Tuesday, June 06, 2017

Stephen Meyer "predicts" there's no junk DNA

Here's an interview with Stephen Meyer on the Evolution 2.0 website: Stephen Meyer Debates Perry Marshall – Intelligent Design vs. Evolution 2.0. I'm posting some remarks by Stephen Meyer in order to preserve them for posterity. Meyer should know by now that the evidence for junk DNA is very solid and the ENCODE declarations are wrong. The fact that he persists in spreading false information about the ID "prediction" is revealing.
We think Intelligent Design has tremendous heuristic value, that is to say it can lead to new discoveries. If you infer that design was at work or an intelligence was at work in producing a system, you’re going to look at it differently.

For example, we predicted very early on that the junk DNA was not junk. We did that on the basis of an ID perspective. The neo-Darwinians thought that the non-coding regions in the genome were the natural, expected result of random changes accumulating the flotsam and jetsam of the evolutionary process accumulating over time.

It was just what they expected—that 3% would be functional the rest would be residue of the trial and error process.

We’ve looked from an ID perspective said the opposite. We said: “Look, we accept that mutations are real processes, but we wouldn’t expect that the signal should be dwarfed by the noise. So we expect to claim function in that allegedly non-functional region that vast allegedly non-functional region with genome.”

Lo and behold, over the last ten years, and especially with the publication or the Encode Project, our ID perspective has been borne out. And in fact Jim Shapiro, one of the scientists who was writing papers with him on this, gave credit to Rick Sternberg. He said Richard Sternberg, formerly of the Smithsonian, and one of our ID colleagues, was the first guy to see this.

And Shapiro said so in the Huffington Post of all places. That’s just one of many examples where ID has heuristic value. It anticipates certain things: You’re going to get in, you’re going to look at it, you’re going to try to figure out: What is the functional logic? What can I be expecting to find here that’s going to make this work in accord with a rational plan?

So we think this is the science-stopper, but it’s a science-starter.
It seems to me that when somebody keeps repeating a "fact" that has been refuted, or at least challenged, then that's like telling a lie. I struggle with the concept of "lie." I don't think Meyer is deliberately saying something that he knows to be untrue—he seems like too nice a guy to do that—but the alternative is that he is deliberately deceiving himself into believing that falsehoods are true. That's just as bad.


36 comments :

  1. In before creationists change the subject to the origin of life!

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    1. Diognenes, could you repost the link to your dissection of Meyer's quote mining of Henry Quastler? That was a great bit of detective work on your part that should be better known.

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    2. Gimme a few hours. If I can't find the link, I'll rewrite it.

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    3. Diogenes, please contact me by email.

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    4. In before creationists change the subject to the origin of life!

      Maybe if you've learned something about quantum information conservation, the origin of life wouldn't be such a thorn in your ass...

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  2. Rather confused and impresise statement. He doesn't really put any numbers on how much function he thinks there is. Is he implying it's 100%? Somewhere above the 80% suggested by Encode?

    And when he cites the 3% figure, he's apparently insinuating that molecular biologists thought only protein coding DNA was functional. That was just never the case. This also highlights the human-centric thinking, because it's mostly just humans that happen to have 3% of their genome constitute protein coding DNA. No creationist has even tried to deal with the onion test with anything other than vague hints and handwaving.

    Perhaps even worse, he tries to swing this one on the "neo-darwinians", which are of course the adaptationists who "predicted" from natural selection that there'd be little to no junk DNA, by reasoning that natural selection would get rid of most of the waste.

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  3. The other aspect is that, even if Meyer's claim was true, the researchers who attributed function to DNA were evolutionists. Generally, in fact, of the most strictly Darwinian kind. So the claim that evolution is a science stopper on this issue is not borne out.

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  4. Meyer robotically emits a greatest hits' package of lies.

    I was wondering why the IDers insist on saying "neo-Darwinists" were the ones to predict junk-- a myth easy to shoot down since Jukes & King wrote that article predicting mostly junk, back about 1970, and titled it "Non-Darwinian Evolution." You can't get more clear than that that junk is a prediction of NON-Darwinism. And they referred to their opponents-- the panglossian "Everything is Awesome" no-junkers-- as "Darwinists." So every single IDer has knowingly reversed the controversors even after being corrected 10,000 times.

    But why? Why lie and call those who predicted junk "neo-Darwinists"? I think it has to do with the propaganda of the right. For the right, a feeling of emotional, visceral disgust is very important, and their propaganda is designed to train or inculcate in the public a Pavlovian disgust-response to certain words or classifiers. For example, around 1980 or so the Christian right in the USA decided they would never use "liberal" in a positive or even neutral sense, they would only use "liberal" as a pejorative, in order to train their followers to have a Pavlovian disgust-response whenever they hear the word liberal. Then, they hope, they can shame people into never calling themselves liberal, and they get to control the dialogue and define the word. This programming makes them stupid. I see more and more US conservatives who just blurt certain disgust keywords at random, as if this makes the world comprehensible to them. It's like a kind of Tourettes. E.g. conservatives will suddenly blurt "George Soros!" into any discussion of anything, because the trained disgust-response makes the world understandable.

    So, I think this is why the IDers use the word "neo-Darwinist" to describe the non-Darwinists who predicted junk. The Disco Tute made a political decision that they would only use "neo-Darwinst" in a pejorative sense, in order to train their followers in the Pavlovian disgust-response. If they were to succeed, it would only make their followers dumber.

    To be fair, we're guilty as well, by consistently calling them IDiots.

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  5. How many times does it have to be explained that creationism does not actually predict no junk DNA and that the arguments for junk DNA do not even depend on evolution being true?

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  6. I'm curious. Does anyone know what Shapiro said in the HuffPo and when he said it? And does anyone know what Sternberg said and where he said it?

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    1. I doubt that any such prediction was made, and I doubt Shapiro mentioned it. This lie about IDers 'predicting' no junkDNA has been debunked so many times and it is so easy - I saw an email exchange between a biologist and John West, and West made the 'prediction' claim. He was asked for clarification, and he mentioned Mims' rejected letter to Science in 1993 and Demsbki's 1996 essay. The biologist then provided a handful of quotes and citations from the 1970s in which real scientists were not only predicting that SOME junkDNA had function, but actually documenting it. He was asked what one calls predictions made decades after discoveries. He stopped responding.

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    2. @N. Manning

      I'm not sure what you mean when you say, "This lie about IDers 'predicting' no junk DNA has been debunked so many times ..."

      Are you focusing on the "no" part of the phrase and arguing that ID proponents are willing to accept some junk DNA, or are you questioning whether Intelligent Design Creationists actually predicted that our genome would have very little junk DNA?

      I found your comment to be very confusing.

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    3. The supposed predictions made by IDcreationists that there will be little or no 'junkDNA' and/or that junkDNA will have function is in my view are lies, sorry if it came out jumbled. One cannot predict that which has already been shown (for example, a paper in Cell in 1975 'predicted' that a function of junk DNA was to help maintain optimal concentration based on the authors' work on the lac operon). To come along in 1993 or 1996 and "predict" function in junkDNA based on ID/creationists ideology is at best disingenuous, at worst a lie. And I tend to see, based on history, the worst in creationists.

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    4. @N. Manning

      I still don't understand what you are trying to say. Knowledgeable scientists think that 90% of our genome is junk but Intelligent Design Creationists are still "predicting" that most of our genome is functional.

      Who's lying?

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  7. Meyer also loves to say that it has been discovered that DNA contains "digital information". His audiences are wowed -- a special digital signal!

    What Meyer means by that is that DNA codes for proteins, RNAs, and contains regulatory sequences. Not exactly a new discovery ...

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    1. Ah, but then there's Sal Cordova and "DNA steganography," by which he means that God has placed an actual identifier in our DNA that this was His work (kind of like those "Body by Fisher" plates on old Chevys).

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  8. As an outsider here, I must say that I don't understand the argument that natural selection would eliminate non-functional DNA from the genome in the absence of any reproductive fitness advantage in doing so. Am I missing something here?

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    1. Junk DNA is a burden because it uses up the cell's resources for no reason. If you are a strict Darwinian, you must conclude that this excess DNA will eventually be eliminated by natural selection.

      If you have grasped the essence of modern population genetics and the importance of random genetic drift then you understand the effect of population size and the the drift-barrier hypothesis. In that case, you understand why slightly deleterious alleles (junk DNA) can be retained.

      Intelligent Design Creationists don't get this at all. They think that Darwinists predict junk DNA when, in fact, they predict the exact opposite.

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    2. Even worse, after they thoroughly fail to get it, they then use the objection to primitive panadaptationist Darwinianism raised by people who actually understand evolution as "evidence" for how evolution has been discredited within the scientific community....

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    3. As someone once said, "They know not what they do." They're just looking for quotes that sound like someone is objecting to something in evolutionary theory. When there are arguments on issues large or small among scientists (quelle surprise!), it does not matter whether that they have no idea what the scientific issue actually is, as long as there's something that can have enough context chopped out of it to sound critical.

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    4. I found this article on the drift-barrier hypothesis coauthored by Paul Sniegowski very interesting: http://www.sciencedirect.com/science/article/pii/S0960982213000213

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    5. As Dr. Moran mentions, junk DNA is only slightly deleterious in the vast majority of cases. Therefore, there just isn't a whole lot of selective pressure to remove it.

      On top of that, I have to wonder how junk DNA removing systems would even work. How would proteins identify junk DNA and remove it with precision? How would an evolutionary pathway even start down that road?

      As long as there is a tolerable rate of both random addition and removal of DNA, then that appears to be the strategy of choice.

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    6. I have never bought the 'cell resources' argument, even when JM Smith made it. It seems to me that the amount of resources devoted to DNA replication would be minuscule compared to the amount of energy cells use on a daily basis just getting things across their membrane.

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    7. @N. Manning

      What is your explanation for why most bacteria species have so little junk DNA? The common explanation is that the population size is large so that the slight selective disadvantage of having extra DNA causes it to be eliminated.

      Do you have a better explanation since you reject the "cell resources" argument?

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    8. How about replication speed? Time is not exactly a "cell resource" in the sense intended.

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    9. Hi Larry,

      No, I don't have a better explanation, but I am not sure why I must accept an explanation because I don't have a better one, I have just not seen convincing data for the 'cell resources' argument. Do you know of data on, for example, ATP use during DNA synthesis compared to that used by a typical non-mitotically active cell during its lifespan? I've looked for such data in the past and came up short.

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    10. N. Manning says," I have just not seen convincing data for the 'cell resources' argument."

      Lynch, M., and Marinov, G.K. (2015) The bioenergetic costs of a gene. Proc. Natl. Acad. Sci. (USA) [doi: 10.1073/pnas.1514974112]

      "An enduring mystery of evolutionary genomics concerns the mechanisms responsible for lineage-specific expansions of genome size in eukaryotes, especially in multicellular species. One idea is that all excess DNA is mutationally hazardous, but weakly enough so that genome-size expansion passively emerges in species experiencing relatively low efficiency of selection owing to small effective population sizes. Another idea is that substantial gene additions were impossible without the energetic boost provided by the colonizing mitochondrion in the eukaryotic lineage. Contrary to this latter view, analysis of cellular energetics and genomics data from a wide variety of species indicates that, relative to the lifetime ATP requirements of a cell, the costs of a gene at the DNA, RNA, and protein levels decline with cell volume in both bacteria and eukaryotes. Moreover, these costs are usually sufficiently large to be perceived by natural selection in bacterial populations, but not in eukaryotes experiencing high levels of random genetic drift. Thus, for scaling reasons that are not yet understood, by virtue of their large size alone, eukaryotic cells are subject to a broader set of opportunities for the colonization of novel genes manifesting weakly advantageous or even transiently disadvantageous phenotypic effects. These results indicate that the origin of the mitochondrion was not a prerequisite for genome-size expansion."

      He second author, Georgi Marinov, is a frequent contributor to comments on this blog. He'll set you straight.

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  9. Id really like to see a reference for this prediction. I've read most of the output of the prominent IDers over the decades and I dont remember ever seeing such a prediction. What I do remember is long arguments on why junk DNA wasn't a problem for ID

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    1. If you follow the link in the post, you'll find the prediction.

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    2. I didnt exhaustively follow links but it looks like the prediction was 2004 from Sternberg. For 15 years before that they were arguing as above and by 2004 I think there were enough lncRNAs discovered that it wasn't much of a prediction. At least not one that can be claimed to be based entirely on a belief in ID

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  10. I would guess Meyer knows the universe is designed and therefore there will be less ‘junk’ than has been proposed. He would then see ENCODE as confirming. It seems there is function being discovered in sequences that were considered ‘junk’ before.

    If one views this from a Bayesian perspective, one would say Meyer’s priors are such that the current information is confirming to the view there is little or no junk.

    The power of any evidence is always weighted by one’s priors.

    Using my family history as an example, one of the amazing things about humans is how they can be completely wrong about so much and still survive and reproduce and live happy and glorious lives.

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  11. If Meyer worked on the bladderwort genome he would largely be correct if he said that most of the genome was functional, if that is any consolation.

    Overall, Meyer seems to have fallen into the trap of only hearing what he wants. He hears ENCODE saying that 80% of the genome has function, but stops listening when ENCODE's definition of function is little else than RNA transcription. Like most IDers, he just doesn't understand that junk DNA can and will be described into RNA, and it is still junk.

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    1. That should be "transcribed into RNA" at the end. Strange autocorrect error.

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  12. Perry Marshall is still hawking the gibberish he got demolished over on the old Secular Web forum years ago. The ego of these clowns...

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    1. Such is the way with these underappreciated geniuses. They eventually slink away to find the company of fellow underappreciated geniuses, who can then stroke each others' egos and tell each other how much they appreciate each others' genius.

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