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!?

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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]