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One of the problems in cell research has been ignoring parts of cells that appear to have no use and have been considered 'junk'. Like junk DNA discussed on the site many times. Most of it has a use or purpose. Now a tiny organelle appearing in cell division called a 'midbody', previously ignored as of no interest, looks like it is useful in some way.-http://the-scientist.com/2011/09/11/obscure-organelle-in-stem-cells-and-cancer/-
 The lesson is in cellular life, everything seems to be purposeful. Ignore nothing. Living matter is extremely complex. When DNA gets torn and is repaired, the molecules move along the strands and bring them back together as if the molecules could think while they work. - http://www.sciencedaily.com/releases/2010/03/100311123522.htm

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Pseudogenes have function; are not junk, without function:-http://www.landesbioscience.com/journals/rnabiology/article/18277/?nocache=1093064241

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Pseudogenes have function; are not junk, without function:
> 
> http://www.landesbioscience.com/journals/rnabiology/article/18277/?nocache=1093064241-A massive study of DNA reported this week in multiple papers shows that 'junk' DNA is not junk.It is filled with switches to control genes. Now instead of 80% junk, it turns out most is useful. This turns Neo-Darwinism on its head. One of the key tenets of Neo-Darwin theory was that much of DNA was left over from evolution, and just an evidence of the past. Yes, there is some viral DNA in our DNA, as a past history but most DNA turns out to be 'switches' controlling genes and in the coiled state the switches are close to the genes they control.-"The thought before the start of the project, said Thomas Gingeras, an Encode researcher from Cold Spring Harbor Laboratory, was that only 5 to 10 percent of the DNA in a human being was actually being used." -The big surprise was not only that almost all of the DNA is used but also that a large proportion of it is gene switches. Before Encode, said Dr. John Stamatoyannopoulos, a University of Washington scientist who was part of the project, "if you had said half of the genome and probably more has instructions for turning genes on and off, I don't think people would have believed you."-http://www.nytimes.com/2012/09/06/science/far-from-junk-dna-dark-matter-proves-crucial-to-health.html?pagewanted=1&_r=1&nl=todaysheadlines&emc=edit_th_20120906-
http://the-scientist.com/2012/09/05/getting-to-know-the-genome/

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More sources:-http://medicalxpress.com/news/2012-09-encode-massive-genome-analysis-gene.html-http://blogs.discovermagazine.com/notrocketscience/2012/09/05/encode-the-rough-guide-to-the-human-genome/#ENCODEfunctional-Screams from the atheists:-http://sandwalk.blogspot.com/ Look for Sept. 5th

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More sources:
> 
> http://medicalxpress.com/news/2012-09-encode-massive-genome-analysis-gene.html... 
> http://blogs.discovermagazine.com/notrocketscience/2012/09/05/encode-the-rough-guide-to... 
> Screams from the atheists:
> 
> http://sandwalk.blogspot.com/ Look for Sept. 5th-From the Guardian:-http://www.guardian.co.uk/science/2012/sep/05/genes-genome-junk-dna-encode-"The researchers found that it is far from useless: within these regions they have identified more than 10,000 new "genes" that code for components that control how the more familiar protein-coding genes work. Up to 18% of our DNA sequence is involved in regulating the less than 2% of the DNA that codes for proteins. In total, Encode scientists say, about 80% of the DNA sequence can be assigned some sort of biochemical function."-80% is functional. Intelligent design, anyone?

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More sources:
> > 
> > http://medicalxpress.com/news/2012-09-encode-massive-genome-analysis-gene.html... > 
> 
> 80% is functional. Intelligent design, anyone?-An explosion of comment. A more nuanced approach with 20% of DNA very active and perhaps up to 80% 'functional' :-http://www.genomeweb.com//node/1123136?hq_e=el&hq_m=1339145&hq_l=1&hq_v=917fb9b80b

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Larry Moran at Sandwalk has listed a group of objections. The Guardian was most accurate in its assessment of these early findings: very active DNA 9%, quite active 20%, somewhat functional 80%. But the major point is having slight attention. This is an 11 year preliminary study, with only a little of DNA carefully studied despite the massive number of lab assets being used so far. With a six-plus-foot molecule, when stretched out having 3.2 billion bases, they have looked at 10,000 places. Undoubtedly, in another 11 years, the complexity will be even more amazing. -Moran is correct: inbetween the active spots, there is inactive stuff. Darwinists theorize this is left over stuff from evolution, now abandoned. There is no proof of this supposition. It sounds good. Since DNA works in a 3-D arrangement, the strung out version is a man-made aberration of how things work. The active triggers controlling gene expression are close by the genes they work with. The inactive material could be spacers to provide the right 3-D proximity of each gene complex (gene plus triggers).-My obvious point: given enough research time, it is all going to get even more complex, and complexer than that. So now Darwinists must explain complex information, in a very complex information code (better than anything we have invented for our computers), all by a purposeless scenario. No wonder several phnilosophers of science have their doubts.-http://sandwalk.blogspot.com/

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A very measured account by a research biologist of the various stories and blogs. But the blogger avoids my point: This is just a first step and DNA holds much more information and complexity. We are at the beginning of the road which will explain how extremely advanced H. sapiens get by with 20,000 genes. Just coding was never the answer. It is the modulation of gene action with 10,000 new active area isolated as triggers.-http://www.michaeleisen.org/blog/?p=1167-This quote makes my point, from Nature:
"So far, ENCODE has sampled 119 of 1,800 known transcription factors and general components of the transcriptional machinery on a limited number of cell types, and 13 of more than 60 currently known histone or DNA modifications across 147 cell types. DNase I, FAIRE and extensive RNA assays across subcellular fractionations have been undertaken on many cell types, but overall these data reflect a minor fraction of the potential functional information encoded in the human genome. An important future goal will be to enlarge this data set to additional factors, modifications and cell types, complementing the other related projects in this area"-http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html

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> This quote makes my point, from Nature:
> "So far, ENCODE has sampled 119 of 1,800 known transcription factors and general components of the transcriptional machinery on a limited number of cell types, and 13 of more than 60 currently known histone or DNA modifications across 147 cell types. DNase I, FAIRE and extensive RNA assays across subcellular fractionations have been undertaken on many cell types, but overall these data reflect a minor fraction of the potential functional information encoded in the human genome. An important future goal will be to enlarge this data set to additional factors, modifications and cell types, complementing the other related projects in this area"
> 
> http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html-Another blogger objects, but the key is still that only a tiny portion of DNA has been studied. Junk DNA is not gone and there always will be some, but no one at this juncture knows how much is junk and how much has some function:-http://www.forbes.com/sites/johnfarrell/2012/09/07/reports-of-junk-dnas-demise-have-been-greatly-exaggerated/

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DAVID: Another blogger objects, but the key is still that only a tiny portion of DNA has been studied. Junk DNA is not gone and there always will be some, but no one at this juncture knows how much is junk and how much has some function:-http://www.forbes.com/sites/johnfarrell/2012/09/07/reports-of-junk-dnas-demise-have-bee...-From the article: "This is, unfortunately, another case of a scientist acting irresponsibly by distorting the importance and the significance of the data. It's getting to be a serious problem and it makes it hard to convey real science to the general public. The public now believes that the concept of junk DNA has been rejected by scientists and that our huge genome really is full of wonderful sophisticated control elements regulating the expression of every gene."-The heading of this article is: "Reports of Junk DNA's Demise Have Been Greatly Exaggerated", which may be so, but when the author writes how hard it is to convey "real science" to the general public, perhaps he should keep in mind that the uselessness of all junk DNA was also conveyed as "real science" until not so long ago. There is always going to be a gap between scientific fact and scientific interpretation, and every broadside fired at the creationists can be fired with equal justification at the atheists.
 
Regardless of religious beliefs and non-beliefs, and of how much DNA is or isn't junk, I have no difficulty whatsoever in believing that "our huge genome really is full of wonderful sophisticated control elements", even if not of every gene. If it wasn't, why has it taken so long for our scientists to unravel the vast number of governing codes? By all means let theists attribute these to a designing intelligence, and let atheists attribute them to random mutations and Nature's process of selecting whatever works best, but why pretend the control elements aren't even there? Is that "real science"?

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> The heading of this article is: "Reports of Junk DNA's Demise Have Been Greatly Exaggerated", which may be so, but when the author writes how hard it is to convey "real science" to the general public, perhaps he should keep in mind that the uselessness of all junk DNA was also conveyed as "real science" until not so long ago. -Many of the articles has conveyed the idea that 'junk' is now gone. Not true. The functionality of many segemnts is minimal.-http://blogs.nature.com/news/2012/09/fighting-about-encode-and-junk.html
 
> Regardless of religious beliefs and non-beliefs, and of how much DNA is or isn't junk, I have no difficulty whatsoever in believing that "our huge genome really is full of wonderful sophisticated control elements", even if not of every gene. -The key statistic is that these electrifying discoveries come from only 147 cell types and there are over a thousand cell types in humans. Those cells all use the same DNA, but express different parts of DNA. Obviously with more research into more cell types, more junk will disappear. -Also this research has emphasized the 3-D nature of DNA. Tightly coiled around histones the double helix presents genes to midifier sections in close proximity, while if the model of DNA is presented strung out in straight lines the modifying triggers seem far apart. My thought is that some junk is conserved simply as buffer material to allow for proper 3-D spacing. DNA looks to be brilliantly conceived, much to atheist dismay.

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> Also this research has emphasized the 3-D nature of DNA. Tightly coiled around histones the double helix presents genes to midifier sections in close proximity, while if the model of DNA is presented strung out in straight lines the modifying triggers seem far apart. My thought is that some junk is conserved simply as buffer material to allow for proper 3-D spacing. DNA looks to be brilliantly conceived, much to atheist dismay.-"Feng comments: 
September 10th, 2012 at 2:31 am
The quote from Sydney above that "the "junk" DNA might be required to maintain the viscosity of the nucleus" is really interesting. In a similar vein, we have done some studies, which show that some DNA sequences in the genome may just be "filler" sequences to keep adjacent functional ones from doing too much."-Sean Eddy comments: 
September 10th, 2012 at 6:10 am
 
Feng: I agree, and I think that's part of the slipperiness of the term "function", and why the term "junk" is only a colloquialism. The junk on my desk is junk, but if you suddenly removed it, my coffee cup would fall over and spill into my laptop; the junk has become part of the system.-These comments are from a very decisive discussion by knowledgeable researchers on a very interesting blog:-http://selab.janelia.org/people/eddys/blog/?p=683-And more secearch on gene regulation:-http://medicalxpress.com/news/2012-09-uncovering-genome-regulatory-code.html

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"ENCODE remains a phenomenally successful effort, one that will continue to pay dividends by accelerating basic science research for decades to come. And the issue of what constitutes junk DNA is likely to remain controversialâI expect we'll continue to find more individual pieces of it that perform useful functions, but the majority will remain evolutionary baggage that doesn't do enough harm for us to eliminate it."-"If the confused coverage of ENCODE has done anything positive, it has provoked a public response by a number of scientists. Their criticisms may help convince their colleagues to be more circumspect in the future. And maybe a few more reporters will be aware that this is an area of genuine controversy, and it will help them identify a few of the scientists they should be talking to when covering it in the future."-http://arstechnica.com/staff/2012/09/most-of-what-you-read-was-wrong-how-press-releases-rewrote-scientific-history/2/ -Only some commentators recognize the 3-D spacing requirements. This fellow doesn't. Also that only a tiny portion of cell types were studied. In future studies more functionality in junk will be found, as more cell types are studied. But there will always be 'spacer junk'

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Shapiro's science blog on the controversy. What he calls formatting of DNA I have referred to as setting up spacers in a 3-D setup of DNA so that modifying regions are in the correct position.-http://www.huffingtonpost.com/james-a-shapiro/bob-dylan-encode-and-evol_b_1873935.html

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How DNA moves to bring control sections together:-http://the-scientist.com/2012/09/13/dna-with-a-twist/

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"What the EP results show (though they're not the first or only ones to do so) is how complex and multiply interlinked even our minutest processes are."-It is the complexity, which keeps increasing with every piece of research, that leads me to believe that evolution did not occur by chance and purposelessness:- http://blogs.scientificamerican.com/guest-blog/2012/09/17/junk-dna-junky-pr/?WT_mc_id=S...

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More evidence that junk DNA has purposes. Pineal control of circadian rhythms:- http://medicalxpress.com/news/2012-09-dark-dna-brain-day-night.html

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An evenhanded comment by a creationist says the science is beautiful but does't prove design by God:-http://toddcwood.blogspot.com/2012/09/everyones-excited-about-encode.html

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DAVID: An evenhanded comment by a creationist says the science is beautiful but doesn't prove design by God:-http://toddcwood.blogspot.com/2012/09/everyones-excited-about-encode.html-Good to hear of an even-handed creationist. Of course nothing can "prove" design by God, any more than anything can "prove" design by chance. Nor, if it comes to that, can anyone "prove" that Neo-Darwinism is dead. -As I see it, the junk/not junk argument cuts both ways. An atheist can argue that design has to be functional, anything non-functional suggests lack of design, and so even 20% is 20% too much. A theist can argue that a mechanism capable of adaptation and innovation will have to contain elements that are POTENTIALLY functional, even if they are not used all the time, and we can't know the potential without knowing the full range of possible conditions. However, I would have thought a creationist who believes in the separate creation of all organs and organisms would be hard pressed to justify any non-functional DNA, whatever the percentage. This is where the argument gets muddied. Theism and creationism are not the same thing, though some atheists like to pretend they are. -Only creationists deny the process of evolution, and even in America, a hotbed of creationism, it seems that the population is evenly divided on the subject, according to the article David posted under "Americans and Creationism". 46% believe in creationism, 32% in God-guided evolution and 15% in evolution without God, which = 47% who believe in some form of Darwinism. I'm surprised that only 7% appear not to have any firm belief either way, but can we trust these polls? -If God designed the initial mechanism for reproduction, heredity, adaptation and innovation, the process of evolution can follow precisely the same course as a non-designed mechanism. Once it is in place, it will use what needs to be used in accordance with varying conditions. The only question is whether you believe the INITIAL mechanism is or is not too complex to have arisen by chance.-As regards the overall heading of this thread, if Neo-Darwinism means belief in Natural Selection as the driving force of gradualistic evolution, and random mutations as the cause of innovations, I would agree that it is at least on the way out. If it means that all species descended from earlier forms of life, that changing environments may bring about sudden as well as gradual genetic changes, and hence new organs and organisms, and that Natural Selection decides which of these survive, then it is not dead. But I don't think the percentage of junk DNA makes any difference either way.

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More evidence of important activity in 'junk DNA' No junk here:-"These results also raise the tantalizing question of why transposable elements, derived from viruses, regulate stem cell-specific expression in mammals. Rinn hypothesizes that "transposable elements may not be limited to giving rise to new lincRNA genes, but may also provide an engine for the evolution of RNA-encoding genes. I like to think of it as the 'genome getting dirty': in the same way that kids that play in the dirt develop better immune systems, the genome may be 'getting dirty' with transposable elements, and once in a while, this has an advantageous effect of producing a new lincRNA gene."
 
"What is clear is that transposable elements may control the tissue-specific expression of lincRNAs, thereby affecting the evolution and function of lincRNAs with important regulatory roles. Following on from these results, it will be interesting to determine other ways hopping genes may have shaped lincRNA evolution. Kelley notes that "This study merely scratches the surface of the possible roles of transposable elements influencing lincRNA function.'"-http://www.sciencedaily.com/releases/2012/11/121125192838.htm

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More jumping genes:-"(Phys.org)âTransposable elementsâor transposonsâare DNA sequences that move in the genome from one location to another. Discovered in the 1940s, for years they were thought to be unimportant and were called "junk DNA." But now scientists recognize that these bits of DNA play vital roles in gene and genome evolution, and are important genetic tools for genome engineering." -Read more at: http://phys.org/news/2012-11-scientists-transposons-human-cells.html#jCp

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MicroRNA in the junk areas drives the formation of the three embryologic layers, ectoderm mesoderm and endoderm:-http://medicalxpress.com/news/2012-12-junk-dna-embryonic.html

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Junk DNA is not really junk. Some is non-functional, some is for 3-D spacing and some does contribute as Encode shows. This paper does more explaining:-http://selab.janelia.org/publications/Eddy12/Eddy12-preprint.pdf

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They are all over the place at all levels of complexity in organisms from single cells upwards:-https://aeon.co/essays/genes-that-jump-species-does-this-shake-the-tree-of-life?utm_source=Aeon+Newsletter&utm_campaign=224349e1e1-Saturday_newsletter_19_March_20163_18_2016&utm_medium=email&utm_term=0_411a82e59d-224349e1e1-68942561-"What has become increasingly clear in the past 10 years is that this liberal genetic exchange is definitely not limited to the DNA of the microscopic world. It likewise happens to genes that belong to animals, fungi and plants, collectively known as eukaryotes because they boast nuclei in their cells. The ancient communion between ferns and hornworts is the latest in a series of newly discovered examples of horizontal gene transfer: when DNA passes from one organism to another generally unrelated one, rather than moving vertically' from parent to child. In fact, horizontal gene transfer has happened between all kinds of living things throughout the history of life on the planet - not just between species, but also between different kingdoms of life. Bacterial genes end up in plants; fungal genes wind up in animals; snake and frog genes find their way into cows and bats. It seems that the genome of just about every modern species is something of a mosaic constructed with genes borrowed from many different forms of life.-"What scientists have seen is just a little tip of an immense iceberg,' says Antonio Teixeira, a biologist at the University of Brasilia. W Ford Doolittle, a biochemist at Dalhousie University in Nova Scotia, agrees: horizontal gene transfer, he wrote recently is far more pervasive and more radical in its consequences than we could have guessed just a decade ago'. Researchers have now discovered so many examples of gene transfer between species and kingdoms of life - with many more surely to come - that they have to adjust their understanding of how evolution works. -***-"At this point, the tally is too high to ignore. Scientists can no longer write off gene-swapping among eukaryotes - and between prokaryotes and eukaryotes - as inconsequential. Clearly genes have all kinds of ways of journeying between the kingdoms of life: sometimes in large and sudden leaps; other times in incremental steps over millennia. -***-"The fact that horizontal gene transfer happens among eukaryotes does not require a complete overhaul of standard evolutionary theory, but it does compel us to make some important adjustments. According to textbook theories of evolution, the major route of genes moving between organisms is parent to child - whether through sex or asexual cloning - not this sneaky business of escorting genes between unrelated organisms. We must now acknowledge that, even among the most complex organisms, vertical is not the only direction in which genes travel.-***-"In some cases, this genetic hopscotching could exert a very powerful evolutionary force', says Li. It can introduce novelties that cannot be achieved by gradual genetic mutations.' -***-"As far as DNA is concerned, however, the supposed walls between species are not nearly so impermeable. Up in the branches of the great tree of life, we are no longer immersed in the ancient communal pool that watered its tangled roots. Yet we cannot escape the winds of promiscuity. Even today - as was true from the start - our' genes are not ours alone.-Comment: This is one guidance mechanism by which God could have directed evolution. The perfect dabble! I've skipped the examples of the studies. Fascinating.

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DAVID: They are all over the place at all levels of complexity in organisms from single cells upwards:-https://aeon.co/essays/genes-that-jump-species-does-this-shake-the-tree-of-life?utm_sou... -David's comment: This is one guidance mechanism by which God could have directed evolution. The perfect dabble! I've skipped the examples of the studies. Fascinating.-Thank you for this extremely stimulating article, and for taking so much trouble to edit it for us. Fascinating indeed. I did skim through it for myself, and found just one additional passage I would like to quote in view of your comment:-QUOTE: Scientists such as Ford Doolittle and Carl Woese at the University of Illinois have argued that this portrayal is an oversimplification. Rather than rising from a single trunk, they say, the tree of life stands on an interweaving root system. Rather than evolving from one last universal ancestor', all life arose from a communal pool of primitive cells with unbridled zeal for exchanging DNA. For relatively simple cells with only a handful of genes each, swapping DNA was an excellent strategy for acquiring and preserving the best adaptations around.-Darwin did actually talk of the Creator breathing life into a few forms or one and the idea that evolution proceeded through cells exchanging DNA is immensely attractive. It was the Nobel Laureate Barbara McClintock who pioneered the concept of the jumping gene. She also championed the concept of cellular intelligence, which as you probably know by now is my proposal for an alternative to your God preprogramming and dabbling.

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DAVID: They are all over the place at all levels of complexity in organisms from single cells upwards:
> 
> https://aeon.co/essays/genes-that-jump-species-does-this-shake-the-tree-of-life?utm_sou... 
> 
> David's comment: This is one guidance mechanism by which God could have directed evolution. The perfect dabble! I've skipped the examples of the studies. Fascinating.
> 
> Thank you for this extremely stimulating article, and for taking so much trouble to edit it for us. Fascinating indeed. I did skim through it for myself, and found just one additional passage I would like to quote in view of your comment:-Thank you for your comment.
> 
> dhw: QUOTE: Scientists such as Ford Doolittle and Carl Woese at the University of Illinois have argued that this portrayal is an oversimplification. Rather than rising from a single trunk, they say, the tree of life stands on an interweaving root system. Rather than evolving from one last universal ancestor', all life arose from a communal pool of primitive cells with unbridled zeal for exchanging DNA. For relatively simple cells with only a handful of genes each, swapping DNA was an excellent strategy for acquiring and preserving the best adaptations around.-This point is well known. Woese found the Achaean branch of life's original three populations-> 
> dhw: Darwin did actually talk of the Creator breathing life into a few forms or one and the idea that evolution proceeded through cells exchanging DNA is immensely attractive.-Yes, very attractive as I noted. -> dhw: It was the Nobel Laureate Barbara McClintock who pioneered the concept of the jumping gene. She also championed the concept of cellular intelligence, which as you probably know by now is my proposal for an alternative to your God preprogramming and dabbling.-Yes, we know. Cells have intelligence through intelligent information they contain.

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