Thursday, June 22, 2017

Jonathan Wells talks about junk DNA

Watch this video. It dates from this year. Almost everything Wells says is either false or misleading. Why? Is he incapable of learning about genomes, junk DNA, and evolutionary theory?



22 comments :

  1. Wow, that is really an amazing assemblage of outright falsehoods.

    Larry, do you happen to know whether Jonathan Wells is even aware of your review of his books? Has he ever interacted with anyone or responded to the case for junk-DNA?

    If he has, then it's pretty clear that he's actually a liar here and can't just feign ignorance.

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    1. I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob. .............. Jonathan Wells

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    2. "I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob."

      Oh, I remember this reply - it was at the end of the closest thing I I ever managed to to a discussion with Wells at Uncommon Descent--which was him critiquing my comments about his work in new posts (but refusing to actually engage in an exchange the comments).

      I called your review extensive and thorough, and his rebuttal was that saturation bombing was also extensive and thorough.

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  2. Let me get this straight:

    The majority of human genome being full of junk DNA (about 90 %) is consistent with evolutionary theory.

    If this is true, ENCODE and other people should not be able to assign real function to the rest of the 90 % of the genome. If they continue to do so, what is this going to mean? Will evolutionary predictions fail?

    However, ENCODE and others claim that the so-called junk DNA could and probably does hold many keys to the answers why some diseases develop, since the majority of junk DNA sequence have regulatory gene functions. It follows that if the regulatory function goes wrong, malfunctioning genes can cause diseases...

    So, while the skeptics like Larry Moran, Dan Grour, PZ Myers, Jerry Coyne, Ricard Dawkins object to the notion that most of human genome is functional, they probably wouldn't object the notion that trying to identify at least some regulatory functions in the junk DNA is a noble cause, even if at the end of the day, some parts of the genome will still be considered junk...

    Many diseases have already been identified to have been caused by the malfunctioning regulatory sequences in the so-called junk DNA. Who says that cancer, diabetes, heart diseased and many more will not be next?

    So, there is no doubt that no rationally and logically thinking human beings would object to phase 2 or 3 or more of ENCODE studies even if in the end some parts of the human genome will remain junk...

    BTW: Since Larry Moran has retired, why can't he support a noble cause and volunteer at some lab to look for regulatory functions of some diseases?

    Wouldn't be ironic, if Larry found a regulatory function for some common disease in the DNA he now considers junk?

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  3. "The majority of human genome being full of junk DNA (about 90 %) is consistent with evolutionary theory."

    Yes.


    "If this is true, ENCODE and other people should not be able to assign real function to the rest of the 90 % of the genome. If they continue to do so, what is this going to mean? Will evolutionary predictions fail?"

    Evolutionary theory shows lines of evidence that all point to one conclusion about the human genome: that about 90% of it is junk, and does not perform a function in any meaningful sense of the word. This evidence includes the lack of sequence conservation of the majority of the genome, the population-genetic impossibility to maintain the majority of the genome by selection, and the origin of much of the genome (being a graveyard of old retrotransposon copies). If somehow it turned out that the majority of the genome was functional in the meaningful, pre-ENCODE sense, then there would probably have to be substantial revision to evolutionary theory. Given that it is hard to conceive of what that could look like, it is hard to know what its impact would be.


    However, ENCODE and others claim that the so-called junk DNA could and probably does hold many keys to the answers why some diseases develop, since the majority of junk DNA sequence have regulatory gene functions. It follows that if the regulatory function goes wrong, malfunctioning genes can cause diseases...

    ENCODErs might think there are sequence-specific causes to many diseases. However, any enthusiasm for such a notion should be tempered by the knowledge that after many decades of searching, few diseases are thoroughly explained in such a way. Although there are genetic correlates for many diseases, just like the correlates of other biologicial traits, genome-wide variation usually explains fleeting percentages of biological variation. This is because phenotype rarely reduces to genotype. As an aside, there is no evidence that the majority of junk DNA sequence regulates genes, unless you mean in indirect ways (i.e. not via regulatory function).


    So, while the skeptics like Larry Moran, Dan Grour, PZ Myers, Jerry Coyne, Ricard Dawkins object to the notion that most of human genome is functional, they probably wouldn't object the notion that trying to identify at least some regulatory functions in the junk DNA is a noble cause...

    No one disputes more regulatory sequences will be discovered in the human genome. It is a matter of how much of the genome this will account for--with the most likely answer being very little.


    Many diseases have already been identified to have been caused by the malfunctioning regulatory sequences in the so-called junk DNA. Who says that cancer, diabetes, heart diseased and many more will not be next?

    Even if we could reduce complex, environmental diseases to gene sequence problems, this does nothing to change what we already know about the origins, structure, or mutation rate of the human genome, nor the limits to natural selection caused by population size.


    So, there is no doubt that no rationally and logically thinking human beings would object to phase 2 or 3 or more of ENCODE studies...

    Some might be quite able to object if they could make a case for the funding going to other more fruitful research. There is no reason based on what we currently know to think we'll solve disease through genomics. Talk to anyone who works on the relationship between genome, transcriptome, proteome, and metabolome to see how limited the application of genomics is to understanding broad molecular biology.


    BTW: Since Larry Moran has retired, why can't he support a noble cause and volunteer at some lab to look for regulatory functions of some diseases?

    I can't imagine that in retirement, a biochemist would want to extensively re-train in human disease genomics.


    Wouldn't be ironic, if Larry found a regulatory function for some common disease in the DNA he now considers junk?

    No.

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    1. Part 1.
      Jass
      "The majority of human genome being full of junk DNA (about 90 %) is consistent with evolutionary theory."

      PM. Yes.

      So ENCODE's and others' saying that most of the human genome is functional YOU view as an attack on the evolutionary theory...


      Jass

      "If this is true, ENCODE and other people should not be able to assign real function to the rest of the 90 % of the genome. If they continue to do so, what is this going to mean? Will evolutionary predictions fail?"

      PM. "Evolutionary theory shows lines of evidence that all point to one conclusion about the human genome: that about 90% of it is junk, and does not perform a function in any meaningful sense of the word. This evidence includes the lack of sequence conservation of the majority of the genome, the population-genetic impossibility to maintain the majority of the genome by selection, and the origin of much of the genome (being a graveyard of old retrotransposon copies). If somehow it turned out that the majority of the genome was functional in the meaningful, pre-ENCODE sense, then there would probably have to be substantial revision to evolutionary theory. Given that it is hard to conceive of what that could look like, it is hard to know what its impact would be."

      So, the conclusions that 90% of the genome must be junk are based on the assumption that evolutionary theory is true. Once the ENCODE and other people came up with evidence that most of human genome is not junk, that threaten that very foundation of that belief that evolution is true. You said it yourself:

      PM. "If somehow it turned out that the majority of the genome was functional in the meaningful, pre-ENCODE sense, then there would probably have to be substantial revision to evolutionary theory. Given that it is hard to conceive of what that could look like, it is hard to know what its impact would be.

      Isn't it why people like Larry, Grour, PZ Myers, J. Felekstein, Hassman, you and many others blindly defend the dogma that 90% of human genome must be junk or it would be"... hard to conceive of what that could look like, it is hard to know what its impact would be..."?

      Yes, I know it would be hard for YOU to conceive what it would be like without evolutionary theory, but not to those who have always seen it as a science fiction story...

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    2. Part 2

      Jass However, ENCODE and others claim that the so-called junk DNA could and probably does hold many keys to the answers why some diseases develop, since the majority of junk DNA sequence have regulatory gene functions. It follows that if the regulatory function goes wrong, malfunctioning genes can cause diseases...

      PM. ENCODErs might think there are sequence-specific causes to many diseases. However, any enthusiasm for such a notion should be tempered by the knowledge that after many decades of searching, few diseases are thoroughly explained in such a way. Although there are genetic correlates for many diseases, just like the correlates of other biologicial traits, genome-wide variation usually explains fleeting percentages of biological variation. This is because phenotype rarely reduces to genotype. As an aside, there is no evidence that the majority of junk DNA sequence regulates genes, unless you mean in indirect ways (i.e. not via regulatory function).

      I don't know whether that has been published yet that the majority of so-called junk DNA sequence regulates genes...I wouldn't be surprised if that turned out to be so. I was referring mainly to the regulatory function as per ENCODE and many others...


      Jass So, while the skeptics like Larry Moran, Dan Grour, PZ Myers, Jerry Coyne, Ricard Dawkins object to the notion that most of human genome is functional, they probably wouldn't object the notion that trying to identify at least some regulatory functions in the junk DNA is a noble cause...

      PM. No one disputes more regulatory sequences will be discovered in the human genome. It is a matter of how much of the genome this will account for--with the most likely answer being very little.

      But if it tuned out to be more than you all expect, what would you do then?


      Jass "Many diseases have already been identified to have been caused by the malfunctioning regulatory sequences in the so-called junk DNA. Who says that cancer, diabetes, heart diseased and many more will not be next??
      This didn't come out as well as I wanted but you got the point...

      PM. Even if we could reduce complex, environmental diseases to gene sequence problems, this does nothing to change what we already know about the origins, structure, or mutation rate of the human genome, nor the limits to natural selection caused by population size.

      Well... that is not written in the stone is it? They would have to be changed if human genome turned out to be ully functional wouldn't it

      Jass "So, there is no doubt that no rationally and logically thinking human beings would object to phase 2 or 3 or more of ENCODE studies..."

      PM. Some might be quite able to object if they could make a case for the funding going to other more fruitful research. There is no reason based on what we currently know to think we'll solve disease through genomics. Talk to anyone who works on the relationship between genome, transcriptome, proteome, and metabolome to see how limited the application of genomics is to understanding broad molecular biology.

      What more fruitful research could there be than trying to save human lives? Isn't it why ENCODE embarked on the project in the first place?

      Jass "BTW: Since Larry Moran has retired, why can't he support a noble cause and volunteer at some lab to look for regulatory functions of some diseases?

      PM. I can't imagine that in retirement, a biochemist would want to extensively re-train in human disease genomics.

      Are you suggesting that it would be to hard to re-train?

      Just this year I became interested in quantum mechanics. I have no official training in it. Now, I got an invitation to submit a paper (unofficially) for the upcoming Consciousness Conference.


      Jass Wouldn't be ironic, if Larry found a regulatory function for some common disease in the DNA he now considers junk?

      PM. No.

      Why not?

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    3. "So ENCODE's and others' saying that most of the human genome is functional YOU view as an attack on the evolutionary theory..."

      No, I view it as inconsistent with population genetics and biochemistry.

      So, the conclusions that 90% of the genome must be junk are based on the assumption that evolutionary theory is true.
      No, it is based on the lines of evidence I outlined.

      Once the ENCODE and other people came up with evidence that most of human genome is not junk, that threaten that very foundation of that belief that evolution is true.
      No, they have provided no such evidence. As discussed extensively on this blog and elsewhere, ENCODE redefined function to come to the conclusion that the majority of the human genome is not junk.

      you and many others blindly defend the dogma that 90% of human genome must be junk
      That's just pointless invective that requires you to have willfully ignored everything I took the time to write above. If you wanna discuss the evidence, go for it (start with the multiple lines of evidence that support the idea that 90% of the human genome is junk). If you wanna throw dumb statements with no substance in them like this around, we're done.

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    4. Paul McBride,

      Looks like the greatest promoter of evolution jumped the ship few years back...

      "Dawkins in 2012:

      I have noticed that there are some creationists who are jumping on [the ENCODE results] because they think that's awkward for Darwinism. Quite the contrary it's exactly what a Darwinist would hope for, to find usefulness in the living world....

      Whereas we thought that only a minority of the genome was doing something, namely that minority which actually codes for protein, and now we find that actually the majority of it is doing something. What it's doing is calling into action the protein-coding genes. So you can think of the protein-coding genes as being sort of the toolbox of subroutines which is pretty much common to all mammals -- mice and men have the same number, roughly speaking, of protein-coding genes and that's always been a bit of a blow to self-esteem of humanity. But the point is that that was just the subroutines that are called into being; the program that's calling them into action is the rest [of the genome] which had previously been written off as junk."


      I think he doesn't want to write fiction anymore... I think you wants to write textbooks now lol

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    5. Paul M

      The dumbest statement I've heard is this:

      "If ENCODE is right, then evolution is wrong".

      This can only mean one thing: Evolution is right no matter what the evidence shows.

      A while back I was wondering what I would do if I were the creator of the most amazing thing in the world for which someone else took credit for...

      Let's just say that you created life and people who have the qualification and insight into it to recognized that life was intelligently designed and created decided to give that credit to dumb luck... What would you do?


      Would you kill them? Well... maybe, but I would humiliate those people to the point that they would be digging holes in the desert to hide...

      I'm no prophet, but starting with ENCODE and others, the humiliation has started...Just watch it! ;-)

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    6. Jass, allow me to refer you to my previous statement: If you wanna discuss the evidence, go for it (start with the multiple lines of evidence that support the idea that 90% of the human genome is junk). If you wanna throw dumb statements with no substance in them like this around, we're done.

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    7. What's your evidence? That ENCODE findings are not compatible with natural selection and population genetics? So-called junk DNA is not conserved so it must me junk!!

      We are done!

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  4. Is he incapable of learning about genomes, junk DNA, and evolutionary theory?

    He is not incapable in the sense of being stupid. He is incapable because he has been brainwashed by his crackpot religious views.

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    1. He's also a liar. I sometimes think with these more educated creationists that their thinking is along these lines: "Evolution convinces people there is no god. If people don't believe in God, they'll go to Hell forever after they die. So it is justifiable for me to lie to them if it saves their souls."

      But that assumes they are holding logically consistent views. That's a big assumption, I realize.

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  5. Jass (above) seems to be confused on two scores:

    1. When people say 90% (or more) of the human genome is junk, they are not calling all of the noncoding sequence "junk". They are not including regulatory sequences in the junk.

    2. The ability to find regulatory sequences in what had been thought to be juink DNA is not the same as the ability to find regulatory functions for most DNA that had been thought to be junk DNA. This tiresome confusion is endlessly used by Wells and his friends -- someone discovers a bit of junk DNA that isn't really junk, and then Wells (and Jass?) go around declaring that this proves that this proves that little or none of the junk DNA is really junk.

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    1. I don't know if it is even accurate in many, if any cases, to say that sequences thought to have been junk were found to be functional. More commonly, sequences that were known to be non-coding were found to have a function, but no one had yet declared them to be junk prior to that. Has, say, a pseudogene ever been found to actually have a function?

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    2. Even if some have been found to have a function, does that establish that all pseudogenes (or even a majority of pseudogenes) have a function?

      Most swans in the world are white (the ones in Australia are black). Wells and his friends are pointing out case after case of individual swans that are black, hoping by this to convince us that almost the great majority of swans are black.

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    3. The swans in South America have black necks. Don't they count for something?

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  6. Wells thinks there should be little ‘junk’ in the DNA .
    He sees ENCODE as confirming evidence.
    He mentions that sequences once thought to be ‘junk’ are now found to have function.
    I would guess he feels he is watching the inevitable ‘filling in’ of function for the genome and the recognition that there is little ‘junk’ in DNA. (Evidence matching his basic premise is given great weight, any evidence contrary is more or less ignored).
    My guess is that he feels that ‘design’ as a viable hypothesis will be recognized by the vast majority in the near future, partly due to this ‘filling in’ of function.

    I don’t think he is lying.

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    1. The genetic load argument says that only a small percentage of our genome can be functional. Wells has never addressed that argument in any meaningful way.

      Less than 10% of our genome is conserved. Wells has never presented a serious explanation to explain why so much unconstrained DNA has a function.

      More than half of our genome consists of broken bits and pieces of once functional transposons and viruses. Has Wells ever explained why most of these are now functional?

      Wells knows that lots of noncoding DNA has a function but he keeps pretending that scientists say something different. He knows that most "Darwinists" are opposed to junk DNA but he keeps telling his followers than junk DNA is a prediction of "Darwinists" like Richard Dawkins.

      Wells knows that the little bits of functional DNA that are discovered make an insignificant contribution to the proportion of junk DNA. In fact, they are encompassed by the 10% of the genome that's presumed to be functional. He doesn't mention this to his followers.

      Wells is familiar with the so-called "C-Value Paradox" and the Onion Test. He is remarkably silent on the implications and ramifications. If some species have very different amounts of DNA in their genome then how does he explain this using Intelligent Design Creationism?

      It's true that he believes goddidit but that doesn't give him the right to ignore and misrepresent facts.

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    2. What gives Wells the right to ignore facts and misrepresent data is that he is human.
      Humans of all religions, no religions, all creeds, no creeds, all sex, no sex, tall people, short people, people with ‘innie’ belly buttons and those with ‘outies’…
      All ignore facts and misrepresent data. It seems to be a birthright.

      Welcome to the human race.

      You list some arguments that lead to the conclusion there is lots of ‘junk’ in the DNA of the life forms on earth.
      The argument against there being junk would be the actual observation that the sequences have function. I think the current claim is there is reason to think the sequences might have function because they are transcribed— something like that.

      I don’t know Wells, I haven’t read his stuff, I’m basing my thoughts on the video— My guess is that Wells thinks function will be found.
      My guess is that ‘wishful thinking’ would be a more appropriate way of categorizing the behavior rather than ‘lying’.

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