Front end loading (Introduction)
by David Turell 
, Saturday, September 20, 2008, 21:07 (5696 days ago)
edited by unknown, Saturday, September 20, 2008, 21:14
There are many examples of front end loading in evolution. Especially in the DNA of ancient organisms. In more complex organisms there are 'exaptations',unused organs that arrive as much as 100,000 years in advance of finally being employed in a real fuction. If one engineers evolution from the beginning, this is how it would be done. - Science 22 August 2008: Vol. 321. no. 5892, pp. 1028 - 1029 DOI: 10.1126/science.321.5892.1028b - GENOMICS: 'Simple' Animal's Genome Proves Unexpectedly Complex - Elizabeth Pennisi - Aptly named "sticky hairy plate," Trichoplax adhaerens barely qualifies as an animal. About 1 millimeter long and covered with cilia, this flat marine organism lacks a stomach, muscles, nerves, and gonads, even a head. It glides along like an amoeba, its lower layer of cells releasing enzymes that digest algae beneath its ever-changing body, and it reproduces by splitting or budding off progeny. Yet this animal's genome looks surprisingly like ours, says Daniel Rokhsar, an evolutionary biologist at the University of California, Berkeley (UCB) and the U.S. Department of Energy Joint Genome Institute in Walnut Creek, California. Its 98 million DNA base pairs include many of the genes responsible for guiding the development of other animals' complex shapes and organs, he and his colleagues report in the 21 August issue of Nature. - Biologists had once assumed that complicated body plans and complex genomes went hand in hand. But T. adhaerens's genome, following on the heels of the discovery of a similarly sophisticated genome in a sea anemone (Science, 6 July 2007, p. 86), "highlights a disconnect between molecular and morphological complexity," says Mark Martindale, an experimental embryologist at the University of Hawaii, Honolulu. Adds Casey Dunn, an evolutionary biologist at Brown University, "It is now completely clear that genomic complexity was present very early on" in animal evolution. - Ever since German zoologist Franz Eilhard Schulze first found Trichoplax more than a century ago in a saltwater aquarium, this disc-shaped animal has stirred debate. It has just four apparent types of cells, prompting Schulze and others to consider it a holdover from the earliest animals. They eventually assigned it to its own phylum, Placozoa. - But not everyone agrees which branch of the animal tree of life is oldest: sponges, comb jellies, or placozoans. And a few researchers have dismissively argued that placozoans are just larvae of cnidarians...jellyfish, sea anemones, and the like...or else a streamlined version of a cnidarian ancestor. - Rokhsar, his graduate student Mansi Srivastava, and their colleagues sequenced a Trichoplax from the Red Sea, finding an estimated 11,514 protein-coding genes. After comparing the sequences of 104 Trichoplax genes with their counterparts in other organisms, they concluded that placozoans aren't the oldest animals; they branched off after sponges but before cnidaria. Placing Trichoplax on the tree "will now allow us to understand how to interpret its biology in the context of animals as a whole," says Dunn. - The sequence is also clarifying what ancient genomes looked like. Trichoplax genes have comparable numbers of introns, noncoding regions interspersed between the coding regions, as vertebrates and as the sea anemone. And many of the same genes were linked on the chromosomes of vertebrates, Trichoplax, and sea anemones, the researchers report. This was not the case with the fruit fly and nematode genomes, whose genes have fewer introns and have moved about quite a bit. - Despite being developmentally simple...with no organs or many specialized cells...the placozoan has counterparts of the transcription factors that more complex organisms need to make their many body parts and tissues. It also has genes for many of the proteins, such as membrane proteins, needed for specialized cells to coordinate their function. "Many genes viewed as having particular 'functions' in bilaterians or mammals turn out to have much deeper evolutionary history than expected, raising questions about why they evolved," says Douglas Erwin, an evolutionary biologist at the Smithsonian National Museum of Natural History (NMNH) in Washington, D.C. - Trichoplax could yet be more complex than observed, perhaps having subtle differences in cell types. Or, the amoeboid form may be just one phase of a complex life cycle that's still undiscovered, says Rokhsar. - The surprises in the Trichoplax genome emphasize the importance of sequencing other early-arising species, such as comb jellies or different kinds of sponges, says evolutionary biologist Allen Collins of the National Marine Fisheries Service and NMNH. "The more taxa we fill in," says Collins, "the clearer our picture will be for how the entire suite of these molecules evolved over the critical time early in metazoan history."
Front end loading
by George Jelliss 
, Crewe, Thursday, September 25, 2008, 20:35 (5691 days ago) @ David Turell
I've not heard of this concept of "front end loading" before. Does it mean that the Intelligent Designer has been identified as the Great front end loader? Does it mean anything other than the metaphor of God as architect or planner? God as project engineer? - This curious story about bedbugs was in the Times on Tuesday. "The females evolved immune organs because of the violent mating techniques adopted by the males, which are armed with needle-like penises that they wield like daggers. Instead of availing themselves of the female genitalia the male bedbugs simply stab them in the abdomen and inject semen into the abdominal cavity. The semen migrates through the female's body to fertilise the eggs." A good example of Intelligent Design, eh? http://www.timesonline.co.uk/tol/news/uk/article4805905.ece - Here's anothet article. Is this an example of "front end loading"? It seems unsurprising to me that structures developed for one function are adapted for other functions by evolution. It is just working with the material it has. "Yale researchers have shown that the origin and evolution of the placenta and uterus in mammals is associated with evolutionary changes in a single regulatory protein." http://www.sciencedaily.com/releases/2008/09/080918171155.htm
Front end loading
by David Turell , Friday, September 26, 2008, 00:29 (5691 days ago) @ George Jelliss
I've not heard of this concept of "front end loading" before. > > Here's anothet article. Is this an example of "front end loading"? It seems unsurprising to me that structures developed for one function are adapted for other functions by evolution. It is just working with the material it has. > "Yale researchers have shown that the origin and evolution of the placenta and uterus in mammals is associated with evolutionary changes in a single regulatory protein." > http://www.sciencedaily.com/releases/2008/09/080918171155.htm - 'Front end loading' is an obvious term if one thinks as I do, and concluded from all the reading I did. It seems curious to me that DNA is arranged million of years in advance to provide a new function when activated probably by RNA in the distant future. It certainly looks like pre-planning, but I agree that certainly doesn't prove that it is. Note that my view comes from the fact that I think DNA and RNA contain coded information, not just making protein by code, but HOX genes RNA managing a group of genes coded with constructional information. Think about building a house. Construction plans have coordinated time lines for various parts. We have recognized some of the controls (HOX and miRNA), but I haven't seen any discoveries in how that control is coded. It has to be very complex, not the simplistic triplet coding for single amino acids. That is why the idea of front-end loading appeals to me. It simplifies the development of complexity. I know that George thinks complexity is just an accident of a chance process, but the arrow of evolution relentlessly pursues complexity. I am not aware of evolution returning to simpler organisms over a prolonged period of time.
Front end loading
I found a science daily article titled "MicroRNAs Found In Animals That Appeared A Billion Years Ago" at http://www.sciencedaily.com/releases/2008/10/081001145018.htm In some of David's post, he has referred to ancient RNA and DNA. Since genetic material doesn't survive in fossils (except small amounts in T-Rex) how can scientists talk about ancient genes. I can see the possibility of finding identical genes in all species within a clade and extrapolating back to the genome for their last common ancestor, but I don't know if that is how it is done, and I don't see how you can then talk about the evolution of that RNA, since all you have is the final product. Does anyone know? Another thought. David talks of "survival of the fittest" being circular. A way to think of it is as a description of a process - "survival of the fittest", "random survival" and "survival of the least fit" in the case of game animals and trophy hunters.
Front end loading
by David Turell , Friday, October 03, 2008, 20:05 (5683 days ago) @ Carl
Carl: I read the article you presented. I interpret it to mean they used living sea anemones and sponges which antidate bilaterians in evolution. Bilaterians appeared just before the Cambrian explosion over 550 million years ago. The scientists appear to have assumed that RNA was present in the genetic material from the appearance of the animals in evolution a billion years ago.
Front end loading
by David Turell , Wednesday, October 08, 2008, 01:43 (5679 days ago) @ David Turell
I was notified about an online discussion for newly discovered RNA molecules with different functions: - "Non-coding RNAs (ncRNAs) are a large group of RNAs that are transcribed, but not translated into protein. They include well-characterized transfer RNAs and ribosomal RNAs, as well as newer and more elusive miRNAs which have been shown to play a crucial role in gene regulation. ncRNAs produce functional RNA molecules rather than encoding proteins and have been found to have roles in a plethora of cellular processes including transcriptional regulation, RNA processing and modification, mRNA stability, and even protein degradation. Even though a large number of genomes have been sequenced, the number and diversity of ncRNA-encoding genes is largely unknown. Many more ncRNAs have been discovered than were predicted, with recent transcriptomic and microarray studies suggesting that, for the mouse genome alone, there exists more than 30,000 long ncRNAs. The challenge now facing researchers is to determine the size of the full compliment of ncRNAs, as well as elucidate their function, particularly in disease. This online discussion will center on the different forms of ncRNAs, and the roles they may play in the biology and pathology of human disease." - The mouse genome contains more functional RNA numerically than the genes themselves. Imagine what our genome will turn up when this research into the different RNA's is completed. This is a master code within a master code. Layer after layer of functionality. Human experience with coding inplies intelligent planning and activity. It still looks like front end loading to me.
Front end loading
David, you say about genomes, "Human experience with coding implies intelligent planning and activity." It seems that sheer genome complexity alone will never provide enough evidence for intelligent design for a researcher to get an article published in a peer reviewed magazine. In your opinion, what type of evidence would be required to get an intelligent design article peer reviewed, published and supported by a moderate percentage of the scientific community?
Front end loading
by David Turell , Tuesday, October 14, 2008, 16:47 (5672 days ago) @ Carl
In your opinion, what type of evidence would be required to get an intelligent design article peer reviewed, published and supported by a moderate percentage of the scientific community? - Carl: I'm sorry, but the way things are set up 90% of leading scientists are atheists and they are very upset by intelligent design proposals. ID folks interpret science findings, but are not on the leading edge of primary research. I would guess in about ten years as more and more evidence builds up some scientists will begin to accept the issue of ID as an area of discussion. God is purposely concealed. He can only be inferred, never proven absolutely, which is why Mortimer J. Adler proposed "proof beyond a reasonable doubt"; which is what I accept. In my book I cover all of the probabalistic odds in favor of reasonable doubt.
Front end loading
by David Turell , Tuesday, November 11, 2008, 18:22 (5644 days ago) @ David Turell
One of the key issues I addressed in my book was the theory that organisms could control their own evolution, known initially as "The Baldwin Effect" but also proposed earlier by Alfred Wallace at a time when Darwin was making his theory known. Reznick's guppies in south american rivers were the first clear proof that something of this sort existed, published about 1998. Here is another new example. The actual article is not on line as yet so that I can not study it directly, but this is the Princeton PR blurb: http://www.princeton.edu/main/news/archive/S22/60/95O56/index.xml?section=topstories All of biology has feedback loops that act as thermostats act for furnace heat. This is another of many loops that have been discovered. A loop of this sort implies that a great deal of information had to be developed to allow this to go on beneath the level of normal mutation. Obviously, an organism that can direct its own evolution to fight a rapidly changing hostile environment is at a great advantage. But if one believes in Darwinian step-by-step development, and feedback loops have several steps, the issue has to be raised, what caused each intermediate step to be conserved through many generations if each step, of its own, has no immediate value?
Front end loading
by David Turell , Wednesday, November 12, 2008, 20:55 (5643 days ago) @ David Turell
No one has commented on this new discovery about evolution. What is startling to me is the implication of pre-planning and what the article says about the authors reaction to their discovery. They are obviously startled also and have to put in the following disclaimers about ID: - "In this paper, we present what is ostensibly the first quantitative experimental evidence, since Wallace's original proposal, that nature employs evolutionary control strategies to maximize the fitness of biological networks," Chakrabarti said. "Control theory offers a direct explanation for an otherwise perplexing observation and indicates that evolution is operating according to principles that every engineer knows." - The scientists do not know how the cellular machinery guiding this process may have originated, but they emphatically said it does not buttress the case for intelligent design, a controversial notion that posits the existence of a creator responsible for complexity in nature. - Chakrabarti said that one of the aims of modern evolutionary theory is to identify principles of self-organization that can accelerate the generation of complex biological structures. "Such principles are fully consistent with the principles of natural selection. Biological change is always driven by random mutation and selection, but at certain pivotal junctures in evolutionary history, such random processes can create structures capable of steering subsequent evolution toward greater sophistication and complexity." - Stated as a result of their faith in science and pure conjecture and speculation, without a shred of evidence to support this view.
Front end loading
I've now read the essays that David recommended: Does Nature Suggest Transcendence? by Neil D. Broom, and Current Stories by Kitta MacPherson. The bulk of the first consists in picking to pieces the arguments of the material biologists, in particular their various analogies, all of which in fact suggest conscious design. Broom's own image of the self-producing internal combustion engine is akin to Hoyle's Boeing 747, and if I may say so, David's own book contains a far clearer and more convincing analysis of the evidence. I shan't pretend to understand the details underlying the new discovery of "control theory" in the second essay, but when researchers talk of self correcting, steering, machinery, fine-tuning etc., again I find it difficult to equate such language with the random actions of chance, as they do. - There was a similar bias in the Sunday Times this week, with an article headlined: A brief encounter and life erupts. The subheading reads: Scientists have pinpointed the single tiny event that created all plants, and the opening paragraph reads: "Scientists have identified the single chance encounter about 1.9 billion years ago to which almost all life on Earth owes its existence." We are told that an amoeba-like organism engulfed a bacterium that had developed the power to use sunlight to break down water and liberate oxygen. The bacterium was probably intended as prey but instead it became incorporated into its attacker's body ... turning it into the ancestor of every tree, flowering plant and seaweed on Earth. Paul Falkowski, professor of biogeochemistry and biophysics at Rutgers University says: "The descendants of that tiny organism transformed our atmosphere, filling it with oxygen needed for animals and, eventually, humans to evolve." One of the accompanying diagrams (headed "How it all began") contains the following caption: "First plants colonised land 475m years ago, creating conditions for primitive land animals to follow 75m years later." - There is more in the article about chloroplasts and cyanobacteria, and what one researcher calls "a series of unique chance events". One presumably shouldn't ask where the amoeba and the bacterium, or for that matter the "primitive land animals" came from. Is it to be taken for granted that once you have plants, you will automatically have animals evolving to feed off them? But even if one grants the possibility that this whole process may have been the result of chance encounters, why do such researchers say categorically that it was? Every new discovery gives us insights into the extraordinary complexity of life and reproduction. Shouldn't scientists remain objective and tell us what may have happened without insisting that they also know the force that made it happen? I'm not taking sides here. It just seems to me that there's no difference between one scientist saying God did it, and another saying Chance did it. In both cases, faith subverts science.
Front end loading
by George Jelliss , Crewe, Thursday, November 13, 2008, 20:06 (5642 days ago) @ dhw
dhw: "I'm not taking sides here. It just seems to me that there's no difference between one scientist saying God did it, and another saying Chance did it. In both cases, faith subverts science." - We know Chance exists, God is a wee bit more doubtful.
Front end loading
by David Turell , Thursday, November 13, 2008, 20:44 (5642 days ago) @ George Jelliss
In both cases, faith subverts science.[/i]" > We know Chance exists, God is a wee bit more doubtful. - George you are quite right. I think it really is an equal flip of the coin, because of the prodigious odds against chance having done the creation of what does exist. And where we differ is that I see a continuous development by science of evidence of engineering, the coding in DNA/RNA to guide the process of evolution. The scientists are only at the beginning of this area of research, and I 'sense' that complexity after complexity will appear with all sorts of 'feed back loop' engineering, back-checking the process.
Front end loading
by George Jelliss , Crewe, Friday, November 14, 2008, 10:30 (5641 days ago) @ David Turell
DT: "George you are quite right." - I'm always immediately suspicious when David says he agrees with me! - DT: "I think it really is an equal flip of the coin, because of the prodigious odds against chance having done the creation of what does exist." - The odds against the existence of Chance and the existence of God are not a 50-50 flip of the coin. Chance we know exists. It obeys the laws of ststistics. God I'm pretty certain doesn't exist, but that is the whole subject of this forum. - I can only repeat what I've said many times before. Evolution depends on an initial chance event, but that is only the trigger for an inevitable sequence of events that follow, due to the action of laws of nature, such as gravity or chemical reactivity. It is not chance alone that does the creation. You may recall the golfing tragedy I used as an illustration. The overall event dhw insisted on calling an "accident" even though most of it was inevitable. Given enough time and enough variation in the situations an accident of the right creative type is inevitable.
Front end loading
by David Turell , Friday, November 14, 2008, 14:40 (5641 days ago) @ George Jelliss
DT: "I think it really is an equal flip of the coin, because of the prodigious odds against chance having done the creation of what does exist." - > Given enough time and enough variation in the situations an accident of the right creative type is inevitable. - George: This is where we part ways. There are only 10^18th power seconds in the life of the universe. Calculations of information theory, using statistical Shannon information theory, indicate that there hasn't been enough time available for your 'accident of chance', particularly since life appeared about 3.6 bya leaving only 10 bya for the accident. Saying chance exists is a truism which ignores the proper definition of chance within a scientific framework of study: the scientific study of statistical probabilities and a probability bound of chance. The age of the universe is finite. The chance of your evolution accident approaches infinity. This puts the odds of an intellectual force planning evolution in my favor.
Front end loading
George: "We know Chance exists, God is a wee bit more doubtful." - A great response, George, but not to my initial question, which was: "Shouldn't scientists remain objective and tell us what may have happened without insisting that they also know the force that made it happen?" What I object to is the use of expressions like "chance encounter" and "a series of unique chance events". It's a subversive way of using the supposed objectivity of science to push through a theory that has no scientific basis, i.e. that life originated by chance. I have no problem with someone's belief that this was so, but it should not be stated as if it were a fact, and that is what is implied by these subtle insertions. Imagine the howls of rage if a scientist said, "God made the amoeba engulf the bacterium", or "God used this method to create all plants, and 75m years later created the primitive land animals that followed." That, however, is just the religious equivalent of "chance" encounters, events etc. You and David are both scientists looking at the same sets of facts, and you draw different conclusions, as is clear to anyone following our discussions. But when a popular newspaper publishes a scientific article quoting a team of authoritative-sounding scientists, it's not so clear where science ends and faith begins.
Front end loading
by David Turell , Friday, November 14, 2008, 17:22 (5641 days ago) @ dhw
George: "We know Chance exists, God is a wee bit more doubtful." > A great response, George, but not to my initial question, which was: "Shouldn't scientists remain objective and tell us what may have happened without insisting that they also know the force that made it happen?" But when a popular newspaper publishes a scientific article quoting a team of authoritative-sounding scientists, it's not so clear where science ends and faith begins. - Exactly. All I have said is that it can be mathematically demonstrated that chance DOES NOT have a chance. Darwin thought the universe was eternal, which allowed him time for his step-by-step method. It takes a certain type of planet with a certain type of sun that ages long enough for life to appear, if we can use Earth as the proper example. There is a finite time to allow this to happen.George appears to think the step-by-step method has infinity to work, which is not the case. George is exhibiting faith in Darwin's method. Reason is not involved.
Front end loading
by George Jelliss , Crewe, Saturday, November 15, 2008, 08:57 (5640 days ago) @ David Turell
DT: "All I have said is that it can be mathematically demonstrated that chance DOES NOT have a chance. Darwin thought the universe was eternal, which allowed him time for his step-by-step method. It takes a certain type of planet with a certain type of sun that ages long enough for life to appear, if we can use Earth as the proper example. There is a finite time to allow this to happen. George appears to think the step-by-step method has infinity to work, which is not the case. George is exhibiting faith in Darwin's method. Reason is not involved." - Obviously I dispute your figures. Infinity would be a slight overestimate! I don't have time at present to look more deeply into your mathematics, since I'm in the middle of moving house, but will do so in due course.
Front end loading
by David Turell , Saturday, November 15, 2008, 16:42 (5640 days ago) @ George Jelliss
George, we shall wait for you to return from your house move, but in the meantime please read this article from the N.Y. Times showing how complex the DNA/RNA system is, how far beyond Watson-Crick: http://www.nytimes.com/2008/11/11/science/11gene.html?pagewanted=1&_r=1 I get dizzy thinking about how many complex moves those little molecules have to do, with RNA leading exons around like we take a dog for a walk!
Front end loading
by George Jelliss , Crewe, Saturday, November 15, 2008, 19:37 (5640 days ago) @ David Turell
Yes, I found that article fascinating. But it doesn't seem to me to show the DNA/RNA system to be "complex" in the sense of being designed. It shows just how chaotically "undesigned" it is. Engineers would not design a machine in which one component "drags along unnecessary excess baggage" or which gets contaminated by the "rotting carcases" of extraneous interlopers! - Here are some quotes from the article: - David Haussler, another Encode team member at the University of California, Santa Cruz, agrees with Dr. Birney. "The cell will make RNA and simply throw it away," he said. - Dr. Haussler bases his argument on evolution. If a segment of DNA encodes some essential molecule, mutations will tend to produce catastrophic damage. Natural selection will weed out most mutants. If a segment of DNA does not do much, however, it can mutate without causing any harm. Over millions of years, an essential piece of DNA will gather few mutations compared with less important ones. - Only about 4 percent of the noncoding DNA in the human genome shows signs of having experienced strong natural selection. Some of those segments may encode RNA molecules that have an important job in the cell. Some of them may contain stretches of DNA that control neighboring genes. Dr. Haussler suspects that most of the rest serve no function. - "Most of it is baggage being dragged along," he said. - --- - "Our genome is littered with the rotting carcasses of these little viruses that have made their home in our genome for millions of years," Dr. Haussler said. - --- - These new concepts are moving the gene away from a physical snippet of DNA and back to a more abstract definition. "It's almost a recapture of what the term was originally meant to convey," Dr. Gingeras said. - This is another good example of the way scientific research moves on. Older over-simplified ideas get discarded in light of new information.
Front end loading
by David Turell , Sunday, November 16, 2008, 01:43 (5640 days ago) @ George Jelliss
Yes, I found that article fascinating. But it doesn't seem to me to show the DNA/RNA system to be "complex" in the sense of being designed. It shows just how chaotically "undesigned" it is. Engineers would not design a machine in which one component "drags along unnecessary excess baggage" or which gets contaminated by the "rotting carcases" of extraneous interlopers! > Here are some quotes from the article: - George: It is a fascinating ability of yours to quote only those portions of the article that support your position. The article in totality describes an extraordinary overlay of RNA control which makes many segments of DNA able to make over 5 different proteins, thereby changing our paltry number of genes (now 21,000) into an instrument of heredity that is equal to the 100,000 genes originally predicted before DNA was analyzed into gene structure. - Yes, some junk genes are discarded, viral DNA sequestered, etc., but once again you are confusing 'optimal design' with 'perfect design'. After all what we are seeing is an optimal design if we conclude that evolution proceeded from simple to complex and handled the errors and viral invasions as well as it did. Human engineers are not faced with invaders of their machines, but we do have viruses attacking our computers, and lo-to-behold, engineers have found a way to thwart them! So did the DNA/RNA mechanism. I think it is amazingly complex, junk and all.
Front end loading
by David Turell , Tuesday, November 18, 2008, 22:07 (5637 days ago) @ David Turell
I would like to continue to present the newly found complexities of life by exhibiting science articles written for the lay public: they are easy to follow. This article discusses what happens when DNA is unwound to do some copying, which is the way copying happens, and then DNA has to be rewound. The authors have found an enzyme that does just that. http://www.sciencedaily.com/releases/2008/10/081030144615.htm When Darwin thought his living matter was simply blobs of protoplasm, his theory was easy to concoct. We no know that cells are manufacturing factories with very complex feedback loops, hundreds of different proteins, hundreds of amino acids long, and folded properly in order to fulfill their required fuction.
Front end loading
by David Turell , Tuesday, November 18, 2008, 22:17 (5637 days ago) @ David Turell
This is a second article I discovered today. I have always wondered how cells communicated in adult animals or plants but also in the embryonal stage when the morphology of the organism is being built. We have all seen blueprints for our homes, and there also is a building plan to order the timing of construction so as not to get one part in the way of another. Can't cover the walls until the electric lines are in place, as a simple example. This is a totally new finding in the past four years. http://www.newscientist.com/article/mg20026821.400-tunnelling-nanotubes-lifes-secret-ne...
Microcosms
David is keeping us up to date with the latest discoveries relating to the "complexities of life". - First of all, I'd like to thank you for this invaluable research service, and for the brief summaries with which you comment on the articles. For non-scientists like myself, all of this is extremely helpful. - I was particularly impressed with the "tunnelling nanotubes". David and George disagree on whether such extraordinary mechanisms denote the workings of design or of chance, but reading about them has set me off on another track. Our bodies are simply filled with these organisms over which we have no control, and of which we are not even conscious. It's as if we ourselves are worlds harbouring various kinds of life, which operate independently yet interdependently. The unifying force is our self. This brings us back to the question of our identity: I am the sum of all my parts, but I sense that I am more than that sum, that I have a character that transcends my physical self. - If we stretch the analogy further, we might see the universe as a body. Its parts work independently but interdependently. And just as I am the unifying force for my cells, my DNA, my "tunnelling nanotubes", perhaps there is another unifying "I" that binds together our universe. I don't want to carry the analogy any further at this stage, and am aware that there is nothing original about the idea ... it is, after all, the very basis of David's panentheism ... but it poses the question: are we ourselves microcosms? If so, of what?
Microcosms
by David Turell , Thursday, November 20, 2008, 15:07 (5635 days ago) @ dhw
I am the sum of all my parts, but I sense that I am more than that sum, that I have a character that transcends my physical self. > but it poses the question: are we ourselves microcosms? If so, of what? - Here I am giving a link to a mind/body symposium. I have read several of the participants and they are non-materialistic scientists. Bruce Greyson is a psychiatrist who studies near to death. Newberg scans meditating brains. These folks believe the mind arises from the material brain, and feelings of self as a separate entity are real. Materialist scientists think the self is an illusion. http://www.mindbodysymposium.com/ I do not agree with the materialists. Baby brains are stimulated to grow and develop thru intellectual contact, one mind contacting another developing one. - We are a microcosm of 10 million cells many of which are doing their own thing. We have autonomic and voluntary nervous systems, for example.
Front end loading
by David Turell , Friday, November 21, 2008, 00:45 (5635 days ago) @ David Turell
The new and amazing findings keep pouring out of the literature. Cyanobacteria are blue-green algae, and so ancient (about 3.5 bya) they appeared about the time life started on Earth. They had to come first or we would not be here. They use photosynthesis for energy (as do all plants generally), burning CO2 and making oxygen as a result. At the time they appeared the atmosphere had very little oxygen, and what became present allowed animal life to appear. - Like many organisms they have a circadian rhythm, which allows adaption to light and dark, day by day. The biochemical mechanism has now apparently been found: http://www.sciencemag.org/cgi/content/abstract/322/5902/697 The article itself describes a complex cascade of biochemical reactions, but note the sentence in the summary about the organism's chromosome changing every day and the changes drive the molecular reactions in one direction only. It looks like Paley's watch mechanism has been found! Unless driven by enzymes many organic chemical reactions can result in back and forth reactions. - The moral: Darwin's mechanisms have only a finite time to create all of this complexity, but the apparent complexity of living matter continues to increase and increase exponentially, continuing to raise the issue: was there enough time for Darwin's theory to create us?
Front end loading
by David Turell , Saturday, November 29, 2008, 00:44 (5627 days ago) @ David Turell
There are many examples of front end loading in evolution. > - The Telegraph article cited here raises another issue. Karen Armstrong in her book, 'The History of God', makes the point that we seem to be created to believe. The temporal lobe of the brain contains an area, called the "God Spot", which gives some people religious experiences, and can be set off by epilepsy, for example. The Telegraph article describes research which seems to show that children are programmed to believe. http://www.telegraph.co.uk/news/newstopics/religion/3512686/Children-are-born-believers...
Front end loading
by George Jelliss , Crewe, Sunday, November 30, 2008, 11:49 (5625 days ago) @ David Turell
A. C. Grayling has answered this better and more comprehensively than I can. - http://www.guardian.co.uk/commentisfree/2008/nov/28/religion-children-innateness-barrett - His article is also reproduced on richarddawkins.net, with many more comments. - I also heard Lewis Wolpert express similar views in a radio interview about this "research". - There was also a recent Radio 4 serialisation of a book by a missionary who spent many years with an Amazonian tribe, and lost his faith, when he found that they did not have any belief in a god. They just accepted nature as what it is, but had a concept of other layers of worlds, above and below.
Front end loading
by David Turell , Sunday, November 30, 2008, 22:54 (5625 days ago) @ George Jelliss
A. C. Grayling has answered this better and more comprehensively than I can. < - I agree with Grayling that the conclusion about children is a stretch. In American Child Psychiatry class it is pointed out that children believe in magic, and don't have the initial experience to figure out why certain things happen as if by magic. An extreme example is young chidren can get very angry about restrictions, and wish someone injured or dead. If the injury or death then occurs in close proximity in time to the child's thought, the child thinks he really caused the event, and may need counselling to straighten out the true understanding of what happened. - On the other hand, as I have mentioned in the past, Andrew Newberg's book, "Why God Won't Go Away", tells us of his studies of how the brain responds to religious activities and may enhance them. There appears to be more going on than just chilhood belief in magic.
Front end loading
by George Jelliss , Crewe, Saturday, August 29, 2009, 17:04 (5353 days ago) @ David Turell
I've just been reading this article which was cited on RD.net: - http://www.wired.com/wiredscience/2009/08/reduciblecomplexity/ - It occurred to me that the concept of "neutral evolution" is very similar to "front end loading", but requiring no divine input. - However, as I've expressed before, it seems obvious that evolution can only work with what it has, by cobbling together preexisting bits. How else could it work?
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GPJ
Front end loading
by David Turell , Saturday, August 29, 2009, 18:31 (5353 days ago) @ George Jelliss
http://www.wired.com/wiredscience/2009/08/reduciblecomplexity/ > It occurred to me that the concept of "neutral evolution" is very similar to "front end loading", but requiring no divine input. - Uncommen Descent has an answer for this: - Wired.com has a new article about why ID isn't science because it's been falsified. Usually the tactic against ID is that it isn't a science because it isn't falsifiable. I reckon use whatever club is closest at hand when you're interested only in beating ID instead of being consistent. The article states: - "You look at cellular machines and say, why on earth would biology do anything like this? It's too bizarre," he said. "But when you think about it in a neutral evolutionary fashion, in which these machineries emerge before there's a need for them, then it makes sense." - "In which these machineries emerge before there's a need" for the machineries. I don't see how that makes any sense. Evolution is supposed to be a stepwise mechanism of solving problems, now they get solved before there is a problem. The article basically makes the assertion that if parts of a whole mechanism are found somewhere else, operating or not operating in any other capacity whatsoever, then the whole mechanism in question is explained by virtue of finding some component parts. If I found an engine foreign to me, I would not be overjoyed to explain it, as a whole, by finding bolts and cylinders and iron lying about, and noticing that the engine uses all three. My first inclination would not be "It was simply a matter of time before they came together into a more complex entity." But that is exactly the argument being made: - But new research comparing mitochondria, which provide energy to animal cells, with their bacterial relatives, shows that the necessary pieces for one particular cellular machine — exactly the sort of structure that's supposed to prove intelligent design — were lying around long ago. It was simply a matter of time before they came together into a more complex entity. - The pieces "were involved in some other, different function. They were recruited and acquired a new function..." - It was just a matter of time before they came together into more complexity? Really? That's a belief system showing it's cards. And how this follows, without seeing the "coming together" itself, is fanciful, to use a kind word. - According to evolutionary theory, however, cellular complexity is reducible. It requires only that existing components be repurposed, with inevitable mutations providing extra ingredients as needed. - Repurposed, recruited, with a dash of mutation for the bread to rise. Did we witness this recruitment, or must it be so for an evolutionary explanation? It must be so, and it has not been witnessed. And what was the purpose before that purpose? Do you have an infinite regress of purposes and recruitments until you get to single molecules that had no purpose? It seems so: - The process by which parts accumulate until they're ready to snap together is called preadaptation. It's a form of "neutral evolution," in which the buildup of the parts provides no immediate advantage or disadvantage. Neutral evolution falls outside the descriptions of Charles Darwin. But once the pieces gather, mutation and natural selection can take care of the rest, ultimately resulting in the now-complex form of TIM23. - How does one even begin to sort through the assumptions? That peices gather together somehow, none falling off the wagon, snap together, fit, that somehow even if they did gather together it wouldn't be a total wreckage, but rather become a cohesive and intricately connected and symbiotic whole beginning to operate as a machine at 3:00 pm on a Thursday, with mutation and natural selection thrown in to supervise the whole endeavor and "take care of the rest", whatever that means. - Well, you get the idea. And it is an idea, if nothing else. Not an evidentially discerned causal explanation, only, rather, the only possible explanation that a Darwinist has. Find the parts, add natural selection and mutation, and you get the whole. What about actual observation, you ask? Apparently, not necessary, because we are, after all, only trying to satisfy a philosophical presupposition of explanation that must turn from simple to complex, and finding some scattered parts is good enough. Actually seeing the increase in the complexity is not necessary for this kind of "science."
Front end loading and loss of information
by David Turell , Sunday, June 19, 2016, 19:40 (2867 days ago) @ David Turell
One of the major discoveries in the study of DNA across species, as pointed out by Michael Behe is loss of information is what drives evolution. This is now being confirmed i9n recent studies. This implies that all the information for evolution was present at the beginning of life and with removal of some of it evolution advances, the exact opposite of what one would expect: - http://www.nature.com/nrg/journal/v17/n7/full/nrg.2016.39.html - Abstract: "The recent increase in genomic data is revealing an unexpected perspective of gene loss as a pervasive source of genetic variation that can cause adaptive phenotypic diversity. This novel perspective of gene loss is raising new fundamental questions. How relevant has gene loss been in the divergence of phyla? How do genes change from being essential to dispensable and finally to being lost? Is gene loss mostly neutral, or can it be an effective way of adaptation? These questions are addressed, and insights are discussed from genomic studies of gene loss in populations and their relevance in evolutionary biology and biomedicine." - This is how the ID group views this: - http://www.uncommondescent.com/intelligent-design/the-war-is-over-we-won/ - "Many years ago, I predicted that modern genome sequencing would eventually prove one side of the argument to be right. This review article indicates that ID is the correct side of the argument. What they describe is essentially what ID scientist, Michael Behe, has termed the “First Principle of Adaptation.” (Which says that the organism will basicaly ‘break something' or remove something in order to adapt) This paper ought to be the death-knell of Darwinism, and, of course, “neo-Darwinism,” but, even the authors who report this new “perspective” have not changed their Darwinian perspective. Somehow, they will find a way to tell us that the Darwinian ‘narrative' always had room in it for this kind of discovery. - *** - From the paper: - "However, genomic data, which is accumulating as a result of recent technological and methodological advances, such as next-generation sequencing, is revealing a new perspective of gene loss as a pervasive source of genetic change that has great potential to cause adaptive phenotypic diversity." - Author interview: " The genome sequencing of very different organisms has shown that gene loss has been a usual phenomenon during evolution in all life cycles. In some cases, it has been proven that this loss might mean an adaptive response towards stressful situations when facing sudden environmental changes” says Professor Cristian Cañestro." - “In other cases, there are genetic losses -says Cañestro- which even though they are neutral per se, have contributed to the genetic and reproductive isolation among lineages, and thus, to speciation, or have rather participated in the sexual differentiation in contributing to the creation of a new Y chromosome. The fact that genetic loss patterns are not stochastic but rather biased in the lost genes[pav: IOW, this is where you're going to find the genomic differences between species you compare] (depending on the kind of function of the gen or its situation in the genome in different organism groups) stresses the importance of the genetic loss in the evolution of the species." - Comment: Perhaps God did start life front end loaded!