Science Literature

For many of us, an important characteristic of science is self-correction. We are proud of the way new findings catalyse re-evaluation and, if corrections are needed, the development of new knowledge. If you are like this, be prepared to be shocked when you read Jonathan Wells' latest book. The concept of Junk DNA was widely held by evolutionary biologists during the 1990s, but only a few were prepared to expose the hypothesis to tests of its validity. Yet this is when publications started to accumulate that reported functionality in genetic material widely regarded as "nonsense". Instead of alerting popularisers of science to be cautious, these writers treated the new data as unrepresentative exceptions. They pressed on with their claim that the bulk of the genome is useless. The trickle of challenging research findings became a stream, but the 'consensus' about junk DNA was not corrected. The stream became a river, but still the much-needed correction was lacking. Here is Richard Dawkins' comment from The Ancestor's Tale (2004, page 22):

"DNA differs from written language in that islands of sense are separated by a sea of nonsense, never transcribed. 'Whole' genes are assembled, during transcription, from meaningful 'exons' separated by meaningless 'introns' whose texts are simply skipped by the reading apparatus. And even meaningful stretches of DNA are in many cases never read -presumably they are superseded copies of once useful genes that hang around like early drafts of a chapter on a cluttered hard disk. Indeed, the image of the genome as an old hard disk, badly in need of a spring clean, is one that will serve us from time to time during the book."

(Source here)

Wells' approach is one of analysing and presenting the evidence for functionality. There are two broad categories to consider. The first concerns the transcription of non-protein coding DNA into various RNAs. The research literature suggests that most of this DNA is transcribed and in many cases, functionality has been confirmed. The second category concerns widespread conserved sequences of non-coding DNA. The very fact of it being conserved in different types of organism is supportive of functionality, even when we do not (yet) know the function.

Wells refers to a hierarchy of three levels for genome functionality. The argument is an interesting one, because it points to genetic information being present in both digital and analogue forms. In some examples discussed, the DNA sequence is in itself not important, but the length of the sequence is critical for successful functioning.

"The genome is hierarchical, and it functions at three levels: the DNA molecule itself; the DNA-RNA-protein complex that makes up chromatin; and the three-dimensional arrangement of chromosomes in the nucleus. At all three of these levels, DNA can function in ways that are independent of its exact nucleotide sequence." (p.93) [. . .]
"At the third level, the position of the chromosome inside the nucleus is important for gene regulation. In most cells, the gene-rich portions of chromosomes tend to be concentrated near the center of the nucleus, and a gene can be inactivated by artificially moving it to the periphery. In some cases, however, the pattern is inverted: rod cells in the retinas of nocturnal mammals contain nuclei in which the non-protein-coding pats of chromosomes are concentrated near the center of the nucleus, where hey form a liquid crystal that serves to focus dim rays of light." (p.94-5)

Junk DNA defenders have argued that junk DNA is supportive of Darwinism and that it refutes ID. This is why design advocates have felt it necessary to engage with these arguments. Well's book is compelling - it demolishes the thesis of junk DNA. If the original argument was logical, then the empirical data that we now have in profusion counts against Darwinism and confirms ID. Wells hastens to say that ID advocates have never suggested that all non-coding DNA is functional, only that it is unlikely that most DNA is non-functional. The design inference leads to the research goal of looking for functionality. This refutes the claim that ID is a science-stopper and does not lead to interesting avenues of research. This case shows that it is the Darwinists who have been guilty of science-stopping by their dogmatic claim that non-coding DNA is "nonsense" and not worth investigating.

Despite the onslaught of new data, with new functionalities being reported each week, there are still die-hards who cannot relinquish the junk DNA thesis. As an example of the intellectual gymnastics that are needed to sustain the myth, Wells refers to the "Onion test" proposed by Ryan Gregory in 2007. He claimed to have a "reality test" for those questioning the junk DNA thesis. "Ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?" (p.85) Wells' discussion of this test is worth reading in full, but his conclusion points to a logical flaw:

"So the onion test is a red herring. Why onion cells have five times as much DNA as human cells is an interesting question, but it poses no challenge to the growing evidence against the myth of junk DNA." (p.87)

Wells points out that the champions of junk DNA should be held accountable for keeping the myth alive and failing to demonstrate the self-correcting character of science. By quoting their arguments, he shows how they all demonstrate a vested interest in a Darwinian approach to evolution (i.e. demonstrating past tinkering that has accumulated nonsense DNA in the genome) and a hostility to ID. The individuals who need to retract erroneous arguments and conclusions are primarily John Avise, Francis Collins, Jerry Coyne, Richard Dawkins, Douglas Futuyma, Philip Kitcher, Kenneth Miller and PZ Myers. Science writers Richard Robinson, Michael Shermer and Carl Zimmer are also named for failing to demonstrate critical thinking skills when writing on this subject. Only Francis Collins has shown signs of revising his thinking - Wells puts it quite strongly: "he subsequently recanted his belief in the myth of junk DNA" (p.98). In an interview for Wired Magazine, he said: "I've stopped using the term" junk DNA (p.99) However, Collins gets only a partial reprieve, because his own baby The Biologos Foundation still promotes the junk DNA myth to argue against ID. (p.100)

Wells communicates very effectively in 114 pages of text plus 54 pages of references. The book could easily have been much larger if there was more background to the research findings and more discussion of the key implications brought out in the last chapter. Wells writes in a very restrained way, sparing us rhetorical flourishes that are often found in books and articles that deal with controversial issues. The writing style is concise, clear and compelling. Wells has chosen to communicate as a scientist and not as a polemicist. Consequently, the book is an invaluable resource as a state-of-the-art review of the issues. It provides a convincing rebuttal to anyone seeking to perpetuate the myth of junk DNA and anyone who suggests that the genome is a product of Darwinian tinkering rather than intelligent design.

Strongly recommended.

See also:

Tyler, D. Does the human genome have "serious molecular shortcomings"? (ARN Literature Blog, 7 May 2010)

Tyler, D. The Molecular Revolution's unfulfilled promises of simplicity (ARN Literature Blog, 11 April 2010)

Tyler. D. Hidden biological information via antisense transcription (ARN Literature Blog, 17 December 2008)