Thursday, May 18, 2017

Jonathan Wells illustrates zombie science by revisiting junk DNA

Jonathan Wells has written a new book (2017) called Zombie Science: More Icons of Evolution. He revisits his famous Icons of Evolution from 2000 and tries to show that nothing has changed in 17 years.

I wrote a book in 2000 about ten images images, ten "icons of evolution," that did not fit the evidence and were empirically dead. They should have been buried, but they are still with us, haunting our science classrooms and stalking our children. They are part of what I call zombie science.
I won't bore you with the details. The icons fall into two categories: (1) those that were meaningless and/or trivial in 2000 and remain so today, and (2) those that Wells misunderstood in 2000 and are still misunderstood by creationists today.

I was more interested in seeing what Jonathan Wells has learned about junk DNA. He published another book called The Myth of Junk DNA in 2011. I wrote an extensive review (14 blog posts) of that book back then [The Myth of Junk DNA by Jonathan Wells]. He didn't like it very much because he said,
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
Since then, a few creationists have admitted that there really is a legitimate debate over junk DNA and it may actually be true that most of our genome is junk [see Creationists admit that junk DNA may not be a "myth" after all].

Let's see if Jonathan Wells has changed his mind about junk now that he's learned about the abundant evidence for junk. Let's see if he understands the science that's been explained to him many times or whether he just wants to raise up the same arguments that were killed many years ago. Is he going to practice zombie science?

The relevant material appears in Chapter 4: The Human Appendix and Other So-called Junk (pp. 125-130).

The first few pages are just repeats of material that appeared in The Myth of Junk DNA—sometimes word-for-word. It's clear that he hasn't absorbed any of the criticisms of the original work. The new stuff starts on page 128.
In September 2012, over four hundred ENCODE researchers reported much more comprehensive evidence in thirty articles published in Nature, Genome Research, and Genome Biology. They concluded that the data enabled them to "assign biochemical functions for 80% of the genome." Since the project had not sampled all cell types, the final figure is expected to be even higher.
I think it's safe to say that very few knowledgeable scientists believe this result as stated. He addresses some of the criticism later on but he misleads his readers by leading with this statement.
Since 2012 there's been a virtual flood of new reports of functions in RNAs transcribed from nonprotein coding DNA. Such RNAs help to specify the three-dimensional structure of chromosomes, and their three-dimensional positioning inside the nucleus, both of which have profound effects on gene expression. Nonprotein coding RNAs are involved in fat metabolism, maintenance of the immune system, and proper functioning of stem cells. Nonprotein coding RNAs also are necessary for the development of nerve cells in the nervous system, from the cells and the skeleton, and for muscles. More functions of such RNAs are discovered every month

So the evidence demonstrates that most of our DNA is transcribed into RNA and that many of those RNAs have biological functions. The idea that most of our DNA is junk, it would seem, is dead.
Most Sandwalk readers can see how how disingenuous this passage is. The key question is not whether some functional RNAs exist, that's a given, it's whether most of the ENCODE transcripts have a proven function. The answer to that question is "no" but Wells doesn't want his readers to know that.
But Wait—Evolution Requires Junk DNA!

According to some evolutionary biologists, however, "junk DNA" is very much alive because evolutionary theory demands it.
Nonsense! This is a standard theme among creationists. They actually believe that evolutionary theory was created by Richard Dawkins and Dawkins says that junk DNA is just selfish DNA parasites. Thus, Dawkins' version of evolutionary theory DEMANDS the existence of junk DNA.

The facts are quite different. The Dawkins version of evolutionary theory is very adaptationist and that's INCOMPATIBLE with the presence of junk DNA. Dawkins tried to rationalize the conflict back in 1977 by suggesting that the excess DNA could consist entirely of parasitic DNA elements like transposons whose presence is favored by natural selection (selfish DNA) operating at the gene level.

This isn't junk DNA by my definition [see Restarting the function wars (The Function Wars Part V)] but that's not the important point. The important point is that only a tiny percentage of the genome consists of active transposons or viruses so it cannot be an adaptationist explanation of why 90% of our genome is junk.

This has been explained to Jonathan Wells and other creationists on many occasions but they still don't get it. I don't understand this. Their arguments against junk DNA do not depend on whether it's demanded by evolutionary theory. The facts should speak for themselves.
Canadian biologists Alexander Palazzo and T. Ryan Gregory pointed out that less than 10% of sequences are conserved (that is, similar) between humans and other mammals. Evolutionary theory attributes sequence conservation to function, and Palazzo and Gregory argue that unconserved sequences are not functional, so the number of human sequences that are functional must be much less than the eighty percent reported by ENCODE [Palazzo and Gregory, 2014].
I'm very familiar with this paper. Alex and Ryan lay out the case for junk DNA. This includes excellent descriptions of the C-Value Paradox and the "Onion Test." They cover modern evolutionary theory with an emphasis on why junk DNA is compatible with Neutral Theory and random genetic drift. They explain how junk DNA arises from the degeneration of transposons. They point out the variability of highly repetitive DNA sequences. The discuss why introns are mostly junk. They describe pseudogenes. They discuss genetic load. They explain the debate over pervasive transcription and how it can be explained by spurious events to produce junk RNA.

Jonathan Wells ignores all of this to concentrate on the conservation argument. Palazzo and Gregory point out that only 9% of the genome is conserved. Since conservation is a very reliable indication of function, this suggests that only 9% of the genome is functional. This fact is consistent with all of the other evidence covered in the paper (e.g. genetic load).

It doesn't rule out the possibility that nonconserved DNA is also functional. In fact, Palazzo and Gregory discuss several examples, including transcripts that aren't conserved but still functional. They are also well aware of bulk DNA hypotheses that ascribe function to nonconserved DNA.

Not only does Wells ignore the careful big picture that Palazzo and Gregory describe in their paper, he also makes the false claim that evolutionary theory requires an intimate connection between conservation and function. (In fairness, Dan Graur also makes this mistake.)
Yet function has been identified in many non-protein-coding RNAs whose sequences have not been conserved. As the subtitle of a report in the journal Trends in Genetics put it, a "lack of conservation does not mean lack of function." So any estimate of functionality based on sequence conservation is an underestimate.
Here's what Alex and Ryan say in their paper ...
In an attempt to counter the argument that sequence conservation is a prerequisite for functionality, it has been recently been proposed that certain transcriptional events may serve some role in regulating cellular function, despite the fact that the sequence of the transcriptional product is unconstrained.
Thus, the idea that conservation may not be the only evidence of function is actually discussed in the paper that Jonathan Wells read. I wonder why he doesn't mention that?
Nevertheless defenders of evolution continue to argue that functionality in human DNA is closer to ten percent that eighty percent. In 2013, W. Ford Doolittle (who argued for junk DNA in 1980) distinguished between two definitions of function; "causal role" (what ever does not occur after deleting or blocking the expression of a region of DNA) and "selected affect" (what ever has been or is subject to natural selection). According to Doolittle, only the latter is really significant.
Ford's paper (Doolittle, 2013) is an excellent example of what good science looks like. He discusses the various meaning of function, taking care to point out that none of them are completely correct and unambiguous. He points out, in particular, that there may be functional sequences that are not conserved.

In addition to the selected effect (SE) definition of function and the causal role (CR) definition, Doolittle also discusses a third possible way of deducing function; namely, "mere existence." He points out the obvious flaws in this definition and notes that it's the one promoted by ENCODE when they claim that 80% of the genome is functional. There's a lot more to this debate than Wells is willing to admit. Is it because he doesn't understand it or is it because he's being deliberately disingenuous?

The Doolittle paper makes a strong case for sequence conservation as the most important criterion for determining function. Wells ignores it.
Several dozen members of the ENCODE team replied that that there are three ways to approach biological function: The genetic approach observes the consequences of perturbing DNA, the evolutionary approach measure selection, and the biochemical approach measures molecular activity. Each approach has its strengths and limitations, and the works from ENCODE "reinforce the principle that each approach provides complementary information and that we need to use combinations of all three to elucidate genome function in human biology and disease" [Kellis et al., 2014]. Nevertheless, Doolittle insisted that "only in the light of evolution does biology makes sense," [Brunet and Doolittle, 2014] so the evolutionary approach takes priority. If this means labeling functional DNA junk, so. Be it.
The quote in the Brunet & Doolittle letter is, "others hold that only 'in the light of evolution' does biology make sense." Brunet and Doolttle challenge the conclusions of the ENCODE leaders (Kellis et al., 2014) by saying ...
... clearly they see the take-home message fro ENCODE to be that there is much more function than believed by adherents of the "junk DNA" notion, and apparently Kellis et al. consider arguments based on C-value ("Why do lungfish have 40 times as much DNA as us?") only marginally relevant. The authors do not rise to the challenge of predicting how many functional elements such bloated genomes might boast.
Jonathan Wells is just like Kellis et al. He doesn't tell us how much of the genome is functional and he doesn't explain how we make sense of biology by some other light.
In 2013, biologists Dan Graur criticized the "evolution-free gospel of ENCODE" and accused its researchers of "playing fast and loose with the term 'function,' by divorcing genomic analysis from its evolutionary context." In a lecture at the University of Houston, Graur argued that "if the human gene genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome." In other words: "If ENCODE is right, then evolution is wrong." But for Graur, evolution can't be wrong. His solution to the problem? "Kill ENCODE."
I don't agree with Graur's language and I don't agree with his claim that if ENCODE is right then evolution is wrong. I see his point, but that particular kind of hyperbole is counter-productive. I'm not surprised that creationists use it to discredit evolution.

I am surprised that these same creationists seem incapable of understanding the arguments of scientists like Doolittle, Gregory, and Palazzo.
So zombie science insists paradoxically both that DNA is the secret of life and that most of it is junk. On both counts, zombie science is wrong.

Evolution as a science stopper.

In spite of the evidence, defenders of evolution continue to insist that the human appendix, the human tail, and most nonprotein coding DNA sequences are useless leftovers from a long process of unguided evolution.

One of the surest ways to discourage empirical research into the possible functions of a feature is to decide at the outset that it has none. British anatomist Arthur Keith wrote in 1912 that "for many years the appendix vermiformis has been regarded as one of the vestigial structures of man's body, and opinion which has prejudiced us against any real endeavor to discover its nature and function."

Maybe there are biological features that really have no significant function, but any theory that claims nonfunctional at the outset obstructs scientific progress.

Evolution is not just zombie science. From the perspective of the empirical science, it may also be the biggest science stopper in history.
Wells just doesn't get it. There is solid evidence for junk DNA in our genome. Scientists did not just wake up one day and arbitrarily make up a "theory" that most of our genome is junk. That idea was radical at the time and counter to the popular understanding of evolution.

It looks like Jonathan Wells has learned nothing in the last six years since publication of The Myth of Junk DNA and nothing in seventeen years since publication of Icons of Evolution. Isn't that shocking!?


Brunet, T.D., and Doolittle, W.F. (2014) Getting “function” right. Proc. Natl. Acad. Sci. 111:E3365-E3365. [doi: 10.1073/pnas.1409762111]

Doolittle, W.F. (2013) Is junk DNA bunk? A critique of ENCODE. Proc. Natl. Acad. Sci. (USA) 110:5294-5300. [doi: 10.1073/pnas.1221376110]

Kellis, M., Wold, B., Snyder, M.P., Bernstein, B.E., Kundaje, A., Marinov, G.K., Ward, L.D., Birney, E., Crawford, G.E., and Dekker, J. (2014) Defining functional DNA elements in the human genome. Proc. Natl. Acad. Sci. 111:6131-6138. [doi: 10.1073/pnas.1318948111]

Palazzo, A.F. and Gregory, T.R. (2014) The Case for Junk DNA. PLoS genetics, 10(5), e1004351. [doi: 10.1371/journal.pgen.1004351]

59 comments :

  1. As I keep tabs on antievolutionism for #TIP project, and likely someone in the Wells defense camp will snark on this piece, will be adding this to #TIP www.tortucan.wordpress.com

    The source methods side is that you're citing several technical papers. and hence those are of relevance for anyone who may be criticizing your take on Wells' latest

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  2. This thread is about junk DNA. i don't follow that issue however it came up here about the human tail.
    The claim of there having once be a tail is asserted by evolutionists by noting the occasional 'tail" of new babies etc.
    The creationist answer to this is about probability.
    If we had never had any tails we would also have a tiny percentages of babes born with extensions of the backbone. this due to errors.
    That is that in giving all humans backbones, it would be that error in the Dna/growth would make a overshooting . so relative to numbers a percentage always would have a 'tail". Whether we had tails once or we never did would be unrelated to this error probability.
    The tail is not a old story making its appearance but is just a likely outcome relative to numbers relative to errors in the body as the spine in the fetus gros in uteral.
    In fact saying that all tails in children is from a tail past would mean not EVEN ONCE was there a error in the system that made a simnple overshooting of the spine. very unlikely.
    Children are born with eight fingers often biut its not evidence of a eight finger past. Even if we had one. its just errors and probability.
    so the tail in some is not proof of a ape past or if it was you never would know it.
    Overshooting spines could always explain it plus math.

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    1. If we had never had any tails we would also have a tiny percentages of babes born with extensions of the backbone. this due to errors. [...] That is that in giving all humans backbones, it would be that error in the Dna/growth would make a overshooting .

      HERITABLE errors? You mean like MUTATIONS? Of a NOVEL feature, which could spread and make humans EVOLVE?
      Robert, it really is amusing that in your desperation to explain away atavisms, you reinvent half of evolutionary theory.

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    2. Hmmm. I don't know if the "tails' on some babies are from mutations.
      I just see it as errors that occur in a population.
      By the way that would mean it is just a mutation and not a memory of a former 'taily" past. evolutionists, i have read/heard, do use the tail to say its evidence of a tail past.

      My point was not this.
      It was that, it could only be, that in such large populations one would get errors in the body EXTENDING the spine too far.
      The 'tail" really is that and not a tail for swatting flies.
      Its just a predictable occurance based on probability.
      Many errors, like extra nipples on mens bodies etc etc, occur. yet not sign of some such past.
      I saw on a famous NOVA episode how they made this error relative to some open thing on some peoples necks. Saying it was from our fish past. Neil Shuban, i think is the name, was saying this on a nOVA episode about finding something up north as a intermediate species.

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  3. Of course, it's not just "Junk DNA" that Wells delivers misinformation on. This is something I noted on Puck Mendelssohn's excellent Amazon review of the book

    Note that Well's book, like Meyer's, has has many endnotes, something that another reviewer here holds up as evidence of its scholarship.

    This is the first endnote that I looked up.

    On p, 63 Wells writes: "In 2009 a fossil bird was discovered in China that apparently predated Archaeopteryx, so Archaeopteryx is not even the oldest bird, much less the ancestor of living birds."

    Leaving aside the non-sequitur claim that a bird older than Archaeopteryx would dethrone Archaeopteryx from being ancestral to later birds, let's look at the reference (coincidentally also #63).

    Hu et al. 2009. "A pre-Archaeopteryx troodontid theropod from China with long feathers on the metatarsus". Nature 461.

    Hmm. That's not describing a bird, but a theropod dinosaur ---- of course, birds are also theropod dinosaurs, technically speaking, but this paper is clearly describing a non-avian dinosaur, not a bird. However, what it actually *is* describing is something that Wells declared in "Icons of Evolution" did not exist (which, at the time, was true): a derived dinosaur on the lineage postulated as being ancestral to birds, but that was earlier in time than Archaeopteryx.

    So, rather than admit that yes, we now do have the appropriate older dinosaurs along the bird lineage, he changes it into a bird and declares it further defeat for Archaeopteryx, hoping that nobody will notice, because who actually checks those references. I do, and I call a whopper on this one.

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  4. Thanks, Prof. Moran, for that enlightening piece. I read this book right away when it first came out, and found it quite awful through and through, but the "Junk DNA" chapter is one place where my lack of technical understanding really left me unable to see much of what Wells had wrong. Knowing Wells as I do from his previous works, I knew he wasn't likely to be telling the truth, but I couldn't have easily said precisely what he had wrong in that area.

    As Christine mentioned, I did a review of this awful book on Amazon. Currently, mine is the only negative review out of nineteen reviews -- if anyone else has read it and would like to jump in over there, it would be great. I've treated a couple of areas of Wells' dishonesty in mine, but of course there is so very much wrong with this book and so little space in any one book review -- I'd love to see some other critics cover more of the ground, and also break up the warm consensus of the creationists over there that this is a marvelous book....

    Puck Mendelssohn

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    1. You are accusing him of not telling the truth.Well that, I guess, you document in your review. I don't know how to find it.
      I doubt there is any intent to not tell the truth. Why in these matters would a researcher do that?!
      he expects to impress and persuade. I never find in origin contentions crusading liars.
      People make mistakes, slow to correct, but LYING!!!
      This "awful book" had 18/19 good reviews so those reviewers must be awful too.
      Are they lying too? Do they miss Well's lies?
      I think a public would go more with the 18 then the one.
      At least its another iD author getting attention!

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    2. You do realize, Robert, that Well's book is nothing more than a litany of accusations against evolutionary biologists that they have lied, right? Any thoughts on that?

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    3. I don't but first my criticisms.
      I doubt he accuses them of liying but rather of why there is lingering of outdated, disproven ideas!
      there is suspicions that they are slow to drop these things because of intent to persuade people and they don't have much.
      Well's isn't saying they don't teach their own kids these lingering errors and so its not accusations about deception.
      its something else in human nature.

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    4. "I don't know how to find it."

      Well, you found the other 18 reviews. Shouldn't be too hard to find mine.

      "I doubt there is any intent to not tell the truth. Why in these matters would a researcher do that?!"

      Wells isn't a researcher. Where did you get the idea that he does research?

      "People make mistakes, slow to correct, but LYING!!!"

      Yep, lying. See, in my review, the reference to his whopper about the rate at which mutations could arise and become fixed in whales. Read what he says, and read the paper he cites. It simply is not plausible that Wells is dim enough to think that he has used that paper accurately. That's a lie; the only alternative would be for Wells to be profoundly, bizarrely, stupendously dim. If you like, you can take that position, but that's rescuing his honesty at the cost of his credibility -- and it's implausible anyhow.

      "This 'awful book' had 18/19 good reviews so those reviewers must be awful too.
      Are they lying too? Do they miss Well's lies?"

      Harder to say. What do you think? Obviously they have got to either be fooled by Wells or be dishonest themselves. Some of them are certainly liars themselves; that's very likely for, for example, the guy who heads the ID organization in Scotland. But in most cases they probably simply do not know the underlying science. They see citations to papers and they imagine -- what faith they have! -- that Wells has not lied about what those papers contain.

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    5. That's a great review you wrote, Puck. I hope you can regrow the brain cells you undoubtedly lost from exposing them to Wells's stupidity.

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    6. Thanks, lutesuite. And, yeah. It takes a toll. The DI just keeps churning out material with brain-cell-damaging power. Tom Bethell's book, Darwin's House of Cards, was even worse than the Wells book, if such a thing can be imagined.

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    7. I just found it. After reading your review I greatly want to read his book. I love his attacks on homology concepts. Other stuff. THANKS.
      NOPE . I see no justification for you to emphasize he is acting in deceit to his readers or anyone. I think you mention something about mutations and whale timelines but he is just working with the info he has.
      Thinkers/researchers like Well's are not lying about anything.
      they hope to persuade, and get applauded for it. they hope to extend discussions and not confuse them with dishonesty.
      i was really exicited to see a ID author, i'm YEC, deal with this stuff about drawing conclusions on biological history based on merely scoring traits of body parts in creatures.
      Indeed the presumption that common descent is true makes evolutionists, convince themselves, then say their TREES of relationships prove common descent.
      Excellent point and I hope this becomes standard criticism in the ID intellectual leadership.
      Truly its an embarrassment of riches these days for well read authors striking at old time evolutionism.

      By the way I do insist marine mammals were once landlovers and only in a post flood world took to the empty seas.
      However not by small step evolutionism. Thats impossible.
      Yet this is a very special case.
      By the By.
      I like you brought up about PE. evolutionists today run from stephen Goulds PE idea.
      Remember however its based on the conclusion the fossil record proves gradualism never happened.Not just faulty digging or fossilization action.
      So your trying to say there are intermediates aplenty is unlikely even if there were intermediates.
      That also very unlikely.

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    8. Well, there's no accounting for tastes...

      He certainly is lying about the time required to obtain and fix the mutations in question; all you need to do is read the paper he cites and compare it to what he says in the book. He has a rather long history of lying; his previous book with Dembski, The Design of Life, is quite deeply dishonest.

      "Thinkers/researchers like Well's are not lying about anything.
      they hope to persuade, and get applauded for it. they hope to extend discussions and not confuse them with dishonesty."

      Wrong, of course, except in one very limited sense. Wells hopes to preach to the already-persuaded and get praise for it. But that audience is willfully ignorant about biology, so he does not need to be honest and he does not need to have positions which anyone with the slightest understanding would agree with. Imagine, if you will, what it is like for an actual biologist to pick up a book like this. Does Wells have any hope of persuading such a person? Look at paleontologist Christine Janis' remarks above -- when she catches Wells lying, well, that's pretty much "game over" as far as Wells persuading her of anything is concerned.

      Wells does not think he's telling the truth. But he does want to tell a tale that his existing audience will love to hear, and given the characteristics of his audience, it does not matter that the tale he tells is entirely fictitious.

      "I like you brought up about PE. evolutionists today run from stephen Goulds PE idea.
      Remember however its based on the conclusion the fossil record proves gradualism never happened.Not just faulty digging or fossilization action.
      So your trying to say there are intermediates aplenty is unlikely even if there were intermediates.
      That also very unlikely."

      While it is frankly very hard to understand what you're getting at here, it's clear that you're badly confused. Biologists aren't "running" from Punk Eek. And Punk Eek doesn't mean gradual evolution never happened ("gradualism" never happened, as "gradualism" is a point of view about evolutionary processes, not an evolutionary process itself). What it means, among other things, is that when gradual evolution within a subpopulation, resulting in a speciation event per the allopatric speciation model, occurs, we are fairly likely to not see the subpopulation where this occurred but only see the new species replace older species when it expands out of the original range in which the speciation event happened. This is a sort of what you seem to mean by "faulty digging or fossilization action": that we do not have fossils of everything everywhere, and so we miss the speciation event while seeing its follow-on consequences. Failing to understand PE at all, of course, creationists tend to draw the conclusion that you seem to have drawn: that it proves that evolution does not happen gradually. Gould was not a saltationist; PE is not "hopeful monsters." PE is more an observation about what the fossil record shows -- and why it shows that -- than it is an observation about evolutionary processes themselves.

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    9. Last time. I don't see you showing a case to publiclly accuse Wells of lying. You bring up some mutation thing that eithewr is as he says or its a mistake on details. Likewise bringing up other books is inadmissible as evidence for this book. i'm sure its just as inaccurate.

      Your very wrong that Gould did not reject gradualism. His whole point was that the fossil record proved gradualism did not occur in nature. So his remedy was PE. he had to fight for it.
      It was not just about simple things.
      It was a rejection of Darwins claim EVOLUTION was constantly scanning biology to bring selection influences upon it to change biology as needed.
      Creationism rightly welcomes Goulds proving the fossil record proves gradualism never happened. Evolution never happened in slow steps everywhere.
      Gould didn't realize how he hurt evolutionism because he thought his PE idea would satisfy all things .
      So today PE is almost ignored and gould not welcomed from everything i read.
      Evolutionists today realize Gould did, or tried, to prove the fossil record was not incomplete but it showed darwin was wrong on gradualism.
      Of coarse the fossil record has nothing to do with biology evidence anyways. another error to be corrected.

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    10. I will admit that I wonder if Puck was being a bit uncharitable in accusing Wells of knowingly lying. That would require underestimating Wells' ability to respond to cognitive dissonance by repressing facts of which he should otherwise be perfectly cognizant. But that option does not exactly speak in Wells' favour either, does it?

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    11. Robert Byers:

      The first notable feature of your defense of Wells is that you haven't read the book; you haven't read the paper Wells cites; you do not appear to be familiar with biology in general (witness your discussion of PE); yet you are ready to defend his honesty. People of good mental habits simply do not do things like that. Were Larry Moran, for example, accused of making a dishonest statement, what I know of his reputation might cause me to doubt the charge; but nothing would ultimately satisfy me on the subject other than to review what he had said, see whether it was accurate, and see what his basis for saying it was. At no point would I say, "well, Larry's on my team, so whatever he says MUST be defended."

      But here, prior to any inquiry, you are defending Wells. Surely nothing in Wells' reputation -- which is universally negative among all learned people -- could prompt you to this. Presumably you are lapsing into that sorry mental habit which is so characteristic of creationism: the defense of anybody and anything perceived to be on "your side."

      There is, in fact, objectively no question that Wells has got this badly, badly wrong and that no literate person, reading the paper in question, and possessing even the slightest elementary grasp of the subject matter, would think otherwise. Likewise, as to the dishonesty of Wells cited in Christine Janis's post above, there can be no question that Wells is wrong and there is no possibility of making a contrary case. Now, as lutesuite points out, there is of course a possibility that Wells is so completely, hideously self-deceived that he believes things which are obviously and objectively false. I am reminded of that great line from Medawar, reviewing Teilhard de Chardin's book: "its author can be accused of dishonesty only on the grounds that before deceiving others he has taken great pains to deceive himself." My only area of disagreement, perhaps, with lutesuite is that saying Wells believes these things to be true makes Wells into such a pathetic, profound fool -- a truly ludicrous character warranting the greatest possible contempt -- that I believe that such a suggestion is more dishonoring than the claim that he is simply being dishonest. Ultimately, of course, no one can stare into Wells's heart and say what he feels; and nobody, probably, would wish to engage in such a stare into that abyss of dishonesty and ignorance anyhow. My bet is upon dishonesty; but whatever the bet, there are no odds for him actually being right.

      On Gould, you are of course badly wrong and it appears that what's happening is typical, again, of the creationist mindset. You think you know Gould, but you probably have read nothing but quote-mines of Gould in creationist works. If you were to do some reading in actual biology, you would find that PE is often discussed -- it is better liked by some than by others, and it is not discussed when it isn't particularly germane to the topics under discussion, but it is certainly not being run from. It doesn't mean what you think it means; to understand it you need to understand the fragmentary nature of the fossil record, the nature and mode of speciation, and how these things fit together to explain the fossil record. Gould is NOT a saltationist, though he admittedly thought that things proceeded a bit more by fits and starts -- but still within the realm of what you would deem "gradualism" -- than some people thought. Again: reading creationist works and getting their fun-house mirror image of actual biology is very bad for you; after you do it, you emerge more ignorant than you entered.

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    12. I read your review and you asked your readers to say Well's was a liar sampled by this mutation thing on whales.
      It is against probability that authors on these matters lie about these things on any side. so many reasons not to, and its all about persuading on the facts. eSpecially for iD/YEC which are attacking the fortresses.
      if the mutation thing is wrong its just about details. Lots of ID thinkers take on the mutation steps relative to walking to swimming whales.
      there was no lying or a right to say so.
      Anyways done with that.

      I said i read Goulds biggest finale paper on PE recently.
      He insisted the fossil record was not fragmantory. his origin of thought for PE was that the fossil record was good enough.
      Insteasd iot showed gradualism was never true. Darwin was wrong.
      Instead evolution came from very special fits and starts and then stops. No constant scanning of biology as darwin thought.
      So the starts easily were not fossilized as being to quick.
      This was his hunch. Just like, as he said, Darwins hunch came from observing corals making islands. Not the Galapagos.
      He thought he had a revolutionary correction and replacement.
      I read it right and got it. Is it possible your reading of Gould and Wells is not accurate?

      I do add myself Gould hurt evolutionism badly but he thought his better idea would do the trick. it didn't. He only proved the fossil record proved evolution was not shown in it as it should be if it had happened.

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    13. Wrong, wrong, and wrong. Here's Gould (broken into two posts due to posting length limit):

      "The idea that we eventually called punctuated equilibrium had two sources and one overriding purpose—to provide an exit from the 'disabling rescue' of Darwin's argument on imperfection. First, a statement about mode of change: Most new species do not arise by transformation of entire ancestral populations but by the splitting (branching) of a lineage into two populations. Niles and I had learned the standard evolutionary version of speciation by branching—a notion popularized by Ernst Mayr and called by him the allopatric theory. Allopatric means 'in another place,' and the theory argues that new species may arise when a small population becomes isolated at the periphery of the parental geographic range. Isolation can occur by a variety of geological and geographic contingencies—mountains rising, rivers changing course, islands forming. Without geographic isolation, favorable variants will not accumulate in local populations, for breeding with parental forms is a remarkably efficient way to blur and dilute any change that might otherwise become substantial enough to constitute a new species. Most peripherally isolated populations never become new species; they die out or rejoin the larger parental mass. But as species may have no other common means of origin, even a tiny fraction of isolated populations provide more than enough 'raw material' for the genesis of evolutionary novelty.

      "Second, a statement about rate of change. The simple claim that species arise by splitting, and not by transformation of entire ancestral populations, does not guarantee punctuated equilibrium. Suppose that most splitting events divide large populations into two units of roughly equal size, which then change at the conventional gradualistic rate. Splitting events, in this scenario, would yield two examples of gradualism—and the case for punctuated equilibrium would be compromised, not strengthened. Punctuated equilibrium gains its rationale from the ideal also a standard component of the allopatric speciation theory, that most peripherally isolated populations are relatively small and undergo their characteristic changes at a rate that translates into geological time as an instant.

      "For a variety of reasons, small isolated populations have unusual potential for effective change: for example, favorable genes can quickly spread throughout the population, while the interaction of random change (rarely important in large populations) with natural selection provides another effective pathway for substantial evolution. Even with these possibilities for accelerated change, the formation of a new species from a peripherally isolated population would be glacially slow by the usual standard of our lifetimes. Suppose the process took five to ten thousand years. We might stand in the midst of this peripheral isolate for all our earthly days and see nothing in the way of major change.

      "But now we come to the nub of punctuated equilibrium. Five to ten thousand years may be an eternity in human time, but such an interval represents an earthly instant in almost any geological situation—a single bedding plane (not a gradual sequence through meters of strata). Moreover, peripheral isolates are small in geographic extent and not located in the larger area where parents are living, dying, and contributing their skeletons to the fossil record.

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    14. Gould, continued:

      "What then is the expected geological expression of speciation in a peripherally isolated population? The answer is, and must be, punctuated equilibrium. The speciation event occurs in a geological instant and in a region of limited extent at some distance from the parental population. In other words, punctuated equilibrium—and not gradualism—is the expected geological translation for the standard account of speciation in evolutionary theory. Species arise in a geological moment—the punctuation (slow by our standards, abrupt by the planet's). They then persist as large and stable populations on substantial geological watches, usually changing little (if at all) and in an aimless fashion about an unaltered average—the equilibrium."

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    15. I've left out the bit, in the same piece, where Gould complains about creationists misusing his words as you have done here. I'm sure you already know you are misusing Gould and that you don't really care; dogmatism is more important than honesty to most creationists, and for that reason I am sure you will love Jonathan Wells' book.

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    16. Your accusing me, like you do Wells, for deliberatley "misusing" words.
      I'm not! If i'm wrong its just incompetence. I'm confident of my own intergrity here and Wells too. You prove the reasson for your unjust accusation against him.
      anyways.
      AMEN. Yes this is what Gould said PE was. A rejection of gradualism being found in the fossil record because it never happens.
      Instead its a tiny isolated population that evolved some trait of note, within 5-10 thousand years. which fossilization would be in a tiny layer or none at all.
      Its his answer to why the fossil record shows no evolutionary steps.
      HIS ANSWER is evolution only happens , in a instant, in a tiny population, in a obscure area, and then later becomes a great population covering a large area.
      So gradualism is proven to not happen by the fossil record.
      THus PE is introduced to fix this glaring problem.
      Gradualism only happens, small steps, in isolated populations relative to a large parent population.

      The important thing is Gould proves the fossil record shows, nor could, the gradual steps of this evolving into that.
      He proves evolution is not evidence in the fiossil record.
      This is smelled out and why he and PE are not welcome as I read it.
      His remedy was admittance of a problem.
      The creationists were right about this detail.
      PE is a rejection of gradualism . In the fossil record and in biology as evolutionism taught for a long time.
      Sure it is!

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    17. Your accusing me, like you do Wells, for deliberatley "misusing" words.
      I'm not! If i'm wrong its just incompetence.


      Oh, Robert. How we love you. If nly other creationists had even half your honesty.

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    18. Plainly, Robert Byers, you do not understand the differences between what you said earlier, what you're saying now, and what Gould actually said. You've got this very, very badly wrong. If you do wish to plead incompetence, I can't deny it; you do not appear to be able to compose a coherent post, so it's very likely that you lack the reading comprehension to properly understand Gould. Gould is not denying what you would call "gradualism" in evolution and, indeed, affirms it. But to understand that, of course, you'd have to understand that "gradual" in our terms and "gradual" in geological terms are two rather different things. And despite Gould spelling this out in the passage I have quoted, it appears that you either cannot understand it or do not wish to.  

      Now, as for Wells: I note that you still haven't actually read the paper, read what Wells says about it, or considered whether there is any actual possibility of Wells being so blindingly incompetent as to have actually thought he was using it accurately. But nonetheless, faced with not one but two glaring examples from Wells' book, neither of which you have evaluated in any way, you are sure he is not dishonest -- and that despite his decades-long, well-documented history of complete dishonesty. I am sure that your desperate and ill-founded faith in this charlatan is quite unjustified. But as you dislike the truth, and love error (intentional or incompetence-driven), you will love Wells' book.

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  5. If Wells were digging through a landfill and found a working power drill he would then proclaim that all of the other stuff in the landfill must also be fully functional power drills and is not junk. That's the logic that Wells is using.

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    1. Wells isn't using logic at all, he's just lying for Jesus:

      "Father's [Rev. Moon's] words, my studies, and my prayers convinced me that I should devote my life to destroying Darwinism, just as many of my fellow Unificationists had already devoted their lives to destroying Marxism. When Father chose me (along with about a dozen other seminary graduates) to enter a Ph.D. program in 1978, I welcomed the opportunity to prepare myself for battle."

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  6. Creationists sure love ENCODE. And yet they also say that junk DNA would be perfectly compatible with creationism. Go figure.

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    1. They say
      (1) (When considering things like the Giraffe Recurrent Laryngeal Nerve) We should not speculate about the intentions of the Designer, one shouldn't base any argument about the presence or absence of Design on that.
      (2) (When considering junk DNA) It can't be there because the Designer would not have done things that way.

      Go figure.

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    2. Heh, I have had a creationist do that EXACT thing in a single discussion, using those two exact things. Junk-DNA(which he took to be synonymous with all non-coding DNA) and the recurrent laryngeal nerve.
      Back in 2010 some IDcreationist was simultaneously claiming that the putative functionality of all non-coding DNA was evidence of design, and that the route taken by the recurrent laryngeal nerve cannot be evidence against design, because we simlpy don't know what the designer wants because we don't know the mind of God:

      Gap arguments: what the layman should know.

      "Many things that we did not properly understand use to contradict ID, non-protein coding DNA/RNA, the "poor backward design" of the human eye, the panda's thumb, and this list goes on. The laryngeal nerve is just the most recent member to join this list, and it won't be long, before science will have an answer for this too, as to why this design is not as poor as we might think." (That was 7 years ago, how long is "it won't be long"?)

      "I hope you are walking around with a scepter in your hand when you make religious claims like this? How on earth do you know how a designer would design things and how he wouldn’t? Do you have knowledge about God that you received via divine revelation?"

      The same person in the same thread linked above made those two statements. The assumption seems to be, outright motivated by religious conviction, that everything is designed to be optimal in a way we just have yet to figure out. And if it appears not to be and we use this merely apparent lack of optimality to argue against design, then we are making unwarranted speculations as if we had recieved divine revelation. (And apparently we need scepters to make religious declarations, go figure!)

      A rare very obvious case of textbook psychological compartmentalization.

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  7. Re the RLN. I like Jerry Bergman's explanation that it's nothing to do with evolutionary history, just an accident of development.

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  8. So histone octamers just happened along to spool up all of that junk and package the DNA so that it is useful? Really?

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    1. "Of course not. A wizard did it."

      Do, they did just "happen along"?

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    2. "Do, they did just "happen along"?"

      No, tx, as MRR said, a wizard magically poofed them into existence.

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    3. "No, tx, as MRR said, a wizard magically poofed them into existence."

      Your sarcasm doesn't provide much cover. Don't you wish you had a really juicy, scientific answer?

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    4. I'm glad we agree that "it was wished into existence with magic" isn't a scientific answer.

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    5. Prokaryotes don't have histones. DNA is a big floppy molecule that will wrap around things, like proteins. If having DNA wrapped around proteins (loosely or tightly) makes the cell more efficient, those proteins and that process will be selected for. There's lots of time (millions of years) among eukaryotes and their ancestral archaea for refinement in histone shape. There's also lots of time for junk DNA to accumulate, unless genomes are massively rearranged (e.g. bladderworts) or a mechanism for removing junk DNA evolves (as it has in nothing we know). What's the problem you see with histone evolution?

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    6. "What's the problem you see with histone evolution?"

      First, it wouldn't be proteins just showing up for a floppy DNA molecule to wrap around. It would be dozens of role-specific, histone genes accidentally developing.

      “It also appears that the structure of histones has been evolutionarily conserved, as any deleterious mutations would be severely maladaptive. All histones have a highly positively charged N-terminus with many lysine and arginine residues.”*

      Any way you look at it, being highly-conserved and mutation-sensitive has to mean extremely unlikely to accidentally evolve. Throwing millions of years at it doesn’t improve the odds against it ever happening.

      But to Joe’s interesting point, why would so much packing and packaging energy be devoted to a 91% junk genome? I guess ‘tidy’ must be strongly selected for?

      *https://en.wikipedia.org/wiki/Histone

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    7. "First, it wouldn't be proteins just showing up for a floppy DNA molecule to wrap around." -- actually, at first it would be precisely that. Remember, prokaryotes function fine without histones. As genomes get bigger and especially as chromosomes become linear, not circular, there might well be advantage to the cell in not having them flop all over the place. The cell would be full of proteins by then, and even an imperfect DNA packaging system would be useful. Now, of course, the histones are about as good as they can be as cores for wrapping DNA around; most changes are harmful.

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    8. TX mentions one of the reasons so many biologists have trouble accepting the idea of junk DNA. It's expensive to build and it's expensive to wrap up to keep it out of the way. Why have it? If one understands evolution simply as natural selection, one concludes that junk DNA shouldn't be there, or if it does occur, it should disappear again as fast as it arises.

      However, the selection advantage of having (for example) 1000 extra base pairs in one's genome is tiny. Whether individuals have 1000 more or fewer base pairs just doesn't matter to human survival or reproduction. So as junk forms, it stays around in populations. We would be much more efficient if we got rid of most of our junk DNA. We can't do it bit by little bit because small changes don't matter, and we can't get rid of it all at once because our cells have no good way to distinguish the useful from the useless stuff. So here it is.

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    9. tx,

      From the very link you posted you could have learned that your "dozens of of role-specific" histones belong to just five families. That reduces your problem from dozens to just five proteins to originally evolve. If you pay even better attention, you might notice that having lots of arginines and lysines should not be that hard either.

      You just want to say that it's not possible, but you don't want to contemplate the possibility that it can actually happen. I wonder if you realize that the reduction of dozens to five proteins is, at the very least, a partial answer to your point. Do you realize?

      "why would so much packing and packaging energy be devoted to a 91% junk genome? I guess ‘tidy’ must be strongly selected for?"

      I suspect you were trying to be sarcastic, but it sounds plausible.

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    10. "From the very link you posted you could have learned that your "dozens of of role-specific" histones belong to just five families."

      Yeah, two super-families, five families, thirteen sub-families, and around 75 proteins listed as hyper-links. You can click on any of them and find out what gene codes for them, and what is known about their function.
      -
      “You just want to say that it's not possible, but you don't want to contemplate the possibility that it can actually happen.”

      Oh, I’ll contemplate that right now. Let’s see…Once upon a time, there were no histones, and millions of years later, there are dozens of highly-conserved proteins all doing specific things, and they are all the result of numerous gene duplications, and the duplicates were altered by DNA replication errors and accidentally wound up useful, and were selected for. No, sorry. That’s an asinine thing to believe, but it looks good on you.

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    11. tx,

      Is it really that hard for you to admit that there was a partial answer there? You prefer to go all the way to what seems unexplainable to you than admit that little tiny bit of an answer?

      Let's see if you're able to get out of your denialist bubble: five families means five original proteins. Thus the dozens are reduced to just five proteins to evolve. Now, sure, to you even five is impossible. But imagine that you're not committed to having an all-or-nothing view about whatever it is you believe. Wouldn't you agree that reducing dozens to five is a partial answer?

      If you can agree to that, now think about this: we get many partial answers. One tiny partial answer would not convince me that evolution has anything going for it either, but as those tiny partial answers accumulate, it starts to make a lot of sense. It's not magic. It's not asinine. It's just partial answers. I'm not satisfied about them being partial answers either. About there being so many gaps to fill. But, at least I look at it honestly. Can you do that? Can you understand that we really look at it honestly?

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    12. “Now, sure, to you even five is impossible. But imagine that you're not committed to having an all-or-nothing view about whatever it is you believe. Wouldn't you agree that reducing dozens to five is a partial answer?”

      No, and again I’m sorry. But partial does not cut it when you’re relying on accidents to yield spectacular results. Check out this picture:

      https://www.nature.com/article-assets/npg/nrmicro/journal/v6/n6/images/nrmicro1887-f2.jpg

      How many possible points of failure can you find? Whatever the number is, that is your miracle count. You and I both believe in miracles, but in your religion they are the rule, not the exception.

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    13. "No, sorry. That’s an asinine thing to believe, but it looks good on you."

      Why is it asinine? You merely claim this, but do no work to argue for it. You simply declare that you don't believe it. We already know you don't believe it.

      Why can five new proteins not evolve by duplication and point mutations filtered by selection, from pre-existing protein superfamilies, over geological timescales? Explain what is asinine about it.

      "No, and again I’m sorry. But partial does not cut it when you’re relying on accidents to yield spectacular results. "

      Why? Again you just declare this, you don't explain why. The only thing you seem capable of doing is to proudly declare what you believe or not. You never get around to actually doing any work to persuade anyone why it is you (dis)believe the things you do.

      "Check out this picture:"

      Yeah it's pretty. And... ?

      "How many possible points of failure can you find?"

      Please show how this is relevant. As in show, with arguments and evidence, rather than appeals to your own mere convictions.

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    14. "No, and again I’m sorry. But partial does not cut it when you’re relying on accidents to yield spectacular results."

      I'm not relying on accidents. I'm relying on what's known about natural phenomena. Some parts are "accidents," some parts are not.

      What part of "imagine that you're not committed to this all-or-nothing view" is so hard for you to understand? I didn't ask you to believe any of it, I asked you to try and understand a way of thinking different from your all-or-nothing posture.

      You cannot even try can you?

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    15. Can you understand that we really look at it honestly?

      Obviously not, so why should we waste time trying? To be fair to the discussion so far, I can't really think of fruitful and interesting issues to explore under the general heading "Jonathan Wells is still an IDiot" myself. But I'm a layperson, so I'm hoping people who know more might find something enlightening to talk about instead of playing our familiar game of Creationist Whack-A-Mole.

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    16. "How many possible points of failure can you find?"

      That's the wrong question. The right questions would be how many ways can this still work? For a partial answer, which, of course, you could not care less about, I have checked the sequences of flagellum proteins across bacterial genomes, and found lots of varieties, meaning that there's lots of working options. If we then examined the types of flagella, and other structures, we could get more answers, but I'll stop here. It's not as if you were about to start caring about answers.

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    17. That's the wrong question. The right questions would be how many ways can this still work?

      That's the type of mathematical inversion in which creationists specialize. If you find a fossil showing characteristics midway between two known species, you haven't found a transitional form, you've created two gaps where you had one. If there are a thousand possible ways to accomplish something, you haven't made it more likely, you've shown that the event which actually occurred is a one in a thousand shot.

      A misunderstanding of mathematics, particularly probability (which, often being unintuitive, is ripe for exploitation by the unscrupulous and/or agenda-driven), is fundamental to much of creationist (both YEC and ID) "thought."

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  9. "But, at least I look at it honestly."

    No, you look at it with breathtaking credulity.
    -
    But, if you admire coincidental results, you should love this. All the coiling that happens when that floppy DNA wraps around those proteins doesn’t just reduce a 1.8 meter long molecule it to a tidy wad. The 10,000 loops that result are actually functional:

    “The researchers also found that the protein CTCF often binds to DNA at the point where it forms a loop. Moreover, they found that the two CTCFs, each binding one piece of DNA, usually face each other.

    The researchers further attempted to understand the function of the loops. They confirmed that loops often bring together distant enhancers and promoters and that these pairings often lead to changes in gene expression. Thirty percent of the loops found in a lymphoblastoid cell line (GM12878) were formed by promoters and enhancers coming together, the researchers found.

    And many loops were conserved among cell types, and even between mice and humans. But others seemed to drive cell type-specific gene expression patterns. The researchers said that their map will help scientists to understand the functional effects of mutations to non-coding DNA regions.”

    http://www.the-scientist.com/?articles.view/articleNo/41653/title/DNA-Loop-the-Loops/

    Now that is some lucky stuff right there, though I’m not exactly sure how those kind of functions would actually be selected for. Wouldn't the loops be kinda random while the histones were being refined over millions of years? Any ideas about that?

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    1. .. so a wizard mustadunit. No explanation, no evidence for this at all. No, you declare with brainless conviction that to believe DNA loops evolved is to display "breathtaking credulity". And in contrast you believe that it was magicked into existence in an instant. On no evidence whatsoever. How's that for irony?

      "Any ideas about that?"

      Yeah, you're assuming the genome was already huge before histones evolved, so it was just flapping around randomly and nonfunctionally until, viola! - histones evolved. That's not how it happened.

      Again, bacteria don't have histones. They usually have a single, small circular chromosome. As cells became more complex and genomes became larger (a gradual process, not instantly from one extreme to the other), one or a few proteins at a time evolved to facilitate the wrapping and looping process.

      As usual you have the whole thing wrong, because you can't for some strange reason (aka intense religiously motivated cognitive biases) get yourself to consider that things might have been different and simpler from how they are now. To let go of your assumptions is the first step to enlightenment.

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    2. To let go of your assumptions is the first step to enlightenment.

      Yes, but I think we would be talking about geologic timescales there.

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    3. "No, you look at it with breathtaking credulity."

      You should avoid making these kinds of statements when your own beliefs are based on breathtaking credulity.

      "But, if you admire coincidental results ..."

      Not that coincidental. Amino-acids have physical-chemical properties. So does DNA. Since some amino-acids have positive charges and DNA has negative ones, some proteins can gain binding to DNA in steps adding those positive charges.

      In a cell, proteins whose functions are not related to DNA binding bind with different affinities to DNA just because of the presence of some charged amino-acids. There's a whole spectrum of such events.

      Studying proteins in general, and those that bind DNA as part of their functions in particular, yield very plausible evolutionary pathways. Of course, that requires lots of study and attention that you cannot be bothered to even try and understand. It also requires being willing to understand that answers come in steps. That we cannot have a whole picture, from the origin of life to today, in a single go. That nature does not owe us anything, let alone answers to each and every question. That we have to work to get those answers, and that sometimes we will get nothing. That some knowledge gaps are there to stay.

      It's brutal. But that's the way things are.

      "Wouldn't the loops be kinda random while the histones were being refined over millions of years? Any ideas about that?"

      Several ideas, and data supporting those ideas. But we both know you don't really care. Partial answers won't cut it for you, remember? You said so, which means that you ask questions whose answers you don't care about.

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    4. You said so, which means that you ask questions whose answers you don't care about.

      Yep, rhetorical questions.

      Thanks by the way for laying out just how prosaic a great deal of biochemistry is. This doesn't mean it's not fascinating, just that every elucidation of reactions and functional steps doesn't require any changes to fundamental theory, right down to the quantum level. Yes, we can find new things going on, but those new things operate on fundamental principles as everyday as positive and negative charges attracting.

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    5. Not a problem judmarc. It's good to know that someone is actually reading.

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    6. Nice discussion of histones. TX won't have learned anything, but I did. Thanks.

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    7. Me, too! Thanks, Gabriel, for your educational posts.

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