“Junk DNA”’s defender doesn’t “do politeness”?

_{Denyse O'Leary

May 8, 2014

'Junk DNA', Darwinism, News}

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The Darwinians do seem to be biting back, to judge from yesterday in Nature:

The latest ENCODE report drew wide attention on Twitter. The paper didn’t provide any estimates about the proportion of the human genome that is functional; instead, it laid out the case that any accurate inventory of the functional parts of the genome must include evolutionary, genetic and biochemical data.

Given the history, some Twitter users wondered how Graur would respond. He soon ended the suspense with a series of tweets blasting ENCODE’s statistics and methodology. In one, he wrote that “the recent half-hearted recantation of #ENCODE was published without a press release.” In his blog post, he wondered why the ENCODE consortium seemed so eager to back away from its “80%” claim. Through it all, he admittedly showed very little tact. “I believe science is a search for the truth, not a lesson in manners,” he says. “I don’t do politeness.”

Kellis says that ENCODE isn’t backing away from anything. The 80% claim, he says, was misunderstood and misreported. More. (paywall)

Actually, ENCODE was neither misunderstood nor misreported. Life just wasn’t doing what Darwin’s followers said it was supposed to, and ENCODE reported that fact.

For free highlights of the junk DNA uproar, see:

Anyone remember ENCODE? Not much junk DNA? Still not much. (Paper is open access.)

Yes, Darwin’s followers did use junk DNA as an argument for their position.

Another response to Darwin’s followers’ attack on the “not-much-junk-DNA” ENCODE findings

By the time you can’t tell the difference between Darwin’s elite followers and his trolls, you know something is happening.

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Comments

Fascinating to look back from 2019 at the exchanges. Bits of Junk DNA are now seen as food storage. No vestigials, no junk. Much egg on face.Belfast_{January 19, 2019
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That was supposed to be a quote:
Darwinism is unfalsifiable, because it can handle either extreme prediction.
-QQuerius_{May 10, 2014
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Timaeous @ 80 . . . Nicely put. Darwinism is unfalsifiable, because it can handle either extreme prediction. As well as almost anything else under investigation. The headlines are almost always, "Researchers surprised at X," Prominent evolutionary scientist n at i, attributes this finding to T: "What must have happened is that m and p, led to t, and this gives us new insight on how evolution works." The Theory of Evolution accommodates and explains everything, but predicts nothing. -QQuerius_{May 10, 2014
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Feynman lectures on how Science should be done. I'm afraid he would think Evo Bio is infested with "Cargo Cult" Scientists. http://www.youtube.com/watch?v=yvfAtIJbatg&feature=youtube_gdata_playerppolish_{May 10, 2014
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phoodoo (4): Good question, but jlafan is far too spineless to commit himself to a numerical prediction. After all, if the prediction were falsified, what would he do then? Darwinism is essentially unfalsifiable with reference to the amount of junk DNA. If there is lots of junk, the atheists and TEs will argue (as they have -- Miller, etc.): "and this is just what we would expect from a process like Darwinian evolution, which builds without plan or purpose in an ad hoc manner from whatever is lying around in the DNA junkyard." And if it turns out that 99% of DNA is functional, Darwinians can always change their argument to: "That's just what we would expect if natural selection is as strong as Darwin said it was! Selection would cause organisms not to waste energy conserving junk, and would tend over time to produce DNA that is nearly 100% functional." Darwinism is unfalsifiable, because it can handle either extreme prediction. On the other hand, if Darwinism were a precise enough theory to give a rough number range, say: "We predict that between 5% and 22% will be found useful to the organism," then Darwinism would be a scientific theory. Science has to have numbers attached to it. (Galileo.) To the extent that Darwinian theory can attach no numbers to its prediction of junk DNA, it is not a scientific theory. It's not surprising that jlafan gives no numbers; he hasn't taken a science course since 9th-grade biology. What is shocking is that professors of evolutionary biology at Harvard etc. aren't compelled to give numbers. If they have a viable scientific theory, they should be able to tell us roughly how much junk DNA we can expect. 10%? 50%? 80%? Not one of them will give a numerical prediction. No professor of experimental physics or chemistry could get away with avoiding numerical predictions like that. This shows how loose the scientific standards are in evolutionary biology.Timaeus_{May 10, 2014
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"Nothing in the recent research or commentary on the subject has challenged these observations." I would think challenges are a good thing. The writers of that paper (L.Moran et al) seem a bit defensive. A bit biased. That can't be good science.ppolish_{May 10, 2014
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wd400:
If you are “seriously looking for answers and open to truth”, you might want to do some research on the arguments for junk. here’s a place to start
"Yet, it is simply not true that potential functions for noncoding DNA were ignored until recently. In fact, various early commenters considered the notion that large swaths of the genome were nonfunctional to be “repugnant”, and possible functions were discussed each time a new type of nonprotein-coding sequence was identified..." But that didn't stop the atheists/materialists using "junk DNA" as an argument for materialism/atheism. "In this review, we examine several lines of evidence—both empirical and conceptual—that support the notion that a substantial percentage of the DNA in many eukaryotic genomes lacks an organism-level function and that the junk DNA concept remains viable post-ENCODE." Perhaps looking at the genome of the onion isn't the best way to determine how much "junk" there is in the human genome. So give ENCODE some credit, at least they are looking in the right place.Mung_{May 10, 2014
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Mung’s nearly neutral theory of dumpster diving. Dr JDD:
We are told that a random neutral mutation that confers no advantage can get fixed within the genome. Yet you are not affording the same possibility to a random neutral deletion.
It seems to me that by analogy you are asserting that we can’t argue for the accumulation of junk in the local landfill because we haven’t taken into account dumpster diving.Mung_{May 10, 2014
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I am using a bit of simplistic hyperbole when I say 98% is junk because many pro-evolutionists (several on here) will still state 98% is junk. So there is disparity within naturalists regarding this. I know full well many people do not consider 98% to be junk No one who knows what they are talking abuout thinks all non-coding sequences are junk. I don't know who made that claim here but they are obviously wrong. and some recently posted articles I posted in other threads show publications where secular scientists make statements that we know now a lot of apparent “junk” DNA is not junk after all. These people however tend to be not evolutionary biologists so they do not need to rely on there being junk present and it doesn’t bother their science as much thinking about the implications of much of non-coding DNA having function. It's true that the people who think genomes are near junless don't know much about evolution. It's not true that evolutionary biology "needs" a junky genome. We are told that a random neutral mutation that confers no advantage can get fixed within the genome. Yet you are not affording the same possibility to a random neutral deletion. This is my point – you cannot have it one way and say it cannot work the other way Right, so under neutrality both types of variant get fixed at the rate which they appear in individuals. Since the rate that junky sequences like ALUs and LINEs and (historically) all those now broken transposons get copied it much greater than they appear we have a ratchet by which junk can accrue. (Of course, some of the elements are later co-opted into functional genes, as we see in the human genome) Taking all the current evidence from ENCODE, FANTOM, recent findings about pseudogene function and lncRNAs Of course some non-coding DNA is functional, and the proportion of the genome assinged to biological function can only go up. But the bestfor junk DNA are not about the fact we can't assign most of the genome to biological function (and it's ignorant to pretent they are), so the slow trickle of functional elements (and the silly headlines from which ENCODE has quietly resiled) don't add up to much (all the lncRNAs, for instance, add up to less thatn one percent of the genome)wd400_{May 10, 2014
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For decades, there has been considerable interest in determining what role, if any, the majority of the DNA in eukaryotic genomes plays in organismal development and physiology. The ENCODE data are only the most recent contribution to a long-standing research program that has sought to address this issue. However, evidence casting doubt that most of the human genome possesses a functional role has existed for some time. This is not to say that none of the nonprotein-coding majority of the genome is functional—examples of functional noncoding sequences have been known for more than half a century, and even the earliest proponents of “junk DNA” and “selfish DNA” predicted that further examples would be found. Nevertheless, they also pointed out that evolutionary considerations, information regarding genome size diversity, and knowledge about the origins and features of genomic components do not support the notion that all of the DNA must have a function by virtue of its mere existence. Nothing in the recent research or commentary on the subject has challenged these observations.
The old "there is no non-functional DNA" straw-man.Mung_{May 10, 2014
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Querius, I agree completely. We should refer to these regions as non-classical coding DNA. They may well code for something or have function that involves a "code" however we have not fully ellucidated this yet. The problem is that low-hanging fruit looks the most tempting - and it is too easy for people to use unknown function to advance their theory of life. Sadly you are correct, much is antithetical in neo-Darwinism. wd400: I am using a bit of simplistic hyperbole when I say 98% is junk because many pro-evolutionists (several on here) will still state 98% is junk. So there is disparity within naturalists regarding this. I know full well many people do not consider 98% to be junk and some recently posted articles I posted in other threads show publications where secular scientists make statements that we know now a lot of apparent "junk" DNA is not junk after all. These people however tend to be not evolutionary biologists so they do not need to rely on there being junk present and it doesn't bother their science as much thinking about the implications of much of non-coding DNA having function.
Selection can only work on genetic variance withing on generation. The ~20% less junk version will never exist if mutations only come in the 0.0001% chunks you yourself admit will make no difference. At the same time mutations increasing junk in tiny chunks are almost undetectable, so we have ratchet by which junk can accumulate.
Please read through my points about neutral evolution that I wrote in great simplification. Please think about random drift and neutral theory of evolution. You cannot say that something will not occur (deletion of useless DNA) when little advantage is gained when that is the arguing point of the greatest current advocates of naturalistic evolutionists. We are told that a random neutral mutation that confers no advantage can get fixed within the genome. Yet you are not affording the same possibility to a random neutral deletion. This is my point - you cannot have it one way and say it cannot work the other way. Especially given the amount of new information needed to be generated in evolution and apparently that just happens (de novo genes, etc). One of the greatest explanation for junk DNA being "ratched" into the genome as you say was pseudogenes. However time and time again we are finding function for these apparent pseudogenes. Therefore, the inference of non-coding DNA being left over from evolution is simply that - inference and assumptive. Our current trend of discovering roles for DNA implies that there is more function than we first attributed, not the other way around (despite the original estimates until about 15 years ago saying we should have a higher number of genes than we do). You make a very good point about genome size and selection pressure/population size. This is difficult to understand and certainly fits with the evolutionary mechanism to a degree as you describe. However many organisms much less complex than humans for example have more coding DNA (genes) than humans. The regulation is clearly different and this is something a bit difficult to understand for evolution to. Despite these seemingly odd large genome sizes (e.g. amoeba), I would still say it just shows how little we really know about DNA, genes, genetic coding and its complete function in an organisms lifecycle. I look forward to science that probes this further to try and interrogate why these genomes are so large, rather than simply assume it is a result of evolution (which it could well be - but the assumption I feel is dangerous). Thanks for the referenced article reviewing junk DNA. I will have a good read of it however it is likely to be very reactionary and biased against ENCODE's findings. These findings have quite annoyed evolutionary biologists it would seem. Taking all the current evidence from ENCODE, FANTOM, recent findings about pseudogene function and lncRNAs, I would say the overall evidence is pointing in a trend towards functionality for apparent non-coding DNA in more cases than we initially thought. I don't subscribe to the notion that ENCODE has proved there is no junk DNA. Nowhere have I said there cannot be junk DNA. I am simply saying we are seeing a trend towards identification of function where we previously did not see function and it would be wrong to assume junk when we are limited by our current understanding.Dr JDD_{May 10, 2014
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Dr JDD, Thanks for your cogent post in #64. This is also not in response to anything wd400 says. You wrote
What we should also consider, is that you can knock out plenty of proteins from mice and they look normal. That does not mean the protein is functionless. There are huge numbers of examples of this happening all the time. Therefore simply knocking out sections of non-coding DNA and seeing an apparent normal animal does not prove no function.
Then why not simply leave it at "non-coding DNA" rather than jumping to the conclusion that it's so much junk as Dr. Ohno did in his landmark paper? Proving something is "junk" is extremely difficult because you have to rule out all other possibilities: present, past, and in the case of "neutral" mutations, future. Jumping to unsupported conclusions might be common with Darwinism, but it's antithetical to the scientific method. -QQuerius_{May 9, 2014
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The irony- On one hand evos chide us for just giving up by reaching a design inference. Yet when it comes to alleged junk DNA it appears that they have just given up figuring out possible functions. However that is due to the limiting framework of their dogma.Joe_{May 9, 2014
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Does the guy who wrote a paper called "THe case for junk DNA" sound like an advocate for junk DNA?wd400_{May 9, 2014
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wd400: Of course “advocates for junk DNA do not claim all non-coding DNA is junk (and have never done so).” Gregory: Not only is “junk DNA” an inappropriate moniker for noncoding DNA in general...but it also has the unfortunate consequence of instilling a strong a priori assumption of total nonfunction. Does Gregory really sound like an advocate for junk DNA? Sounds to me like just the opposite. The quote is from Chapter 1 of the linked text, p. 30. Gregory is the editor of that volume, but also the author of chapter 1.
...dismissing it as no more than "junk" in the pejorative sense of "useless" or "wasteful" does little to advance the understanding of genome evolution. For this reason, the far less loaded term "noncoding DNA" is used throughout this chapter and is recommended in preference to "junk DNA" for future treatments of the subject. - p. 31
Mung_{May 9, 2014
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A somewhat neutral theory of junk DNA: Take a computer hard drive, for example. As you add data to it and delete data from it you can be left with segments that can be described as junk. How foolish is it to argue over the functionality of segments on a hard drive? Why is DNA so different from a hard drive?Mung_{May 9, 2014
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I presume so. Of course "advocates for junk DNA do not claim all non-coding DNA is junk (and have never done so)."wd400_{May 9, 2014
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wd400:
If you are “seriously looking for answers and open to truth”, you might want to do some research on the arguments for junk. here’s a place to start
Thank you for the link. Is that the same T. Ryan Gregory who wrote:
Not only is “junk DNA” an inappropriate moniker for noncoding DNA in general because of the minority status of pseudogenes within genome sequences, but it also has the unfortunate consequence of instilling a strong a priori assumption of total nonfunction.
Mung_{May 9, 2014
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Great writing, Dr. JDD. It is nice to have you here at UD.OldArmy94_{May 9, 2014
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You make several common mistakes here Given that apparently 98% of the genome is junk 98% of the genome is non-coding, advocates for junk DNA do not claim all non-coding DNA is junk (and have never done so). ... less chance of deleterious mutations (e.g. if the rate of mutation is 10e-8 then a genome of 10e10 will have more mutations than a genome of 10e8 by simple mathematics). Therefore this could be a small conferred advantage. If most of the genome is junk then the the total number of mutations doesn't make any difference - deleterious mutations can only fall in functional regions. Sure removing 0.0001% on one instance may not seem a advantage but what about the incremental deletion of that DNA to reach say, 20%? Selection can only work on genetic variance withing on generation. The ~20% less junk version will never exist if mutations only come in the 0.0001% chunks you yourself admit will make no difference. At the same time mutations increasing junk in tiny chunks are almost undetectable, so we have ratchet by which junk can accumulate. Interesting, the genomes of organisms with small population size (so weaker selection) are generally larger. And effect that fits with theory junk accumulates when the tiny differences in fitness an extra sequence might create can't be felt by selection. I think if you are seriously looking for answers and open to truth, then you will look at this problem of junk DNA and see how it does not quite make sense for it to be pure junk. ... That has been my argument here – my argument which some people have failed to understand is that junk DNA can be argued to not make much sense based on current evolutionary thinking and thinking about mutation events over vast periods of time. I'm afraid to make that argument you'd have to understand current evolutionary thinking more than you do. If you are "seriously looking for answers and open to truth", you might want to do some research on the arguments for junk. here's a place to startwd400_{May 9, 2014
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I am not replying to Evolve or AVS as we disagree on a fundamental point thus they instantly nullify contemplating my point, but if anyone is interested in some non-linear critical thinking around the subject, perhaps this will interest them, perhaps not. Over millions of years, we would accept that DNA will undergo various changes ("mutations") that can be favourable, or deleterious. The truth is, most are deleterious so they do not get passed on. However we also know that any change that is neutral, can (not will, but can) get passed on. Simply speaking, what changes can occur? Well we can have point mutations, we can have frameshift mutations (deletion or addition of a base changing the reading frame - usually very deleterious), you can have recombination, horizontal gene transfer, you can have whole new chunks of DNA, but you can also have the revervse of modifications that add (duplication, recombination, etc) -i.e. deletions of segments of DNA. Now back to the millions of years time frame. As most mutations are deleterious, you have to go through a lot to get advantage where the gene is likely to be passed on. In that time, you are likely then to get deletion events. These could be single bases, they could be chunks or sections of DNA. Given that apparently 98% of the genome is junk (in humans, as an example - the point is the vast majority), it is likely that such deletions will occur in those non-coding regions. Such a deletion event will at least be neutral (if junk DNA theory is correct) but could be argued to confer advantage. Why? Because there is slightly less to copy, less energy used, less chance of deleterious mutations (e.g. if the rate of mutation is 10e-8 then a genome of 10e10 will have more mutations than a genome of 10e8 by simple mathematics). Therefore this could be a small conferred advantage. Given the number of steps positive evolution (i.e. in coding DNA where you need to mutate one duplicated gene for example into a completely new functional gene) must make, and where each new mutation is likely to either have no benefit (neutral) or very very slight benefit, it is at least equally probable to get the deletion events I describe above, of redundant, junk DNA. Therefore, if we see completely novel proteins that are said to come from mutated genes of other protein's DNA or code in an incremental step-wise fashion, why do we not see the removal of unnecessary DNA in stepwise fashion? Sure removing 0.0001% on one instance may not seem a advantage but what about the incremental deletion of that DNA to reach say, 20%? That is 10x more DNA than there is gene That would definitely be an advantage given the points I raise - less cellular expenditure in copying upon replication and less chance of deleterious mutation. We see the cell tries to avoid mutation - this is why we see events such as proof-reading polymerases and also enzymes to repair DNA. Therefore you have to ask the question, when something so simple as mutation to remove/delete unnecessary DNA is more likely (as it applies to 98% of the genome, not 2% therefore has higher chance of occurring here) does not remove it, yet the mutations in the 2% of coding regions do apparently with incremental steps create novel functionality and protein folds, how is that logical? And why are people using the argument that "if it is not advantagious to reproduction or survival of an organism it won't happen" yet advocating their gurus who claim neutral evolution rules? That simply there is a conflict. I think if you are seriously looking for answers and open to truth, then you will look at this problem of junk DNA and see how it does not quite make sense for it to be pure junk. It would make more sense to have function. And what I say above, and in coming to that conclusion is INDEPENDENT of OOL belief. The consequences of that conclusion have ramifications around OOL, but not the consideration itself. That has been my argument here - my argument which some people have failed to understand is that junk DNA can be argued to not make much sense based on current evolutionary thinking and thinking about mutation events over vast periods of time. You cannot say that the cell can randomly duplicate genes, introduce whole new sections of DNA and that results in functionality yet deny the process of deleting DNA that has no use or function in a similar mechanistic fashion. That makes no sense, and is not the critical thinking scientists should employ. What we should also consider, is that you can knock out plenty of proteins from mice and they look normal. That does not mean the protein is functionless. There are huge numbers of examples of this happening all the time. Therefore simply knocking out sections of non-coding DNA and seeing an apparent normal animal does not prove no function. Given species potential for diversification, given many genes' involvements with stress responses and other non "normal" or essential functions, we cannot conclusively say that removing something and seeing nothing wrong means no function - scientists (especially mouse geneticists) quite readily accept this already. If scientists did not let dogma about things unproven (naturalism) guide them, then the question would always be "why is this here?" or "why does this happen?" etc. That is what science is about. Instead of trying to determine function, naturalists are too keen to attribute something they don't understand, that could lend support to their belief system as a result of that belief system that science loses. Yet time and time again, as we probe deeper and deeper into our understanding of the complex cell (which we are barely scratching the surface, clearly), what we see is that things are there for a reason, there is usually purpose of function. Therefore the natural (logical based on evidence) hypothesis of things we do not initially see function for, is to assume we just do not yet know or cannot yet detect function, but we should certainly invest time and resource looking as it it likely to contain function. ID trumps naturalism time in time out in contribution towards scientific thinking when it comes to such issues around function.Dr JDD_{May 9, 2014
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Nothing tricky about it: Orr maintains that the theory of intelligent design is not falsifiable. He’s wrong. To falsify design theory a scientist need only experimentally demonstrate that a bacterial flagellum, or any other comparably complex system, could arise by natural selection. If that happened I would conclude that neither flagella nor any system of similar or lesser complexity had to have been designed. In short, biochemical design would be neatly disproved.- Dr Behe in 1997 Michael Behe on Falsifying Intelligent Design - video http://www.youtube.com/watch?v=N8jXXJN4o_Abornagain77_{May 8, 2014
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@bornagain Look man, can you tone down the rhetoric here, please? Last I checked, trying to prove a negative is tricky business.VunderGuy_{May 8, 2014
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actually Darwinism is ALWAYS about story telling and never about empirically demonstrating! "There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject." James Shapiro, molecular biologist, National Review, Sept. 16, 1996bornagain77_{May 8, 2014
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////But they are in competition with other cells to divide as fast and efficiently as possible. He who out-replicates the other wins. Natural Selection and Survival of the Fittest and and all that bs./// Wrong. They are in competition with other SPECIES who share the same resources to SURVIVE and REPRODUCE, not to set the Olympic record for the fastest reproduction! ///NSF Study on Green Algae Finds Darwin Was Wrong About Competition//// Did you actually read the title of the NSF article, which says it all: "Study suggests survival may not always be about competition". Nobody ever said that survival is ALWAYS about competition. That's unrealistic; there IS cooperation, symbiosis, mutualism, commensalism etc between species. Species can co-evolve instead of competing with each other. We've known that for many decades. The NSF study gives us one more example of cooperation, that's it.Evolve_{May 8, 2014
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further note: Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome - Oct. 2009 Excerpt: At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. http://www.sciencemag.org/cgi/content/abstract/326/5950/289 3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell - Oct. 2009 Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip -- while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication. http://www.sciencedaily.com/releases/2009/10/091008142957.htm Moreover, since 'form' is not reducible to DNA sequences anyway, then Darwinism in reality has nothing to say about what the genome size should be in the first place, whereas, from a design point of view, we should rightly expect genome sizes to vary within design constraints. Constraints that would obviously be imposed in trying to achieve a ‘optimal design’ in any particular life-form that was designed; a few examples of such constraints,,: "There is strong positive correlation, however, between the amount of DNA and the volume of a cell and its nucleus - which effects the rate of cell growth and division. Furthermore, in mammals there is a negative correlation between genome size and rate of metabolism. Bats have very high metabolic rates and relatively small genomes. In birds, there is a negative correlation between C-value and resting metabolic rate. In salamanders, there is also a negative correlation between genome size and the rate of limb regeneration." Jonathan Wells - The Myth Of Junk DNA - page 85 THE ALLOMETRIC RELATIONSHIP BETWEEN GENOME SIZE (C-VALUE) AND TOTAL METABOLIC ENERGY PER LIFESPAN, PER UNIT BODY MASS IN ANIMALS Excerpt: this show(s) that,,, the higher total life energy per unit body mass leads to smaller C-value. http://www.sustz.com/Proceeding09/Papers/Medical%20Biology%20Studies/A_ATANASOV.pdf Chromosomes' Big Picture: Similarities Found in Genomes Across Multiple Species; Platypus Still out of Place - 2011 Excerpt: "Basically what this all means is that if the chromosome number of a species can be given, the relative sizes of all the chromosomes can instantly be known," Yu said. "Also, if you tell me the genome size in the chromosome base pair, I can tell you the base pair length of each chromosome." According to Yu, the most surprising finding is the extremely consistent distribution pattern of the chromosomes, a result from comparing the full sets of chromosomes -- called genomes -- of the 68 random eukaryotes. The team found that nearly every genome perfectly formed an S-curve of ascending chromosomal lengths when placed on a standardized X-Y axis. That meant the genome from a species of rice expressed the same pattern as the genome from a species of maize, sorghum, fruit fly, dog, chimpanzee, etc.,,,, "We could not believe this the first time the plot was generated," said Chengsong Zhu, research associate in agronomy. http://www.sciencedaily.com/releases/2011/07/110706113450.htm The 's-curve' (1/4 power scaling) generated in the preceding paper can be seen here: http://images.sciencedaily.com/2011/07/110706113450-large.jpg As well, at the 7:00 minute mark of this following video, we find that ‘genome length vs. mass’ also gives a enigmatic 1/4 power scaling on the plotted graph for a wide range of different creatures. Thus, once again, giving strong indication of a design constraint that was/is imposed, top down, on genome length, and which is inexplicable from the neo-Darwinian framework: 4-Dimensional Quarter Power Scaling In Biology – video http://www.metacafe.com/watch/5964041/bornagain77_{May 8, 2014
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Yes wd400, we are well aware that Darwinian evolution is great at breaking things and producing junk: Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - May 2013 Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11]. 1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696. 2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19. 3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358. 4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144. 5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47. 6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. 7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117. 8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526. 9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685. 10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079. 11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006 “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/ The problem for you is not to demonstrate that Darwinism produces junk. That is a given! The problem for you is to explain/demonstrate why we find complexity that our best computer programers and engineers can't come close to imitating: "Complexity Brake" Defies Evolution - August 2012 Excerpt: "This is bad news. Consider a neuronal synapse -- the presynaptic terminal has an estimated 1000 distinct proteins. Fully analyzing their possible interactions would take about 2000 years. Or consider the task of fully characterizing the visual cortex of the mouse -- about 2 million neurons. Under the extreme assumption that the neurons in these systems can all interact with each other, analyzing the various combinations will take about 10 million years..., even though it is assumed that the underlying technology speeds up by an order of magnitude each year.",,, Even with shortcuts like averaging, "any possible technological advance is overwhelmed by the relentless growth of interactions among all components of the system," Koch said. "It is not feasible to understand evolved organisms by exhaustively cataloging all interactions in a comprehensive, bottom-up manner." He described the concept of the Complexity Brake:,,, "Allen and Greaves recently introduced the metaphor of a "complexity brake" for the observation that fields as diverse as neuroscience and cancer biology have proven resistant to facile predictions about imminent practical applications. Improved technologies for observing and probing biological systems has only led to discoveries of further levels of complexity that need to be dealt with. This process has not yet run its course. We are far away from understanding cell biology, genomes, or brains, and turning this understanding into practical knowledge.",,, Why can't we use the same principles that describe technological systems? Koch explained that in an airplane or computer, the parts are "purposefully built in such a manner to limit the interactions among the parts to a small number." The limited interactome of human-designed systems avoids the complexity brake. "None of this is true for nervous systems.",,, to read more go here: http://www.evolutionnews.org/2012/08/complexity_brak062961.html Systems biology: Untangling the protein web - July 2009 Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. "Combine all this and you can start to think that maybe some of the information flow can be captured," he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. "The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent," he says. "The simple pathway models are a gross oversimplification of what is actually happening." http://www.nature.com/nature/journal/v460/n7253/full/460415a.htmlbornagain77_{May 8, 2014
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If anyone wants to consider the evidence for the prevalence of junk in the genomes of most large eukaryotes, there was a review paper on just this published todaywd400_{May 8, 2014
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Mung @45 noted
Trade-off is a design term.
Exactly! Interestingly, in Genesis, the terms "good" and "very good" are used regarding creation, with one exception. But it never says "perfect. Dr JDD, Thank you for your great posts! They were very informative both in content and in what some of the embarrassingly desperate rhetorical responses reveals about the people who responded, as well as the dynamics of argumentation. Thanks for your patience, but we can all see how ideological contamination won't allow some people to appreciate the complexity of cellular processes, denigrating them in several ways. Evolve @ 53, You make an excellent demonstration on how your assumptions that the size of various genomes mean that they just gotta have alotta junk in them, and how this limits your imagination. How would you know that the Norway Spruce, various salamanders, and other living things with large genomes don't have a much greater ability to adapt, or a much greater ability to spawn new species, or were a true common ancestor to a wide range of species, or are the result of merging species, or something else? For all you know, the Norway Spruce can grow its own Christmas ornaments, candles and all. My point is that you don't know, and apparently wouldn't be interested in finding out, since you already have a made your conclusions. At least think about. -QQuerius_{May 8, 2014
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Evolve:
Cells are not in a race with themselves to divide as fast as possible or as efficiently as possible.
Well, duh. But they are in competition with other cells to divide as fast and efficiently as possible. He who out-replicates the other wins. Natural Selection and Survival of the Fittest and and all that bs. Or not. NSF Study on Green Algae Finds Darwin Was Wrong About CompetitionMung_{May 8, 2014
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