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At least Forbes.com’s John Farrell, while trashing Jonathan Wells’ “junk DNA” book, doesn’t threaten to actually read it.

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The Myth of Junk DNAHe sniffs that he might, in the end, review it, as time permits. One hopes he’ll read it first. Some readers of reviews like that sort of thing, and there is simply no accounting for tastes.

PZ Myers, however, has threatened to read the book.

Farrell (“Jonathan Wells’s “The Myth … of the Myth of Junk DNA,” May. 20 2011) claims that the idea that Darwinists ever thought that stuff was junk is itself a “myth”:

T. Ryan Gregory at Genomicron has tirelessly pointed out the problems with the myth argument over the past few years. He cites a number of articles from the journals of the time to show that scientists never dismissed junk DNA in the literature.

Oh? Indeed. But does Gregory cite the ones where they actually did dismiss it explicitly because it was the very junk that Darwinism predicted?

Discovery Institute’s Casey Luskin provides the missing citations in the Forbes combox, suggesting that it sounds as though Farrell has not read the book. That would be in no way unusual. In the context, not reading the book functions as form of censorship, because Farrell can misrepresent without lying, as he has done here. Many Darwinists are quite self-righteous enough to believe that they are rendering the world a service thereby.

Here’s genome mapper Francis Collins on junk DNA as supporting Darwinism, and here’s UD’s interview with Wells where he addresses Darwinists’ support of the concept.

Why is all this so reminiscent of the recent Beckwith-Forrest-Synthese uproar, that made it into the New York Times? Could it be the demand for public belief in an evidently false proposition?

Here’s Casey:

Your point (A) is an attempt to rewrite history, which is a predictable response to the overwhelming mass of evidence Jonathan Wells compiles in his book showing that evolutionary scientists have predicted that much of the genome is junk. In fact, John Avise’s book from which you quote refutes your first point. As Jonathan Wells documents:

In 2010, University of California Distinguished Professor of Ecology & Evolutionary Biology John C. Avise published a book titled Inside the Human Genome: A Case for Non-Intelligent Design, in which he wrote that “noncoding repetitive sequences—‘ junk DNA’—comprise the vast bulk (at least 50%, and probably much more) of the human genome.” Avise argued that pseudogenes, in particular, are evidence against intelligent design. For example, “pseudogenes hardly seem like genomic features that would be designed by a wise engineer. Most of them lie scattered along the chromosomes like useless molecular cadavers.” To be sure, “several instances are known or suspected in which a pseudogene formerly assumed to be genomic ‘ junk’ was later deemed to have a functional role in cells. But such cases are almost certainly exceptions rather than the rule. And in any event, such examples hardly provide solid evidence for intelligent design; instead, they seem to point toward the kind of idiosyncratic tinkering for which nonsentient evolutionary processes are notorious.”

Avise also published an article in Proceedings of the National Academy of Sciences USA titled “Footprints of nonsentient design inside the human genome,” in which he repeated the same argument. “Several outlandish features of the human genome,” he wrote, “defy notions of ID by a caring cognitive agent,” but they are “consistent with the notion of nonsentient contrivance by evolutionary forces.” For example, “the vast majority of human DNA exists not as functional gene regions of any sort but, instead, consists of various classes of repetitive DNA sequences, including the decomposing corpses of deceased structural genes.”

(Jonathan Wells, The Myth of Junk DNA, pp. 26-27 (2011).)

Comments
"It is interesting to point out that neo-Darwinists presuppose non-functionality, i.e. Junk DNA," when we are ignorant as to a particular DNA sequences functionality" I am not sure what is wrong with this reasoning? I think I am missing something. // whereas ID, at least the broader concept of ID, presupposes functionality for sequences of unknown function.// And I am still confused. What is it about ID that causes us to presuppose functionality for all sequences?Chiefley
May 23, 2011
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@bornagain77, thanks for the clarification. But I don't see how the term "broader" makes any difference. We need to demonstrate why optimal design is a logical consequence of the requirement for design. Or conversely, we need to demonstrate by logical consequence why non-optimal design is forbidden. Otherwise our prediction is just someone's opinion.Chiefley
May 23, 2011
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Further reflection on the differences of ID and neo-Darwinism's concept of junk DNA; It is interesting to point out that neo-Darwinists presuppose non-functionality, i.e. Junk DNA, when we are ignorant as to a particular DNA sequences functionality, whereas ID, at least the broader concept of ID, presupposes functionality for sequences of unknown function. The interesting thing in all this is that we now have many, many, instances where functionality is only discovered for a particular 'Junk DNA' sequence when it has a detrimental, disease causing, mutation. A disease causing mutation that reveals the Junk DNA sequence's essential purpose to the integrated whole of the life form. This problem of 'Junk DNA' revealing itself to have essential function, in such a non-modular and thus 'non-Darwinian' way, led to this observation of the severe impediment that Darwinian thought has placed on medical research: International HoloGenomics Society - "Junk DNA Diseases" Excerpt: "elaborated in more detail in my “Obituary of Junk DNA “ http://www.junkdna.com/#obituary_of_junk_dna” uncounted millions of people died miserable deaths while scientists were looking for the “gene” causing their illnesses – and were not even supposed to look anywhere but under the lamp illuminating only 1.3% of the genome (the genes)." https://uncommondescent.com/intelligent-design/the-discovery-institute-needs-to-be-destroyed/#comment-357177 Thus not only does neo-Darwinism not have any solid empirical support to back up its claim of being a serious science, but in so far as neo-Darwinian presuppositions have been taken seriously, it has had a 'deadly' effect on medical research for humans. Moreover, this integrated 'wholeness' that Junk DNA reveals of the genome is of a second order level of irreducible complexity which, while not as stringent as Dr. Behe's first order level of irreducible complexity, none-the-less gives us a outline of a 'oneness' of living systems that is not presupposed in neo-Darwinian thought. i.e. neo-Darwinism presupposes a high level of 'independent modularity' within the genome where functionality can be selected and discarded at will, and not the highly integrated functionality that we find; Poly-Functional Complexity equals Poly-Constrained Complexity http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMjdoZmd2emZncQ DNA - Evolution Vs. Polyfuctionality - video http://www.metacafe.com/watch/4614519 further note; Scott Minnich reveals in this following video that it was not possible to comprehensively study the irreducible complexity of the Bacterial Flagellum unless it had been for the principle of 'specific functionality revealing itself through specific deleterious mutations'; Bacterial Flagella: A Paradigm for Design - Scott Minnich - video http://www.youtube.com/watch?v=0NXElnMuTPIbornagain77
May 23, 2011
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Chiefley notice I stated: ,,, Whereas ID predicts, at least the broader concept of ID predicts, that optimal information/functionality was designed originally in a, or in many, parent species,bornagain77
May 23, 2011
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It seems to me that ID makes no prediction about the presence or absence of non-coding DNA. Such a prediction would require assumptions about the designer. The notion of a wise and caring designer who would not produce non-functional or non-optimum biological constructs seems simply sentimental. If we are to look to the designers we can observe (humans) we produce plenty of non-optimum and even non-functioning designs.Chiefley
May 23, 2011
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Gregory's Onion Test: The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA1. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?Pedant
May 23, 2011
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DrREC, you finally have written something that I can almost agree with. Both ID and neo-Darwinism predict 'junk' but for two VERY dramatically different reasons. neo-Darwinism predicts junk because it presupposes all functionality to arise randomly from non-functionality. Which is something that we have never witnessed occurring in nature.,,, The Law of Physicodynamic Insufficiency - Dr David L. Abel - November 2010 Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.” http://www.scitopics.com/The_Law_of_Physicodynamic_Insufficiency.html ,,, Whereas ID predicts, at least the broader concept of ID predicts, that optimal information/functionality was designed originally in a, or in many, parent species, and that all adaptations away from that, or those, parent species will always come at a cost of that optimal functionality/information that we find in life. The problem for neo-Darwinism in all this is that all of nature testifies against its precept in that all newly created things we see in nature acquire nicks, scratches, dents and dings as they get older, whereas no one has ever witnessed any optimal functional information being created from scratch. ,,, Thus as to predictions, neo-Darwinisn predicts vast swaths of non-functionality, for it is required to arrive at novel functionality in the first place, (a feat which we have never witnessed), whereas ID predicts vast swaths of functionality with 'dents and dings' of non-functionality because this is exactly what we observe in nature, and is of course in complete accord with the second law and Conservation of Information theorems. notes: the evidence for the detrimental nature of mutations in humans is overwhelming for scientists have already cited over 100,000 mutational disorders. 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.biobase-international.com/pages/index.php?id=hgmddatabase I really question their use of the word 'celebrating'. Human Evolution or Human Genetic Entropy? - Dr. John Sanford - video http://www.metacafe.com/w/4585582 This following study confirmed the detrimental mutation rate for humans, of 100 to 300 per generation, estimated by John Sanford in his book 'Genetic Entropy' in 2005: Human mutation rate revealed: August 2009 Every time human DNA is passed from one generation to the next it accumulates 100–200 new mutations, according to a DNA-sequencing analysis of the Y chromosome. (Of note: this number is derived after "compensatory mutations") http://www.nature.com/news/2009/090827/full/news.2009.864.html This 'slightly detrimental' mutation rate of 100 to 200 per generation is far greater than even what evolutionists agree is an acceptable mutation rate for an organism: 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/releases/2007/10/071001172753.htm also of note, all supposed 'beneficial mutations' to humans, such as lactase persistence, and the Tibetan red blood cell mutation, appear to be mutations that arise from some type of Lamarkian evolution, where the environment is influencing the higher levels of epigenetic information to 'calculate' a rapid response to environmental stress. The mutations are 'non-random'. Moreover these precious few examples of 'beneficial mutations' are found to come at a cost of 'optimal functionality', thus staying within the overriding principle of genetic entropy. further notes: “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.(that is a net 'fitness gain' within a 'stressed' environment i.e. remove the stress from the environment and the parent strain is always more 'fit') http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/ Michael Behe talks about the preceding paper on this podcast: Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time - December 2010 http://intelligentdesign.podomatic.com/player/web/2010-12-23T11_53_46-08_00 Evolution Vs Genetic Entropy - Andy McIntosh - video http://www.metacafe.com/watch/4028086bornagain77
May 23, 2011
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Mung:
Preface: 0 cites. Chapter 1. 19 references Gee, that’s a huge number compared to the total number of cites. Let us know when you’ve read the book. Thanks.
So, again you're quoting the number of references as a proxy for quality... So does that mean that Wells shouldn't have written a preface or first chapter to his book, or just that they are above any critique? Still haven't heard your thoughts on the book, Mung. Any good? What proportion of the genome does Wells attribute function to? More than half?, and if so on what grounds?paulmc
May 23, 2011
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I’ve always found the ‘no DNA is junk’ a curious prediction for ID.
Me too! And your evidence for the assertion that no DNA is junk DNA is a prediction of ID is?Mung
May 22, 2011
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I've always found the 'no DNA is junk' a curious prediction for ID. Or is that little junk? Some junk? 10%, 20% 45%...where is it that the prediction kicks in? But back to my point-suppose something was designed, but subject to the ever-popular 'genetic entropy.' BA77-where are your links on this? Thanks. What would that designed thing look like after decay? Junk? Or 'frontloaded' genes-what might they look like? Junk? ( Not trash-after all, junkyards are where we go to pull parts to keep our cars running-grad school isn't profitable after all). So it seems odd to have this notion of 'no junk' when the design hypothesis seems like it warrants 'junk.' Just misinterpretation heaped on misinformation, and no wins for either party here.DrREC
May 22, 2011
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Yes. Although, frankly, if it turns out Wells really is as selective with the evidence as Moran claims in his critique, I might not finish it.
Preface: 0 cites. Chapter 1. 19 references Gee, that's a huge number compared to the total number of cites. Let us know when you've read the book. Thanks.Mung
May 22, 2011
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Mung
One would think that actually reading the book is a minimal prerequisite for a “critic.”
I agree and don't think it is useful for the likes of Farrell to have criticised the book without reading it. However, if that was directed at me, you'll note that barring a single general comment I have only pointed readers to (the start of) Larry's chapter-by-chapter discussion. What I discussed above was Luskin's and Farrell's incorrect characterisation of T. Ryan Gregory, central to the OP, not Well's book. I do find the omission of Larry Moran's critique from the post interesting, considering the context. So, the 'evolutionists' criticise Wells' book without reading it ... except in the cases where they do read it.
It’s not as if Wells does not address “the union test.”
Excellent for Wells. But above I was referring to the onion test being ignored by Luskin in his quote on the Forbes blog, where he makes a fatuous claim about T. Ryan Gregory. Wells' name occurs only in a subsequent general comment about the presence of junk in the human genome, the junk he claims is a myth.
The Preface is 1.5 pages and contains 0 (zero) cites. One can only applaud Moran’s non-effort.
I don't understand your point, if you have one. Moran commented on the preface before he had gotten a copy of the book. He is now going through the book chapter by chapter. Is it a 'non-effort' for him to dissect the book in chapters? Why have you counted up the references for each chapter? Is the work robust because chapter 6 cites >100 references? A review of a narrow topic in the literature will usually cite at least this many references - without any guarantee of doing the topic justice. If Chapter 1 in Wells' book is 4.5 pages long, I wouldn't blame Moran for this.
Do you intend to read the book yourself?
Yes. Although, frankly, if it turns out Wells really is as selective with the evidence as Moran claims in his critique, I might not finish it.paulmc
May 22, 2011
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paulmc, Please do let us know when you've actually read The Myth of Junk DNA. One would think that actually reading the book is a minimal prerequisite for a "critic." It's not as if Wells does not address "the union test."
He finds that, so far (he’s only critiqued Chapter 1 and the preface so far) ...
Bully for him. Do you intend to read the book yourself? The Preface is 1.5 pages and contains 0 (zero) cites. One can only applaud Moran's non-effort. Chapter 1 is 4.5 pages and contains 19 references. Chapter 3 contains 62 references. Chapter 4 contains 63 references. Chapter 5 contains 63 references. Chapter 6 contains 117 references. Good luck Larry.Mung
May 22, 2011
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The greatest spin campaign ever will be executed for optimal damage control over this issue. The reason is simple. This is one concept- "junk dna" that the general public does grasp (concerning the genome.) It is a simple and powerful rhetoric. So therefore when it(junk dna) inevitably slips away from the drawinist/media machine, that detail will not be misunderstood by the general public either. The bottom line is that the "junk dna" fiasco hurts the neo-darwinist more than anything with respect to the general public's perception. This is a topic that has not been kept hidden in the abstracts of biology journals. Because "junk dna" was so catchy, and it clicked with people, like... "if the glove don't fit, you must acquit." That rhetoric worked very well, it helped a killer go free. But only because the glove did not fit. What would have happened to perception if the glove later was found to not fit at all?junkdnaforlife
May 22, 2011
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Problem is (for both Farrell and Luskin) T. Ryan Gregory does not argue what appears to be claimed of him here. He is the deviser of the onion test, after all. Gregory's point was that there has never been a consensus on junk DNA. Neutralists of the 1970s supported the idea, Darwinists often rejected it. There was, in other words, a plurality of views rather than a consensus, why claim otherwise? When Luskin claims in his Forbes post "It’s very convenient for T. Ryan Gregory to argue, in 2011, that the genome isn’t full of useless junk.", Luskin is very badly mistaken. Gregory - as he would know if he read him - does not argue any such thing (again see the onion test). Contra Luskin and Wells, there is substantial evidence that a majority of the human genome is junk. Gregory, being a genomics researcher, knows this. In related news, Larry Moran is dissecting it chapter by chapter. He finds that, so far (he's only critiqued Chapter 1 and the preface so far), Wells makes selective use of quotations ("quote mining" in the common parlance) to make a case that is not supported by the balance of evidence.paulmc
May 22, 2011
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