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

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

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).)

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

  1. 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.

  2. 2

    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?

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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?

  8. 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?

  9. 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_L.....iency.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-internation.....mddatabase

    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/200.....9.864.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/re.....172753.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.co.....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.podom.....3_46-08_00

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

  10. 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?

  11. 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.

  12. 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,

  13. 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).”
    http://www.uncommondescent.com.....ent-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?doc.....Zmd2emZncQ

    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=0NXElnMuTPI

  14. @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.

  15. “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?

  16. Chiefley I agree with you, and I sense that a good size book could be written on just that ‘optimal’ inference, as well, I suppose that by your criteria then neo-Darwinists will also have to justify why they are allowed to use examples of ‘supposed’ sub-optimal design to support their claims for neo-Darwinism, almost exclusively, instead of actually demonstrating the generation of functional information by purely material processes.

  17. Chiefley, when you dig down underneath all of the Darwinian rhetoric, you find that it is at its core a theological argument with no solid empirical support, Thus whatever criticism you are trying to level at ID could also be leveled at neo-Darwinism in full measure. Actually leveled more so against neo-Darwinism since we have no examples of material processes generating information, whereas every time you write a post you yourself, by your own intelligence, are generating more functional information than can reasonable be expected from the material processes of the universe over the entire history of the universe!:

    notes:

    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

    Book Review – Meyer, Stephen C. Signature in the Cell. New York: HarperCollins, 2009.
    Excerpt: As early as the 1960s, those who approached the problem of the origin of life from the standpoint of information theory and combinatorics observed that something was terribly amiss. Even if you grant the most generous assumptions: that every elementary particle in the observable universe is a chemical laboratory randomly splicing amino acids into proteins every Planck time for the entire history of the universe, there is a vanishingly small probability that even a single functionally folded protein of 150 amino acids would have been created. Now of course, elementary particles aren’t chemical laboratories, nor does peptide synthesis take place where most of the baryonic mass of the universe resides: in stars or interstellar and intergalactic clouds. If you look at the chemistry, it gets even worse—almost indescribably so: the precursor molecules of many of these macromolecular structures cannot form under the same prebiotic conditions—they must be catalysed by enzymes created only by preexisting living cells, and the reactions required to assemble them into the molecules of biology will only go when mediated by other enzymes, assembled in the cell by precisely specified information in the genome.
    So, it comes down to this: Where did that information come from? The simplest known free living organism (although you may quibble about this, given that it’s a parasite) has a genome of 582,970 base pairs, or about one megabit (assuming two bits of information for each nucleotide, of which there are four possibilities). Now, if you go back to the universe of elementary particle Planck time chemical labs and work the numbers, you find that in the finite time our universe has existed, you could have produced about 500 bits of structured, functional information by random search. Yet here we have a minimal information string which is (if you understand combinatorics) so indescribably improbable to have originated by chance that adjectives fail.
    http://www.fourmilab.ch/docume.....k_726.html

    Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe:
    Excerpt: The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences.
    http://www.ncbi.nlm.nih.gov/pubmed/15321723

    Correcting Four Misconceptions about my 2004 Article in JMB — May 4th, 2011 by Douglas Axe
    http://biologicinstitute.org/2.....le-in-jmb/

    Measuring the functional sequence complexity of proteins – 2007: Kirk K Durston, David KY Chiu, David L Abel, Jack T Trevors
    In this paper, we provide a method to measure functional sequence complexity (in proteins).
    Conclusion: This method successfully distinguishes between order, randomness, and biological function (for proteins).
    http://www.tbiomed.com/content/4/1/47/

    “a very rough but conservative result is that if all the sequences that define a particular (protein) structure or fold-set where gathered into an area 1 square meter in area, the next island would be tens of millions of light years away.”
    Kirk Durston

    Stability effects of mutations and protein evolvability. October 2009
    Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,,
    http://www.ncbi.nlm.nih.gov/pubmed/19765975

    The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway – Ann K. Gauger and Douglas D. Axe – April 2011
    Excerpt: We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions. But evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth.
    http://bio-complexity.org/ojs/.....O-C.2011.1

    When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
    Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
    http://biologicinstitute.org/2.....t-collide/

  18. “neo-Darwinism predicts junk because it presupposes all functionality to arise randomly from non-functionality.”

    Really? Where does that come from? I would think that neo-Darwinism would simply point to the ability of genetic mutation to disable a gene.

    Also, don’t we have sections of viruses inserted into genomes backwards?

  19. “Chiefley, when you dig down underneath all of the Darwinian rhetoric, you find that it is at its core a theological argument with no solid empirical support,”

    Actually, I understand the empirical support offered by ToE. I just find it hard to believe. And for my own reasons I am looking for evidence of design in nature.

    ” Thus whatever criticism you are trying to level at ID could also be leveled at neo-Darwinism in full measure.”

    So you are not helping by telling me that both ToE and ID are theological with no empirical support.

    If we are to be making claims about the requirement for design in nature, we should be doing it rigorously. At least it should stand up to my simple questions.

    I don’t like to see misrepresentation and bad logic in ToE arguments either.

    I can understand how the basic axioms of ToE predict non-functioning DNA by logical necessity, but I do not see how it is falsifiable. Doesn’t it represent an argument from ignorance? Or do I have that wrong?

  20. Chiefley, I’m sorry but I do not follow your logic when you state.

    So you are not helping by telling me that both ToE and ID are theological with no empirical support.

    For ID works primary from a design inference not from a theological inference as Darwinism does;

    i.e.

    “A code system is always the result of a mental process (it requires an intelligent origin or inventor). It should be emphasized that matter as such is unable to generate any code. All experiences indicate that a thinking being voluntarily exercising his own free will, cognition, and creativity, is required. ,,,there is no known law of nature and no known sequence of events which can cause information to originate by itself in matter. Werner Gitt 1997 In The Beginning Was Information pp. 64-67, 79, 107.”
    (The retired Dr Gitt was a director and professor at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt, Braunschweig), the Head of the Department of Information Technology.)

    The Capabilities of Chaos and Complexity – David L. Abel – 2009
    Excerpt: “A monstrous ravine runs through presumed objective reality. It is the great divide between physicality and formalism. On the one side of this Grand Canyon lies everything that can be explained by the chance and necessity of physicodynamics. On the other side lies those phenomena than can only be explained by formal choice contingency and decision theory—the ability to choose with intent what aspects of ontological being will be preferred, pursued, selected, rearranged, integrated, organized, preserved, and used. Physical dynamics includes spontaneous non linear phenomena, but not our formal applied-science called “non linear dynamics”(i.e. language,information).
    http://www.mdpi.com/1422-0067/10/1/247/pdf

    The DNA Enigma – Where Did The Information Come From? – Stephen C. Meyer – video
    http://www.metacafe.com/watch/4125886

    Stephen C. Meyer – Signature In The Cell:
    “DNA functions like a software program,” “We know from experience that software comes from programmers. Information–whether inscribed in hieroglyphics, written in a book or encoded in a radio signal–always arises from an intelligent source. So the discovery of digital code in DNA provides evidence that the information in DNA also had an intelligent source.”
    http://www.evolutionnews.org/2.....ligen.html

    Thus ID is not basing its inference on Theology, but is basing its argument for what our uniform experience of reality tells us. i.e. intelligence is required to generate information!!! Whereas Chiefley for you to prove that neo-Darwinism is not a theological argument you would have to provide concrete evidence of purely material generating information instead of the plethora of ‘bad design’ arguments we continually see Darwinists make.

  21. From the responses here, it seems ID makes no prediction on ‘Junk’ DNA because-

    It is impossible to tell if something was designed to function, but fell into disuse/disarray due to ‘genetic entropy.’

    Saying a design must function infers the will of the designer-that the design was good, efficient, and seamless (not leaving ‘junky’ artifacts or non-functional bits about).

    It is impossible to tell if something was designed to one day emerge as functional.

    Ok. But these are hardly testable hypotheses. Lots of ‘junk’, little ‘junk’ or no ‘junk’, still designed?

    ID scores again!

  22. DrREC, but why should it matter to you at all what ID predicts since neo-Darwinism has no rigorously established foundation in science in the first place??? i.e. Your theory ain’t even in the ballpark as to being a rational explanation, and yet you act as if it does have credence??? It seems VERY DISINGENUOUS of you to ignore the fact that your ‘preferred’ theory of neo-Darwinism is devoid of any rigorous foundation in physical science, all the while sniping about just how much genetic entropy should be allowed into play, on top of the already established design inference. DrREC, perhaps you care to prove the ID inference wrong by generating functional information by material processes??? Until then why in the world should anyone give your unfounded opinions any thought whatsoever???

  23. //DrREC, but why should it matter to you at all what ID predicts since neo-Darwinism has no rigorously established foundation in science in the first place???//

    It matters because this question is what distinguishes a scientific hypothesis from just someone’s opinion. I am actually interested in the answer.

    Can I ask it again so we can discuss ID or is this simply a ToE bashing forum?

    From what basic premises in ID theory does the prediction that all aspects of a designed system must be optimally functional or even just functional come from?

  24. BA77: Even if you’re right and neo-Darwinism is a busted flush that doesn’t mean that ID is automatically true. It still needs to be examined and questioned and put to the test like any other scientific notion.

    There are options/explanations other than neo-Darwinsism and ID. No free lunch in this part of the forum I’m afraid.

    And now I’ve got to go to bed. See y’all later!!

  25. So…..no other comments on ‘junk DNA’?

    I thought this was supposed to be a big win for ID, but now most commenters agree it is not even a prediction of ID.

    Interesting, and I really welcome any other comments as we return to the original topic despite attempts to derail it.

  26. 26

    This appears to be some sort of id prediction:

    “As far back as 1994, pro-ID scientist and Discovery Institute fellow Forrest Mims had warned in a letter to Science[1] against assuming that ‘junk’ DNA was ‘useless.’” Science wouldn’t print Mims’ letter, but soon thereafter, in 1998, leading ID theorist William Dembski repeated this sentiment in First Things: “[Intelligent] design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term “junk DNA.” Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as “junk” merely cloaks our current lack of knowledge about function. Design encourages scientists to look for function where evolution discourages it.”

    http://www.firstthings.com/art.....-design-10

  27. The prediction is not very specific though. ” . . . we expect, as much as possible, to exhibit function.” Too bad Dr Dembski did put some numbers or estimates down.

    Another good area for ID research??

  28. 28

    point made ell, a little yes, but he(dembski) seemed to be on the right track, whereas the dawkins types about the same time time (98ish) were saying the exact opposite, trumpeting the junk dna rhetoric. naturally the dawkins types do not represent everyone in biology. But they are the loudest and the media loves them.

    I’ll have to look through On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life again, because i’m close to 100% certain that darwin made some less than specific predictions but still gets a pat on the ass for them.

    About specific numbers… if id claims that intelligence is the source of information in dna. And dna is digital code, analogous to binary computer code, functioning like an operating system, with complex algorithms ect, then it should be within computer programming that an id person should be looking to draw a baseline. Computer code is never perfect. Run ebay.com through an html validator and you will see hundreds of errors and warnings. same with php or ajax or whatever they are using. And that is just a website. genes are subject to entropy, computer codes are not closed systems, they have teams constantly working on them, so in nature the error rate may be higher than ebay or windows. so scale the size of a coded system, function, complexity ect along with the error, broken string etc % to that of a genome, factor in for entropy tweak for other intangibles and toss out a range of percentages of predicted genome function and hope its falls within the margin of error

  29. junk: Sounds like a good idea! You’re certainly right about most websites, so much is just kludged until the output is ‘correct’.

  30. “As far back as 1994, pro-ID scientist and Discovery Institute fellow Forrest Mims had warned in a letter to Science against assuming that ‘junk’ DNA was ‘useless.’” Science wouldn’t print Mims’ letter….:

    I Don’t think this rejection was out of ideology
    Science, Feb 1994:

    Mining treasures from ‘junk DNA.’
    http://www.sciencemag.org/cont.....08.extract
    “….so-called junk DNA is turning out to have vital roles in genome function.”

    In 1998, leading ID theorist William Dembski repeated this sentiment in First Things….

    This is 5 years further into the exploration of non-coding DNA.

    These would be a lot more interesting predictions, if for example in 1993, Victor Ambros lab hadn’t already cloned lin-4, and shown it to be a non-coding RNA whose deletion caused development to go wrong in C. elegans.

    http://www.sciencedirect.com/s.....749390529Y

    It just feels a bit like the ID crowd was postdicting a role for ‘junk’ DNA. Not all of it, not most of it, just some of it-years after it the function of some of it had flashed across the pages of Science, Nature, and Cell.

    And there are still plenty of non-functional bits around, who are broken in ways that indicate common ancestry.

  31. DrREC,

    You need more than common broken stuff for universal common ancestry.

    Just sayin’…

  32. Joseph: I think there is more than common broken stuff implying common descent with modification.

    To be honest, I’m a bit shaken by the points raised in the Lynn Margulis interview that BA77 flagged up for me in another thread. I’m churning it all over in my mind and . . . I’m thinking she has a real point. I’m think she just might have an insight into some of the jumps we see in the fossil record. It’ll be interesting to see how the follow on research pans out. It’s a good time to be alive! Lots going on.

  33. paulmc:

    Still haven’t heard your thoughts on the book, Mung. Any good?

    As an ID book I’d rate it above median. But that may not be saying much, as there are so many crappy ID books making their way on to the market, lol.

    IMO, it does not make a positive case for ID, so it doesn’t rank up there with DBB and SitC.

    What proportion of the genome does Wells attribute function to? More than half?, and if so on what grounds?

    He doesn’t. Sorry to disappoint.

    Would you say though that what was once thought to be “junk DNA” is now a vibrant area of research?

    What Darwinian principle(s) motivated the research?

  34. Can I explain why an onion needs about five times more non-coding DNA for this function than a human?

    Stupid question.

    Might make sense of humans were onions, or onions were humans.

  35. Mung:

    He doesn’t. Sorry to disappoint.

    Haha, yeah. Why am I not surprised?

    Would you say though that what was once thought to be “junk DNA” is now a vibrant area of research?

    It certainly is an active area of research, yes. Small fragments of DNA are found to be functional from time to time.

    These are always interesting finds. But – as I keep coming back to – the real argument here is over numbers. We are talking about changes to our understanding of a tiny, tiny percentage of the genome. Broken fragments of pseudogenes and LINES in intergenic regions and introns remain without known function, nor reason to suspect function when considering their apparent origins.

    What Darwinian principle(s) motivated the research?

    The Darwinian fixation on natural selection and adaptation (i.e. the pervasive view that if it’s not promoted by selection it shouldn’t be there) probably goes a long way towards explaining it.

    All this searching should make for a rigorous test of the junk DNA theory.

    Might make sense of humans were onions, or onions were humans.

    I find the other half of the onion test more interesting: why does one species in the onion genus (Allium ursinum) require a genome that is 4.5 times larger than another similar one (Allium altyncolicum)?

  36. …and introns remain without known function, nor reason to suspect function when considering their apparent origins.

    Been a long time since I’ve done any reading on this subject, but what are “the apparent origins” of introns?

    Do I need to abandon my “eukaryotes first” position?

    We are talking about changes to our understanding of a tiny, tiny percentage of the genome. Broken fragments of pseudogenes and LINES in intergenic regions and introns remain without known function, nor reason to suspect function when considering their apparent origins.

    So now we expect these portions to be “junk” because we know where they come from?

    why does one species in the onion genus (Allium ursinum) require a genome that is 4.5 times larger than another similar one (Allium altyncolicum)

    Why are they in a separate genus?

    My guess is that the larger/smaller genomes are there to confuse evolutionists.

  37. So now we expect these portions to be “junk” because we know where they come from?

    I should have expanded my thoughts. This is what I was meaning:

    We have large, sections of the genome where long and short sequences are repeated. Lots of these sequences have subsequently degraded via mutation, showing little sign of conservation.

    The lack of conservation indicates they are not subject to purifying selection. They don’t show greater-than-expected variation like the MHC where heterogeneity is known to be beneficial.

    So why are these sequences in the genome? When – on top of their lack of known function and lack of conservation – we consider the mechanism of reverse transcription and its consequence (insertions of additional copies of these transposible elements into the genome) – then where they come from does become an additional line of evidence regarding their status as junk.

    That there are transposible elements at all appears to be beneficial; hence active transposons are not considered junk. Such stochastic insertions can be a good thing in the long run as sources of evolutionary novelty. But because their insertion is haphazard, the bulk of those not immediately removed by purifying selection because of serious fitness effects have either no consequence of significance and are destined to be degraded by mutation.

  38. Haha, yeah. Why am I not surprised?

    Why should you be surprised? I already told you what I thought Wells’ argument was, and that it did not include the idea that there was no “junk” DNA.

    Wells appears to be keeping an open mind on the issue. Why you think that should be held against him is beyond me. (Not really. It’s obvious where you are coming from.)

    Seriously. Wells is a scientist. What did you want him to say? There is no junk DNA? (Yes. That’s what you wanted him to say. Admit it.)

    I just love how you translate the refusal to take an absurd and probably indefensible position as somehow a lack of character on the person who fails to do so.

  39. Lots of these sequences have subsequently degraded via mutation, showing little sign of conservation.

    Interesting choice of language.

    You mean that if you examine different species, that these sequences show differences, and that because they show differences, it must be the case that these sequences are not being selected for, and since they are not obviously being selected for, they must be degrading.

    Sez who?

    How can non-functional junk be degrading? Is that a scientific term, degrading? How do you measure the level of degradation in the genome, over time?

    Cites please.

  40. Why should you be surprised? I already told you what I thought Wells’ argument was, and that it did not include the idea that there was no “junk” DNA.

    Yes, but the problem here is that Wells attempts to make a forceful case against the existence of junk DNA. In the preface to Myth, he claims:“[t]he idea that most of our DNA is junk became the dominant view among biologists. That view has turned out to be spectacularly wrong.

    Far from consisting mainly of junk that provides evidence against intelligent design, our genome is increasingly revealing itself to be a multidimensional, integrated system”
    .

    Wells has made a clear claim. Less than 50% of the genome is junk, probably much less. This is a qualitative claim that Wells does not support.

    Wells appears to be keeping an open mind on the issue. Why you think that should be held against him is beyond me. (Not really. It’s obvious where you are coming from.)

    An open mind? Our views diverge, sir, considering what I have discussed above.

    Seriously. Wells is a scientist. What did you want him to say? There is no junk DNA? (Yes. That’s what you wanted him to say. Admit it.)

    I just love how you translate the refusal to take an absurd and probably indefensible position as somehow a lack of character on the person who fails to do so.

    Sorry, you’re barking up the wrong tree. I don’t want him to take any viewpoint in particular. I want him to make cohesive, evidence-based arguments. I have already said in a couple threads that I don’t see junk DNA as necessarily a for-or-against ID issue (even if some ID proponents do).

    All I can do is say that I don’t have any vested interest in junk DNA existing or not existing. You can choose to believe me or not. Wells appears to have a vested interest – he appears to believe that junk is harmful to ID (as quoted above).

  41. You mean that if you examine different species, that these sequences show differences, and that because they show differences, it must be the case that these sequences are not being selected for, and since they are not obviously being selected for, they must be degrading.

    Sez who?

    Sez population genetics theorists since the 1950s.

    The inference of being free from purifying selection does not come from the fact that the sequences show differences, but because the rate at which those differences accumulate (i.e. relative to conserved sequences such as genes) is relatively fast. The rate of change alone indicates they are not conserved by purifying natural selection for a function, but there is another good reason for this inference.

    In the 1930s, Haldane had shown an upper limit on the rate of positive selection, because of the ‘cost of natural selection’, i.e. death. This was developed further in the 1950s. We term the cost ‘genetic load’.

    So, if the sequences were evolving under selection at that rate, their change must come with a genetic load, a cost in terms of differential survival.

    The genetic load argument was used in the 1960s to show that the rates of amino acid changes in mammals was too fast to have been caused by selection (e.g. Kimura 1968). If you want the numbers, grab a copy of Kimura’s paper. Such a rate of positively selected changes would result in extinction. Most of the changes must have resulted from genetic drift – i.e. they must not affect survival to the extent that they are noticeably subject to natural selection.

    This is also independently evidenced by the mutation rate in humans. The mutational load is too high for all (or even many) of the mutations to be subject to purifying selection – if it were the case again we would necessarily be extinct because the action of selection is on differential survival and reproduction.

    How can non-functional junk be degrading? Is that a scientific term, degrading? How do you measure the level of degradation in the genome, over time?

    Cites please.

    It was a shorthand term = changing from a previously functional sequence, through the accumulation of random mutations. This can be measured through numbers of changes from the inferred ancestral node on a molecular phylogeny and calibrated to time via the fossil record where possible. Yes, this assumes common descent. On the balance of evidence, is this an unsafe assumption? If so, why?

  42. All I can do is say that I don’t have any vested interest in junk DNA existing or not existing. You can choose to believe me or not. Wells appears to have a vested interest – he appears to believe that junk is harmful to ID (as quoted above).

    I also see no problem with the existence of “junk” DNA.

    But I don’t agree that Wells believes junk DNA is harmful to ID.

    In my opinion, and I offer this up without quote from Wells (’cause right now I’m just to lazy to haul the book off my shelf, which is probably less than three feet away), is that “the argument from junk DNA” is a metaphysical or religiously based argument, and is outside of science.

  43. In the 1930s, Haldane had shown an upper limit on the rate of positive selection, because of the ‘cost of natural selection’, i.e. death. This was developed further in the 1950s. We term the cost ‘genetic load’.

    If your beliefs are based on genetic death or genetic load I invite you to re-think.

    In order for an allele to increase in number/frequency in the population the carriers of that allele must out-reproduce the non-carriers.

    Is that statement controversial?

  44. I also see no problem with the existence of “junk” DNA.

    If you were to take this one step further and momentarily accept the existence of junk DNA: How would you interpret nested hierarchical patterns of similarities and differences in junk DNA between species (i.e. with regards to common descent versus common design)?

    Apologies for the long sentence.

  45. In order for an allele to increase in number/frequency in the population the carriers of that allele must out-reproduce the non-carriers.

    Is that statement controversial?

    No – that’s not controversial. However, because neutral loci evolve independently under genetic drift, multiple substitutions are able to occur at once without increasing genetic load (whereas selections ‘sweep’ through populations, thereby increasing load). This is one of the central arguments made in support of the view that genetic drift is a major evolutionary process for us metazoans.

    In any case, my argument does not depend on genetic load – mutational load provides evidence that most loci in the human genome are not and cannot be under strong selection (because of the number of individuals that would need to die to prevent an inescapable build up of deleterious mutations).

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