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Function, the evolution-free gospel of ENCODE

There is no better title for this post than the very title some Darwinists chose for themselves:

On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE

Darwinists are still struggling to come to terms with the idea, from the ENCODE project, that 80% of the genome is functional. Whatever Dawkins now says, according to their model, only about 10% should be subject to natural selection, leaving 70% unexplained. This cannot be!

Apparently, ENCODE are to be criticised for using an ‘evolution-free’ definition of function. Yep, you heard that right. You thought that function was function was function, but oh no, you must use a evolution-y definition or you will not get the ‘correct’ evolution-y answer. It seems awfully like you need to presuppose Darwinism or you will not find Darwinism. Can that be right?

The excuse for this is some interesting Darwinian philosophy (or do I mean sophistry? – make up your mind below): the authors believe that function means nothing (is purely subjective) unless it is selected for. For example, the heart causes the pericardium (the membrane around the heart) to not collapse by filling space, so we could call that a function, but it is selected for pumping blood.

Well, yes, that’s an interesting point, and that’s where it ends for a Darwinist because Darwinists resist the possibility of purpose. But it is nonsense to an engineer. An engineer would not make the mistake of seeing the pericardium as more important than the heart. A broken watch may still contain many functional components even if overall it does nothing. A TV switched off is still a TV even if it never functions. Is that subjective?

It depends what you mean by subjective. If your only ultimate reference frame is physics (and biology as a derivative of physics), then of course all intelligent agents are in fact subjective! For much of what we know, never mind religion and ethics, even in something solid like the definition of a motor, there is no way of translating it into physical equations (you could describe an instance of a motor but that would not capture all possible motors or what ‘motorness’ is – physics makes motors work but it doesn’t know what they are). However, what if all intelligent agents shared that ‘subjective’ knowledge? Then it isn’t really subjective anymore is it? At very least, a being that knows what a motor is, or that a bacterial flagellum is a motor, is more intelligent than one that does not. When we say there is an intelligence out there, we mean there must be a being like us in this respect. A being who wouldn’t be so stupid as to think that the heart was put in to hold up the pericardium. We might not be able to explain why that is stupid, but that doesn’t stop it from being objectively stupid. See my point? Darwinians effectively deny intelligence full stop, writing it off as subjectivity.

Amongst other things the ENCODE authors are lambasted for not distinguishing between ‘Junk DNA’ and ‘Garbage DNA’. No seriously, ‘junk’ now means stuff that is functional, but not used very often, but could be used, like stuff in your attic is ‘junk’. It is different from ‘garbage’, which is the stuff that you would put straight in the bin. ‘junk’ is now a rather misleading word for ‘functional’. So our genome is full of ‘junk’ that is useful and functional, but to a Darwinian it does not count until it starts getting used so that natural selection can get the credit. How convenient! The possibility of design is sidestepped by careful choice of language. Welcome to 1984! A better word might be ‘archived’ rather than ‘junk’.

This article tells us a lot about what is wrong with the whole project. The way to find out if the genome is functional or not, is to look directly for actual function. No presuppositions, just objectivity. But they criticise the attempts of ENCODE to do that. Instead these guys are focussing on searching for indirect evidence of natural selection, with models replete with assumptions and complexities, all presupposing that Darwinism is true. If the Darwinist approach was followed (thankfully many scientists ignore it!) the simple question “functional or not?” could potentially get buried for decades more, under the continuing assumption that most is not. A few more valuable decades in which Darwinists tell us not to bother go looking for function, so slowing down scientific progress.

I, and many of us, hold to an ID worldview firstly and most securely because of what we know about prebiotic chemistry and thus the origin of the first life form. Based on that, because I know there has been a designer involved, I think probably a lot of ‘junk’ will turn out to be ‘brought down from the attic’ at various stages of an organisms life, especially in the developing stages. Time will tell.

Scientific means finding out what is actually there. ENCODE are to be praised for doing that. Darwinism has always been about telling creation myths from the point of view of naturalism (roughly, physics only), and shoehorning every fact into the story. ENCODE are now receiving scorn because they did not wait for the Darwinian imprimatur. Intelligent Design people and creationists (in fact everyone who is not a Darwinist) should take courage from this, jump in and start driving forward ordinary mainstream science, but just make sure they sidestep the attempts to sign them up to that cult.

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56 Responses to Function, the evolution-free gospel of ENCODE

  1. AJ: Very interesting take. And, you are right to prioritise OOL as the pivot where the whole issue turns on. There is a reason why modern design thought in science began there on the bio side. KF

  2. Some Darwinists have tried to have it both ways and say that some Darwinists predicted that the majority of DNA would be functional, but,,,

    Carter: Why Evolutionists Need Junk DNA – December 2009
    Excerpt: Junk DNA is not just a label that was tacked on to some DNA that seemed to have no function, but it is something that is required by evolutionary theory. Mathematically, there is too much variation, too much DNA to mutate, and too few generations in which to get it all done. This was the essence of Haldane’s work. Without junk DNA, evolutionary theory cannot currently explain how everything works mathematically. Think about it; in the evolutionary model there have only been 3-6 million years since humans and chimps diverged. With average human generation times of 20-30 years, this gives them only 100,000 to 300,000 generations to fix the millions of mutations that separate humans and chimps. This includes at least 35 million single letter differences, over 90 million base pairs of non-shared DNA, nearly 700 extra genes in humans (about 6% not shared with chimpanzees), and tens of thousands of chromosomal rearrangements. Also, the chimp genome is about 13% larger than that of humans, but mostly due to the heterochromatin that caps the chromosome telomeres. All this has to happen in a very short amount of evolutionary time. They don’t have enough time, even after discounting the functionality of over 95% of the genome–but their position becomes grave if junk DNA turns out to be functional. Every new function found for junk DNA makes the evolutionists’ case that much more difficult.
    Robert W. Carter – biologist
    http://indicium.us/2009/12/car.....k-dna.html

    A short history of how junk DNA was mathematically necessitated by Darwinian thought:
    https://docs.google.com/document/d/14-TXfGxPu-3YeCHtLmxTmL4UZN90Odt135c59yTIFsw/edit

  3. Great entry, Andy, thanks. And thanks also for highlighting this supposedly peer-reviewed article which perfectly illustrates what happens when you try to disguise idealogy with science… and fail, badly.

    Dan Graur, Yichen Zheng, Nicholas Price, Ricardo B. R. Azevedo, Rebecca A. Zufall and Eran Elhaik have let their emotions and evolutionist faith cloud their judgement about ENCODE’s findings… in the name of science too. It’s toe-curlingly dreadful. They do neither themselves, nor science any favours with such desperate attempts to put so-called junk DNA back in the garbage again.

    Just goes to show how important junk DNA is to evolution. Once we discover and indisputably establish function in all DNA (worth more than a million rabbits in the Cambrian!), will the aforementioned scientists agree that neo-darwinism has been falsified?

    I seriously doubt it.

  4. Dawkins, 2009: on “junkDNA”
    “it’s full of junk, which is just as Darwinism predicted… how embarrassing for those creationists who say it shouldn’t be!”

    Dawkins, 2012: on non-junkDNA…
    “it’s not full of junk, which is just as Darwinism predicted… nothing for the creationists to take advantage of here, move along!”

    Richard Dawkins ENCODE 2013 “Junk DNA”
    http://www.youtube.com/watch?f.....pRB0#t=94s

  5. Wolfgang Pauli, thou shouldst be living now…

    Now they’ve done the maths, they still don’t want to know.

    Ironically, it is they who should be banned from any teaching post relating to empirical science, since they so doggedly hold it back, yet batten, as parasites on the discoveries of genuine scientists; most notably, of course, in the sphere of quantum physics – which their self-applied blinkers would never have allowed them to contemplate in very principle, never mind, research the informed conjectures.

    It is no coincidence that all the late, great paradigm-changers of the last century were ABSOLUTELY convinced of Intelligent Design, Einstein in particular, seemingly, having nothing but the most profound contempt for the fatuity of his Consensus peers. I use that term, ‘peers’, of course, very loosely.

    Ironically, it he, the awe-filled panentheist, that the dunderheads most often accuse of being a pantheist!

  6. Andy,

    This is a brilliant article. I learned a lot from reading it. Thank you.

  7. BA77 @ 2

    Very good of you to bring up those points from Dr Carter et.al.

    It seems to be something less talked about, but that actually should be more talked about regarding so called “junk” DNA claim. The problem with Darwinism that first required to call so much of DNA “junk”. It shows red handed that Darwinian thinking directly stifled real scientific progress.

    So, it’s interesting now. If Darwinist want to backtrack and call those portions of the DNA that they called “junk” (meaning “garbage”) as not “garbage” but more in the sense that it is archived useful stuff (LOL!), then they will pour copious amounts of gasoline on the fire of Haldane’s dilemma. Can’t win for losing. It must be really uncomfortable as a faithful Darwinist.

  8. A couple excerpts from J.Wells book “The Myth of Junk DNA”, quoting Richard Dawkins. Bold emphasis added by me:

    SEVERAL RECENT books have likewise used junk DNA as evidence for Darwinism and evidence against design or a creator. In 2004, Richard Dawkins wrote: “Genomes are littered with nonfunctional pseudogenes, faulty duplicates of functional genes that do nothing, while their functional cousins (the word doesn’t even need scare quotes) get on with their business in a different part of the genome. And there’s lots more DNA that doesn’t even deserve the name pseudogene. It too is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, ‘tandem repeats’, and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself. Once again, creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.”23

    The following quote is perhaps the most interesting to me. Almost everyone exposed to much of Dawkins speakings, has repeatedly heard him refer to evolution as a fact as any other fact we know. That is quite emphatic!…but as we can see, being an emphatic Dawkins just doesn’t make it so:

    Richard Dawkins continued to rely on junk DNA in his 2009 book The Greatest Show on Earth: The Evidence for Evolution. “It is a remarkable fact,” Dawkins wrote, “that the greater part (95 per cent in the case of humans) of the genome might as well not be there, for all the difference it makes.” In particular, pseudogenes “are genes that once did something useful but have now been sidelined and are never transcribed or translated.” Dawkins concluded: “What pseudogenes are useful for is embarrassing creationists. It stretches even their creative ingenuity to make up a convincing reason why an intelligent designer should have created a pseudogene… unless he was deliberately setting out to fool us.”30

    If he asserted this as a remarkable fact so remarkably wrong….how could anyone trust any emphatic assertion from his mouth.

    Dawkins now —-> http://www.youtube.com/watch?v=_bjKH43pRB0

  9. Yes JGuy, Dr. Carter is a powerhouse when it comes to this area. Here are a few clips from a presentation he gave:

    What Is The Genome? It’s Certainly Not Junk! – Dr. Robert Carter – video – (Notes in video description)
    http://www.metacafe.com/w/8905583

    Multidimensional Genome – Dr. Robert Carter – video (Notes in video description)
    http://www.metacafe.com/w/8905048

    Moreover, Dr. Carter’s work even extends to the point of falsifying neo_Darwinian’ (and theistic evolutionists) claims as to coherently explaining what we find in the human genome:

    Here is a paper which, though technical, shows that the modern genetic evidence we now have actually supports Adam and Eve. Moreover, the evidence it presents from the latest genetic research is completely inexplicable to neo-Darwinism, i.e. neo-Darwinism, once again, completely falls apart upon rigid scrutiny; (and although I don’t agree with the extreme 6000 year Young Earth model used as a starting presumption in the paper for deriving the graphs, the model, none-the-less, can be amended quite comfortably to a longer time period. Which I, personally, think provides a much more ‘comfortable’ fit to the overall body of evidence)

    The Non-Mythical Adam and Eve! – Refuting errors by Francis Collins and BioLogos
    http://creation.com/historical-adam-biologos

    CMI has a excellent video of the preceding paper by Dr. Carter, that makes the technical aspects of the paper much easier to understand;

    The Non Mythical Adam and Eve (Dr Robert Carter) – video
    http://www.youtube.com/watch?v=8ftwf0owpzQ

    Moreover this genetic evidence for ‘Adam and Eve’, elucidated by Dr. Carter, is corroborated by other lines of genetic evidence:

    Human Evolution? – The Compelling Genetic Evidence For Adam and Eve
    Dr. Fazale Rana – video
    http://www.metacafe.com/watch/4284482

    Dr. Fazale Rana defends the integrity of the genetic evidence for Adam and Eve, on the following site, from some pretty high level criticism:

    Were They Real? The Scientific Case for Adam and Eve by Fazale Rana – November 2010
    http://www.thepoachedegg.net/t.....d-eve.html

  10. @ba77
    regarding you post about humans and chimps, Les Sherlock expands on that a little more over here:
    the challenge

    It is indeed an interesting question, I wonder if we will see another revision of timescales to help account for this intriguing problem.

  11. The ENCODE project has the possibility of demolishing population genetics, and with it, neo-Darwinism. Such a demise would render Darwinism hollowed-out.

    That is what the authors are pushing back against in their critique of ENCODE.

    Two articles removed (and it’s free) is an article whose coauthor is John Stomatoyannoupolos. He apparently is the “villian” in all of this.

    Here’s what they report :

    Our results demonstrate that regulatory variation is pervasive throughout the genome, on average mildly deleterious, and individuals likely harbor more functionally important variants in noncoding compared with protein-coding DNA.

    The bolded section is the true blasphemy Stomatoyannoupolos utters.

    For, as Graur, Zheng, et. al. mention, to have ‘positive selection’ occuring throughout the entire genome, a seeming necessity if “deleterious” mutations are to be weeded out, implies a “mutational load” that is prohibitive.

    Let’s remember it was precisely on this basis that Motoo Kimura proffered his “Neutral Theory.”

    If Stomatoyannoupolos (sto-ma-toy-an-nop-o-los) is correct, then Darwinism makes very little sense. And, of course, EVOLUTION IS A FACT. So, Stomatoyannoupolos must be wrong.

    I must say that having read bits of Graur, Zheng, et.al’s article, the contrast they try to develop between “selective function” and “causal function” seems a bit contrived. It leaves you scratching your head some.

    Years ago, probably on these pages, I said that whole genome analysis would either prove Darwinism right, or prove it wrong. And Graur, et. al.’s article seems evidence that Darwinism has been proven wrong . . . . . . but not accepted.

    In sum, Kimura looks at protein polymorphisms and says there’s too many for positive selection to explain. So he proposes the Neutral Theory.

    Now, WGA comes along and finds that the total amount of DNA that is “functional” is way more than ‘positive selection’ can explain. Stomatoyannoupolos is proposing a new understanding of how the genome works because Darwinian positive selection isn’t the answer.

    When will they ever give up??!!

  12. Here’s a quote from Stomatoyannoupolos’ article that Graur, Zheng, et. al., find so objectionable.

    At the outset of ENCODE in 2003, it was widely assumed that evolutionary conservation would prove to be the ultimate arbiter of functional elements in the human genome sequence—all that was lacking was a sufficiently deep sampling of vertebrate genomes for comparative analysis. Correspondingly, highly conserved noncoding sequences were frequently equated with regulatory DNA. For a variety of reasons, both of these expectations missed the mark widely. Following on studies of transcriptional regulation in the RET locus (Fisher et al. 2006), The ENCODE Pilot Project raised a general alarm: Most elements defined by biochemical signatures lacked strong evolutionary conservation (The ENCODE Project Consortium 2007). Conversely, most highly conserved elements escaped annotation using biochemical or other functional assays (Attanasio et al. 2008; McGaughey et al. 2008; Taher et al. 2011). These initial findings have been considerably amplified by the vast volume of data accumulated during the current production phase (The ENCODE Project Consortium 2012) and by other functional studies (Blow et al. 2012).

    IOW, this is “population genetics” standing on its head!

    Now we know the reason for the push-back.

  13. Pav @ 11 & 12.

    Excellent comments! Makes me wonder if Darwinist actually regret the discovery of DNA. :D

    And I see that “push-back” isn’t just the name of another dieting plan.

  14. I don’t much like the Graur et al. article, because the silly tone of it lets people gloss over the more substantive criticisms.

    But, doesn’t anyone want to tackle the actual critique of ENCODE’s magic number? Is transcription really a function? Is there any good reason to say transcription is a function and DNA replication isn’t (other than that would leave us with a 100% functional genome)

    This is also another case when this verbal-tic of calling evolutionary biology “Darwinism” looks particularly stupid – junk DNA, after all, arises because of the weakness of natural selection

  15. But, doesn’t anyone want to tackle the actual critique of ENCODE’s magic number? Is transcription really a function? Is there any good reason to say transcription is a function and DNA replication isn’t (other than that would leave us with a 100% functional genome)

    Assume for a moment that 95% of the DNA was junk as Dawkins et.al. have said and assumed. How much energy would a cell be wasting then?

    Suppose it can be shown that an organism would only need to consume 1/10th as much of the available resources of the environment to survive. I’d say that would be a pretty serious advantage. But the need for less energy would not be the only advantage: the organisms strength to weight ratio would be greater than it’s dense counterpart, and the organisms speed & agility would both be greater… among potentially other possible benefits. Selection is good at destroying and removing genetic sequences. So, wouldn’t selection travel an easily found path to remove the useless portions? In that case, if it can be shown that so much energy would be saved, then how can it be possible that it is still there and not selected? Saying that, well it’s there..would of course not be an explanation. And invoking chance would not make sense given the ease we would expect such junk to be removed. Dawkins said he thinks Darwinist would hope to find function, but that is bologna..who would hope to find more complexity in a problem? The reason it was called junk was to avoid obvious problems – as noted above in comments and in linked source.

    In the recent video posted on UD, Behe made a strong point regarding this, where he shows that finding solutions that destroys to the end that an organism gained beneficial resistance to malaria was always the case, and added that no examples are found where there was a non destructive solution.

  16. How much energy would a cell be wasting then?

    Hardly any. Especially not comparing one junky-genome to another (the evolutionary process doesn’t, after all, allow us to compare with a ‘prefect’ state, only what exists in a given generation).

    What “obvious problem” was Ohno avoiding in calling this DNA ‘junk’?

  17. That site appears to be the collected ravings of madman, but there is no sign of the “obvious problem” Ohno was avoiding in using the term ‘junk’.

  18. The link wasn’t sent to critique a website, but to see scanned paper of Ohno’s. In fact, it’s easy to find, the paper consumes ~95% of the page while ~5% of the web page is so called junk. :)

  19. @wd400 comment 14

    Like ‘evolution’, ‘Darwinism’ is a slippery word. Here it is used for the grand narrative of materialism in biology. That is what Darwin pioneered and why he made such an impact. Natural selection in itself is a trivial concept. His idea was that it could do and had done a lot of creative work.

    Transcription might not necessarily be function, but it was a surprise to people who were thinking according to the Darwinian big picture. Only ‘stupid’ people like us expected a lot more activity in the genome, rather than inert junk.

    To be fair, it remains to be seen how much of this material is truly functional now, especially in embryos, how much could trivially be switched on to become functional (like archived material), and how much is genuinely damaged or useless ‘garbage’. Darwin and Intelligent Design continue to make opposite predictions in that regard. Who will win? Time will tell.

  20. 21
    englishmaninistanbul

    Wow. Just wow. 20 comments in and still nothing from our friends on the other side…

  21. There is nothing slippery about Darwinism, it’s a word with a meaning. Creationists use it as a stand in for evolutionary biology, presumably because it’s easier to fight and -ism than an entire field of study. This example proves the point, as many materialists biologists are unhappy with our junky genome and are always looking for ways to add more function.

    JGuy,

    You still haven’t told me what porblems Ohno was avoiding in using the term junk.

  22. JGuy posted this:

    Selection is good at destroying and removing genetic sequences.

    No it isn’t.

    Selection does not act on sequences, it acts on bodies. If the sequence isn’t expressed in the phenotype, then the sequence can’t be selected for or against.

  23. wd400

    I’m not an expert in this area, but I see some things as obvious enough. Perhaps, I’m mistaken. Ifso, so-be-it. But I was hoping you would have come to the same thought…

    Question:
    Would Ohno’s paper have come to a different conclusion regarding the “junkness” of 94% of the DNA if the mutation rate was 10^-9 instead of 10^-5?

    My thinking is that:
    Yes, he would have. Why? Because if that is true, that he would have had a different conclusion, then it seems obvious enough (to me at least) that he is avoiding/circumventing the problem, not in conspiracy, but in the sense that he is assuming there actually should be no problem b/c all that other stuff must be junk at the given mutation rate.

  24. JGuy,

    The 10^-9 mutation rate that is often cited is an estiamte of the rate per nucleotide per generation. In Ohno’s time we couldn’t get that sort of resolution, so he was talking about the rate per locus per generation. If the exonic bits of an average locus is 3,000 bp then that’s a 1e-6 mutation rate per locus. If most mutations are harmless of no consequence the 1e-5 sounds about right.

    When Ohno was developing these idea evolutionary biologists where a lot more Darwinian than we are today, and though that pretty much everything in the genome would be there for some reason. Ohno was saying that’s not possible. Subsequent studies have vindicated him, and, unless you really think transcription is a function then ENCODE does little to change that.

  25. wd400, I’m just trying to square your belief that the majority of sequences are non-functional (merely transcribed) with the unfathomed complexity being revealed in the cell. For instance:

    DNA – Replication, Wrapping & Mitosis – video
    http://vimeo.com/33882804

    Unwinding the Double Helix: Meet DNA Helicase – Jonathan M. February 20, 2013 – article with video
    Excerpt: With a rotational speed of up to 10,000 rotations per minute, the helicase rivals the rotational speed of jet engine turbines.
    http://www.evolutionnews.org/2.....69371.html

    Harvard Scientists Write the Book on Intelligent Design—in DNA – Dr. Fazale Rana – September 10, 2012
    Excerpt: One gram of DNA can hold up to 455 exabytes (one exabyte equals 10^18 bytes). In comparison, a CD-ROM holds about 700 million (7 x 10^8) bytes of data. (One gram of DNA holds the equivalent amount of data as 600 billion CD-ROMs. Assuming a typical book requires 1 megabyte of data-storage capacity, then one gram of DNA could harbor 455 trillion books.)
    http://www.reasons.org/article.....ign-in-dna

    The data compression of some stretches of human DNA is estimated to be up to 12 codes thick (12 different ways of DNA transcription) (Trifonov, 1989). (This is well beyond the complexity of any computer code ever written by man). John Sanford – Genetic Entropy

    DNA – The Genetic Code – Optimal Error Minimization & Parallel Codes – Dr. Fazale Rana – video
    http://www.metacafe.com/watch/4491422

    ‘Quadruple helix’ DNA discovered in human cells – January 20, 2013
    Excerpt: In 1953, Cambridge researchers Watson and Crick published a paper describing the interweaving ‘double helix’ DNA structure – the chemical code for all life. Now, in the year of that scientific landmark’s 60th Anniversary, Cambridge researchers have published a paper proving that four-stranded ‘quadruple helix’ DNA structures – known as G-quadruplexes – also exist within the human genome.,,,
    Physical studies over the last couple of decades had shown that quadruplex DNA can form in vitro – in the ‘test tube’, but the structure was considered to be a curiosity rather than a feature found in nature. The researchers now know for the first time that they actually form in the DNA of human cells.
    “This research further highlights the potential for exploiting these unusual DNA structures to beat cancer –,,,
    “It’s been sixty years since its structure was solved but work like this shows us that the story of DNA continues to twist and turn.”,,,
    While quadruplex DNA is found fairly consistently throughout the genome of human cells and their division cycles, a marked increase was shown when the fluorescent staining grew more intense during the ‘s-phase’ – the point in a cell cycle where DNA replicates before the cell divides.,,,
    It’s a philosophical question as to whether they are there by design or not – but they exist and nature has to deal with them.,,,
    “The ‘quadruple helix’ DNA structure may well be the key to new ways of selectively inhibiting the proliferation of cancer cells. The confirmation of its existence in human cells is a real landmark.”
    http://phys.org/news/2013-01-q.....cells.html

    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/.....6/5950/289

    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/re.....142957.htm

    Biochemical Turing Machines “Reboot” the Watchmaker Argument – Fazale Rana – July 2012
    Excerpt: Researchers recognize several advantages to DNA computers.(7) One is the ability to perform a massive number of operations at the same time (in parallel) as opposed to one at a time (serially) as demanded by silicon-based computers. Secondly, DNA has the capacity to store an enormous quantity of information. One gram of DNA can house as much information as nearly 1 trillion CDs. And a third benefit is that DNA computing operates near the theoretical capacity with regard to energy efficiency.
    http://stevebrownetc.com/2012/.....-argument/

    etc.. etc.. etc..

    I just don’t see where the presupposition of non-functional sequences in the DNA is justified wd400. It, the presupposition, certainly is not fruitful to spurring further research, and from what I can tell, the necessity of the presupposition arises solely from the neo-Darwinian framework i.e. genetic reductionism. A framework that is fairing none to well these days. Shoot, as if all the preceding was not bad enough to your presupposition that ‘filtered accidents’ can build unfathomed complexity, I think you guys are about to lose the the ‘concept of a gene’ entirely!

    Landscape of transcription in human cells – Sept. 6, 2012
    Excerpt: Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.
    http://www.nature.com/nature/j.....11233.html

  26. It’s a conclusion, not a presupposition. I don’t doubt cells are complex, most messy things are complex.

  27. timothya:

    Selection does not act on sequences, it acts on bodies.

    Actually, it depends on which Darwinist you’re talking to on which day. It must be nice to have a theory that enables you talk out of both sides of your mouth.

  28. Selection does not act on sequences, it acts on bodies.

    Actually, it depends on which Darwinist you’re talking to on which day. It must be nice to have a theory that enables you talk out of both sides of your mouth.

    Yet the truth is that evolutionary theory predicts that selection acts on the phenotype, the whole body. You’re very fond of calling people you disagree with liars, mung. Prove us liars by finding a Darwinist who says selection acts on the genotype.

  29. The next evolutionary synthesis: Jonathan BL Bard (2011)
    Excerpt: We now know that there are at least 50 possible functions that DNA sequences can fulfill [8], that the networks for traits require many proteins and that they allow for considerable redundancy [9]. The reality is that the evolutionary synthesis says nothing about any of this; for all its claim of being grounded in DNA and mutation, it is actually a theory based on phenotypic traits. This is not to say that the evolutionary synthesis is wrong, but that it is inadequate – it is really only half a theory!
    http://www.biosignaling.com/co.....X-9-30.pdf

  30. “It’s a conclusion, not a presupposition.”

    But alas, in Darwinian fantasy land of science the conclusion of evolution is derived from its presupposition!

    Excerpt: The fact of evolution assures us that the species arose spontaneously, but it doesn’t tell us how. That’s for the theory of evolution to figure out.

    This all makes sense to evolutionists because the fact of evolution does not come from science. – Cornelius Hunter
    http://darwins-god.blogspot.co.....yotes.html

  31. as to the conclusion of evolution being derived from its presupposition,,,

    There are two definitions of Science in our Culture – Phillip E. Johnson – audio
    http://www.youtube.com/watch?f.....Xo#t=1596s

  32. Alan Fox:

    Yet the truth is that evolutionary theory predicts that selection acts on the phenotype, the whole body. You’re very fond of calling people you disagree with liars, mung. Prove us liars by finding a Darwinist who says selection acts on the genotype.

    Wow. That’s a tough one!

    I didn’t call timothya a liar. Maybe he really believes it.

    I would not be at all surprised to find that you, on the other hand, argued against the need for any genotype/phenotype distinction as a requirement for darwinian evolution.

    The relevant thread, however:

    UB Sets It Out Step-By-Step

    How quickly they forget.

  33. Alan Fox:

    Yet the truth is that evolutionary theory predicts that selection acts on the phenotype, the whole body.

    Reference please. We can’t just take your word for it.

    Prove us liars by finding a Darwinist who says selection acts on the genotype.

    Only artificial selection acts, Alan. Perhaps sexual selection also acts.

  34. The insurmountable ‘princess and the pea’ problem is pointed out by Dr. John Sanford, at the 8:14 minute mark, of this following video,,,

    Genetic Entropy – Dr. John Sanford – Evolution vs. Reality – video
    http://vimeo.com/35088933

    ,,,In which Dr. Sanford points out ‘selection’ acts at the coarse level of the entire organism and yet the vast majority of mutations have effects that are only ‘slightly detrimental’ and are far below the power of selection to remove from genomes before they spread throughout the population.

    Further notes on the princess and the pea paradox of natural selection:

    Evolution Vs Genetic Entropy – Andy McIntosh – video
    http://www.metacafe.com/watch/4028086/

    The GS Principle (The Genetic Selection Principle) – Abel – 2009
    Excerpt: The GS Principle, sometimes called “The 2nd Law of Biology,” states that selection must occur at the molecular/genetic level, not just at the fittest phenotypic/organismic level, to produce and explain life.,,, Natural selection cannot operate at the genetic level.
    http://www.bioscience.org/2009.....lltext.htm

    Natural Selection’s Reach – Ann Gauger – February 12, 2013
    Excerpt: What is the mutational reach of natural selection in general? It’s very short. For bacteria, our work suggests the reach is only a few mutations at a time. That’s not enough to get a genuinely new function for a protein, let alone a new pathway made up of a handful of proteins, or a metabolism made up of hundreds of proteins. For larger multicellular organisms like us, with slower generation times and smaller populations, the problem gets worse. Much worse.
    http://www.evolutionnews.org/2.....69121.html

    Using Computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load:
    Excerpt: We apply a biologically realistic forward-time population genetics program to study human mutation accumulation under a wide-range of circumstances.,, Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space.
    http://bioinformatics.cau.edu......aproof.pdf
    MENDEL’S ACCOUNTANT: J. SANFORD†, J. BAUMGARDNER‡, W. BREWER§, P. GIBSON¶, AND W. REMINE
    http://mendelsaccount.sourceforge.net/

  35. BA,

    Does Sanford’s (nutty) theory suggest there should be more or less junk DNA than mainstream science?

  36. When a darwinist gets sick, he sits down with his doctor, (like anyone else), who tells him which part of his body is not functioning, how it’s not functioning, and what needs to be done to effect repair, to get it functioning “properly” again. The doctor will tell him how this component of his body should “normally function” And the explanation is often crystal clear. When he arrives home he has to struggle to remind himself it was all just a useful metaphor. There is no ‘real’: “repair, no “function”, no “proper”, no “normal”. Just his ‘preferences’ (like staying alive and healthy). This is another example of how they can’t live without constant contradicition, if they really think about their condition

  37. wd400 you state:

    Does Sanford’s (nutty) theory suggest there should be more or less junk DNA than mainstream science?

    Nutty theory??? That’s funny for you to say that because Avise uses the same data for overwhelmingly negative rate of mutations, that Sanford uses to support Genetic Entropy, to argue that Darwinism is correct because it is proof of ‘non-Intelligent Design’:

    Inside the Human Genome: A Case for Non-Intelligent Design – Pg. 57 By John C. Avise
    Excerpt: “Another compilation of gene lesions responsible for inherited diseases is the web-based Human Gene Mutation Database (HGMD). Recent versions of HGMD describe more than 75,000 different disease causing mutations identified to date in Homo-sapiens.”

    I went to the mutation database website cited by John Avise and found:

    HGMD®: Now celebrating our 100,000 mutation milestone!
    http://www.hgmd.org/

    But note how Avise uses such a high rate of negative mutations as a Theological argument:

    If, on the other hand, natural causation is denied, and a caring Intelligent Designer is to be held directly responsible for life’s imperfect features, then the theodicy challenge remains poignant. How could a Creator God have engineered such a deeply flawed biological world, right down to its most elemental molecular features? Unless we pretend that biological defects do not exist, we seem forced to conclude that any Intelligent Designer is either technically fallible, morally challenged, or both. Furthermore, if the intelligent designer is deemed to be the Abrahamic God (rather than a Martian, for example), then are we not guilty of blasphemy in ascribing to Him a direct hand in sponsoring the molecular genomic flaws that plague human health? [156] – John Avise – In his chapter on non intelligent design
    http://darwins-god.blogspot.co.....ation.html

    Did it even cross John Avise’s mind that the evidence, that he himself cited, is absolutely SCIENTIFICALLY crushing for Darwinism???

    We Are All Mutants: First Direct Whole-Genome Measure of Human Mutation Predicts 60 New Mutations in Each of Us – June 2011
    http://www.sciencedaily.com/re.....012758.htm

    *3 new mutations every time a cell divides in your body
    * Average cell of 15 year old has up to 6000 mutations
    *Average cell of 60 year old has 40,000 mutations
    Reproductive cells are ‘designed’ so that, early on in development, they are ‘set aside’ and thus they do not accumulate mutations as the rest of the cells of our bodies do. Regardless of this protective barrier against the accumulation of slightly detrimental mutations still we find that,,,
    *60-175 mutations are passed on to each new generation. – Dr. John Sanford

    Interestingly, this ‘slightly detrimental’ mutation rate of 100 to 200, or even 60, per generation is far greater than what even evolutionists agree is an acceptable mutation rate since detrimental mutations will accumulate far faster than ‘selection’ can eliminate them in any given genome:

    Beyond A ‘Speed Limit’ On Mutations, Species Risk Extinction
    Excerpt: Shakhnovich’s group found that for most organisms, including viruses and bacteria, an organism’s rate of genome mutation must stay below 6 mutations per genome per generation to prevent the accumulation of too many potentially lethal changes in genetic material.
    http://www.sciencedaily.com/re.....172753.htm

    Human evolution or extinction – discussion on acceptable mutation rate per generation from population genetics (with clips from Dr. John Sanford) – video
    http://www.youtube.com/watch?v=aC_NyFZG7pM

    wd400 it is really not a matter of how much ‘junk’ DNA ID predicts, all that really matters is that on evolution, because of such a overwhelmingly negative mutation rate’ everything should be 100% junk if Darwinism were true!

  38. wd400, do you consider Avise’s theological argument a scientific argument?

    Here, at about the 55:00 minute mark in the following video, Phillip Johnson sums up his, in my opinion, excellent lecture by noting that the refutation of his book, ‘Darwin On Trial’, in the Journal Nature, the most prestigious science journal in the world, was a theological argument about what God would and would not do and therefore Darwinism must be true, and the critique from Nature was not a refutation based on any substantiating scientific evidence for Darwinism that one would expect to be brought forth in such a prestigious venue to support such a, supposedly, well supported scientific theory:

    Darwinism On Trial (Phillip E. Johnson) – lecture video
    http://www.youtube.com/watch?v=gwj9h9Zx6Mw

    In this following video Dr. William Lane Craig is surprised to find that evolutionary biologist Dr. Ayala uses theological argumentation in his book to support Darwinism and invites him to present evidence, any evidence at all, that Darwinism can do what he claims it can:

    Refuting The Myth Of ‘Bad Design’ vs. Intelligent Design – William Lane Craig – video
    http://www.youtube.com/watch?v=uIzdieauxZg

    In fact, it has been pointed out, by many people besides Dr. Craig, that the whole neo-Darwinian argument is, at its core beneath all the rhetoric, a theological argument:

    On the Vastness of the Universe
    Excerpt: Darwin’s objection to design inferences were theological. And in addition, Darwin overlooked many theological considerations in order to focus on the one. His one consideration was his assumption about what a god would or wouldn’t do. The considerations he overlooked are too numerous to mention here, but here’s a few:,,,
    http://www.uncommondescent.com.....ent-362918

    Here are peer-reviewed papers which point out the fact that many arguments for Darwinian evolution turn out to be primarily theological arguments at their core:

    The role of theology in current evolutionary reasoning – Paul A. Nelson – Biology and Philosophy, 1996, Volume 11, Number 4, Pages 493-517
    Excerpt: Evolutionists have long contended that the organic world falls short of what one might expect from an omnipotent and benevolent creator. Yet many of the same scientists who argue theologically for evolution are committed to the philosophical doctrine of methodological naturalism, which maintains that theology has no place in science. Furthermore, the arguments themselves are problematical, employing concepts that cannot perform the work required of them, or resting on unsupported conjectures about suboptimality. Evolutionary theorists should reconsider both the arguments and the influence of Darwinian theological metaphysics on their understanding of evolution.
    http://www.springerlink.com/co.....34/?MUD=MP

    Charles Darwin, Theologian: Major New Article on Darwin’s Use of Theology in the Origin of Species – May 2011
    http://www.evolutionnews.org/2.....46391.html

    The Descent of Darwin – Pastor Joe Boot – (The Theodicy of Darwinism) – video
    http://www.youtube.com/watch?v=HKJqk7xF4-g

    “The strength of materialism is that it obviates the problem of evil altogether. God need not be reconciled with evil, because neither exists. Therefore the problem of evil is no problem at all.,,, And of course since there is no evil, the materialist must, ironically, not use evil to justify atheism. The problem of evil presupposes the existence of an objective evil-the very thing the materialist seems to deny. The argument (from Theodicy) that led to materialism is exhausted just when it is needed most. In other words, the problem of evil is only generated by the prior claims that evil exists. One cannot then conclude, with Dawkins, that there is ‘no evil and no good’ in the universe.,,,
    The fact that evolution’s acceptance hinges on a theological position would, for many, be enough to expel it from science. But evolution’s reliance on metaphysics is not its worst failing. Evolution’s real problem is not its metaphysics but its denial of its metaphysics.,,,
    Cornelius Hunter – Darwin’s God – pg. 154 & 159
    http://www.amazon.com/Darwins-.....1587430118

  39. BA,

    I don’t read the link the link-spam, if you have something meaningful to say do so in your own words. As for Avise’s comments – no one is arguing there are no bad mutations, just that Sanford erects a lot of silly ideas ontop of the observation that mutation is a net-negative (i.e. most mutations are neutral, a few bad and only a very small number benificial).

  40. Joe posted this:

    Alan Fox:

    Yet the truth is that evolutionary theory predicts that selection acts on the phenotype, the whole body.

    Reference please. We can’t just take your word for it.

    Darwin’s Origin of Species provides an excellent introduction to how the external environment selects for or against particular phenotypes in a breeding population.

    Combine that with any scientific treatment of Mendelian genetics and you will understand how the external environment, by acting on the bodies of organisms, causes differential reproduction rates between body types and subsequent changes in the population’s gene allele frequency.

    I don’t know of any evolutionary biologists who believe that natural selection acts directly on gene structures, but I’m prepared to be surprised.

  41. wd400:

    “and only a very small number beneficial”

    But alas, even the beneficial mutations that Darwinists are dependent on to make their atheistic theory seem plausible are only ‘beneficial’ in a limited context:

    “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.co.....evolution/

    Michael Behe’s Blog – October 2007
    Excerpt: As I showed for mutations that help in the human fight against malaria, many beneficial mutations actually are the result of breaking or degrading a gene. Since there are so many ways to break or degrade a gene, those sorts of beneficial mutations can happen relatively quickly. For example, there are hundreds of different mutations that degrade an enzyme abbreviated G6PD, which actually confers some resistance to malaria. Those certainly are beneficial in the circumstances. The big problem for evolution, however, is not to degrade genes (Darwinian random mutations can do that very well!) but to make the coherent, constructive changes needed to build new systems.
    http://behe.uncommondescent.com/page/6/

    Blink and You’ll Miss It: Jerry Coyne Turns His Attention to the “Engine of Evolution” (Lenski, Lynch, Hall, Antibiotic resistance, Insecticide resistance) – December 7, 2012
    http://www.evolutionnews.org/2.....67161.html

    Richard Lenski’s Long-Term Evolution Experiments with E. coli and the Origin of New Biological Information
    Excerpt: Even if there were several possible pathways by which to construct a gain-of-FCT mutation, or several possible kinds of adaptive gain-of-FCT features, the rate of appearance of an adaptive mutation that would arise from the diminishment or elimination of the activity of a protein is expected to be 100-1000 times the rate of appearance of an adaptive mutation that requires specific changes to a gene.
    (Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010).)

    The sort of loss-of-function examples seen in the Lenski’s LTEE (Long Term Evolution Experiment) will never show that natural selection can increase high CSI. To understand why, imagine the following hypothetical situation.

    Consider an imaginary order of insects, the Evolutionoptera. Let’s say there are 1 million species of Evolutionoptera, but ecologists find that the extinction rate among Evolutionoptera is 1000 species per millennium. The speciation rate (the rate at which new species arise) during the same period is 1 new species per 1000 years. At these rates, every thousand years 1000 species of Evolutionoptera will die off, while one new species will develop–a net loss of 999 species. If these processes continue, in 1,000,001 years there will be no species of Evolutionoptera left on earth.
    http://www.evolutionnews.org/2.....51051.html

    Mutations : when benefits level off – June 2011 – (Lenski’s e-coli after 50,000 generations)
    Excerpt: After having identified the first five beneficial mutations combined successively and spontaneously in the bacterial population, the scientists generated, from the ancestral bacterial strain, 32 mutant strains exhibiting all of the possible combinations of each of these five mutations. They then noted that the benefit linked to the simultaneous presence of five mutations was less than the sum of the individual benefits conferred by each mutation individually.
    http://www2.cnrs.fr/en/1867.htm?theme1=7

    New Research on Epistatic Interactions Shows “Overwhelmingly Negative” Fitness Costs and Limits to Evolution – Casey Luskin June 8, 2011
    Excerpt: In essence, these studies found that there is a fitness cost to becoming more fit. As mutations increase, bacteria faced barriers to the amount they could continue to evolve. If this kind of evidence doesn’t run counter to claims that neo-Darwinian evolution can evolve fundamentally new types of organisms and produce the astonishing diversity we observe in life, what does?
    http://www.evolutionnews.org/2.....47151.html

  42. @wd400

    Let me try again.

    Darwinism and evolutionary biology are different things. I am not using it to refer to evolutionary biology, which contains much stuff that is valid scientific methodology, but to an *ideology* which says that natural selection can create substantial new function. If you want to split hairs about, for example, neutral theories of evolution not being Darwinian, then I will let you have that pedantic point, but neutral evolution is about chance, which is pre-Darwinian, hardly progress, and I dont think anyone is going to be misled by this terminology.

    If you think my terminology sounds to ‘creationist’, then how would you word it?

  43. @wd400

    Again, transcription is *indicative* of function, so it does change things.

  44. Since, as far as I’m aware, every evolutionary biologist thinks natural selection can be constructive (and a few, like me, don’t think you even need selection eg this paper) you could maybe say “evolutionary biology”.

    It’s good to see you are at least admitting the genome isn’t 80% functional.

  45. wd400 snips: “It’s good to see you are at least admitting the genome isn’t 80% functional.”

    And yet,,,

    Shoddy Engineering or Intelligent Design? Case of the Mouse’s Eye – April 2009
    Excerpt: — The (entire) nuclear genome is thus transformed into an optical device that is designed to assist in the capturing of photons. This chromatin-based convex (focusing) lens is so well constructed that it still works when lattices of rod cells are made to be disordered. Normal cell nuclei actually scatter light. — So the next time someone tells you that it “strains credulity” to think that more than a few pieces of “junk DNA” could be functional in the cell – remind them of the rod cell nuclei of the humble mouse.
    http://www.evolutionnews.org/2.....ellig.html

    Demolishing Junk DNA as an icon of evolution – July 2011
    Excerpt: “The genome is hierarchical, and it functions at three levels: the DNA molecule itself; the DNA-RNA-protein complex that makes up chromatin; and the three-dimensional arrangement of chromosomes in the nucleus. At all three of these levels, DNA can function in ways that are independent of its exact nucleotide sequence.” (p.93) [. . .] “At the third level, the position of the chromosome inside the nucleus is important for gene regulation. In most cells, the gene-rich portions of chromosomes tend to be concentrated near the center of the nucleus, and a gene can be inactivated by artificially moving it to the periphery. In some cases, however, the pattern is inverted: rod cells in the retinas of nocturnal mammals contain nuclei in which the non-protein-coding parts of chromosomes are concentrated near the center of the nucleus, where they form a liquid crystal that serves to focus dim rays of light.” (p.94-5) (The Myth of Junk DNA)
    http://www.arn.org/blogs/index.....n_of_evolu

    Jonathan Wells on Darwinism, Science, and Junk DNA – November 2011
    Excerpt: Mice without “junk” DNA. In 2004, Edward Rubin?] and a team of scientists at Lawrence Berkeley Laboratory in California reported that they had engineered mice missing over a million base pairs of non-protein-coding (“junk”) DNA—about 1% of the mouse genome—and that they could “see no effect in them.”
    But molecular biologist Barbara Knowles (who reported the same month that other regions of non-protein-coding mouse DNA were functional) cautioned that the Lawrence Berkeley study didn’t prove that non-protein-coding DNA has no function. “Those mice were alive, that’s what we know about them,” she said. “We don’t know if they have abnormalities that we don’t test for.”And University of California biomolecular engineer David Haussler? said that the deleted non-protein-coding DNA could have effects that the study missed. “Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years,” he argued.
    In 2010, Rubin was part of another team of scientists that engineered mice missing a 58,000-base stretch of so-called “junk” DNA. The team found that the DNA-deficient mice appeared normal until they (along with a control group of normal mice) were fed a high-fat, high-cholesterol diet for 20 weeks. By the end of the study, a substantially higher proportion of the DNA-deficient mice had died from heart disease. Clearly, removing so-called “junk” DNA can have effects that appear only later or under other circumstances.
    http://www.uncommondescent.com.....-junk-dna/

  46. Michael Behe on the theory of constructive neutral evolution – February 2012
    Excerpt: In brief, the idea is that neutral interactions evolve serendipitously in the cell, spread in a population by drift, get folded into a system, and then can’t be removed because their tentacles are too interconnected. It would be kind of like trying to circumvent the associate director of licensing delays in the Department of Motor Vehicles — can’t be done.

    The authors think the evolution of such a complex is well beyond the powers of positive natural selection: “Even Darwin might be reluctant to advance a claim that eukaryotic spliceosomal introns remove themselves more efficiently or accurately from mRNAs than did their self-splicing group II antecedents, or that they achieved this by ‘numerous, successive, slight modifications’ each driven by selection to this end.” (1)

    I don’t mean to be unkind, but I think that the idea seems reasonable only to the extent that it is vague and undeveloped; when examined critically it quickly loses plausibility. The first thing to note about the paper is that it contains absolutely no calculations to support the feasibility of the model. This is inexcusable. – Michael Behe
    http://www.uncommondescent.com.....evolution/

  47. wd400:

    Since, as far as I’m aware, every evolutionary biologist thinks natural selection can be constructive (and a few, like me, don’t think you even need selection eg this paper) you could maybe say “evolutionary biology”.

    There is a paper out that shows that synonymous substitutions are involved in the determining the rate at which proteins are transcribed. This puts further restrictions on the genome, and means that “neutral” mutations are perhaps rarer than thought.

    It looks like Darwinism is being squeezed at both ends. Neutral ‘evolution’, certainly, is becoming less and less tenable.

    What options are left? Intelligent design, perhaps??

  48. There’s been papers on that since the 1960s. Works in bacteria where populations are large and small selective effects can have an influence, not likely relevant to smaller populations.

    I think that’ the 12,000th time someone here has conflate neutral theory with Darwinism, which, as I keep trying to point out, our opposed to each other! Perhaps I should stop bothering.

  49. I think that’ the 12,000th time someone here has conflate neutral theory with Darwinism, which, as I keep trying to point out, our opposed to each other! Perhaps I should stop bothering.

    Darwinism swallowed up neutral theory like a proto-eukaryote.

  50. timothya:

    Darwin’s Origin of Species provides an excellent introduction to how the external environment selects for or against particular phenotypes in a breeding population.

    Except the environment does NOT select. And whatever is good enough survives.

    But anyway I asked for a reference for the prediction Alan stated. Do you have one?

  51. wd400:

    I think that’ the 12,000th time someone here has conflate neutral theory with Darwinism, which, as I keep trying to point out, our opposed to each other! Perhaps I should stop bothering.

    Well I’ve read Kimura’s book. I wonder if you have. And I know that Kimura proposed the Neutral Theory because positive selection, and the mutational load associated with it, does not accord with the very high level of polymorphisms found in the genome. (Were you aware of that? And, if not, why not? Because evol biol/Darwinists don’t talk about such things? If that’s the case, it’s quite telling.)

    It’s not us here at UD who don’t understand the difference, it’s the evolutionary biologists who don’t seem to get it. IOW, we, here at UD, have to deal with people who, at one and the same time, espouse Darwinism and purport the neutral theory to help explain it.

    You cited a reference to CNE. Maybe you can argue it’s some kind of hybrid, but it’s like saying if you put two theories that both have trouble explaining macroevolution, all the problems go away when you combine them. You’ll have a hard time selling that one here.

    The paper I cited above limits the true configuration space of putative “neutral evolution”—which, as you mention, would work for most bacterial populations simply because of their growth rate—and, so, makes invoking NT for sexually reproducing organisms ring even more hollow.

  52. Yeah, I’ve read Kimura, and I even understand it, which is why I don’t called NT “Darwinism”.

    Of course most biologists working in relevant fields know about Kimura’s load arguments, that’s why no one (apart from certain molecular biologists…) think every polymorphism is the result of Darwinian selection.

    The paper I cited above limits the true configuration space of putative “neutral evolution”—which, as you mention, would work for most bacterial populations simply because of their growth rate—and, so, makes invoking NT for sexually reproducing organisms ring even more hollow.

    You didn’t actually cite a paper, you referred to a commonly known fact about molecular evolution. But, why would “invoking NT for sexually reproducing organisms” ring hollow? A polymorohism will act as if netural if 2NeS < 1, and Ne is usually much smaller in sexually reducing species that bacteria, thus more nearly-neutral mutations behave as if they were neutral.

  53. @wd400

    You are misrepresenting what a number of us are saying, and thus not helping.

    To most people, at the popular level, Darwinism means a natural theory of evolution, with natural selection as the main driver of creation. Now, of course, we all know that natural selection doesnt actually create anything; it only selects from options available. Even in Darwinism, variants are generated by chance, whether one-step mutations or a process of genetic drift and ‘neutral evolution’, so there is not really a very big distinction. As for the difference between Darwinism and evolutionary biology: if evolutionary biology *assumes* that evolution is creative and mimics design, then it is not scientific, but that is what Darwinists (in the traditional sense of the word) do.

    I did not say that less than 80% of the genome is functional. Indeed it may be more. We dont know exactly, but the indications we have are, currently, roughly 80%.

  54. Clarification:
    Instead of assuming evolution is creative or has been in the past, evolutionary biologists, including the ID sort, should ask the question, ‘Is evolution creative in practice now?’ Does it produce new designs? Does it increase information* content? Or does it, in fact, as seems to be the case, exclusively use old designs and existing information?

    * Information can be defined rigorously in principle:
    Information required for a function F is -log(P(F))
    http://www.tbiomed.com/content/4/1/47

  55. ‘most messy things are complex.’

    You don’t call something that’s integrated and purposeful, and thus, clearly been designed, ‘messy’, WD400. Well, rational people don’t.

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