Jonathan Wells on the junk DNA myth

_{Denyse O'Leary

August 30, 2013

'Junk DNA'}

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Yesterday, we noted the Abstract and Conclusion of Jonathan Wells’s Cornell Origin of Biological Information paper, “Not Junk After All.”

Here is an interview with Wells on the junk myth, “Yes, it is a Darwinist myth and he nails it as such”, here’s an excerpt from his book, The Myth of Junk DNA, and here’s his response to critics, “Jonathan Wells on Darwinism, Science, and Junk DNA”.

One thing you can be sure of, now that it is clear that very little DNA is junk, you will no longer hear how it prove ID is wrong; a future discard will be substituted.

Comments

Mung, I did not claim that either Egnor or Jerry Fodor and Massimo Piatelli-Palmarini wrote what I said before I quoted them directly. Thus I amend my notes to include this following quote from Egnor: Natural selection is not a level of explanation. In F&P-P’s cogent phrase, natural selection is empty. I hope this is to your satisfaction as I have removed any personal interpretation I may have had, that you may have objected to, from my notes and let Egnor's own words speak for themselves. I'm quite happy to have Natural selection is not a level of explanation. In F&P-P’s cogent phrase, natural selection is empty. in my notes and to remove any false interpretation I may have imposed on it.bornagain77_{September 1, 2013
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BA77:
mung so you do not object to what Egnor or from Fodor and Piattelli-Palmarini wrote but to what I wrote preceding the quote
There was no quote, there was an alleged quote. I object to your assertion that you were quoting anyone. BA77:
Natural selection is ‘empty’ of true explanatory power and to the extent that it does do anything, it is found that Natural Selection reduces genetic information instead of creates it.
Reference please? Who are you quoting?Mung_{September 1, 2013
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mung so you do not object to what Egnor or from Fodor and Piattelli-Palmarini wrote but to what I wrote preceding the quote? Okie Dokie hows this for splitting hairs: Natural Selection Is Empty – Michael Egnor – August 30, 2013 Excerpt: "What’s essential about adaptationism, as viewed from this perspective, is precisely its claim that there is a level of evolutionary explanation. We think this claim is just plain wrong. We think that successful explanations of the fixation of phenotypic traits by ecological variables typically belong not to evolutionary theory but to natural history, and that there is just no end of the sorts of things about a natural history that can contribute to explaining the fixation of some or other feature of a creature’s phenotype. Natural history isn’t a theory of evolution; it’s a bundle of evolutionary scenarios. That’s why the explanations it offers are so often post hoc and unsystematic." - Jerry Fodor and Massimo Piatelli-Palmarini’s – What Darwin Got Wrong – 2010 Natural selection is not a level of explanation. In F&P-P's cogent phrase, natural selection is empty. http://www.evolutionnews.org/2013/08/natural_selecti_2075991.htmlbornagain77_{September 1, 2013
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BA77: I read the Egnor article. Nothing I said contradicts what he wrote. The problem for me is what you appended to what he wrote that he did not in fact himself write. Nor did Foder and Piattelli-Palmarini write it. This was your exact "quote": ‘Natural selection is ‘empty’ of true explanatory power and to the extent that it does do anything, it is found that Natural Selection reduces genetic information instead of creates it.’ The quote marks are yours, not mine. If you can show me where that's an actual quote from either Egnor or from Fodor and Piattelli-Palmarini I'l gladly withdraw my objection. I can gladly provide you with quotes from their book, they just won't look like the one you've given. "If nobody believes Skinner any more, why does everybody still believe Darwin?" p. 3Mung_{August 31, 2013
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Mung, funny, what I quoted is verbatim of how Fodor and Piattelli-Palmarini sum up their argument, before Egnor states,, Natural selection is not a level of explanation. In F&P-P's cogent phrase, natural selection is empty. - See more at: http://www.evolutionnews.org/2013/08/natural_selecti_2075991.html#sthash.qQhYUxbv.dpuf mung, Perhaps you have a better quote from them? If so I will be glad to amend my notes.bornagain77_{August 31, 2013
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BA77:
Mr. Fox, as to my claim that ‘Natural selection is ‘empty’ of true explanatory power and to the extent that it does do anything, it is found that Natural Selection reduces genetic information instead of creates it.’
That's NOT why it's an empty concept, or at least that's not the argument Fodor and Piattelli-Palmarini make.Mung_{August 31, 2013
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Alan Fox:
Breckmin asks where to get an ID argument. Well yes. UD is about the only place left for that. What you won´t get is any kind of evidence -based explanation.
Well no, Alan, that's jut not true, and you know it's not true. As you speak there are multiple threads at TSZ defending ID, and both Upright BiPed and gpuccio have put in appearances over there in spite of it's obvious echo-chamber qualities. Take, for example, the thread on Darwin's Doubt, the new book by Stephen Meyer. But it seems that Elizabeth is the only "critic" there to have actually read the book! So on that score alone Breckmin should be asking here rather than there. At least we try to do our homework here.Mung_{August 31, 2013
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"What you won´t get is any kind of evidence -based explanation." Says the man who can't produce evidence for a single molecular machine being generated by Darwinian processes: ,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’ Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205. *Professor Emeritus of Biochemistry, Colorado State University, USA Michael Behe - No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines http://www.metacafe.com/watch/5302950/ of related note to the fact that Darwinists have ZERO empirical evidence of Darwinian processes EVER producing a molecular machine, here is an example that intelligence can do as such: (Man-Made) DNA nanorobot – video https://vimeo.com/36880067 Also of note, Dr. James Tour, who builds the most sophisticated man-made molecular machines in the world,,, Science & Faith — Dr. James Tour – video http://www.youtube.com/watch?v=CdU5ojTpyzg ,,will buy lunch for anyone who can explain to him exactly how Darwinian evolution works: Top Ten Most Cited Chemist in the World Knows That Evolution Doesn’t Work – James Tour, Phd. – video http://www.youtube.com/watch?v=WCyAOCesHv0bornagain77_{August 31, 2013
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Breckmin asks where to get an ID argument. Well yes. UD is about the only place left for that. What you won´t get is any kind of evidence -based explanation.Alan Fox_{August 31, 2013
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Mr. Fox, as to my claim that 'Natural selection is ‘empty’ of true explanatory power and to the extent that it does do anything, it is found that Natural Selection reduces genetic information instead of creates it.'
Natural Selection Is Empty - Michael Egnor - August 30, 2013 Excerpt: What's essential about adaptationism, as viewed from this perspective, is precisely its claim that there is a level of evolutionary explanation. We think this claim is just plain wrong. We think that successful explanations of the fixation of phenotypic traits by ecological variables typically belong not to evolutionary theory but to natural history, and that there is just no end of the sorts of things about a natural history that can contribute to explaining the fixation of some or other feature of a creature's phenotype. Natural history isn't a theory of evolution; it's a bundle of evolutionary scenarios. That's why the explanations it offers are so often post hoc and unsystematic. - Jerry Fodor and Massimo Piatelli-Palmarini's - What Darwin Got Wrong - 2010 http://www.evolutionnews.org/2013/08/natural_selecti_2075991.html Can Purifying Natural Selection Preserve Biological Information? - published online May 2013 - Paul Gibson, John R. Baumgardner, Wesley H. Brewer, John C. Sanford http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0010 Natural Selection Reduces Genetic Information - No Beneficial Mutations - Lee Spetner - Michael Denton - video http://www.metacafe.com/watch/4036816
Though on top of all that CS Lewis's argument from reason and Plantinga's Evolutionary Argument Against Naturalism, in which it is shown neo-Darwinism results in the epistemological failure of naturalism itself,,
“One absolutely central inconsistency ruins [the popular scientific philosophy]. The whole picture professes to depend on inferences from observed facts. Unless inference is valid, the whole picture disappears… unless Reason is an absolute, all is in ruins. Yet those who ask me to believe this world picture also ask me to believe that Reason is simply the unforeseen and unintended by-product of mindless matter at one stage of its endless and aimless becoming. Here is flat contradiction. They ask me at the same moment to accept a conclusion and to discredit the only testimony on which that conclusion can be based.” —C.S. Lewis, Is Theology Poetry (aka the Argument from Reason)
Then perhaps you can begin to understand why I find you assertion that ID is 'unscientific' to be laughable Mr. Fox:
"Modern science was conceived, and born, and flourished in the matrix of Christian theism. Only liberal doses of self-deception and double-think, I believe, will permit it to flourish in the context of Darwinian naturalism." ~ Alvin Plantinga
Verse and Music:
Proverbs 21:30 There is no wisdom, no insight, no plan that can succeed against the LORD. Better Than A Hallelujah - Amy Grant http://myktis.com/songs/better-than-a-hallelujah/
bornagain77_{August 31, 2013
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Mr. Fox, someone pointed out a while back that while on UD you are fairly well behaved but once on TSZ you revert back to the boorish behavior that is typical of internet atheists. Why is this? But regardless of your hypocrisy in your treatment of us, let's take a look at your claim that Darwinism is scientific and Intelligent Design is unscientific and see what we can find. This morning another atheistic neo-Darwinist, like yourself, claimed, as you frequently do, that ID was untestable and unscientific to which I responded:
I hold that Darwinism is unscientific and ID is scientific for the former has no discernible demarcation criteria so as to delineate it as scientific whereas the later, ID, does,,, Moreover all the foundational presuppositions undergirding neo-Darwinism are found to be false. Reductive materialism is falsified by advances quantum mechanics. ‘Randomness’ (entropic processes of the universe) consistently destroy functional information instead of build it. Natural selection is ‘empty’ of true explanatory power and to the extent that it does do anything, it is found that Natural Selection reduces genetic information instead of creates it. see also Denis Nobel’s lecture on the modern synthesis being false.
As to neo-Darwinism having no discernible falsification criteria so as to delineate it as scientific:
“nobody to date has yet found a demarcation criterion according to which Darwin can be described as scientific” – Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, quote as stated in 1973 LSE Scientific Method Lecture Oxford University Seeks Mathemagician — May 5th, 2011 by Douglas Axe Excerpt: Grand theories in physics are usually expressed in mathematics. Newton’s mechanics and Einstein’s theory of special relativity are essentially equations. Words are needed only to interpret the terms. Darwin’s theory of evolution by natural selection has obstinately remained in words since 1859. … http://biologicinstitute.org/2011/05/05/oxford-university-seeks-mathemagician/ “On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?” (Berlinski, D., “A Scientific Scandal?: David Berlinski & Critics,” Commentary, July 8, 2003) Macroevolution, microevolution and chemistry: the devil is in the details – Dr. V. J. Torley – February 27, 2013 Excerpt: After all, mathematics, scientific laws and observed processes are supposed to form the basis of all scientific explanation. If none of these provides support for Darwinian macroevolution, then why on earth should we accept it? Indeed, why does macroevolution belong in the province of science at all, if its scientific basis cannot be demonstrated? https://uncommondescent.com/intelligent-design/macroevolution-microevolution-and-chemistry-the-devil-is-in-the-details/
In fact all the foundational presuppositions undergirding neo-Darwinism, in the modern synthesis, are now shown to be false:
Modern Synthesis Of Neo-Darwinism Is False – Denis Nobel – video http://www.metacafe.com/w/10395212
Whereas ID does not suffer such an embarrassment as to having no discernible falsification criteria so as to delineate it as scientific:
Evolutionary Informatics Lab – Main Publications http://evoinfo.org/publications/
,, the empirical falsification criteria of ID is much easier to understand than the math is, and is as such:
"Orr maintains that the theory of intelligent design is not falsifiable. He’s wrong. To falsify design theory a scientist need only experimentally demonstrate that a bacterial flagellum, or any other comparably complex system, could arise by natural selection. If that happened I would conclude that neither flagella nor any system of similar or lesser complexity had to have been designed. In short, biochemical design would be neatly disproved." - Dr Behe in 1997 Michael Behe on Falsifying Intelligent Design – video http://www.youtube.com/watch?v=N8jXXJN4o_A
As to my claim, 'Reductive materialism (which is the main philosophy underpinning the atheistic version of neo-Darwinism) is falsified by advances quantum mechanics':
the argument for God from consciousness can be framed like this: 1. Consciousness either preceded all of material reality or is a 'epi-phenomena' of material reality. 2. If consciousness is a 'epi-phenomena' of material reality then consciousness will be found to have no special position within material reality. Whereas conversely, if consciousness precedes material reality then consciousness will be found to have a special position within material reality. 3. Consciousness is found to have a special, even central, position within material reality. 4. Therefore, consciousness is found to precede material reality. Four intersecting lines of experimental evidence from quantum mechanics that shows that consciousness precedes material reality (Wigner’s Quantum Symmetries, Wheeler’s Delayed Choice, Leggett’s Inequalities, Quantum Zeno effect): https://docs.google.com/document/d/1G_Fi50ljF5w_XyJHfmSIZsOcPFhgoAZ3PRc_ktY8cFo/edit
As to my claim that '‘Randomness’ (entropic processes of the universe) consistently destroy functional information in the cell instead of build it up'
Shining Light on Dark Energy – October 21, 2012 Excerpt: It (Entropy) explains time; it explains every possible action in the universe;,, Even gravity, Vedral argued, can be expressed as a consequence of the law of entropy. ,,, The principles of thermodynamics are at their roots all to do with information theory. Information theory is simply an embodiment of how we interact with the universe —,,, http://crev.info/2012/10/shining-light-on-dark-energy/ “Is there a real connection between entropy in physics and the entropy of information? …. The equations of information theory and the second law are the same, suggesting that the idea of entropy is something fundamental…” Tom Siegfried, Dallas Morning News, 5/14/90 – Quotes attributed to Robert W. Lucky, Ex. Director of Research, AT&T, Bell Laboratories & John A. Wheeler, of Princeton & Univ. of TX, Austin in the article Demonic device converts information to energy – 2010 Excerpt: “This is a beautiful experimental demonstration that information has a thermodynamic content,” says Christopher Jarzynski, a statistical chemist at the University of Maryland in College Park. In 1997, Jarzynski formulated an equation to define the amount of energy that could theoretically be converted from a unit of information2; the work by Sano and his team has now confirmed this equation. “This tells us something new about how the laws of thermodynamics work on the microscopic scale,” says Jarzynski. http://www.scientificamerican.com/article.cfm?id=demonic-device-converts-inform
,,having a empirically demonstrated direct connection between entropy and the information inherent within a cell is extremely problematic for Darwinists because,,,
“Bertalanffy (1968) called the relation between irreversible thermodynamics and information theory one of the most fundamental unsolved problems in biology.” Charles J. Smith – Biosystems, Vol.1, p259. “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/
bornagain77_{August 31, 2013
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@ 5 Mung makes a good point, where else would I go? (to get the ID side of the argument)Breckmin_{August 31, 2013
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@ 5 Well Mr. Fox, I take it you have lost faith in Uncommon Descent's ability to scientifically analyze the data of a specific find? Do you have anything specific in mind that was not scientifically understood here at uncommondescent?Breckmin_{August 31, 2013
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@ 3 kairosfocus particularly interested in a hydrothermal vent as it relates to Jack Szostak's work on creating (watching them form)stable vesicles which can break and then later form self-replicating proto-cells capable of making RNA chains. It is amazing to me that we could postulate the chemicals for nucleotides all being in the same place in the universe, let alone ribose, etc... how do they end up with useful or meaningful information? My suspicion is they don't... and this is light years away from DNA let alone small functional RNA.Breckmin_{August 31, 2013
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Alan Fox:
You’d be better directing your questions in a venue frequented by scientists.
Like TSZ, lol?Mung_{August 31, 2013
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@ Breckmin You'd be better directing your questions in a venue frequented by scientists.Alan Fox_{August 31, 2013
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KF @ 3 How would you make the case for peer-review? I think that the objector in this case would say that it is a different "type" of information that occurs as a natural phenomenon rather than as a result of intelligence. If you were refuting his 5 points, how would you approach it? What different points would you make?Breckmin_{August 31, 2013
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B: The diagnosis is simple: selectively hyperskeptical dismissal of otherwise uncontroversial facts. With D/RNA coding for proteins, we are looking at a plain case of object code -- which has been cracked for decades now, used in a string data structure. The objector needs to ponder whether a punched paper tape or the prongs on a Yale lock key hold information. And those proteins are a part of a complex, functionally specific key-lock fitting molecular nanotech system that we can only begin to glimpse. Their function is specifically dependent on folding driven by specific sequence. KFkairosfocus_{August 31, 2013
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http://debunkingchristianity.blogspot.com/2013/08/one-reason-and-one-reason-only-to.html Another comment he made from the same link:
It is not "obvious" to you because you barely understand what you are saying - you wish it would be obviously true, but all you have are your intuitions and experiences with systems that are not analogous. "Ink doesn´t arrange itself on a blank page to produce a newspaper article, ergo abiogenesis is impossible" is not "practical wisdom" it´s foolish nonsense - you let your intuitions and experiences with one system dictate what should be possible (or not) for every other system, including those that are absolutely not analogous. The analogy doesn´t make sense on any level: 1. There is a virtually infinite number of possible arrangements for ink molecules on paper, only a tiny subset of which would correspond to letters from the english alphabet, while for chemical reactions that create polymers of nucleotides, EVERY possible arrangement would correspond to a string of "letters" (to stay in the analogy). 2. Ink molecules arranging themselves to form a newspaper article again implies that there is this one tiny tiny needle in the HUUUUUGE haystack of possibilities that "random processes" have to stumble upon, but as I already explained to you, this is false. There isn´t just one "needle", there isn´t even just one kind of "needle". There is substantial evidence to support that the earliest replicators relied heavily on RNA to store and transmit genetic information and to catalyze chemical reactions. But it didn´t have to be any specific instance of these molecules - ANYTHING capable of autonomous replication would have done. For all instances of autonomously replicating RNA systems that we found so far, we know that there are variations of the system with equal, better, or worse replication fidelity, and it doesn´t matter which of those was the first. It didn´t even have to be RNA, it has also been demonstrated that other XNAs could do the same job (the 'X' is a placeholder for various alternatives to 'R' (="Ribose") that have been tested). 3. "Information" in polymers of nucleotides has little to do with "information" in a human language. DNA / RNA / XNA polymers are not analogous to "words" in a human language (well, in some sense they are - but this analogy is completely misleading at best and your intutions and experiences based on the english language do not apply here). 4. DNA / RNA / XNA polymers are not "symbolic codes". 5. The chemistry that happens and the reactions that are possible on a sheet of paper is not the chemistry that happens and is possible in a hydrothermal vent (for example).</blockquote?
Breckmin_{August 30, 2013
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link to thread that was closed during debate: http://debunkingchristianity.blogspot.com/2013/08/one-reason-and-one-reason-only-to.html A few days ago I was on another blog discussing theodicy which eventually turned ID. After 686 posts the topic was closed before I could really dissect the information aspect of nucleotide arrangements/sequences as programming. Andy_Schueler said:
You seem to believe that naturally occuring sequences have an invisible property called "information" which a random amino acid sequence doesn´t have, and if only you´d "knew this language", you could tell these two kinds of proteins apart based on finding this "information". No. You couldn´t. There are naturally occuring sequences which have no biologically meaningful function (or have biologically meaningful functions that are actually harmful to the organism...) and there are proteins in randomized synthetic libraries that have biologically meaningful functions. And even if that wouldn´t be the case, for any useful definition of "information" (yours is not one them), it is trivial to show that evolutionary processes are able to create it. You have no case.
The appeal is often made to coding which didn't appear to produce functional information (or did produce a harmful protein) to skirt away from Information/programming being from Intelligence. It seems like a clear red herring to me since there is still functional information produced as a result of other programming (programmed information) regardless whatever random processes are rearranging the code. I argued that if I was omniscient regarding human proteins I could identify the good coding from the bad based on the specific sequences. What am I missing here?Breckmin_{August 30, 2013
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