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

Did I own up to 'mendacity', franklin? I tell a lie. I have quite a clear memory now of trying to fashion a small parachute out of a handkerchief with the corners knotted and sewing threads attached, and dropping it with a small payload from the roof of the lean-to at the back of our house. Unfortunately, even today my technical nous is not what it might be, thinking the masthead of this blog was a fancy kind of exhaust-pipe, for quite a while, but it must have been all the more deficient in my childhood, because I feel a twinge of shame now that my expectations had been so high, for such a primitive design and technology. I believe Charles would never have been so naive, and that's not necessarily any great tribute, is it?Axel_{September 12, 2013
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I was hoping for an answer from Alan Fox, but I think he's drawn 'one of his lines in the sand'. For which, alas, there is no remedy, but a stoical resignation.Axel_{September 12, 2013
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I would categorise my response, franklin, not as a literal statement of fact, but as an example of trivial mendacity evidently used as a metaphor, in casual disparagement. As reported on here to me, I have no way of knowing whether our famous theology graduate, who apparently died a convinced Christian, had the results of his experiments peer-reviewed, without following WD400's advice and reading Darwinian literature. Indeed, only the context suggests that the subject of such experiments could be classified as being of a scientific nature. But, alas, I have read enough on here to know that Darwin, for all his limitations, was brighter than his modern-day followers, who have at their disposal information totally discrediting his hypotheses; and have read quotes of his stating why he, himself, regarded his conjectures with enormous reservations. He would surely set you all straight, today, were he alive.Axel_{September 12, 2013
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Axel, How many of the results of your experiments have you managed to publish? Would you be so kind to provide the citations to your published manuscripts?franklin_{September 12, 2013
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wd400, I've performed a lot of experiments in my home too.Axel_{September 12, 2013
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Nice cryptic answer. Why don't you spell it it out, Alan. Be a good chap and briefly spell it out for us, will you.Axel_{September 12, 2013
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Where’s the flaw in Lewis’ logic?
I think Elizabeth Anscombe spotted that a while ago.Alan Fox_{September 1, 2013
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By the way, what’s your response to Philip’s #7?
Comment name and number doesn't tally. Best to paste a quote and ideally use the permalink facility.Alan Fox_{September 1, 2013
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Plants!!! not plats Is it just me or does the odd missing letter plague other posters?Alan Fox_{September 1, 2013
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In his case, plants.
Barnacles are generally considered animalia. On the other hand, plats are a wonderful example f how evolution works so I am glad you brought it up!Alan Fox_{September 1, 2013
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Always fatuous jibes devoid of any sense, on your part, Reynard, and a seemingly endless silence in response to the questions put to you by IDers, destroying your position. If reason and logic meant anything to you, this quotation by Philip from C S Lewis should make you cringe and whimper (especially in response to your 'laughable assertion that ID is unscientific'): “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) Come on... Where's the flaw in Lewis' logic? Speak up.Axel_{September 1, 2013
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Axel, You should probably read a bit more about Darwin, who, as well as collected facts of naturalists breeders and gardeners, performed many experiments at his house in Down.wd400_{September 1, 2013
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'Darwin spent most of his adult life in the study of biology.' Stamp-collecting, Reynard. In his case, plants. Not a scientist, however theoretical. Although, at least he expressed a definite awareness of the insuperable problems the direction he was taking would lead to; which is more than can be said for his 'groupies'. In fact, he dropped out of his medical studies. I expect he couldn't 'cut it'. As for Hunter not being a scientist, because he didn't work in a commercial lab, Einstein pointed to a draw in his desk in his patent office, remarking that that was his Physics Department (having been turned down for a post as junior lecturer). And, as I suggested earlier, he didn't do too bad for a dilettante. By the way, what's your response to Philip's #7?Axel_{September 1, 2013
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"I build molecules for a living, I can't begin to tell you how difficult that job is. I stand in awe of God because of what he has done through his creation. Only a rookie who knows nothing about science would say science takes away from faith. If you really study science, it will bring you closer to God. James Tour - one of the leading nano-tech engineers in the world Strobel, Lee (2000), The Case For Faith, p. 111, Your PhD Mr. Fox?bornagain77_{September 1, 2013
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Now Mr. Fox, I know you think it beneath yourself to have to actually provide empirical proof, (seeing as you are so enamored with your own intelligence, which you deny is real by the way) but why is Dr. Axe asking for just a single gene to be created by Darwinian processes? I mean, certainly you are not foolish enough to believe all the wondrous complexity we see in life all around us happened by accident without even a single gene of proof to prove it did happen by accident? Or are you really that gullible? A yes or no answer will suffice!bornagain77_{September 1, 2013
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Of Note: Dr. Axe challenges a Darwinist to create a single new gene by Darwinian processes: Show Me: A Challenge for Martin Poenie - Douglas Axe August 16, 2013 Excerpt: Poenie want to be free to appeal to evolutionary processes for explaining past events without shouldering any responsibility for demonstrating that these processes actually work in the present. That clearly isn't valid. Unless we want to rewrite the rules of science, we have to assume that what doesn't work didn't work. It isn't valid to think that evolution did create new enzymes if it hasn't been demonstrated that it can create new enzymes. And if Poenie really thinks this has been done, then I'd like to present him with an opportunity to prove it. He says, "Recombination can do all the things that Axe thinks are impossible." Can it really? Please show me, Martin! I'll send you a strain of E. coli that lacks the bioF gene, and you show me how recombination, or any other natural process operating in that strain, can create a new gene that does the job of bioF within a few billion years. http://www.evolutionnews.org/2013/08/a_challenge_for075611.htmlbornagain77_{September 1, 2013
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Your PhD Mr Fox?bornagain77_{September 1, 2013
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ad hominem Mr Fox? So your boorish atheistic behavior finally surfaces on UD! Perhaps now that you sunk to that level we can now just bow at your feet at how much smarter you are than theists and forget evidence altogether?
So, Phil, can you tell me about Cornelius Hunter's work in biology. A published paper? A coherent sentence?Alan Fox_{September 1, 2013
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And might I be so bold as to ask what your particular PhD is in Mr. Fox so that I might know how you acquired such great wisdom to call another PhD ignorant?bornagain77_{September 1, 2013
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ad hominem Mr Fox? So your boorish atheistic behavior finally surfaces on UD! Perhaps now that you sunk to that level we can now just bow at your feet at how much smarter you are than theists and forget evidence altogether?bornagain77_{September 1, 2013
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Oops re missing HAlan Fox_{September 1, 2013
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And when I said "hunter is not a biologist" I meant he does no work as a biologist and never has done. Published papers, for instance? Darwin spent most of his adult life in the study of biology.Alan Fox_{September 1, 2013
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Dr. Hunter has a PhD in biophysics.
Yes, you're right. So, he has less excuse than you for the amazing level of ignorance e exhibits.Alan Fox_{September 1, 2013
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Mr. Fox, Dr. Hunter has a PhD in biophysics. Cornelius G. Hunter is a graduate of the University of Illinois where he earned a Ph.D. in Biophysics and Computational Biology. http://www.discovery.org/p/208 But since you bring it up, Darwin's degree was in theology, which explains why most of the arguments for Darwinism are based in Theodicy instead of science. (numerous references upon request supporting that fact) As to your Szostak reference, you've been shown to be wrong on this before, but to let others know where Szostak's work fails,,, This following paper was the paper that put the final nail in the coffin for Szostak's work: A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial Cells - 2009 Excerpt: "Recent advances in de novo protein evolution have made it possible to create synthetic proteins from unbiased libraries that fold into stable tertiary structures with predefined functions. However, it is not known whether such proteins will be functional when expressed inside living cells or how a host organism would respond to an encounter with a non-biological protein. Here, we examine the physiology and morphology of Escherichia coli cells engineered to express a synthetic ATP-binding protein evolved entirely from non-biological origins. We show that this man-made protein disrupts the normal energetic balance of the cell by altering the levels of intracellular ATP. This disruption cascades into a series of events that ultimately limit reproductive competency by inhibiting cell division." http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0007385 To show how ludicrous this is,, How Proteins Evolved - Cornelius Hunter - December 2010 Excerpt: Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane. And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function. http://darwins-god.blogspot.com/2010/12/how-proteins-evolved.html And yet you are not allowed teach such problems in the classroom! No wonder Darwinists have to sue people to keep them from talking about this evidence in schools!bornagain77_{September 1, 2013
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Hunter's not a biologist, Phil.Alan Fox_{September 1, 2013
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Mr. Fox, Now Evolution Must Have Evolved Different Functions Simultaneously in the Same Protein - Cornelius Hunter - Dec. 1, 2012 Excerpt: In one study evolutionists estimated the number of attempts that evolution could possibly have to construct a new protein. Their upper limit was 10^43. The lower limit was 10^21. These estimates are optimistic for several reasons, but in any case they fall short of the various estimates of how many attempts would be required to find a small protein. One study concluded that 10^63 attempts would be required for a relatively short protein. And a similar result (10^65 attempts required) was obtained by comparing protein sequences. Another study found that 10^64 to 10^77 attempts are required. And another study concluded that 10^70 attempts would be required. In that case the protein was only a part of a larger protein which otherwise was intact, thus making the search easier. These estimates are roughly in the same ballpark, and compared to the first study giving the number of attempts possible, you have a deficit ranging from 20 to 56 orders of magnitude. Of course it gets much worse for longer proteins. http://darwins-god.blogspot.com/2012/12/now-evolution-must-have-evolved.html?showComment=1354423575480#c6691708341503051454 Correcting Four Misconceptions about my 2004 Article in JMB - Doug Axe - 2011 http://www.biologicinstitute.org/post/19310918874/correcting-four-misconceptions-about-my-2004-article-in Shortcuts to new protein folds - October 2010 Excerpt: Axe concludes that all of these putative shortcuts are dead ends. The Darwinian search mechanism is not capable of finding new protein folds by random sampling and all the shortcuts to new folds are dead ends. http://idintheuk.blogspot.com/2010/10/shortcuts-to-new-protein-folds.html Here is an article that clearly illustrate that the protein evidence, no matter how crushing to Darwinism, is always, 'unscientifically', crammed into the Darwinian framework by Evolutionists instead of the Darwinists ever considering the fact that they might have a problem: The Hierarchy of Evolutionary Apologetics: Protein Evolution Case Study - Cornelius Hunter - January 2011 http://darwins-god.blogspot.com/2011/01/hierarchy-of-evolutionary-apologetics.htmlbornagain77_{September 1, 2013
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OT: Is Richard Dawkins proving the existence of God after all? The scientist in the following video, who works within the field of Quantum Mechanics, shows how one of Richard Dawkins presuppositions, that he used in a recent debate, actually proves the existence of God: Is Richard Dawkins proving the existence of God after all? - Antoine Suarez - video http://www.youtube.com/watch?v=jIXXqv9zKEwbornagain77_{September 1, 2013
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Oops not young trees sampling!Alan Fox_{September 1, 2013
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If we compare the number of 150-amino-acid sequences that correspond to some sort of functional protein to the total number of possible 150-amino-acid sequences, we find that only a tiny proportion of possible amino acid sequences are capable of performing a function of any kind.
With respect, this is rubbish, Vincent. The unexplored space of all theoretically synthesizable proteins is vast, theoretically infinite. What cannot be claimed is what level of potentially functional (in some context) proteins lies within that space. Random sapling (Szostak for example) suggests functionality is widespread.Alan Fox_{September 1, 2013
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Hi Breckmin, Just a few comments in response to #2 above. 1. Comparing amino acid sequences to ink dots may be off the mark; comparing them to Scrabble letters is not. The same goes for the nucleotides in RNA. 2. In a discussion hosted by Edge in 2008, entitled, Life! What a Concept, with scientists Freeman Dyson, Craig Venter, George Church, Dimitar Sasselov and Seth Lloyd, Professor Robert Shapiro (1935-2011) explained why he found the RNA world hypothesis so incredible:
... I looked at the papers published on the origin of life and decided that it was absurd that the thought of nature of its own volition putting together a DNA or an RNA molecule was unbelievable. I'm always running out of metaphors to try and explain what the difficulty is. But suppose you took Scrabble sets, or any word game sets, blocks with letters, containing every language on Earth, and you heap them together and you then took a scoop and you scooped into that heap, and you flung it out on the lawn there, and the letters fell into a line which contained the words "To be or not to be, that is the question," that is roughly the odds of an RNA molecule, given no feedback — and there would be no feedback, because it wouldn't be functional until it attained a certain length and could copy itself — appearing on the Earth.
3. Now let's consider proteins. Specifically, let's consider a protein made up of 150 amino acids - which is a fairly modest length. If we compare the number of 150-amino-acid sequences that correspond to some sort of functional protein to the total number of possible 150-amino-acid sequences, we find that only a tiny proportion of possible amino acid sequences are capable of performing a function of any kind. The vast majority of amino-acid sequences are good for nothing. So, what proportion are we talking about here? An astronomically low proportion: 1 in 10 to the power of 74, according to work done by Dr. Douglas Axe. When we add the requirement that a protein has to be made up of amino acids that are either all left-handed or all right-handed, and when we finally add the requirement that the amino acids have to be held together by peptide bonds, we find that only 1 in 10 to the power of 164 amino-acid sequences of that length are suitable proteins. I'd certainly call that a needle in a haystack, and I think you would, too. 4. Regarding the reality of the genetic code, this topic was covered in a post of mine entitled, Is the genetic code a real code? where I quoted Barry Arrington's argument that the genetic code is a semiotic code, as well as a statement by Chance Ratcliff that "the DNA to polypeptide mapping function is in the form F:A?B, where F: is performed essentially by RNA polymerase, aminoacyl trna synthetase, and the ribosome, and works by mechanism to convert elements of A (codons) into elements of B (amino acids)." I hope that helps answer Andy Schueler's objections.vjtorley_{September 1, 2013
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