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]


  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

    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

  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.

    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.

    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.

  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.

  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

    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!

    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?

  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.

    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."

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

    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.

    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.

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

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

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

      Do, they did just "happen along"?

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

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