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Definitely not:-"The finding, published online today in Nature, overturns the notion that this repetitive, non-coding DNA, popularly called "junk" DNA, is necessary for life."- http://news.sciencemag.org/sciencenow/2013/05/scienceshot-carnivorous-plant-ej.html?ref... article:-http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12132.html-More complete commentary:-http://phys.org/news/2013-05-carnivorous-bladderwort-genome-contradicts-notion.html

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Since their evolutionary split 87 million years ago, both plants have experienced episodes of genetic duplication where the plants' DNA doubled in size. But while the tomato has held onto a lot of those duplicates, the bladderwort has thrown out anything it doesn't need, and now has a genome only a tenth as long as the tomato's. The finding, published online today in Nature, overturns the notion that this repetitive, non-coding DNA, popularly called "junk" DNA, is necessary for life. [/i]-@Assumption from hell, unless they have genetic samples all along the way that prove it. -I am wondering how long it is before they find out they were dead wrong about this, as they have been with so many other 'remarkable discoveries' lately.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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Since their evolutionary split 87 million years ago, both plants have experienced episodes of genetic duplication where the plants' DNA doubled in size. But while the tomato has held onto a lot of those duplicates, the bladderwort has thrown out anything it doesn't need, and now has a genome only a tenth as long as the tomato's. The finding, published online today in Nature, overturns the notion that this repetitive, non-coding DNA, popularly called "junk" DNA, is necessary for life. [/i]
> 
> @Assumption from hell, unless they have genetic samples all along the way that prove it. 
> 
> I am wondering how long it is before they find out they were dead wrong about this, as they have been with so many other 'remarkable discoveries' lately.-What is overlooked is the 3-d arrangement of DNA on the histone spools which generally puts modifying segments of DNA next to genes to control specific expressions of genes. This is what ENCODE tended to show. For very complex DNA, some 3-d spacing arangments are necessary, and so the so-called junk really is useful, but not in a coding way. I think Nature is not clear in their thinking My conclousion is: 'it depends' on which DNA is at work for which organism. One snowball doesn't make a snow storm.

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Latest discovery. Most junk DNa seems to be functional:-"The remaining 150,000 initiation machinesâthose Pugh and Venters did not find right at genesâremained somewhat mysterious. "These initiation machines that were not associated with genes were clearly active since they were making RNA and aligned with fragments of RNA discovered by other scientists," Pugh said. "In the early days, these fragments of RNA were generally dismissed as irrelevant since they did not code for proteins." Pugh added that it was easy to dismiss these fragments because they lacked a feature called polyadenylationâa long string of genetic material, adenosine basesâthat protect the RNA from being destroyed. Pugh and Venters further validated their surprising findings by determining that these non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating that they have a specific origin and that their production is regulated, just like it is at coding genes.
 
"These non-coding RNAs have been called the 'dark matter' of the genome because, just like the dark matter of the universe, they are massive in terms of coverageâmaking up over 95 percent of the human genome. However, they are difficult to detect and no one knows exactly what they all are doing or why they are there," Pugh said. "Now at least we know that they are real, and not just 'noise' or 'junk.' Of course, the next step is to answer the question, 'what, in fact, do they do?'"-
 Read more at: http://phys.org/news/2013-09-genomic-dark.html#jCp-Study this carefully. We know DNA makes proteins, but a collection of proteins is just that, an amorphous collection. Each body plan must have instructions, which to this point have not been found. If most of DNA is functional, not junk, then the plan is there and we will find it.

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I am certainly not going even to hazard a guess as to how much of DNA is "junk" and how much is functional, and we have already had a detailed discussion on how important the question is for The God Theory anyway, since ID-ers and materialists will still put their own slant on the findings. I just want to point out one rather revealing passage:-"Now at least we know that they are real, and not just 'noise' or 'junk'. Of course the next step is to answer the question, 'what, in fact, do they do?'"-Before we are able to say goodbye to junk DNA, shouldn't we find out what, in fact, it does?

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> dhw: Before we are able to say goodbye to junk DNA, shouldn't we find out what, in fact, it does?-The point is junk was supposed to be inactive and now we find a great deal of it is active. It is doing something, therefore it is not junk

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ENCODE research has done a major job of chipping away at junk DNA. Junk DNA has been important 'evidence' that chance mutations left behind lots of unnecessary stuff in DNA during all the time of evolution. ENCODE suggested that 80% of DNA has some function. Now a new study using a different type of approch is dicussing the possibility that 95% of DNA is useful:-http://science.psu.edu/news-and-events/2013-news/Pugh9-2013-"A duo of scientists at Penn State University has achieved a major milestone in understanding how genomic "dark matter" originates. This "dark matter" -- called non-coding RNA -- does not contain the blueprint for making proteins and yet it comprises more than 95 percent of the human genome. The researchers have discovered that essentially all coding and non-coding RNA originates at the same types of locations along the human genome. The team's findings eventually may help to pinpoint exactly where complex-disease traits reside, since the genetic origins of many diseases reside outside of the coding region of the genome."-"Pugh added that it was easy to dismiss these fragments because they lacked a feature called polyadenylation -- a long string of genetic material, adenosine bases -- that protect the RNA from being destroyed. Pugh and Venters further validated their surprising findings by determining that these non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating that they have a specific origin and that their production is regulated, just like it is at coding genes.
 
"These non-coding RNAs have been called the 'dark matter' of the genome because, just like the dark matter of the universe, they are massive in terms of coverage -- making up over 95 percent of the human genome. However, they are difficult to detect and no one knows exactly what they all are doing or why they are there," Pugh said. "Now at least we know that they are real, and not just 'noise' or 'junk.' Of course, the next step is to answer the question, 'what, in fact, do they do?'"

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DAVID (quoting): "These non-coding RNAs have been called the 'dark matter' of the genome because, just like the dark matter of the universe, they are massive in terms of coverage -- making up over 95 percent of the human genome. However, they are difficult to detect and no one knows exactly what they all are doing or why they are there," Pugh said. "Now at least we know that they are real, and not just 'noise' or 'junk.' Of course, the next step is to answer the question, 'what, in fact, do they do?'"-You have drawn our attention to this before, and I pointed out that if we still can't answer the question "what, in fact, do they do?" we can hardly say they are not junk. However, we also discussed the fact that even if it turns out DNA is 100% functional, it still won't prove anything either way about design. I think you yourself told us how Dawkins brazenly changed his argument from "shows you what a bad designer your God is" to "just what you would expect from natural selection" (I'm only paraphrasing). No credit to Dawkins, but the argument itself is fair enough.

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> dhw: You have drawn our attention to this before, and I pointed out that if we still can't answer the question "what, in fact, do they do?" we can hardly say they are not junk. However, we also discussed the fact that even if it turns out DNA is 100% functional, it still won't prove anything either way about design. -You miss the main point. "Junk" supports a chance mechanism discarding stuff, a la Darwinian style unguided evoluton. A 100% functional DNA demands design. You can't just slough it off. It doesn't prove design, but what else is there?

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dhw: You have drawn our attention to this before, and I pointed out that if we still can't answer the question "what, in fact, do they do?" we can hardly say they are not junk. However, we also discussed the fact that even if it turns out DNA is 100% functional, it still won't prove anything either way about design.
 
DAVID: You miss the main point. "Junk" supports a chance mechanism discarding stuff, a la Darwinian style unguided evoluton. A 100% functional DNA demands design. You can't just slough it off. It doesn't prove design, but what else is there?-It's all a question of your starting point. One person looks at DNA, sees how complex it is, and concludes that it must have been designed; this means that no matter how unlikely it may seem, there must be a designer of whose origin, nature and even existence we know absolutely nothing. The atheist doesn't believe in such an unknown and unknowable being, and concludes that no matter how unlikely it may seem, the first self-replicating molecule must have assembled itself by chance, and then evolution followed its natural course. If "junk" is not junk, that is because natural selection ensures that what is useful survives and what isn't useful disappears. People can always find an explanation to fit in with their beliefs. The atheist can learn to accommodate non-junk just as the theist can learn to accommodate evolution.

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DHW: It's all a question of your starting point. One person looks at DNA, sees how complex it is, and concludes that it must have been designed; this means that no matter how unlikely it may seem, there must be a designer of whose origin, nature and even existence we know absolutely nothing. .... People can always find an explanation to fit in with their beliefs. The atheist can learn to accommodate non-junk just as the theist can learn to accommodate evolution.-What you are not recognizing in how important atheists like Larry Moran are trying to preserve the concept of junk. It is considered very vital to their concept of the edvolutionary theory. They are refusing to accept the sort of material I am presenting as valid.

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DAVID: What you are not recognizing in how important atheists like Larry Moran are trying to preserve the concept of junk. It is considered very vital to their concept of the edvolutionary theory. They are refusing to accept the sort of material I am presenting as valid.-It's far too early even for you to say whether DNA is 100% functional or not, so at this stage some atheists can carry on junking, while others like Dawkins have already adjusted their argument to cope with non-junk. Creationists refused at first to accept evolution (and many still do), since separate creation was "considered very vital" to their concept of the God theory, but eventually even the Catholic Church officially accepted theistic evolution. What you are not recognizing is that just as evolution did not knock out theism, functional DNA will not knock out atheism. As I said before, people can always find an explanation to fit in with their beliefs (and disbeliefs).

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dhw: What you are not recognizing is that just as evolution did not knock out theism, functional DNA will not knock out atheism. As I said before, people can always find an explanation to fit in with their beliefs (and disbeliefs).-Very sage comment. You are correct, but some folks will allow for thoughful change in their original position. Antony Flew and I did.

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dhw: What you are not recognizing is that just as evolution did not knock out theism, functional DNA will not knock out atheism. As I said before, people can always find an explanation to fit in with their beliefs (and disbeliefs).
> 
> Very sage comment. You are correct, but some folks will allow for thoughful change in their original position. Antony Flew and I did.-An example of one who resists change, Larry Moran:-http://sandwalk.blogspot.com/2013/09/dark-matter-is-real-not-just-noise-or.html

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More helpful findings in the 'junk' areas of DNA:-http://www.sciencedaily.com/releases/2013/10/131003142321.htm

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"Eukaryotic cells use alternative pre-mRNA splicing to generate protein diversity in development and in response to the environment. By selectively including or excluding regions of pre-mRNAs, cells make on average ten versions of each of the more than 20,000 genes in the genome. RNA-binding proteins are the class of proteins most closely linked to these decisions, but very little is known about how they actually perform their roles in cells.
 
"For most genes, protein-coding space is distributed in segments on the scale of islands in an ocean," Lovci said. "RNA processing machinery, including RNA-binding proteins, must pick out these small portions and accurately splice them together to make functional proteins. Our work shows that not only is the sequence space nearby these 'islands' important for gene regulation, but that evolutionarily conserved sequences very far away from these islands are important for coordinating splicing decisions.'"-
 Read more at: http://phys.org/news/2013-11-un-junking-junk-dna.html#jCp-It is a matter of understanding that DNA is a 3-D object and spacing is needed to coordinate sections of the DNA. Note 10 versions of 20,000 genes makes 200,000.

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Another review article showing that most of DNA is active in regulation of gene production:-http://www.genengnews.com/insight-and-intelligence/what-junk-dna-it-s-an-operating-system/77899872/

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Another paper showing how miRNA and ncRNA are n ot junk and modulated gene expression:-"In this study, we tried to simulate the naturally occurring pseudogene phenomena, initially reported for PTENP1 (ref. 32) and later termed as the competing endogenous RNA model. Pseudogenes have been discovered in equal abundance to functional genes and therefore represent a large component of the genome. The human genome has been estimated to have ~20,000 putative pseudogenes33. Previously, pseudogenes were classified as 'junk DNA' based on the fact that they did not code for proteins. However, it has been recently shown that certain pseudogenes have important roles in maintaining homeostasis, specifically as modulators of miRNAs"-
http://www.nature.com/ncomms/2014/140107/ncomms3914/full/ncomms3914.html

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Long non-coding RNA has function:-"In the second phase of the research, a comparison among the different species allowed the scientists to pinpoint the emergence of these genes in the evolutionary history. While 11,000 long non-coding RNAs are shared by all primates, 2,500 go back to an ancestor common to man and mouse, about 90 million years ago. Only a hundred genes of this kind stem from an ancestor common to all eleven species considered, including birds and amphibians. "One of our main findings is that the activity of these non-coding genes is controlled by the same transcription factors that regulate protein-coding gene activity. Even more strikingly, we found that the 2,500 oldest long noncoding RNA genes are regulated by factors that are important for embryonic development. This suggests that, among the 2500 long non-coding RNAs conserved during the evolution of placental mammals, a large percentage may function specifically in embryonic development."
 
New network of interactions
 
The third phase of the research allowed the scientists to highlight a network of interactions (specifically, co-expression interactions, that is: genes are activated in the same organs or cell types) involving both long non-coding RNAs and protein-coding genes. For instance, they found that some non-coding genes are strongly associated to protein coding genes involved in brain function or in spermatogenesis, which suggests similar functions for these long non-coding RNA genes.
 
In the case of the H19X gene - one of the most ancient long noncoding RNA genes identified in this study - its association to the placental mammals' H19 gene (which was the first long non-coding RNA identified years ago) helped to uncover its functioning: "The H19 prevents the placenta from excessively growing inside the mother's womb," said Anamaria Necsulea. "We can assume that H19X also contributes to this function. We now plan to disable this gene in mice to test its functions in the placenta."
 
Among the subcategories of RNA producing genes, are these long RNA genes more useful than it originally seemed? By tracking them in 11 different species, this new study of unprecedented scale suggests that some of our genomes' "dark matter" may play a role in the development and functioning of the most vital organs of our bodies. Future experimental studies will further clarify the role of these genes that have just revealed their first secrets to us."-
 Read more at: http://phys.org/news/2014-01-scientists-biological-dark.html#jCp

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More uses found for lincRNA, long intergenic non-coding RNA, by deletion studies in mice:-"Ever since the Human Genome Project decoded the genome, the prevailing scientific view has been that only the 2 percent that makes proteinsâthe building blocks of cellsâwas important. The rest was deemed not functional, or "junk." But from his days in graduate school, through his postdoctoral fellowship, and now as a Harvard Stem Cell scientist, John Rinn has been digging through the genome, challenging that prevailing belief.-"Now, Rinn and his Harvard Stem Cell Institute colleagues, including neurobiologist Paola Arlotta, have carried out an elegant and important experiment in which they have demonstrated that much of what had been dismissed in fact plays as vital a role as protein-coding genes.
 
"Rinn and his colleagues have generated 18 strains of mutant mice, removing from each a different piece of "junk" genome, or so-called long intergenic noncoding RNAs (lincRNAs). If the lincRNA truly had been "junk," nothing should have happened.
 
What the researchers found was the opposite. Obvious defects were observed in seven of the 18 mutant strains. Three died shortly after birth, and there is reason to believe many others also are defective." -http://medicalxpress.com/news/2014-01-lincrna-believed-useless-role-genome.html

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Here junk DNA is found in non-coding RNA to produce new beneficial genes in fruit flies:-http://www.sciencedaily.com/releases/2014/01/140123142029.htm

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More information on ENCODE type studies in fruit flies. Very complex genome:-http://www.evolutionnews.org/2014/03/not_so_simple_f083491.html

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More junk DNA bites the dust:-http://www.sciencedaily.com/releases/2014/03/140326141644.htm-
"Researchers studied human and mouse cells using a new technology called Cap Analysis of Gene Expression (CAGE), developed at RIKEN, to discover how 95% of all human genes are switched on and off. These "switches" -- called "promoters" and "enhancers" -- are the regions of DNA that manage gene activity. The researchers mapped the activity of 180,000 promoters and 44,000 enhancers across a wide range of human cell types and tissues and, in most cases, found they were linked with specific cell types."

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New Encode research finds 70-75% of DNA may have activity in modifying gene expression, (in body of the article), but firm evidence of activity is not fully established. The conclusion of the article:-"Conclusion:
In contrast to evolutionary and genetic evidence,
biochemical data offer clues about
both the molecular function served by underlying
DNA elements and the cell types
in which they act, thus providing a launching
point to study differentiation and development,
cellular circuitry, and human
disease (14, 35, 69, 111, 112). The major
contribution of ENCODE to date has been
high-resolution, highly-reproducible maps of
DNA segments with biochemical signatures
associated with diverse molecular functions.
We believe that this public resource is far
more important than any interim estimate
of the fraction of the human genome that
is functional.
By identifying candidate genomic elements
and placing them into classes with shared
molecular characteristics, the biochemical
maps provide a starting point for testing
how these signatures relate to molecular,
cellular, and organismal function. The data
identify very large numbers of sequence elements
of differing sizes and signal strengths.
Emerging genome-editing methods (113,
114) should considerably increase the
throughput and resolution with which
these candidate elements can be evaluated
by genetic criteria. Given the limitations of
our current understanding of genome function,
future work should seek to better define
genome elements by integrating all three
methods to gain insight into the roles they
play in human biology and disease."-http://www.pnas.org/content/early/2014/04/23/1318948111.long

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A careful study in failing hearts shows that long non-coding RNA is active and responds to treatment:-"In the new study, the investigators found that unlike other RNA molecules, expression patterns of long noncoding RNAs could distinguish between two major types of heart failure and between failing hearts before and after they received LVAD support.
 
"We don't know whether these changes in long noncoding RNAs are a cause or an effect of heart failure," Nerbonne said. "But it seems likely they play some role in coordinating the regulation of multiple genes involved in heart function."
 
"Nerbonne pointed out that all types of RNA molecules they examined could make the obvious distinction: telling the difference between failing and nonfailing hearts. But only expression of the long noncoding RNAs was measurably different between heart failure associated with a heart attack (ischemic) and heart failure without the obvious trigger of blocked arteries (nonischemic). Similarly, only long noncoding RNAs significantly changed expression patterns after implantation of left ventricular assist devices."- Note: lncRNA was part of the original 'junk' DNA.-
http://www.sciencedaily.com/releases/2014/04/140425134022.htm

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Finding areas of DNA thoght to be non-coding that do code:-"Among the proteins whose data patterns have been characterized for the first time are many that were never predicted to exist. (Within the genome, in addition to the DNA sequences that encode proteins, there are stretches of DNA whose sequences do not follow a conventional protein-coding gene pattern and have therefore been labeled "noncoding.") The team's most unexpected finding was that 193 of the proteins they identified could be traced back to these supposedly noncoding regions of DNA.
 
""This was the most exciting part of this study, finding further complexities in the genome," says Pandey. "The fact that 193 of the proteins came from DNA sequences predicted to be noncoding means that we don't fully understand how cells read DNA, because clearly those sequences do code for proteins.""-
http://www.sciencedaily.com/releases/2014/05/140528133149.htm

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Long non-coding RNA segments do code:-""Our work establishes that lncRNAs in yeast can encode proteins, and we provide evidence that this is probably true also in mammals, including humans," Baker said. "Our investigation has expanded our knowledge of the genetic coding potential of already well-characterized genomes."
 
"Collaborating with researchers including Case Western Reserve University graduate and undergraduate students, Baker analyzed yeast and mouse cells, which serve as model organisms because of their functional resemblance to human cells.
 
"Previously, lncRNAs were thought to lack the information and capacity to encode for proteins, distinguishing them from the messenger RNAs that are expressed from known genes and act primarily as templates for the synthesis of proteins. Yet this team demonstrated that a subset of these lncRNAs is engaged by the translation machinery and can function to produce protein products."-http://www.sciencedaily.com/releases/2014/06/140623131331.htm-
My point is still the same. The less DNA is junk, the more likely it was designed

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There is a secondary effect as well that is not mentioned at all. The more functional DNA that they discover the greater the gap between humans and other species becomes. Traditionally, they only compared functional DNA when measuring the disparity between species.-Right now, even an extremely conservative estimate of differentiation between base pairs is likely in the 500,000,000 base range, and one base pair is enough to change an essential function. -->>Point Mutations are changes involving only one base pair of the DNA. (Very small mutations--ie, two or three base pairs--are generally also considered point mutations, although they don't strictly meet the definition.)
1.
Base substitutions involve the replacement of one base (and its complementary partner) by one of the other bases (and its complementary partner). Base subsitutions affect only the amino acid coded for by the codon affected.
a.
Transition mutations involve replacing a purine with another purine (and its partnering pyrimidine with another pyrimidine), or replacing a pyrimidine with a pyrimidine (and its partnering purine with another purine). For example, if an A-T pair is replaced by a G-C pair, this is a transition.
b.
Transversion mutations involve replacing a purine with a pyrimidine (and its partnering pyrimidine with a purine), or replacing a pyrimidine with a puring (and its partnering purine with a pyrimidine). For example, if an A-T pair is replaced by either a T-A pair or a C-G pair, this is a transversion.
2.
Frame shifts are created when one or a few bases are inserted or deleted, thus altering the ultimate reading frame of the ribosome. Frame shift mutations affect all of the protein following the position of the inserted or deleted base. Ribosomes read in a strict 3-base-codon frame, regardless of whether the final amino acid sequence "makes sense." --Since even one base change can change the environment, and the environment can change the expression, 500,000,000 differences in base pairs is nothing to sneeze at.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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http://www.ncbi.nlm.nih.gov/books/NBK21955/

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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Another paper finding function in repeated segments:-We've come to understand that not all repeat sequences are junk DNA, said Pawel Michalak, an associate professor at the Virginia Bioinformatics Institute. These repetitive sequences are increasingly being recognized as agents of adaptive change. We discovered a larger than expected amount of genetic variation in these repeating sequences between the fly populations and saw that the variation resulted in potentially functional differences in important biological processes, such as stress resistance and mating.-http://www.alphagalileo.org/ViewItem.aspx?ItemId=143443&CultureCode=en

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DAVID: Another paper finding function in repeated segments:-http://www.alphagalileo.org/ViewItem.aspx?ItemId=143443&CultureCode=en-Below is the section that really interests me:-QUOTE: The two slopes of the canyon are about two football fields apart at their bases  between 100 meters and 400 meters  but the south-facing slope is tropical and may receive eight times as much sun, while the north-facing slope is darker, more like a European forest.
Animals genetically adapt depending on whether they live on the drier, hotter side of the canyon, or the more humid, cooler side.
Researchers extracted DNA from flies collected in the canyon, then identified and mapped repeating patterns of what genomics researchers call transposable elements  DNA sequences capable of spontaneously changing position within the genome.
The scientists discovered flies taken from the opposing sides of the canyon displayed a significant difference in the contents and distribution of mobile elements.
The biological roles of these place-jumping, repetitive elements are mysterious. 
They are largely viewed as genomic parasites, but in this study, researchers found the mobile DNA can provide genetic novelties recruited as certain population-unique, functional enrichments that are nonrandom and purposeful.-This would seem to be yet another example of the way in which cell communities intelligently adapt and innovate in accordance with their environment. Of course you insist that such changes are preprogrammed by your God, because according to you these communities behave automatically. It is truly amazing how many programmes he must have packed into those first few living cells to be passed down to all succeeding species over the next few billion years, especially when apparently all he really wanted to do was create human beings!

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dhw: This would seem to be yet another example of the way in which cell communities intelligently adapt and innovate in accordance with their environment. Of course you insist that such changes are preprogrammed by your God, because according to you these communities behave automatically.-No, you misinterpret! The organisms (flies) have the ability to adapt to their environments, with their epigenetic abiliities on board. The preplanning is in the ablitity, not innumerable life plans. Keep it simple, not complex is the rule.

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dhw: This would seem to be yet another example of the way in which cell communities intelligently adapt and innovate in accordance with their environment. Of course you insist that such changes are preprogrammed by your God, because according to you these communities behave automatically.-DAVID: No, you misinterpret! The organisms (flies) have the ability to adapt to their environments, with their epigenetic abiliities on board. The preplanning is in the ablitity, not innumerable life plans. Keep it simple, not complex is the rule.
-Then why not acknowledge that the ability of the various cell communities to perceive and process information from the environment, to communicate with other cell communities, to decide which steps are necessary - even to the extent of innovation - constitutes a form of intelligence? If the life plan has not been preprogrammed, the cell communities must take the decisions themselves. They are therefore not automata.

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> dhw: Then why not acknowledge that the ability of the various cell communities to perceive and process information from the environment, to communicate with other cell communities, to decide which steps are necessary - even to the extent of innovation - constitutes a form of intelligence? If the life plan has not been preprogrammed, the cell communities must take the decisions themselves. They are therefore not automata.-Our only difference is that the biologic systems run under tight controls with feedback loops and other controls. They are engineered to make automatic decisions.-Note this discussion of systems biology which fits what I know from my education:-http://www.evolutionnews.org/2014/07/when_biologists087871.html

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dhw: Then why not acknowledge that the ability of the various cell communities to perceive and process information from the environment, to communicate with other cell communities, to decide which steps are necessary - even to the extent of innovation - constitutes a form of intelligence? If the life plan has not been preprogrammed, the cell communities must take the decisions themselves. They are therefore not automata.-DAVID: Our only difference is that the biologic systems run under tight controls with feedback loops and other controls. They are engineered to make automatic decisions.-Your first sentence describes all biologic systems including our own and that of those fellow animals to which you are willing to ascribe a mental capacity we call intelligence, an essential part of which is the ability to make decisions. However, as usual, you insist that humans and - to a lesser degree - our fellow animals are capable of making their own spontaneous decisions, whereas other life forms from bacteria onwards are automata. THAT is the difference between us.
 
DAVID: Note this discussion of systems biology which fits what I know from my education:-http://www.evolutionnews.org/2014/07/when_biologists087871.html-It makes a good case for intelligent design. How does it exclude the concept of cells and cell communities designed to make their own intelligent decisions? Once again, let me point out that if the different life plans of the fruit flies were not preprogrammed, the cell communities of which the fruit flies are composed must have cooperated in making all the decisions that led to their particular life plan. If those decisions were not preprogrammed, they cannot have been automatic. -Incidentally, the article - like many you have recently quoted on this thread - emphasizes that so-called junk DNA is not junk. An article in today's Guardian reports on the claim by researchers at Oxford University that: More than 90% of human DNA is doing nothing very useful, and large stretches may be no more than biological baggage that has built up over years of evolution. As is so often the case, scientists themselves can't agree. Back to the picket fence, everybody!

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dhw:However, as usual, you insist that humans and - to a lesser degree - our fellow animals are capable of making their own spontaneous decisions, whereas other life forms from bacteria onwards are automata. THAT is the difference between us.-Again, either I've not been clear or you misunderstand. we humans hae different sets of cellular controls. My kidney acts autonomously and automatically on its ow, just like a bacterial cell. But I have a brain which is some sort of a basis for consciousness, and I am in control of my consciousness
> 
> dhw: let me point out that if the different life plans of the fruit flies were not preprogrammed, the cell communities of which the fruit flies are composed must have cooperated in making all the decisions that led to their particular life plan. If those decisions were not preprogrammed, they cannot have been automatic. -Let me point out that we both accept evolution, and in my concept of it, life and body forms respond to various challenges of nature. Life forms are designed to contain the information to make appropriate responses, and that response can be inheritable as shown in recent epigenetic research. They have plans of adaptation, not pre-programming to the tinest degree. 
> 
> dhw: Incidentally, the article - like many you have recently quoted on this thread - emphasizes that so-called junk DNA is not junk. An article in today's Guardian reports on the claim by researchers at Oxford University that: More than 90% of human DNA is doing nothing very useful, and large stretches may be no more than biological baggage that has built up over years of evolution. As is so often the case, scientists themselves can't agree. Back to the picket fence, everybody!-You have quoted the atheistic version of the battle about junk, and in my opinion the Guardian always represents that side. You have forgotten ENCODE with its consortium of hundreds of scientists who showed function in 80% of DNA.

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dhw: However, as usual, you insist that humans and - to a lesser degree - our fellow animals are capable of making their own spontaneous decisions, whereas other life forms from bacteria onwards are automata. THAT is the difference between us.DAVID: Again, either I've not been clear or you misunderstand. we humans hae different sets of cellular controls. My kidney acts autonomously and automatically on its ow, just like a bacterial cell. But I have a brain which is some sort of a basis for consciousness, and I am in control of my consciousness.-Your view is perfectly clear: you reject the case Margulis, Shapiro, Albrecht-Buehler & Co have made for regarding cells (including bacteria) as intelligent, sentient beings. Under Cell Memories I wrote: ...much cellular behaviour is undoubtedly automatic once an innovation has established itself. It is not the repetition of established modes of behaviour that led the above researchers to their conclusion, but the solving of new problems through innovation and adaptation. No-one is claiming that bacterial intelligence is the same as human consciousness. The parallel lies in the capacity for processing information, communicating, and taking decisions.-dhw: ..let me point out that if the different life plans of the fruit flies were not preprogrammed, the cell communities of which the fruit flies are composed must have cooperated in making all the decisions that led to their particular life plan. If those decisions were not preprogrammed, they cannot have been automatic.-DAVID: Let me point out that we both accept evolution, and in my concept of it, life and body forms respond to various challenges of nature. [I agree.] Life forms are designed to contain the information to make appropriate responses, and that response can be inheritable as shown in recent epigenetic research. [I agree.] They have plans of adaptation, not pre-programming to the tinest degree.-Either detailed plans for adaptations and innovations are already present in all life forms (= preprogramming), or they have to be worked out by the organisms themselves as and when the need or opportunity arises (= autonomous intelligence). Even the tiniest details must work perfectly or the response will fail.
 
dhw: Incidentally, the article - like many you have recently quoted on this thread - emphasizes that so-called junk DNA is not junk. An article in today's Guardian reports on the claim by researchers at Oxford University that: More than 90% of human DNA is doing nothing very useful, and large stretches may be no more than biological baggage that has built up over years of evolution. As is so often the case, scientists themselves can't agree. Back to the picket fence, everybody!-DAVID: You have quoted the atheistic version of the battle about junk, and in my opinion the Guardian always represents that side. You have forgotten ENCODE with its consortium of hundreds of scientists who showed function in 80% of DNA.-You have been quoting ENCODE on this thread, which is what I meant when I said scientists themselves can't agree. ENCODE scientists claim 80% function, Oxford scientists claim to have found very different figures. So long as there is no scientific consensus, how can the layman believe or disbelieve the claims of the different researchers, let alone the conclusions they draw from them?

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dhw: No-one is claiming that bacterial intelligence is the same as human consciousness. The parallel lies in the capacity for processing information, communicating, and taking decisions.-Agreed, but with the proviso that those processes are automatic.-
> dhw: Either detailed plans for adaptations and innovations are already present in all life forms (= preprogramming), or they have to be worked out by the organisms themselves as and when the need or opportunity arises (= autonomous intelligence). Even the tiniest details must work perfectly or the response will fail.-Again, agreed, with the proviso that while the organisms are adapting they are doing it automatically within certain genetically provided guidelines of response.
> 
> 
> dhw: You have been quoting ENCODE on this thread, which is what I meant when I said scientists themselves can't agree. ENCODE scientists claim 80% function, Oxford scientists claim to have found very different figures. So long as there is no scientific consensus, how can the layman believe or disbelieve the claims of the different researchers, let alone the conclusions they draw from them?- "How" is by following what I report of continous findings since ENCODE of more and more functions by other researchers. It seems never ending and all the while junk shrinks. The patern is obvious. Look to the future. The exact %age of junk is continuously shrinking. At some point we will find the right figure representing junk, but the Darwinists use junk as a proof of evolution by pointing to discarded DNA from the past. Only much of it is not discarded. Junk =s Darwin-type evolution, and loss of junk suggests Darwin-type evolution is not correct.

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dhw: No-one is claiming that bacterial intelligence is the same as human consciousness. The parallel lies in the capacity for processing information, communicating, and taking decisions.
DAVID: Agreed, but with the proviso that those processes are automatic.-As I understand it, automatic intelligence entails no autonomous decision-making. It has to be preprogrammed, and you have agreed that adaptations and innovations are not preprogrammed. No deal. (But see Cell Memories.)-dhw: Either detailed plans for adaptations and innovations are already present in all life forms (= preprogramming), or they have to be worked out by the organisms themselves as and when the need or opportunity arises (= autonomous intelligence). Even the tiniest details must work perfectly or the response will fail.
DAVID: Again, agreed, with the proviso that while the organisms are adapting they are doing it automatically within certain genetically provided guidelines of response.-I can accept that all forms of intelligence, including our own, may be within genetically provided guidelines of response, since all forms of intelligence appear to be limited by physical capacity. That does not make them automatic. (But see Cell Memories.)-dhw: You have been quoting ENCODE on this thread, which is what I meant when I said scientists themselves can't agree. ENCODE scientists claim 80% function, Oxford scientists claim to have found very different figures. So long as there is no scientific consensus, how can the layman believe or disbelieve the claims of the different researchers, let alone the conclusions they draw from them?
DAVID: "How" is by following what I report of continous findings since ENCODE of more and more functions by other researchers. It seems never ending and all the while junk shrinks. The patern is obvious. Look to the future. -I am not prepared to say that the Oxford researchers are all fakes and charlatans following their own junky agenda. My point is that if scientists disagree, the neutral layman cannot make a choice.
 
DAVID: The exact %age of junk is continuously shrinking. At some point we will find the right figure representing junk, but the Darwinists use junk as a proof of evolution by pointing to discarded DNA from the past. Only much of it is not discarded. Junk =s Darwin-type evolution, and loss of junk suggests Darwin-type evolution is not correct.-Atheist Darwinists use junk to prove that DNA was not designed, or at best was badly designed. Junk = whatever you want it to =. Both sides are so desperate to find evidence for their God / anti-God theories that they simply ignore anything counter to their entrenched beliefs. If junk DNA is junk, it doesn't alter the fact that the mechanism is still too complex for us to understand, let alone reproduce, and what is junk now may have served an essential purpose earlier. On the other hand, Darwin-type evolution stresses the idea that natural selection preserves whatever is useful. And so if junk DNA is not junk, a Darwinist evolutionist can perfectly reasonably point out that natural selection has preserved what is useful. It's also worth reminding ourselves that a Darwinist evolutionist does not have to be an atheist.

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> dhw: As I understand it, automatic intelligence entails no autonomous decision-making. It has to be preprogrammed, and you have agreed that adaptations and innovations are not preprogrammed. No deal. (But see Cell Memories.)-Cells do not plan, they have responses to choose from.-
>> dhw: I can accept that all forms of intelligence, including our own, may be within genetically provided guidelines of response, since all forms of intelligence appear to be limited by physical capacity. That does not make them automatic. (But see Cell Memories.)-I repeat, cells do not plan. They are organized to work together within resonse guidences.- 
> 
> dhw: Atheist Darwinists use junk to prove that DNA was not designed, or at best was badly designed. And so if junk DNA is not junk, a Darwinist evolutionist can perfectly reasonably point out that natural selection has preserved what is useful. It's also worth reminding ourselves that a Darwinist evolutionist does not have to be an atheist.-You keep skipping the point that as function is discovered in DNA, and we are getting to understand more and more of DNA, there is less 'junk'. we have no true idea as of yet what portion of DNA is real junk. We are in the middle of a research process. The apparent end point is that there will be much less junk, and less support for the Darwinist contention that DNA is a helter-skelter result of an aimless process. I don't think that is hard to predict.

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DAVID: Cells do not plan, they have responses to choose from.-As new situations arise, cells/cell communities must find ways to respond. Some succeed, and some don't. No-one is claiming that they anticipate the new situation and plan ahead for it. The point is that successful cells work together to find an appropriate response. Unless that response has been preprogrammed (and you say it hasn't), they must make their own decisions.
 
dhw: I can accept that all forms of intelligence, including our own, may be within genetically provided guidelines of response, since all forms of intelligence appear to be limited by physical capacity. That does not make them automatic. 
DAVID: I repeat, cells do not plan. They are organized to work together within resonse guidences.-As above. I don't know what you mean by response guidances, other than the physical limitations within which the cells have to work. Are you suggesting that your God has built in a series of multiple choice solutions for every possible problem throughout the history of evolution? Even if you are, it would still require intelligence and individual decision-making to choose the right answer.-DAVID: You keep skipping the point that as function is discovered in DNA, and we are getting to understand more and more of DNA, there is less 'junk'. we have no true idea as of yet what portion of DNA is real junk. We are in the middle of a research process. The apparent end point is that there will be much less junk, and less support for the Darwinist contention that DNA is a helter-skelter result of an aimless process. I don't think that is hard to predict.-My point was that Oxford scientists clearly disagree with ENCODE scientists, and so the layman can hardly make a decision. You now say we don't know how much is junk, but you predict that there will be less, and no doubt the Oxford scientists would predict there will be more. I don't think more or less junk will make the slightest difference to Darwinist evolutionists. However, it will be a blow to atheists, since they use junk as an argument against design. As regards a helter-skelter result, natural selection would explain the lack of junk, and an aimless process would refer to the higgledy-pigglediness of all the comings and goings, regardless of how much DNA is junk.

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DAVID: Cells do not plan, they have responses to choose from.
> 
> dhw: As new situations arise, cells/cell communities must find ways to respond. Some succeed, and some don't. No-one is claiming that they anticipate the new situation and plan ahead for it. The point is that successful cells work together to find an appropriate response. Unless that response has been preprogrammed (and you say it hasn't), they must make their own decisions.-No, cells have decision trees, a range of responses dictated by the chemical stimuli they intercept or receive. So these decisions are very limited to what response is allowed. There is no decisions making as we do, and I know you understand that. -
> 
> dhw: I can accept that all forms of intelligence, including our own, may be within genetically provided guidelines of response, since all forms of intelligence appear to be limited by physical capacity. That does not make them automatic. 
> DAVID: I repeat, cells do not plan. They are organized to work together within resonse guidences.
> 
> dhw: My point was that Oxford scientists clearly disagree with ENCODE scientists, and so the layman can hardly make a decision. You now say we don't know how much is junk, but you predict that there will be less, and no doubt the Oxford scientists would predict there will be more. -You are missing the point. Until a few years ago it was a clearly state point that 80% of DNA was left-over non-coding segments that did nothing, i.e., junk. Bit by bit function has been found in large areas, not so much coding as controls and modifications of gene action. Therefore the 80% is receding and junk is now obviously much less than 80%. Will it recede to 50% or 20%, no one can predict, but until the studies are completed over the next 10-20 years, we don't have an answer? As bit by bit the shrinkage of junk is proceding, there is only one expectation. the final %age will be much less than 80%. And you clearly understand what this means to each side of the debate.

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ENCODE research marches on, finding more function in DNA across species in transcription regions:-http://www.the-scientist.com/?articles.view/articleNo/40891/title/Expanding-ENCODE/-We still have no idea how little junk there really is. Another article:-http://www.sciencedaily.com/releases/2014/08/140827131751.htm

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That fits nicely with my analogy of a program>class>method hierarchy.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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Tony: That fits nicely with my analogy of a program>class>method hierarchy.-Yes, it does.

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More evidence of 'junk' DNA functionality:-http://wfas2014.acaom.edu/wfas-registration-landing-page/?gclid=CNmbitGbnsECFSyCMgodpSsAFA-"Aldrich's findings, published today in the online edition of the journal PLOS ONE, showed that differences in the heterochromatin exist, confirming that the junk DNA is not stagnant as researchers originally had believed and that mutations which could affect other parts of the genome are capable of occurring.
 
"We know that there is hidden variation there, like disease proclivities or things that are evolutionarily important, but we never knew how to study it," Maggert said. "We couldn't even do the simplest things because we didn't know if there was a little DNA or a lot of it.
 
"This work opens up the other non-coding half of the genome."

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More tRNA found scattered through human DNA:-http://medicalxpress.com/news/2014-10-conspicuous-trna-lookalikes-riddle-human.html-I believe that more and more DNA will be found to be functional. The human being is too complex for a DNA that has less than 30,000 genes. One of the keystones of Darwinian theory as a 'proof' that evolution is a random purposeless process has been the proposal that junk DNA is the garbage left over from such a process. As junk disappears design rears its ugly head. The vicious and vindictive howls of protest from some atheist blogs, Larry Moran, PZ Myers, Jerry Coyne, etc. are evidence that atheistic underpinnings in evolutionary theory are threatened.

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More useful stretches of non-coding DNA:-"Increases or decreases in transcriptionas dictated by a regulatory stretch of DNA called an enhancer, which serves as a binding site for transcription factors and associated proteinscan produce an aberrant composition of proteins, metabolites, and signaling molecules that drives pathologic states. Identifying the root causes of these changes may lead to new therapeutic approaches for many different diseases. -"Although few therapies for human diseases aim to alter gene expression, the outstanding examplesincluding antiestrogens for hormone-positive breast cancer, antiandrogens for prostate cancer, and PPAR-? agonists for type 2 diabetesdemonstrate the benefits that can be achieved through targeting gene-control mechanisms. Now, thanks to recent papers from laboratories at MIT, Harvard, and the National Institutes of Health, researchers have a new, much bigger transcriptional target: large DNA regions known as super-enhancers or stretch-enhancers. Already, work on super-enhancers is providing insights into how gene-expression programs are established and maintained, and how they may go awry in disease. Such research promises to open new avenues for discovering medicines for diseases where novel approaches are sorely needed. -"Super-enhancers cover stretches of DNA that are 10- to 100-fold longer and about 10-fold less abundant in the genome than typical enhancer regions (Cell, 153:307-19, 2013). They also appear to bind a large percentage of the transcriptional machinery compared to typical enhancers, allowing them to better establish and enforce cell-type specific transcriptional programs"-http://www.the-scientist.com//?articles.view/articleNo/41281/title/Enhanced-Enhancers/

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More areas of DNA function:-
"Special Issue on microRNAs - the smallest RNA regulators of gene expression-
"It is now well recognised that the majority of non-protein-coding genomic DNA is not junk but specifies a range of regulatory RNA molecules which finely tune protein expression. This issue of CDD contains an editorial and 5 reviews on a particular class of these regulatory RNAs, the microRNAs (miRs) of around 22 nucleotides, and which exert their effects by binding to consensus sites in the 3?UTRs of mRNAs. The reviews cover the role of miRs from their early association with CLL to other forms of cancer, their importance in the development of the epidermis and their potential as disease biomarkers as secreted in exosomes. In addition, we publish a News and Commentary on CRISPR, a technology which is not only revolutionising genetic manipulation in the lab, but which has the potential to treat genetic disease in vivo."-http://www.nature.com/cdd/journal/v22/n1/pdf/cdd2014114a.pdf?WT.ec_id=CDD-201501-"Following their discovery in C. elegans in 19931 and
subsequent rediscovery' in 2001, microRNAs (miRNAs) have
been intensively studied and currently more than 31 000
scientific papers have been published on the subject. So, a
massive amount of information has been gathered on the
expression and biological impact of miRNAs in normal
physiological processes and in pathologies and we understand
much more about the mechanisms underlying miRNAmediated
gene regulation. In addition, strategies for exploiting
miRNAs as biomarkers and therapeutic targets are beginning
to mature.
"This issue of Cell Death and Differentiation features a series
of interesting reviews on miRNAs focusing on the mode of
action, their involvement in stemness, and their usefulness as
markers and in novel therapies."

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About 5% of our DNA is retrovirus occupiers. And their abilities are used to regulate brain function!- http://www.sciencedaily.com/releases/2015/01/150112093129.htm-"Researchers have long been aware that endogenous retroviruses constitute around five per cent of our DNA. For many years, they were considered junk DNA of no real use, a side-effect of our evolutionary journey.-"In the current study, Johan Jakobsson and his colleagues show that retroviruses seem to play a central role in the basic functions of the brain, more specifically in the regulation of which genes are to be expressed, and when. The findings indicate that, over the course of evolution, the viruses took an increasingly firm hold on the steering wheel in our cellular machinery. The reason the viruses are activated specifically in the brain is probably due to the fact that tumours cannot form in nerve cells, unlike in other tissues.-"We have been able to observe that these viruses are activated specifically in the brain cells and have an important regulatory role. We believe that the role of retroviruses can contribute to explaining why brain cells in particular are so dynamic and multifaceted in their function. It may also be the case that the viruses' more or less complex functions in various species can help us to understand why we are so different," says Johan Jakobsson, head of the research team for molecular neurogenetics at Lund University."-Note to dhw: could retroviruses be the inventive mechanism? Is it one of God's evolutionary trick? :-)

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7.5% of non-genic (junk DNA) controls genes and makes us human:-https://www.sciencenews.org/article/human-evolution-tied-small-fraction-genome-"Only about 7.5 percent of the human genetic instruction book shaped the evolution of human traits, a new study suggests. And it's often not genes, but the how-to instructions for using those genes that are most important, researchers report January 19 in Nature Genetics.-"Those findings emerged from a new method of analyzing how natural selection has tinkered with the genome since humans split from chimpanzees.-Remarkably we use nearly the same building blocks as chimpanzees, but we end up with very different results, says Brad Gulko, a computer scientist at Cornell University."-.......-"Researchers have developed a new computational approach to understanding which single nucleotide polymorphisms (SNPs) in the human genome might have conferred species-specific advantages. Researchers from Cornell University in Ithaca, New York, and colleagues found that many such point mutations related to human evolution actually reside in noncoding regions of the genome."-http://www.the-scientist.com//?articles.view/articleNo/41948/title/Fraction-of-SNPs-Can-Affect-Fitness/

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A paper from 2005 demonstrating the enormous amount of genetic controls that surround genes that remove genes from the one gene one protein concept from the early years of research and predicting there was more to come. The moral is that it is the entire DNA, not just the genes that create a living multicellular organism.- http://embor.embopress.org/content/embor/6/9/808.full.pdf-"Today, however, it is harder and harder to maintain that genes determine
even a unique protein sequence. The classical molecular concept of one gene,
one enzyme', embedded in Francis Crick's central dogma, began to unravel with the
discovery of reverse transcriptase in the 1970s. Then came introns, exons, jumping
genes, alternative reading frames, and the whole machinery of post-transcriptional
and post-translational processing. Even before the Human Genome Project was
complete, Evelyn Fox Keller from the Massachusetts Institute of Technology
(Cambridge, MA, USA) suggested that the term gene' might have become a hindrance
to understanding, both for biologists and lay readers, misleading as often as it
informs (Keller, 2000). Since then, genes have become even more deeply embedded
in complex cellular and genomic networks. DNA methylation, microRNAs and a multiplicity of regulatory DNA sequences all alter the context in which the basic genetic information is interpreted." -What bothers me today is the research that claims to identify one gene with one function, just like one gene one protein. Yes, one gene may well be related to one function, but it just isn't that simple, as this article predicts.

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Excellent summary of the history of discovery in the analysis of human DNA. Junk and anti-junk proponents are discussed. What is seen is that more and more areas of non-coding do have other functions:-"As the scientists find new RNA molecules that look to be important, they are picking out a few to examine in close molecular detail. I'm totally in love with this one, Rinn said, standing at a whiteboard wall and drawing a looping line to illustrate yet another RNA molecule, one that he calls firre. The experiments that Rinn's team has run on firre suggest that it performs a spectacular lasso act, grabbing onto three different chromosomes at once and drawing them together. Rinn suspects that there are thousands of RNA molecules encoded in our genomes that perform similar feats: bending DNA, unspooling it, bringing it in contact with certain proteins and otherwise endowing it with a versatility it would lack on its own.-It's genomic origami, Rinn said about this theory. In every cell, you have the same piece of paper. Stem cell, brain cell, liver cell, it's all made from the same piece of paper. How you fold that paper determines if you get a paper airplane or a duck. It's the shape that you fold it into that matters. This has to be the 3-D code of biology.-"To some biologists, discoveries like Rinn's hint at a hidden treasure house in our genome. Because a few of these RNA molecules have turned out to be so crucial, they think, the rest of the noncoding genome must be crammed with riches. But to Gregory and others, that is a blinkered optimism worthy of Dr. Pangloss. They, by contrast, are deeply pessimistic about where this research will lead. Most of the RNA molecules that our cells make will probably not turn out to perform the sort of essential functions that hotair and firre do. Instead, they are nothing more than what happens when RNA-making proteins bump into junk DNA from time to time."-http://www.nytimes.com/2015/03/08/magazine/is-most-of-our-dna-garbage.html?emc=edit_th_20150308&nl=todaysheadlines&nlid=60788861&_r=0

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I've said it before, and I will say it again. Scientist, whether it is conscious or not, do not WANT to believe that all DNA is useful, because if they do their pet theory of evolution is dead. If the genome were to be proven 100% useful, as I strongly suspect it is, then there is no possibility of chance. There is no room for the trial and error ideology that they cling to in order to escape the inescapable conclusion that life was designed.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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A useful retrovirus steers human embryology:-http://www.nature.com/nsmb/journal/v21/n4/full/nsmb.2799.html-Abstract: "Human endogenous retrovirus subfamily H (HERVH) is a class of transposable elements expressed preferentially in human embryonic stem cells (hESCs). Here, we report that the long terminal repeats of HERVH function as enhancers and that HERVH is a nuclear long noncoding RNA required to maintain hESC identity. Furthermore, HERVH is associated with OCT4, coactivators and Mediator subunits. Together, these results uncover a new role of species-specific transposable elements in hESCs."

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Tony; I've said it before, and I will say it again. Scientist, whether it is conscious or not, do not WANT to believe that all DNA is useful, because if they do their pet theory of evolution is dead. If the genome were to be proven 100% useful, as I strongly suspect it is, then there is no possibility of chance. There is no room for the trial and error ideology that they cling to in order to escape the inescapable conclusion that life was designed.-That is the reason for my 'goodbye' in the headline. I suspect that Encode's 80% is close to correct.

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TONY: I've said it before, and I will say it again. Scientist, whether it is conscious or not, do not WANT to believe that all DNA is useful, because if they do their pet theory of evolution is dead. If the genome were to be proven 100% useful, as I strongly suspect it is, then there is no possibility of chance. There is no room for the trial and error ideology that they cling to in order to escape the inescapable conclusion that life was designed.-I've said it before, and I will say it again, both sides will always find an answer to any discovery. Whether you think God designed life, it came about by chance, or it came about via some kind of panpsychist evolution, you can twist any scenario to fit your hypothesis. Do you really mean to tell me that if scientists could prove there WAS junk, you would immediately lose your faith in the existence of a designer? Of course you wouldn't. If DNA is 100% useful, the trial and error ideology can simply claim that successful trials preserved what worked, and errors eliminated what didn't work. That is the process known as Natural Selection.

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dhw: Do you really mean to tell me that if scientists could prove there WAS junk, you would immediately lose your faith in the existence of a designer?-I wouldn't be as sure as I am if the 90% that they claim is junk is really junk..-
> dhw: If DNA is 100% useful, the trial and error ideology can simply claim that successful trials preserved what worked, and errors eliminated what didn't work. That is the process known as Natural Selection.-You always skip the point. If DNA is 80% functional, that makes it so complex it could not have developed by natural selection or chance. Only a mind could have created the code.

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TONY: I've said it before, and I will say it again. Scientist, whether it is conscious or not, do not WANT to believe that all DNA is useful, because if they do their pet theory of evolution is dead. If the genome were to be proven 100% useful, as I strongly suspect it is, then there is no possibility of chance. There is no room for the trial and error ideology that they cling to in order to escape the inescapable conclusion that life was designed.
> 
>DHW: I've said it before, and I will say it again, both sides will always find an answer to any discovery. Whether you think God designed life, it came about by chance, or it came about via some kind of panpsychist evolution, you can twist any scenario to fit your hypothesis. Do you really mean to tell me that if scientists could prove there WAS junk, you would immediately lose your faith in the existence of a designer? Of course you wouldn't. If DNA is 100% useful, the trial and error ideology can simply claim that successful trials preserved what worked, and errors eliminated what didn't work. That is the process known as Natural Selection.-No trial and error methodology can produce a 100% useful product, particularly not on par with the complexity of DNA. The chances of even 80% percent appearing via random mutation is so staggering that you would have a higher chance of securing a peaceful dinner date with the Queen of England, the Israeli and Palestinian Prime ministers, Richard Dawkins, the Easter Bunny, Santa Clause the Pope, and and Rabbi Raskin and that little leprechaun fellow off the Lucky Charms commercial while the American congress was hard at work and politicians tell the truth.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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TONY: I've said it before, and I will say it again. Scientist, whether it is conscious or not, do not WANT to believe that all DNA is useful, because if they do their pet theory of evolution is dead. If the genome were to be proven 100% useful, as I strongly suspect it is, then there is no possibility of chance. There is no room for the trial and error ideology that they cling to in order to escape the inescapable conclusion that life was designed.-DHW: I've said it before, and I will say it again, both sides will always find an answer to any discovery. Whether you think God designed life, it came about by chance, or it came about via some kind of panpsychist evolution, you can twist any scenario to fit your hypothesis. Do you really mean to tell me that if scientists could prove there WAS junk, you would immediately lose your faith in the existence of a designer? Of course you wouldn't. If DNA is 100% useful, the trial and error ideology can simply claim that successful trials preserved what worked, and errors eliminated what didn't work. That is the process known as Natural Selection.-DAVID: You always skip the point. If DNA is 80% functional, that makes it so complex it could not have developed by natural selection or chance. Only a mind could have created the code.-The same argument is used of all life's complexities, but many scientists remain atheists and argue for a chance beginning. I neither skip nor reject the design argument. I am pointing out that atheists will still find a means of incorporating new discoveries into their scenario, just as theists do. In the days before ENCODE began to unravel the purposes of so-called junk, I don't recall theists getting into a mighty panic over the then prevalent view that DNA was not 100% functional. I repeat: "You can twist any scenario to fit your hypothesis."
 
TONY: No trial and error methodology can produce a 100% useful product, particularly not on par with the complexity of DNA. The chances of even 80% percent appearing via random mutation is so staggering that you would have a higher chance of securing a peaceful dinner date with the Queen of England, the Israeli and Palestinian Prime ministers, Richard Dawkins, the Easter Bunny, Santa Clause the Pope, and and Rabbi Raskin and that little leprechaun fellow off the Lucky Charms commercial while the American congress was hard at work and politicians tell the truth. -Great post, Tony, and I am no supporter of the random mutations theory. But I still maintain that both sides will always find an answer to any discovery. The very fact that life exists defies all the odds, and that was true even before the discovery of DNA. My point is exemplified by the fact that Francis Crick was an agnostic with a strong inclination towards atheism and James Watson is an atheist.

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DHW:I neither skip nor reject the design argument. I am pointing out that atheists will still find a means of incorporating new discoveries into their scenario, just as theists do. In the days before ENCODE began to unravel the purposes of so-called junk, I don't recall theists getting into a mighty panic over the then prevalent view that DNA was not 100% functional. I repeat: "You can twist any scenario to fit your hypothesis...But I still maintain that both sides will always find an answer to any discovery. The very fact that life exists defies all the odds, and that was true even before the discovery of DNA. My point is exemplified by the fact that Francis Crick was an agnostic with a strong inclination towards atheism and James Watson is an atheist.-This is not a case of trying to fit anything to a theory. This is a case of either something is possible, or it is not. Saying that it must have happened because we are here is a cop out that ignores the fact that it is, by sciences/maths own definitions, impossible. They don't even stand by their own definitions of what makes something impossible.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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DHW:I neither skip nor reject the design argument. I am pointing out that atheists will still find a means of incorporating new discoveries into their scenario, just as theists do. In the days before ENCODE began to unravel the purposes of so-called junk, I don't recall theists getting into a mighty panic over the then prevalent view that DNA was not 100% functional. I repeat: "You can twist any scenario to fit your hypothesis...But I still maintain that both sides will always find an answer to any discovery. The very fact that life exists defies all the odds, and that was true even before the discovery of DNA. My point is exemplified by the fact that Francis Crick was an agnostic with a strong inclination towards atheism and James Watson is an atheist.
> 
> Tony: This is not a case of trying to fit anything to a theory. This is a case of either something is possible, or it is not. Saying that it must have happened because we are here is a cop out that ignores the fact that it is, by sciences/maths own definitions, impossible. They don't even stand by their own definitions of what makes something impossible.-Crick and Watson's opinions are just that, individual human opinions, not adding any thing factual. Darwinists twist any finding beyond recognition to fit their agenda. the story of junk DNA is that it fits the idea of uncontrolled chance evolution which results in many discarded elements of DNA because of the chance advance producing junk along the way.

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DHW:I neither skip nor reject the design argument. I am pointing out that atheists will still find a means of incorporating new discoveries into their scenario, just as theists do. In the days before ENCODE began to unravel the purposes of so-called junk, I don't recall theists getting into a mighty panic over the then prevalent view that DNA was not 100% functional. I repeat: "You can twist any scenario to fit your hypothesis...But I still maintain that both sides will always find an answer to any discovery. The very fact that life exists defies all the odds, and that was true even before the discovery of DNA. My point is exemplified by the fact that Francis Crick was an agnostic with a strong inclination towards atheism and James Watson is an atheist.-TONY: This is not a case of trying to fit anything to a theory. This is a case of either something is possible, or it is not. Saying that it must have happened because we are here is a cop out that ignores the fact that it is, by sciences/maths own definitions, impossible. They don't even stand by their own definitions of what makes something impossible.-I am as ill at ease representing atheism in discussions with you as I am representing theism in discussions with atheists, but I will put my own atheistic case. (George, can you not be tempted to join in the junketing?) Firstly, if I were an atheist, I would point out that it is only theist scientists who claim the odds are impossible. I find it perfectly feasible that either this universe has existed for eternity, or first cause energy has spawned an infinite number of universes throughout eternity. That offers an infinity of combinations of matter, and if you have an infinity of combinations, anything is possible.-Secondly, the argument that life is too complex to have come about by chance is counterbalanced by the argument that there is no evidence for a universal mind capable of creating life and universes. To maintain that such a mind must exist though we don't know how it could have come into existence is just as huge a cop-out as the argument that we are here but we don't know how we got here.
 
Thirdly, if I were an atheist, I would suggest that once chance (or some sort of panpsychist evolution) had assembled the mechanisms for life and evolution (no more of a miracle than an infinite, eternal consciousness that came from nowhere), the survival of every beneficial change would have increased complexity, whereas any unsuccessful change would have disappeared. And so if DNA does prove to be 100% useful, that is because any non-useful component would have been jettisoned in the process known as natural selection. You don't have to accept the argument. I don't accept it either. But I don't find it any less acceptable than the case for an infinite, eternal consciousness without a cause.
 
DAVID: Crick and Watson's opinions are just that, individual human opinions, not adding any thing factual. Darwinists twist any finding beyond recognition to fit their agenda. the story of junk DNA is that it fits the idea of uncontrolled chance evolution which results in many discarded elements of DNA because of the chance advance producing junk along the way.-Of course those are just individual opinions and add nothing factual. Your belief in God comes under exactly the same category. I am merely pointing out that as the scientists who discovered DNA they were not exactly ignorant of life's complexities, and yet like so many other specialists in so many other fields of science, they see no reason to believe in your God. Do you take them all for fools? I have pointed out that both sides can twist any scenario to fit their hypothesis, but you can only see one side doing it. I am well aware of the atheist argument concerning junk, but just as theists have changed their argument to accommodate evolution, atheists can change their argument to accommodate functioning DNA, as I have pointed out in my response to Tony.

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> dhw: I find it perfectly feasible that either this universe has existed for eternity, or first cause energy has spawned an infinite number of universes throughout eternity. That offers an infinity of combinations of matter, and if you have an infinity of combinations, anything is possible.-Very large numbers of chances can be very comforting. Unfortunately there is no evidence of many universes, and we are trapped in one universe which had can obvious beginning. It is easier to decide upon an intelligent first cause.
> 
> dhw: Secondly, the argument that life is too complex to have come about by chance is counterbalanced by the argument that there is no evidence for a universal mind capable of creating life and universes. To maintain that such a mind must exist though we don't know how it could have come into existence is just as huge a cop-out as the argument that we are here but we don't know how we got here.-It is not a cop-out. It is reasoning to the best solution to the puzzle.

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Theists are not the only ones that look at the probabilities. That is why people like Steven Hawking agree that the probabilities for life occurring our infinitesimally small. Moreover, that is why they have to keep coming up with older ages, multi-verses, and other increasingly absurd theories to try and bolster the probabilities. String Theory is a direct response to the fact that the chances of our universe existing without divine intervention are practically nil. The chances of both the universe, planet earth, AND life existing are beyond nil, that is to say, far beyond statistically impossible.-
And this, my friend, is the atheist answer: http://www.science20.com/stars_planets_life/calculating_odds_life_could_begin_chance-They dodge the bullet again by trying to say that well, it didn't have to start with life, and then inventing another million monkeys scenario. -The skip DNA, and go to RNA:-"For the purposes of today's column I will go through the probability calculation that a specific ribozyme might assemble by chance. Assume that the ribozyme is 300 nucleotides long, and that at each position there could be any of four nucleotides present. The chances of that ribozyme assembling are then 4^300, a number so large that it could not possibly happen by chance even once in 13 billion years, the age of the universe."-Then they skip a specific RNA and say, well.. just any assemblage will do, and then we can use natural selection.-"The calculation assumes that a single specific ribozyme must be synthesized for life to begin, but that's not how it works. Instead, let's make the plausible assumption that an enormous number of random polymers are synthesized, which are then subject to selection and evolution. This is the alternative hypothesis, and we can test it."-And yes, experiments show that could work, but ONLY if the RNA elements were ENGINEERED to begin with. "In vitro RNA selection does not demonstrate that complex ribozymes could have arisen naturally in a prebiotic soup, because the in vitro experimental conditions are wholly unrealistic, revealing at every turn the fingerprints of intervening intelligence. RNA World researchers have taken their own engineering of ribozymes as analogous to plausible prebiotic processes, when in fact the two situations are profoundly different. Indeed, aspects of ribozyme engineering, together with other lines of evidence, support a very different view of biological origins from that advocated by RNA World researchers."-So, you have the atheistic acknowledgement that it is statistically impossible, then they engineer a solution and say "Look! Randomness works!" (provided that some intelligent being first creates a perfect environment and randomly generates trillions of RNA strands and binds them all together at the same spot and the same time....shhhhhhh)

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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This article is especially for DHW. -http://idscience.hubpages.com/hub/Why-Darwinian-Evolution-Is-Impossible

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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TONY: This article is especially for DHW. - [i]http://idscience.hubpages.com/hub/Why-Darwinian-Evolution-Is-Impossible[/i]-I'm afraid the technicalities are way beyond me, but if I've understood the general gist, it is not the conventional attack on chance, but a direct assertion that organisms are incapable of undergoing innovations because these would be destabilizing. Since nobody has ever witnessed the innovations that have led to new species, and since life itself is unique and so it is highly doubtful whether we can draw ANY analogies, I'm not sure that anyone is qualified to say what is and isn't possible. We know organisms can adapt, which clearly involves change without destabilisation, but that is all we know. -Towards the end of the article, the author's reference to the designer creating pairs (capable only of minor variations) suggests that he is advocating separate creation of all species (broad sense). Since David believes that evolution did take place, thanks to God preprogramming the first cells in such a way that innovations could happen in existing organisms without destabilisation, perhaps I could call upon him to comment on the scientific details.

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> dhw: I'm afraid the technicalities are way beyond me,-> dhw:Since David believes that evolution did take place, thanks to God preprogramming the first cells in such a way that innovations could happen in existing organisms without destabilisation, perhaps I could call upon him to comment on the scientific details.-Just one very obvious comment about the article. In error correction there must be a mechanism, and we know there is. Therefore, imagine this scenario: initially RNA and DNA form and begin to reproduce more generations. How did RNA/DNA 'know' that errors might occur? Molecules do not plan or think. Obviously, error correction mechanisms had to be simultaneously created or early life would not have reproduced properly and continued to live. We know the correct copy rate is about 99.9%, so errors occurred from the beginning. Further, part of innovation mutations come from uncorrected errors, but since most mutations are deleterious, the control mechanisms were vital. It takes a planning mind to set up both sides of this at once.

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TONY: This article is especially for DHW. -http://idscience.hubpages.com/hub/Why-Darwinian-Evolution-Is-Impossible-dhw:Since David believes that evolution did take place, thanks to God preprogramming the first cells in such a way that innovations could happen in existing organisms without destabilisation, perhaps I could call upon him to comment on the scientific details.-DAVID: Just one very obvious comment about the article. In error correction there must be a mechanism, and we know there is. Therefore, imagine this scenario: initially RNA and DNA form and begin to reproduce more generations. How did RNA/DNA 'know' that errors might occur? Molecules do not plan or think. Obviously, error correction mechanisms had to be simultaneously created or early life would not have reproduced properly and continued to live. We know the correct copy rate is about 99.9%, so errors occurred from the beginning. Further, part of innovation mutations come from uncorrected errors, but since most mutations are deleterious, the control mechanisms were vital. It takes a planning mind to set up both sides of this at once.-Thank you, but that does not answer my question.He seems to be advocating separate creation of the species (broad sense). I know how reluctant you are to contradict anyone who says nasty things about Darwinian evolution, but do you agree with him that evolution through innovation in existing organisms (even if preprogrammed by your God) could not have happened because of destabilization?

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> dhw: Thank you, but that does not answer my question.He seems to be advocating separate creation of the species (broad sense). I know how reluctant you are to contradict anyone who says nasty things about Darwinian evolution, but do you agree with him that evolution through innovation in existing organisms (even if preprogrammed by your God) could not have happened because of destabilization?-The issue of destabilization is simply a view that if arbitrary constants are required for fine tuning, one can look at biology and find the same issue. It requires design. The fine tuning constants are just simply there, without a way to explain why they are that way. In life very specified organic molecules must be of a certain length and folding to have their function fit the requirements for life. There are millions of these molecules, all interlocking like a giant puzzle to create the spark of life. It is like a giant jigsaw puzzle which then creates a giant picture. As Tony just pointed out today ( March 14, 2015, 21:00) it is so complex it requires design. That is why my thoughts about evolution is that God guided it. Did He personally create each species or just guided a process He set in motion? I don't know, but it is one or the other. In other words, the universe is stable because God has set up the mechanism to keep it that way, and the same for evolution. Life, once started with its spark, must continue on the same path from the very first life. -This excerpt makes perfect sense to me, and I've known it for years from my thinking and research:-"Moreover the genome is filled with highly conserved functional elements, that if changed, will cause the biological system to become unstable. We know of the 50 billion proteins (and counting) in life, they all have extremely precise parameters for proper folding & function. If these precise parameters are changed, proper protein function will cease and problems soon arise in the organism. Herein lies the fatal dilemma for abiogenesis and Darwinian evolution, 100% of the biological system must slowly evolve, thus precise fixed elements are impossible to establish.-"This is why naturalists have no choice but to jump over the origins of life, because the cell has scores of highly conserved functional elements that can not be explained by gradual continual random changes. Any evolutionary mechanism with the ability to create a functional arrangement of sequences, also , because its blind, has the ability to destroy that same functional arrangement of sequences.-"An intelligent designer on the other hand would have the foresight to prevent essential functional sequences from being subject to random changes in order to keep the system stable and running, just as PC program codes, parts of a machine, or a buildings infrastructure are prevented from randomly changing for that same reason. Time and unimaginably phenomenal luck produce miracles that defy natural laws for - oddly enough - naturalists."

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dhw: I know how reluctant you are to contradict anyone who says nasty things about Darwinian evolution, but do you agree with him that evolution through innovation in existing organisms (even if preprogrammed by your God) could not have happened because of destabilization?-You have responded with your usual detailed account of why life could only have originated by design, but since my focus is on how evolution itself might work, and since the author insists it couldn't have worked at all, I'll accept everything you say and home in on one statement tucked away in your argument: That is why my thought about evolution is that God guided it. Did He personally create each species or just guided a process He set in motion? I don't know. But it is one or the other. This is a radical departure from your original stance. Dabbling is one thing, but the personal creation of each species would make you into an Old Earth Creationist and not a theistic evolutionist. Your dilemma seems to be deepening as our discussions continue.
 
Because of this I took a quick look at what you said about Creationism in your book The Atheist Delusion, and to my delight (I'd forgotten it) found the following:
I am not arguing, however, that God engineered all these intricate processes separately (Dawkins loves to equate design with biblical Creationism, so that he can ignore all other aspects of the argument.) My point is that living organisms have been provided with mechanisms that enable them to adapt and invent. It is the astonishing versatility of these mechanisms that makes chance so unlikely a provider.-So you actually got there before me: the autonomous inventive mechanism (theistic version). Sounds good to me!

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> dhw: Because of this I took a quick look at what you said about Creationism in your book The Atheist Delusion, and to my delight (I'd forgotten it) found the following:
> I am not arguing, however, that God engineered all these intricate processes separately (Dawkins loves to equate design with biblical Creationism, so that he can ignore all other aspects of the argument.) My point is that living organisms have been provided with mechanisms that enable them to adapt and invent. It is the astonishing versatility of these mechanisms that makes chance so unlikely a provider.
> 
> So you actually got there before me: the autonomous inventive mechanism (theistic version). Sounds good to me!-Remember I don't know how God guided evolution, and I've agreed an onboard IM may really exist in most species. Where you and I disagree is whether it is autonomous vs. semi-autonomous, and I favor semi, so God stays in control. He is not ful,ly in control with semi-autonomous

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DAVID (15 March): That is why my thought about evolution is that God guided it. Did He personally create each species or just guided a process He set in motion? I don't know. But it is one or the other. -DAVID (in The Atheist Delusion): "I am not arguing, however, that God engineered all these intricate processes separately (Dawkins loves to equate design with biblical Creationism, so that he can ignore all other aspects of the argument.) My point is that living organisms have been provided with mechanisms that enable them to adapt and invent. It is the astonishing versatility of these mechanisms that makes chance so unlikely a provider.-Dhw: So you actually got there before me: the (theistic version of) the autonomous inventive mechanism. Sounds good to me!-DAVID: Remember I don't know how God guided evolution, and I've agreed an onboard IM may really exist in most species. Where you and I disagree is whether it is autonomous vs. semi-autonomous, and I favor semi, so God stays in control. He is not fully in control with semi-autonomous.-I remain surprised at your sudden willingness to abandon evolution altogether and accept the possibility that God personally created each species. You now appear to be torn between four (not necessarily mutually exclusive) options: 1) God preprogrammed evolution; 2) God dabbled in the evolutionary process; 3) God gave organisms an inventive mechanism with which to drive evol- while he drove -ution; 4) evolution never happened, and God did it all (= Creationism). I must say I prefer the clear version in your book, in which the astonishingly versatile mechanisms enable organisms to adapt and invent. Ah, the good old days!

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> DAVID: Remember I don't know how God guided evolution, and I've agreed an onboard IM may really exist in most species. Where you and I disagree is whether it is autonomous vs. semi-autonomous, and I favor semi, so God stays in control. He is not fully in control with semi-autonomous.
> 
> dhw: I remain surprised at your sudden willingness to abandon evolution altogether and accept the possibility that God personally created each species. You now appear to be torn between four (not necessarily mutually exclusive) options: 1) God preprogrammed evolution; 2) God dabbled in the evolutionary process; 3) God gave organisms an inventive mechanism with which to drive evol- while he drove -ution; 4) evolution never happened, and God did it all (= Creationism). I must say I prefer the clear version in your book, in which the astonishingly versatile mechanisms enable organisms to adapt and invent. Ah, the good old days!-For some reason you have interpreted my position into four parts. You are a splitter and I'm not. Basically as stated over and over, I believe God used evolution to produce humans. How He did it is alluded to in my comment before yours above. I did mistype my very last comment. It should read "he is not fully in control with an autonomous IM, and in more control with semi-autonomous.

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DAVID: Remember I don't know how God guided evolution, and I've agreed an onboard IM may really exist in most species. Where you and I disagree is whether it is autonomous vs. semi-autonomous, and I favor semi, so God stays in control. He is not fully in control with semi-autonomous.-dhw: I remain surprised at your sudden willingness to abandon evolution altogether and accept the possibility that God personally created each species. You now appear to be torn between four (not necessarily mutually exclusive) options: 1) God preprogrammed evolution; 2) God dabbled in the evolutionary process; 3) God gave organisms an inventive mechanism with which to drive evol- while he drove -ution; 4) evolution never happened, and God did it all (= Creationism). I must say I prefer the clear version in your book, in which the astonishingly versatile mechanisms enable organisms to adapt and invent. Ah, the good old days!-David: For some reason you have interpreted my position into four parts. You are a splitter and I'm not. Basically as stated over and over, I believe God used evolution to produce humans. How He did it is alluded to in my comment before yours above. I did mistype my very last comment. It should read "he is not fully in control with an autonomous IM, and in more control with semi-autonomous.-Autonomous v semi-autonomous is quite a recent split in our discussion. Earlier you said your dilemma lay between preprogramming and dabbling. No problem if you've given up on the preprogramming hypothesis, which even stretched so far as to include the weaverbird's nest and the monarch's lifestyle, and always seemed to me to be way, way over the top. 
 
DAVID (15 March): That is why my thought about evolution is that God guided it. Did He personally create each species or just guided a process He set in motion? I don't know. But it is one or the other.-So now it would seem that your dilemma lies between a semi-autonomous inventive mechanism by which God semi-guided evolution, and the personal creation of each species (Creationism). At least it's being narrowed down.

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> dhw: Autonomous v semi-autonomous is quite a recent split in our discussion. Earlier you said your dilemma lay between preprogramming and dabbling. No problem if you've given up on the preprogramming hypothesis, which even stretched so far as to include the weaverbird's nest and the monarch's lifestyle, and always seemed to me to be way, way over the top. 
> 
> DAVID (15 March): That is why my thought about evolution is that God guided it. Did He personally create each species or just guided a process He set in motion? I don't know. But it is one or the other.
> 
> dhw: So now it would seem that your dilemma lies between a semi-autonomous inventive mechanism by which God semi-guided evolution, and the personal creation of each species (Creationism). At least it's being narrowed down.-Not necessarily. My thinking must remain open-ended. Pre-programming and dabbling are still options, none of which are provable. But God-guided evolution I find very reasonable as in the comment I made about the essay I presented today.

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Dhw (16 March): I remain surprised at your sudden willingness to abandon evolution altogether and accept the possibility that God personally created each species. You now appear to be torn between four (not necessarily mutually exclusive) options: 1) God preprogrammed evolution; 2) God dabbled in the evolutionary process; 3) God gave organisms an inventive mechanism with which to drive evol- while he drove -ution; 4) evolution never happened, and God did it all (= Creationism). -David (17 March): For some reason you have interpreted my position into four parts. You are a splitter and I'm not.-Dhw (18 March): So now it would seem that your dilemma lies between a semi-autonomous inventive mechanism by which God semi-guided evolution, and the personal creation of each species (Creationism). At least it's being narrowed down.-DAVID (19 March): Not necessarily. My thinking must remain open-ended. Pre-programming and dabbling are still options, none of which are provable. But God-guided evolution I find very reasonable as in the comment I made about the essay I presented today.-Of course you do, and so it is. But you have gone straight back to the four-part position that I put to you on 16 March and which you rejected on 17 March! I even pointed out that the positions were not necessarily mutually exclusive. I could hardly have been more helpful!

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dhw: But you have gone straight back to the four-part position that I put to you on 16 March and which you rejected on 17 March! I even pointed out that the positions were not necessarily mutually exclusive. I could hardly have been more helpful!-I believe God did not do it absent some form of evolutionary process. I reject Number 4! If I accepted straight creationism, I wouldn't have all the puzzlement. Some form of evolution appears present. Would God be fooling me and lots of us? Not reasonable. But there are enough discrepancies' in simple common descent such as no genetic tree, convergence, saltation's, punctuated equilibrium contrived theory, etc. to strongly suggest theistic guidance as more complex life unfolded.

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dhw: But you have gone straight back to the four-part position that I put to you on 16 March and which you rejected on 17 March! I even pointed out that the positions were not necessarily mutually exclusive. I could hardly have been more helpful!-DAVID: I believe God did not do it absent some form of evolutionary process. I reject Number 4! If I accepted straight creationism, I wouldn't have all the puzzlement. Some form of evolution appears present. Would God be fooling me and lots of us? Not reasonable. But there are enough discrepancies' in simple common descent such as no genetic tree, convergence, saltation's, punctuated equilibrium contrived theory, etc. to strongly suggest theistic guidance as more complex life unfolded.-Number 4 was the separate creation of species, as referred to in your post of 15 March: "That is why my thought about evolution is that God guided it. Did He personally create each species or just guided a process He set in motion? I don't know. But it is one or the other."-The Creationists will be disappointed now, but we move on. It seems to me that all the so-called discrepancies can be explained by the intelligent, inventive mechanism, whether this was designed by your God or not. Contrived theory is a term I don't know, though. Perhaps you could explain.

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> dhw: The Creationists will be disappointed now, but we move on. It seems to me that all the so-called discrepancies can be explained by the intelligent, inventive mechanism, whether this was designed by your God or not. Contrived theory is a term I don't know, though. Perhaps you could explain.-Punc Eq is a contrived theory to try to explain speciation. When one sees species appearing in the fossil record without intermediates, something has to be invented to explain it. Thus the invention of Punc Eq. It only names what is seen, nothing more. Therefore contrived.

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dhw: The Creationists will be disappointed now, but we move on. It seems to me that all the so-called discrepancies can be explained by the intelligent, inventive mechanism, whether this was designed by your God or not. Contrived theory is a term I don't know, though. Perhaps you could explain.-DAVID: Punc Eq is a contrived theory to try to explain speciation. When one sees species appearing in the fossil record without intermediates, something has to be invented to explain it. Thus the invention of Punc Eq. It only names what is seen, nothing more. Therefore contrived.-Ah! So God is a contrived theory to try to explain life. When one sees the complexity of life without any indication of its origins, something has to be invented to explain it. Thus the invention of God. In this case, it only names what is not known, nothing more. Therefore contrived. I understand it now. Thank you.

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> dhw: Ah! So God is a contrived theory to try to explain life. When one sees the complexity of life without any indication of its origins, something has to be invented to explain it. Thus the invention of God. In this case, it only names what is not known, nothing more. Therefore contrived. I understand it now. Thank you.-Exactly. It fits every problem and issue.

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dhw: I find it perfectly feasible that either this universe has existed for eternity, or first cause energy has spawned an infinite number of universes throughout eternity. That offers an infinity of combinations of matter, and if you have an infinity of combinations, anything is possible.-(A note for Tony: if you believe, as David does, in an eternal God, it is not unreasonable to assume that he did not spend past eternity doing nothing. If he made this universe, he might well have made others, and so the idea of other universes should not seem quite as absurd as you make out.)
 
DAVID: Very large numbers of chances can be very comforting. Unfortunately there is no evidence of many universes, and we are trapped in one universe which had can obvious beginning. It is easier to decide upon an intelligent first cause.-Easier? You do yourself an injustice. In your two books you have taken it upon yourself to pursue (with much scholarship and skill) the extremely difficult task of enrolling science to your aid in the battle against atheism. Unfortunately, there is no evidence of a universal mind, and we are trapped in one universe which prevents access to any information prior to or outside that universe. It is easier to take no decision, though easiness should not be our criterion (and is certainly not mine)! -TONY: Theists are not the only ones that look at the probabilities. That is why people like Steven Hawking agree that the probabilities for life occurring our infinitesimally small. Moreover, that is why they have to keep coming up with older ages, multi-verses, and other increasingly absurd theories to try and bolster the probabilities. String Theory is a direct response to the fact that the chances of our universe existing without divine intervention are practically nil. The chances of both the universe, planet earth, AND life existing are beyond nil, that is to say, far beyond statistically impossible.-Thank you for this and for the rest of your post. For brevity's sake I shan't repeat the rest of your excellent arguments, which echo my own at the end of the brief guide, as an example of our mad world: humans believe that if they ever can consciously and deliberately design such an organism, it will prove that they themselves were not designed. I agree with you: life is almost infinitely improbable, and yes people come up with unprovable theories such as older ages, multiverses (though please see the first paragraph in this post), string theory, and...God theory. Of course you can ridicule atheist theories, just as they ridicule your own - and for the same reasons. There is nothing here but imagination and speculation. (I appreciate the fact that you are not bringing the Bible into this discussion, because that would lead us down other tracks.) You and David see the absurdity of the atheist argument, but not that of your own: nobody knows how life and the universe came into being, so let's invent an eternal, all-knowing designer of no origin, who simply IS, and let's call him God. Unprovable, unknown, unknowable, devoid of any scientific basis, but providing an easy (David's word) answer to the mystery of our origins, as well as providing scope for the human imagination to work on (hence the vast variety of gods, and stories about gods). Life is a mystery, so we solve it by creating an even greater mystery.-That should not be taken as a sign of disrespect for your beliefs. I'm merely trying to explain why I keep seeing pots calling kettles black. One side has to be closer to the truth than the other, but reason certainly won't help me decide which one it is!

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As David has pointed out many times, either everything was created, or it wasn't. It is a pretty short list of options. That means that there either is a God(s), or there isn't. There really is no middle ground. Finding the least absurd answer then mean's that it is most likely the correct on. -In order to recognize design, there are some thing that we can typically look for:-

Specified complexity - that is, that the chance of something reach a given level of complexity is impossible by random chance. 

Purpose - There is a clear purpose to the item in question.

Need - In many cases, a design fills a specific need.

Efficiency - This is one of those weird ones, the best example I can think of right off the top of my head is, if you toss a box of chips(fries) into the air, random chance will not pack them neatly and efficiently into the most ideal configuration.

Redundancy - Randomness does not produce effective redundancy

Error Correct - Randomness does not produce error correction

Stability - Randomness can produce stability, so stability has to be taken in conjunction with, and in the context of, other elements on the list.

Simplicity - This may seem at odds with complexity, but it is not. Randomly generated events are typically needlessly complex. In this case, simplicity is the combination of Specified Complexity coupled with Efficiency in order to fill a purpose or need. 

Aesthetics - Randomness is typically not aesthetically pleasing to the senses.

Balance - Randomness does not typically produce a balanced system, it may produce a seemingly balanced distribution(like the probability of a dice roll), but that is not really the same thing.

-These are just a few things. Yet, they are all things that we see in nature. If randomness can not create these attributes repeatably, then how do we explain that they all repeatedly exist? If it is not random, the ONLY other possibility is design.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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Dhw: You and David see the absurdity of the atheist argument, but not that of your own: nobody knows how life and the universe came into being, so let's invent an eternal, all-knowing designer of no origin, who simply IS, and let's call him God. Unprovable, unknown, unknowable, devoid of any scientific basis, but providing an easy (David's word) answer to the mystery of our origins, as well as providing scope for the human imagination to work on (hence the vast variety of gods, and stories about gods). Life is a mystery, so we solve it by creating an even greater mystery.
That should not be taken as a sign of disrespect for your beliefs. I'm merely trying to explain why I keep seeing pots calling kettles black. One side has to be closer to the truth than the other, but reason certainly won't help me decide which one it is!-TONY: As David has pointed out many times, either everything was created, or it wasn't. It is a pretty short list of options. That means that there either is a God(s), or there isn't. There really is no middle ground. Finding the least absurd answer then mean's that it is most likely the correct on. 
In order to recognize design, there are some thing that we can typically look for....-You go on to offer us a brilliant résumé (thank you) of all the factors integral to design, most of which are incontrovertible when applied to human activity. I shan't repeat the above brief list of problems with what you consider to be the less absurd answer (God), but will explain how I think your own list can be drastically reduced. I will happily acknowledge that randomness as the initial trigger for life and the mechanism for evolution is every bit as absurd as a universal intelligence that had no beginning and (cop-out of cop-outs) simply IS. Six of one and half a dozen of the other. But from that initial step, once cells reproduced themselves and were able to combine and learn from one another (no more absurd than eternal, unsourced energy already knowing everything there is to know), the majority of your factors automatically come into play. Living organisms have the purpose to survive and propagate and improve their quality of life. Those that are efficient prosper, the rest fail; there is no randomness except through changing environments, to which successful organisms adapt, while some even change in order to exploit the new conditions. Simplicity is a keynote - only that which is necessary will be carried forward; balance will continually change as the environment changes, or individual species become particularly efficient. Aesthetics are a matter of subjective judgement. I myself do not find Mrs Hippopotamus irresistibly beautiful, but I'm sure Mr Hippo does (or did). You create a scenario in which every change and progression is random (and this, I agree, is a major fault in Darwin's theory), but it ain't necessarily so. Instead of an absurd eternal and universal intelligence, you now have an absurd initial concatenation of materials whose intelligence evolves. Once a form of intelligence is in place, it designs itself. That is why David is so bitterly opposed to the findings of many scientists that even single cells are intelligent, communicative, problem-solving, decision-making beings. But he grants that there is a 50/50 possibility that they are. Yes, the chance birth of that intelligence is as incredible as the non-birth of divine intelligence. But at least the former option confines us to the world we know, as opposed to a reality wildly beyond the scope of the imagination.-I'd better repeat that I am not championing atheism, and my intelligent cell hypothesis can also be viewed theistically. I am simply explaining my agnosticism, which in discussions with you and David inevitably entails putting my own case for atheism.

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DHW: But from that initial step, once cells reproduced themselves and were able to combine and learn from one another (no more absurd than eternal, unsourced energy already knowing everything there is to know), the majority of your factors automatically come into play. -That 'initial step' is a few trillion 'initial steps' totally disregarded, each of which that had to happen 'just so', each of which had to happen a few trillion times. -> 
>DHW: I'd better repeat that I am not championing atheism, and my intelligent cell hypothesis can also be viewed theistically. I am simply explaining my agnosticism, which in discussions with you and David inevitably entails putting my own case for atheism.-That would be because you are. And you are doing it in much the same fashion that Atheists do. You are trivializing that "initial step", and trivializing the fact that it would have had to to happen a tremendous number of times both consecutively and concurrently in order for that initial step to have occurred. And you are trivializing the absurd number of things that aren't subject to evolutionary trial and error, such as the "just so" laws of physics and the "just so" location of the planet and the a whole slew of other "just so" parameters, none of which are even remotely possible statistically and are wholly unaffected by evolution.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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DHW: But from that initial step, once cells reproduced themselves and were able to combine and learn from one another (no more absurd than eternal, unsourced energy already knowing everything there is to know), the majority of your factors automatically come into play. -TONY: That 'initial step' is a few trillion 'initial steps' totally disregarded, each of which that had to happen 'just so', each of which had to happen a few trillion times. -DHW: I'd better repeat that I am not championing atheism, and my intelligent cell hypothesis can also be viewed theistically. I am simply explaining my agnosticism, which in discussions with you and David inevitably entails putting my own case for atheism.-TONY: That would be because you are. And you are doing it in much the same fashion that Atheists do. You are trivializing that "initial step", and trivializing the fact that it would have had to to happen a tremendous number of times both consecutively and concurrently in order for that initial step to have occurred. And you are trivializing the absurd number of things that aren't subject to evolutionary trial and error, such as the "just so" laws of physics and the "just so" location of the planet and the a whole slew of other "just so" parameters, none of which are even remotely possible statistically and are wholly unaffected by evolution.-As always, you mount what I view as a perfectly justified case against atheism, but you ignore the framework of our discussion, which is that both sides trivialize and place their faith in hypotheses that beggar belief. Must I spell it out for you? You like figures. Well, nobody knows the size of the universe - it may even be infinite. Based on what can be observed, some folk estimate that there are 100 billion stars in our galaxy alone. There may be 10 billion galaxies. Do the maths yourself. If the universe is finite, some websites suggest it may be 92 billion light years in diameter. There are stars constantly being born while others die - to what purpose we have no idea. You believe that this unimaginable, ever changing vastness (our sun and our planet will also die one day) was created by, and is controlled and contained by (or contains) a conscious mind, perhaps even a being at least 92 billion light years in diameter (for maybe the universe itself IS your God), though you don't know what it is made of, how it acquired its consciousness, why it is constantly making new stars and allowing others to die, or what it might have done or even consisted of before it created this universe. Some people even believe that this unimaginably vast mind created this unimaginably vast universe with its unimaginably vast number of stars past, present and future, just for the sake of producing us humans on the tiny speck we call Earth. They even think that the spirit of 92 times whatever billion light years' worth of materials and energy (sorry, I can't do the real maths) loves and cares about Mr Ugg, who died a thousand years ago in the village of Ugg in Uggland.-You think that I am trivializing the origin of life and the conditions that allow for life because of the odds against them. In the context of what may be the infinity of our universe, or at least of numbers so vast that they might just as well be infinite, you argue that our pathetically limited life and consciousness can only have been designed, whereas the eternal consciousness creating and controlling let's say 92 times whatever billion light years of space and matter and the zillions of stars and the intricate complexities of our own life and consciousness simply IS. Yet you regard the view that our own life simply IS as a cop-out. -If one side in the battle between theism and atheism is guilty of trivialization, so is the other. (And I haven't even mentioned the history of the gods.) However, one of you is closer to the truth than the other, so my scepticism towards both chance AND a designer is patently wrong. Therefore you and David, Dawkins and Hawking are quite right to cherish your respective faiths, and I can only sit on my fence and let myself be pelted from both sides. Fortunately, the folk on this website are relatively gentle throwers!

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So many of those 'finely tuned' things that I mentioned, the ones that aren't subject to evolution or natural selection are what make those billions and billions of stars even possible. If 'gravity' were just a slight bit stronger, the universe would not have formed. -Things Atheist trivialize in regards to just the existence of our universe:-
ratio of electromagnetic force constant to gravitational force constant
if larger: all stars would be at least 40% more massive than the sun; hence, stellar burning would be too brief and too uneven for life support
if smaller: all stars would be at least 20% less massive than the sun, thus incapable of producing heavy elements-
ratio of number of protons to number of electrons
if larger: electromagnetism would dominate gravity, preventing galaxy, star, and planet formation
if smaller: same as above-expansion rate of the universe
if larger: no galaxies would form
if smaller: universe would collapse, even before stars formed-entropy level of the universe
if larger: stars would not form within proto-galaxies
if smaller: no proto-galaxies would form-
initial uniformity of radiation
if more uniform: stars, star clusters, and galaxies would not have formed
if less uniform: universe by now would be mostly black holes and empty space-average distance between galaxies
if larger: star formation late enough in the history of the universe would be hampered by lack of material
if smaller: gravitational tug-of-wars would destabilize the sun's orbit-density of galaxy cluster
if denser: galaxy collisions and mergers would disrupt the sun's orbit
if less dense: star formation late enough in the history of the universe would be hampered by lack of material-
fine structure constant (describing the fine-structure splitting of spectral lines) if larger: all stars would be at least 30% less massive than the sun
if larger than 0.06: matter would be unstable in large magnetic fields
if smaller: all stars would be at least 80% more massive than the sun-decay rate of 8Be
if slower: heavy element fusion would generate catastrophic explosions in all the stars
if faster: no element heavier than beryllium would form; thus, no life chemistry-ratio of neutron mass to proton mass
if higher: neutron decay would yield too few neutrons for the formation of many life-essential elements
if lower: neutron decay would produce so many neutrons as to collapse all stars into neutron -stars or black holes-initial excess of nucleons over anti-nucleons
if greater: radiation would prohibit planet formation
if lesser: matter would be insufficient for galaxy or star formation-polarity of the water molecule
if greater: heat of fusion and vaporization would be too high for life
if smaller: heat of fusion and vaporization would be too low for life; liquid water would not work as a solvent for life chemistry; ice would not float, and a runaway freeze-up would result-supernovae eruptions
if too close, too frequent, or too late: radiation would exterminate life on the planet
if too distant, too infrequent, or too soon: heavy elements would be too sparse for rocky planets to form-white dwarf binaries
if too few: insufficient fluorine would exist for life chemistry
if too many: planetary orbits would be too unstable for life
if formed too soon: insufficient fluorine production
if formed too late: fluorine would arrive too late for life chemistry-ratio of exotic matter mass to ordinary matter mass
if larger: universe would collapse before solar-type stars could form
if smaller: no galaxies would form-number of effective dimensions in the early universe
if larger: quantum mechanics, gravity, and relativity could not coexist; thus, life would be impossible
if smaller: same result-number of effective dimensions in the present universe
if smaller: electron, planet, and star orbits would become unstable
if larger: same result-mass of the neutrino
if smaller: galaxy clusters, galaxies, and stars would not form
if larger: galaxy clusters and galaxies would be too dense-big bang ripples
if smaller: galaxies would not form; universe would expand too rapidly
if larger: galaxies/galaxy clusters would be too dense for life; black holes would dominate; universe would collapse before life-site could form-size of the relativistic dilation factor
if smaller: certain life-essential chemical reactions will not function properly
if larger: same result-uncertainty magnitude in the Heisenberg uncertainty principle
if smaller: oxygen transport to body cells would be too small and certain life-essential elements would be unstable
if larger: oxygen transport to body cells would be too great and certain life-essential elements would be unstable-cosmological constant
if larger: universe would expand too quickly to form solar-type stars--Things Creationist Trivialize:-How God Exists.-
It isn't just that the universe is fine tuned for life, it is fine tuned for the universe as we know it to even exist! So yes, there IS some trivialization going on. That is not throwing stones at anyone, it is simply pointing out what should be painfully obvious.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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dhw: You think that I am trivializing the origin of life and the conditions that allow for life because of the odds against them. In the context of what may be the infinity of our universe, or at least of numbers so vast that they might just as well be infinite, you argue that our pathetically limited life and consciousness can only have been designed, whereas the eternal consciousness creating and controlling let's say 92 times whatever billion light years of space and matter and the zillions of stars and the intricate complexities of our own life and consciousness simply IS. Yet you regard the view that our own life simply IS as a cop-out. -What does size have to do with anything? You have a strange approach to the discussion. The issue is why are there human being on Earth? That fact is more in favor of a God than if the universe were teeming with life. That fact suggests a special creation doesn't it. We know the Earth is very, very special. Tony has told you how special the universe is. And the CMB was created 350,000 years after the BB; the universe is 3.78 billion years old so it is not so infinite after all. The 'infinite universe' is a is a claim the atheist folks are making as a substitute for the multiverse, if that unprovable conjecture doesn't fly. Two unprovable conjectures are just that, nothings. 
> 
> dhw: If one side in the battle between theism and atheism is guilty of trivialization, so is the other. (And I haven't even mentioned the history of the gods.) However, one of you is closer to the truth than the other, so my scepticism towards both chance AND a designer is patently wrong.-Thanks for admitting that you are wrong. The only trivial point the atheists make is to refuse to accept a first cause. That is why we get the jokingly stupid 'something-from-nothing' junk being published (see Krauss as a philosophic marvel). Tony and I are not trivial. We are making pointed criticisms of the atheists argument. They don't have one. Non-belief is a difficult position. Proving a negative is an almost impossible proposition. Reasoning to a reasonable positive solution makes the most sense, but I admit at that point one has to take Pascal's leap. You are a jumper or you are not, hence agnosticism as a refuge.

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DAVID: What does size have to do with anything? You have a strange approach to the discussion. The issue is why are there human beings on Earth? -As frequently happens on this forum, the discussion between Tony and myself has changed the subject. Both of you constantly explain why you reject chance and therefore believe in a designer, but in the post you are referring to, I have spelled out the unimaginable scale and unfathomable nature of the power you expect us to believe in although you have no direct, observable, provable evidence that such a power exists. It is nothing more than a theory to explain why we exist, and it has no more substance than the multiverse, string theory or any other hypothesis offered to solve the great mystery. Your answer is that one has to take Pascal's leap. No, one doesn't.-Tony has come up with another admirable list of designer arguments, which he summarizes: It isn't just that the universe is fine tuned for life, it is fine tuned for the universe as we know it to even exist. This is none other than the nebulous anthropic principle, with which both theists and atheists try to justify their beliefs: if the universe (and life) was not as it is, it would either not exist or it would not be as it is. The atheist says it has to be like this because it IS, and the theist says it has to be like this, God made it this way, and God IS. Since we have absolutely nothing with which to compare our universe (or our life), the argument is a dead end.
 
DAVID: The only trivial point the atheists make is to refuse to accept a first cause. [...] Tony and I are not trivial. We are making pointed criticisms of the atheists argument. [...] Reasoning to a reasonable positive solution makes the most sense, but I admit at that point one has to take Pascal's leap. -I have accepted first cause. I do not accept (or reject) first cause consciousness. Reasonableness and the most sense are totally subjective concepts, and while I accept your criticisms of atheistic faith in chance, I do not accept the reasonableness of faith in the nebulous being described in my earlier post. Tony says the only thing Creationists trivialize is How God Exists. That is the equivalent of saying the only thing atheists trivialize is How We Exist, but I'll accept your summary if you'll accept mine. However, belief in God is not the default position. If there is no evidence for something, why should we believe in it? As David says of the infinite universe and the multiverse: "Two unprovable conjectures are just that, nothings." I'm afraid the same applies to the God conjecture.
 
I still respect and admire you both for your Pascalian athleticism, but I'd respect and admire you even more if you would acknowledge just what a mighty leap is required!

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> dhw: Tony has come up with another admirable list of designer arguments, which he summarizes: It isn't just that the universe is fine tuned for life, it is fine tuned for the universe as we know it to even exist. This is none other than the nebulous anthropic principle, with which both theists and atheists try to justify their beliefs: if the universe (and life) was not as it is, it would either not exist or it would not be as it is.-
I would remind you: John Leslie in his book Universes uses fine tuning to conclude: (paraphrased) "either there is a God and/or a multiverse". The anthropic principal, of which I want no part and never would use, is circular reasoning. We are here because of fine tuning and if we were not here there would be no fine tuning. It is philosophic garbage invented as usual by a cosmology scientist. It is only if fine tuning is used as a teleological argument that theists and Leslie go into action.-> 
> dhw: I have accepted first cause..... However, belief in God is not the default position. If there is no evidence for something, why should we believe in it? As David says of the infinite universe and the multiverse: "Two unprovable conjectures are just that, nothings." I'm afraid the same applies to the God conjecture.
> 
> I still respect and admire you both for your Pascalian athleticism, but I'd respect and admire you even more if you would acknowledge just what a mighty leap is required!-I understand the leap.

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DHW: It is nothing more than a theory to explain why we exist, and it has no more substance than the multiverse, string theory or any other hypothesis offered to solve the great mystery. Your answer is that one has to take Pascal's leap. No, one doesn't... Tony has come up with another admirable list of designer arguments, which he summarizes: It isn't just that the universe is fine tuned for life, it is fine tuned for the universe as we know it to even exist. This is none other than the nebulous anthropic principle, with which both theists and atheists try to justify their beliefs: if the universe (and life) was not as it is, it would either not exist or it would not be as it is. The atheist says it has to be like this because it IS, and the theist says it has to be like this, God made it this way, and God IS. Since we have absolutely nothing with which to compare our universe (or our life), the argument is a dead end.-
First, my argument was not the anthropic principle, as that is based on the existence of the humans that observe it (from Greek anthropos, meaning "human"). My argument had nothing to do with life, and I intentionally went through and tried to remove all references to life from the points listed. If I missed one, my apologies. However, "if the universe (and life) was not as it is, it would either not exist or it would not be as it is" is not the argument at all. It would be better stated as "If the parameters of physics were not as they are, the universe could not exist. Period." Not that it could not exist in it's current state, it simply could not exist. -
>DHW: I have accepted first cause. I do not accept (or reject) first cause consciousness. Reasonableness and the most sense are totally subjective concepts, and while I accept your criticisms of atheistic faith in chance, I do not accept the reasonableness of faith in the nebulous being described in my earlier post. Tony says the only thing Creationists trivialize is How God Exists. That is the equivalent of saying the only thing atheists trivialize is How We Exist, but I'll accept your summary if you'll accept mine. However, belief in God is not the default position. If there is no evidence for something, why should we believe in it? As David says of the infinite universe and the multiverse: "Two unprovable conjectures are just that, nothings." I'm afraid the same applies to the God conjecture.
> -I've never denied that believing in God was a leap of faith, but a person of reason is lead to the edge of that chasm by reason and careful consideration of the facts. I would love for someone to show me the proof of dark matter or dark energy outside of what is needed to balance an equation on paper, or even the proof of evolution outside of speculative fairy tales with minimal substance (that need constant revision, I might add, when the data does not fit the theory).

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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TONY: First, my argument was not the anthropic principle, as that is based on the existence of the humans that observe it (from Greek anthropos, meaning "human"). My argument had nothing to do with life, and I intentionally went through and tried to remove all references to life from the points listed. -Brandon Carter himself apparently said the term anthropic was a misnomer. I deliberately put life' in brackets, but the term is applied both to life and to the cosmos. Dawkins devotes two chapters to it, claiming that it is an alternative to design, and laughing at the fact that theists use the same principle to justify their faith - all as I have described in my post, and as you describe below:
 
TONY: However, "if the universe (and life) was not as it is, it would either not exist or it would not be as it is" is not the argument at all. It would be better stated as "If the parameters of physics were not as they are, the universe could not exist. Period." Not that it could not exist in it's current state, it simply could not exist.-You wrote that the universe is fine tuned for the universe as we know it to even exist. I see no difference between as we know it and in its current state. If the parameters of physics were not as they are, they would be different, and so we might have a different universe. Nobody knows what is possible because we have nothing to compare our universe to, and so both sides insist that because the universe is as it is, it has to be as it is, and somehow that supports their case. I still see this if as a dead end.
 
TONY: I've never denied that believing in God was a leap of faith, but a person of reason is lead to the edge of that chasm by reason and careful consideration of the facts. I would love for someone to show me the proof of dark matter or dark energy outside of what is needed to balance an equation on paper, or even the proof of evolution outside of speculative fairy tales with minimal substance (that need constant revision, I might add, when the data does not fit the theory).-There are two chasms. A person of reason will agree that there is no evidence that chance can create life. A person of reason will agree that there is no evidence of a vast, eternal, sourceless, superintelligent mind/power/being that somehow knew from nothing how to create a universe and life. A person of reason can then decide to leap towards chance, or leap towards God, and fill the gaps in his/her knowledge with all kinds of unprovable theories. Or a person of reason can decide not to leap at all.

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> dhw: You wrote that the universe is fine tuned for the universe as we know it to even exist. I see no difference between as we know it and in its current state. If the parameters of physics were not as they are, they would be different, and so we might have a different universe. Nobody knows what is possible because we have nothing to compare our universe to, and so both sides insist that because the universe is as it is, it has to be as it is, and somehow that supports their case. I still see this if as a dead end.-It is not a dead end. The concept of fine tuning is tied to life as we know it. It cannot be known if another type of life is possible. Carbon-based life based on our periodic table of elements is the best arrangement for what we have available. What I am saying that this is possibly the only life-bearing universe possible.

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DHW: You wrote that the universe is fine tuned for the universe as we know it to even exist. I see no difference between as we know it and in its current state. If the parameters of physics were not as they are, they would be different, and so we might have a different universe. Nobody knows what is possible because we have nothing to compare our universe to, and so both sides insist that because the universe is as it is, it has to be as it is, and somehow that supports their case. I still see this if as a dead end.
>-Actually I wrote ""If the parameters of physics were not as they are, the universe could not exist. Period." Not that it could not exist in it's current state, it simply could not exist."-"If the parameters of physics were not as they are, they would be different, and so we might have a different universe." is pure speculation on your part, and is in essence the Multiverse theory. -> 
>>DHW: There are two chasms. A person of reason will agree that there is no evidence that chance can create life. A person of reason will agree that there is no evidence of a vast, eternal, sourceless, superintelligent mind/power/being that somehow knew from nothing how to create a universe and life. A person of reason can then decide to leap towards chance, or leap towards God, and fill the gaps in his/her knowledge with all kinds of unprovable theories. Or a person of reason can decide not to leap at all.-If "A person of reason will agree that there is no evidence that chance can create life" then there is only one other possibility.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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> Tony: If "A person of reason will agree that there is no evidence that chance can create life" then there is only one other possibility.-I hate to gang up, but that has been my constant refrain. Dhw keeps looking for a third way, but there is none. His day dream of the interaction of matter and energy somehow conjuring up the design of this universe when they are both two aspects of the same thing, makes no sense at all. The hope for a third way is Nagelistic, whose bookish hope also made no sense. Reasoning to the simplest solution which can explain all is a reasonable approach. It doesn't explain the mind of God, but there has to be a planning first cause, which requires mentation, surprise! we have the 120 precise parameters of the universe which make it as it is, and then the essay I just presented sees how hard it is to find the right combination of functional proteins to create life if a blind (Darwinian) search is employed.

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TONY: Actually I wrote If the parameters of physics were not as they are, the universe could not exist. Period. Not that it could not exist in it's current state, it simply could not exist.-Aw shucks! On Sunday 15 March at 20.20 (at the end of your analysis of the cosmos) you wrote: It isn't just that the universe is fine tuned for life, it is fine tuned for the universe as we know it to even exist! On Monday 16 March at 21.22, I said I regarded this argument as a dead end, and on Tuesday 17 March at 06.50 (what were you doing up so early?) you rejected the current state - or as we know it - argument you yourself had put forward, and replaced it with the quote above about physics. Frankly, it doesn't make much difference. I agree that it's pure speculation to argue that If the parameters of physics were not as they are, they would be different, and so we might have a different universe, but I am not championing the multiverse theory. I am not championing any theory. We only know (a little of)what we have, and it's also pure speculation to assume that what we have is all there is, or that we know all the possibilities of what we have, or that what we have is specially designed by an unknown designer to be the way it is, or that what we have has to be as it is because that's how it is and so there's no need for a designer.-Dhw: A person of reason will agree that there is no evidence that chance can create life. A person of reason will agree that there is no evidence of a vast, eternal, sourceless, superintelligent mind/power/being that somehow knew from nothing how to create a universe and life. A person of reason can then decide to leap towards chance, or leap towards God, and fill the gaps in his/her knowledge with all kinds of unprovable theories. Or a person of reason can decide not to leap at all.-Tony: If "A person of reason will agree that there is no evidence that chance can create life" then there is only one other possibility.-Why do you ignore the rest of my post? If a person of reason agrees that there is no evidence of Big Daddy in the sky (Our Father who art in Heaven), then there is only one other possibility. That is why so many scientists are atheists. Then they and you try to fill the gaps with your nebulous theories.
 
DAVID: I hate to gang up, but that has been my constant refrain. Dhw keeps looking for a third way, but there is none. His day dream of the interaction of matter and energy somehow conjuring up the design of this universe when they are both two aspects of the same thing, makes no sense at all. [...] Reasoning to the simplest solution which can explain all is a reasonable approach. It doesn't explain the mind of God...-Ganging up is perfectly natural. Theists and atheists do it all the time, and theists even gang up against each other, because it's so difficult to read a mind that might not exist. You personally like to distance yourself from such conflicts by refusing to give any attributes to the designer. I must say that for me a God without attributes might just as well not be there, so I wonder why you don't just say SOMETHING caused life but we don't know what it is. Wouldn't that be "the simplest solution"?

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> DAVID: I hate to gang up, but that has been my constant refrain. Dhw keeps looking for a third way, but there is none. His day dream of the interaction of matter and energy somehow conjuring up the design of this universe when they are both two aspects of the same thing, makes no sense at all. [...] Reasoning to the simplest solution which can explain all is a reasonable approach. It doesn't explain the mind of God...
> 
> Ganging up is perfectly natural......You personally like to distance yourself from such conflicts by refusing to give any attributes to the designer. I must say that for me a God without attributes might just as well not be there, so I wonder why you don't just say SOMETHING caused life but we don't know what it is. Wouldn't that be "the simplest solution"?-I don't give attributes to God simply because I don't believe I can know them. Why do you want to personalize Him, other then to conjure up straw man arguments about what He means to accomplish? Yes, something caused life. The complexity of life's biochemistry forces me to conclude it needs a designer. You stick to a simplistic form of negative thinking, by stopping short of reaching any conclusion which cannot be proven. Again, it takes some faith that your reasoning carries logic. Chance or design is all there can be.

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DAVID: I don't give attributes to God simply because I don't believe I can know them. Why do you want to personalize Him, other then to conjure up straw man arguments about what He means to accomplish? Yes, something caused life. The complexity of life's biochemistry forces me to conclude it needs a designer. You stick to a simplistic form of negative thinking, by stopping short of reaching any conclusion which cannot be proven. Again, it takes some faith that your reasoning carries logic. Chance or design is all there can be. -It cannot be proven that one political party, one partner, one job is better than another, and yet believe it or not, there are agnostics who make such judgements and decisions all the time! Agnosticism does not consist of not reaching a conclusion which cannot be proven, but of not reaching a conclusion because the two sides are evenly balanced and there is no need to shut one eye. As for simplistic, many of the world's worst problems are caused by the simplistic thinking of those who refuse to acknowledge that most issues have more than one side. The history of religion is a prime example.

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> dhw: As for simplistic, many of the world's worst problems are caused by the simplistic thinking of those who refuse to acknowledge that most issues have more than one side. The history of religion is a prime example.-Currently we only know of two possibilities to explain this reality of ours, chance or design. You want a third, fourth or fifth. Can you describe e one reasonable alternative?

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DAVID: Currently we only know of two possibilities to explain this reality of ours, chance or design. You want a third, fourth or fifth. Can you describe one reasonable alternative?-Too simplistic! When does chance begin? When does design begin? Over and over again you quote articles illustrating the complexities of life, and as often as not you comment: All by chance? We spend hours debating how evolution works, and you have conceded the possibility that organisms themselves may contain a mechanism that dispenses with the randomness espoused by Darwin. If this mechanism exists, you will have to confine your ironic question to the origin of the mechanism (maybe God, maybe chance), because then evolution itself does not proceed by chance. So that puts paid to one of your constant beefs about chance. However, when we discuss the origin, I try in vain to point out the irrationality of the belief that conscious beings have to be designed, whereas the conscious being that created those conscious beings doesn't have to be designed. When you do register the illogicality, you tell me that is the point at which one must take the leap of faith.
 
Here are the real alternatives: either the story of life began from the top with an undesigned supercolossal intelligence that always knew everything, or it began from the bottom with the tiniest intelligence that evolved into all the intelligence we now know. How the supercolossal intelligence came to be so intelligent you cannot tell me. How the tiniest intelligence came to be intelligent I cannot tell you. Both choices demand a leap of faith - or of course we choose not to leap.

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> dhw: Here are the real alternatives: either the story of life began from the top with an undesigned supercolossal intelligence that always knew everything, or it began from the bottom with the tiniest intelligence that evolved into all the intelligence we now know. How the supercolossal intelligence came to be so intelligent you cannot tell me. How the tiniest intelligence came to be intelligent I cannot tell you. Both choices demand a leap of faith - or of course we choose not to leap.-I don't believe 'tiny intelligences' can grow themselves. An powerful existing intelligence is the only choice that makes sense to me.

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DHW: Here are the real alternatives: either the story of life began from the top with an undesigned supercolossal intelligence that always knew everything, or it began from the bottom with the tiniest intelligence that evolved into all the intelligence we now know. How the supercolossal intelligence came to be so intelligent you cannot tell me. How the tiniest intelligence came to be intelligent I cannot tell you. Both choices demand a leap of faith - or of course we choose not to leap.-Why does God have to start out as knowing everything? Or more to the point, if all of this did not exist until it was designed and created, what "everything" was there for him to know?

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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> tony: Why does God have to start out as knowing everything? Or more to the point, if all of this did not exist until it was designed and created, what "everything" was there for him to know?-Now I am confused. Didn't God know what he was going to create, and didn't He know how to do it?

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> > tony: Why does God have to start out as knowing everything? Or more to the point, if all of this did not exist until it was designed and created, what "everything" was there for him to know?
> 
>David: Now I am confused. Didn't God know what he was going to create, and didn't He know how to do it?-Did he have to know that from the instant that he sprang into existence? You and DHW both seem to treat him like he has to be Houdini, springing into existence (or always existing) already having all the answers, and completely disregarding the possibility that maybe he didn't do any creating for a REALLY long time. If WE, as imperfect as we are, understand that sitting down and working out a plan BEFORE you start production of something is a good idea, how much more so would God understand that. Do you REALLY look at creation and think, "Eh, he must have made it up as he went along"?

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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> Tony:.... If WE, as imperfect as we are, understand that sitting down and working out a plan BEFORE you start production of something is a good idea, how much more so would God understand that. Do you REALLY look at creation and think, "Eh, he must have made it up as he went along"?-No, I've always accepted the idea that God always knew what He was planning.

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> > Tony:.... If WE, as imperfect as we are, understand that sitting down and working out a plan BEFORE you start production of something is a good idea, how much more so would God understand that. Do you REALLY look at creation and think, "Eh, he must have made it up as he went along"?
> 
>David: No, I've always accepted the idea that God always knew what He was planning.-Well, if he had a the time to plan, that also implies that he time to find and correct any problems during the planning phase, which means that he didn't HAVE to know everything right from the beginning.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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> >David: No, I've always accepted the idea that God always knew what He was planning.
> 
> Tony: Well, if he had a the time to plan, that also implies that he time to find and correct any problems during the planning phase, which means that he didn't HAVE to know everything right from the beginning.-I'm sure He had time to plan. I'm not sure that He knew every complication that might arise. This is why if evolution occurred, it happened under His guidance.

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dhw: Here are the real alternatives: either the story of life began from the top with an undesigned supercolossal intelligence that always knew everything, or it began from the bottom with the tiniest intelligence that evolved into all the intelligence we now know. How the supercolossal intelligence came to be so intelligent you cannot tell me. How the tiniest intelligence came to be intelligent I cannot tell you. Both choices demand a leap of faith - or of course no leap at all. 
DAVID: I don't believe tiny intelligences' can grow themselves. A powerful existing intelligence is the only choice that makes sense to me.-So you believe a supercolossal intelligence can grow itself.-TONY: Why does God have to start out as knowing everything? Or more to the point, if all of this did not exist until it was designed and created, what "everything" was there for him to know?
David: Now I am confused. Didn't God know what he was going to create, and didn't He know how to do it?
TONY: Did he have to know that from the instant that he sprang into existence? You and DHW both seem to treat him like he has to be Houdini, springing into existence (or always existing) already having all the answers, and completely disregarding the possibility that maybe he didn't do any creating for a REALLY long time. If WE, as imperfect as we are, understand that sitting down and working out a plan BEFORE you start production of something is a good idea, how much more so would God understand that. Do you REALLY look at creation and think, "Eh, he must have made it up as he went along"?-I don't treat him like that at all. I don't even know if he exists! And I have repeatedly challenged David's idea that God, if he exists, could know it all in advance. I could actually imagine him making a lot of it up as he goes along (or experimenting) - after all, he may have had eternity to mess around with different ideas and even with different universes. And of course if HE had eternity, unconscious first cause energy would also have had eternity to produce whatever unconscious first cause energy might produce, including perhaps different universes. Who knows? But I'd best leave the two of you to fight over what God might have known and not known, since you are a lot closer to him than I am.

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TONY: Did he have to know that from the instant that he sprang into existence? You and DHW both seem to treat him like he has to be Houdini, springing into existence (or always existing) already having all the answers, and completely disregarding the possibility that maybe he didn't do any creating for a REALLY long time. If WE, as imperfect as we are, understand that sitting down and working out a plan BEFORE you start production of something is a good idea, how much more so would God understand that. Do you REALLY look at creation and think, "Eh, he must have made it up as he went along"?
> 
>DHW: I don't treat him like that at all. I don't even know if he exists! And I have repeatedly challenged David's idea that God, if he exists, could know it all in advance. I could actually imagine him making a lot of it up as he goes along (or experimenting) - after all, he may have had eternity to mess around with different ideas and even with different universes. And of course if HE had eternity, unconscious first cause energy would also have had eternity to produce whatever unconscious first cause energy might produce, including perhaps different universes. Who knows? But I'd best leave the two of you to fight over what God might have known and not known, since you are a lot closer to him than I am.-Err... But you just said "dhw: Here are the real alternatives: ...the story of life began from the top with an undesigned supercolossal intelligence that always knew everything,"-
I'm no closer to God than anyone else, and please do not put those words in my mouth. I do strive to cut out habits/practices from my life that I find to be at odds wit what the bible teaches, but the only one that has the right to say who is closer and who is not is God himself, and I would not presume to claim to speak for him. That is why I try to reference the bible when talking about God.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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TONY: Did he have to know that from the instant that he sprang into existence? You and DHW both seem to treat him like he has to be Houdini, springing into existence (or always existing) already having all the answers, and completely disregarding the possibility that maybe he didn't do any creating for a REALLY long time....
DHW: I don't treat him like that at all. I don't even know if he exists! And I have repeatedly challenged David's idea that God, if he exists, could know it all in advance. I could actually imagine him making a lot of it up as he goes along (or experimenting) - after all, he may have had eternity to mess around with different ideas and even with different universes. -TONY: Err... But you just said "dhw: Here are the real alternatives: ...the story of life began from the top with an undesigned supercolossal intelligence that always knew everything,"-Well spotted. I was of course responding to David, who holds that belief. I must be careful to distinguish between your different brands of theism. I should have written that the real alternative beginnings were an inexplicable undesigned superintelligence at the top and an inexplicable tiny intelligence at the bottom. Thank you.-Dhw: But I'd best leave the two of you to fight over what God might have known and not known, since you are a lot closer to him than I am.-TONY: I'm no closer to God than anyone else, and please do not put those words in my mouth. I do strive to cut out habits/practices from my life that I find to be at odds wit what the bible teaches, but the only one that has the right to say who is closer and who is not is God himself, and I would not presume to claim to speak for him. That is why I try to reference the bible when talking about God.-I'm sorry if I offended you. You wrote: God says: The dead are conscious of nothing. That suggests you know or think you know God's mind. David also thinks he knows God's mind (e.g. God planned everything in advance so that he could create human beings). As a mere speculating agnostic, I must confess I am always surprised by the confidence of such beliefs, and so I'm afraid there was a gentle irony in my remark. My apologies. Perhaps the irony would have been clearer if I had said: "I'd best leave the two of you to fight over what God might have known and not known, since you both seem to know more about God's mind than I do."

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dhw: I must confess I am always surprised by the confidence of such beliefs, and so I'm afraid there was a gentle irony in my remark. My apologies. Perhaps the irony would have been clearer if I had said: "I'd best leave the two of you to fight over what God might have known and not known, since you both seem to know more about God's mind than I do."-I wish we knew God as well as you imply. Tony reaches Him through the Bible, and I infer His activities through science, two very different approaches.

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dhw: I must confess I am always surprised by the confidence of such beliefs, and so I'm afraid there was a gentle irony in my remark. My apologies. Perhaps the irony would have been clearer if I had said: "I'd best leave the two of you to fight over what God might have known and not known, since you both seem to know more about God's mind than I do."
> 
>David: I wish we knew God as well as you imply. Tony reaches Him through the Bible, and I infer His activities through science, two very different approaches.-I use both!(As directed by the bible to do..)

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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TONY: I'm no closer to God than anyone else, and please do not put those words in my mouth. I do strive to cut out habits/practices from my life that I find to be at odds wit what the bible teaches, but the only one that has the right to say who is closer and who is not is God himself, and I would not presume to claim to speak for him. That is why I try to reference the bible when talking about God.
> 
>DHW: I'm sorry if I offended you. You wrote: God says: The dead are conscious of nothing. That suggests you know or think you know God's mind. David also thinks he knows God's mind (e.g. God planned everything in advance so that he could create human beings). As a mere speculating agnostic, I must confess I am always surprised by the confidence of such beliefs, and so I'm afraid there was a gentle irony in my remark. My apologies. Perhaps the irony would have been clearer if I had said: "I'd best leave the two of you to fight over what God might have known and not known, since you both seem to know more about God's mind than I do."-I'm not offended. The key difference, I think, is that I view the bible as the divinely inspired word of God, and you don't. (Course if you did, you couldn't be agnostic...) So, when I say "God says.." it is equivalent to "it is written in the bible..."

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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DAVID: I don't believe tiny intelligences' can grow themselves. A powerful existing intelligence is the only choice that makes sense to me.
> 
> dhw: So you believe a supercolossal intelligence can grow itself.-No, I think it is eternal. A first cause.

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> DAVID: Very large numbers of chances can be very comforting. Unfortunately there is no evidence of many universes, and we are trapped in one universe which had can obvious beginning. It is easier to decide upon an intelligent first cause.
> 
> dhw: Easier? You do yourself an injustice. ... Unfortunately, there is no evidence of a universal mind, and we are trapped in one universe which prevents access to any information prior to or outside that universe. It is easier to take no decision, though easiness should not be our criterion (and is certainly not mine)!-I appreciate your compliments, but I still insist there has to be a first cause, and one can reason to a likely description.
 
> dhw: You and David see the absurdity of the atheist argument, but not that of your own: nobody knows how life and the universe came into being, so let's invent an eternal, all-knowing designer of no origin, who simply IS, and let's call him God. Unprovable, unknown, unknowable, devoid of any scientific basis,....Life is a mystery, so we solve it by creating an even greater mystery.... That should not be taken as a sign of disrespect for your beliefs. I'm merely trying to explain why I keep seeing pots calling kettles black. One side has to be closer to the truth than the other, but reason certainly won't help me decide which one it is!-Your rejection of chance tells me that your reasoning is closer to Tony and I than you may realize.

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Another review article of the latest findings:-http://www.evolutionnews.org/2015/03/these_sequences094801.html-"A "News & Views" piece in Nature, "Coding in non-coding RNAs," states: "The discovery of peptides encoded by what were thought to be non-coding -- or 'junk' -- regions of precursors to microRNA sequences reveals a new layer of gene regulation. These sequences may not be junk, after all." It then describes a new study just published in Nature which finds that precursors of microRNAs can in fact encode proteins. The news article tells a familiar story: Evolutionary biologist meets new type of DNA. Evolutionary biologist doesn't know what DNA does. Evolutionary biologists assumes DNA is junk and ignores it. Molecular biologist comes along, doesn't think about evolution, and finds out DNA isn't junk and does something important. Here's how the Nature piece puts it:-"In the 1970s, as it started to become clear that the genomic regions that encode proteins (the genes) swim in a sea of non-protein- coding sequences, the idea of meaningless, or 'junk', DNA became a hot topic of discussion. Biologists are now well aware of introns, the sequences within genes that separate the coding regions (exons) and which are spliced out at the messenger-RNA level, as well as their notable regulatory roles. However, the term junk DNA has survived and is used loosely to describe genomic sequences between genes, giving them an implied lack of importance.-"The debate about the usefulness of non-protein-coding DNA sequences continues to rage. However, within these intergenic regions of a genome are the sequences that produce most plant and many animal pri-miRs. Clearly, these sequences are not useless. Yet the regions of a pri-miR that do not generate the miRNA or the highly structured adjacent sequences have suffered the similar fate of being largely ignored and possibly thought of as junk RNA lacking function.
Essentially, pri-miRs are RNAs from which microRNAs are derived. Researchers have long known that microRNAs can regulate gene expression, but most thought that the pri-miR DNA didn't do anything if it didn't help generate microRNAs. Now it turns out that they are actually a class of DNA that can encode functional proteins, called miPEpS: "Lauressergues and colleagues identified short open reading frames (ORFs) -- sequences that can potentially encode proteins -- in many different pri-miRs of two plant species." Indeed, the proteins generated by pri-miR transcripts also have the ability to promote transcription, ensuring that these proteins stay at certain levels within the cytoplasm. So add a gene-regulation function to these pri-miR sequences. The article concludes:
The experimental discovery of miPEPs and other small peptides such as these raises an inconvenient question: are we missing a vast library of biologically important peptide signals...?"

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The book is Junk DNA:-Nessa Carey
Columbia University Press, March 2015- "Can we please stop calling non-protein-coding DNA junk? We've had more than a decadesince researchers first sequenced the human genome in 2001to come to grips with the fact that 98 percent of our DNA doesn't get translated directly into proteins. And in the intervening years, what was initially considered perplexingly abundant detritus has evolved into a wondrous genomic landscape that hasn't disappointed intrepid explorers. Imperial College London molecular biologist and author Nessa Carey details this transformation and the progress science has made in her latest book, Junk DNA.-"Carey examines the importance of noncoding DNA, from its role in controlling gene expression to the ways in which it influences RNA behavior, disease progression, and sex determination. Although we can now be sure that 98 percent of the human genome is anything but junk, researchers are only just beginning to fully appreciate the complex influence of all that once-maligned genomic material.-"Junk DNA serves as a nice primer for the still-uninitiated, but here's to hoping that continued research, and the emerging view that genomes behave like networks rather than a string of isolated genes, soon relegates the J-word to the junk pile of science history."-http://cup.columbia.edu/book/junk-dna/9780231170840

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Another review, in great detail, of Nessa Carry's book, Junk DNA. She thinks many more functions will be found:-http://www.evolutionnews.org/2015/04/a_new_book_on_j095611.html-"The other shock from the sequencing of the human genome was the realisation that the extraordinary complexities of human anatomy, physiology, intelligence and behaviour cannot be explained by referring to the classical model of genes. In terms of numbers of genes that code for proteins, humans contain pretty much the same quantity (around 20,000) as simple microscopic worms. Even more remarkably, most of the genes in the worms have directly equivalent genes in humans.-"As researchers deepened their analyses of what differentiates humans from other organisms at the DNA level, it became apparent that genes could not provide the explanation. In fact, only one genetic factor generally scaled with complexity. The only genomic features that increased in number as animals became more complicated were the regions of junk DNA. The more sophisticated an organism, the higher the percentage of junk DNA it contains. Only now are scientists really exploring the controversial idea that junk DNA may hold the key to evolutionary complexity. (p. 4)-"Carey doesn't openly take a side in the debate over ENCODE, and she doesn't claim that our genome will eventually turn out to contain no "junk" DNA whatsoever. But she is clear that the trend line in research is away from junk DNA, and she notes that one reason for our lack of understanding of what a lot of junk DNA does is that we haven't yet developed the technologies to study it:-"Part of the problem is that the systems we can use to probe the functions of junk DNA are still relatively underdeveloped. This can sometimes make it hard for researchers to use experimental approaches to test their hypotheses. We have only been working on this for a relatively short space of time. (p. 6)
of the important functions going on in the genome. -"As Carey notes, "We now know that in some cases just a single base-pair change in an apparently irrelevant region of the genome can have a definite effect" (p. 201), meaning there's a lot of work left to be done. After all, she points out: "One stretch of DNA can include a protein-coding gene, long non-coding RNAs, small RNAs, antisense RNAs, splice signal sites, untranslated regions, promoters and enhancers." (p. 287) Thus, she concludes, "When we really think about the complexity of our genomes, it isn't surprising that we can't understand everything yet." (p. 288) And that, along with much else in this excellent book, hits the nail on the head."

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The midbody which is part of the process in cell division cell was thought to be junk, but that doesn't seem so with new research. The lesson here is consistent with the observation that as research progresses junk recedes. 'Junk' is very important to Darwin philosophy, in that a build up of discarded DNA/RNA supports the conception of a random process. The less junk, the more complexity must lead to considerations of design:-http://phys.org/news/2015-04-scientists-discoveries-specific-protein-effects.html-"A new study conducted by scientists at UC Santa Barbara reveals a novel function for WDR5, a protein known for its critical role in gene expression whereby information encoded in genes is converted into products like RNA (ribonucleic acid) and protein. In cells, WDR5 is a subunit of a five-protein complex. Mutations in members of this complex can result in childhood leukemia and other disorders affecting numerous organ systems in the body. The UCSB team worked with WDR5 in cultured human cell lines. The results of the study appear in the Journal of Biological Chemistry.-"'We found that when two cells divide, WDR5 is localized to a very interesting cellular structure called the midbody," said lead author Jeff Bailey, a graduate student in UCSB's Department of Molecular, Cellular and Developmental Biology (MCDB). "In the past, although associated with cell division, the midbody was considered 'junk,' but that has changed in the last decade. Now the midbody is believed to be important during stem cell differentiation." (my bold)-"When a stem cell divides to produce a differentiated type of cell like a skin cell or a neuron, stem cells retain the midbody while differentiated cells do not. "This suggests that the midbody has important functions," Bailey explained. "Also, when the midbody isn't cut correctly, the cells can re-fuse, creating one cell with two nuclei. This is thought to be part of what happens when a tumor forms.'"

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It really is disappearing. At least 80% is not junk, and although these areas do not code, they control gene expression. They run the genes:-http://theconversation.com/explainer-microrna-the-puppet-master-of-the-genome-39641-"For biologists, those important emails that slipped into the junk mail folder and were disregarded were miRNAs. That was until the first functional miRNA, lin-4, was officially discovered in 1993. Scientists were looking at the development of the nematode worm, Caenorhabditis elegans, and found that lin-4 inhibited protein synthesis of the lin-14 gene.-"They subsequently found that miRNA can physically bind to mRNA and stop it creating proteins. Thus it effectively suppresses the activity of a gene. This discovery was the first evidence of miRNA negatively regulating RNA coding for proteins.-"So, it turns out that the 98% of our genome that was regarded as junk might have a function after all.-"The second miRNA was not discovered for another seven years. But since then, more than 1,800 human miRNAs have been found. We now understand that miRNA control numerous genes and processes vital for cellular life such as metabolism, development and the immune system"-And from the 'junk' silencing function:-http://www.sciencemag.org/content/348/6230/41.summary-"All molecular machines have imperfections, and the biological ones are no exception. One type of flaw is a quantitative one: Although all the cells within an organ are genetically identical, the concentrations of many of their proteins can be noisythat is, vary and fluctuate between all the cells. Biologists decompose such noise into two sources: an intrinsic one, which results from the stochastic nature of the biochemistry operating within cells, and an extrinsic one that manifests global differences between cells, such as the number of protein production facilities (e.g., ribosomes) (1). A major question is whether organisms have evolved means to control noise, especially when imprecisions are detrimental. On page 128 in this issue, Schmiedel et al. (2) report combining mathematical modeling and a synthetic gene approach to establish a complex role for microRNAs (miRNAs) in controlling cellular protein content. "-Abstract:
"MicroRNAs (miRNAs) repress the expression of many genes in metazoans by accelerating messenger RNA degradation and inhibiting translation, thereby reducing the level of protein. However, miRNAs only slightly reduce the mean expression of most targeted proteins, leading to speculation about their role in the variability, or noise, of protein expression. We used mathematical modeling and single-cell reporter assays to show that miRNAs, in conjunction with increased transcription, decrease protein expression noise for lowly expressed genes but increase noise for highly expressed genes. Genes that are regulated by multiple miRNAs show more-pronounced noise reduction. We estimate that hundreds of (lowly expressed) genes in mouse embryonic stem cells have reduced noise due to substantial miRNA regulation. Our findings suggest that miRNAs confer precision to protein expression and thus offer plausible explanations for the commonly observed combinatorial targeting of endogenous genes by multiple miRNAs, as well as the preferential targeting of lowly expressed genes. "-New book I've mentioned, Nessa Carey's "Junk DNA":-http://www.evolutionnews.org/2015/04/a_new_book_on_j095611.html-"Don't miss that last line: "The whole organization only works when all the components are in place. And so it is with our genomes." Doesn't that sound exactly like irreducible complexity? So here we have a biologist, unaffiliated with the intelligent-design community, arguing that junk DNA must be functional because it's like a car factory where all the components are needed in order for the entire system to function. Critics might claim that ID has had no impact on biological thinking, but the evidence shows otherwise."

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Further evidence from research that ENCODE is correct that most of DNA has some function, even if we do not know them all as yet:-http://www.salvomag.com/new/articles/salvo32/the-encode-embroilment-part-II.php-"The fact that DNA transcription is immenseand nonrandomwas confirmed in a 2013 paper that studied RNA transcripts in yeast. It found that while the yeast genome contains only about 6,000 genes, there were over 1.8 million unique RNA transcripts, which were "arranged in a remarkably complex, overlapping pattern across the genome."-***-"ENCODE's results suggest that a cell's type and functional role in an organism are critically influenced by complex and carefully orchestrated patterns of expression of RNAs inside that cell. As Stamatoyannopoulos observes, ENCODE found that "the majority of regulatory DNA regions are highly cell type-selective," and "the genomic landscape rapidly becomes crowded with regulatory DNA as the number of cell types" studied increases.7 Thus, as two pro-ENCODE biochemists explain, "Assertions that the observed transcription represents random noise . . . is more opinion than fact and difficult to reconcile with the exquisite precision of differential cell- and tissuespecific transcription in human cells."-***-"In marked contrast to the prevailing wisdom, ENCODE chromatin and transcription studies now suggest that a large number of transposable elements encode highly cell type-selective regulatory DNA that controls not only their own cell-selective transcription, but also those of neighboring genes. Far from an evolutionary dustbin, transposable elements appear to be active and lively members of the genomic regulatory community, deserving of the same level of scrutiny applied to other genic or regulatory features.-***-"More of the human genome sequence appears to be used for some reproducible, biochemically defined activity than was previously imagined. Contrary to the initial expectations of many, the overwhelming majority of these activities appear to be state-specificeither restricted to specific cell types or lineages, or evokable in response to a stimulus. . . . Biochemical signatures of many ENCODE-defined elements exhibit complex trans-cellular patterns of activity. . . . Together, these observations suggest that the genome may, in fact, be extensively multiply encodedi.e., that the same DNA element gives rise to different activities in different cell types.-***
"Finally, transcription doesn't just happen by accident. It can't start without special stretches of DNA, called promoter sequences, which bind to special enzymes called transcription factors (TFs). And just any enzyme won't doTFs must be able to recognize the specific DNA promoter sequence that they're keyed to unlock for transcription. Without that precise biochemical correspondence, transcription can't occur. Once the right TFs bind to a promoter sequence, a molecular machine called RNA polymerase can then find the right place on the DNA to start converting the genomic message into a strand of RNA. The fact that the vast majority of the genome is transcribed suggests that these specified moleculesDNA promoter sequences and TFsexist and are carefully matched throughout the genome. If all that RNA is junk, why do these innumerable specified molecules exist throughout our cells? "

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"The fact that DNA transcription is immenseand nonrandomwas confirmed in a 2013 paper that studied RNA transcripts in yeast...
> 
> ***
> 
> "..a cell's type and functional role in an organism are critically influenced by complex and carefully orchestrated patterns of expression of RNAs inside that cell...."Assertions that the observed transcription represents random noise . . . is more opinion than fact and difficult to reconcile with the exquisite precision of differential cell- and tissuespecific transcription in human cells."
> 
> -> 
> ***
> "Finally, transcription doesn't just happen by accident. It can't start without special stretches of DNA, called promoter sequences, which bind to special enzymes called transcription factors (TFs). And just any enzyme won't doTFs must be able to recognize the specific DNA promoter sequence that they're keyed to unlock for transcription...---Heresy!! Burn 'em at the stake!! RANDOM CHANCE!!

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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RNA's are produced in about 85% of DNA, but the functions of these twisting and turning RNA's is just now being uncovered:-http://www.nature.com/news/a-cellular-puzzle-the-weird-and-wonderful-architecture-of-rna-1.18014?WT.ec_id=NATURE-20150723&spMailingID=49156958&spUserID=MjA1NjE2NDU5MwS2&spJobID=722865381&spReportId=NzIyODY1MzgxS0-" In November 2013, they and their teams became the first to describe the shapes of thousands of RNAs in a living cell  revealing a veritable sculpture garden of different forms in the weedy thale cress, Arabidopsis thaliana1. One month later, a group at the University of California, San Francisco, reported a comparable study of yeast and human cells2. The number of RNA structures they managed to resolve was unprecedented, says Alain Laederach, an RNA biologist at the University of North Carolina at Chapel Hill (UNC).-"Scientists' view of RNA has transformed over the past few decades. Once, most RNAs were thought to be relatively uninteresting pieces of limp spaghetti that ferried information between the molecules that mattered, DNA and protein. Now, biologists know that RNAs serve many other essential functions: they help with protein synthesis, control gene activity and modify other RNAs. At least 85% of the human genome is transcribed into RNA, and there is vigorous debate about what, if anything, it does. (my bold)-"But a key mystery has remained: its convoluted structures. Unlike DNA, which forms a predictable double helix, RNA comprises a single strand that folds up into elaborate loops, bulges, pseudo-knots, hammerheads, hairpins and other 3D motifs. These structures flip and twist between different forms, and are thought to be central to the operation of RNA, albeit in ways that are not yet known. It's a big missing piece of the puzzle of understanding how RNAs work, says Jonathan Weissman, a biophysicist and leader of the yeast and human RNA study.-"In the past few years, researchers have begun to get a toehold on the problem. Bevilacqua, Weissman and others have devised techniques that allow them to take snapshots of RNA configurations en masse inside cells  and found that the molecules often look nothing like what is seen when RNA folds under artificial conditions. The work is helping them to decipher some of the rules that govern RNA structure, which might be useful in understanding human variation and disease  and even in improving agricultural crops."

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From an obituary on a leading expert:-http://www.caltech.edu/news/developmental-biologist-eric-h-davidson-passes-away-47772-"Inherent in the idea of gene regulatory networks was the concept that genome sequences that provided information about how genes should be expressed would be as important as the genome sequences that coded for the proteins themselves. Although non-protein-coding DNA was long considered to be "junk," Davidson recognized that the key regulatory code resided in this genetic material. In 2006, Davidson co-led a group of 240 researchers from more than 70 institutions that sequenced the purple sea urchin's genome. In 2008, a consortium of institutions led by Davidson's lab characterized the 23,000 genes of that genome.-In parallel, the Davidson group systematically created a comprehensive functional testing strategy to detect all of the control connections between the genes involved in the key events in the earliest stages of sea urchin embryo development, and to determine how the activity of each gene affected the ability of every other gene in that part of the embryo to be expressed. The network model, first described in 2002 and elucidated and extended over the next 13 years, revealed that the regulatory networks governing high-level processes such as the formation of a specific type of cell are built from gene circuits that can have striking similarities even when the identities of the genes in the circuits are different. These circuits can be viewed as a few dozen types of modules that perform specific functions. Because similar modular systems appear to exist in flies, frogs, chicks, mice, and zebrafish, they may be a universal feature of higher organisms.

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Blocking a long noncoding RNA in rats helps protect their brain from a large stroke. This lncRNA was previously considered junk, but the study below uncovered its function:-http://www.sciencedaily.com/releases/2015/12/151215185858.htm-"A study of rats shows that blocking a type of RNA produced by what used to be called "junk DNA" can prevent a significant portion of the neural destruction that follows a stroke. The research points toward a future treatment for post-stroke damage, which is often more extensive than the initial destruction that results when blood to the brain is temporarily shut off.-***-"'Less than 2 percent of the RNAs formed from the genome code for proteins, leaving 98 percent that we call 'noncoding RNA,'" says senior author Raghu Vemuganti, a professor of neurological surgery at the University of Wisconsin-Madison.-***-"This lncRNA can bind to other RNA, to a protein, or to a protein on one side and DNA on the other," says first author Suresh Mehta, a scientist in the Department of Neurological Surgery. "Among many other jobs, lncRNAs can regulate gene activity.'"-Comment: This is presented for the lncRNA functional control demonstration. How much junk DNA is really present. ENCODE says about 20%.

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A non-coding RNA has been found to control chromosome number in dividing cells:-http://medicalxpress.com/news/2015-12-scientists-role-rna-safeguarding-human.html-
"Molecular biologists at UT Southwestern Medical Center have identified a gene called NORAD that helps maintain the proper number of chromosomes in cells, and that when inactivated, causes the number of chromosomes in a cell to become unstable, a key feature of cancer cells. -"Previously, genes that encode the recipe for making proteins have been implicated in maintaining the proper number of chromosomes in a cell. The NORAD gene, however, does not encode a protein. Instead, NORAD produces a long noncoding RNA, a type of molecule that was not previously known to be important in chromosome maintenance, the researchers report in the journal Cell.-"In the absence of the NORAD RNA, the number of chromosomes in cells becomes highly abnormal," explained Dr. Joshua Mendell, Professor of Molecular Biology at UT Southwestern and a Howard Hughes Medical Institute Investigator. "This is an entirely new function for a noncoding RNA and may have implications in cancer biology since genomic instability is a hallmark of tumor cells."-"Researchers began studying this particular molecule because the RNA kicks into action after DNA is damaged; they therefore termed it Noncoding RNA Activated by DNA Damage, or NORAD.-"The scientists unexpectedly found that NORAD plays a critical role in keeping the genome stable, and conducted experiments showing that when NORAD is absent, cells frequently lose or gain whole chromosomes. Microscopic imaging revealed that cells lacking NORAD are unable to properly pass on chromosomes as they divide. NORAD controls chromosome segregation during cell division by regulating the activity of a family of proteins called PUMILIO proteins. In cells lacking NORAD, overactivity of PUMILIO leads to an unstable genome. Since most cancer cells also exhibit genomic instability, Dr. Mendell and his team are now exploring whether abnormal function of NORAD or PUMILIO proteins contribute to human tumors."-Comment: Junk DNA keeps disappearing. Darwinist scientists have used 'junk' to claim that evolution is a random process which produces junk DNA that is left in place.

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David: Comment: Junk DNA keeps disappearing. Darwinist scientists have used 'junk' to claim that evolution is a random process which produces junk DNA that is left in place.-David
Interestingly non coding (junk) DNA and evolution live quite happily together.-https://en.wikipedia.org/wiki/Noncoding_DNA-Can I suggest you try editing this Wiki page to correct any misconceptions the authors have.

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Romansh: Interestingly non coding (junk) DNA and evolution live quite happily together.
> 
> https://en.wikipedia.org/wiki/Noncoding_DNA
> 
> Can I suggest you try editing this Wiki page to correct any misconceptions the authors have.-I'm finally back from an AT&T internet outage for four days. I looked at Wiki and found it rather evenhanded. I recognize there is a debate over the ENCODE results, but the ENCODE authors are quite adamant there interpretation is correct. My point is, since then more non-coding DNA is turning up with some biologic function. I'm sure there is useless DNA, but its percentage is still up for debate. And a massive portion of DNA as evidence for evolution discarding "junk" seems to be disappearing.

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David: My point is, since then more non-coding DNA is turning up with some biologic function. I'm sure there is useless DNA, but its percentage is still up for debate. And a massive portion of DNA as evidence for evolution discarding "junk" seems to be disappearing.-My bad; I thought you point was as more of the non coding DNA was found to have function, it made evolution somehow more impossible.

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DAVID's Comment: Junk DNA keeps disappearing. Darwinist scientists have used 'junk' to claim that evolution is a random process which produces junk DNA that is left in place.-As always, one can fit the facts to one's beliefs. If junk is not junk, your Darwinian scientist can point out that natural selection gets rid of junk. If junk is junk, he can say it's all random. If junk is not junk, your theist can say it's evidence of God's supreme planning. If junk is junk, he can say, Wait and see. Or: Told you so, we're already 80% of the way there. Or: We have no idea how (or why) God did what he did.

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> dhw: As always, one can fit the facts to one's beliefs. If junk is not junk, your Darwinian scientist can point out that natural selection gets rid of junk. If junk is junk, he can say it's all random. If junk is not junk, your theist can say it's evidence of God's supreme planning. If junk is junk, he can say, Wait and see. Or: Told you so, we're already 80% of the way there. Or: We have no idea how (or why) God did what he did.-Originally 'junk' was proposed as a proof of evolution. With research finding function with what is considered 'junk', useful junk is not junk but functional DNA. Natural selection has nothing to do with it. The issue relates to initial theories proposed by Darwinists before DNA was more clearly understood.

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dhw: As always, one can fit the facts to one's beliefs. If junk is not junk, your Darwinian scientist can point out that natural selection gets rid of junk. If junk is junk, he can say it's all random. If junk is not junk, your theist can say it's evidence of God's supreme planning. If junk is junk, he can say, Wait and see. Or: Told you so, we're already 80% of the way there. Or: We have no idea how (or why) God did what he did.-DAVID: Originally 'junk' was proposed as a proof of evolution. With research finding function with what is considered 'junk', useful junk is not junk but functional DNA. Natural selection has nothing to do with it. The issue relates to initial theories proposed by Darwinists before DNA was more clearly understood.
-I think you have missed my point. No matter what discoveries are made about so-called junk, both sides will use them to prove their point. From a materialist atheist standpoint, natural selection would have everything to do with it, because if junk is NOT junk, it can be claimed that natural selection ensures the disappearance of whatever is not needed. The fact that the materialist atheist has to change the original line of argument could be classed as flexibility in the face of new research, just as many religious folk have adjusted from creationism to evolution.

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dhw:I think you have missed my point. No matter what discoveries are made about so-called junk, both sides will use them to prove their point. From a materialist atheist standpoint, natural selection would have everything to do with it, because if junk is NOT junk, it can be claimed that natural selection ensures the disappearance of whatever is not needed.-You are still incorrect. 99% of species are gone. Junk represents previous useful DNA bases used by those lost organisms, thus proving evolution. Natural selection kills off organisms, which leave the junk behind. Now it turns out about 80% of DNA has some function, which puts this evidence for evolution in some doubt.

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dhw:I think you have missed my point. No matter what discoveries are made about so-called junk, both sides will use them to prove their point. From a materialist atheist standpoint, natural selection would have everything to do with it, because if junk is NOT junk, it can be claimed that natural selection ensures the disappearance of whatever is not needed.-DAVID: You are still incorrect. 99% of species are gone. Junk represents previous useful DNA bases used by those lost organisms, thus proving evolution. Natural selection kills off organisms, which leave the junk behind. Now it turns out about 80% of DNA has some function, which puts this evidence for evolution in some doubt.-You're quite right, I should have put it the other way round. Natural selection ensures the survival of what is useful. But if useful material is passed onto subsequent organisms, how does that cast doubt on evolution? (I am not trying to defend the atheist line - I am merely pointing out that both sides can twist any discovery to fit in with their hypotheses.)

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> dhw: You're quite right, I should have put it the other way round. Natural selection ensures the survival of what is useful. But if useful material is passed onto subsequent organisms, how does that cast doubt on evolution? (I am not trying to defend the atheist line - I am merely pointing out that both sides can twist any discovery to fit in with their hypotheses.)-You've got it, but, evolution will always pass on useful information in the newly reconstructed DNA. It is generally found that mutations that cause 'advances' actually delete existing information! An initial hailing of junk as 'proof' is now being walked back.-Afterthought: The finding that information is lost when advancing adaptations occur, is part of the reasoning I use to think that DNA was coded for all of evolution from the beginning of life.

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dhw: You're quite right, I should have put it the other way round. Natural selection ensures the survival of what is useful. But if useful material is passed onto subsequent organisms, how does that cast doubt on evolution? (I am not trying to defend the atheist line - I am merely pointing out that both sides can twist any discovery to fit in with their hypotheses.)-DAVID: You've got it, but, evolution will always pass on useful information in the newly reconstructed DNA. It is generally found that mutations that cause 'advances' actually delete existing information! An initial hailing of junk as 'proof' is now being walked back.
Afterthought: The finding that information is lost when advancing adaptations occur, is part of the reasoning I use to think that DNA was coded for all of evolution from the beginning of life.-This is very much in line with hard determinism, as explained in the article Romansh referred us to: Hard determinists will dispute that subatomic particle behaviour is really random and instead claim that the way they behave is exactly as predetermined as everything else in the universe has been since the Big Bang. (My bold) According to you all evolutionary innovations, lifestyles and natural wonders are predetermined (by your God). Romansh himself doesn't like "predetermined", and prefers caused, but of course random events have causes too, which removes the distinction between random and predetermined. The question is whether evolution is directed by an intention, and that is where the three of us probably diverge: you think there is an overall purpose directed by your God, and basically only humans have the ability to determine their own way of life, though maybe other large organisms have a small degree of freedom to modify your God's work; I tend to opt for all levels of life pursuing their own evolutionary purposes (and if God exists, that would have been his intention); Romansh will have to speak for himself...

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A review article by the authors of ENCODE is now saying that some of the biochemically functional areas may not result in gene produced results:-http://www.pnas.org/content/111/17/6131-"Abstract:-"With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types. The resulting genome-wide data reveal sites of biochemical activity with high positional resolution and cell type specificity that facilitate studies of gene regulation and interpretation of noncoding variants associated with human disease. However, the biochemically active regions cover a much larger fraction of the genome than do evolutionarily conserved regions, raising the question of whether nonconserved but biochemically active regions are truly functional. Here, we review the strengths and limitations of biochemical, evolutionary, and genetic approaches for defining functional DNA segments, potential sources for the observed differences in estimated genomic coverage, and the biological implications of these discrepancies. We also analyze the relationship between signal intensity, genomic coverage, and evolutionary conservation. Our results reinforce the principle that each approach provides complementary information and that we need to use combinations of all three to elucidate genome function in human biology and disease."-Their conclusion:-"In contrast to evolutionary and genetic evidence,biochemical data offer clues about
both the molecular function served by underlying DNA elements and the cell types
in which they act, thus providing a launching point to study differentiation and development,cellular circuitry, and human disease (14, 35, 69, 111, 112). The major
contribution of ENCODE to date has been high-resolution, highly-reproducible maps of
DNA segments with biochemical signatures associated with diverse molecular functions.
We believe that this public resource is far more important than any interim estimate
of the fraction of the human genome that is functional.-"By identifying candidate genomic elements and placing them into classes with shared
molecular characteristics, the biochemical maps provide a starting point for testing
how these signatures relate to molecular,cellular, and organismal function. The data
identify very large numbers of sequence elements of differing sizes and signal strengths. Emerging genome-editing methods should considerably increase the
throughput and resolution with which these candidate elements can be evaluated
by genetic criteria. Given the limitations of our current understanding of genome function,future work should seek to better define genome elements by integrating all three methods to gain insight into the roles they play in human biology and disease."-Comment: The resulting function of 'active' areas, being still unknown, it is best not to conclude that non-junk is up to 80%. The percent may be less and needs more research. Honest hindsight.

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David's comment: The resulting function of 'active' areas, being still unknown, it is best not to conclude that non-junk is up to 80%. The percent may be less and needs more research. Honest hindsight.-And, as always, honest reporting by you. Thank you. Whatever the percentage, I do not think for one moment that theists or atheists will change their opinions, and I do not doubt for one moment that each of them will fit the facts to their theories.

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David's comment: The resulting function of 'active' areas, being still unknown, it is best not to conclude that non-junk is up to 80%. The percent may be less and needs more research. Honest hindsight.
> 
> dhw: And, as always, honest reporting by you. Thank you. Whatever the percentage, I do not think for one moment that theists or atheists will change their opinions, and I do not doubt for one moment that each of them will fit the facts to their theories.-The size of DNA is a major issue in the discussion. The length (size) of amoebic DNA is larger/longer than human with only a few genes present. Amoebas have not evolved much since the beginning of life. Following Darwinist logic makes no sense here. Did the amoeba evolve with mostly all junk in its DNA to start with? The junk is supposed to be 'left- over' material from evolution. My thought has always been early organisms had large DNA's to allow for future modifications to drive complexity. It is like a small family building a great big house from the start, to allow for new arrivals coming later.-The same with the organization of DNA in single celled prokaryotes, floating around with minor 3-D relationships. In multicellular eukaryotes the coiling of DNA allows for complex 3-D relationships to permit complex controls of gene expression.

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some more places to look-https://whyevolutionistrue.wordpress.com/2016/01/01/is-the-discovery-institute-falling-apart/

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Romansh: some more places to look
> 
> https://whyevolutionistrue.wordpress.com/2016/01/01/is-the-discovery-institute-falling-... been fully aware of this opinion, and have seen it before.

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David's comment: The resulting function of 'active' areas, being still unknown, it is best not to conclude that non-junk is up to 80%. The percent may be less and needs more research. Honest hindsight.-dhw: And, as always, honest reporting by you. Thank you. Whatever the percentage, I do not think for one moment that theists or atheists will change their opinions, and I do not doubt for one moment that each of them will fit the facts to their theories.-DAVID: The size of DNA is a major issue in the discussion. [...]-Thank you for your interesting thoughts on amoeba and prokaryote DNA junk as preparation for later developments. I'm not sure how this would account for the junk in those later developments, but at the moment I'm more interested in responses to the news. For argument's sake, if it turns out to be say 70/30 or 50/50, how will you interpret the figures in terms of God's grand design? And how do you think an atheist will interpret them?

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> DAVID: The size of DNA is a major issue in the discussion. [...]
> 
> dhw: Thank you for your interesting thoughts on amoeba and prokaryote DNA junk as preparation for later developments. I'm not sure how this would account for the junk in those later developments, but at the moment I'm more interested in responses to the news. For argument's sake, if it turns out to be say 70/30 or 50/50, how will you interpret the figures in terms of God's grand design? And how do you think an atheist will interpret them?-The term junk was introduced in the 1970's by a Dr. Ohno, as not much seemed functional. More and more is found in varying degrees of functionality. We don't know what the final result will be over the ensuing years.

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More so called junk DNA is now seen functional:-http://www.evolutionnews.org/2016/02/junk_dna_is_pre102591.html-"The news release is titled, "'Junk' DNA plays role in preventing breast cancer." It's based on an open-access paper in Nature Communications. Most readers scanning the paper will see what researchers are up against. Discussion of the complex interactions of parts -- lncRNAs transcripts, small interfering RNAs (siRNAs), promoters, exons, introns, alleles, interference in cis and trans and all the rest -- gets into the technical weeds fast. Thankfully, the release simplifies the essence of the finding. Basically, a piece of non-coding DNA "keeps cells healthy" by preventing a genetic "switch" from getting stuck.-***-"The researchers found that the lncRNA GNG12-AS1 acts as a molecular "rheostat" (their term) that controls the expression of an adjacent gene, DIRAS3, a tumor suppressor. It does it by two mechanisms. One is by regulating the number of transcripts of the tumor suppressor. But if that gets out of control, it can even suppress the "network of genes that prepare cells to change their shape and prepare for metastasis."-"By experimentally reducing the amount of GNG12-AS1 produced, either by preventing its transcription or destroying the transcripts, they found that cells start becoming cancerous. This explains why in cancer patients, the switch is stuck:-"DIRAS3 is downregulated in 70% of breast and ovarian cancer, and its loss of expression correlates with cancer progression and metastasis. The mechanism responsible for DIRAS3 downregulation to date involves different epigenetic mechanisms and loss of heterozygosity. We hypothesized that TI [transcriptional interference] by GNG12-AS1 could represent an additional layer of regulating DIRAS3 dosage.-"The interactions are far more complex than can be described here. Suffice it to say that this long non-coding RNA, which would have been considered "junk" previously, plays a crucial role in regulating the amount of an important tumor suppressor gene. It's a "stable lncRNA localized in the nucleus" with a half-life of 20 to 25 hours, meaning it needs to be transcribed often. Other processes regulate the amount of the lncRNA in a very complex choreography of enhancers, suppressors, and feedback loops. Levels of expression also vary depending on the tissue involved.-"It has become increasingly clear that non-coding parts of the genome play vital roles in regulating the coding parts. Regulation is an important function. A system that generates parts without regard to the amount needed is a system out of control." -My usual comment: How much complexity has to be found before design is accepted?

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Transposable elements in plants have helped direct evolution, a problem Darwin was troubled by: - http://gbe.oxfordjournals.org/content/5/10/1886.full.pdf+html: - From the abstract: - "Transposable elements (TEs) are a dominant feature of most flowering plant genomes. Together with other accepted facilitators of evolution, accumulating data indicate that TEs can explain much about their rapid evolution and diversification. Genome size in angiosperms is highly correlated with TE content and the overwhelming bulk (>80%) of large genomes can be composed of TEs. Among retro-TEs, long terminal repeats (LTRs) are abundant, whereas DNA-TEs, which are often less abundant than retro-TEs, are more active. Much adaptive or evolutionary potential in angiosperms is due to the activity of TEs (active TE-Thrust), resulting in an extraordinary array of genetic changes, including gene modifications, duplications, altered expression patterns, and exaptation to create novel genes, with occasional gene disruption. TEs implicated in the earliest origins of the angiosperms include the exapted Mustang, Sleeper, and Fhy3/Far1 gene families. Passive TE-Thrust can create a high degree of adaptive or evolutionary potential by engendering ectopic recombination events resulting in deletions, duplications, and karyotypic changes. TE activity can also alter epigenetic patterning, including that governing endosperm development, thus promoting reproductive isolation. Continuing evolution
of long-lived resprouter angiosperms, together with genetic variation in their multiple meristems, indicates that TEs can facilitate somatic evolution in addition to germ line evolution. Critical to their success, angiosperms have a high frequency of polyploidy and hybridization, with resultant increased TE activity and introgression, and beneficial gene duplication. Together with traditional explanations, the enhanced genomic plasticity facilitated by TE-Thrust, suggests a more complete and satisfactory explanation for Darwin's abominable mystery: the spectacular success of the angiosperms. - Article: - Although once said to be junk, or parasitic, DNA (Doolittle and Sapienza 1980; Orgel and Crick 1980), a recent large and rapid accumulation of evidence indicates
that transposable elements (TEs) have been a significant factor in the evolution of a wide range of eukaryotic taxa (Bennetzen 2000; Kazazian 2004; Bie´mont and Vieira 2006; Feschotte and Pritham 2007; Bo¨ hne et al. 2008; Hua-Van et al. 2011). We have proposed TEs as powerful facilitators of evolution (Oliver and Greene 2009), formalized this proposal into the TE-Thrust hypothesis (Oliver and Greene 2011),
and more recently, expanded and strengthened this hypothesis (Oliver and Greene 2012). The TE-Thrust hypothesis has great explanatory power with regard to adaptation and evolution and was developed from empirical evidence among the metazoans, principally mammals. It has offered an explanation for the great fecundity of some lineages and the paucity of species in other lineages, for
stasis, and for living fossils (Oliver and Greene 2009, 2011, 2012). Owing to variable TE activity over time, TE-Thrust also suggests strong support for punctuated equilibrium (Eldredge andGould 1972; Gould 2002). - *** - "By assessing the available evidence, we conclude that TE-Thrust operates in, and has been crucial to, the evolution of flowering plants. The additional involvement of TEs in the artificial arena of plant domestication provides direct and relatively recent evidence for the importance of TEs in the generation of selectable variation in angiosperms. TE-Thrust is therefore potentially a general phenomenon that may have
very widespread significance to many lineages of life on earth. Nevertheless, TE-Thrust is only one of the many facilitators of evolution, and its relative importance may vary from lineage to lineage and from age to age. A comprehension of the full magnitude of the contributions that TEs have made to angiosperm evolution will require complete genome sequencing and detailed trait characterization in a wide range of plant species, including nondomesticated species of angiosperms and species from other plant phyla. However, any measure of TE impact will likely be an underestimate owing to important contributions having been made by ancient TEs that have been lost or are no longer recognizable." - Comment: As usual more research ,less junk

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An article that tries to explain some of the functions of non-coding RNA (ncRNA):-http://phys.org/news/2016-05-dark-genome.html-"What used to be dismissed by many as "junk DNA" is back with a vengeance as growing data points to the importance of non-coding RNAs (ncRNAs)genome's messages that do not code for proteinsin development and disease.-***-"Of the 3 billion letters in the human genome, only two per cent make up the protein-coding genes. The genes are copied, or transcribed, into messenger RNA (mRNA) molecules, which provide templates for building proteins that do most of the work in the cell. Much of the remaining 98 per cent of the genome was initially considered by some as lacking in functional importance. However, large swaths of the non coding genomebetween half and three quarters of itare also copied into RNA- *** -"It is emerging that many ncRNAs have important roles in gene regulation. This view is supported in that some ncRNAs act as carriages for shuttling the mRNAs around the cell, or provide a scaffold for other proteins and RNAs to attach to and do their jobs.-***-"ncRNAs come in multiple flavours: there's rRNA, tRNA, snRNA, snoRNA, piRNA, miRNA, and lncRNA, to name a few, where prefixes reflect the RNA's place in the cell or some aspect of its function. But the truth is that no one really knows the extent to which these ncRNAs control what goes on in the cell, nor how they do this. The new technology developed by Blencowe's group has been able to pick up new interactions involving all classes of RNAs and has already revealed some unexpected findings.-"The team discovered new roles for small nucleolar RNAs (snoRNAs) that normally guide chemical modifications of other ncRNAs. It turns out that some snoRNAs can also regulate stability of a set of protein-coding mRNAs. In this way, snoRNAs can also directly influence which proteins are made, as well as their abundance, adding a new level of control in cell biology. And this is only the tip of the iceberg as the researchers plan to further develop and apply their technology to investigate the ncRNAs in different settings."-Comment: One of the initial basic tenets of hard-Darwinists is evolution discarded lots of junk into DNA, because only 2% codes form proteins, and the junk proves evolution was a random process leaving junk behind. Instead, the obvious issue in retrospect was ignored: it is fine that we know the origin of proteins, but what was left out was the question of how is everything managed. Now in the so-called junk the management processes are being elucidated. Lots of planned complexity is my view. The 80% active DNA may be correct.

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Introns are the spacers in the DNA. They signal the start and stop of gene instruction areas (exons) and are spliced out in the transcription process when protein instructions are stitched together. How they evolved from bacteria how they might change is still being studied:-http://scienmag.com/rare-evolutionary-event-detected-in-university-of-texas-lab/-"It took nearly a half trillion tries before researchers at The University of Texas at Austin witnessed a rare event and perhaps solved an evolutionary puzzle about how introns, non-coding sequences of DNA located within genes, multiply in a genome. The results, published today in the Proceedings of the National Academy of Sciences, address fundamental questions about the evolution of new species and could expand our understanding of gene expression and the causes of diseases such as cancer.-***-"For a long time, scientists have known that much of the DNA within any given organism's genome does not code for functional molecules or protein. However, recent research has found that these genetic sequences, misnamed "junk" DNA in the past, often do have functional significance. -"These introns are no exception. Now known to play a role in which genes are expressed, introns are the portion of gene sequences that are removed or spliced out of RNA before genes are translated into protein. When eukaryotes first diverged from bacteria, there was a massive invasion of introns into the genome. All living eukaryotes-from yeast to mammals-share this common ancestor, and while simpler organisms like yeast have eliminated most of their introns, organisms such as mammals have considerably expanded their intron inventory. Humans have over 200,000 introns which take up about 40 percent of the genome. (my bold)
***-"Normally, to make proteins, RNA reads instructions from DNA, skipping the code contained in the introns. But in these two instances, the cell read the DNA in reverse and allowed the introns to make it into the RNA, thus creating a permanent genetic change. These are called intron gains, and if these accumulate over time, they can contribute to the development of new species as well as human disease.-"'We showed in this project that introns continue to be gained, although infrequently at any point in time," says Stevens. "But can introns drive evolution? If these sequences give organisms a selective advantage and become fixed in a population, others have shown that it can be a major factor in the creation of new species." -"These evolutionary advances come at a cost, however, because diseases such as cancer correlate with the improper removal of introns from RNA. Stevens adds, "We are continuing this work to further understand how this process impacts our genetic history, our future, and the prospects of curing disease.'"-Comment: 80% of DNA is not junk. Note the bold. The fact that humans have 40% introns and yeast only a few is a product of our complexity. Lack of junk DNA negates the 'random theory' about evolution, much to the discomfort of strict Darwinians.

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As an additional point to discussion introns and splicing, there is a huge difference in chimp DNA splicing and ours. They do very little, we do a lot:-http://darwins-god.blogspot.com/2016/05/the-naked-ape-open-letter-to-biologos_27.html-"When it was discovered that the human genome contained about twenty five thousand genes it seemed too few. Are not more genes required for a human body? More recently it has been discovered that we make up for that small number of genes with alternative splicing schemes. Most of our genes may undergo such editing, and the result can be a completely different function for the resulting protein.- "We have an enormous alternative splicing program in our cells, far more than chimps have. And this is another inconsistency with evolutionary theory.-"Given the high similarity between the chimp and human genomes, and the relatively few beneficial mutations in protein-coding genes (discussed above), evolutionists have considered the possibility of evolution by splicing. In other words, our enormous alternative splicing program may have been an important factor in our evolving from a small, primitive ape.- "But there are many thousands of these gene splicing changes that would have to evolve. And unlike bacteria whose populations are large and generation times are short, our gene splicing changes would have to evolve in smaller populations with longer generation times.- "It is difficult to see how evolution would have the resources to make this happen. The problem quickly becomes astronomically improbable if groups of genes would need to implement their new splicing logic together. And how could that not be the case?-"In fact, even if only the order of implementing splicing for a small number of genes is important, the problem quickly becomes astronomically improbable. And again, how could that not be the case?-" But this is only the beginning. In addition to the fact that the evolution of our enormous gene splicing changes is unlikely, it also represents an enormous serendipity problem. We would have to say that random mutations constructed complicated genes, with exons and introns and splicing codes, and the incredible splicing machinery, which, it would just so happen, would luckily be just what was needed to evolve humans.-" It is even worse than this when one considers the exons themselves. Those random mutations would have divided the genetic instructions into so many exons, and it just so happened that they would be the right building blocks that, when rearranged, would lead to humans. The serendipity is astronomical here."-Comment: This is part of a large blog article from Dr. Hunter, who does not believe in Darwin common descent, but what he describes in genomic evolution from the chimp is a saltation! And I'm with him. God did it, perhaps through a complexification mechanism or by direct dabble.

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As study of DNA becomes more refined, short segments in open reading frames are found to code small peptides:-http://www.the-scientist.com/?articles.view/articleNo/46150/title/Noncoding-RNAs-Not-So-Noncoding/&utm_campaign=NEWSLETTER_TS_The-Scientist-Daily_2016&utm_source=hs_email&utm_medium=email&utm_content=30186776&_hsenc=p2ANqtz--qrPQXRxBG6mcSqI8C5S11sCRe8FyHrl_pzT0ug0glBuJuXgm2GmXWsqwhpGO72phj5KxFMZFt3_ZxS91gUxsIT8_ckA&_hsmi=30186776/-"In 2002, a group of plant researchers studying legumes at the Max Planck Institute for Plant Breeding Research in Cologne, Germany, discovered that a 679-nucleotide RNA believed to function in a noncoding capacity was in fact a protein-coding messenger RNA (mRNA).1 It had been classified as a long (or large) noncoding RNA (lncRNA) by virtue of being more than 200 nucleotides in length. The RNA, transcribed from a gene called early nodulin 40 (ENOD40), contained short open reading frames (ORFs)putative protein-coding sequences bookended by start and stop codonsbut the ORFs were so short that they had previously been overlooked. When the Cologne collaborators examined the RNA more closely, however, they found that two of the ORFs did indeed encode tiny peptides: one of 12 and one of 24 amino acids. Sampling the legumes confirmed that these micropeptides were made in the plant, where they interacted with a sucrose-synthesizing enzyme.-***-"Turning his attention to how the RNA functioned, Kageyama thought he should first rule out the possibility that it encoded proteins. But he couldn't. We actually found it was a protein-coding gene, he says. It was an accidentwe are RNA people! The pri gene turned out to encode four tiny peptidesthree of 11 amino acids and one of 32that Kageyama and colleagues showed are important for activating a key developmental transcription factor.4-"Since then, a handful of other lncRNAs have switched to the mRNA ranks after being found to harbor micropeptide-encoding short ORFs (sORFs)those less than 300 nucleotides in length. And given the vast number of documented lncRNAsmost of which have no known functionthe chance of finding others that contain micropeptide codes seems high.-***-"ORFs can exist in practically any stretch of RNA sequence by chance, but many do not encode actual proteins. Because the chance that an ORF encodes a protein increases with its length, most ORF-finding algorithms had a size cut-off of 300 nucleotidestranslating to 100 amino acids. This allowed researchers to filter out garbagethat is, meaningless ORFs that exist randomly in RNAs, says Eric Olson of the University of Texas Southwestern Medical Center in Dallas.-"Of course, by excluding all ORFs less than 300 nucleotides in length, such algorithms inevitably missed those encoding genuine small peptides. I'm sure that the people who came up with [the cut-off] understood that this rule would have to miss anything that was shorter than 100 amino acids, says Nicholas Ingolia of the University of California, Berkeley. As people applied this rule more and more, they sort of lost track of that caveat. Essentially, sORFs were thrown out with the computational trash and forgotten.-***-"That paper was really a milestone in terms of showing that there is a lot of translation outside of [known] coding regions, says Pauli.-"But just how much is still unclear. While Ingolia and Weissman's findings could have pointed to a transcriptome littered with micropeptide-encoding sORFs, they also found some fully characterized lncRNAs with well-known nuclear functions to be associated with ribosomes in their analysis. Classical noncoding RNAs such as telomerase RNA, which acts as a template for telomeric DNA replication, for example, and small nuclear RNAs known to be involved in splicing come up as very highly translated in ribosome profiling assays, says Caltech's Mitch Guttman. That's what originally clued us in to the fact that . . . this ribosome-occupancy measure is not [always] indicative of real translation.-***-"And as researchers continue to more carefully comb small snippets of genomes, it's likely that even more cellular roles for micropeptides will be uncovered. Their diminutive size may have caused these peptides to be overlooked, their sORFs to be buried in statistical noise, and their RNAs to be miscategorized, but it does not prevent them from serving important, often essential functions, as the micropeptides characterized to date demonstrate.-"In short, size isn't everything. Indeed, says Pauli, the only reason researchers haven't identified more peptide-encoding sORFs to date is because one just didn't know that these things existed.'-Comment: Same point. Not much DNA is junk, and a major Darwinian theory goes out the window.

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David's comment: Same point. Not much DNA is junk, and a major Darwinian theory goes out the window. - Atheistic evolutionists have argued that junk DNA contradicts the theory of design. Since Darwin knew nothing about DNA, it is absurd to link their arguments with his theory.

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David's comment: Same point. Not much DNA is junk, and a major Darwinian theory goes out the window.
> 
> dhw; Atheistic evolutionists have argued that junk DNA contradicts the theory of design. Since Darwin knew nothing about DNA, it is absurd to link their arguments with his theory.-Of course Darwin didn't know, but atheists claim that junk DNA supports the basis of his theory.I'm discussing the present. His theory has more than one part. His theory of common descent is intact. His proposed method of evolution is by chance and that is denied by the loss of junk as an argument.

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David's comment: Same point. Not much DNA is junk, and a major Darwinian theory goes out the window.-dhw; Atheistic evolutionists have argued that junk DNA contradicts the theory of design. Since Darwin knew nothing about DNA, it is absurd to link their arguments with his theory.-DAVID: Of course Darwin didn't know, but atheists claim that junk DNA supports the basis of his theory.I'm discussing the present. His theory has more than one part. His theory of common descent is intact. His proposed method of evolution is by chance and that is denied by the loss of junk as an argument.-His proposed method of evolution is by random mutation (chance) and natural selection (which decides what changes are beneficial). You and I reject chance because we do not believe that random mutations are capable of producing the complexities of functioning organs. Atheists, however, have the best of both worlds: they can argue that junk is evidence against design, but they can just as easily argue that non-junk is evidence that evolution preserves what is useful (natural selection). Non-junk does not provide evidence against random mutations; it only removes the argument that junk contradicts design. In other words, you can still believe in random mutations whether there is junk or no junk.

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dhw: Atheists, however, have the best of both worlds: they can argue that junk is evidence against design, but they can just as easily argue that non-junk is evidence that evolution preserves what is useful (natural selection). Non-junk does not provide evidence against random mutations; it only removes the argument that junk contradicts design. In other words, you can still believe in random mutations whether there is junk or no junk.-You are not reading what some of the atheist professors are saying. They are still defending junk as an argument against design. Look up Larry Moran's blog "Sandwalk". He rails against ENCODE's findings.-http://sandwalk.blogspot.com/

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dhw: Atheists, however, have the best of both worlds: they can argue that junk is evidence against design, but they can just as easily argue that non-junk is evidence that evolution preserves what is useful (natural selection). Non-junk does not provide evidence against random mutations; it only removes the argument that junk contradicts design. In other words, you can still believe in random mutations whether there is junk or no junk.-DAVID: You are not reading what some of the atheist professors are saying. They are still defending junk as an argument against design. Look up Larry Moran's blog "Sandwalk". He rails against ENCODE's findings.-http://sandwalk.blogspot.com/-You have forgotten the point of this discussion. You wrote that a major Darwinian theory goes out the window, and I pointed out that the junk versus non-junk debate has no bearing on Darwin's theory of random mutations, for all the reasons given above (please reread). The fact that an atheist rejects ENCODE is irrelevant, and his argument against design confirms what I wrote.

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dhw: You have forgotten the point of this discussion. You wrote that a major Darwinian theory goes out the window, and I pointed out that the junk versus non-junk debate has no bearing on Darwin's theory of random mutations, for all the reasons given above (please reread). The fact that an atheist rejects ENCODE is irrelevant, and his argument against design confirms what I wrote.-Your sentence is correct:
Non-junk does not provide evidence against random mutations; it only removes the argument that junk contradicts design. In other words, you can still believe in random mutations whether there is junk or no junk.-But the bold is my main point. We emphasize differently. The atheist insists the presence of junk contradicts design. They want all the junk preserved, which is why Moran constantly denigrates ENCODE. Of course random mutations occur. Note when I use the word 'Darwinian' I'm not referring to the great man, but his pigmy followers.

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dhw: You have forgotten the point of this discussion. You wrote that a major Darwinian theory goes out the window, and I pointed out that the junk versus non-junk debate has no bearing on Darwin's theory of random mutations, for all the reasons given above (please reread). The fact that an atheist rejects ENCODE is irrelevant, and his argument against design confirms what I wrote.-DAVID: Your sentence is correct:
"Non-junk does not provide evidence against random mutations; it only removes the argument that junk contradicts design. In other words, you can still believe in random mutations whether there is junk or no junk."-But the bold is my main point. We emphasize differently. The atheist insists the presence of junk contradicts design. They want all the junk preserved, which is why Moran constantly denigrates ENCODE. Of course random mutations occur. Note when I use the word 'Darwinian' I'm not referring to the great man, but his pigmy followers.-Fair comment, so long as you now agree that a major Darwinian theory has not gone out the window!

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> David But the bold is my main point. We emphasize differently. The atheist insists the presence of junk contradicts design. They want all the junk preserved, which is why Moran constantly denigrates ENCODE. Of course random mutations occur. Note when I use the word 'Darwinian' I'm not referring to the great man, but his pigmy followers.[/i]
> 
> dhw: Fair comment, so long as you now agree that a major Darwinian theory has not gone out the window!-Random mutation is out the window also. What is left of Darwin is common descent and the competition implicit in natural selection as a passive recipient of variation. Darwin does not explain speciation.

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DAVID: Your sentence is correct:
Non-junk does not provide evidence against random mutations; it only removes the argument that junk contradicts design. In other words, you can still believe in random mutations whether there is junk or no junk.
But the bold is my main point. We emphasize differently. The atheist insists the presence of junk contradicts design. They want all the junk preserved, which is why Moran constantly denigrates ENCODE. Of course random mutations occur. Note when I use the word 'Darwinian' I'm not referring to the great man, but his pigmy followers.-dhw: Fair comment, so long as you now agree that a major Darwinian theory has not gone out the window!-DAVID: Random mutation is out the window also. What is left of Darwin is common descent and the competition implicit in natural selection as a passive recipient of variation. Darwin does not explain speciation.-Random mutation is out the window for you and me because we reject the idea that chance can create the complexities of organic life, and not because of junk versus non-junk. But I agree with you: The Origin of Species does not explain the origin of species!

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A new function for 'junk' DNA is found. Junk DNA is an important part of Darwinian proof that DNA shows that evolution is random and produces non-functional DNA. Not true as research progresses:-https://www.sciencedaily.com/releases/2016/10/161005091648.htm-"Researchers have shown that when parts of a genome known as enhancers are missing, the heart works abnormally, a finding that bolsters the importance of DNA segments once considered "junk" because they do not code for specific proteins.-"The team, led by scientists at the Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab), examined the role of two heart enhancers in the mouse genome, showing that the loss of either one resulted in symptoms that resemble human cardiomyopathy, a disease in which the heart muscle often becomes enlarged or rigid.-***-"In that same paper, the researchers provided a comprehensive genome-wide map of more than 80,000 enhancers considered relevant to human heart development and function. The two heart enhancers that they tested were the mouse equivalent of enhancers chosen from among that catalog.
"The cardiac changes that we observed in knockout mice lacking these enhancers highlight the role of noncoding sequences in processes that are important in human disease," said study co-senior author Axel Visel, senior staff scientist.-***-"When scientists sequenced the human genome, they discovered that less than 5 percent of our DNA were genes that actually coded for protein sequences. The biological functions of the noncoding portions of the genome were unclear.
Over the past fifteen years, however, there has been a growing appreciation for the importance of these noncoding regions, thanks in large part to the efforts of individual labs and, more recently, large international efforts such as the Encyclopedia of DNA Elements (ENCODE) project.-"What became clear from this work is that there are many elements of the genome, including enhancers, that are involved in regulating gene expression, even though they do not encode for proteins directly.-"This realization meant that there were vast sections of the genome that needed to be explored and understood. Dickel noted that there are about 20,000 genes in the mouse genome, and in many cases, scientists have a fairly good understanding of what will happen if any one of them is disabled. In contrast, there are 80,000 candidate heart enhancers in the human genome, and it is still unclear how important they are for human development.-***-"...the researchers picked two enhancers located near genes associated with human heart disease. They then determined their equivalent enhancers on the mouse genome and disabled them in mice.-"They compared the mice with the disabled enhancers with control mice that had no mutation and saw very large changes in gene expression in the test mice.
Echocardiograms used to image the hearts from the two groups of mice confirmed that the heart tissue of mice with a disabled enhancer was pumping with less power than normal, consistent with the signs of human cardiomyopathy.-"'Prior to this work, no study had looked at what happens to heart function as a result of knocking out the heart enhancers in the genome," said Dickel. "What was surprising to me was that outwardly, the knockout mice seemed fine. If you just looked at them, you wouldn't necessarily see anything wrong."-"With so many enhancers to test, the map could help scientists prioritize which ones to assess in animal studies and in disease research, the researchers said."-Comment: The idea of junk DNA supporting Darwin's theory is essentially dead. With the absence of any tiny steps in the fossil evidence and faced with the huge gap evidence of speciation, a new theory must be found. How does one plan for the complex changes required in the biochemistry and phenotypic new forms? With a mental understanding of how to plan and coordinate all he new parts. Of course there is no proof, but an assumption of a powerful mental God is reasonable.

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David's comment: The idea of junk DNA supporting Darwin's theory is essentially dead. With the absence of any tiny steps in the fossil evidence and faced with the huge gap evidence of speciation, a new theory must be found. How does one plan for the complex changes required in the biochemistry and phenotypic new forms? With a mental understanding of how to plan and coordinate all he new parts. Of course there is no proof, but an assumption of a powerful mental God is reasonable.-The absence of tiny steps has already been covered by the now far from new theory of punctuated equilibrium. Darwin's theories of common descent and natural selection do not preclude the existence of a powerful mental God. His theory that innovation was caused by random mutations does, in my view, require replacement. A divine 3.7-billion-year-old computer programme and divine dabbling have been offered by a dear friend of mine. I myself have offered cellular intelligence. Any other suggestions?

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> dhw: The absence of tiny steps has already been covered by the now far from new theory of punctuated equilibrium. Darwin's theories of common descent and natural selection do not preclude the existence of a powerful mental God. His theory that innovation was caused by random mutations does, in my view, require replacement. A divine 3.7-billion-year-old computer programme and divine dabbling have been offered by a dear friend of mine. I myself have offered cellular intelligence. Any other suggestions? - We equate intelligence with the ability to think and plan. Remember that first life must have worked automatically in some simple way. How did that then develop intelligence and where were the ideas stored? We will not answer the question of the gaps between species until we find the mechanism for speciation.

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A guess is more like 20% but more and more modifying areas for gene expression are found in 'dark' or junk DNA as newer techniques tease apart DNA:

http://www.nature.com/nature/journal/v538/n7624/full/538275a.html?WT.ec_id=NATURE-20161...

"Fifteen years ago, scientists celebrated the first draft of the sequenced human genome. At the time, they predicted that humans had between 25,000 and 40,000 genes that code for proteins. That estimate has continued to fall. Humans actually seem to have as few as 19,000 such genes1 — a mere 1–2% of the genome. The key to our complexity lies in how these genes are regulated by the remaining 99% of our DNA, known as the genome's 'dark matter'.

***

"So far, the data suggest that there are hundreds of thousands of functional regions in the human genome whose task is to control gene expression: it turns out that much more space in the human genome is devoted to regulating genes than to the genes themselves. Scientists are now trying to validate each predicted element experimentally to ascertain its function — a mammoth task, but one for which they now have a powerful new tool.

***

"How much of DNA's dark matter has a function in gene control is still up for debate. In 2012, ENCODE scientists proposed on the basis of biochemical-assay predictions that 80% of the non-coding genome has a function2. But this figure soon proved to be an overestimate as researchers narrowed the definition of 'function' and devised experimental methods, such as reporter assays, to test these functions. “The number still isn't fully known”, in part because the mapping isn't complete, says Michael Snyder, a geneticist at Stanford University in California and a member of ENCODE. “Most people would say between 10% and 20% of the [non-coding] genome is likely to have a function where, if you disrupt it, you will affect something.”

"But regulatory elements have a bewildering array of functions and forms, which makes tackling them a formidable challenge. Even the best-known types, such as spots in the genome known as promoters, which lie next to a gene where transcription begins, and enhancers — regions that when bound by specific transcription factors alter the likelihood of a gene being read — are hard to study. In addition to the sheer number of these sites, estimated at 15 million, enhancers may be positioned thousands of base pairs away from the gene that they control. This makes it tough to predict where their target genes are located and what they do.

***

"...the researchers also discovered mysterious sections that they dubbed 'unmarked regulatory elements', or UREs, that do not fit into any category of functional elements. The team is currently exploring how widespread these UREs might be in the genome. This new type of assay, along with other gene-editing-based screens, will play an increasingly important part in the validation of ENCODE candidates, says Sherwood.

***

"It's possible that there are still elements in the genome that existing assays have missed. After all, regulatory signals still crop up unexpectedly, such as the UREs in Sherwood's screen. And a team of scientists led by Harvard Medical School immunologist Daniel Tenen discovered10 a potential new class of regulators that seem to control whether a gene is turned on or off by blocking the enzyme DNA methyltransferase 1, which adds methyl groups to silence genes. These elements are dubbed 'extracoding RNAs', and because they can influence silencing in a gene-specific way, have therapeutic potential. Earlier this year, neuroscientist Jeremy Day of the University of Alabama at Birmingham and his colleagues showed in rat neurons that an extracoding RNA influences the transcription of a gene important for memory formation.

***

" A spatial understanding of how DNA is packaged into a cell, and of the 3D folding that positions genes in close contact with their regulatory elements, will be key to predicting an element's target genes. The NIH Common Fund has begun the '4D Nucleome' project, for instance, which aims to predict the target genes for every regulatory element. That knowledge will help to fill in the picture of how a given regulatory element influences health and disease."

Comment: Still no idea of how much DNA is useful, as the article explains. Not 80% but how much? Note the idea of 3,4-D relationships I've noted before. With a huge regulatory system, chance invention of human DNA is not possible.

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This article discusses pseudo-pseudogenes ( in so-called junk DNA areas) that may well function to understand and recognize odors. This is much like immune cells building antibodies by modifying DNA as new infectious organisms are recognized by invasion:

http://www.uncommondescent.com/intelligent-design/our-junk-dna-hard-at-work-pseudo-pseu...

"Abstract: Pseudogenes are generally considered to be non-functional DNA sequences that arise through nonsense or frame-shift mutations of protein-coding genes. Although certain pseudogene-derived RNAs have regulatory roles, and some pseudogene fragments are translated, no clear functions for pseudogene-derived proteins are known. Olfactory receptor families contain many pseudogenes, which reflect low selection pressures on loci no longer relevant to the fitness of a species. Here we report the characterization of a pseudogene in the chemosensory variant ionotropic glutamate receptor repertoire of Drosophila sechellia, an insect endemic to the Seychelles that feeds almost exclusively on the ripe fruit of Morinda citrifolia. This locus, D. sechellia Ir75a, bears a premature termination codon (PTC) that appears to be fixed in the population. However, D. sechellia Ir75a encodes a functional receptor, owing to efficient translational read-through of the
PTC. Read-through is detected only in neurons and is independent of the type of termination codon, but depends on the sequence downstream of the PTC. Furthermore, although the intact Drosophila melanogaster Ir75a orthologue detects acetic acid-a chemical cue important for locating fermenting food found only at trace levels in Morinda fruit-D. sechellia Ir75a has evolved distinct odour-tuning properties through amino-acid changes in its ligand-binding domain. We identify functional PTC-containing loci within different olfactory receptor repertoires and species, suggesting that such ‘pseudo-pseudogenes’ could represent a widespread phenomenon. "(my bold)

Comment: More and junk DNA is found to function.

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Another area of 'junk' DNA is found to be active in stress in mice. Darwinists have claimed the so-called non-functional DNA proved their point that evolution was a chance random process. That proof has disappeared:

https://www.sciencedaily.com/releases/2016/12/161215143340.htm

"A study from Massachusetts General Hospital (MGH) investigators has found a surprising role for what had been considered a nonfunctional "junk" RNA molecule: controlling the cellular response to stress. In their report in the Dec. 15 issue of Cell, the researchers describe finding that a highly specific interaction between two elements previously known to repress gene transcription -- B2 RNA and EZH2, an enzyme previously known only to silence genes -- actually induces the expression of stress-response genes in mouse cells.

***

"Less than 2 percent of the genome in mammals actually codes for proteins, and for many years it was thought that noncoding DNA was a useless artifact. While some is translated into RNA molecules required for maintaining and regulating cellular functions -- such as transfer RNA and microRNAs -- the impression that most noncoding RNA serves no function has persisted. This has been particularly true for long noncoding RNAs and is even more the case for molecules transcribed from "parasitic" retrotransposons -- repetitive DNA sequences inserted throughout the genome. But recent studies in mouse cells have indicated that RNA transcribed from the B2 retrotransposon binds to stress genes and suppresses their transcription.

***

"Their cellular experiments confirmed that EZH2 binds to B2 RNA and, when subjected to heat, cuts or cleaves the RNA molecule. That cleavage of B2 RNA -- which otherwise binds to and silences genes that protect against cellular damage by heat shock -- allowed the transcription of those heat-shock genes.

"'Our findings imply that B2 is a key regulator of the stress response and probably has that role in all types of cells," says Lee, who is a professor of Genetics at Harvard Medical School. "We and others have studied B2 cells in mice, but these same types of short interspersed nuclear elements are found in human cells, where they are quite different. While it remains to be seen whether human SINEs have similar properties, I wouldn't be surprised if they do.'"

Comment: It is the same old story. The more DNA is researched the more functional areas are found. Most of it is not leftover junk from previous evolution. It is complex and it is purposeful.

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Long non-coding RNA's are yielding their functions to new studies:

http://www.the-scientist.com/?articles.view/articleNo/47786/title/Nearly-500-New-lncRNA...

"Long noncoding RNAs (lncRNAs) comprise a mysterious class of molecules that are more than 200 nucleotides in length, but do not code for any proteins. Now, in a December 15 study published in Science, researchers identify 499 new lncRNAs and have made strides toward understanding the functions of these molecules. Unlike most coding genes, which tend to be essential across diverse cell lines, nearly 90 percent of the lncRNAs genes identified appear to affect robust cell growth in just one of the six cell lines tested, the team reported.

“'Long noncoding RNAs are a pretty mysterious set of transcripts that are abundantly present in most cells,” said coauthor Daniel Lim, a neuroscientist and clinician at the University of California, San Francisco (UCSF). “What wasn’t known is how many there are, and which are important for basic biological functions. Our surprising finding is that . . . most lncRNAs function in only one cell type. This exquisite specificity in RNA function is a result that I do not think I would have believed, had we not done a study on this scale.”

***

"The most surprising finding, the authors wrote, was that the vast majority of lncRNA genes appear to modify cell growth in only one cell type. “Unlike protein-coding genes, which are often essential in many different types of cells, the lncRNAs that were essential in one cell rarely played an important role in the other cell types,” Weissman said. “That suggests lncRNAs play a role in giving each cell its own identity.”

"Rinn praised the findings. “This heroic effort is the first genome-wide screen for lncRNA biology across specific cell types,” he said. “From this study we can now conclude that a majority of lncRNAs are important to cell viability, as had been suspected. But now the proof is in the pudding, so to speak.”

"He cautioned, however, that it is still unclear how the 499 lncRNA loci identified might affect cell growth. “This study took great care to control for numerous shortcomings of genome-wide screens,” Rinn said. “However, this study can’t rule out if it is the act of transcription of these lncRNAs that is important or the final RNA product acting as a functional molecule.'”

Comment: More 'junk' DNA bites the dust. Most of DNA seems to have functional purposes contrary to Darwinist theories about it.

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An RNA in the so-called 'junk' area of DNA both controls expression of genes by allowing and stopping expression:

https://www.sciencedaily.com/releases/2016/12/161215143340.htm

"A study from Massachusetts General Hospital (MGH) investigators has found a surprising role for what had been considered a nonfunctional "junk" RNA molecule: controlling the cellular response to stress. ... the researchers describe finding that a highly specific interaction between two elements previously known to repress gene transcription -- B2 RNA and EZH2, an enzyme previously known only to silence genes -- actually induces the expression of stress-response genes in mouse cells.

"'EZH2 is part of a structure called the Polycomb Repressive Complex 2, which silences target genes," says Jeannie T. Lee, MD, PhD,of the MGH Department of Molecular Biology, senior author of the report. "But a big paradox in the field has been that EZH2 is found at the sites of both active and inactive genes. We have shown, for the first time, that EZH2 can act outside of the PRC2 complex to activate genes through another mechanism -- in this case by cleaving the B2 RNA molecule, which then activates stress response genes."

"Less than 2 percent of the genome in mammals actually codes for proteins, and for many years it was thought that noncoding DNA was a useless artifact. While some is translated into RNA molecules required for maintaining and regulating cellular functions -- such as transfer RNA and microRNAs -- the impression that most noncoding RNA serves no function has persisted. This has been particularly true for long noncoding RNAs and is even more the case for molecules transcribed from "parasitic" retrotransposons -- repetitive DNA sequences inserted throughout the genome. But recent studies in mouse cells have indicated that RNA transcribed from the B2 retrotransposon binds to stress genes and suppresses their transcription.

***

"Their cellular experiments confirmed that EZH2 binds to B2 RNA and, when subjected to heat, cuts or cleaves the RNA molecule. That cleavage of B2 RNA -- which otherwise binds to and silences genes that protect against cellular damage by heat shock -- allowed the transcription of those heat-shock genes.

"'Our findings imply that B2 is a key regulator of the stress response and probably has that role in all types of cells," says Lee, who is a professor of Genetics at Harvard Medical School. "We and others have studied B2 cells in mice, but these same types of short interspersed nuclear elements are found in human cells, where they are quite different. While it remains to be seen."

Comment: Another example that most of DNA is useful and active in some way, even though it does not code for protein. Classic Darwinism claimed that the 'junk' DNA was created and discarded by the pointless chance mechanism of evolution. How wrong!

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The research continues to show 'junk' DNA is not junk. Another study into long non-coding RNA functions. Only 2% of DNA codes for protein, but a huge percentage of the remaining 98% does modulating function:

http://medicalxpress.com/news/2016-12-reveals-importance-non-coding-rna-cellular.html

"The investigators used computational analyses to predict potential polypeptides that could be encoded by known lncRNA molecules, and then they used mass spectrometry to determine if these putative polypeptides were actually expressed. "With this approach we actually identified many expressed hidden polypeptides and went on to characterize one in particular," Pandolfi explained. This specific lncRNA molecule is termed LINC00961 and encodes a 90 amino acid polypeptide.

"A variety of molecular and biochemical experiments revealed that the LINC00961 encoded polypeptide played an important role in modulating the activity of the mTORC1 protein complex, which is a critical sensor of nutrient availability within cells. The complex also regulates a variety of cellular processes including translation, metabolism, cell growth, and proliferation, and alterations in its function can lead to diseases such as cancer. Because the LINC00961 polypeptide appeared to specifically block mTORC1's ability to sense stimulation with amino acids, the investigators named the peptide encoded by the lncRNA SPAR (Small regulatory Polypeptide of Amino acid Response).

Pandolfi and his team found that the SPAR encoding lncRNA is highly expressed in a number of tissue types, including muscle. Experiments conducted in mice demonstrated that through its effects on mTORC1, the SPAR polypeptide helps regulate the muscle's ability to regenerate and repair after injury. Specifically, expression of LINC00961 is blocked following muscle injury in mice, leading to reduced levels of SPAR and maximal mTORC1 activity to promote tissue regeneration.

"The experimental approach we used allowed us to eliminate expression of the SPAR polypeptide, while maintaining expression of the host lncRNA," said lead author Akinobu Matsumoto, PhD, research fellow at the Cancer Center at BIDMC and lead author of the study. "We are able to ascribe this function to the coding function of the lncRNA rather than any non-coding function it may also have." The findings suggest that therapeutic strategies that restrict expression of SPAR in injured muscle may promote a more rapid regeneration of tissue.

"The results suggest that lncRNAs may have diverse roles and functions. Although they may not code for large proteins, lncRNAs may produce small polypeptides that can fine tune the activity of critical cellular components. The findings also expand the repertoire of peptide-coding genes in the human genome that should be studied and annotated.

"The study also provides insights on how mTORC1 activity may be attuned to meet the distinct needs of a specific tissue. "An ability to target such modulators could be of great advantage from a therapeutic perspective, allowing for control of mTORC1 activity in cells or tissues that express such modulators while not affecting its activity and function in other tissue and cell types," explained co-author John Clohessy, PhD, Instructor in Medicine at BIDMC and a senior member of Pandolfi's research team. Indeed, a key feature of many lncRNAs is that their expression is often highly tissue-specific. Thus, targeting small polypeptides encoded by lncRNA molecules may provide the key to regulating common cellular components in a tissue-specific manner."

Comment: It is obvious that DNA is changed to be tissue specific and organ specific in the cells in the liver, in the kidney, in the lung, etc. lncRNA is one of the results. It is obvious that the function of DNA must be production of protein, but that simply creates the structures of life. DNA must also be able to also manage the functions of life through modifiers.

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Now most lncRNA function:

http://www.the-scientist.com/?articles.view/articleNo/48691/title/Study--Most-Long-Nonc...

"Researchers have now catalogued nearly 28,000 long noncoding RNAs (lncRNAs) present in human cells, and found that roughly 20,000 are likely functional. The study, published yesterday (March 1) in Nature, also suggests that about 2,000 lncRNAs are associated with diseases.

“'There is strong debate in the scientific community on whether the thousands of long non-coding RNAs generated from our genomes are functional or simply byproducts of a noisy transcriptional machinery,” coauthor Alistair Forrest, a genomicist at the University of Western Australia and a visiting scientist at the RIKEN Center for Life Science Technologies, said in a press release. “By integrating the improved gene models with data from gene expression, evolutionary conservation and genetic studies, we find compelling evidence that the majority of these long non-coding RNAs appear to be functional.” (my bold)

"Forrest’s team used 1,829 human samples to build the lncRNA atlas, which is available for researchers to probe genetic and cell-type information.

"The roles of lncRNAs in the cell are only recently beginning to take shape. In December, for instance, another group of scientists identified nearly 500 such molecules important for cellular growth. “Our surprising finding is that . . . most lncRNAs function in only one cell type,” coauthor Daniel Lim of the University of California, San Francisco (UCSF), told The Scientist at the time. “This exquisite specificity in RNA function is a result that I do not think I would have believed, had we not done a study on this scale.”

"The authors of the newest study note there is still much to be understood about the biogenesis and activity of lncRNAs. Even among those lncRNAs not presumed to be functional, “to what extent [that proportion] represents spurious transcription initiation by RNA polymerase II42 is still an open question,” Forrest and colleagues write in the study."

Comment: The levels of control and complexity keep increasing as research go on. Chance cannot do this.

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Found studying paramecia:

https://phys.org/news/2017-03-unique-dna-function.html

"Researchers at the University of Bern have for the first time described a mechanism in detail how so-called "junk DNA" is transcribed before being degraded – and this mechanism is remarkably clever

"sounds a bit like the winning proposal in a design contest: How can small pieces of information be read when they are too short to fit into the reading apparatus? Stitch them together into a longer string and close the string to produce a handy loop that can even be read off repeatedly. That's how a little organism called Paramecium tetraurelia, a species of unicellular ciliate, organises the transcription of small excised DNA segments into RNAs, which have a regulatory function.

"But the story actually goes the other way round: When Mariusz Nowacki from the Institute of Cell Biology of the University of Bern found small RNAs with a regulatory function in the elimination of segments out of paramecium DNA, he and his team started to investigate the molecular mechanisms – where do these RNAs come from, and what exactly is their role? They soon found out that there seems to be a sort of a feedback loop in the deletion of DNA segments. These, previously thought to be useless pieces of DNA, are cut out of the genome and then degraded by the cell machinery. However, before degradation, they serve as templates for small RNAs which in turn help with cutting out more of these DNA pieces. Once started, this pyramid system keeps reinforcing itself, via the production of RNA.

***

"And their guess proved to be right: Paramecium has figured out a way to stitch DNA pieces together randomly into strings and, once the strings have the right length (of about 200 base pairs), to connect the ends and form circular concatemers of DNA segments.

"The finding has interesting implications: DNA thought to be non-coding "junk" – of no use for the organism whatsoever and degraded quickly after being removed from the genome –is actually a functional template for a biologically important class of small RNAs. It is actually one of the big emerging fields in molecular biology, whether "junk" DNA is really worthless or rather, as is increasingly becoming clear, whether it actually has regulatory functions. Nowacki believes that in this work his group was for the first time able to pin down a precise mechanism for the transcription of deleted "junk DNA"– which would strengthen the case for an inevitable name change.

"The research group studies a class of molecules that has long been neglected: RNA (ribonucleic acid) is pivotal for many vital processes and much more complex than initially assumed. For instance, RNA defines the conditions, in a given cell, under which a given gene is or is not activated. If any part of this process of genetic regulation breaks down or does not run smoothly, this can cause heart disease, cancer, brain disease and metabolic disorders."

Comment: As usual more research, less junk DNA, and another Darwin evolutionary theory dies.

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DAVID's comment: As usual more research, less junk DNA, and another Darwin evolutionary theory dies.

Please tell us where Darwin talks of junk DNA. Alternatively, please stop sniping at poor old Darwin every time you attack atheistic interpretations of his theory.

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DAVID's comment: As usual more research, less junk DNA, and another Darwin evolutionary theory dies.

dhw: Please tell us where Darwin talks of junk DNA. Alternatively, please stop sniping at poor old Darwin every time you attack atheistic interpretations of his theory.

My comment is just a reminder that most scientists supporting Darwin's concept of how evolution works declared that over 80% of DNA was junk produced by random and useless mutations. Now shown terribly wrong. Poor Darwin was misused by his followers. To educate new readers of this website they must see this reminder.

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DAVID's comment: As usual more research, less junk DNA, and another Darwin evolutionary theory dies.

dhw: Please tell us where Darwin talks of junk DNA. Alternatively, please stop sniping at poor old Darwin every time you attack atheistic interpretations of his theory.

DAVID: My comment is just a reminder that most scientists supporting Darwin's concept of how evolution works declared that over 80% of DNA was junk produced by random and useless mutations. Now shown terribly wrong. Poor Darwin was misused by his followers. To educate new readers of this website they must see this reminder.

Then perhaps it would be fairer to attack atheistic neo-Darwinians than to attack Darwin.

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DAVID: My comment is just a reminder that most scientists supporting Darwin's concept of how evolution works declared that over 80% of DNA was junk produced by random and useless mutations. Now shown terribly wrong. Poor Darwin was misused by his followers. To educate new readers of this website they must see this reminder.

dhw: Then perhaps it would be fairer to attack atheistic neo-Darwinians than to attack Darwin.

Yes, poor Darwin is miss-used by his supporters.

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A junk area gene, actually a lncRNA, has been found to help with familial hypercholesterolemia:

https://www.sciencedaily.com/releases/2017/08/170827101841.htm

"Scientists from UCLA and the Howard Hughes Medical Institute successfully used a gene that suppresses cholesterol levels as part of a treatment to reduce plaque in mice with a disorder called familial hypercholesterolemia. In a preclinical study, researchers found that the gene, LeXis, lowered cholesterol and blockages in the arteries, and the treatment appeared to reduce the build-up of fat in liver cells.

"Familial hypercholesterolemia is an inherited condition characterized by extremely high levels of low-density lipoprotein cholesterol (commonly referred to as "bad cholesterol") and an increased risk of early heart disease.

"The LeXis gene belongs to a unique group of genes that until recently were considered "junk DNA" because scientists believed they served little purpose. However, evidence from the human genome project led to the discovery that genes like LeXis are actually active. The study of these genes, now referred to as long noncoding ribonucleic acids, or lncRNAs, is a rapidly evolving area in biology.

"Researchers wanted to test whether a single injection of LeXis could slow the development of heart disease. To do so, they gave the mice either LeXis or a control gene, and fed them a 15-week diet consisting of food high in sodium and cholesterol -- the mouse equivalent of fast-food hamburgers and french fries. Researchers then measured the progression of heart disease."

Comment: 'Junk' DNA, as a concept, is important to atheists, who point to so-called junk areas in DNA as a proof that the process of evolution is really at random, and these areas are evidence of discarded useless genes from past attempts at evolution. The less evidence of purpose, the more likely it is all a chance mechanism, no God needed. It appears more and more about 805 of DNA is functional.

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David’s comment: 'Junk' DNA, as a concept, is important to atheists, who point to so-called junk areas in DNA as a proof that the process of evolution is really at random, and these areas are evidence of discarded useless genes from past attempts at evolution. The less evidence of purpose, the more likely it is all a chance mechanism, no God needed. It appears more and more about 805 of DNA is functional.

Junk DNA may be important to atheists who wish to debunk the idea that God created every species separately (i.e. why would he specially design something useless?) but (a) it tells us nothing whatsoever about how life and the mechanism for evolution began, and (b) a theist evolutionist can simply argue that God allowed the mechanism to run its own course, and so it was perfectly natural that different species should retain those elements of the mechanism that were no longer of use to them. If there is no junk DNA, the theist can say: “There you are, perfect design”, and the atheist can say that evolution gets rid of any material that is not useful. Both sides can take it or leave it, and it won’t make the slightest difference to their beliefs.

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David’s comment: 'Junk' DNA, as a concept, is important to atheists, who point to so-called junk areas in DNA as a proof that the process of evolution is really at random, and these areas are evidence of discarded useless genes from past attempts at evolution. The less evidence of purpose, the more likely it is all a chance mechanism, no God needed. It appears more and more about 805 of DNA is functional.

dhw: Junk DNA may be important to atheists who wish to debunk the idea that God created every species separately (i.e. why would he specially design something useless?) but (a) it tells us nothing whatsoever about how life and the mechanism for evolution began, and (b) a theist evolutionist can simply argue that God allowed the mechanism to run its own course, and so it was perfectly natural that different species should retain those elements of the mechanism that were no longer of use to them. If there is no junk DNA, the theist can say: “There you are, perfect design”, and the atheist can say that evolution gets rid of any material that is not useful. Both sides can take it or leave it, and it won’t make the slightest difference to their beliefs.

But that is not what the atheists say. They are still insisting DNA is 80-90% junk, despite the mounting evidence:

https://evolutionnews.org/2017/06/dan-graur-darwins-reactionary/

In 2013, biologist Dan Graur criticized the “evolution-free gospel of ENCODE” and accused its researchers of “playing fast and loose with the term ‘function,’ by divorcing genomic analysis from its evolutionary context.”81 In a lecture at the University of Houston, Graur argued that “if the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome.” In other words: “If ENCODE is right, then evolution is wrong.” But for Graur, evolution can’t be wrong. His solution to the problem? “Kill ENCODE.”

Just my point

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David’s comment: 'Junk' DNA, as a concept, is important to atheists, who point to so-called junk areas in DNA as a proof that the process of evolution is really at random, and these areas are evidence of discarded useless genes from past attempts at evolution. The less evidence of purpose, the more likely it is all a chance mechanism, no God needed. It appears more and more about 805 of DNA is functional.

dhw: Junk DNA may be important to atheists who wish to debunk the idea that God created every species separately (i.e. why would he specially design something useless?) but (a) it tells us nothing whatsoever about how life and the mechanism for evolution began, and (b) a theist evolutionist can simply argue that God allowed the mechanism to run its own course, and so it was perfectly natural that different species should retain those elements of the mechanism that were no longer of use to them. If there is no junk DNA, the theist can say: “There you are, perfect design”, and the atheist can say that evolution gets rid of any material that is not useful. Both sides can take it or leave it, and it won’t make the slightest difference to their beliefs.

DAVID: But that is not what the atheists say. They are still insisting DNA is 80-90% junk, despite the mounting evidence:
https://evolutionnews.org/2017/06/dan-graur-darwins-reactionary/
In 2013, biologist Dan Graur criticized the “evolution-free gospel of ENCODE” and accused its researchers of “playing fast and loose with the term ‘function,’ by divorcing genomic analysis from its evolutionary context.”81 In a lecture at the University of Houston, Graur argued that “if the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome.” In other words: “If ENCODE is right, then evolution is wrong.” But for Graur, evolution can’t be wrong. His solution to the problem? “Kill ENCODE.”
Just my point

I’m surprised to hear you agree that if ENCODE is right, then evolution is wrong. I thought you believed that your God used evolution as his method and directed it. I myself am in no position to say whether ENCODE is right or wrong. My point is that whether ENCODE is right or wrong won’t make the slightest different to people’s beliefs, as I have explained above.

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DAVID: But that is not what the atheists say. They are still insisting DNA is 80-90% junk, despite the mounting evidence:
https://evolutionnews.org/2017/06/dan-graur-darwins-reactionary/
In 2013, biologist Dan Graur criticized the “evolution-free gospel of ENCODE” and accused its researchers of “playing fast and loose with the term ‘function,’ by divorcing genomic analysis from its evolutionary context.”81 In a lecture at the University of Houston, Graur argued that “if the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome.” In other words: “If ENCODE is right, then evolution is wrong.” But for Graur, evolution can’t be wrong. His solution to the problem? “Kill ENCODE.”

David Just my point

dhw: I’m surprised to hear you agree that if ENCODE is right, then evolution is wrong. I thought you believed that your God used evolution as his method and directed it. I myself am in no position to say whether ENCODE is right or wrong. My point is that whether ENCODE is right or wrong won’t make the slightest different to people’s beliefs, as I have explained above.

I'm sorry if I've confused you. Graur is a confirmed atheist evolutionist. Note the bold. He is defending undirected evolution. ENCODE implies evolution is designed (directed) if 80% of DNA is functional and I present evidence to that effect all the time. Concept: more junk means more undirection to the athiests. Read the link I presented above.

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DAVID: I'm sorry if I've confused you. Graur is a confirmed atheist evolutionist. Note the bold. He is defending undirected evolution. ENCODE implies evolution is designed (directed) if 80% of DNA is functional and I present evidence to that effect all the time. Concept: more junk means more undirection to the athiests. Read the link I presented above.

You made it plain that Graur was an atheist, and I am perfectly aware that the less junk there is, the more a theist will argue that it supports design. My point is that even if it turned out that there was no junk at all, atheists could say that evolution dispenses with junk. People with fixed beliefs can always find a way to adapt them to new findings. These days many theists, including yourself, have turned their backs on Creationism and believe in evolution. At present, though, atheists are still arguing for junk, and I’m afraid even 20% junk is junk. I can only repeat that “I myself am in no position to say whether ENCODE is right or wrong. My point is that whether ENCODE is right or wrong won’t make the slightest different to people’s beliefs...” There is no disagreement here between us – I am simply offering a different perspective on the subject.

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DAVID: I'm sorry if I've confused you. Graur is a confirmed atheist evolutionist. Note the bold. He is defending undirected evolution. ENCODE implies evolution is designed (directed) if 80% of DNA is functional and I present evidence to that effect all the time. Concept: more junk means more undirection to the athiests. Read the link I presented above.

dhw: You made it plain that Graur was an atheist, and I am perfectly aware that the less junk there is, the more a theist will argue that it supports design. My point is that even if it turned out that there was no junk at all, atheists could say that evolution dispenses with junk. People with fixed beliefs can always find a way to adapt them to new findings. These days many theists, including yourself, have turned their backs on Creationism and believe in evolution. At present, though, atheists are still arguing for junk, and I’m afraid even 20% junk is junk. I can only repeat that “I myself am in no position to say whether ENCODE is right or wrong. My point is that whether ENCODE is right or wrong won’t make the slightest different to people’s beliefs...” There is no disagreement here between us – I am simply offering a different perspective on the subject.

Fair enough.

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Using viruses to explore the possible function of long non-coding RNA, 200 or more bases long, a study shows functions, a further dagger in the heart of Darwinist claims about junk DNA:

https://www.nature.com/articles/d41586-017-07692-w

"Could a class of host RNA known as long non-coding RNAs (lncRNAs) also be targeted to achieve a similar goal? Analysis of the roles of cellular and viral lncRNAs in infection has previously focused mainly on modulation of innate immune responses2. Now, writing in Science, Wang et al.3 reveal a different mechanism by which the virus appropriates host-derived lncRNA: activation of a host-cell metabolic pathway required for viral replication.

"Long non-coding RNAs (non-coding RNAs more than 200 nucleotides long) have roles in many aspects of cell biology. In the nucleus, they are involved in transcriptional regulation and remodelling of chromosomes, and in the cytoplasm, they regulate microRNA function as well as the translation of mRNAs to generate proteins. But there are scores of lncRNAs whose functions have not been identified, so there are potentially many more roles to uncover.

***

"They next analysed gene expression in cells deficient in lncRNA-ACOD1 and identified changes in the expression of many metabolic genes, suggesting that this lncRNA indirectly affects virus replication by modulating host metabolism.

"Wang et al. then recovered lncRNA-ACOD1 from cells and analysed the proteins associated with it. This revealed that lncRNA-ACOD1 specifically bound to the host protein glutamic-oxaloacetic transaminase 2 (GOT2) — an enzyme involved in a variety of metabolic pathways, including the tricarboxylic acid (TCA) cycle, which generates energy, and the uptake of long-chain fatty acids, which can be used as metabolic fuel by cells. Subsequent mechanistic analyses showed that lncRNA-ACOD1 not only bound GOT2, but also strongly potentiated its enzymatic activity (Fig. 1). This activation was, in turn, crucial for the generation of metabolites required for viral replication.

***

"Wang and colleagues’ work adds to the list of known mechanisms by which lncRNAs can regulate crucial physiological processes. Much previous work has focused on the roles of mRNAs, even though they comprise only about 2% of the human genome. But some 80% of the genome is actively transcribed6, resulting in RNAs with no obvious coding potential, many of which may well have regulatory functions. Viruses have extremely limited genomic space relative to that of their hosts, and targeting a host-cell factor central to many metabolic processes, such as a key host lncRNA, would be an efficient way of adjusting the host-cell environment to suit their own needs. Clearly, further work that focuses on how viruses manipulate non-coding RNA function (and, in particular, the relatively under-studied lncRNAs) has the potential to greatly increase our understanding of how viruses take control of the cells they infect.

"Despite the elegance of Wang and colleagues’ story, questions remain about both lncRNA-ACOD1 and other viral metabolic targeting strategies. Prominent among these is understanding why decreasing GOT2 activity has such a marked effect on virus replication without detectably affecting host-cell viability. Wang et al. found that GOT2 depletion led to decreased levels of l-aspartate (an amino acid required for the biosynthesis of almost all proteins) and α-ketoglutarate (a key molecule in the TCA cycle, and hence central to energy production in the cell) — both of which are expected to have vital roles in host-cell metabolism. It is reasonable to expect that virus-infected cells, which produce thousands of viral progeny, would have higher energy requirements than uninfected cells. However, the finding that lncRNA-ACOD1 is largely dispensable for normal host-cell metabolism raises the question of why the molecule would be evolutionarily conserved when it is potentially so harmful to the host."

Comment: This article is on a study of viral mechanisms, but in the research they have uncoverd unknown normal incRNA functional controls. It is obvious that coding DNA does not do the whole job of maintaining live organisms. The other control layers are being uncovered and in doing so commpletely destroying the Darwinists claims that 'junk DNA' proves teh Darwin theory of a purposeless chance mmchanism that discards many mistakes along the way through natural selection for only good results. I've mentioned Dan Graur before:

"Remember Dan Graur and the debate about “junk DNA”? That 'if we permit the ENCODE consortium to claim 80% of non-coding DNA is useful, then Darwinists have lost' a game to ID?"

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Protection is from non-coding RNA's activities. They are part of so-called junk DNA, since they don't code for proteins:

https://www.sciencedaily.com/releases/2018/03/180302124842.htm

"Thousands of molecules of ribonucleic acid make salt-loving microbes known as "extremophiles" highly resistant to the phenomenon oxidative stress -- the uncontrollable production of unstable forms of oxygen called "free radicals," which can negatively affect DNA, proteins, and lipids in cells.

"In a study published recently in the Journal of Bacteriology, Johns Hopkins University scientists found that a group of RNAs -- that do not form protein -- orchestrate this resilience in extremophiles requiring high salt concentrations called Haloarchaea, to grow without signs of damage.

***

"To understand the extremophile's resistance to oxidative stress, Gelsinger examined its ribonucleic acid profile under hydrogen peroxide as an agent of the stress. Along with messenger RNA, which is needed to create proteins, he observed large quantities of something surprising -- small noncoding RNA. Unlike messenger RNA, which acts as the go-between for DNA and proteins, noncoding RNAs do not seem to turn into protein.

"'My findings strongly suggest that the [noncoding RNA] actually causes the messenger RNA to degrade and be cut up," Gelsinger said. By effectively blocking the production of protein or breaking down the messenger RNA, the proteins that play a role in oxidative stress were simply not made.

"Moreover, Gelsinger said, these noncoding RNAs affect multiple targets, having a large-scale effect. Pieces of DNA that are jumpy, particularly in times of stress, and hop around in the genome of organisms, called transposons, are targets for such regulatory small RNAs. By disrupting the disruptors, these RNAs possibly keep in check further damage caused by transposons, allowing extremophiles to repair the damage caused by oxidative stress.

"'What we found is that a lot of these noncoding RNAs are causing the degradation of those transposons, so they are essentially silencing them," said Gelsinger. With fewer transposons hopping around, damage to the DNA is reduced.

"Among other targets of the small noncoding RNAs were messenger RNAs that aid in guiding microbes towards or away from food or other chemical agents, as well as those that reign in damaged proteins and prevent injured cells from growing. These noncoding RNAs also targeted a class of molecules that decide which proteins -- and how many of them -- are formed. "If you can regulate the regulator, you can get a much faster, larger effect than just directly regulating your target," said Gelsinger. The enveloping effect of these noncoding RNAs appears to contribute heavily to the oxidative stress resistance found within Haloarchaea.'

Comment: More evidence that much so-called junk DNA isn't junk. According to Darwin current theory junk DNA is useless stuff produced by chance mutations during purposeless evolution, but 80% of it has been found to have function, small and large effects.

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New research shows junk DNA must be studied in cancers to direct therapy against so-called junk DNA that is functional:

https://medicalxpress.com/news/2018-04-genetic-material-junk-key-cancer.html

"Material left out of common processes for sequencing genetic material in cancer tumors may actually carry important information about why only some people respond to immunotherapy, possibly offering better insight than the type of material that is being sequenced, according to a study by Mount Sinai researchers published on April 3 in Cell Reports.

"Sequencing a type of genetic material in cancer tumors called messenger RNA has transformed personalized cancer therapy and revealed biomarkers for early detection. Advances in this field have transformed scientists' understanding of the differences between healthy tissue and tumors.

"To date, gene expression in tumors has been typically profiled by capturing messenger RNAs; however, they represent only a fraction of the molecules detected. A different type of RNA, called non-coding RNA, had long been dismissed as "junk" and left out of sequencing processes. However, recent advances in genetics have shown that many non-coding RNAs can carry critical functions for cell biology, and a class of RNA known as repetitive elements may interact with the immune system in a way that may be important to develop new and personalized cancer immunotherapies.

"In their study, the researchers used a process called total RNA sequencing to identify many non-coding RNAs that would normally remain undetected with the more common sequencing method. They showed that several of these RNAs were specifically expressed in tumors that responded to checkpoint blockade immunotherapy in bladder cancer patients, while others were associated with tumors that escaped being sensed by the immune system.

"'Our conclusions make the case that non-coding RNA in tumors, particularly repetitive elements, is under-quantified," said the study's senior author, Benjamin Greenbaum, PhD, Assistant Professor of Oncological Sciences, Pathology, and Medicine (Hematology and Medical Oncology) at The Tisch Cancer Institute at the Icahn School of Medicine at Mount Sinai. "We feel that critical findings will arise from analysis of the full breadth of a tumor's non-coding RNA interplay with the immune system."

"One specific finding of this study was that one repetitive element in non-coding RNA is a better predictor of immunotherapy response to PDL1 inhibitors, a type of cancer immunotherapy drug, than conventional immune signatures in certain patients. Mount Sinai researchers, in partnership with the Ting Lab at the Massachusetts General Hospital Cancer Center, found that these repeat RNAs appear to alter the immune response in colon and pancreatic cancers. These have implications for future research on how non-coding RNA could be novel targets for cancer therapy and how they influence patients' response to cancer therapies. "

Comment: Non-coding RNA's are not junk, in normal tissues and in cancer. Not surprising. So-called junk no longer supports a current version of Darwin theory.

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Satellite DNA thought to be junk is very important in cell division:

https://www.sciencedaily.com/releases/2018/04/180411131659.htm

"Their findings, published recently in the journal eLife, indicate that this genetic "junk" performs the vital function of ensuring that chromosomes bundle correctly inside the cell's nucleus, which is necessary for cell survival. And this function appears to be conserved across many species.

"This pericentromeric satellite DNA consists of a very simple, highly repetitive sequence of genetic code. Although it accounts for a substantial portion of our genome, satellite DNA does not contain instructions for making any specific proteins. What's more, its repetitive nature is thought to make the genome less stable and more susceptible to damage or disease. Until fairly recently, scientists believed this so-called "junk" or "selfish" DNA did not serve any real purpose.

***

'Yamashita and her colleagues decided to see what would happen if cells could not use this pericentromeric satellite DNA. Because it exists in long, repetitive sequences, the researchers could not simply mutate or cut the entire satellite DNA out of the genome. Instead, they approached the question through D1, a protein known to bind to satellite DNA.
The researchers removed D1 from the cells of a commonly used model organism, Drosophila melanogaster (fruit flies). And the team quickly noticed that germ cells -- the cells that ultimately develop into sperm or eggs -- were dying.

"Further analysis revealed that the dying cells were forming micro-nuclei, or tiny buds, outside the nucleus that included pieces of the genome. Without the entire genome encapsulated in the nucleus, the cells could not survive.

"The researchers believe that the D1 protein binds onto the satellite DNA to pull all of the chromosomes together in the nucleus. If the D1 protein cannot grab the satellite DNA, the cell loses its ability to form a complete nucleus and ultimately dies.

"It's like forming a bouquet," said Yamashita, who is also a professor of cell and developmental biology at the U-M Medical School and an HHMI investigator. "The protein has multiple binding sites, so it can bind onto multiple chromosomes and package them together in one place, preventing individual chromosomes from floating out of the nucleus."

"The team conducted similar experiments using mouse cells and found the same results: When they removed a protein that normally binds to mouse satellite DNA, the cells again formed micro-nuclei and did not survive.

"The similar findings from both fruit fly and mouse cells lead Yamashita and her colleagues to believe that satellite DNA is essential for cellular survival, not just in model organisms, but across species that embed DNA into the nucleus -- including humans."

Comment: Most junk DNA is not junk but purposeful. There are Darwinist scientists who are frightened by these findings, since in their minds a random theory of mutations should produce 'junk'. If most DNA shows purposeful activity, it is highly suggestive of design.

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DAVID's comment: Most junk DNA is not junk but purposeful. There are Darwinist scientists who are frightened by these findings, since in their minds a random theory of mutations should produce 'junk'. If most DNA shows purposeful activity, it is highly suggestive of design.

As I have said before, I don’t know why they should be frightened. One would expect natural selection to dispose of ”junk”.

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DAVID's comment: Most junk DNA is not junk but purposeful. There are Darwinist scientists who are frightened by these findings, since in their minds a random theory of mutations should produce 'junk'. If most DNA shows purposeful activity, it is highly suggestive of design.

dhw: As I have said before, I don’t know why they should be frightened. One would expect natural selection to dispose of ”junk”.

Again, the theory has been chance mutations produced useless DNA which was kept as evolution swept along as living proof only chance mutations apply to the theory. 'Nuff said

9803 views

DAVID's comment: Most junk DNA is not junk but purposeful. There are Darwinist scientists who are frightened by these findings, since in their minds a random theory of mutations should produce 'junk'. If most DNA shows purposeful activity, it is highly suggestive of design.

dhw: As I have said before, I don’t know why they should be frightened. One would expect natural selection to dispose of ”junk”.

DAVID: Again, the theory has been chance mutations produced useless DNA which was kept as evolution swept along as living proof only chance mutations apply to the theory. 'Nuff said.

I am as sceptical as you about chance mutations, but “junk DNA” does not in itself invalidate that theory, because the die-hards can still argue that natural selection will do away with unnecessary material. If they haven’t thought of that, then more fool them.

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DAVID's comment: Most junk DNA is not junk but purposeful. There are Darwinist scientists who are frightened by these findings, since in their minds a random theory of mutations should produce 'junk'. If most DNA shows purposeful activity, it is highly suggestive of design.

dhw: As I have said before, I don’t know why they should be frightened. One would expect natural selection to dispose of ”junk”.

DAVID: Again, the theory has been chance mutations produced useless DNA which was kept as evolution swept along as living proof only chance mutations apply to the theory. 'Nuff said.

dhw: I am as sceptical as you about chance mutations, but “junk DNA” does not in itself invalidate that theory, because the die-hards can still argue that natural selection will do away with unnecessary material. If they haven’t thought of that, then more fool them.

Fair enough.

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Why it is important to recognize the Darwin scientists were wrong:

https://evolutionnews.org/2013/11/darwin_in_the_d_3/

in the field of Darwinian evolution itself, which is based on the inviolable assumption that everything in biology must be the result of unguided material processes. Over the past century, this assumption has undoubtedly inspired many interesting research questions and scientific advances. At the same time, it also has undoubtedly discouraged and delayed many other important research questions. Witness the unhelpful Darwinian preoccupation with “vestigial” organs over the past century. Time and again, biological features we do not fully understand have been dismissed by advocates of Darwinian evolution as non-functional leftovers from a blind evolutionary process. Time and again, researchers who eventually bothered to look discovered that such supposedly “vestigial” features — the appendix and tonsils, to name two — actually perform important biological functions. The evidence of function was there all along, but scientists were discouraged by the existing paradigm from asking the questions that would elicit the evidence.

More recently, one of the biggest mistakes in the history of modern biology may turn out to be the belief that the human genome is riddled with “junk DNA.” Random mutations in protein-coding DNA are supposed to drive Darwinian evolution, and so when it was discovered that the vast majority of DNA does not code for proteins, some leading Darwinists jumped to the conclusion that non-protein-coding DNA must be mere “junk” left over from the evolutionary process just like some vestigial organs. Not only that, leading evolutionists ranging from atheist Richard Dawkins to Christian Francis Collins championed “junk DNA” as proof that human beings were the result of a Darwinian process rather than intentional design.

However, when scientists finally started to look more closely at non-coding DNA, they were shocked to learn that reality did not correspond to their ideological assumptions. Indeed, over the past decade science journals have been flooded with new research showing the rich and varied functionality of so-called “junk DNA.” In the words of biologist Jonathan Wells: “Far from consisting mainly of junk that provides evidence against intelligent design, our genome is increasingly revealing itself to be a multidimensional, integrated system in which non-protein-coding DNA performs a wide variety of functions.” Again, the evidence of functionality in non-protein-coding DNA was always there to find; but the evidence was not forthcoming because few people were asking the right questions.

Comment: The point is obvious.

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More junk says goodbye as function is found:

https://evolutionnews.org/2018/05/genetics-leaves-central-dogma-and-junk-dna-in-the-rea...

"'How often have we heard about new roles for junk DNA? Here’s another: “A conserved function for pericentromeric satellite DNA” announced in the journal eLife by researchers at the University of Michigan. This one got promoted from junk to captain:

"A universal and unquestioned characteristic of eukaryotic cells is that the genome is divided into multiple chromosomes and encapsulated in a single nucleus. However, the underlying mechanism to ensure such a configuration is unknown. Here we provide evidence that pericentromeric satellite DNA, which is often regarded as junk, is a critical constituent of the chromosome, allowing the packaging of all chromosomes into a single nucleus.

"'Old-school geneticists considered this kind of DNA as “junk” or “selfish” DNA that perpetuated itself for no purpose, says Science Daily. But lead author Yukiko Yamashita and colleagues “were not quite convinced by the idea that this is just genomic junk.” For one thing, it is highly conserved, so “If we don’t actively need it, and if not having it would give us an advantage, then evolution probably would have gotten rid of it. But that hasn’t happened.” When they took a closer look, they found that cells in fruit flies, mice, humans and probably all vertebrates cannot survive without it. Using a protein named D1 that binds to the satellite DNA, they found it provides vital attachment points for molecular machines that keep chromosomes in the nucleus. Without it, DNA would float off into buds with only part of the genome, and the cell would die.

"The similar findings from both fruit fly and mouse cells lead Yamashita and her colleagues to believe that satellite DNA is essential for cellular survival, not just in model organisms, but across species that embed DNA into the nucleus — including humans.

***

"The old genetics of the late 20th century was powerful enough evidence of intelligent design, with its systems of highly-accurate transcription and translation of encoded information. Now, we find that the old picture was far too simplistic. And the surprising lack of “genes” found by the Human Genome Project, feeding rumors of useless “junk” pervading our genome, is rapidly being supplanted by evidence of hierarchical codes and functions everywhere.

"If the old genetics was sufficient to allow A.E. Wilder-Smith to help convince Matti Leisola to become a Darwin Heretic in the 1970s (pp. 40-41), how much more will the flood of new discoveries, illustrated by these few examples, persuade the next generation of geneticists that Darwinism is hopelessly inadequate to account for the complexity of life? It’s like having to account for half a dozen codes instead of one. The future looks bright for ID in next-generation genetics, embedded in epigenetics. The nucleus is a whole new ball game."

Comment: The genome has all sorts of control and layers of instruction. Darwinism is dead.

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QUOTE: […] how much more will the flood of new discoveries, illustrated by these few examples, persuade the next generation of geneticists that Darwinism is hopelessly inadequate to account for the complexity of life? It’s like having to account for half a dozen codes instead of one. The future looks bright for ID in next-generation genetics, embedded in epigenetics. The nucleus is a whole new ball game."

David’s comment: The genome has all sorts of control and layers of instruction. Darwinism is dead.

What aspect of Darwinism is “hopelessly inadequate to account for the complexity of life”? What is dead? His theory of evolution begins at Chapter Two of life (i.e. not the beginning), does not and cannot analyse how cells work, and does not exclude the possibility that the mechanisms of life and evolution are the product of design, but in later editions even credits the Creator with having set it all up. His focus was on common descent, which you accept. His reliance on random mutations and gradualism may well prove to be “dead”, but the rest remains and, as I have said repeatedly, the concept of junk DNA has absolutely no bearing on his theory. The fact that some atheistic evolutionists take junk DNA to be evidence of bad or no design is not Darwinism. And in any case, if it’s not junk, they can argue that natural selection preserves what is useful. I do wish you and your fellow ID-ers would vent your spleen on atheistic evolutionists, and would stop pretending that they represent all evolutionists (many of whom are theists), let alone Darwin himself.

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QUOTE: […] how much more will the flood of new discoveries, illustrated by these few examples, persuade the next generation of geneticists that Darwinism is hopelessly inadequate to account for the complexity of life? It’s like having to account for half a dozen codes instead of one. The future looks bright for ID in next-generation genetics, embedded in epigenetics. The nucleus is a whole new ball game."

David’s comment: The genome has all sorts of control and layers of instruction. Darwinism is dead.

dhw: What aspect of Darwinism is “hopelessly inadequate to account for the complexity of life”? What is dead? His theory of evolution begins at Chapter Two of life (i.e. not the beginning), does not and cannot analyse how cells work, and does not exclude the possibility that the mechanisms of life and evolution are the product of design, but in later editions even credits the Creator with having set it all up. His focus was on common descent, which you accept. His reliance on random mutations and gradualism may well prove to be “dead”, but the rest remains and, as I have said repeatedly, the concept of junk DNA has absolutely no bearing on his theory. The fact that some atheistic evolutionists take junk DNA to be evidence of bad or no design is not Darwinism. And in any case, if it’s not junk, they can argue that natural selection preserves what is useful. I do wish you and your fellow ID-ers would vent your spleen on atheistic evolutionists, and would stop pretending that they represent all evolutionists (many of whom are theists), let alone Darwin himself.

Darwinism is the false view of atheist evolutionists that have created a religion espousing a naturalistic explanation for the evolutionary theory of common descent and insisting 'junk DNA' proves it. Nothing more. If Darwin could see this, of course he would be upset. You miss the point.

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David’s comment: The genome has all sorts of control and layers of instruction. Darwinism is dead.

dhw: I do wish you and your fellow ID-ers would vent your spleen on atheistic evolutionists, and would stop pretending that they represent all evolutionists (many of whom are theists), let alone Darwin himself.

DAVID: Darwinism is the false view of atheist evolutionists that have created a religion espousing a naturalistic explanation for the evolutionary theory of common descent and insisting 'junk DNA' proves it. Nothing more. If Darwin could see this, of course he would be upset. You miss the point.

Darwinism is Charles Darwin’s theory of evolution as set out in his book On the Origin of Species. Darwinism is not dead. What is dead is the false view of atheistic evolutionists who insist that ‘junk DNA’ proves them right. You have made the point and missed it at the same time!

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David’s comment: The genome has all sorts of control and layers of instruction. Darwinism is dead.

dhw: I do wish you and your fellow ID-ers would vent your spleen on atheistic evolutionists, and would stop pretending that they represent all evolutionists (many of whom are theists), let alone Darwin himself.

DAVID: Darwinism is the false view of atheist evolutionists that have created a religion espousing a naturalistic explanation for the evolutionary theory of common descent and insisting 'junk DNA' proves it. Nothing more. If Darwin could see this, of course he would be upset. You miss the point.

dhw: Darwinism is Charles Darwin’s theory of evolution as set out in his book On the Origin of Species. Darwinism is not dead. What is dead is the false view of atheistic evolutionists who insist that ‘junk DNA’ proves them right. You have made the point and missed it at the same time!

All that is left is his theory of common descent. His 'small, successive changes' is gone. What he did was establish that common descent is a reasonable view.

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In the non-coding region of DNA is an enhancer that controls sex organ development:

https://evolutionnews.org/2018/06/an-intimate-reminder-about-what-was-once-thought-to-b...

"Male mice grow ovaries instead of testes if they are missing a small region of DNA that doesn’t contain any genes, finds a new paper published in Science.

"The study, led by researchers at the Francis Crick Institute, could help explain disorders of sex development in humans, at least half of which have an unknown genetic cause.

"Mammals will develop ovaries and become females unless the early sex organs have enough of a protein called SOX9 at a key stage in their development. SOX9 causes these organs to become testes, which then direct the rest of the embryo to become male.

"The amount of SOX9 produced is controlled initially by the SRY protein encoded by the Sry gene, which is located on the Y chromosome. This is why males, who have an X chromosome and a Y chromosome, usually develop testes while females, who have two X chromosomes, do not.

"Only 2% of human DNA contains the ‘code’ to produce proteins, key building blocks of life. The remaining 98% is ‘non-coding’ and was once thought to be unnecessary ‘junk’ DNA, but there is increasing evidence that it can play important roles.

"The latest study adds to this evidence, showing that a small piece of DNA called enhancer 13 (Enh13), located over half a million bases away from the Sox9 gene, boosts SOX9 protein production at the right moment to trigger testes development. When the team genetically removed Enh13 from male (XY) mice, they developed ovaries and female genitalia.

"'Our study also highlights the important role of what some still refer to as ‘junk’ DNA, which makes up 98% of our genome. If a single enhancer can have this impact on sex determination, other non-coding regions might have similarly drastic effects.”

"The “junk” view, once a prized piece of evidence for neo-Darwinian theory, is thus reduced to the province of the benighted, the reactionaries who “still refer to [it] as ‘junk’ DNA,” after science has already passed them by. Having volumes of garbage lying around was a logical prediction of Darwinism that is in the process of being falsified. Now, it seems likely that non-coding regions have not trivial but “drastic effects.”

"This reversal helps explain why evolutionists like Richard Dawkins have radically revised a key claim. Dawkins himself, in the space of three years, went from assuring us that junk validates Darwinism to claiming that function is what it expects. What a theory! It can never, ever be wrong."

Comment: Junk DNA is disappearing, although there must be some that will exist after DNA is thoroughly studied. Dawkins was forced to change his view of the theory.

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QUOTE: "This reversal helps explain why evolutionists like Richard Dawkins have radically revised a key claim. Dawkins himself, in the space of three years, went from assuring us that junk validates Darwinism to claiming that function is what it expects. What a theory! It can never, ever be wrong."

DAVID’s comment: Junk DNA is disappearing, although there must be some that will exist after DNA is thoroughly studied. Dawkins was forced to change his view of the theory.

As I keep saying, both sides will always find a way of accommodating new discoveries into their theories. Hence the Catholic Church’s acceptance of evolution.

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QUOTE: "This reversal helps explain why evolutionists like Richard Dawkins have radically revised a key claim. Dawkins himself, in the space of three years, went from assuring us that junk validates Darwinism to claiming that function is what it expects. What a theory! It can never, ever be wrong."

DAVID’s comment: Junk DNA is disappearing, although there must be some that will exist after DNA is thoroughly studied. Dawkins was forced to change his view of the theory.

dhw: As I keep saying, both sides will always find a way of accommodating new discoveries into their theories. Hence the Catholic Church’s acceptance of evolution.

And you will watch both sides from atop your fence.

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One is found that is necessary for embryo development:

https://phys.org/news/2018-06-junk-gene-critical-early-embryo.html

"A so-called "jumping gene" that researchers long considered either genetic junk or a pernicious parasite is actually a critical regulator of the first stages of embryonic development, according to a new study in mice led by UC San Francisco scientists and published June 21, 2018 in Cell.

"Only about 1 percent of the human genome encodes proteins, and researchers have long debated what the other 99 percent is good for. Many of these non–protein coding regions are known to contain important regulatory elements that orchestrate gene activity, but others are thought to be evolutionary garbage that is just too much trouble for the genome to clean up.

"For example, fully half of our DNA is made up of "transposable elements," or "transposons," virus-like genetic material that has the special ability of duplicating and reinserting itself in different locations in the genome, which has led researchers to dub them genetic parasites. Over the course of evolution, some transposons have left hundreds or thousands of copies of themselves scattered across the genome. While most of these stowaways are thought to be inert and inactive, others create havoc by altering or disrupting cells' normal genetic programming and have been associated with diseases such as certain forms of cancer.

"Now UCSF scientists have revealed that, far from being a freeloader or parasite, the most common transposon, called LINE1, which accounts for fully 24 percent of the human genome, is actually necessary for embryos to develop past the two-cell stage. (my bold)

***

"..although the LINE1 gene is expressed in the early embryo and stem cells, its role is not to insert itself elsewhere in the genome. Instead, its RNA is trapped within the cell nucleus, where it forms a complex with gene regulatory proteins Nucleolin and Kap1. This complex is necessary to turn off the dominant genetic program that orchestrates embryos' two-cell state—controlled by a gene called Dux—and to turn on genes that are needed for the embryo to move on with further cell divisions and development.

***

"'These genes have been with us for billions of years and have been the majority of our genomes for hundreds of millions of years," Ramalho-Santos said. "I think it's fair to ask if the 1.5 percent of protein-coding genes are the free-riders, and not the other way around."

"Ramalho-Santos speculates that transposons like LINE1 may make the delicate early stages of development more robust precisely because they are so ubiquitous. Because LINE1 is repeated thousands of times in the genome, it's virtually impossible for a mutation to disrupt its function: if one copy is bad, there are thousands more to take its place.

"'We now think these early embryos are playing with fire but in a very calculated way," Ramalho-Santos said. "This could be a very robust mechanism for regulating development."

"'Scientists have done so much work on protein-coding genes, and they're less than 2 percent of the genome, whereas transposons make up nearly 50 percent," Percharde added. "I'm personally excited to continue exploring novel functions of these elements in development and disease.'"

Comment: Junk DNA was a strong line of defense for Darwin theorists who believed evolution was a chanced event. That defense is gone. The junk isn't junk

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The latest finding:

https://medicalxpress.com/news/2018-07-imaging-cells-reveals-junk-dna.html

"These pieces of DNA are part of over 90 percent of the genetic material that are not genes. Researchers now know that this "junk DNA" contains most of the information that can turn on or off genes. But how these segments of DNA, called enhancers, find and activate a target gene in the crowded environment of a cell's nucleus is not well understood.

"Now a team led by researchers at Princeton University has captured how this happens in living cells. The video allows researchers to see the enhancers as they find and connect to a gene to kick-start its activity.

***

"As their name suggests, enhancers switch on the expression of other genes. In the mammalian genome, there are an estimated 200,000 to 1 million enhancers, and many are located far away on the DNA strand from the gene they regulate, raising the question of how the regulatory segments can locate and connect with their target genes.

"Many previous studies on enhancers were conducted on non-living cells because of the difficulty in imaging genetic activity in living organisms. Such studies give only snapshots in time and can miss important details.

"In the new study, researchers used imaging techniques developed at Princeton to track the position of an enhancer and its target gene while simultaneously monitoring the gene's activity in living fly embryos.

"'This study provides the unique opportunity to observe in real time how two regions of DNA interact with each other," said Michal Levo, a postdoctoral research fellow in the Lewis-Sigler Institute. "We can monitor in time where the enhancer and the gene are physically located and simultaneously measure the gene's activity in an attempt to relate these processes."

***

"As their name suggests, enhancers switch on the expression of other genes. In the mammalian genome, there are an estimated 200,000 to 1 million enhancers, and many are located far away on the DNA strand from the gene they regulate, raising the question of how the regulatory segments can locate and connect with their target genes.

"Many previous studies on enhancers were conducted on non-living cells because of the difficulty in imaging genetic activity in living organisms. Such studies give only snapshots in time and can miss important details.

"In the new study, researchers used imaging techniques developed at Princeton to track the position of an enhancer and its target gene while simultaneously monitoring the gene's activity in living fly embryos.

"'This study provides the unique opportunity to observe in real time how two regions of DNA interact with each other," said Michal Levo, a postdoctoral research fellow in the Lewis-Sigler Institute. "We can monitor in time where the enhancer and the gene are physically located and simultaneously measure the gene's activity in an attempt to relate these processes.'"

Comment: Once again we see that the 3-D relationships are very important in how sections of DNA relate to each other. 80% of DNA is useful.

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The latest finding:

https://medicalxpress.com/news/2018-07-imaging-cells-reveals-junk-dna.html

"These pieces of DNA are part of over 90 percent of the genetic material that are not genes. Researchers now know that this "junk DNA" contains most of the information that can turn on or off genes. But how these segments of DNA, called enhancers, find and activate a target gene in the crowded environment of a cell's nucleus is not well understood.

"Now a team led by researchers at Princeton University has captured how this happens in living cells. The video allows researchers to see the enhancers as they find and connect to a gene to kick-start its activity.

***

"As their name suggests, enhancers switch on the expression of other genes. In the mammalian genome, there are an estimated 200,000 to 1 million enhancers, and many are located far away on the DNA strand from the gene they regulate, raising the question of how the regulatory segments can locate and connect with their target genes.

"Many previous studies on enhancers were conducted on non-living cells because of the difficulty in imaging genetic activity in living organisms. Such studies give only snapshots in time and can miss important details.

"In the new study, researchers used imaging techniques developed at Princeton to track the position of an enhancer and its target gene while simultaneously monitoring the gene's activity in living fly embryos.

"'This study provides the unique opportunity to observe in real time how two regions of DNA interact with each other," said Michal Levo, a postdoctoral research fellow in the Lewis-Sigler Institute. "We can monitor in time where the enhancer and the gene are physically located and simultaneously measure the gene's activity in an attempt to relate these processes."

***

"As their name suggests, enhancers switch on the expression of other genes. In the mammalian genome, there are an estimated 200,000 to 1 million enhancers, and many are located far away on the DNA strand from the gene they regulate, raising the question of how the regulatory segments can locate and connect with their target genes.

"Many previous studies on enhancers were conducted on non-living cells because of the difficulty in imaging genetic activity in living organisms. Such studies give only snapshots in time and can miss important details.

"In the new study, researchers used imaging techniques developed at Princeton to track the position of an enhancer and its target gene while simultaneously monitoring the gene's activity in living fly embryos.

"'This study provides the unique opportunity to observe in real time how two regions of DNA interact with each other," said Michal Levo, a postdoctoral research fellow in the Lewis-Sigler Institute. "We can monitor in time where the enhancer and the gene are physically located and simultaneously measure the gene's activity in an attempt to relate these processes.'"

David Comment: Once again we see that the 3-D relationships are very important in how sections of DNA relate to each other. 80% of DNA is useful.

I suspect more than 80%.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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***David:

"As their name suggests, enhancers switch on the expression of other genes. In the mammalian genome, there are an estimated 200,000 to 1 million enhancers, and many are located far away on the DNA strand from the gene they regulate, raising the question of how the regulatory segments can locate and connect with their target genes.

"Many previous studies on enhancers were conducted on non-living cells because of the difficulty in imaging genetic activity in living organisms. Such studies give only snapshots in time and can miss important details.

"In the new study, researchers used imaging techniques developed at Princeton to track the position of an enhancer and its target gene while simultaneously monitoring the gene's activity in living fly embryos.

"'This study provides the unique opportunity to observe in real time how two regions of DNA interact with each other," said Michal Levo, a postdoctoral research fellow in the Lewis-Sigler Institute. "We can monitor in time where the enhancer and the gene are physically located and simultaneously measure the gene's activity in an attempt to relate these processes.'"

David Comment: Once again we see that the 3-D relationships are very important in how sections of DNA relate to each other. 80% of DNA is useful.

Tony: I suspect more than 80%.

That is the currently accepted amount except the diehard Darwinists.

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So-called junk DNA controls regeneration in animals that can regenerate:

https://www.sciencedaily.com/releases/2018/08/180821114432.htm

"cientists have discovered that genetic material in the cell that was previously thought to be 'junk' because of its apparent lack of function likely plays a part in regulating genetic circuits responsible for regeneration in highly regenerative animals.

***

"In particular, the scientists looked at the role of noncoding RNAs, or RNAs that were formerly considered "junk" because they do not make proteins, in the early stages of heart regeneration in the zebrafish, a common aquarium fish that is one of nature's champions of regeneration.

"RNA, or ribonucleic acid, typically acts as a messenger that transports instructions from the DNA, the carrier of genetic information, to the machinery in the cell that manufactures proteins involved in biological functions.

"'One of the secrets to decoding why zebrafish can regenerate their hearts while adult humans cannot may lie with these noncoding RNAs," said King, the paper's lead author. "The protein-coding genes in zebrafish and humans are more or less the same -- what's different is how they are regulated during regeneration by noncoding RNAs."

***

"'The biological role of more than 90 percent of the genetic material in the cell is unknown, which raises the question: Why is it there?" said Hermann Haller, M.D., president of the MDI Biological Laboratory. "This extraordinary discovery demonstrates the power of computational biology to map this uncharted genetic landscape."

"Yin and King studied the roles of two types of noncoding RNAs -- microRNAs and long noncoding RNAs -- in zebrafish heart regeneration.

"In addition to further elucidating the role of microRNAs, which are known to play a regulatory role in heart regeneration, the scientists also characterized the role of known and previously unknown long noncoding RNAs and the genes they potentially regulate through genetic proximity searches that King called "guilt by association."

***

"The paper also introduced the RegenDbase, a new database that allows scientists to compare and contrast gene regulatory pathways within and across tissues and research models, with a focus on noncoding RNAs.

"The database was created using a new dataset for heart regeneration in zebrafish created at the MDI Biological Laboratory, as well as existing data on multiple types of injured tissues from various species. The utility of the database, which is available to the public, is expected to grow as more data is added, including from human tissues."

Comment: Note the bold. 'Junk DNA' is a point of view proposed and promoted by ardent Darwinists to protect the very weak theory now that DNA is becoming m ore understood. The new data base is a response to the previously improper view of DNA. Other than common descent the whole theory is dead and Tony thinks that doesn't exist.

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DAVID: Comment: Note the bold. 'Junk DNA' is a point of view proposed and promoted by ardent Darwinists to protect the very weak theory now that DNA is becoming m ore understood. The new data base is a response to the previously improper view of DNA. Other than common descent the whole theory is dead and Tony thinks that doesn't exist.

As I keep saying, the gradual disappearance of the “junk” theory can be explained by “ardent Darwinists” as natural selection at work – only what is useful survives. For obvious reasons Junk DNA was never part of Darwin’s theory! At least you still believe in common descent, so perhaps you could explain to Tony why you think he’s wrong.

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DAVID: Comment: Note the bold. 'Junk DNA' is a point of view proposed and promoted by ardent Darwinists to protect the very weak theory now that DNA is becoming m ore understood. The new data base is a response to the previously improper view of DNA. Other than common descent the whole theory is dead and Tony thinks that doesn't exist.

dhw: As I keep saying, the gradual disappearance of the “junk” theory can be explained by “ardent Darwinists” as natural selection at work – only what is useful survives. For obvious reasons Junk DNA was never part of Darwin’s theory! At least you still believe in common descent, so perhaps you could explain to Tony why you think he’s wrong.

You again are blinded by Darwin. The Darwin scientists have used junk DNA to justify Darwin theory by saying the 'useless junk DNA' shows evolution evolved by chance and the junk is left over evidence of chance attempts at evolution that did not work out. I've explained this before. Dan Graur, an ardent Darwinist professor, has said if junk does not exist Darwin is dead. I can probably find the quote for you, as I remember publishing it here.

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DAVID: Note the bold. 'Junk DNA' is a point of view proposed and promoted by ardent Darwinists to protect the very weak theory now that DNA is becoming m ore understood. The new data base is a response to the previously improper view of DNA. Other than common descent the whole theory is dead and Tony thinks that doesn't exist.

dhw: As I keep saying, the gradual disappearance of the “junk” theory can be explained by “ardent Darwinists” as natural selection at work – only what is useful survives. For obvious reasons Junk DNA was never part of Darwin’s theory! At least you still believe in common descent, so perhaps you could explain to Tony why you think he’s wrong.

DAVID: You again are blinded by Darwin. The Darwin scientists have used junk DNA to justify Darwin theory by saying the 'useless junk DNA' shows evolution evolved by chance and the junk is left over evidence of chance attempts at evolution that did not work out. I've explained this before. Dan Graur, an ardent Darwinist professor, has said if junk does not exist Darwin is dead. I can probably find the quote for you, as I remember publishing it here.

You are again blinded by your hatred of Darwin. If these “ardent Darwinists” have not latched on to the answer that non-junk can be explained as natural selection at work – i.e. what is useful survives – then more fool them. Why don’t you consider this explanation instead of banging your anti-Darwin drum?

Under "pointy end eggs"):

QUOTE: “In general, an egg's conicality was the most reliable predictor of its likelihood of staying put on inclined surfaces," Hauber says. "This finding provides experimental support for natural selection shaping the unique form of murre eggs amongst all bird eggs.”

DAVID: These eggs cannot have been developed by chance attempts if the birds were to survive. Only design fits.

When you say only design fits, what exactly do you mean? That your God preprogrammed pointed murre eggs 3.8 billion years ago, or that he saw murre eggs falling off the cliff, and in order to preserve the balance of nature so that life could go on until he produced the brain of Homo sapiens, stepped in to change round to pointy? How about Hauber’s suggestion that natural selection fits: round eggs didn’t survive, and pointy eggs did?

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By what process does an egg shell evolve, I wonder.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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Tony: By what process does an egg shell evolve, I wonder.

It requires a major change in cloacal design!

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DAVID: Note the bold. 'Junk DNA' is a point of view proposed and promoted by ardent Darwinists to protect the very weak theory now that DNA is becoming m ore understood. The new data base is a response to the previously improper view of DNA. Other than common descent the whole theory is dead and Tony thinks that doesn't exist.

dhw: As I keep saying, the gradual disappearance of the “junk” theory can be explained by “ardent Darwinists” as natural selection at work – only what is useful survives. For obvious reasons Junk DNA was never part of Darwin’s theory! At least you still believe in common descent, so perhaps you could explain to Tony why you think he’s wrong.

DAVID: You again are blinded by Darwin. The Darwin scientists have used junk DNA to justify Darwin theory by saying the 'useless junk DNA' shows evolution evolved by chance and the junk is left over evidence of chance attempts at evolution that did not work out. I've explained this before. Dan Graur, an ardent Darwinist professor, has said if junk does not exist Darwin is dead. I can probably find the quote for you, as I remember publishing it here.

dhw: You are again blinded by your hatred of Darwin. If these “ardent Darwinists” have not latched on to the answer that non-junk can be explained as natural selection at work – i.e. what is useful survives – then more fool them. Why don’t you consider this explanation instead of banging your anti-Darwin drum?

Under "pointy end eggs"):

QUOTE: “In general, an egg's conicality was the most reliable predictor of its likelihood of staying put on inclined surfaces," Hauber says. "This finding provides experimental support for natural selection shaping the unique form of murre eggs amongst all bird eggs.”

DAVID: These eggs cannot have been developed by chance attempts if the birds were to survive. Only design fits.

dhw: When you say only design fits, what exactly do you mean? That your God preprogrammed pointed murre eggs 3.8 billion years ago, or that he saw murre eggs falling off the cliff, and in order to preserve the balance of nature so that life could go on until he produced the brain of Homo sapiens, stepped in to change round to pointy? How about Hauber’s suggestion that natural selection fits: round eggs didn’t survive, and pointy eggs did?

If you understood how difficult it is to make a shelled egg of any shape, it is difficult to see how the birds arrived at changing their cloaca to do that all at once on cliffs. Natural selection is the usual tautology true Darwinists fall back upon. Really!

9509 views

dhw: You are again blinded by your hatred of Darwin. If these “ardent Darwinists” have not latched on to the answer that non-junk can be explained as natural selection at work – i.e. what is useful survives – then more fool them. Why don’t you consider this explanation instead of banging your anti-Darwin drum?

Thank you for dropping this subject.

Under "pointy end eggs"):

QUOTE: “In general, an egg's conicality was the most reliable predictor of its likelihood of staying put on inclined surfaces," Hauber says. "This finding provides experimental support for natural selection shaping the unique form of murre eggs amongst all bird eggs.”

DAVID: These eggs cannot have been developed by chance attempts if the birds were to survive. Only design fits.

dhw: When you say only design fits, what exactly do you mean? That your God preprogrammed pointed murre eggs 3.8 billion years ago, or that he saw murre eggs falling off the cliff, and in order to preserve the balance of nature so that life could go on until he produced the brain of Homo sapiens, stepped in to change round to pointy? How about Hauber’s suggestion that natural selection fits: round eggs didn’t survive, and pointy eggs did?

DAVID: If you understood how difficult it is to make a shelled egg of any shape, it is difficult to see how the birds arrived at changing their cloaca to do that all at once on cliffs. Natural selection is the usual tautology true Darwinists fall back upon. Really!

I do not believe they did it all at once. I am suggesting that lots and lots of round eggs fell off the cliff, and only pointy ones survived, and so in the end there were only pointy ones. Meanwhile, why don’t you answer my question? Do you believe your God preprogrammed pointy eggs 3.8 billion years ago, or personally dabbled them when he saw so many falling off the cliff?

9488 views

Under "pointy end eggs"):

QUOTE: “In general, an egg's conicality was the most reliable predictor of its likelihood of staying put on inclined surfaces," Hauber says. "This finding provides experimental support for natural selection shaping the unique form of murre eggs amongst all bird eggs.”

DAVID: These eggs cannot have been developed by chance attempts if the birds were to survive. Only design fits.

dhw: When you say only design fits, what exactly do you mean? That your God preprogrammed pointed murre eggs 3.8 billion years ago, or that he saw murre eggs falling off the cliff, and in order to preserve the balance of nature so that life could go on until he produced the brain of Homo sapiens, stepped in to change round to pointy? How about Hauber’s suggestion that natural selection fits: round eggs didn’t survive, and pointy eggs did?

DAVID: If you understood how difficult it is to make a shelled egg of any shape, it is difficult to see how the birds arrived at changing their cloaca to do that all at once on cliffs. Natural selection is the usual tautology true Darwinists fall back upon. Really!

dhw: I do not believe they did it all at once. I am suggesting that lots and lots of round eggs fell off the cliff, and only pointy ones survived, and so in the end there were only pointy ones. Meanwhile, why don’t you answer my question? Do you believe your God preprogrammed pointy eggs 3.8 billion years ago, or personally dabbled them when he saw so many falling off the cliff?

Again, your fealty to Darwin's hunt and peck chance approach. The pointed eggs require a specific type of cloacal shape, which must be created by a changed DNA. Either the cloaca makes round or pointed, not the possibility of both types. I'm sure God helped in design of the proper shaped egg for cliff-side dwelling with no nest to control the eggs.

9478 views

dhw: I do not believe they did it all at once. I am suggesting that lots and lots of round eggs fell off the cliff, and only pointy ones survived, and so in the end there were only pointy ones. Meanwhile, why don’t you answer my question? Do you believe your God preprogrammed pointy eggs 3.8 billion years ago, or personally dabbled them when he saw so many falling off the cliff?

DAVID: Again, your fealty to Darwin's hunt and peck chance approach. The pointed eggs require a specific type of cloacal shape, which must be created by a changed DNA. Either the cloaca makes round or pointed, not the possibility of both types. I'm sure God helped in design of the proper shaped egg for cliff-side dwelling with no nest to control the eggs.

I must confess that I’m not sure about most of the things we discuss, and I really have no idea of the history of pointy eggs. It is clear that the species would not have survived without them. And so we go back to your theory that your God preprogrammed or dabbled (= "helped") every innovation, lifestyle and natural wonder in order to balance nature so that life would continue until he could produce the brain of Homo sapiens. But I’ll be a real devil here, and suggest to you that even if the murre had gone extinct, our brain would still have evolved. And so, as with the turtle, I wonder why your God bothered with murres and pointy eggs. Alternatively, he may have designed a mechanism that would enable organisms to work out their own ways to cope with the environment. In which case, congratulations to the cell communities of the murre for pointy-shaping their cloacae and not having to join the other 90%+ of organisms that couldn’t cope.

9482 views

dhw: I do not believe they did it all at once. I am suggesting that lots and lots of round eggs fell off the cliff, and only pointy ones survived, and so in the end there were only pointy ones. Meanwhile, why don’t you answer my question? Do you believe your God preprogrammed pointy eggs 3.8 billion years ago, or personally dabbled them when he saw so many falling off the cliff?

DAVID: Again, your fealty to Darwin's hunt and peck chance approach. The pointed eggs require a specific type of cloacal shape, which must be created by a changed DNA. Either the cloaca makes round or pointed, not the possibility of both types. I'm sure God helped in design of the proper shaped egg for cliff-side dwelling with no nest to control the eggs.

dhw: I must confess that I’m not sure about most of the things we discuss, and I really have no idea of the history of pointy eggs. It is clear that the species would not have survived without them. And so we go back to your theory that your God preprogrammed or dabbled (= "helped") every innovation, lifestyle and natural wonder in order to balance nature so that life would continue until he could produce the brain of Homo sapiens. But I’ll be a real devil here, and suggest to you that even if the murre had gone extinct, our brain would still have evolved. And so, as with the turtle, I wonder why your God bothered with murres and pointy eggs. Alternatively, he may have designed a mechanism that would enable organisms to work out their own ways to cope with the environment. In which case, congratulations to the cell communities of the murre for pointy-shaping their cloacae and not having to join the other 90%+ of organisms that couldn’t cope.

I know you live your life with purpose and certainty. But in this area of 'theory of the immaterial' you are hoist onto your personal picket fence with both feet planted firmly in mid air.

9488 views

dhw: I do not believe they did it all at once. I am suggesting that lots and lots of round eggs fell off the cliff, and only pointy ones survived, and so in the end there were only pointy ones. Meanwhile, why don’t you answer my question? Do you believe your God preprogrammed pointy eggs 3.8 billion years ago, or personally dabbled them when he saw so many falling off the cliff?

DAVID: Again, your fealty to Darwin's hunt and peck chance approach. The pointed eggs require a specific type of cloacal shape, which must be created by a changed DNA. Either the cloaca makes round or pointed, not the possibility of both types. I'm sure God helped in design of the proper shaped egg for cliff-side dwelling with no nest to control the eggs.

dhw: I must confess that I’m not sure about most of the things we discuss, and I really have no idea of the history of pointy eggs. It is clear that the species would not have survived without them. And so we go back to your theory that your God preprogrammed or dabbled (= "helped") every innovation, lifestyle and natural wonder in order to balance nature so that life would continue until he could produce the brain of Homo sapiens. But I’ll be a real devil here, and suggest to you that even if the murre had gone extinct, our brain would still have evolved. And so, as with the turtle, I wonder why your God bothered with murres and pointy eggs. Alternatively, he may have designed a mechanism that would enable organisms to work out their own ways to cope with the environment. In which case, congratulations to the cell communities of the murre for pointy-shaping their cloacae and not having to join the other 90%+ of organisms that couldn’t cope.

Can you show me that 90% of the birds that laid round eggs on cliffs died? Also, can you show me the 10% of birds of this variety with round nests on cliffs that did survive? Or evidence that they ever laid round eggs on these cliffs? Or perhaps you could show me two of the same species of birds that have the genetic differences needed to go from round egg to pointy, with the round egg layer being an older specimen?

What about 10% of the whales that did not go into the water but survived? Where did they go? Where is the record of them? And don't tell me another damn fairy tale that has no objective evidence, no record, no traceable, documented process that took them from form A to form B.

Show me something that can be repeated in a lab, step-wise. We can manipulate DNA now, at will. Show me one, just one, scientist that has managed to make stepwise adjustments to DNA to take a creature from an amphibian to a reptile, or reptile to a bird or mammal. Hell, show me one that has managed to change one mammal into another. Hell, change one single celled organism into another single celled organism. Say, e coli to yeast.

In chemistry, we can prove the claims made by chemist by doing it. We have the technology now. So show me the evidence by reproducing the process. That is science.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

9483 views

DAVID: Again, your fealty to Darwin's hunt and peck chance approach. The pointed eggs require a specific type of cloacal shape, which must be created by a changed DNA. Either the cloaca makes round or pointed, not the possibility of both types. I'm sure God helped in design of the proper shaped egg for cliff-side dwelling with no nest to control the eggs.

dhw: I must confess that I’m not sure about most of the things we discuss, and I really have no idea of the history of pointy eggs. It is clear that the species would not have survived without them. And so we go back to your theory that your God preprogrammed or dabbled (= "helped") every innovation, lifestyle and natural wonder in order to balance nature so that life would continue until he could produce the brain of Homo sapiens. But I’ll be a real devil here, and suggest to you that even if the murre had gone extinct, our brain would still have evolved. And so, as with the turtle, I wonder why your God bothered with murres and pointy eggs. Alternatively, he may have designed a mechanism that would enable organisms to work out their own ways to cope with the environment. In which case, congratulations to the cell communities of the murre for pointy-shaping their cloacae and not having to join the other 90%+ of organisms that couldn’t cope.

Tony: Can you show me that 90% of the birds that laid round eggs on cliffs died? Also, can you show me the 10% of birds of this variety with round nests on cliffs that did survive? Or evidence that they ever laid round eggs on these cliffs? Or perhaps you could show me two of the same species of birds that have the genetic differences needed to go from round egg to pointy, with the round egg layer being an older specimen?

What about 10% of the whales that did not go into the water but survived? Where did they go? Where is the record of them? And don't tell me another damn fairy tale that has no objective evidence, no record, no traceable, documented process that took them from form A to form B.

Show me something that can be repeated in a lab, step-wise. We can manipulate DNA now, at will. Show me one, just one, scientist that has managed to make stepwise adjustments to DNA to take a creature from an amphibian to a reptile, or reptile to a bird or mammal. Hell, show me one that has managed to change one mammal into another. Hell, change one single celled organism into another single celled organism. Say, e coli to yeast.

In chemistry, we can prove the claims made by chemist by doing it. We have the technology now. So show me the evidence by reproducing the process. That is science.

Thank you Tony.

dhw: "I wonder why your God bothered with murres and pointy eggs." You wonder why God bothered with anything. I'm glad He did, we are here!

9462 views

A new method for understanding these strange parts of DNA and find their function:

https://phys.org/news/2018-09-scientists-reveal-vast-unknown-territory.html

"'Long non-coding RNAs are part of what you might call the 'dark matter' of the genome, and this tool we've developed should help us understand much better how they work in health and disease," said study senior author Mauro Calabrese, Ph.D., assistant professor of pharmacology and member of the UNC Lineberger Comprehensive Cancer Center.

"Genetic information in animals and plants is stored in DNA, and cells make use of that genetic information by transcribing the DNA into closely related molecules known as RNAs. Many RNAs go on to be translated into proteins. But scientists in recent decades have been forced to reckon with the fact that less than 2 percent of the genome is used that way. Most of the DNA is transcribed into RNAs that do not encode proteins. These are called non-coding RNAs, and the ones over 200 nucleotides in length are classified as long non-coding RNAs.

"Many of these RNAs bind to proteins or other molecules to switch genes on or off, thus regulating cellular processes. One of the best known lncRNAs is called Xist, which is important for normal development in females. High levels of another called MALAT, have been linked to more aggressive and metastatic cancers. On the whole, biologists are sure that many lncRNAs have key regulatory roles whose disruption contributes to disease. So far, however, they have characterized the functions of only a small fraction of the many thousands of lncRNAs that are thought to exist in mammalian cells.

"One reason biologists have been slow to understand what these molecules do is that a lncRNA's function is not readily apparent when you study how it's put together from its sequence of nucleotide building-blocks. Often two lncRNAs with similar functions appear to have very different sequences.

"Calabrese and his team, including first author Jessime Kirk and Peter Mucha, Ph.D., professor of mathematics and applied physical sciences in the UNC College of Arts and Sciences, tried to decipher the otherwise obscure relationship between lncRNA sequence and function. They started with two key clues: Firstly, there is evidence that lncRNAs function mainly by binding to proteins. Secondly, RNAs connect to proteins using short sequences within their overall structures.

***

"The team developed a computer-based method called SEEKR to find and compare protein-binding sequences they called "kmers" in lncRNAs, regardless of the kmers' precise locations. The team found that about half of all human and mouse lncRNAs could be grouped into five different communities, based on similarities in their kmer content. The kmer-based approach also could help predict where lncRNAs are normally found within cells and to what kinds of protein they bind.

"'We can now take sequence information from a well-studied lncRNA, and use it to discover lncRNAs that may be functioning through a related mechanism. In a way, it's like being able to finally understand the different scripts in the Rosetta Stone." Calabrese said.

"Surprisingly, the team found that kmer-content communities were often highly similar between species. Human and mouse lncRNA communities resembled each other closely, but some mammalian lncRNA communities had clear counterparts even among distantly related animals. One mammalian lncRNA community, represented by an lncRNA called HOTTIP, appeared to have cousin lncRNA communities in other vertebrates and even in sea urchins.

"'In terms of kmer content, subsets of human lncRNAs may be more similar to lncRNAs from evolutionarily distant species than they are to other human lncRNAs," Calabrese said. "This supports the idea that groups of lncRNAs have similar functions in different organisms despite lacking obvious linear sequence similarity."

***

"'Our genomes produce so many lncRNAs, and now we have a much better idea of how to look at the sequences of these molecules to predict which ones are doing important things in our cells," Calabrese said."

Comment: There is very little junk DNA, to the disappointment of Darwinists

9257 views

A new method for understanding these strange parts of DNA and find their function:

https://phys.org/news/2018-09-scientists-reveal-vast-unknown-territory.html

"'Long non-coding RNAs are part of what you might call the 'dark matter' of the genome, and this tool we've developed should help us understand much better how they work in health and disease," said study senior author Mauro Calabrese, Ph.D., assistant professor of pharmacology and member of the UNC Lineberger Comprehensive Cancer Center.

"Genetic information in animals and plants is stored in DNA, and cells make use of that genetic information by transcribing the DNA into closely related molecules known as RNAs. Many RNAs go on to be translated into proteins. But scientists in recent decades have been forced to reckon with the fact that less than 2 percent of the genome is used that way. Most of the DNA is transcribed into RNAs that do not encode proteins. These are called non-coding RNAs, and the ones over 200 nucleotides in length are classified as long non-coding RNAs.

"Many of these RNAs bind to proteins or other molecules to switch genes on or off, thus regulating cellular processes. One of the best known lncRNAs is called Xist, which is important for normal development in females. High levels of another called MALAT, have been linked to more aggressive and metastatic cancers. On the whole, biologists are sure that many lncRNAs have key regulatory roles whose disruption contributes to disease. So far, however, they have characterized the functions of only a small fraction of the many thousands of lncRNAs that are thought to exist in mammalian cells.

"One reason biologists have been slow to understand what these molecules do is that a lncRNA's function is not readily apparent when you study how it's put together from its sequence of nucleotide building-blocks. Often two lncRNAs with similar functions appear to have very different sequences.

"Calabrese and his team, including first author Jessime Kirk and Peter Mucha, Ph.D., professor of mathematics and applied physical sciences in the UNC College of Arts and Sciences, tried to decipher the otherwise obscure relationship between lncRNA sequence and function. They started with two key clues: Firstly, there is evidence that lncRNAs function mainly by binding to proteins. Secondly, RNAs connect to proteins using short sequences within their overall structures.

***

"The team developed a computer-based method called SEEKR to find and compare protein-binding sequences they called "kmers" in lncRNAs, regardless of the kmers' precise locations. The team found that about half of all human and mouse lncRNAs could be grouped into five different communities, based on similarities in their kmer content. The kmer-based approach also could help predict where lncRNAs are normally found within cells and to what kinds of protein they bind.

"'We can now take sequence information from a well-studied lncRNA, and use it to discover lncRNAs that may be functioning through a related mechanism. In a way, it's like being able to finally understand the different scripts in the Rosetta Stone." Calabrese said.

"Surprisingly, the team found that kmer-content communities were often highly similar between species. Human and mouse lncRNA communities resembled each other closely, but some mammalian lncRNA communities had clear counterparts even among distantly related animals. One mammalian lncRNA community, represented by an lncRNA called HOTTIP, appeared to have cousin lncRNA communities in other vertebrates and even in sea urchins.

"'In terms of kmer content, subsets of human lncRNAs may be more similar to lncRNAs from evolutionarily distant species than they are to other human lncRNAs," Calabrese said. "This supports the idea that groups of lncRNAs have similar functions in different organisms despite lacking obvious linear sequence similarity."

***

"'Our genomes produce so many lncRNAs, and now we have a much better idea of how to look at the sequences of these molecules to predict which ones are doing important things in our cells," Calabrese said."

Comment: There is very little junk DNA, to the disappointment of Darwinists

That sounds eerily familiar. In fact, it sounds exactly as I predicted in my hypothesis on the programmatic nature of DNA.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

9250 views

A new method for understanding these strange parts of DNA and find their function:

https://phys.org/news/2018-09-scientists-reveal-vast-unknown-territory.html

"'Long non-coding RNAs are part of what you might call the 'dark matter' of the genome, and this tool we've developed should help us understand much better how they work in health and disease," said study senior author Mauro Calabrese, Ph.D., assistant professor of pharmacology and member of the UNC Lineberger Comprehensive Cancer Center.

"Genetic information in animals and plants is stored in DNA, and cells make use of that genetic information by transcribing the DNA into closely related molecules known as RNAs. Many RNAs go on to be translated into proteins. But scientists in recent decades have been forced to reckon with the fact that less than 2 percent of the genome is used that way. Most of the DNA is transcribed into RNAs that do not encode proteins. These are called non-coding RNAs, and the ones over 200 nucleotides in length are classified as long non-coding RNAs.

"Many of these RNAs bind to proteins or other molecules to switch genes on or off, thus regulating cellular processes. One of the best known lncRNAs is called Xist, which is important for normal development in females. High levels of another called MALAT, have been linked to more aggressive and metastatic cancers. On the whole, biologists are sure that many lncRNAs have key regulatory roles whose disruption contributes to disease. So far, however, they have characterized the functions of only a small fraction of the many thousands of lncRNAs that are thought to exist in mammalian cells.

"One reason biologists have been slow to understand what these molecules do is that a lncRNA's function is not readily apparent when you study how it's put together from its sequence of nucleotide building-blocks. Often two lncRNAs with similar functions appear to have very different sequences.

"Calabrese and his team, including first author Jessime Kirk and Peter Mucha, Ph.D., professor of mathematics and applied physical sciences in the UNC College of Arts and Sciences, tried to decipher the otherwise obscure relationship between lncRNA sequence and function. They started with two key clues: Firstly, there is evidence that lncRNAs function mainly by binding to proteins. Secondly, RNAs connect to proteins using short sequences within their overall structures.

***

"The team developed a computer-based method called SEEKR to find and compare protein-binding sequences they called "kmers" in lncRNAs, regardless of the kmers' precise locations. The team found that about half of all human and mouse lncRNAs could be grouped into five different communities, based on similarities in their kmer content. The kmer-based approach also could help predict where lncRNAs are normally found within cells and to what kinds of protein they bind.

"'We can now take sequence information from a well-studied lncRNA, and use it to discover lncRNAs that may be functioning through a related mechanism. In a way, it's like being able to finally understand the different scripts in the Rosetta Stone." Calabrese said.

"Surprisingly, the team found that kmer-content communities were often highly similar between species. Human and mouse lncRNA communities resembled each other closely, but some mammalian lncRNA communities had clear counterparts even among distantly related animals. One mammalian lncRNA community, represented by an lncRNA called HOTTIP, appeared to have cousin lncRNA communities in other vertebrates and even in sea urchins.

"'In terms of kmer content, subsets of human lncRNAs may be more similar to lncRNAs from evolutionarily distant species than they are to other human lncRNAs," Calabrese said. "This supports the idea that groups of lncRNAs have similar functions in different organisms despite lacking obvious linear sequence similarity."

***

"'Our genomes produce so many lncRNAs, and now we have a much better idea of how to look at the sequences of these molecules to predict which ones are doing important things in our cells," Calabrese said."

David: Comment: There is very little junk DNA, to the disappointment of Darwinists

Tony:That sounds eerily familiar. In fact, it sounds exactly as I predicted in my hypothesis on the programmatic nature of DNA.

DNA is way more complex than the Darwin theory. Not only is most of it active, the 3-D relationships of various parts to each other are vital. Only two precent codes but 80% is active.

9247 views

A new method for understanding these strange parts of DNA and find their function:

https://phys.org/news/2018-09-scientists-reveal-vast-unknown-territory.html

"'Long non-coding RNAs are part of what you might call the 'dark matter' of the genome, and this tool we've developed should help us understand much better how they work in health and disease," said study senior author Mauro Calabrese, Ph.D., assistant professor of pharmacology and member of the UNC Lineberger Comprehensive Cancer Center.

"Genetic information in animals and plants is stored in DNA, and cells make use of that genetic information by transcribing the DNA into closely related molecules known as RNAs. Many RNAs go on to be translated into proteins. But scientists in recent decades have been forced to reckon with the fact that less than 2 percent of the genome is used that way. Most of the DNA is transcribed into RNAs that do not encode proteins. These are called non-coding RNAs, and the ones over 200 nucleotides in length are classified as long non-coding RNAs.

"Many of these RNAs bind to proteins or other molecules to switch genes on or off, thus regulating cellular processes. One of the best known lncRNAs is called Xist, which is important for normal development in females. High levels of another called MALAT, have been linked to more aggressive and metastatic cancers. On the whole, biologists are sure that many lncRNAs have key regulatory roles whose disruption contributes to disease. So far, however, they have characterized the functions of only a small fraction of the many thousands of lncRNAs that are thought to exist in mammalian cells.

"One reason biologists have been slow to understand what these molecules do is that a lncRNA's function is not readily apparent when you study how it's put together from its sequence of nucleotide building-blocks. Often two lncRNAs with similar functions appear to have very different sequences.

"Calabrese and his team, including first author Jessime Kirk and Peter Mucha, Ph.D., professor of mathematics and applied physical sciences in the UNC College of Arts and Sciences, tried to decipher the otherwise obscure relationship between lncRNA sequence and function. They started with two key clues: Firstly, there is evidence that lncRNAs function mainly by binding to proteins. Secondly, RNAs connect to proteins using short sequences within their overall structures.

***

"The team developed a computer-based method called SEEKR to find and compare protein-binding sequences they called "kmers" in lncRNAs, regardless of the kmers' precise locations. The team found that about half of all human and mouse lncRNAs could be grouped into five different communities, based on similarities in their kmer content. The kmer-based approach also could help predict where lncRNAs are normally found within cells and to what kinds of protein they bind.

"'We can now take sequence information from a well-studied lncRNA, and use it to discover lncRNAs that may be functioning through a related mechanism. In a way, it's like being able to finally understand the different scripts in the Rosetta Stone." Calabrese said.

"Surprisingly, the team found that kmer-content communities were often highly similar between species. Human and mouse lncRNA communities resembled each other closely, but some mammalian lncRNA communities had clear counterparts even among distantly related animals. One mammalian lncRNA community, represented by an lncRNA called HOTTIP, appeared to have cousin lncRNA communities in other vertebrates and even in sea urchins.

"'In terms of kmer content, subsets of human lncRNAs may be more similar to lncRNAs from evolutionarily distant species than they are to other human lncRNAs," Calabrese said. "This supports the idea that groups of lncRNAs have similar functions in different organisms despite lacking obvious linear sequence similarity."

***

"'Our genomes produce so many lncRNAs, and now we have a much better idea of how to look at the sequences of these molecules to predict which ones are doing important things in our cells," Calabrese said."

David: Comment: There is very little junk DNA, to the disappointment of Darwinists

Tony:That sounds eerily familiar. In fact, it sounds exactly as I predicted in my hypothesis on the programmatic nature of DNA.

David: DNA is way more complex than the Darwin theory. Not only is most of it active, the 3-D relationships of various parts to each other are vital. Only two precent codes but 80% is active.

It is a five dimensional information structure: X,Y,Z,Time,Information

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

9241 views

"'Our genomes produce so many lncRNAs, and now we have a much better idea of how to look at the sequences of these molecules to predict which ones are doing important things in our cells," Calabrese said."

David: Comment: There is very little junk DNA, to the disappointment of Darwinists

Tony:That sounds eerily familiar. In fact, it sounds exactly as I predicted in my hypothesis on the programmatic nature of DNA.

David: DNA is way more complex than the Darwin theory. Not only is most of it active, the 3-D relationships of various parts to each other are vital. Only two precent codes but 80% is active.

Tony: It is a five dimensional information structure: X,Y,Z,Time,Information

Please explain your concept of 'time' as it relates to the code of DNA. I understand the others

9215 views

"'Our genomes produce so many lncRNAs, and now we have a much better idea of how to look at the sequences of these molecules to predict which ones are doing important things in our cells," Calabrese said."

David: Comment: There is very little junk DNA, to the disappointment of Darwinists

Tony:That sounds eerily familiar. In fact, it sounds exactly as I predicted in my hypothesis on the programmatic nature of DNA.

David: DNA is way more complex than the Darwin theory. Not only is most of it active, the 3-D relationships of various parts to each other are vital. Only two precent codes but 80% is active.

Tony: It is a five dimensional information structure: X,Y,Z,Time,Information

David: Please explain your concept of 'time' as it relates to the code of DNA. I understand the others

Things must happen at the right time, in the right sequence. Time and timing.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

9212 views

"'Our genomes produce so many lncRNAs, and now we have a much better idea of how to look at the sequences of these molecules to predict which ones are doing important things in our cells," Calabrese said."

David: Comment: There is very little junk DNA, to the disappointment of Darwinists

Tony:That sounds eerily familiar. In fact, it sounds exactly as I predicted in my hypothesis on the programmatic nature of DNA.

David: DNA is way more complex than the Darwin theory. Not only is most of it active, the 3-D relationships of various parts to each other are vital. Only two precent codes but 80% is active.

Tony: It is a five dimensional information structure: X,Y,Z,Time,Information

David: Please explain your concept of 'time' as it relates to the code of DNA. I understand the others

Tony: Things must happen at the right time, in the right sequence. Time and timing.

Yes, all biological processes require exact steps, one after the other.

9199 views

The neutral DNA theory is now questioned:

https://www.sciencedaily.com/releases/2018/10/181010105536.htm

"Researchers recently discovered that 95 percent of our genome seems to be affected by selection and other genetic biases and that markers previously thought to be neutral appear to provide skewed estimates. Their study calls for the re-examination of a plethora of results and provides the tools and recommendations to correct such issues in the future.

"Geneticists use standards to reconstruct the history of a species or to evaluate the impact of mutations, in the form of genetic markers scattered throughout the genome. Provided these markers are neutral, i.e. that they have evolved randomly rather than through a selective process, they can be reliably used as "standards" to compare various parameters across populations.

"However, what scientist Fanny Pouyet and colleagues from the Group of Laurent Excoffier at the SIB Swiss Institute of Bioinformatics and University of Bern recently discovered, is that 95% of our genome actually seems to be affected by selection and other genetic biases and that markers previously thought to be neutral appear to provide skewed estimates. Their study, published in eLife, calls for the re-examination of a plethora of results and provides the tools and recommendations to correct such issues in the future.

***

"'What we find is that less than 5% of the human genome can actually be considered as "neutral"," says Fanny Pouyet, lead author of the study. "This is a striking finding: it means that 95% of the genome is indirectly influenced by functional sites, which themselves represent only 10% to 15% of the genome," she concludes. These functional sites encompass both genes and regions involved in gene regulation.

***

"'We re-examined all existing sets of markers presented as "neutral" and found that they provided, under one aspect or another, skewed estimates" indicates Pouyet. The team then went on to identify a new set of markers that matched, this time, all the neutrality criteria, using two whole genome datasets of over a hundred individuals in total. This neutral dataset has now been made available for humans, but the method could in theory be used to find such markers in any other species."

Comment: What this indicates is most of DNA is actively involved, and it not just limited to coding, as originally thought, and gene regulation is DNA-wide function. Not much is junk. From the original study is this comment:

"Pouyet, Aeschbacher et al. created a measure of genetic diversity that is only affected by selection or transmission bias. The results showed that negative selection influences as much as 85 percent of our genome, whereas transmission bias affects a majority of the rest of the genome. After removing these two biases, less than 5 percent of the human genome is found to evolve by chance. This suggests that while most of our genetic material is formed of non-functional sequences, the vast majority of it evolves indirectly under some type of selection."

https://elifesciences.org/articles/36317

And who or what is doing the selecting?

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"This suggests that while most of our genetic material is formed of non-functional sequences, the vast majority of it evolves indirectly under some type of selection."

https://elifesciences.org/articles/36317

DAVID: And who or what is doing the selecting?

Nature, as in natural selection? Whatever is useful will survive?

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"This suggests that while most of our genetic material is formed of non-functional sequences, the vast majority of it evolves indirectly under some type of selection."

https://elifesciences.org/articles/36317

DAVID: And who or what is doing the selecting?

dhw: Nature, as in natural selection? Whatever is useful will survive?

Unless there are extinctions. We don't know what is natural and what is controlled.

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"This suggests that while most of our genetic material is formed of non-functional sequences, the vast majority of it evolves indirectly under some type of selection."
https://elifesciences.org/articles/36317

DAVID: And who or what is doing the selecting?

dhw: Nature, as in natural selection? Whatever is useful will survive?

DAVID: Unless there are extinctions. We don't know what is natural and what is controlled.

Extinctions are the natural consequence of organisms not having the necessary equipment to cope with changing conditions. But we are talking about so-called “junk DNA”. Why do you find it so difficult to accept the idea that something useful is more likely to survive than something which is of no use?

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"This suggests that while most of our genetic material is formed of non-functional sequences, the vast majority of it evolves indirectly under some type of selection."
https://elifesciences.org/articles/36317

DAVID: And who or what is doing the selecting?

dhw: Nature, as in natural selection? Whatever is useful will survive?

DAVID: Unless there are extinctions. We don't know what is natural and what is controlled.

dhw: Extinctions are the natural consequence of organisms not having the necessary equipment to cope with changing conditions. But we are talking about so-called “junk DNA”. Why do you find it so difficult to accept the idea that something useful is more likely to survive than something which is of no use?

The point of the poorly thought out 'junk DNA' theory is that the junk was supposed to have survived despite being useless. It appears 80% of DNA has some form of function. Think about survival after Chixculub: the rat-like mammals that survived did it immediately because they had the existing ability to survive without any adaptations. Subsequent evolution produced more forms that were/could adapt to the new conditions on Earth. They were designed for it. .

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"This suggests that while most of our genetic material is formed of non-functional sequences, the vast majority of it evolves indirectly under some type of selection."
https://elifesciences.org/articles/36317

DAVID: And who or what is doing the selecting?

dhw: Nature, as in natural selection? Whatever is useful will survive?

DAVID: Unless there are extinctions. We don't know what is natural and what is controlled.

dhw: Extinctions are the natural consequence of organisms not having the necessary equipment to cope with changing conditions. But we are talking about so-called “junk DNA”. Why do you find it so difficult to accept the idea that something useful is more likely to survive than something which is of no use?

David: The point of the poorly thought out 'junk DNA' theory is that the junk was supposed to have survived despite being useless. It appears 80% of DNA has some form of function.

This is a big rub for me with evolution. 'Random mutations' have to magically hit on not one, not two, but hundreds, if not thousands' of proper permutations for even some of the least complex adaptations before 'natural selection' can passively filter it.Yet, many such adaptations would be useless, in a two way fashion, without each other. Call it biological codependency.

This mindset of negating biological codependency has led, I believe, to a fundamental misunderstanding of how genetics work. Further, because of the chaotic nature of life, and the random nature of misfortunes, I do not think 'survival of the fittest' has any real explanatory power. The fittest may have been called by sheer dumb luck, thus reducing natural selection as nothing more than random chance.

All of the mad scrambling to recover from one fire after another about evolutionary theory should clue them in, but they see their marginal successes as grand victories, impressing themselves with their own cleverness, and become blind to the evidence in front of their eyes.

It makes me sad, not angry, though it used to make me angry as well. If only they (research scientist) could ever set their ego aside, along with their own preconceived notions. I know DHW will likely chime in and say we all have our preconceived notions, including me, and he would be right. But a person can learn to let go of those .

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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dhw: Extinctions are the natural consequence of organisms not having the necessary equipment to cope with changing conditions. But we are talking about so-called “junk DNA”. Why do you find it so difficult to accept the idea that something useful is more likely to survive than something which is of no use?

David: The point of the poorly thought out 'junk DNA' theory is that the junk was supposed to have survived despite being useless. It appears 80% of DNA has some form of function.

TONY: This is a big rub for me with evolution. 'Random mutations' have to magically hit on not one, not two, but hundreds, if not thousands' of proper permutations for even some of the least complex adaptations before 'natural selection' can passively filter it.Yet, many such adaptations would be useless, in a two way fashion, without each other. Call it biological codependency.

You are preaching to the converted. Both David and I have long since jettisoned the whole concept of random mutations as the generator of evolution, and what you call biological co-dependency is what Lynn Margulis called cooperation. (She was also a firm believer in cellular intelligence.) I agree with you and her.

TONY: This mindset of negating biological codependency has led, I believe, to a fundamental misunderstanding of how genetics work. Further, because of the chaotic nature of life, and the random nature of misfortunes, I do not think 'survival of the fittest' has any real explanatory power. The fittest may have been called by sheer dumb luck, thus reducing natural selection as nothing more than random chance.

Biological cooperation is central to my whole hypothesis. And I agree that natural selection, or “survival of the fittest” has no explanatory power if we are discussing how evolution progresses, because nature can only select from what already exists. However, you have raised a crucial point with your “chaotic nature of life and the random nature of misfortune”. This is a major problem if you want to discuss your God’s purpose for creating life. David’s anthropocentric view of life’s history hardly fits in with chaos and randomness, and so it raises the whole question of the extent to which his God remains in control of events and environmental changes. I don’t know your views on this. Was Chixculub, for instance, due to random chance, or do you think your God threw it at the dinosaurs?

TONY: All of the mad scrambling to recover from one fire after another about evolutionary theory should clue them in, but they see their marginal successes as grand victories, impressing themselves with their own cleverness, and become blind to the evidence in front of their eyes.

How many fires are you talking about in relation to evolutionary theory, i.e. the theory that all life is descended from a few forms or one? I myself do not accept Darwin’s explanation of how the process works, but he himself forecast that new discoveries would result in new approaches. He also left wide open the problem of the origin of life itself (he was an agnostic). To be blind to evidence means the evidence is there, so (let me put on my atheist’s hat) please tell us what evidence there is for a sourceless supermind which produces species out of thin air.

TONY: It makes me sad, not angry, though it used to make me angry as well. If only they (research scientist) could ever set their ego aside, along with their own preconceived notions. I know DHW will likely chime in and say we all have our preconceived notions, including me, and he would be right. But a person can learn to let go of those.

A true and honest perception. Most of our discussions revolve around those preconceptions (or around notions which we have come to regard as more believable than others), but I would like to think that none of us are trying to impress the others with our own clever ego. The object of this forum is to question all the notions to see which ones, if any, make sense to us. I can quite understand your sadness and earlier anger at atheistic insistence that life and speciation is all a matter of chance. This indeed is what prompted me to start the website in the first place. But why would you be sad or angry at the suggestion that your God (let me put on my theist's hat) may have created a mechanism which enabled living organisms to diversify autonomously from the original few forms or one?

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DHW: Biological cooperation is central to my whole hypothesis. And I agree that natural selection, or “survival of the fittest” has no explanatory power if we are discussing how evolution progresses, because nature can only select from what already exists. However, you have raised a crucial point with your “chaotic nature of life and the random nature of misfortune”. This is a major problem if you want to discuss your God’s purpose for creating life. David’s anthropocentric view of life’s history hardly fits in with chaos and randomness, and so it raises the whole question of the extent to which his God remains in control of events and environmental changes. I don’t know your views on this. Was Chixculub, for instance, due to random chance, or do you think your God threw it at the dinosaurs?

I do not think that co-dependency and cooperation are the same thing. Co-dependency means that one can not function independently, while cooperation implies that each is independently successful, but becomes more successful by working with another. I think this difference is crucial a proper analysis of genetics because the 'chicken and egg' problems can not be wished away or magicked away by random chance.

There are a couple of interesting scriptures in the bible that refer to 'time and unforeseen circumstances', and there is also the concept of free will, and as well a concept of 'consequence of action'. So we have, at a minimum, three different vectors upon which, at least from a biblical context, God does not profess to assert control. It is also important to understand that the lack of assertion does not preclude the ability to assert control. The latter two are inextricably intertwined, and one can not be had without the other while still maintaining a sense of fairness and justice. The former, however, is a little harder to unpack.

As best I can reason, the idea is that chaotic events provoke opportunities to grow. This is not saying that such chaos is unavoidable, or that it can not be mitigated, but rather that it is absolutely necessary for life to exist and thrive. Without it we would be weak, lazy, complacent, ignorant, and frail. There is also the idea expressed that Jehovah is 'the one teaching you to benefit yourself', and that by 'keeping his commandments' you would be a long way ahead in avoiding the chaotic catastrophes of life. I have no way of knowing, nor does anyone else, whether or not Chixculub was God directed or not. Either is possible, and both sides of the argument have their merits. Yet, I can say with some degree of certainty that if Chiculub had not happened something else would have. Either atmospheric conditions would have changed, or the food supply would have ran short, or drought, or any number of other events would have eventually wiped out the dinosaurs as a dominant species.

TONY: All of the mad scrambling to recover from one fire after another about evolutionary theory should clue them in, but they see their marginal successes as grand victories, impressing themselves with their own cleverness, and become blind to the evidence in front of their eyes.

DHW: How many fires are you talking about in relation to evolutionary theory, i.e. the theory that all life is descended from a few forms or one? ... To be blind to evidence means the evidence is there, so (let me put on my atheist’s hat) please tell us what evidence there is for a sourceless supermind which produces species out of thin air.

To the first question: the fossil record, the genetic record, the complexity issue, the information origin issue, the abiogenesis issue, the speciation issue, the invention before selection issue, the co-dependency issue, the evolution of sex issue, the inter-species co-evolvement issue, etc. Pick one.

The answer to the second question is in the answers to the first.

TONY: It makes me sad, not angry, though it used to make me angry as well. If only they (research scientist) could ever set their ego aside, along with their own preconceived notions. I know DHW will likely chime in and say we all have our preconceived notions, including me, and he would be right. But a person can learn to let go of those.

DHW: A true and honest perception. Most of our discussions revolve around those preconceptions (or around notions which we have come to regard as more believable than others), but I would like to think that none of us are trying to impress the others with our own clever ego... But why would you be sad or angry at the suggestion that your God may have created a mechanism which enabled living organisms to diversify autonomously from the original few forms or one?

I think we all struggle with our ego, myself being no exception. That does not make me angry, though in all honesty the panpsychism answer does irritate me because the evidence for it is only overwhelming in that it is underwhelming. We have no evidence for panpsychism that can not be explained better by a more programmatic approach. However, there is also the case that could be made that the very stability of species over large scales of time is indicative of many things, but Darwinian evolution and panpsychism are not among them.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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I am editing comments in order to keep the arguments more focused.

DHW: Biological cooperation is central to my whole hypothesis.

TONY: I do not think that co-dependency and cooperation are the same thing. […]

Agreed. Co-dependency is Margulis’s theory of symbiosis, but that still requires cooperation. The body is a mass of symbiotic relationships requiring cooperation between the different cell communities.

Dhw: […] you have raised a crucial point with your “chaotic nature of life and the random nature of misfortune”. […] it raises the whole question of the extent to which his God remains in control of events and environmental changes. I don’t know your views on this. Was Chixculub, for instance, due to random chance, or do you think your God threw it at the dinosaurs?

TONY: […] God does not profess to assert control. It is also important to understand that the lack of assertion does not preclude the ability to assert control.

With my theist’s hat on, I’m happy with this. Your God’s renunciation of control would explain the higgledy-piggledy history of evolution, with its unpredictability adding interest to the spectacle. (This may irritate you, but it fits in with your views on control.)

TONY: As best I can reason, the idea is that chaotic events provoke opportunities to grow.

This again fits in with the hypothesis that your God enjoys seeing change, which would include growth,

TONY: This is not saying that such chaos is unavoidable, or that it can not be mitigated, but rather that it is absolutely necessary for life to exist and thrive. Without it we would be weak, lazy, complacent, ignorant, and frail.

I don’t understand why you are confining your comments to humans. My questions concern the whole history of life.

TONY: I have no way of knowing, nor does anyone else, whether or not Chixculub was God directed or not. Either is possible, and both sides of the argument have their merits. Yet, I can say with some degree of certainty that if Chiculub had not happened something else would have. […]

Agreed. The history of life is one of change, and your account seems to suggest your God let it run its own course rather than preprogramming or dabbling every change for the sake of the human brain, as proposed by David.

TONY: All of the mad scrambling to recover from one fire after another about evolutionary theory should clue them in, but they […] become blind to the evidence in front of their eyes.

DHW: How many fires are you talking about in relation to evolutionary theory, i.e. the theory that all life is descended from a few forms or one? ... To be blind to evidence means the evidence is there, so (let me put on my atheist’s hat) please tell us what evidence there is for a sourceless supermind which produces species out of thin air.

TONY: To the first question: the fossil record, the genetic record, the complexity issue, the information origin issue, the abiogenesis issue, the speciation issue, the invention before selection issue, the co-dependency issue, the evolution of sex issue, the inter-species co-evolvement issue, etc. Pick one. The answer to the second question is in the answers to the first.

I’m sorry, but firstly the fact that there are issues over origins (which are not the subject of the theory) and over the means by which evolution progresses, does not disprove the theory that all life descended from one or a few forms. Even you have agreed that these were single cells. However, even more to the point, not one of these issues provides a shred of evidence that there is a sourceless supermind which produces species out of thin air. Issues are issues, not evidence!

DHW: …why would you be sad or angry at the suggestion that your God may have created a mechanism which enabled living organisms to diversify autonomously from the original few forms or one?

TONY: [..] in all honesty the panpsychism answer does irritate me because the evidence for it is only overwhelming in that it is underwhelming. We have no evidence for panpsychism that can not be explained better by a more programmatic approach.

This does not answer the above question. However, most forms of panpsychism (including David’s panentheism, which includes programmes for just about everything that wasn’t dabbled)) revolve around your God. I have suggested an atheistic form, and although you will reject it, I don’t know why you regard a bottom-up evolution of complexity and consciousness as a poorer explanation than a top-down one that has a supreme but sourceless consciousness creating a programme for consciousness.

TONY: However, there is also the case that could be made that the very stability of species over large scales of time is indicative of many things, but Darwinian evolution and panpsychism are not among them.

Of course they are among them. Evolution proceeds in bursts (see Gould’s punctuated equilibrium). Darwinian evolution does not discount there being long periods of environmental stasis leading to long periods of stable species. Panpsychism endows all things with some form of mental ability. Why do you think it impossible for organisms to have mental abilities just because their species is stable for a long time?

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DHW:Co-dependency is Margulis’s theory of symbiosis, but that still requires cooperation. The body is a mass of symbiotic relationships requiring cooperation between the different cell communities.

This presents chicken and egg problems, as well as communication and planning problems in regards to intelligence.

TONY: […] God does not profess to assert control. It is also important to understand that the lack of assertion does not preclude the ability to assert control.

DHW: With my theist’s hat on, I’m happy with this. Your God’s renunciation of control would explain the higgledy-piggledy history of evolution, with its unpredictability adding interest to the spectacle. (This may irritate you, but it fits in with your views on control.)

I should amend to clarify that there are times when he asserts control, meaning that he is capable and has done so.

TONY: As best I can reason, the idea is that chaotic events provoke opportunities to grow.

This again fits in with the hypothesis that your God enjoys seeing change, which would include growth,

TONY: This is not saying that such chaos is unavoidable, or that it can not be mitigated, but rather that it is absolutely necessary for life to exist and thrive. Without it we would be weak, lazy, complacent, ignorant, and frail.

I don’t understand why you are confining your comments to humans. My questions concern the whole history of life.

Why is my statement limited to humans?

TONY: I have no way of knowing, nor does anyone else, whether or not Chixculub was God directed or not. Either is possible, and both sides of the argument have their merits. Yet, I can say with some degree of certainty that if Chiculub had not happened something else would have. […]

DHW: Agreed. The history of life is one of change, and your account seems to suggest your God let it run its own course rather than preprogramming or dabbling every change for the sake of the human brain, as proposed by David.

Degrees of Freedom, DHW, degrees of freedom. Freedom and variation within limits.

TONY: All of the mad scrambling to recover from one fire after another about evolutionary theory should clue them in, but they […] become blind to the evidence in front of their eyes.

DHW: How many fires are you talking about in relation to evolutionary theory, i.e. the theory that all life is descended from a few forms or one? ... To be blind to evidence means the evidence is there, so (let me put on my atheist’s hat) please tell us what evidence there is for a sourceless supermind which produces species out of thin air.

TONY: To the first question: the fossil record, the genetic record, the complexity issue, the information origin issue, the abiogenesis issue, the speciation issue, the invention before selection issue, the co-dependency issue, the evolution of sex issue, the inter-species co-evolvement issue, etc. Pick one. The answer to the second question is in the answers to the first.

DHW: I’m sorry, but firstly the fact that there are issues over origins (which are not the subject of the theory) and over the means by which evolution progresses, does not disprove the theory that all life descended from one or a few forms. Even you have agreed that these were single cells. However, even more to the point, not one of these issues provides a shred of evidence that there is a sourceless supermind which produces species out of thin air. Issues are issues, not evidence!

Um... that makes no logical or scientific sense. A hypothesis is disproved by its failed predictions. Evolution has made lots of failed predictions.

TONY: However, there is also the case that could be made that the very stability of species over large scales of time is indicative of many things, but Darwinian evolution and panpsychism are not among them.

Of course they are among them. Evolution proceeds in bursts (see Gould’s punctuated equilibrium). Darwinian evolution does not discount there being long periods of environmental stasis leading to long periods of stable species. Panpsychism endows all things with some form of mental ability. Why do you think it impossible for organisms to have mental abilities just because their species is stable for a long time?

I do not think it impossible. I think there is no evidence for the degree of intelligence you attribute to them.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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DHW:Co-dependency is Margulis’s theory of symbiosis, but that still requires cooperation. The body is a mass of symbiotic relationships requiring cooperation between the different cell communities.

Tony: This presents chicken and egg problems, as well as communication and planning problems in regards to intelligence.

TONY: […] God does not profess to assert control. It is also important to understand that the lack of assertion does not preclude the ability to assert control.

DHW: With my theist’s hat on, I’m happy with this. Your God’s renunciation of control would explain the higgledy-piggledy history of evolution, with its unpredictability adding interest to the spectacle. (This may irritate you, but it fits in with your views on control.)

Tony: I should amend to clarify that there are times when he asserts control, meaning that he is capable and has done so.

TONY: As best I can reason, the idea is that chaotic events provoke opportunities to grow.

dhw: This again fits in with the hypothesis that your God enjoys seeing change, which would include growth,

TONY: This is not saying that such chaos is unavoidable, or that it can not be mitigated, but rather that it is absolutely necessary for life to exist and thrive. Without it we would be weak, lazy, complacent, ignorant, and frail.

Tony: I don’t understand why you are confining your comments to humans. My questions concern the whole history of life.

Tony: Why is my statement limited to humans?

TONY: I have no way of knowing, nor does anyone else, whether or not Chixculub was God directed or not. Either is possible, and both sides of the argument have their merits. Yet, I can say with some degree of certainty that if Chiculub had not happened something else would have. […]

DHW: Agreed. The history of life is one of change, and your account seems to suggest your God let it run its own course rather than preprogramming or dabbling every change for the sake of the human brain, as proposed by David.

Tony: Degrees of Freedom, DHW, degrees of freedom. Freedom and variation within limits.

TONY: All of the mad scrambling to recover from one fire after another about evolutionary theory should clue them in, but they […] become blind to the evidence in front of their eyes.

DHW: How many fires are you talking about in relation to evolutionary theory, i.e. the theory that all life is descended from a few forms or one? ... To be blind to evidence means the evidence is there, so (let me put on my atheist’s hat) please tell us what evidence there is for a sourceless supermind which produces species out of thin air.

TONY: To the first question: the fossil record, the genetic record, the complexity issue, the information origin issue, the abiogenesis issue, the speciation issue, the invention before selection issue, the co-dependency issue, the evolution of sex issue, the inter-species co-evolvement issue, etc. Pick one. The answer to the second question is in the answers to the first.

DHW: I’m sorry, but firstly the fact that there are issues over origins (which are not the subject of the theory) and over the means by which evolution progresses, does not disprove the theory that all life descended from one or a few forms. Even you have agreed that these were single cells. However, even more to the point, not one of these issues provides a shred of evidence that there is a sourceless supermind which produces species out of thin air. Issues are issues, not evidence!

Tony: Um... that makes no logical or scientific sense. A hypothesis is disproved by its failed predictions. Evolution has made lots of failed predictions.

TONY: However, there is also the case that could be made that the very stability of species over large scales of time is indicative of many things, but Darwinian evolution and panpsychism are not among them.

dhw: Of course they are among them. Evolution proceeds in bursts (see Gould’s punctuated equilibrium). Darwinian evolution does not discount there being long periods of environmental stasis leading to long periods of stable species. Panpsychism endows all things with some form of mental ability. Why do you think it impossible for organisms to have mental abilities just because their species is stable for a long time?

Tony: I do not think it impossible. I think there is no evidence for the degree of intelligence you attribute to them.

dhw uses a massive illogical extrapolation from observed intelligent responses by single cells which are automatically functioning every second to maintain the homeostasis of life. Life requires that cells are constantly functioning. Many of them keep on functioning, even after death, which is why we can transplant organs.

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DHW:Co-dependency is Margulis’s theory of symbiosis, but that still requires cooperation. The body is a mass of symbiotic relationships requiring cooperation between the different cell communities.

TONY: This presents chicken and egg problems, as well as communication and planning problems in regards to intelligence.

You were distinguishing between cooperation and co-dependency, so I tried to explain that co-dependency is a form of cooperation. All forms of cooperation involve some sort of communication and they take place whether you think your God preprogrammed them, dabbled them, or enabled organisms to work them out for themselves.

TONY: […] God does not profess to assert control. It is also important to understand that the lack of assertion does not preclude the ability to assert control.

DHW: With my theist’s hat on, I’m happy with this. Your God’s renunciation of control would explain the higgledy-piggledy history of evolution, with its unpredictability adding interest to the spectacle. (This may irritate you, but it fits in with your views on control.)

TONY: I should amend to clarify that there are times when he asserts control, meaning that he is capable and has done so.

No problem. If God exists and created the great spectacle, he could certainly interfere if he wanted to. “I’ve had enough of these damned dinosaurs. I’ll chuck an asteroid at ‘em an’ see what happens next.”

TONY: This is not saying that such chaos is unavoidable, or that it can not be mitigated, but rather that it is absolutely necessary for life to exist and thrive. Without it we would be weak, lazy, complacent, ignorant, and frail.

dhw: I don’t understand why you are confining your comments to humans. My questions concern the whole history of life.

TONY: Why is my statement limited to humans?

I didn’t think “we would be weak etc.”, meant you were identifying “us” with bacteria, dinosaurs or the duckbilled platypus.

DHW: The history of life is one of change, and your account seems to suggest your God let it run its own course rather than preprogramming or dabbling every change for the sake of the human brain, as proposed by David.

TONY: Degrees of Freedom, DHW, degrees of freedom. Freedom and variation within limits.

With my theist’s hat on, I’ll settle for that. How much freedom/limitation is open to question, but my objection was to David’s hypothesis.

DHW: I’m sorry, but firstly the fact that there are issues over origins (which are not the subject of the theory) and over the means by which evolution progresses, does not disprove the theory that all life descended from one or a few forms. Even you have agreed that these were single cells. However, even more to the point, not one of these issues provides a shred of evidence that there is a sourceless supermind which produces species out of thin air. Issues are issues, not evidence!

TONY: Um... that makes no logical or scientific sense. A hypothesis is disproved by its failed predictions. Evolution has made lots of failed predictions.

You can’t “disprove” the hypothesis of common descent any more than you can "disprove" the hypothesis of separate creation until you actually know the truth about speciation! They both remain hypotheses. And I’m afraid your list of “issues” still doesn’t provide a single shred of evidence for your own hypothesis that a sourceless supermind produces species out of thin air.

TONY: However, there is also the case that could be made that the very stability of species over large scales of time is indicative of many things, but Darwinian evolution and panpsychism are not among them.

dhw: Of course they are among them. Evolution proceeds in bursts (see Gould’s punctuated equilibrium). Darwinian evolution does not discount there being long periods of environmental stasis leading to long periods of stable species. Panpsychism endows all things with some form of mental ability. Why do you think it impossible for organisms to have mental abilities just because their species is stable for a long time?

TONY: I do not think it impossible. I think there is no evidence for the degree of intelligence you attribute to them.

I was responding to your claim that stability was not "indicative" of Darwinian evolution or panpsychism. But I agree with your comment. That is why my hypothesis remains a hypothesis. There is no evidence for any of the theories relating to the origin of species, and that is why the debate continues.

DAVID: dhw uses a massive illogical extrapolation from observed intelligent responses by single cells which are automatically functioning every second to maintain the homeostasis of life. Life requires that cells are constantly functioning. Many of them keep on functioning, even after death, which is why we can transplant organs.

Of course most functions are automatic. Intelligence comes into play when there are problems to be solved. Those are the “observed intelligent responses”. And of course life requires cells to function! That does not mean they are not intelligent! But, as above, my hypothesis is a hypothesis, and remains as hypothetical as your own hypotheses.

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TONY: […] God does not profess to assert control. It is also important to understand that the lack of assertion does not preclude the ability to assert control.

DHW: With my theist’s hat on, I’m happy with this. Your God’s renunciation of control would explain the higgledy-piggledy history of evolution, with its unpredictability adding interest to the spectacle. (This may irritate you, but it fits in with your views on control.)

TONY: I should amend to clarify that there are times when he asserts control, meaning that he is capable and has done so.

dhw: No problem. If God exists and created the great spectacle, he could certainly interfere if he wanted to. “I’ve had enough of these damned dinosaurs. I’ll chuck an asteroid at ‘em an’ see what happens next.”

TONY: This is not saying that such chaos is unavoidable, or that it can not be mitigated, but rather that it is absolutely necessary for life to exist and thrive. Without it we would be weak, lazy, complacent, ignorant, and frail.

dhw: I don’t understand why you are confining your comments to humans. My questions concern the whole history of life.

TONY: Why is my statement limited to humans?

I didn’t think “we would be weak etc.”, meant you were identifying “us” with bacteria, dinosaurs or the duckbilled platypus.

DHW: The history of life is one of change, and your account seems to suggest your God let it run its own course rather than preprogramming or dabbling every change for the sake of the human brain, as proposed by David.

TONY: Degrees of Freedom, DHW, degrees of freedom. Freedom and variation within limits.

dhw: With my theist’s hat on, I’ll settle for that. How much freedom/limitation is open to question, but my objection was to David’s hypothesis.

DHW: I’m sorry, but firstly the fact that there are issues over origins (which are not the subject of the theory) and over the means by which evolution progresses, does not disprove the theory that all life descended from one or a few forms. Even you have agreed that these were single cells. However, even more to the point, not one of these issues provides a shred of evidence that there is a sourceless supermind which produces species out of thin air. Issues are issues, not evidence!

TONY: Um... that makes no logical or scientific sense. A hypothesis is disproved by its failed predictions. Evolution has made lots of failed predictions.

dhw: You can’t “disprove” the hypothesis of common descent any more than you can "disprove" the hypothesis of separate creation until you actually know the truth about speciation! They both remain hypotheses. And I’m afraid your list of “issues” still doesn’t provide a single shred of evidence for your own hypothesis that a sourceless supermind produces species out of thin air.

TONY: However, there is also the case that could be made that the very stability of species over large scales of time is indicative of many things, but Darwinian evolution and panpsychism are not among them.

dhw: Of course they are among them. Evolution proceeds in bursts (see Gould’s punctuated equilibrium). Darwinian evolution does not discount there being long periods of environmental stasis leading to long periods of stable species. Panpsychism endows all things with some form of mental ability. Why do you think it impossible for organisms to have mental abilities just because their species is stable for a long time?

TONY: I do not think it impossible. I think there is no evidence for the degree of intelligence you attribute to them.

dhw: I was responding to your claim that stability was not "indicative" of Darwinian evolution or panpsychism. But I agree with your comment. That is why my hypothesis remains a hypothesis. There is no evidence for any of the theories relating to the origin of species, and that is why the debate continues.

DAVID: dhw uses a massive illogical extrapolation from observed intelligent responses by single cells which are automatically functioning every second to maintain the homeostasis of life. Life requires that cells are constantly functioning. Many of them keep on functioning, even after death, which is why we can transplant organs.

dhw: Of course most functions are automatic. Intelligence comes into play when there are problems to be solved. Those are the “observed intelligent responses”. And of course life requires cells to function! That does not mean they are not intelligent! But, as above, my hypothesis is a hypothesis, and remains as hypothetical as your own hypotheses.

What you skip over about 'observed intelligent responses' is I view those responses as continuous to keep life alive and therefor totally automatic, with no evidence that cellular intelligence can be stretched to design for future changes. Therefore the basis of your hypothesis fails from the beginning.

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dhw: Of course most functions are automatic. Intelligence comes into play when there are problems to be solved. Those are the “observed intelligent responses”. And of course life requires cells to function! That does not mean they are not intelligent! But, as above, my hypothesis is a hypothesis, and remains as hypothetical as your own hypotheses.

DAVID: What you skip over about 'observed intelligent responses' is I view those responses as continuous to keep life alive and therefor totally automatic, with no evidence that cellular intelligence can be stretched to design for future changes. Therefore the basis of your hypothesis fails from the beginning.

The basis of my hypothesis is the belief of several experts in the field that cells are intelligent. The fact that you believe your own view and not theirs does not mean my hypothesis fails from the beginning! Of course responses must be continuous, and if they are not, and the cell communities fail to provide intelligent solutions to new problems, the life of the organism ends! I have acknowledged a hundred times that we do not have evidence that their intelligence can stretch so far as to the innovations that cause speciation, which is why my hypothesis remains just as unproven as your own.

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dhw: Of course most functions are automatic. Intelligence comes into play when there are problems to be solved. Those are the “observed intelligent responses”. And of course life requires cells to function! That does not mean they are not intelligent! But, as above, my hypothesis is a hypothesis, and remains as hypothetical as your own hypotheses.

DAVID: What you skip over about 'observed intelligent responses' is I view those responses as continuous to keep life alive and therefor totally automatic, with no evidence that cellular intelligence can be stretched to design for future changes. Therefore the basis of your hypothesis fails from the beginning.

dhw: The basis of my hypothesis is the belief of several experts in the field that cells are intelligent. The fact that you believe your own view and not theirs does not mean my hypothesis fails from the beginning! Of course responses must be continuous, and if they are not, and the cell communities fail to provide intelligent solutions to new problems, the life of the organism ends! I have acknowledged a hundred times that we do not have evidence that their intelligence can stretch so far as to the innovations that cause speciation, which is why my hypothesis remains just as unproven as your own.

OK. Well skip over the need for design again.

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dhw: Extinctions are the natural consequence of organisms not having the necessary equipment to cope with changing conditions. But we are talking about so-called “junk DNA”. Why do you find it so difficult to accept the idea that something useful is more likely to survive than something which is of no use?

David: The point of the poorly thought out 'junk DNA' theory is that the junk was supposed to have survived despite being useless. It appears 80% of DNA has some form of function.

TONY: This is a big rub for me with evolution. 'Random mutations' have to magically hit on not one, not two, but hundreds, if not thousands' of proper permutations for even some of the least complex adaptations before 'natural selection' can passively filter it.Yet, many such adaptations would be useless, in a two way fashion, without each other. Call it biological codependency.

You are preaching to the converted. Both David and I have long since jettisoned the whole concept of random mutations as the generator of evolution, and what you call biological co-dependency is what Lynn Margulis called cooperation. (She was also a firm believer in cellular intelligence.) I agree with you and her.

TONY: This mindset of negating biological codependency has led, I believe, to a fundamental misunderstanding of how genetics work. Further, because of the chaotic nature of life, and the random nature of misfortunes, I do not think 'survival of the fittest' has any real explanatory power. The fittest may have been called by sheer dumb luck, thus reducing natural selection as nothing more than random chance.

dhw: Biological cooperation is central to my whole hypothesis. And I agree that natural selection, or “survival of the fittest” has no explanatory power if we are discussing how evolution progresses, because nature can only select from what already exists. However, you have raised a crucial point with your “chaotic nature of life and the random nature of misfortune”. This is a major problem if you want to discuss your God’s purpose for creating life. David’s anthropocentric view of life’s history hardly fits in with chaos and randomness, and so it raises the whole question of the extent to which his God remains in control of events and environmental changes. I don’t know your views on this. Was Chixculub, for instance, due to random chance, or do you think your God threw it at the dinosaurs?

TONY: All of the mad scrambling to recover from one fire after another about evolutionary theory should clue them in, but they see their marginal successes as grand victories, impressing themselves with their own cleverness, and become blind to the evidence in front of their eyes.

dhw: How many fires are you talking about in relation to evolutionary theory, i.e. the theory that all life is descended from a few forms or one? I myself do not accept Darwin’s explanation of how the process works, but he himself forecast that new discoveries would result in new approaches. He also left wide open the problem of the origin of life itself (he was an agnostic). To be blind to evidence means the evidence is there, so (let me put on my atheist’s hat) please tell us what evidence there is for a sourceless supermind which produces species out of thin air.

TONY: It makes me sad, not angry, though it used to make me angry as well. If only they (research scientist) could ever set their ego aside, along with their own preconceived notions. I know DHW will likely chime in and say we all have our preconceived notions, including me, and he would be right. But a person can learn to let go of those.

dhw: A true and honest perception. Most of our discussions revolve around those preconceptions (or around notions which we have come to regard as more believable than others), but I would like to think that none of us are trying to impress the others with our own clever ego. The object of this forum is to question all the notions to see which ones, if any, make sense to us. I can quite understand your sadness and earlier anger at atheistic insistence that life and speciation is all a matter of chance. This indeed is what prompted me to start the website in the first place. But why would you be sad or angry at the suggestion that your God (let me put on my theist's hat) may have created a mechanism which enabled living organisms to diversify autonomously from the original few forms or one?

I'll enter here to note we have had long discussion about the possibility that God gave organisms an inventive mechanism to cause designed advances. My version contains God's guidelines.

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"This suggests that while most of our genetic material is formed of non-functional sequences, the vast majority of it evolves indirectly under some type of selection."
https://elifesciences.org/articles/36317

DAVID: And who or what is doing the selecting?

dhw: Nature, as in natural selection? Whatever is useful will survive?

DAVID: Unless there are extinctions. We don't know what is natural and what is controlled.

dhw: Extinctions are the natural consequence of organisms not having the necessary equipment to cope with changing conditions. But we are talking about so-called “junk DNA”. Why do you find it so difficult to accept the idea that something useful is more likely to survive than something which is of no use?

David: The point of the poorly thought out 'junk DNA' theory is that the junk was supposed to have survived despite being useless. It appears 80% of DNA has some form of function.

Tony: This is a big rub for me with evolution. 'Random mutations' have to magically hit on not one, not two, but hundreds, if not thousands' of proper permutations for even some of the least complex adaptations before 'natural selection' can passively filter it.Yet, many such adaptations would be useless, in a two way fashion, without each other. Call it biological codependency.

This mindset of negating biological codependency has led, I believe, to a fundamental misunderstanding of how genetics work. Further, because of the chaotic nature of life, and the random nature of misfortunes, I do not think 'survival of the fittest' has any real explanatory power. The fittest may have been called by sheer dumb luck, thus reducing natural selection as nothing more than random chance.

All of the mad scrambling to recover from one fire after another about evolutionary theory should clue them in, but they see their marginal successes as grand victories, impressing themselves with their own cleverness, and become blind to the evidence in front of their eyes.

It makes me sad, not angry, though it used to make me angry as well. If only they (research scientist) could ever set their ego aside, along with their own preconceived notions. I know DHW will likely chime in and say we all have our preconceived notions, including me, and he would be right. But a person can learn to let go of those .

The complexity of the genome does not allow for chance evolution to work as Tony shows. Survi val of the fittest tells us nothing.

8245 views

“This suggests that while most of our genetic material is formed of non-functional sequences, the vast majority of it evolves indirectly under some type of selection."
https://elifesciences.org/articles/36317

DAVID: And who or what is doing the selecting?

dhw: Nature, as in natural selection? Whatever is useful will survive?

DAVID: Unless there are extinctions. We don't know what is natural and what is controlled.

dhw: Extinctions are the natural consequence of organisms not having the necessary equipment to cope with changing conditions. But we are talking about so-called “junk DNA”. Why do you find it so difficult to accept the idea that something useful is more likely to survive than something which is of no use?

DAVID: The point of the poorly thought out 'junk DNA' theory is that the junk was supposed to have survived despite being useless. It appears 80% of DNA has some form of function. Think about survival after Chixculub: the rat-like mammals that survived did it immediately because they had the existing ability to survive without any adaptations. Subsequent evolution produced more forms that were/could adapt to the new conditions on Earth. They were designed for it.

I know the junk theory, and I know that it is being increasingly discredited. You asked who are what is doing the selecting (i.e. of useful DNA). I suggested that it is natural for something useful to survive and for something that is not useful not to survive. What is your objection?

8221 views

“This suggests that while most of our genetic material is formed of non-functional sequences, the vast majority of it evolves indirectly under some type of selection."
https://elifesciences.org/articles/36317

DAVID: And who or what is doing the selecting?

dhw: Nature, as in natural selection? Whatever is useful will survive?

DAVID: Unless there are extinctions. We don't know what is natural and what is controlled.

dhw: Extinctions are the natural consequence of organisms not having the necessary equipment to cope with changing conditions. But we are talking about so-called “junk DNA”. Why do you find it so difficult to accept the idea that something useful is more likely to survive than something which is of no use?

DAVID: The point of the poorly thought out 'junk DNA' theory is that the junk was supposed to have survived despite being useless. It appears 80% of DNA has some form of function. Think about survival after Chixculub: the rat-like mammals that survived did it immediately because they had the existing ability to survive without any adaptations. Subsequent evolution produced more forms that were/could adapt to the new conditions on Earth. They were designed for it.

dhw: I know the junk theory, and I know that it is being increasingly discredited. You asked who are what is doing the selecting (i.e. of useful DNA). I suggested that it is natural for something useful to survive and for something that is not useful not to survive. What is your objection?

The point is the reliance on 'survival of the fittest', which is what you just did, is a very minor unproven aspect of evolution. Your statement is correct if understood in the right context.

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dhw: I know the junk theory, and I know that it is being increasingly discredited. You asked who are what is doing the selecting (i.e. of useful DNA). I suggested that it is natural for something useful to survive and for something that is not useful not to survive. What is your objection?

DAVID: The point is the reliance on 'survival of the fittest', which is what you just did, is a very minor unproven aspect of evolution. Your statement is correct if understood in the right context.

You asked who or what did the selection. Since the context is useful DNA versus junk DNA and you accept that it is natural for something useful to survive and for something that is not useful not to survive, there is no disagreement here.

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Inflammation has to be controlled to the area needed. This is how lncRNA does it:

https://medicalxpress.com/news/2018-11-noncoding-rna-key-inflammation.html

"Scientists have identified an RNA molecule with broad powers to regulate the body's inflammatory response to infection and injury. Called lincRNA-Cox2, it belongs to a recently discovered, highly abundant class of RNAs whose functions are only beginning to be understood.

"The sequencing of the human genome revealed that only a small fraction of the DNA in our chromosomes comprises genes that encode instructions for making proteins. Those genes are transcribed into messenger RNA, which directs the synthesis of proteins that carry out various functions in the cell. The rest of the genome, about 98 percent of it, was sometimes referred to as the "dark matter" of the genome or dismissed as "junk DNA."

"In the past decade, however, new RNA sequencing technologies have revealed that much of the genome is transcribed into noncoding RNA molecules of various types. Long intergenic noncoding RNA (lincRNA) is the largest class of these RNAs.

"'We now know of about 16,000 long noncoding RNAs, about as many as there are protein-coding genes, but we know the functions of less than one percent of them," said Susan Carpenter, an assistant professor of molecular, cell and developmental biology at UC Santa Cruz.

"Carpenter's lab is interested in how these lincRNAs control the processes involved in inflammation. The new study, published November 6 in Cell Reports, shows that lincRNA-Cox2 functions in several different ways to regulate the activity of genes involved in inflammation and other immune system responses.

"Inflammation is a normal part of the body's response to infection and injury, but unresolved or chronic inflammation is associated with a wide range of diseases. LincRNA-Cox2 was named for its proximity in the genome to a gene called Cox2, which Carpenter calls "the most important inflammatory gene in the body." Aspirin, ibuprofen, and other nonsteroidal anti-inflammatory drugs (NSAIDs) reduce inflammation by inhibiting the Cox2 enzyme encoded by this gene.

"One of the major findings of the new study is that lincRNA-Cox2 regulates the activity of this neighboring gene, boosting production of the enzyme. Carpenter's team found that levels of the Cox2 enzyme were 70 to 80 percent lower than normal in mice lacking the lincRNA-Cox2 gene.

"But Cox2 is not the only gene regulated by lincRNA-Cox2. It also influences the expression of genes scattered all across the genome, and these other genes are important in the innate immune response to infections. LincRNA-Cox2 can inhibit some genes and enhance the expression of others.

***

"'We've now made animal models that show lincRNA-Cox2 is important in the whole organism, and this is probably one of the first examples to show a lincRNA controls not only a neighboring gene but other genes as well," Carpenter said.

"One of the functions of lincRNA-Cox2 is to inhibit the expression of a number of genes that are important in the innate immune response to viral infections. "You want those genes to turn on when you have an infection, but when they get turned on in the absence of infection it's associated with autoimmune diseases like lupus," Carpenter said."

Comment: like any other generalized reaction, think of blood clotting, the area to be affected must be limited to that area and not allowed to spread around the whole body which would b e a disastrous outcome. This must be designed and cannot be developed by chance. Chance would kill.

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This study says retrotransposons use junk DNA to advance evolution within DNA:

https://phys.org/news/2018-11-genes-advanced-life-emerged.html

"A previously unappreciated interaction in the genome turns out to have possibly been one of the driving forces in the emergence of advanced life, billions of years ago.

"This discovery began with a curiosity for retrotransposons, known as "jumping genes," which are DNA sequences that copy and paste themselves within the genome, multiplying rapidly. Nearly half of the human genome is made up of retrotransposons, but bacteria hardly have them at all.

"When retrotransposons copy themselves within the genome, they first find a spot in the DNA and cut it open. To survive, the organism then has to repair this cut. Some bacteria, like E. coli, only have one way to perform this repair, which usually ends up removing the new retrotransposon. But advanced organisms (eukaryotes) have an additional "trick" called nonhomologous end-joining, or NHEJ, that gives them another way to repair cuts in their DNA.

"Goldenfeld and Kuhlman decided to see what would happen if they gave bacteria the ability to do NHEJ, thinking that it would help them tolerate the damage to their DNA. But it just made the retrotransposons better at multiplying, causing even more damage than before.

"It just completely killed everything," Kuhlman said. "At the time, I thought I was just doing something wrong."
They realized that the interaction between NHEJ and retrotransposons may be more important than they previously thought.

***

"Eukaryotes typically have many retrotransposons in their genome, along with a lot of other "junk" DNA, which doesn't have a well-understood function. Within the genome, there must be a constant interplay between NHEJ and retrotransposons, as NHEJ tries to control how rapidly the retrotransposons multiply. This gives the organism more power over their genome, and the presence of "junk" DNA is important.

"'As you get more and more junk in your DNA, you can start taking these pieces and combining them together in different ways, more ways than you could without all the junk in there," Kuhlman said.

"These conditions—the accumulation of "junk" DNA, the presence of retrotransposons and their interactions with NHEJ—make the genome more complex. This is one feature that may distinguish advanced organisms, like humans, from simpler ones, like bacteria.
"Advanced organisms can also manage their genome by using their spliceosome, a molecular machine that sorts through the "junk" DNA and reconstructs the genes back to normal.

"Some parts of the spliceosome are similar to group II introns, bacteria's primitive version of retrotransposons. Introns are also found in eukaryotes, and along with the spliceosome are evolutionarily derived from group II introns. Goldenfeld said this poses an evolutionary question.

"'What came first, the spliceosome or the group II introns? Clearly the group II introns," he said. "So then you can ask: where did the eukaryotic cell first get those group II introns in order to build up the spliceosome early on?"

"This study suggests that group II introns, the ancestors of introns in the spliceosome and retrotransposons in eukaryotes, somehow invaded early eukaryotic cells. Then, their interactions with NHEJ created a "selection pressure" that helped lead to the emergence of the spliceosome, which helped life become advanced billions of years ago.

"The spliceosome helped life become advanced by enabling eukaryotes to do more with their DNA. For example, even though humans have roughly the same number of genes as C. elegans, a worm, humans can do more with those genes. (my bold)

"'There's not much difference between this very simple worm and humans, which is obviously insane," Goldenfeld said. "What's happening is that humans are able to take these genes and mix and match them in many combinations to do much more complicated functions than C. elegans does."

"Not only did NHEJ and retrotransposons help with the creation of the spliceosome; this study suggests that they may also have assisted in making chromosomes—DNA molecules that contain genetic material—more advanced. Interactions between NHEJ and retrotransposons may have aided in the transition from circular chromosomes (which bacteria generally have) to linear ones (which more advanced organisms have), another indicator of advanced life.

"Goldenfeld said that before this research, many researchers studied the role of retrotransposons, but the importance of NHEJ was not fully appreciated. This research proves that it played a part, billions of years ago, in eukaryotes becoming the advanced organisms we know today.

"'This certainly was not the only thing that was going on," Goldenfeld said. "But if it hadn't happened, it's hard to see how you could have complex life.'"

Comment: Once again junk DNA is necessary. This could well explain how advances in evolution were coded into DNA, by simply rearranging DNA, with no need for enlargement. Perhaps this is what ID scientists view as devolution. The authors assume chance evolution. I think God used this method .

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Introns are the spacers between genes, but it found they have a real function in food scarcity:

https://www.nature.com/articles/d41586-019-00183-0?utm_source=Nature+Briefing&utm_c...

"Two studies published in Nature on 16 January suggest that these stretches of non-coding DNA called introns help to control the rate at which cells grow, conserving energy when food becomes scarce.

***

"At first, the team found that modified yeast strains grew just like the unmodified, ‘wild-type’ strain under laboratory conditions.

"But when the researchers grew the altered yeast in nutrient-poor conditions alongside wild-type yeast, 64% of the modified strains died out, whereas the wild types survived.

"The researchers surmised that many of the introns helped the wild yeast to cope with a lack of food. Further experiments illuminated the mechanism behind the introns’ role in a cell.

***

"When a cell makes a protein from a gene, the gene sequence is first copied from the DNA onto a messenger RNA, which is the template for the protein. Before the protein is assembled, the introns are cut out of the RNA by a molecular machine called a spliceosome.

"Abou Elela’s team found that in many of the yeasts lacking one of their introns, the remaining introns weren’t cut out of the messenger RNAs.

"And when nutrients were scarce, the genes for proteins that make up the ribosomes ― cellular machines that assemble proteins ― were more active than those in wild-type yeast.

"Ribosomes require a lot of energy, and during periods of starvation, cells normally repress ribosomal-protein-related genes to conserve energy. The modified yeast strains, however, did not generally do this.

"The team concluded that in normal cells with introns, those introns repress ribosomal-protein genes when food is in short supply to conserve energy.

"Abou Elela says that “70 to 80% of the introns have the same effect. We have found an entirely new way for the cell to regulate itself when nutrients are depleted.”

"In the second study2, Jeffrey Morgan, a biomedical engineer at the Massachusetts Institute of Technology in Cambridge, and his colleagues examined how efficiently yeast make proteins when under nutritional stress.

"They found that in normal cells with introns in their DNA, the introns were cut out of the messenger RNA and destroyed unless a cell was starved. When a cell was starved, those cut-out RNA introns were accumulating in the cell.

"And the team has linked this accumulation to a protein called TORC1, which regulates cell growth and the production of ribosomes. When they inhibited TORC1, introns were not destroyed anymore, Morgan says.

"This led the team to a similar conclusion as Abou Elela. “We think the ultimate way these introns are affecting cell growth is to help [suppress] ribosome production,” says Morgan.

"Although the details are different, both studies found that introns can repress the production of ribosomal proteins, helping the yeast cells to save energy when food is short.

“'I do find the core observation of both pieces convincing,” says Manuel Ares, Jr, a molecular biologist at the University of California, Santa Cruz. “It seems unlikely two groups would come to something this unexpected if it wasn’t true.'”

Comment: More and more DNA is found to be importantly functional

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More on introns function:

https://medicalxpress.com/news/2019-02-exploring-dark-side-genome.html

"Research published in PLOS Genetics, led by Alfonso Valencia, ICREA, director of the Life Sciences department of the Barcelona Supercomputing Center-National Supercomputing Center (BSC) and Dr. Daniel Rico of the Institute of Cellular Medicine, Newcastle University has analysed how introns are affected by copy number variants (CNV). CNVs are genomic variants that result in the presence (even in multiple copies) or absence of regions of the genome in different individuals.

***

"The results show that introns tend to be lost less frequently than other non-coding regions of the dark side of the genome. This suggests that there is a selective pressure to not lose them during evolution. This finding can be interpreted as a consequence of their functional importance. Confirming this hypothesis, this work has revealed that the loss of intron fragments tends to selectively exclude those parts of introns that contain known regulatory signals and therefore are more likely to affect the organism. The analysis of these regulatory signals has required the study of their organization in the three-dimensional structure of the nucleus of cells.

"Dr. Rico explained: "When we compare human genomes from different people, we see that they are way more different than we initially expected when the Human Genome Project was declared to be "completed" in 2003. One of the main contributions to these differences are the so called Copy Number Variable (CNV) regions. CNV regions are in different copy number depending on each individual, and their variability can be greater in some human populations than others. The number of copies of CNV regions can contribute to both normal phenotypic variability in the populations and susceptibility to certain diseases.

"Genes are mainly composed of exons, genomic regions with information that encode for proteins, and long stretches of DNA found between exons. Until now, most studies have focused into CNV regions that include entire genes, affecting their dosage in each individual. We discovered that CNV regions that exclusively affect introns can also affect the gene dosage of these genes. The DNA is folded inside the nucleus of cells, so exons and introns of different genes can be in close proximity of each other. Strikingly, our data also suggests that the length of certain introns can also influence the gene dosage of different genes that in their proximity, including some associated with disease."

"'The data was there, but no one had paid attention to it: as introns are not usually given importance, nobody had noticed that more than 6000 genes have introns with variable sizes in different people," comments Maria Rigau of the BSC, principal author of the paper, who adds that "the size of the genes matters, since we see a significant number of genes in which having shorter or longer introns affects the amount of RNA that is produced, which could be associated with changes in transcriptional regulation and could be related to different diseases.' "

Comment: The DNA is much more complex than originally thought. Litte is junk and 3-D relationships are very important.

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It continues as more functions are found in non-coding DNA:

https://www.sciencenews.org/article/rna-molecules-crucial-roles-human-health-disease?tg...

"RNAs, composed of strings of genetic letters called nucleotides, are best known for ferrying instructions from the genes in our DNA to ribosomes, the machines in cells that build proteins. But in the last decade or so, researchers have realized just how much more RNAs can do — how much they control, even. In particular, scientists are finding RNAs that influence health and disease yet have nothing to do with being messengers.

"The sheer number and variety of noncoding RNAs, those that don’t ferry protein-building instructions, give some clues to their importance. So far, researchers have cataloged more than 25,000 genes with instructions for noncoding RNAs in the human genome, or genetic instruction book (SN: 10/13/18, p. 5). That’s more than the estimated 21,000 or so genes that code for proteins.

"Those protein-coding genes make up less than 2 percent of the DNA in the human genome. Most of the rest of the genome is copied into noncoding RNAs, and the vast majority of those haven’t been characterized yet, says Pier Paolo Pandolfi of Boston’s Beth Israel Deaconess Medical Center. “We can’t keep studying just two volumes of the book of life. We really need to study them all.”

"Scientists no longer see the RNAs that aren’t envoys between DNA and ribosomes as worthless junk. “I believe there are hundreds, if not thousands, of noncoding RNAs that have a function,” says Harvard University molecular biologist Jeannie Lee. She and other scientists are beginning to learn what these formerly ignored molecules do. It turns out that they are involved in every step of gene activity, from turning genes on and off to tweaking final protein products. Those revelations were unthinkable 20 years ago."

Comment: The article goes on at much length to describe five different types of RNA's with functions. Apparently there is not much junk DNA and Darwinists have said if there is no junk DNA Darwin is wrong.

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Non-coding RNA is necessary to maintain chromosome integrity in cell division:

https://phys.org/news/2019-05-cell-division-requires-non-coding-rna.html

"One chromosomal element that is important for proper chromosome segregation is the centromere, a unique region of DNA on the chromosome that directs chromosome movement during cell division.

"Assistant Professor Dr. Karen Wing Yee Yuen and Postdoctoral Fellow Dr. Yick Hin Ling from the School of Biological Sciences, University of Hong Kong (HKU), discovered that centromeric DNA is used as a template to produce a non-protein coding, centromeric RNA (ribonucleic acid), that is essential for chromosome stability. If there is too much or too little centromeric RNA (cenRNA), the centromere will be defective and chromosomes will be lost.

***

"The DNA of our chromosomes codes for about 20,000 proteins. When the cell needs to produce a particular protein, such as insulin, the segment of DNA molecule coding for insulin, known as a gene, is first used as a template to copy into a RNA molecule. That RNA then serves as a recipe for directing the cells to make the specific protein. However, only 2% of our DNA is protein-coding. Yet, another 70% of our DNA is still copied into RNAs, which are not recipes to make proteins. Those are called non-coding RNA. These non-coding RNAs are once considered as "junk". In recent years, however, researches have revealed vital roles of non-coding RNA, such as in gene regulation and maintaining chromosome structure.

"Dr. Karen Wing Yee Yuen, who leads HKU's Chromosome Biology Laboratory in the School of Biological Sciences, said, "Our current study is performed in single-cell organism, the baker's yeast, but non-coding RNA copied from the DNA of the centromere is also found in multicellular organisms such as humans, mice and flies, suggesting that centromeric RNA (cenRNA) is a fundamentally important molecule that is commonly used by nature to control cell division.'"

Comment: Obviously most of DNA has a purpose.

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Another finding shows function in 'junk DNA':

https://www.sciencedaily.com/releases/2019/05/190527111726.htm

"Leveraging artificial intelligence techniques, researchers have demonstrated that mutations in so-called 'junk' DNA can cause autism. The study, published May 27 in Nature Genetics, is the first to functionally link such mutations to the neurodevelopmental condition.

***

"The analysis predicted the ramifications of genetic mutations in parts of the genome that do not encode proteins, regions often mischaracterized as 'junk' DNA. The number of autism cases linked to the noncoding mutations was comparable to the number of cases linked to protein-coding mutations that disable gene function.

"The implications of the work extend beyond autism, Troyanskaya says. "This is the first clear demonstration of non-inherited, noncoding mutations causing any complex human disease or disorder."

***

"Noncoding mutations in many of the children with autism altered gene regulation, the analysis suggested. Moreover, the results suggested that the mutations affected gene expression in the brain and genes already linked to autism, such as those responsible for neuron migration and development. "This is consistent with how autism most likely manifests in the brain," says study co-author Christopher Park, a research scientist at CCB. "It's not just the number of mutations occurring, but what kind of mutations are occurring."

"The researchers tested the effects of some of the noncoding mutations in laboratory experiments. They inserted predicted high-impact mutations found in children with autism into cells and observed the resulting changes in gene expression. These changes affirmed the model's predictions."

Comment: The point is, if a mutation can cause function in a non-coding part of DNA, it is not junk, but genetically active. Not much 'junk' in DNA

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Circular RNA's have a disposal function in cell damage:

https://www.sciencedaily.com/releases/2019/09/190920081901.htm

"The human genetic blueprint is like a string of code. To follow it, the code, or DNA, is transcribed into shorter strings of RNA. While some of these shorter strings carry instructions for making proteins -- the functional units of cells -- most RNA is not involved in protein production. Among these noncoding RNAs are the recently discovered circular RNAs, so-named because of their unusual ring shape (most other RNAs are linear).

"Circular RNAs, like other noncoding RNAs, were thought to be nonfunctional, but recent evidence suggests otherwise. Circular RNAs may in fact act like sponges to "soak up," or bind, other molecules, including microRNAs and proteins, and now, new work by researchers at the Lewis Katz School of Medicine at Temple University (LKSOM) and colleagues supports this idea. They describe, for the first time, a circular RNA that fills a critical role in tissue repair after heart attack, thanks to its ability to soak up harmful molecules.

***

"Dr. Kishore and colleagues focused their investigation on circFndc3b after finding that this particular circular RNA was significantly decreased in the heart in mice that had experienced a heart attack. "This observation led us to wonder whether the change in circFndc3b expression meant that it was important functionally in the heart," Dr. Kishore said.

"To investigate this possibility, a gene product to induce circFndc3b overexpression was injected into the heart in mice after heart attack. Subsequent examination showed that within eight weeks of injection, treated mice experienced gains in heart function and in survival compared to their untreated counterparts. There was also evidence within heart tissue that new blood vessels had started to form, greatly aiding the tissue repair process.

"The findings offer exciting insight into circular RNAs and the significance of their potential role as molecular sponges that limit the activity of damaging molecules. "CircFndc3b specifically soaked up an RNA binding protein that suppresses blood vessel formation," Dr. Kishore explained. "In doing so, it made way for new vessels to grow.'"

Comment: As before, the point Darwinists made for years is that junk DNA (non-coding DNA) proved chance evolution with much DNA useless. Obviously not true. All studies show most DNA cannot be from chance mechanisms, such as accidental mutations.

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This claims that there are overriding patterns to DNA which constitute an overall genetic code which controls DNA in a different organization and functional way:

https://www.advancedsciencenews.com/that-junk-dna-is-full-of-information/

"It should not surprise us that even in parts of the genome where we don’t obviously see a “functional” code (i.e., one that’s been evolutionarily fixed as a result of some selective advantage), there is a type of code, but not like anything we’ve previously considered as such. And what if it were doing something in three dimensions as well as the two dimensions of the ATGC code?

***

"Hence a sequence of DNA can code for a protein and, in addition, for something else. This “something else”, according to Giorgio Bernardi, is information that directs the packaging of the enormous length of DNA in a cell into the relatively tiny nucleus. Primarily it is the code that guides the binding of the DNA-packaging proteins known as histones. Bernardi refers to this as the “genomic code”—a structural code that defines the shape and compaction of DNA into the highly-condensed form known as “chromatin”.

***

"As Bernardi reviews, synthesizing his and others’ groundbreaking work, in the core sequences of the eukaryotic genome, the GC content in structural organizational units of the genome termed “isochores” increased during the evolutionary transition between so-called cold-blooded and warm-blooded organisms. And, fascinatingly, this sequence bias overlaps with sequences that are much more constrained in function: these are the very protein-coding sequences mentioned earlier, and they—more than the intervening non-coding sequences—are the clue to the “genomic code”.

***

"These regions of DNA may then be regarded as structurally important elements in forming the correct shape and separation of condensed coding sequences in the genome, regardless of any other possible function that those non-coding sequences have: in essence, this would be an “explanation” for the persistence in genomes of sequences to which no “function” (in terms of evolutionarily-selected activity), can be ascribed (or, at least, no substantial function).

"A final analogy—this time much more closely related—might be the very amino acid sequences in large proteins, which do a variety of twists, turns, folds etc. We may marvel at such complicated structures and ask “but do they need to be quite so complicated for their function?” Well, maybe they do in order to condense and position parts of the protein in the exact orientation and place that generates the three-dimensional structure that has been successfully selected by evolution. But with a knowledge that the “genomic code” overlaps protein coding sequences, we might even start to become suspicious that there is another selective pressure at work as well."

Comment: What is being described in the very complex original article are 'isochores' which are sections of the DNA which are similar in structure and are packed in chromatin as recognized sections. So we again see the 3-D aspect of DNA being critical, and the importance of 'junk' DNA as defining Darwinian evolution by chance and mistake as flying out the window, resulting in a recognition that all of DNA and its organization are most likely designed, purposeful, and not a slap-dash chance structure predicted by Darwin's theory.

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There was no comment upon the last entry on 3-D DNA, and n ow an other article with a different approach, showing how loops are arranged for by cohesin:

https://phys.org/news/2019-11-groundbreaking-cohesin-molecular-motor-genome.html

"It took many decades to identify the chromosomes as strands of DNA neatly folded into loops, and even longer to realize that DNA is folded into such structures in all cells and at all times; it took until 2019 to find out how this folding is accomplished. In a paper published by the journal Science, researchers from Jan-Michael Peters' lab at the Institute of Molecular Pathology (IMP) in Vienna have demonstrated for the first time that a molecular machine actively and purposefully folds DNA via "loop extrusion," and thereby fulfills several important functions in the interphase cell.

"That the process of looping DNA is neither random nor arbitrary is evident from how evolutionarily ancient it is. Cells of all organisms perform this function, from bacteria to humans. The primeval function of the folding mechanism is still unknown, and we may never find out, but some vital tasks have been discovered in recent years. By looping DNA, distant regions on the large molecule are brought into close proximity and are able to interact. This physical contact plays an important role in gene regulation, in which DNA segments called enhancers influence which genes are active. Looping is also essential for the ability of immune cells to produce a diverse array of antibodies.

"The team involving Davidson, a senior postdoc in the Peters lab at the IMP, was able to reconstitute cohesin function in a simplified system in vitro. Thus, he could watch how single cohesin molecules rapidly extruded single pieces of DNA into loops, exactly as Mirny and others had postulated. His findings, published online on 21 November 2019, are far-reaching and change the entire perception of the genome in several ways:

"Rather than being static, the genome is a highly dynamic structure.

"The folding of genomic DNA is an actively regulated process. It involves looping the DNA molecule by way of extrusion, with many loops in constant motion.

"The looping process is mediated by cohesin, which must therefore be a molecular motor, similar to other motor proteins such as myosin, which activates muscles.

"The cohesin molecule does not just form carabiner-like rings around DNA, but must attach to DNA dynamically via several binding sites to be able to fold it. This must also be true for a related molecule, condensin, as was shown last year.

"'This is a real paradigm shift," says IMP director Jan-Michael Peters. "Earlier observations gave us some hints, but the work of Iain Davidson is now proof. In my scientific life, few other discoveries were as far-reaching as this one.'"

Comment: More about the arrangement that allows 3-D relationships between genes that are spread over a six-foot long DNA. The packing is purposeful for it allows more close relationships than would otherwise be possible. Certainly by design.

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DAVID: There was no comment upon the last entry on 3-D DNA, and n ow an other article with a different approach, showing how loops are arranged for by cohesin:
https://phys.org/news/2019-11-groundbreaking-cohesin-molecular-motor-genome.html

DAVID: More about the arrangement that allows 3-D relationships between genes that are spread over a six-foot long DNA. The packing is purposeful for it allows more close relationships than would otherwise be possible. Certainly by design.

I can’t comment on every post, and especially on such highly technical articles! You have my blanket agreement that the complexities of cells and of all organisms represent the best possible argument for design. You also have my blanket response that as far as I am concerned, the mystery of design is not solved by the mystery of an unknown, sourceless, hidden superintelligence that is simply there and has always been there; nor is it solved by faith in chance; nor is it solved by some form of panpsychism. That is why I am an agnostic.

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DAVID: There was no comment upon the last entry on 3-D DNA, and n ow an other article with a different approach, showing how loops are arranged for by cohesin:
https://phys.org/news/2019-11-groundbreaking-cohesin-molecular-motor-genome.html

DAVID: More about the arrangement that allows 3-D relationships between genes that are spread over a six-foot long DNA. The packing is purposeful for it allows more close relationships than would otherwise be possible. Certainly by design.

dhw: I can’t comment on every post, and especially on such highly technical articles! You have my blanket agreement that the complexities of cells and of all organisms represent the best possible argument for design. You also have my blanket response that as far as I am concerned, the mystery of design is not solved by the mystery of an unknown, sourceless, hidden superintelligence that is simply there and has always been there; nor is it solved by faith in chance; nor is it solved by some form of panpsychism. That is why I am an agnostic.

Is there any point where the demonstration of design complexity in 'such highly technical articles' would convince you a designing mind is necessary? This is a key point in my thinking, as with Dr. Tour. I know design keeps you from becoming an atheist, but it is the increasing complexity that research keeps uncovering that makes me hopeful here is a tipping point that can lead to a final decision, as I stated in my first book.

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dhw: I can’t comment on every post, and especially on such highly technical articles! You have my blanket agreement that the complexities of cells and of all organisms represent the best possible argument for design. You also have my blanket response that as far as I am concerned, the mystery of design is not solved by the mystery of an unknown, sourceless, hidden superintelligence that is simply there and has always been there; nor is it solved by faith in chance; nor is it solved by some form of panpsychism. That is why I am an agnostic.

DAVID: Is there any point where the demonstration of design complexity in 'such highly technical articles' would convince you a designing mind is necessary? This is a key point in my thinking, as with Dr. Tour. I know design keeps you from becoming an atheist, but it is the increasing complexity that research keeps uncovering that makes me hopeful here is a tipping point that can lead to a final decision, as I stated in my first book.

Of course it is a key point in your thinking, and I have always accepted its logic. But for some reason you still don’t understand why I cannot take the leap of faith required to believe in the unknown, unknowable and inexplicable superintelligence described above. If you asked me how life’s complexities came into existence, and if I answered: “Blojibloji invented them,” wouldn’t you want to know a bit more about Blojibloji before you started worshipping it? The source of life’s complexities is unknown, and you don’t solve the mystery by saying the inventor of life’s complexities is unknown but if you call it God or Blojibloji, then you need look no further. Maybe the source is chance combinations of materials or rudimentary intelligences evolving. I just don’t know.

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dhw: I can’t comment on every post, and especially on such highly technical articles! You have my blanket agreement that the complexities of cells and of all organisms represent the best possible argument for design. You also have my blanket response that as far as I am concerned, the mystery of design is not solved by the mystery of an unknown, sourceless, hidden superintelligence that is simply there and has always been there; nor is it solved by faith in chance; nor is it solved by some form of panpsychism. That is why I am an agnostic.

DAVID: Is there any point where the demonstration of design complexity in 'such highly technical articles' would convince you a designing mind is necessary? This is a key point in my thinking, as with Dr. Tour. I know design keeps you from becoming an atheist, but it is the increasing complexity that research keeps uncovering that makes me hopeful here is a tipping point that can lead to a final decision, as I stated in my first book.

dhw: Of course it is a key point in your thinking, and I have always accepted its logic. But for some reason you still don’t understand why I cannot take the leap of faith required to believe in the unknown, unknowable and inexplicable superintelligence described above. If you asked me how life’s complexities came into existence, and if I answered: “Blojibloji invented them,” wouldn’t you want to know a bit more about Blojibloji before you started worshipping it? The source of life’s complexities is unknown, and you don’t solve the mystery by saying the inventor of life’s complexities is unknown but if you call it God or Blojibloji, then you need look no further. Maybe the source is chance combinations of materials or rudimentary intelligences evolving. I just don’t know.

Your answer is that you will never accept Blojibloji, despite how much information is given. We're back to Pascal's leap of faith. Fair enough.

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DAVID: Is there any point where the demonstration of design complexity in 'such highly technical articles' would convince you a designing mind is necessary? This is a key point in my thinking, as with Dr. Tour. I know design keeps you from becoming an atheist, but it is the increasing complexity that research keeps uncovering that makes me hopeful here is a tipping point that can lead to a final decision, as I stated in my first book.

dhw: Of course it is a key point in your thinking, and I have always accepted its logic. But for some reason you still don’t understand why I cannot take the leap of faith required to believe in the unknown, unknowable and inexplicable superintelligence described above. If you asked me how life’s complexities came into existence, and if I answered: “Blojibloji invented them,” wouldn’t you want to know a bit more about Blojibloji before you started worshipping it? The source of life’s complexities is unknown, and you don’t solve the mystery by saying the inventor of life’s complexities is unknown but if you call it God or Blojibloji, then you need look no further. Maybe the source is chance combinations of materials or rudimentary intelligences evolving. I just don’t know.

DAVID: Your answer is that you will never accept Blojibloji, despite how much information is given. We're back to Pascal's leap of faith. Fair enough.

How much “information” do you have about Blojibloji? Who gave it to you? Yes of course we are back to the leap of faith (I think that was Kierkegaard), or Pascal’s wager if you like.

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DAVID: Is there any point where the demonstration of design complexity in 'such highly technical articles' would convince you a designing mind is necessary? This is a key point in my thinking, as with Dr. Tour. I know design keeps you from becoming an atheist, but it is the increasing complexity that research keeps uncovering that makes me hopeful here is a tipping point that can lead to a final decision, as I stated in my first book.

dhw: Of course it is a key point in your thinking, and I have always accepted its logic. But for some reason you still don’t understand why I cannot take the leap of faith required to believe in the unknown, unknowable and inexplicable superintelligence described above. If you asked me how life’s complexities came into existence, and if I answered: “Blojibloji invented them,” wouldn’t you want to know a bit more about Blojibloji before you started worshipping it? The source of life’s complexities is unknown, and you don’t solve the mystery by saying the inventor of life’s complexities is unknown but if you call it God or Blojibloji, then you need look no further. Maybe the source is chance combinations of materials or rudimentary intelligences evolving. I just don’t know.

DAVID: Your answer is that you will never accept Blojibloji, despite how much information is given. We're back to Pascal's leap of faith. Fair enough.

dhw: How much “information” do you have about Blojibloji? Who gave it to you? Yes of course we are back to the leap of faith (I think that was Kierkegaard), or Pascal’s wager if you like.

I'll keep pouring in the info as I find it.

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Changes in gene suppression areas can callow cancer to occur:

https://www.sciencedaily.com/releases/2019/12/191205224221.htm

"A person's risk of developing cancer is affected by genetic variations in regions of DNA that don't code for proteins, previously dismissed as 'junk DNA', according to new research published in the British Journal of Cancer today (Friday).

"This new study shows that inherited cancer risk is not only affected by mutations in key cancer genes -- known as oncogenes and tumour suppressor genes -- but that variations in the DNA that controls the expression of these genes can also drive the disease.

***

"Unlike mutations in coding DNA, such as BRCA, that are rare but significantly raise a person's risk of developing cancer, non-coding SNPs are relatively common in the population but only slightly increase cancer risk.

"The team analysed whether there was a correlation between the presence of a particular SNP and the expression of particular genes. In total, they looked at over 6 million genetic variants across 13 different body tissues.

"They found that variations in the regions that regulate the expression of oncogenes and tumour suppressor genes affect cancer risk. The study also revealed that these cancer-risk SNPs tend to be specifically located in regions that regulate the immune system and tissue-specific processes -- highlighting the importance of these cellular processes to the development of cancer.

"Professor John Quackenbush, lead researcher of the study from Harvard T.H. Chan School of Public Health, said: "What we found surprised us as it had never been reported before -- our results show that small genetic variations work collectively to subtly shift the activity of genes that drive cancer. We hope that this approach could one day save lives by helping to identify people at risk of cancer, as well as other complex diseases.'"

Comment: More non-coding DNA is found to have function. The estimate from the ENCODE study of a few years ago estimated 80% percent of DNA has function. It looks more and more as correct.

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The evidence keeps piling up:

https://www.nature.com/articles/s41576-019-0196-1

"Abstract
Pseudogenes are defined as regions of the genome that contain defective copies of genes. They exist across almost all forms of life, and in mammalian genomes are annotated in similar numbers to recognized protein-coding genes. Although often presumed to lack function, growing numbers of pseudogenes are being found to play important biological roles. In consideration of their evolutionary origins and inherent limitations in genome annotation practices, we posit that pseudogenes have been classified on a scientifically unsubstantiated basis. We reflect that a broad misunderstanding of pseudogenes, perpetuated in part by the pejorative inference of the ‘pseudogene’ label, has led to their frequent dismissal from functional assessment and exclusion from genomic analyses. With the advent of technologies that simplify the study of pseudogenes, we propose that an objective reassessment of these genomic elements will reveal valuable insights into genome function and evolution."

***

"Many pseudogenes contain a frequency of mutations that render them unlikely to be (or incapable of being) translated into proteins. However, such mutations do not necessarily preclude pseudogenes from performing a biological function.

***

"Another mechanism through which pseudogenes can function is by influencing chromatin or genomic architecture. HBBP1, a pseudogene residing within the haemoglobin locus, enables the dynamic chromatin changes that regulate expression of fetal and adult globin genes during development. Notably, although inhibiting HBBP1 transcription has no effect, deletion of the genomic locus reactivates fetal globin expression. HBBP1 DNA contacts, but not transcription, are required for suppressing the expression of fetal globin genes in adult erythroid cells.

***

"The examples of pseudogene function elaborated on here should not imply that pseudogene functionality is likely to be confined to isolated instances. At least 15% of pseudogenes are transcriptionally active across three phyla, many of which are proximal to conserved regulatory regions. It is estimated that at least 63 new human-specific protein-coding genes were formed by retrotransposition since the divergence from other primates. Numerous ‘retrogenes’ continue to be recognized as functional protein-coding genes rather than pseudogenes across species. High-throughput mass spectrometry and ribosomal profiling approaches have identified hundreds of pseudogenes that are translated into peptides. Although the functions of these peptides remain to be experimentally determined, such examples illustrate the challenge in substantiating a gene–pseudogene dichotomy.

***

"In addition to the demotivation into exploring pseudogene function by the a priori assumption that they are functionless, their systematic study has also been hindered by a lack of robust methodologies capable of distinguishing the biological activities of pseudogenes from the functions of the genes from which they are derived."

Comment: More evidence that even Darwinist scientist are recognizing their mistake in not looking carefully at genes and portions of the genome that do not simply code for protein. Most of DNA is not junk (about 80%) and removes a 'proof' for random discarded mutations and other stretches of DNA as the backbone of Darwinian style of evolution. If not by chance, then design is required.

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A possible control gene is found in the'junk':

https://medicalxpress.com/news/2020-02-discovery-illuminate-link-atherosclerosis-aging....

"Investigators from Brigham and Women's Hospital have made a potentially exciting discovery by jumping into the abyss of the dark side of the genome. Once dismissed as "junk DNA," roughly 75 percent of the human genome do not code for proteins. But these dark regions of the genome are far from junk—instead, they may hold tantalizing clues about disease states. A team of Brigham investigators led by Mark Feinberg, MD, of the Division of Cardiovascular Medicine, and an associate professor of Medicine at Harvard Medical School, recently plunged into these regions in search of clues about atherosclerosis—a disease in which the arteries become increasingly hardened and narrow, obstructing blood flow and leading to heart disease. Using a preclinical model of atherosclerosis, Feinberg and colleagues have uncovered a long, noncoding RNA (lncRNA) that may point the way toward new therapies for atherosclerosis and shed light on why the likelihood of the disease increases with age.

"'We have identified a new actor in controlling aging in the vessel wall and, surprisingly, it's not a traditional gene or protein. It's part of the non-coding genome. That was unexpected," said Feinberg. "We know a lot about the importance of cholesterol and inflammation in heart disease, but this is a new, additional pathway. We need to think carefully about how it might impact the development of therapeutics for cardiovascular disease."

"Feinberg and colleagues used a mouse model of atherosclerosis in which mice begin to develop atherosclerotic lesions at 12 weeks. The investigators isolated RNA from the inner-most lining of the blood vessel wall and looked across the entire genome at all RNAs, searching for which ones had changes in activity during disease progression or regression. One of the most dynamic was SNHG12, a long stretch of RNA that does not code for a protein but is found across multiple species, including humans, pigs and mice.

"To better understand SNHG12's role, the researchers conducted experiments in which they either knocked down its activity or ramped it up. They found that less SNHG12 led to a profound increase in atherosclerosis but more SNHG12 dramatically reduced disease progression. To understand what SNHG12 was doing, the team looked for who its partners were. One of them turned out to be a molecule involved with DNA damage repair and aging. Without these partners working together, vessel walls became leaky and permeable to bad cholesterol. The team could reverse this phenomenon by adding a small molecule that promotes DNA damage repair, suggesting a potential therapeutic avenue to pursue."

Comment: Aspectx of aging must be under genome control, as this shows. Another blow against the theory of junk DNA proving Darwin. at least 80% of DNA has functions. It is not a wasteland of trail and error formed by chance mutations.

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DAVID: Aspectx of aging must be under genome control, as this shows. Another blow against the theory of junk DNA proving Darwin. at least 80% of DNA has functions. It is not a wasteland of trail and error formed by chance mutations.

Just to restore the balance, as usual: if something is useful, it is likely to survive. If it is not useful, it is likely to disappear. The process is called natural selection.

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DAVID: Aspectx of aging must be under genome control, as this shows. Another blow against the theory of junk DNA proving Darwin. at least 80% of DNA has functions. It is not a wasteland of trail and error formed by chance mutations.

dhw: Just to restore the balance, as usual: if something is useful, it is likely to survive. If it is not useful, it is likely to disappear. The process is called natural selection.

If DNA is not helter-skelter, it makes a wonderful case for design.

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A new highly technical article on mutation load negates his arguments:

https://evolutionnews.org/2020/05/paper-shows-that-mutational-load-arguments-dont-refut...

"Perhaps one of ENCODE’s staunchest critics has been Dan Graur, a molecular evolutionary biologist at the University of Houston. He argued in 2017 in the journal Genome, Biology and Evolution that ENCODE’s empirically based conclusions could not possibly be correct because “Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 15%.” What exactly is “mutational load”?

"Mutational load is based upon the principal that populations of organisms can only tolerate a certain number of deleterious mutations before they reach a critical level and the population crashes. If every element of a genome is functional, then every possible mutation stands to have a non-neutral effect, and could be potentially deleterious. But if only a small portion of the genome is functional, then most mutations will happen to occur in functionally unimportant regions, and this spreads out mutations in a manner that greatly decreases the likelihood of experiencing a deleterious mutation. Thus, when your genome is filled with “junk,” you can tolerate a much higher “mutational load.”

***

"because now in 2020 serious criticisms have been made of the assumptions in Graur’s “mutational load” arguments. Recently three scientists writing in the journal Genome Biology and Evolution noted that these arguments wrongly assume that there could potentially exist a person with no deleterious mutations in their genome:

"Our approach is different from previous work that compared mean fitness at mutation-selection equilibrium with the fitness of an individual who has no deleterious mutations; we show that such an individual is exceedingly unlikely to exist. We find that the functional fraction is not very likely to be limited substantially by mutational load, and that any such limit, if it exists, depends strongly on the selection coefficients of new deleterious mutations.

"By comparing the population mean fitness at mutation-selection equilibrium to that of an individual who possesses no deleterious mutations, Graur (2017) reached the conclusion that, for likely values of the human per-base deleterious mutation rate, the functional fraction must be small.

***

"We conclude — while making no claims about the actual functional fraction as determined by comparative studies—that a mutational load argument is unlikely to set a low limit on the functional fraction of the human genome, and that any attempt to set such a limit must take into account the fitness effects of new deleterious mutations.

***

"Graur is an eminent scientist — about whom the journal Science said, “Graur’s atheism inflamed his anger at ENCODE.” In an online talk, Graur explained what’s at stake:

"If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome. If, on the other hand, organisms are designed, then all DNA, or as much as possible, is expected to exhibit function. If ENCODE is right, then evolution is wrong. (my bold)

"He then admits in the talk that his goal is to “Kill ENCODE.”

"Dr. Graur should be commended for his honesty, which makes clear that there’s a lot at stake here. We should not expect ENCODE-critics to go away quietly. But if this latest paper indicates anything, it’s that “mutational load” arguments aren’t the ENCODE-killers that they have been made out to be."

Comment: The 'no junk DNA' is important for atheists to fight as Graur explains. Despite Darwin's later protestations following his first edition that God did it, atheists need his natural evolution theory to stay intact.

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QUOTES: "If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome. If, on the other hand, organisms are designed, then all DNA, or as much as possible, is expected to exhibit function. If ENCODE is right, then evolution is wrong. (David’s bold)

"He then admits in the talk that his goal is to “Kill ENCODE.”

DAVID: The 'no junk DNA' is important for atheists to fight as Graur explains. Despite Darwin's later protestations following his first edition that God did it, atheists need his natural evolution theory to stay intact.

We have discussed this over and over again. If ENCODE is right, and there is no junk, any self-respecting atheist should be able to say: there you are, natural selection ensures that only useful things survive. And just to keep the record clear: Darwin was an agnostic, and there is absolutely nothing in his theory of evolution that precludes the existence of God. Atheists are as guilty as theists in their constant misuse of that theory.

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QUOTES: "If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome. If, on the other hand, organisms are designed, then all DNA, or as much as possible, is expected to exhibit function. If ENCODE is right, then evolution is wrong. (David’s bold)

"He then admits in the talk that his goal is to “Kill ENCODE.”

DAVID: The 'no junk DNA' is important for atheists to fight as Graur explains. Despite Darwin's later protestations following his first edition that God did it, atheists need his natural evolution theory to stay intact.

dhw: We have discussed this over and over again. If ENCODE is right, and there is no junk, any self-respecting atheist should be able to say: there you are, natural selection ensures that only useful things survive. And just to keep the record clear: Darwin was an agnostic, and there is absolutely nothing in his theory of evolution that precludes the existence of God. Atheists are as guilty as theists in their constant misuse of that theory.

You miss Graur's point. His atheism is based on chance as the only cause of evolution so there MUST be junk DNA which proves that point. I doubt there are atheists who think as you do.

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QUOTES: "If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome. If, on the other hand, organisms are designed, then all DNA, or as much as possible, is expected to exhibit function. If ENCODE is right, then evolution is wrong." (David’s bold)

"He then admits in the talk that his goal is to “Kill ENCODE.”

DAVID: The 'no junk DNA' is important for atheists to fight as Graur explains. Despite Darwin's later protestations following his first edition that God did it, atheists need his natural evolution theory to stay intact.

dhw: We have discussed this over and over again. If ENCODE is right, and there is no junk, any self-respecting atheist should be able to say: there you are, natural selection ensures that only useful things survive. And just to keep the record clear: Darwin was an agnostic, and there is absolutely nothing in his theory of evolution that precludes the existence of God. Atheists are as guilty as theists in their constant misuse of that theory.

DAVID: You miss Graur's point. His atheism is based on chance as the only cause of evolution so there MUST be junk DNA which proves that point. I doubt there are atheists who think as you do.

You miss my point. If he is trying to prove that chance created life by rubbishing ENCODE’s findings, he won’t have much of a case, will he? Now please tell me what is wrong with my argument.

3269 views

QUOTES: "If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome. If, on the other hand, organisms are designed, then all DNA, or as much as possible, is expected to exhibit function. If ENCODE is right, then evolution is wrong." (David’s bold)

"He then admits in the talk that his goal is to “Kill ENCODE.”

DAVID: The 'no junk DNA' is important for atheists to fight as Graur explains. Despite Darwin's later protestations following his first edition that God did it, atheists need his natural evolution theory to stay intact.

dhw: We have discussed this over and over again. If ENCODE is right, and there is no junk, any self-respecting atheist should be able to say: there you are, natural selection ensures that only useful things survive. And just to keep the record clear: Darwin was an agnostic, and there is absolutely nothing in his theory of evolution that precludes the existence of God. Atheists are as guilty as theists in their constant misuse of that theory.

DAVID: You miss Graur's point. His atheism is based on chance as the only cause of evolution so there MUST be junk DNA which proves that point. I doubt there are atheists who think as you do.

dhw: You miss my point. If he is trying to prove that chance created life by rubbishing ENCODE’s findings, he won’t have much of a case, will he? Now please tell me what is wrong with my argument.

You are missing Graur's point. The key to his argument is chance mutations should fill DNA if most of them were useless and abandoned by natural selection.

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QUOTE: "If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome. If, on the other hand, organisms are designed, then all DNA, or as much as possible, is expected to exhibit function. If ENCODE is right, then evolution is wrong." (David’s bold)

DAVID: The 'no junk DNA' is important for atheists to fight as Graur explains. Despite Darwin's later protestations following his first edition that God did it, atheists need his natural evolution theory to stay intact.

dhw: We have discussed this over and over again. If ENCODE is right, and there is no junk, any self-respecting atheist should be able to say: there you are, natural selection ensures that only useful things survive.

DAVID: You are missing Graur's point. The key to his argument is chance mutations should fill DNA if most of them were useless and abandoned by natural selection.

You are missing your own point! You bolded: "if ENCODE is right, evolution is wrong", and you said that junk DNA was important for atheists and Graur’s atheism “is based on chance as the only cause of evolution so there MUST be junk DNA which proves that point.” In other words, if ENCODE is right, there is no junk, Graur is wrong, and evolution and atheism are wrong! Now please tell me what is wrong with my bolded argument above – i.e. that whatever was useless WAS abandoned by natural selection.

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QUOTE: "If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome. If, on the other hand, organisms are designed, then all DNA, or as much as possible, is expected to exhibit function. If ENCODE is right, then evolution is wrong." (David’s bold)

DAVID: The 'no junk DNA' is important for atheists to fight as Graur explains. Despite Darwin's later protestations following his first edition that God did it, atheists need his natural evolution theory to stay intact.

dhw: We have discussed this over and over again. If ENCODE is right, and there is no junk, any self-respecting atheist should be able to say: there you are, natural selection ensures that only useful things survive.

DAVID: You are missing Graur's point. The key to his argument is chance mutations should fill DNA if most of them were useless and abandoned by natural selection.

dhw: You are missing your own point! You bolded: "if ENCODE is right, evolution is wrong", and you said that junk DNA was important for atheists and Graur’s atheism “is based on chance as the only cause of evolution so there MUST be junk DNA which proves that point.” In other words, if ENCODE is right, there is no junk, Graur is wrong, and evolution and atheism are wrong! Now please tell me what is wrong with my bolded argument above – i.e. that whatever was useless WAS abandoned by natural selection.

You are right and a mistake by me fooled you. The bold in my original statement should read "if encode is right, then any theory that evolution was naturally caused is wrong." Your bolded comment is correct but off the point also.

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QUOTE: "[…] If ENCODE is right, then evolution is wrong." (David’s bold)

DAVID: The 'no junk DNA' is important for atheists to fight as Graur explains. Despite Darwin's later protestations following his first edition that God did it, atheists need his natural evolution theory to stay intact.

dhw: We have discussed this over and over again. If ENCODE is right, and there is no junk, any self-respecting atheist should be able to say: there you are, natural selection ensures that only useful things survive.

DAVID: You are missing Graur's point. The key to his argument is chance mutations should fill DNA if most of them were useless and abandoned by natural selection.

dhw: You are missing your own point! You bolded: "if ENCODE is right, evolution is wrong", and you said that junk DNA was important for atheists and Graur’s atheism “is based on chance as the only cause of evolution so there MUST be junk DNA which proves that point.” In other words, if ENCODE is right, there is no junk, Graur is wrong, and evolution and atheism are wrong! Now please tell me what is wrong with my bolded argument above – i.e. that whatever was useless WAS abandoned by natural selection.

DAVID: You are right and a mistake by me fooled you. The bold in my original statement should read "if encode is right, then any theory that evolution was naturally caused is wrong." Your bolded comment is correct but off the point also.

Then what on earth was the point of raising the subject of Graur and ENCODE in the first place? You are trying to prove that atheists have got it wrong. Now please tell me what is wrong with my bolded response.

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QUOTE: "[…] If ENCODE is right, then evolution is wrong." (David’s bold)

DAVID: The 'no junk DNA' is important for atheists to fight as Graur explains. Despite Darwin's later protestations following his first edition that God did it, atheists need his natural evolution theory to stay intact.

dhw: We have discussed this over and over again. If ENCODE is right, and there is no junk, any self-respecting atheist should be able to say: there you are, natural selection ensures that only useful things survive.

DAVID: You are missing Graur's point. The key to his argument is chance mutations should fill DNA if most of them were useless and abandoned by natural selection.

dhw: You are missing your own point! You bolded: "if ENCODE is right, evolution is wrong", and you said that junk DNA was important for atheists and Graur’s atheism “is based on chance as the only cause of evolution so there MUST be junk DNA which proves that point.” In other words, if ENCODE is right, there is no junk, Graur is wrong, and evolution and atheism are wrong! Now please tell me what is wrong with my bolded argument above – i.e. that whatever was useless WAS abandoned by natural selection.

DAVID: You are right and a mistake by me fooled you. The bold in my original statement should read "if encode is right, then any theory that evolution was naturally caused is wrong." Your bolded comment is correct but off the point also.

dhw: Then what on earth was the point of raising the subject of Graur and ENCODE in the first place? You are trying to prove that atheists have got it wrong. Now please tell me what is wrong with my bolded response.

The problem is you. I told you it was off the point of the so-called importance of junk DNA to a small group of very vocal atheists who must have junk DNA to support their atheism. It shows the fanaticism involved. They should become reasoned agnostics like you.

3278 views

QUOTE: "[…] If ENCODE is right, then evolution is wrong." (David’s bold)

dhw: We have discussed this over and over again. If ENCODE is right, and there is no junk, any self-respecting atheist should be able to say: there you are, natural selection ensures that only useful things survive.
[…]
DAVID: The bold in my original statement should read "if encode is right, then any theory that evolution was naturally caused is wrong." Your bolded comment is correct but off the point also.

dhw: Then what on earth was the point of raising the subject of Graur and ENCODE in the first place? You are trying to prove that atheists have got it wrong. Now please tell me what is wrong with my bolded response.

DAVID: The problem is you. I told you it was off the point of the so-called importance of junk DNA to a small group of very vocal atheists who must have junk DNA to support their atheism. It shows the fanaticism involved. They should become reasoned agnostics like you.

I’m not sure why this makes me a problem, but I presume that your kind compliment means you accept my reasoning and we can now put to bed the argument that ENCODE disproves Darwinian evolution.

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QUOTE: "[…] If ENCODE is right, then evolution is wrong." (David’s bold)

dhw: We have discussed this over and over again. If ENCODE is right, and there is no junk, any self-respecting atheist should be able to say: there you are, natural selection ensures that only useful things survive.
[…]
DAVID: The bold in my original statement should read "if encode is right, then any theory that evolution was naturally caused is wrong." Your bolded comment is correct but off the point also.

dhw: Then what on earth was the point of raising the subject of Graur and ENCODE in the first place? You are trying to prove that atheists have got it wrong. Now please tell me what is wrong with my bolded response.

DAVID: The problem is you. I told you it was off the point of the so-called importance of junk DNA to a small group of very vocal atheists who must have junk DNA to support their atheism. It shows the fanaticism involved. They should become reasoned agnostics like you.

dhw: I’m not sure why this makes me a problem, but I presume that your kind compliment means you accept my reasoning and we can now put to bed the argument that ENCODE disproves Darwinian evolution.

It leaves us with the conclusion that DNA looks like a designed code, which throws out the Darwin insistence on chance mutation. All we have left from Darwin definitely is common descent and the probabilistic theory about natural selection, which logically sounds good, but is not proven as a sorting mechanism to somehow advance evolution through its choices. Since it is a judge looking at what organisms appear on the scene, the arrival of new forms is not explained by Darwin. All of this lies behind the junk or almost-no-junk argument. You should agree with this analysis.

3271 views

QUOTE: "[…] If ENCODE is right, then evolution is wrong." (David’s bold)

dhw: We have discussed this over and over again. If ENCODE is right, and there is no junk, any self-respecting atheist should be able to say: there you are, natural selection ensures that only useful things survive[/i].
[…]
DAVID: The bold in my original statement should read "if encode is right, then any theory that evolution was naturally caused is wrong." Your bolded comment is correct but off the point also.

dhw: Then what on earth was the point of raising the subject of Graur and ENCODE in the first place? You are trying to prove that atheists have got it wrong. Now please tell me what is wrong with my bolded response.

DAVID: The problem is you. I told you it was off the point of the so-called importance of junk DNA to a small group of very vocal atheists who must have junk DNA to support their atheism. It shows the fanaticism involved. They should become reasoned agnostics like you.

dhw: I’m not sure why this makes me a problem, but I presume that your kind compliment means you accept my reasoning and we can now put to bed the argument that ENCODE disproves Darwinian evolution.

DAVID: It leaves us with the conclusion that DNA looks like a designed code, which throws out the Darwin insistence on chance mutation. All we have left from Darwin definitely is common descent and the probabilistic theory about natural selection, which logically sounds good, but is not proven as a sorting mechanism to somehow advance evolution through its choices. Since it is a judge looking at what organisms appear on the scene, the arrival of new forms is not explained by Darwin. All of this lies behind the junk or almost-no-junk argument. You should agree with this analysis.

Yes, I do, but you have left the ENCODE argument far behind and have focused on the overall argument for design! ENCODE is strictly limited to proving that there is no junk. That would demolish the atheists’ argument that a designer would not have left any junk behind. But it does not demolish the atheists’ belief in Darwin’s theory of chance mutations, because no matter what caused the changes leading to speciation, they can argue that natural selection would have removed any unnecessary material.

3284 views

QUOTE: "[…] If ENCODE is right, then evolution is wrong." (David’s bold)

dhw: We have discussed this over and over again. If ENCODE is right, and there is no junk, any self-respecting atheist should be able to say: there you are, natural selection ensures that only useful things survive[/i].
[…]
DAVID: The bold in my original statement should read "if encode is right, then any theory that evolution was naturally caused is wrong." Your bolded comment is correct but off the point also.

dhw: Then what on earth was the point of raising the subject of Graur and ENCODE in the first place? You are trying to prove that atheists have got it wrong. Now please tell me what is wrong with my bolded response.

DAVID: The problem is you. I told you it was off the point of the so-called importance of junk DNA to a small group of very vocal atheists who must have junk DNA to support their atheism. It shows the fanaticism involved. They should become reasoned agnostics like you.

dhw: I’m not sure why this makes me a problem, but I presume that your kind compliment means you accept my reasoning and we can now put to bed the argument that ENCODE disproves Darwinian evolution.

DAVID: It leaves us with the conclusion that DNA looks like a designed code, which throws out the Darwin insistence on chance mutation. All we have left from Darwin definitely is common descent and the probabilistic theory about natural selection, which logically sounds good, but is not proven as a sorting mechanism to somehow advance evolution through its choices. Since it is a judge looking at what organisms appear on the scene, the arrival of new forms is not explained by Darwin. All of this lies behind the junk or almost-no-junk argument. You should agree with this analysis.

dhw: Yes, I do, but you have left the ENCODE argument far behind and have focused on the overall argument for design! ENCODE is strictly limited to proving that there is no junk. That would demolish the atheists’ argument that a designer would not have left any junk behind. But it does not demolish the atheists’ belief in Darwin’s theory of chance mutations, because no matter what caused the changes leading to speciation, they can argue that natural selection would have removed any unnecessary material.

What causes my confusion is your bolded and oft repeated comment. Natural selection removes failed species, but does not affect DNA code. ENCODE says there are very few chance mutations

3278 views

DAVID: It leaves us with the conclusion that DNA looks like a designed code, which throws out the Darwin insistence on chance mutation. All we have left from Darwin definitely is common descent and the probabilistic theory about natural selection, which logically sounds good, but is not proven as a sorting mechanism to somehow advance evolution through its choices. Since it is a judge looking at what organisms appear on the scene, the arrival of new forms is not explained by Darwin. All of this lies behind the junk or almost-no-junk argument. You should agree with this analysis.

dhw: Yes, I do, but you have left the ENCODE argument far behind and have focused on the overall argument for design! ENCODE is strictly limited to proving that there is no junk. That would demolish the atheists’ argument that a designer would not have left any junk behind. But it does not demolish the atheists’ belief in Darwin’s theory of chance mutations, because no matter what caused the changes leading to speciation, they can argue that natural selection would have removed any unnecessary material.

DAVID: What causes my confusion is your bolded and oft repeated comment. Natural selection removes failed species, but does not affect DNA code. ENCODE says there are very few chance mutations.

A very sudden switch of argument! I’m not going to pretend to understand the science, but I strongly object to the suggestion that “natural selection” can only be applied to species. It works in any number of contexts. As I understand it, ENCODE’s task is to find out the functions of all the different parts of the genome. Since the genomes of different species have different numbers/sequences/ functions, and you believe in common descent, I can’t see any reason why you should assume that the inner workings of the cell communities of which all organisms consist have not undergone a continuous process of changing numbers/sequences/ functions, which survive or don’t survive according to natural selection. Unless you can prove otherwise, our atheists can carry on using natural selection as a reason for the absence of junk.

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DAVID: What causes my confusion is your bolded and oft repeated comment. Natural selection removes failed species, but does not affect DNA code. ENCODE says there are very few chance mutations.

dhw: A very sudden switch of argument! I’m not going to pretend to understand the science, but I strongly object to the suggestion that “natural selection” can only be applied to species. It works in any number of contexts. As I understand it, ENCODE’s task is to find out the functions of all the different parts of the genome. Since the genomes of different species have different numbers/sequences/ functions, and you believe in common descent, I can’t see any reason why you should assume that the inner workings of the cell communities of which all organisms consist have not undergone a continuous process of changing numbers/sequences/ functions, which survive or don’t survive according to natural selection. Unless you can prove otherwise, our atheists can carry on using natural selection as a reason for the absence of junk.

Talk about a switch. Natural selection works at the level of living organisms. Changes in the DNA depends upon who survives and that they pass on their specific code to progeny. Natural selection is an active judge of what is presented to it but is a passive producer of evolution in that strict sense. You seem to imply DNA change is an active cellular process all by itself. There are many reasons for mutations, but cells don't just purposely churn them out. Darwin's' view is chance accidental mutations are the source of evolution and as such the junk proponents are sure the DNA must contain lots of remnants of discarded genes. Why is Graur so distressed if logically he can use your argument?

3282 views

DAVID: What causes my confusion is your bolded and oft repeated comment. Natural selection removes failed species, but does not affect DNA code. ENCODE says there are very few chance mutations.

dhw: A very sudden switch of argument! I’m not going to pretend to understand the science, but I strongly object to the suggestion that “natural selection” can only be applied to species. It works in any number of contexts. As I understand it, ENCODE’s task is to find out the functions of all the different parts of the genome. Since the genomes of different species have different numbers/sequences/ functions, and you believe in common descent, I can’t see any reason why you should assume that the inner workings of the cell communities of which all organisms consist have not undergone a continuous process of changing numbers/sequences/ functions, which survive or don’t survive according to natural selection. Unless you can prove otherwise, our atheists can carry on using natural selection as a reason for the absence of junk.

DAVID: Talk about a switch. Natural selection works at the level of living organisms.

It can work in lots of other contexts, but in any case cells are living organisms.

DAVID: Changes in the DNA depends upon who survives and that they pass on their specific code to progeny. Natural selection is an active judge of what is presented to it but is a passive producer of evolution in that strict sense.

Of course it’s passive in that sense. And of course permanent changes in the genome will depend on who survives – that is the role of natural selection. It doesn’t create the changes, it determines which changes survive. And I am pointing out that if there is no junk, your atheist can argue that whenever there was a change, whatever was not needed did not survive.

DAVID: You seem to imply DNA change is an active cellular process all by itself. There are many reasons for mutations, but cells don't just purposely churn them out. Darwin's' view is chance accidental mutations are the source of evolution and as such the junk proponents are sure the DNA must contain lots of remnants of discarded genes. Why is Graur so distressed if logically he can use your argument?

We are discussing the theory of cellular intelligence (Shapiro’s “natural genetic engineering”) elsewhere, and I know what the junk proponents are saying. And if there is no junk, they are wrong. You have not offered a single logical objection to my proposal. You will have to ask Graur why he doesn’t use the argument.

3268 views

DAVID: Changes in the DNA depends upon who survives and that they pass on their specific code to progeny. Natural selection is an active judge of what is presented to it but is a passive producer of evolution in that strict sense.

dhw: Of course it’s passive in that sense. And of course permanent changes in the genome will depend on who survives – that is the role of natural selection. It doesn’t create the changes, it determines which changes survive. And I am pointing out that if there is no junk, your atheist can argue that whenever there was a change, whatever was not needed did not survive.

DAVID: You seem to imply DNA change is an active cellular process all by itself. There are many reasons for mutations, but cells don't just purposely churn them out. Darwin's' view is chance accidental mutations are the source of evolution and as such the junk proponents are sure the DNA must contain lots of remnants of discarded genes. Why is Graur so distressed if logically he can use your argument?

dhw: We are discussing the theory of cellular intelligence (Shapiro’s “natural genetic engineering”) elsewhere, and I know what the junk proponents are saying. And if there is no junk, they are wrong. You have not offered a single logical objection to my proposal. You will have to ask Graur why he doesn’t use the argument.

The history of this point is that a key argument by Darwinists was the junk theory. As Encode and its general acceptance shows that it has been pushed into a corner where a few furious proponents are fighting a rear guard action. I've been explaining how their thinking goes, and as it is destroyed, what is happening is more support for the design argument. Your comment is an exhibit of your clear thinking.

3271 views

DAVID: You seem to imply DNA change is an active cellular process all by itself. There are many reasons for mutations, but cells don't just purposely churn them out. Darwin's' view is chance accidental mutations are the source of evolution and as such the junk proponents are sure the DNA must contain lots of remnants of discarded genes. Why is Graur so distressed if logically he can use your argument?

dhw: We are discussing the theory of cellular intelligence (Shapiro’s “natural genetic engineering”) elsewhere, and I know what the junk proponents are saying. And if there is no junk, they are wrong. You have not offered a single logical objection to my proposal. You will have to ask Graur why he doesn’t use the argument.

DAVID: The history of this point is that a key argument by Darwinists was the junk theory. As Encode and its general acceptance shows that it has been pushed into a corner where a few furious proponents are fighting a rear guard action. I've been explaining how their thinking goes, and as it is destroyed, what is happening is more support for the design argument. Your comment is an exhibit of your clear thinking.

Thank you.

3284 views

New techniques elicit more understanding:

https://phys.org/news/2020-05-technology-rna-gene.html

"It was previously believed that RNA functions mostly as an intermediary in building proteins based on a DNA template (fig. 1a), with very rare exceptions such as ribosomal RNAs. However, with the development of genomic analysis, it turned out that not all DNA regions encode RNA, and not all transcribed RNA encodes proteins.

"Although the number of noncoding RNAs and those that encode proteins is about the same, the function of most noncoding RNA is still not entirely clear.

"Scientists are now coming to the conclusion that RNA is one of the factors that determine which genes are expressed, or active.

"Long noncoding RNAs are known to interact with chromatin—DNA tightly packaged with proteins (fig. 1b). Chromatin has the ability to change its conformation, or "shape," so that certain genes are either exposed for transcription or concealed. Long noncoding RNAs contribute to this conformation change and the resulting change in gene activity by interacting with certain chromatin regions. To understand the regulatory potential of RNA—in addition to it being a template for protein synthesis—it is important to know which chromatin region any given RNA interacts with.

"RNAs interact with chromatin inside the cell nucleus by binding to chromatin-associated proteins that fold a DNA molecule.

***

"The research confirmed that long noncoding RNAs play an important role in the regulation of gene expression occurring at a considerable distance from the regulated gene.

"This technology can also be used to study cell type-specific RNA-chromatin interactions. The scientists proved it by looking at two noncoding RNAs in a mouse cell, one of them possibly associated with schizophrenia. They found that an interaction pattern between chromatin and those RNAs in two different cells—the embryonic stem cell and the oligodendrocyte progenitor cell—correlated with preferential gene expression in those cell types.

***

"The analysis performed by bioinformaticians from the Research Center of Biotechnology and MIPT showed that not only the standard double helix interactions between DNA and RNA but also those involving RNA-DNA triplexes could participate in gene regulation. Also, such interactions highlight the significance of noncoding RNA in protein targeting to particular gene loci."

Comment: Bit by bit the layers of the genome onion are being uncovered and it turns out to be complexly designed.

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" A spatial understanding of how DNA is packaged into a cell, and of the 3D folding that positions genes in close contact with their regulatory elements(emphasis mine), will be key to predicting an element's target genes. The NIH Common Fund has begun the '4D Nucleome' project, for instance, which aims to predict the target genes for every regulatory element. That knowledge will help to fill in the picture of how a given regulatory element influences health and disease."

I know this is an old post, but a particular line caught my eye. What regulates the protein folding spatially? What puts the protein in close proximity to the right regulatory section? How is the information of that spatial awareness stored?

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

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" A spatial understanding of how DNA is packaged into a cell, and of the 3D folding that positions genes in close contact with their regulatory elements(emphasis mine), will be key to predicting an element's target genes. The NIH Common Fund has begun the '4D Nucleome' project, for instance, which aims to predict the target genes for every regulatory element. That knowledge will help to fill in the picture of how a given regulatory element influences health and disease."

Tony: I know this is an old post, but a particular line caught my eye. What regulates the protein folding spatially? What puts the protein in close proximity to the right regulatory section? How is the information of that spatial awareness stored?

Try this previous entry: Thursday, April 30, 2020, 21:28

https://phys.org/news/2020-04-hidden-symmetry-chemical-kinetic-equations.html

"In each case, the researchers demonstrated that a simple mathematical ratio shows that the likelihood of errors is controlled by kinetics rather than thermodynamics.

"'It could be a protein folding into the correct versus the incorrect conformation, an enzyme incorporating the right versus the wrong amino acid into the polypeptide chain, or a motor protein mistakenly stepping backward instead of going forward," said Igoshin, a CTBP investigator and professor of bioengineering at Rice. "All of those properties can be expressed as a ratio of two steady-state fluxes, and we found that biological properties expressed in these terms are under kinetic control."

***

"Before it folds, a protein has energy, like a ball sitting atop a hill. Folding is the downhill run from this high-energy starting point to the place where the ball stops rolling. Chemists often use a visual aid called a "free-energy landscape" to chart energy levels in chemical reactions. The landscape looks like a mountain range with peaks and valleys, and the downhill run from a protein's unfolded starting point to its fully folded finishing point can look like a mountain road that winds through a series of valleys. Even if one town along the road is lower in elevation, a traveler might have to climb hills to get from one valley to the next on the way downhill.

"'We've shown it's the barriers, the high points between valleys, that determine these ratios," Igoshin said. "The depths of the valleys don't matter.

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A new study finding junk is not junk:

https://phys.org/news/2020-06-dark-dna-vital-rice-reproduction.html

"Researchers from the Okinawa Institute of Science and Technology Graduate University (OIST) have shed light on the reproductive role of 'dark matter' DNA—non-coding DNA sequences that previously seemed to have no function.

"Their findings, published today in Nature Communications, have revealed that a specific non-coding genomic region is essential for the proper development of the male and female reproductive organs in rice.

***

"The vast expanse of this 'junk DNA' has long puzzled biologists, with many dubbing it the 'dark matter' of the genome. But recent research suggests that many of these non-coding genomic regions may have a function after all, giving rise to non-coding RNA.

***

"Dr. Komiya's group therefore proposes that the Argonaute proteins may interact with microRNA2118 to trigger production of the secondary small RNAs. The proteins may also interact with the secondary small RNAs to silence specific regions of the genome. The team hopes to elucidate exactly how the Argonaute proteins and secondary small RNAs affect development of the plant reproductive system in further research.

"'Reproduction is an important phenomenon of passing genetic information to the next generation and is essential for maintaining a stable yield supply. However, development of the reproductive system is complicated, and many aspects remain unknown," concluded Dr. Komiya. "This study shows that non-coding RNAs, derived from regions of the genome that were thought to be non-functional, are vital for plant reproduction. Exploring non-coding RNAs further is an exciting and important area of research."

Comment: continuing confirmation there is very little junk in DNA

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It is very active in many processes:

https://evolutionnews.org/2020/06/in-new-research-rna-takes-center-stage/

"Long thought to be a mere template for transcription and translation of DNA with the names messenger RNA (mRNA) and transfer RNA (tRNA), RNA with its more transient lifetime serves many other functions that have been coming to light in the 21st century. New terms are being added to the vocabulary of epigenetics: among them, long noncoding RNA (lncRNA), micro-RNA (miRNA), dietary RNA, and extracellular RNA (exRNA).

***

"RNA is not only a linear copy of the genetic information, but often folds into complex structures. The combination of single-stranded and partially folded double-stranded regions is of central importance for the function and stability of RNAs. “If we want to learn something about RNAs, we must also understand their structure,” says Franz Narberhaus.

***

"The regulatory functions of miRNAs usually take place in the cytoplasm, where they interact with target RNA transcripts to inhibit their translation into protein or promote their decay...By investigating a miRNA named miR-126-5p, Weber’s team demonstrates that this molecule can unexpectedly be transferred into the cell nucleus and, by simply interacting with it, suppresses the activity of an enzyme, named caspase-3, which is responsible for killing the cell by programmed cell death. In this way, the molecule protects vascular integrity and reduces the extent of atherosclerotic lesions.

***

" So fascinating is this new concept of “extracellular RNA” (exRNA), Nature devoted a special issue to the subject. Herb Brody writes,

The molecule best known for its part in translating genetic code into protein-assembly instructions is finding a new role in medicine. RNA, once thought to exist only in cells, is now known to travel to tissues all over the body through the blood, under the protection of tiny lipid sacs known as extracellular vesicles. The study of this extracellular RNA (exRNA) has led to a quiet revolution in biology, as scientists endeavour to understand why cells release RNA, and how the molecules might be used to improve the detection and treatment of disease.

"Micro-RNA (miRNA), “Once overlooked as genetic junk,” (my bold) is proving its worth in many ways. “By attaching to matching strands of messenger RNA, which is involved in protein synthesis, miRNA can effectively turn mRNA off and on, and alter what proteins are made,” Nguyen adds. In the case of mother’s milk, one researcher started asking the right questions:

"Bo Lönnerdal, a biochemist at the University of California, Davis, has spent decades studying the bioactive components of breast milk. When Lönnerdal learnt that researchers had found miRNAs in breast milk, he remembers wondering what the molecules were doing there. There must be a reason why these seemingly random bits of RNA are present in milk, he recalls thinking.

"He wondered if the miRNAs provided nutrition, or were regulating some other substance. It’s a tedious process to solve — 1,400 miRNA’s have been identified in breast milk — but so far, it appears that these packages of code do regulate genes within the baby, perhaps tuning immune responses or speeding up rates of development for pre-term babies.

***

"The body’s tissues routinely communicate with each other through RNA messages sent back and forth between cells. So, it seemed obvious to scientists that, by eavesdropping on these extracellular communiqués carried in blood, saliva, urine and other fluids, they should be able to intercept dispatches indicative of health and disease.

***

"Evolutionists have already failed this burgeoning field by relegating RNAs they didn’t understand to the “genetic junk” bin. And ever since, after all these years of discovery, all they can do is speculate about what “might have evolutionary underpinnings.” This is a great time for design advocates to read the messages in RNA and find out what they are saying." (my bold)

Comment: A typical ID article pointing out how the research in RNA has opened a huge field for new discoveries. As the last paragraph sows, ID design experts will have different interpretations of the 'facts'.

3153 views

**

"Evolutionists have already failed this burgeoning field by relegating RNAs they didn’t understand to the “genetic junk” bin. And ever since, after all these years of discovery, all they can do is speculate about what “might have evolutionary underpinnings.” This is a great time for design advocates to read the messages in RNA and find out what they are saying." (my bold)

Davids Comment: A typical ID article pointing out how the research in RNA has opened a huge field for new discoveries. As the last paragraph sows, ID design experts will have different interpretations of the 'facts'.

Well, he's not wrong. Evolutionary biologist did relegate what they didn't understand, and have thus spent decades being surprised. The reason that their 'surprise' is so telling is that a good scientific theory makes predictions, and you're only surprised when the predictions are wrong. The extreme level of complexity makes the entire prospect of random chance and natural selection relatively ludicrous, but then, the entire theory of evolution has too much of a strangle hold to be dislodged by something as inconvenient as facts or the scientific method. As theories go, it has been wrong a lot.... like a lot a lot.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

3176 views

QUOTE: "Evolutionists have already failed this burgeoning field by relegating RNAs they didn’t understand to the “genetic junk” bin. And ever since, after all these years of discovery, all they can do is speculate about what “might have evolutionary underpinnings.” This is a great time for design advocates to read the messages in RNA and find out what they are saying." (David’s bold)

David's comment: A typical ID article pointing out how the research in RNA has opened a huge field for new discoveries. As the last paragraph sows, ID design experts will have different interpretations of the 'facts'.

TONY: Well, he's not wrong. Evolutionary biologist did relegate what they didn't understand, and have thus spent decades being surprised. The reason that their 'surprise' is so telling is that a good scientific theory makes predictions, and you're only surprised when the predictions are wrong. The extreme level of complexity makes the entire prospect of random chance and natural selection relatively ludicrous, but then, the entire theory of evolution has too much of a strangle hold to be dislodged by something as inconvenient as facts or the scientific method. As theories go, it has been wrong a lot.... like a lot a lot.

On this website we have long since agreed that random chance as the source of all the complexities is “relatively ludicrous”. Natural selection in itself simply means that Nature will preserve whatever works, and will get rid of what doesn’t. What is ludicrous is the claim that it creates anything. Darwin’s “Origin of species by means of natural selection” is therefore horribly misleading, as his form of speciation depends initially on random mutations, not natural selection. However, none of this invalidates the theory of evolution itself in the sense of common descent, and indeed as Darwin says at the end of his book (later editions): “There is grandeur in the view of life, with its several powers, having been originally breathed by the Creator into a few forms or one.” For years now, we have been discussing the theory that evolution has advanced by means of cooperation between intelligent cell communities (as opposed to random mutations), possibly created by your God and responding in their different ways to different conditions. I don't remember hearing your views on this theory, but if you have told us, perhaps you could give us a reminder?

3164 views

QUOTE: "Evolutionists have already failed this burgeoning field by relegating RNAs they didn’t understand to the “genetic junk” bin. And ever since, after all these years of discovery, all they can do is speculate about what “might have evolutionary underpinnings.” This is a great time for design advocates to read the messages in RNA and find out what they are saying." (David’s bold)

David's comment: A typical ID article pointing out how the research in RNA has opened a huge field for new discoveries. As the last paragraph shows, ID design experts will have different interpretations of the 'facts'.

TONY: Well, he's not wrong. Evolutionary biologist did relegate what they didn't understand, and have thus spent decades being surprised. The reason that their 'surprise' is so telling is that a good scientific theory makes predictions, and you're only surprised when the predictions are wrong. The extreme level of complexity makes the entire prospect of random chance and natural selection relatively ludicrous, but then, the entire theory of evolution has too much of a strangle hold to be dislodged by something as inconvenient as facts or the scientific method. As theories go, it has been wrong a lot.... like a lot a lot.

dhw: On this website we have long since agreed that random chance as the source of all the complexities is “relatively ludicrous”. Natural selection in itself simply means that Nature will preserve whatever works, and will get rid of what doesn’t. What is ludicrous is the claim that it creates anything. Darwin’s “Origin of species by means of natural selection” is therefore horribly misleading, as his form of speciation depends initially on random mutations, not natural selection. However, none of this invalidates the theory of evolution itself in the sense of common descent, and indeed as Darwin says at the end of his book (later editions): “There is grandeur in the view of life, with its several powers, having been originally breathed by the Creator into a few forms or one.” For years now, we have been discussing the theory that evolution has advanced by means of cooperation between intelligent cell communities (as opposed to random mutations), possibly created by your God and responding in their different ways to different conditions. I don't remember hearing your views on this theory, but if you have told us, perhaps you could give us a reminder?

I think Tony has given much of what He thinks right here. It seems he has just trashed natural selection, and I've said I don't think very much of it as having any value in any form of the theory such as expressed by dhw. But I hope Tony will pitch in a little more.

3147 views

dhw: For years now, we have been discussing the theory that evolution has advanced by means of cooperation between intelligent cell communities (as opposed to random mutations), possibly created by your God and responding in their different ways to different conditions. I don't remember hearing your views on this theory, but if you have told us, perhaps you could give us a reminder?

DAVID: I think Tony has given much of what He thinks right here. It seems he has just trashed natural selection, and I've said I don't think very much of it as having any value in any form of the theory such as expressed by dhw. But I hope Tony will pitch in a little more.

Tony has not mentioned the theory as expressed by Talbott, Shapiro and myself. I also hope we will hear more from him! Are you there, Tony?

3168 views

Turned off, it allows stem cells to become neurons:

https://phys.org/news/2020-07-junk-dna-free-stem-cells.html

"NIH researchers report for the first time that ancient viral genes that were once considered "junk DNA" may play a role in this process. The article describes a series of preclinical experiments that showed how some human endogenous retrovirus (HERV-K) genes inscribed into chromosomes 12 and 19 may help control the differentiation, or maturation, of human stem cells into the trillions of neurons that are wired into our nervous systems.

"Over the course of evolution, the human genome has absorbed thousands of human endogenous retrovirus genes. As a result, nearly eight percent of the DNA that lines our chromosomes includes remnants of these genes. Although once thought to be inactive, or "junk", recent studies have shown that these genes may be involved in human embryonic development, the growth of some tumors, and nerve damage during multiple sclerosis. Previously, researchers in Dr. Nath's lab showed that amyotrophic lateral sclerosis (ALS) may be linked to activation of the HERV-K gene. In this study, led by Tongguang (David) Wang, M.D., Ph.D., staff scientist at NINDS, the team showed that deactivation of the gene may free stem cells to become neurons.

***

"Surprisingly, they found that the surfaces of the stem cells were lined with high levels of HERV-K, subtype HML-2, an envelope protein, that viruses often use to latch onto and infect cells. These proteins progressively disappeared as the cells were served two rounds of "cocktails." One round nudged the cells into an intermediate, neural stem cell state followed by a second round that pushed the cells into finally becoming neurons. The researchers sped up this process by turning off HERV-K, HML-2 genes in the stem cells or by treating the cells with antibodies against the HML-2 protein. In contrast, they delayed neural differentiation by artificially overloading the cells with the HML-2 genes. Finally, the team discovered that interactions on the stem cell surfaces between HML-2 and another immune cell protein called CD98HC may restrain differentiation by triggering internal chemical reactions that are known to control cell growth and tumors. In the future, the team plans to explore how HERV-K genes may shape the wiring of a nervous system."

Comment: So called 'junk' is not junk, yet again. Our newer abilities to study and tailor DNA had produced many surprises. Most DNA, even with added viral DNA appears to be quite useful. It has been noted here, in the past that, that viral DNA has contributed to the advance of evolution.

3114 views

A series of articles in Nature reveal the new regulatory findings:

https://www.nature.com/articles/d41586-020-02139-1

"Less than 2% of the human genome encodes proteins. A grand challenge for genomic sciences has been mapping the functional elements — the regions that determine the extent to which genes are expressed — in the remaining 98% of our DNA. The Encyclopedia of DNA Elements (ENCODE) project, among other large collaborative efforts, was established in 2003 to create a catalogue of these functional elements and to outline their roles in regulating gene expression. In nine papers in Nature5–13, the ENCODE consortium delivers the third phase of its valuable project.

***

"Highly occupied target regions have been described before, but — by analysing the patterns in which proteins co-assemble at these regions, and the DNA sequences to which they bind — Partridge et al. have provided the first comprehensive evidence to support a speculative model of HOT-region formation. Under this model, a set of anchor DNA sequences first recruit specific transcription factors. These proteins increase chromatin accessibility, then serve as a core around which other binding proteins aggregate in a manner that is independent of DNA sequence. This could happen through protein–protein interactions and chromatin loops, which might link together multiple distant CREs.

"To further understand how distant CREs work together, Grubert et al.9 mapped chromatin loops in 24 human cell types. They showed that differences in chromatin looping between cell types can affect gene expression, by changing which distant enhancer elements regulate a gene, and which sections of a gene are retained after transcription (a process called alternative splicing). Their most intriguing finding was that housekeeping genes (those involved in day-to-day cell maintenance) often interact with just a few enhancer elements, whereas many enhancers make contact with genes that cause disease if one of two copies is mutated. This implies that a simpler circuitry favours steady and constant expression, whereas more-complex circuitry is needed to safeguard the expression of ‘dosage-sensitive’ genes.

***

"This catalogue of RNA elements substantially expands our knowledge of the regulatory components encoded in the human genome. It should enable researchers to predict genetic variants that alter RNA processing, and will constitute an invaluable resource for research into how protein–RNA interactions are regulated.

"The third phase of the ENCODE project is a tour de force. But because many regulatory elements act only in specific cell types or at particular times, it is not possible to precisely assess the completeness of the encyclopedia. It would be interesting to see how the project might incorporate single-cell technologies to tease out spatio-temporal-specific elements and so to further unveil the fundamentals of gene regulation."

Comment: Little junk left. This highly complex review article of over 6,000 papers cannot be reproduced here. CRE's are highly specific regulatory loop areas in DNA. Log in to see the diagrams. Amazingly complex. Our small genome, producing amazingly complex us, had to have these many levels of control and modifications.

3107 views

More DNA so-called 'junk' found to function in aging:

https://phys.org/news/2020-08-clues-aging-junk-dna.html

"Tom LaRocca, an assistant professor in the Department of Health and Exercise Science and faculty member in the Columbine Heath Systems Center for Healthy Aging at CSU, led the study to investigate a growing body of evidence that repetitive elements—transposons and other sequences that occur in multiple copies in the human genome—may become active over time as we age.

***

"To carry out the study, the researchers began by analyzing an existing RNA sequencing dataset gathered from skin cells in healthy human subjects aged 1-94 years old. Just as the Human Genome Project of the 1990s sought to sequence and map the approximately 20,500 genes in human DNA, RNA sequencing can provide a map of the entire transcriptome in the cells under study. From that analysis, which was all computational, the researchers found that transcripts from most major types of repetitive elements were increased in older subjects.

"In a second wave of study, the researchers verified their initial findings by performing their own lab analyses on skin cells from a biobank. Using fluorescent microscopy, the researchers tagged the transcript of a specific transposon, Charlie5, to see how it fluctuates with the age of cells: the brighter the tag appears under the microscope, the more Charlie5 transcript is detectable.

"As hypothesized, skin cells from older adults revealed a marked accumulation of Charlie5 transcript compared to cells from younger individuals, showing that repetitive element RNAs appear to accumulate with age.

"While an important observation, the grander outcome of this study is that repetitive RNA transcripts might be linked with biological age, or the health of a person's cells, as opposed to chronological age in years.

***

"A link between repetitive element transcripts and biological age was further confirmed by studying skin cells from patients with Hutchinson-Gilford progeria syndrome (HGPS), a premature aging syndrome, and by studying an RNA-sequencing dataset from the roundworm Caenorhabditis elegans.

"Why might repetitive element transcripts increase with age? The researchers suspect that chromatin—the complex of DNA and protein in cells that typically represses repetitive elements from being expressed—might become disrupted, allowing for the transcription of repetitive elements.

"All in all, for a portion of the genome that scientists used to ignore, evidence is growing that noncoding RNAs and repetitive elements play vital roles in regulating the rest of the human genome, and in this case, as potentially targetable biomarkers of aging.

"'This is a really big chunk of the genome that, for the longest time, no one really knew what it did, so they just kind of assumed it was junk. But we're finding more and more that these noncoding regions might not only be doing something, but they might have actual health implications," Cavalier said."

Comment: As more and more DNA is found to function, the stronger the evidence for design.

3025 views

Difficult to demonstrate in DNA, but this is a new approach using sea sponge DNA"

https://phys.org/news/2020-11-sea-sponge-scientists-unravel-million-year-old.html

"Australian scientists have found that humans, and most likely the entire animal kingdom, share important genetic mechanisms with a jelly-like sea sponge that comes from the Great Barrier Reef.

"Published in Science today, the research reveals some elements of the human genome—an organism's complete set of DNA—are functioning in the same way as the prehistoric sea sponge. This mechanism—which drives gene expression, key to species diversity across the animal kingdom—has therefore been preserved across 700 million years of evolution.

***

"'We collected sea sponge samples from the Great Barrier Reef, near Herron Island. At the University of Queensland, we extracted DNA samples from the sea sponge and injected it into a single cell from a zebrafish embryo. Without harming the zebrafish, we then repeated the process at the Victor Chang Cardiac Research Institute with hundreds of embryos, inserting small DNA samples from humans and mice as well."

"Dr. Wong says despite a lack of similarity between the sponge and humans due to millions of years of evolution, the team identified a similar set of genomic instructions that controls gene expression in both organisms.

"We were blown away by the results," Dr. Wong says.

"According to scientists, the sections of DNA that are responsible for controlling gene expression are notoriously difficult to find, study and understand. Even though they make up a significant part of the human genome, researchers are only starting to understand this genetic "dark matter".

"'We are interested in an important class of these regions called 'enhancers'," Dr. Wong says.

"'Trying to find these regions based on the genome sequence alone is like looking for a light switch in a pitch-black room. And that's why, up to this point, there has not been a single example of a DNA sequence enhancer that has been found to be conserved across the animal kingdom.

"'We are still a long way from a clear understanding of how DNA precisely shapes morphology in health and disease but our work is an important step in that direction."

***

"The team focused on an ancient gene that is important in our nervous system but which also gave rise to a gene critical in heart development.'"

Comment: As usual the 'dark areas' of DNA are purposeful. I cannot image a designing God who created a bunch of useless DNA. God, as I view Him, is purely purposeful, and never shows frivolous human thoughts or desires.

2894 views

How new genes appear when necessary:

https://www.sciencenews.org/article/essential-genes-fast-evolution-junk-dna-heterochrom...

"A new study in fruit flies may help solve that puzzle. It shows that some new genes quickly become crucial because they regulate a type of DNA called heterochromatin. Once considered “junk DNA,” heterochromatin actually performs many important jobs, including acting like a tightly guarded prison: It locks up “bad actor” genes, preventing them from turning on and doing damage.

"Heterochromatin is also one of the fastest-changing bits of DNA in the body, so the genes that regulate it have to adapt quickly just to keep up, evolutionary biologist Harmit Malik at the Fred Hutchinson Cancer Research Center in Seattle and his colleagues report.

“'The work is a milestone,” said Manyuan Long, an evolutionary biologist at the University of Chicago who was not involved in the research. “It is really amazing seeing such an important role the heterochromatin plays in gene evolution.”

***

"About a decade ago, researchers discovered that new genes don’t just confer new functions; some may actually be necessary for survival. In the fruit fly Drosophila melanogaster, as many as 30 percent of essential genes are “new,” with some arising as recently as 3 million years ago — a flash in evolutionary timescales. The discovery overturned a long-held belief that important genes don’t really change much over the course of evolution.

***

"The team found that one of the new essential genes, dubbed Nicknack, issues instructions for a protein that binds to heterochromatin, although the details remain unknown.

***

"They tested this theory by swapping the gene from D. simulans into the D. melanogaster fly, expecting that if the genes were the same, the trade would have no effect. But instead, the female files survived the swap just fine, but all the males died. Malik thinks the difference between the sexes has to do with heterochromatin: The Y chromosome contains a lot of it.

“'It’s as if [D.] simulans’ [Nicknack gene] comes in with its hand tied behind its back,” Malik says. “It’s good enough to do its function in female flies, but in male flies, where there is a huge block of heterochromatin, it can’t.” In other words, the gene from one species is no match for its counterpart in the other.

"The result suggests that in the 2.5 million years since the two species split, D. melanogaster evolved its own version of Nicknack. And because the swap adversely affected the males, with their abundance of heterochromatin in the Y chromosome, the researchers concluded that Nicknack must play some crucial role in regulating heterochromatin. And since heterochromatin evolves so rapidly, the Nicknack gene has to evolve rapidly too, so it doesn’t become obsolete."

Comment: This study suggests much support for my theory that God dabbles as evolution proceeds. And. of course, more 'junk DNA' disappears.

Another report also covers this study:

https://www.quantamagazine.org/scientists-find-vital-genes-evolving-in-genomes-junkyard...

To dig deeper into this puzzling result, Kasinathan looked for clues to the functions of Nicknack and Oddjob, two essential ZAD-ZNF genes that evolved quickly.

***
According to Malik, this explains why Oddjob and Nicknack evolve so rapidly: They have to adjust to the changing DNA environment of the heterochromatin to remain functional. In some ways, they are like the genes of the immune system, which change quickly to keep up with rapidly evolving pathogens in a kind of arms race. But in this case, Malik said, “It’s almost like an arms race happening in the genome, just to preserve an essential function.”

***

Species today face problems that their ancestors didn’t, and those new problems require new solutions. But “what if it’s actually the evolution of these heterochromatin sequences that created the need for this essential function first?” Malik asked.

“The essential function itself may not be conserved, and that’s a heretical concept,” he continued. “We’re not just saying that the essential genes are not conserved. We are actually saying that it’s possible that the essential functions are not conserved, because it’s all context-specific.” (My bold)

Kasinathan and Malik are now turning their attention to the other ZAD-ZNF transcription factors, many of which also localize to the heterochromatin. “This compartment of the genome that we basically ignored because it’s so gene-poor … is actually, at least for the ZAD-ZNFs, the answer to this paradox of young genes becoming essential,” Malik said.

“If you’re interested in centromere function, if you only look at the genes that are totally conserved across humans, yeast and flies, you could be missing really important genes that are potential therapeutic targets,” Malik said. “We’ve let our intuition and dogma kind of bias us to the point where we might be missing a lot of important biology.”

Comment: The bold suggest s God edits as necessary

2876 views

Human regions are hard to find without comparisons to other species:

https://cosmosmagazine.com/nature/marine-life/sea-sponge-with-quite-a-story-to-tell/?ut...

"Many human traits, such as height and disease susceptibility, depend on genes that are encoded in our DNA. These genes are switched on and off and further fine-tuned by important but hard-to-find regions in the genome.

"A particularly important class of these regions are known as enhancers, which boost the likelihood that a particular gene will be activated. Trying to find enhancers based on the genome sequence alone is incredibly difficult, like finding a light switch in a dark room.

***

"In a new study published in Science, we found that humans, mice, zebrafish — and most likely the entire animal kingdom — share enhancer regions with a sea sponge that comes from the Great Barrier Reef. Because sea sponges and humans last shared a common ancestor more than 700 million years ago, this means the functional mechanism has been preserved across all this time.

***

"...we extracted enhancer DNA from the sea sponge and injected it into a single cell from a zebrafish embryo. We found that while the sea sponge enhancer sequences were very different from zebrafish enhancer sequences, they still worked: they successfully and consistently drove the expression of a fluorescent protein in certain types of zebrafish cells.

"Based on computational predictions, we also identified and tested similar enhancers from humans and mice, to show that these sequences drive the expression of a fluorescent protein in similar zebrafish cell types during development.

"We discovered that despite differences between the genetic sequences of sponges and humans due to millions of years of evolution, we could identify a similar set of genomic instructions that controls gene expression in both organisms.

"Our findings represent a fundamental discovery in understanding the connection between our genomes and our physical traits.

"The sections of DNA that are responsible for controlling gene expression are notoriously difficult to find, study and understand. Even though they make up a significant part of the human genome, researchers are only beginning to understand this genetic “dark matter”."

Comment: Complete proof of common descent, if we ever needed it. More junk DNA gone, and more complexity understood. Genes primarily code for protein but networks of other DNA regions perform lots of the organizational work making phenotypes and physiological systems..

2872 views

Yes, in so=called junk:

https://www.sciencedaily.com/releases/2021/01/210104145943.htm

"new research reveals the discovery of a new cog in the circadian clock - a genome-wide regulatory layer made up of small chains of non-coding nucleotides known as micro RNAS (miRNAs).

***

"Formerly thought to be "junk DNA," miRNAs are now known to affect gene expression by preventing messenger RNA from making proteins. Past research has indicated miRNAs may have a role in the function of circadian clocks but determining which of the hundreds of miRNAs in the genome might be involved remained a problem.

"Kay and his team, led by Lili Zhou, a research associate in the Keck School's Department of Neurology, turned to the Genomics Institute of the Novartis Research Foundation (GNF) in San Diego which has created robots capable of high throughput experiments. Working with scientists at the institute, Zhou developed a high throughput screen for a robot to test the close to 1000 miRNAs by individually transferring them into cells the team had engineered to glow on and off, based on the cell's 24-hour circadian clock cycle.

"'The collaboration with GNF made it possible for us to conduct the first cell-based, genome-wide screening approach to systematically identify which of the hundreds of miRNAs might be the ones modulating circadian rhythms," said Zhou."

"'Much to our surprise," said Kay, "we discovered about 110 to 120 miRNAs that do this.'"

Comment: Most DNA is purposeful which means it developed from design rather than by chance. The 'junk theory' to support Darwinism is totally dead as this article demonstrates.

2723 views

How much 'junk' is really there?:

https://medicalxpress.com/news/2021-02-epigenomic-reveals-circuitry-human-disease.html

"Over the past two decades, it has become apparent that those noncoding stretches of DNA, originally thought to be "junk DNA," play critical roles in development and gene regulation. In a new study published today, a team of researchers from MIT has published the most comprehensive map yet of this noncoding DNA.

"This map provides in-depth annotation of epigenomic marks—modifications indicating which genes are turned on or off in different types of cells—across 833 tissues and cell types, a significant increase over what has been covered before. The researchers also identified groups of regulatory elements that control specific biological programs, and they uncovered candidate mechanisms of action for about 30,000 genetic variants linked to 540 specific traits.

***

"Layered atop the human genome—the sequence of nucleotides that makes up the genetic code—is the epigenome. The epigenome consists of chemical marks that help determine which genes are expressed at different times, and in different cells. These marks include histone modifications, DNA methylation, and how accessible a given stretch of DNA is.

***

"Since the final draft of the human genome was completed in 2003, researchers have performed thousands of genome-wide association studies (GWAS), revealing common genetic variants that predispose their carriers to a particular trait or disease.

"These studies have yielded about 120,000 variants, but only 7 percent of these are located within protein-coding genes, leaving 93 percent that lie in regions of noncoding DNA.

"How noncoding variants act is extremely difficult to resolve, however, for many reasons. First, genetic variants are inherited in blocks, making it difficult to pinpoint causal variants among dozens of variants in each disease-associated region. Moreover, noncoding variants can act at large distances, sometimes millions of nucleotides away, making it difficult to find their target gene of action. They are also extremely dynamic, making it difficult to know which tissue they act in. Lastly, understanding their upstream regulators remains an unsolved problem.

"In this study, the researchers were able to address these questions and provide candidate mechanistic insights for more than 30,000 of these noncoding GWAS variants. The researchers found that variants associated with the same trait tended to be enriched in specific tissues that are biologically relevant to the trait. For example, genetic variants linked to intelligence were found to be in noncoding regions active in the brain, while variants associated with cholesterol level are in regions active in the liver.

"The researchers also showed that some traits or diseases are affected by enhancers active in many different tissue types. For example, they found that genetic variants associated with coronary heart disease (CAD) were active in adipose tissue, coronary arteries, and the liver, among many other tissues."

Comment: This brings us back to errors where a disease happens, but much of it involves 'traits' which may not be bad. This system God designed for adaptation has both good and bad, as we interpret the results. Is God required to produce perfection?

2702 views

Needs lots of 'junk' to work:

https://evolutionnews.org/2021/05/noncoding-junk-dna-is-important-for-limb-formation/

"A 2021 article in Nature, “Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator,” reports important new functions for non-coding or “junk” DNA that underlie limb formation.

***

"The technical paper in Nature describes the research. The investigators examined the chromosomes of people who had naturally occurring limb malformation, and found that these people had deletions of DNA encoding long non-coding RNA sequences (lncRNAs) from human chromosome 2. They deleted corresponding DNA sequences in mice and found similar “severe congenital limb malformation,” suggesting these lncRNA sequences are functionally important:

"Here we show that genetic ablation of a lncRNA locus on human chromosome 2 causes a severe congenital limb malformation. We identified homozygous 27–63-kilobase deletions located 300 kilobases upstream of the engrailed-1 gene (EN1) in patients with a complex limb malformation featuring mesomelic shortening, syndactyly and ventral nails (dorsal dimelia). Re-engineering of the human deletions in mice resulted in a complete loss of En1expression in the limb and a double dorsal-limb phenotype that recapitulates the human disease phenotype. Genome-wide transcriptome analysis in the developing mouse limb revealed a four-exon-long non-coding transcript within the deleted region, which we named Maenli. Functional dissection of the Maenli locus showed that its transcriptional activity is required for limb-specific En1 activation in cis, thereby fine-tuning the gene-regulatory networks controlling dorso-ventral polarity in the developing limb bud.

***

"In the era of whole-genome sequencing, the findings described here underscore the need for a systematic annotation and functional characterization of lncRNA loci to interpret and classify non-coding genetic variants. They highlight the importance of elucidating the complex diversity of lncRNA modes of action to assess their role in organ development and disease.

***

"Another 2021 article in Nature shows why it’s no longer tenable for evolutionists to hide behind such an argument from ignorance. The article explains that over 130,000 functional “genomic elements, previously called junk DNA” have now been discovered, highlighting how important these “junk” segments have turned out to be: (my bold)

"t is now appreciated that the majority of functional sequences in the human genome do not encode proteins. Rather, elements such as long non-coding RNAs, promoters, enhancers and countless gene-regulatory motifs work together to bring the genome to life. Variation in these regions does not alter proteins, but it can perturb the networks governing protein expression With the HGP draft in hand, the discovery of non-protein-coding elements exploded. So far, that growth has outstripped the discovery of protein-coding genes by a factor of five, and shows no signs of slowing. Likewise, the number of publications about such elements also grew in the period covered by our data set. For example, there are thousands of papers on non-coding RNAs, which regulate gene expression."

Comment: All of these discoveries show that most human complaints about God's 'bad' designs are as my bold shows, arguments from ignorance. Human judgement is not God's judgement. What seems bad must be proven bad to have any honest discussion about God and His works.

2430 views

ERV's are ENDOGENOUS RETROVIRAL PROTEINS throughout our DNA:

https://journals.asm.org/doi/full/10.1128/JVI.02299-20

"Long disregarded as junk DNA or genomic dark matter, endogenous retroviruses (ERVs) have turned out to represent important components of the antiviral immune response. These remnants of once-infectious retroviruses not only regulate cellular immune activation, but may even directly target invading viral pathogens. In this Gem, we summarize mechanisms by which retroviral fossils protect us from viral infections. One focus will be on recent advances in the role of ERVs as regulators of antiviral gene expression.

***

"...we see that ERVs work to initiate immune responses to viruses in a variety of ways:

"(A) ERVs use “viral mimicry” where ERV-encoded long non-coding RNA (lncRNA) molecules bind with viral RNA to activate pattern recognition receptors (PRRs) which activate an immune response.

"(B) LncRNAs produced by ERVs can also induce expression of antiviral cytokines, creating a “positive feedback loop enhancing antiviral immune responses.”

"(C) Proteins encoded by ERV DNA can also enhance immune responses by binding with toll-like receptors.

"(D) ERV envelope proteins (called ENVs) are the outer layer of viruses which protects the genetic material inside. ENVs can bind to receptors which harmful viruses might use to enter host cells, blocking them from entering.

"(E) ENV proteins can enter viruses themselves and interfere with the viral life-cycle, inactivating viruses before they infect new host cells.

"(F) ERV proteins can also stop viruses by interfering with viral capsids that have already entered host cells.

'(G) Some ERVs that are neither transcribed nor translated can promote recombination which increases the number of host genes that can be used to target viruses. This is an evolutionary mechanism, but it could explain how ERVs can be a built-in designed mechanism to increase immune responses within a species.

"(H) There are also very important ERV functions for regulating gene expression, as ERVs can act as promoters, enhancers, or transcription start sites for gene expression. The article explains just how common this is:

"This cooption of regulatory elements is not a rare phenomenon, and it has been estimated that about 20% of all transcription factor binding sites in humans are found in HERVs and other transposable elements. In line with this, a meta-analysis of chromatin immunoprecipitation sequencing (ChIP-Seq) data sets identified about 800,000 transcription factor binding sites within HERVs.

"Intriguingly, almost 90% of all HERVs represent so-called solo LTRs [long terminal repeats, which can serve as binding sites to regulate gene expression]. These HERVs lost the prototypical retroviral genes gag, pol, and env due to homologous recombination of their flanking LTR sequences, leaving single LTR promoters in the genome. Due to their activation upon immune stimulation, ERV LTRs have already been termed “landing strips for inflammatory transcription factors” (90), and evidence for their role in regulating cellular immune responses is growing."

Comment: So it turns out viruses can also be good, not bad. My view is God has a reason for everything, and as yesterday's essay shows, we are innocent bystanders in the war of eat or be eaten.

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More junk removed as a segment controlling telomere length is found:

https://www.sciencedaily.com/releases/2021/07/210723105258.htm

"Researchers have recently identified a DNA region known as VNTR2-1 that appears to drive the activity of the telomerase gene, which has been shown to prevent aging in certain types of cells. Knowing how the telomerase gene is regulated and activated and why it is only active in certain cell types could someday be the key to understanding how humans age and how to stop the spread of cancer.

***

"Their finding is based on a series of experiments that found that deleting the DNA sequence from cancer cells -- both in a human cell line and in mice -- caused telomeres to shorten, cells to age, and tumors to stop growing. Subsequently, they conducted a study that looked at the length of the sequence in DNA samples taken from Caucasian and African American centenarians and control participants in the Georgia Centenarian Study, a study that followed a group of people aged 100 or above between 1988 and 2008. The researchers found that the length of the sequence ranged from as short as 53 repeats -- or copies -- of the DNA to as long as 160 repeats.

"'It varies a lot, and our study actually shows that the telomerase gene is more active in people with a longer sequence," Zhu said.

"Since very short sequences were found only in African American participants, they looked more closely at that group and found that there were relatively few centenarians with a short VNTR2-1 sequence as compared to control participants. However, Zhu said it was worth noting that having a shorter sequence does not necessarily mean your lifespan will be shorter, because it means the telomerase gene is less active and your telomere length may be shorter, which could make you less likely to develop cancer.

***

"Zhu noted that since African Americans have been in the United States for generations, many of them have Caucasian ancestors from whom they may have inherited some of this sequence. So as a next step, he and his team hope to be able to study the sequence in an African population."

Comment: just more evidence there is little 'junk DNA' in our genome. The African white difference shows our human variant types are really somewhat different.

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DNA seems to have function in most places:

https://www.quantamagazine.org/the-complex-truth-about-junk-dna-20210901/

"Many mysteries still surround the issue of what noncoding DNA is, and whether it really is worthless junk or something more. Portions of it, at least, have turned out to be vitally important biologically. But even beyond the question of its functionality (or lack of it), researchers are beginning to appreciate how noncoding DNA can be a genetic resource for cells and a nursery where new genes can evolve.

"Abstractions navigates promising ideas in science and mathematics. Journey with us and join the conversation. “Slowly, slowly, slowly, the terminology of ‘junk DNA’ [has] started to die,” said Cristina Sisu, a geneticist at Brunel University London.

***

"Cells use some of their noncoding DNA to create a diverse menagerie of RNA molecules that regulate or assist with protein production in various ways. The catalog of these molecules keeps expanding, with small nuclear RNAs, microRNAs, small interfering RNAs and many more. Some are short segments, typically less than two dozen base pairs long, while others are an order of magnitude longer. Some exist as double strands or fold back on themselves in hairpin loops. But all of them can bind selectively to a target, such as a messenger RNA transcript, to either promote or inhibit its translation into protein.

***

"By far the biggest category of noncoding DNA in the genomes of humans and many other organisms consists of transposons, segments of DNA that can change their location within a genome. These “jumping genes” have a propensity to make many copies of themselves — sometimes hundreds of thousands — throughout the genome, says Seth Cheetham, a geneticist at the University of Queensland in Australia. Most prolific are the retrotransposons, which spread efficiently by making RNA copies of themselves that convert back into DNA at another place in the genome. About half of the human genome is made up of transposons; in some maize plants, that figure climbs to about 90%.

***

"One category of noncoding DNA that intrigues many scientists these days is the pseudogenes, which are usually viewed as the remnants of working genes that were accidentally duplicated and then degraded through mutation. As long as one copy of the original gene works, natural selection may exert little pressure to keep the redundant copy intact.

"Akin to broken genes, pseudogenes might seem like quintessential genomic junk. But Cheetham warns that some pseudogenes may not be “pseudo” at all. Many of them, he says, were presumed to be defective copies of recognized genes and labeled as pseudogenes without experimental evidence that they weren’t functional.

"Pseudogenes can also evolve new functions. “Sometimes they can actually control the activity of the gene from which they were copied,” Cheetham said, if their RNA is similar enough to that of the working gene to interact with it. Sisu notes that the discovery in 2010 that the PTENP1 pseudogene had found a second life as an RNA regulating tumor growth convinced many researchers to look more closely at pseudogene junk.

***

"But how much of this DNA therefore qualifies as true “junk” in the sense that it serves no useful purpose for a cell? This is hotly debated. In 2012, the Encyclopedia of DNA Elements (Encode) research project announced its findings that about 80% of the human genome seemed to be transcribed or otherwise biochemically active and might therefore be functional. However, this conclusion was widely disputed by scientists who pointed out that DNA can be transcribed for many reasons that have nothing to do with biological utility.

***

"In the future, researchers may be less and less inclined to describe any of the noncoding sequences as junk because there are so many other more precise ways of labeling them now. For Sisu, the field’s best way forward is to keep an open mind when assessing the eccentricities of noncoding DNA and RNA and their biological importance. People should “take a step back and realize that one person’s trash is another person’s treasure,” she said."

Comment: This is a carefully drawn article, but as I have presented here most non-coding DNA has some alternative function so the 80% estimate of function from ENCODE is reasonable. The argument about the importance pf 'junk' is that chance mutations in evolution should produce lots of junk. That is not true from this evidence, so that suggests DNA may be designed as I believe.

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It relates to red cell production:

https://evolutionnews.org/2022/01/blast-from-the-past-eugenie-scotts-failed-prediction-...

"Humans have six copies of the beta-globin gene. Five produce beta-globin proteins, but the sixth, the pseudogene copy, has a premature stop codon (and other mutations) that prevent translation into a protein. In Scott’s telling this means that the pseudogene cannot have any function whatsoever. But molecular biology now knows that pseudogenes can produce transcripts which can regulate protein-coding versions of the same gene—and that’s exactly what the researchers propose is going on here.

***

"The beta-globin pseudogene’s inability to produce a translatable RNA transcript does not preclude it from being functional. The researchers argue the pseudogene HBBP1 works something like an on/off switch, regulating expression of protein-coding beta-globin genes. Here’s a lengthy quote from the paper:

"n the light of recent studies on the chromatin conformation of the β-globin cluster, we present evidence sustaining that the strong functional constraints underlying the decreased contemporary diversity at these two regions were not driven by protein function but instead are likely due to a regulatory role in ontogenic switches of gene expression. … Over the past years, the β-globin cluster has been regarded as a complex genetic system and a paradigm of gene expression regulation. More recently, a boost of studies on the β-globin cluster have contributed to a better understanding of the mechanisms underlying the regulation of each gene in the cluster.

***

"But there’s a lot more to this story. You’ll note that they “hypothesize” function based upon clear genetic evidence and knowledge of how gene regulation operates. The precise function of the HBBP1 pseudogene was confirmed and identified in a 2021 paper published in Developmental Cell titled “Genome-wide analysis of pseudogenes reveals HBBP1’s human-specific essentiality in erythropoiesis and implication in b-thalassemia.

"The 2021 paper was unmistakable in reporting the important function of this pseudogene, stating: “Pseudogenic HBBP1 confers human-specific essentiality in erythropoiesis.” Erythropoiesis is the process of producing red blood cells, and they report “human-specific indispensability of the HBBP1 transcript” in erythropoiesis and find “HBBP1 is essential for erythroid development and differentiation.”

***

"In conclusion, pseudogenes represent a new layer in the flow of genetic information. The highly integrative framework implemented in this study provides a prototype for determining the function of pseudogenes under normal and pathological conditions. Exploration of species-specific regulatory functions of pseudogenes or even studies of population-specific pseudogenes are expected to blossom in future.

"In other words, the “traditional view” that pseudogenes are “functionless evolutionary relics” has hindered research into understanding the true nature of pseudogenes. But now that we’re overcoming that old view, they expect studies elucidating specific functions of pseudogenes to “blossom” in the future.

"The implication of this story is that in their rush to oppose intelligent design, Darwin defenders like Eugenie Scott and Ken Miller not only made an argument that has turned out to be completely wrong. It may also have slowed the progress of science."

Comment: this is a review from non-ID source material. Who named pseudogenes? Darwinists!! Who named junk DNA? Darwinists!! Note current research, not done by IDers, is demolishing false conclusions by Darwin defenders. Almost all DNA is shown to function. Nothing seems accidental from chance mutations. With no evidence of chance, design emerges as required.

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As usual in non-coding DNA (junk):

https://qbi.uq.edu.au/article/2022/03/junk-dna-key-controlling-fear

"A piece of “junk DNA” could be the key to extinguishing fear-related memories for people struggling with post-traumatic stress disorder (PTSD) and phobia, according to a study from The University of Queensland.

"An international research project, led by the Queensland Brain Institute’s Associate Professor Timothy Bredy, discovered the new gene while investigating how the genome responds to traumatic experiences.

“'Until recently, scientists thought the majority of our genes were made up of junk DNA, which essentially didn’t do anything.” Dr Bredy said.

“'But when researchers began to explore these regions, they realised that most of the genome is active and transcribed.”

***

"A new gene, labelled ADRAM by the researchers, was found to not only act as a scaffold for molecules inside the cell, but also helped coordinate the formation of fear-extinction memory.

***

"Until now, there have been no studies devoted to understanding these genes, let alone how they might influence brain function in the context of learning and memory.

“Our findings suggest that long non-coding RNAs provide a bridge, linking dynamic environmental signals with the mechanisms that control the way our brains respond to fear,” Dr Bredy said.

“'With this new understanding of gene activity, we can now work towards developing tools to selectively target long non-coding RNAs in the brain that directly modify memory, and hopefully, develop a new therapy for PTSD and phobia.”

"This study was published in Cell Reports (doi.org/10.1016/j.celrep.2022.110546)"

Comment: it may be boring to have me produce more findings on what seemed to be 'junk' in DNA. However Larry Moran is publishing a book still claiming most of it is junk. He won't give up despite his lonely position. I think Dan Graur is still with him. What they realize is teh old Darwin theory is dead unless junk exists showing chance appearing useless mutations in the genome.

1239 views

A new important paper:

https://onlinelibrary.wiley.com/doi/full/10.1002/bies.202300080

"Abstract
Thomas Kuhn described the progress of science as comprising occasional paradigm shifts separated by interludes of ‘normal science’. The paradigm that has held sway since the inception of molecular biology is that genes (mainly) encode proteins. In parallel, theoreticians posited that mutation is random, inferred that most of the genome in complex organisms is non-functional, and asserted that somatic information is not communicated to the germline. However, many anomalies appeared, particularly in plants and animals: the strange genetic phenomena of paramutation and transvection; introns; repetitive sequences; a complex epigenome; lack of scaling of (protein-coding) genes and increase in ‘noncoding’ sequences with developmental complexity; genetic loci termed ‘enhancers’ that control spatiotemporal gene expression patterns during development; and a plethora of ‘intergenic’, overlapping, antisense and intronic transcripts. These observations suggest that the original conception of genetic information was deficient and that most genes in complex organisms specify regulatory RNAs, some of which convey intergenerational information."

From evolution news: https://evolutionnews.org/2023/11/newly-paper-in-bioessays-recognizes-kuhnian-paradigm-...

"This brings us to the article recently published in BioEssays, written by John Mattick, an Australian molecular biologist and Professor of RNA Biology at the University of New South Wales, Sydney. I have no evidence that Mattick has any affinities with intelligent design — but he’s a prime example of a bold scientist who has embraced new theories that challenge the reigning paradigm. Mattick has been indefatigable in following the evidence where it leads regarding evidence of function for “junk DNA.” In part because of his work, biology today has experienced a paradigm shift away from the concept of junk DNA. In fact, Mattick’s new BioEssays article, “A Kuhnian revolution in molecular biology: Most genes in complex organisms express regulatory RNAs,” frames the revolution in thinking over junk DNA precisely in “Kuhnian paradigm shift” terms.

***

" Mattick describes the previously reigning “junk DNA” paradigm in biology as having come from “prevailing assumptions.” The assumptions hold that “‘genes’ encode proteins, that genetic information is transacted and regulated by proteins, and that there is no heritable communication between somatic and germ cells.” This view that genes encode proteins is a key part of the “central dogma” of biology. Of course, no one denies that genes encode proteins — Mattick’s point is that they can do much more than this. They can also encode RNAs and the evidence shows that many non-protein-coding sequences of DNA actually encode RNAs that perform many types of vital functions in the cell."

Comment: the whole concept of junk DNA was a direct result of early concepts, which were wrong. Mattick explains:

"[T]heoretical biologists were integrating Mendelian genetics with Darwinian evolution, leading in 1942 to the so-called Modern Synthesis, which made two primary claims: mutations are random and somatic mutations are not inherited. … In 1968 Kimura proposed the neutral theory of molecular evolution, which posited that “an appreciable fraction” of the genome was evolving independently of natural selection. In 1969, Nei concluded that, given the “high probability of accumulating … lethal mutations in duplicated genomes … it is to be expected that higher organisms carry a considerable number of nonfunctional genes (nonsense DNA) in their genome”, leading Ohno to promote the concept of “junk DNA”, also arguing that “in order not to be burdened with an unbearable mutation load, the necessary increase in the number of regulatory systems had to be compensated by simplification of each regulatory system”. [Emphasis in the original."]

Evolution news: " Against this backdrop — permeated with evolutionary thinking about the origin of the genome — the idea of junk DNA flourished and spread throughout the biology community."

Comment: it is about time.

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The role of RNA:

https://evolutionnews.org/2023/11/the-new-post-junk-dna-paradigm-of-molecular-biology-r...

“'Another Class of Genes That Produce RNAs”
The main point of Mattick’s new paradigm is that in addition to protein-coding genes, there’s “another class of genes that produce RNAs.” These “RNA genes” perform many diverse functions, but primarily they “act as regulatory molecules to control gene expression and organise nuclear territories and cytoplasmic domains during ontogeny.” He summarizes the new paradigm this way:

"n simplified Kuhnian terms, the dominant paradigm in molecular biology since its foundation that “genes encode proteins and sequences that do not are mainly junk” should be replaced by “genes encode proteins and regulatory RNAs, the latter required for the epigenetic control of developmental trajectories”. RNA is not simply an intermediate between gene and protein, but a major player in gene regulation and a contributor to inheritance.

"These RNA genes have many functions but a large proportion entail gene regulation-related functions that fall within the category of epigenetics. Mattick identifies multiple types of RNAs that perform these important functions:

"Small regulatory RNAs (e.g., microRNAs) which regulate translation of proteins, regulate epigenetic process, and are also involved in alternative splicing.

"Long non-coding RNAs (called “lncRNAs”) which also influence gene expression by controlling transcription factors and transcription-splicing and also modulate many genetically variable traits. Some may even encode peptides.

"Transposable elements are important for gene structure and function, and gene regulatory networks.

"Overall these types of functional RNAs undergo much post-transcriptional editing and are important for brain function, and also can foster “transgenerational epigenetic inheritance.”

"Mattick has explained this new paradigm elsewhere as well. In a weighty academic book published earlier this year, RNA: The Epicenter of Genetic Information (Taylor & Francis), Mattick along with bioengineer Paulo Amaral argue that “the genomes of humans and other complex organisms are not full of junk.” They acknowledge that this is “contrary to long-held … dogmas of evolutionary theory.” Here’s the striking quote in full:

"While the story is still unfolding, we conclude that the genomes of humans and other complex organisms are not full of junk but rather are highly compact information suites that are largely devoted to the specification of regulatory RNAs. These RNAs drive the trajectories of differentiation and development, underpin brain function and convey transgenerational memory of experience, much of it contrary to long-held conceptions of genetic programming and the dogmas of evolutionary theory."

JOHN MATTICK AND PAULO AMARAL, RNA: THE EPICENTER OF GENETIC INFORMATION (CRC-TAYLOR & FRANCIS, 2023), P. VII.

Comment: it is not my intent to beat the subject to death. This article teaches us more about RNA's many functions.

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