Does Darrel Falk's Junk DNA Argument for Common Descent Commit "One of the Biggest Mistakes in the History of Molecular Biology"?
Recently I was e-mailed by an individual who had read the book Coming to Peace with Science, by Darrel Falk, president of the BioLogos Foundation. This person was interested in a response to the arguments for human/ape common ancestry in Dr. Falk's book. Not having read Dr. Falk's book before, I wrote back that I hadn't yet read the book but had a strong suspicion that it would argue that shared non-functional (aka "junk") DNA between humans, apes, and other species is evidence of their common ancestry. This is an extremely common argument from theistic evolutionists--Francis Collins made it in The Language of God (and Collins wrote the foreword to Dr. Falk's book). Of course in 2010, we're seeing more and more that such "junk" DNA arguments are factually weak because a myriad of functions have been discovered for non-coding DNA. As Helen Pearson put it in Nature a couple years ago, scientists are finding that "DNA previously written off as junk actually carries biological information."1
Some who aren't aware of recent developments in this field find "junk" DNA arguments for common ancestry persuasive, especially when they are made by highly credible individuals with Ph.D.s in biology -- individuals like Dr. Falk, who unfortunately are known to dismiss criticisms by asserting that if you don't have a Ph.D. in biology, then you've got no business commenting on biological origins. (These types of dismissals are utterly unpersuasive to laypersons who like think of themselves as reasonably intelligent people.)
The fact that "junk" DNA arguments for common ancestry are made by some highly-credible scientists doesn't mean the arguments are good ones -- it just shows how deeply these views have penetrated into the evolutionary scientific community. As I wrote with Logan Gage in response to Francis Collins, "That such an eminent geneticist as Collins would make so dubious an assumption, given its well-documented history of failure, makes clear how entrenched the 'junk' DNA mind-set is within the Darwinian scientific community."
So after buying Dr. Falk's book, did my suspicions turn out to be right or wrong?
What surprised me after reading Coming to Peace with Science wasn't that Dr. Falk makes much the same fundamental mistakes as Francis Collins, arguing that shared "junk" DNA is evidence for common ancestry when it isn't actually "junk." What surprised me was the depth to which Dr. Falk's book relies on the dubious "junk" DNA argument (he uses the word "gibberish" instead of "junk")--even regarding types of DNA which we have long known are neither "junk" nor "gibberish."
Dr. Falk identifies a variety of types of DNA which he claims are non-functional and thereby demonstrate our common ancestry with apes. He first focuses on pseudogenes, discussing a pseudogene found in primates wherein apes share an 11-base deletion. He argues this marked pseudogene provides evidence for common ancestry. To Dr. Falk's credit, he notes the possibility of common design for this shared genetic feature, but he claims this is not a viable argument because "The gene has no function" and therefore it's wrong to say that "the reason why God put a deletion into the ape lineage is because it would make the gene more ideally suited to carrying out its purpose." (p. 188) He thus argues that such "marked pseudogenes  leave telltale signs of common descent." (p. 188)
He uses the same kind of reasoning when discussing introns, which he calls "meaningless gibberish." (p. 189) Specifically, Dr. Falk writes, "A stretch of gibberish, when it occurs within a gene, is termed an intron" (p. 189), and "[g]enetic instructions contain stretches of gibberish called introns" (p. 190), because they are virus instructions that got inserted into a gene. He calls these allegedly non-functional stretches of DNA "scars" (p. 196) and argues that "organisms that share a specific 'scarred' section of DNA do so because of their shared ancestry." (p. 196) He argues that shared introns, retrotransposons, and repetitive DNA (such as SINE elements) indicate common ancestry.
It's worth highlighting just how much Dr. Falk relies upon the argument that introns are junk and are largely the result of viral DNA that got inserted (and thus "scarred") our genome:
Recall our three mechanisms for God's mechanism of creation. Possibility 2 was that animals share ancestry, but only within prototypes. The retrotransposon data ... are not consistent with possibility 2 but are completely consistent with possibility 3. Since gibberish is inserted within the same intron (which is gibberish itself) at the same position in two different species from different prototypes, virtually all geneticists are convinced about the reasons: they share common ancestors. (p. 192)
So Dr. Falk relies heavily upon the argument that introns are "gibberish" DNA that we share with other species at the same position, and this supposedly demonstrates common ancestry. The problem for the argument is that introns are not "gibberish," but have important functions, such as regulating gene expression. And if there's function, then a perfectly valid explanation for the functional genetic similarities we see is common design, not necessarily common descent. His argument that introns comprise functionless genetic "gibberish" is simply not correct.
Dr. Falk's book was published in 2004. A stark admission of the false assumption that non-coding intronic DNA is useless genetic "gibberish" was highlighted in a 2003 article in Scientific American titled, "The Unseen Genome: Gems Among the Junk."2
Though written from an evolutionary perspective, the article explains how "the introns within genes and the long stretches of intergenic DNA between genes ... were immediately assumed to be evolutionary junk" and "long ago written off as irrelevant" by molecular biologists using neo-Darwinian assumptions. The article admits that "[t]hat assumption was too hasty" and quotes a molecular biologist explaining how this Darwinian-based dogma stifled research, calling the failure to recognize introns as functional possibly "one of the biggest mistakes in the history of molecular biology." As the article stated:
"I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century," Mattick says. "The failure to recognize the full implications of this-particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules-may well go down as one of the biggest mistakes in the history of molecular biology."
The article summarizes John Mattick's view with these striking words: "The failure to recognize the importance of introns 'may well go down as one of the biggest mistakes in the history of molecular biology.'" Yet that is what Dr. Falk does in Coming to Peace with Science by repeatedly calling introns "gibberish."
Falk also cites shared retrotransposons such as SINE elements and other forms of repetitive DNA as evidence for common ancestry. But here, too, evidence of function has been found for SINE elements. In a 2005 paper in Biological Reviews of the Cambridge Philosophical Society, influential geneticist James Shapiro and pro-ID biologist Richard Sternberg conclude, "There are clear theoretical reasons and many well-documented examples which show that repetitive DNA is essential for genome function."3
In 2002, Sternberg wrote a review article in Annals of the New York Academy of Sciences titled, "On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic-Epigenetic System" which documents a variety of known functional roles for repetitive DNA, including:
Indeed, here on ENV Sternberg recently posted some fascinating insights showing unexpected conserved patterns of SINE elements which not only could hint at their function, but entail similarities that are not due to common descent. So like introns, SINE elements should also not be written off as "gibberish."
telomeric tandem repeats and LINE elements SINEs as nucleation centers for methylation SINEs as chromatin boundary/insulator elements SINEs involved in cell proliferation SINEs involved in cellular stress responses SINEs involved in translation (may be connected to stress response) SINEs involved in binding cohesin to chromosomes and LINEs involved in DNA repair4
What about endogenous retroviruses or ERVs? Even these--also cited by Dr. Falk--have shown hints of function--or at the very least, what we presume is inserted viral DNA might actually be functional DNA in our genomes, and it was false evolutionary assumptions that made us think it was viral DNA. If you want to learn more about function for this type of DNA, two great commentaries are "'Large Scale' Function for Endogenous Retroviruses: Intelligent Design Prediction Fulfilled While Another Darwinist Argument Bites the Dust" and "When 'Junk DNA' Isn't Junk: Farewell to a Darwinist Standard Response."
None of this intends to single out Dr. Falk for these inaccuracies. Essentially, he's repeating the consensus of his peers--a consensus of many in the evolutionary scientific community which just happens to be wrong.
Some of these peers bucked this consensus and predicted function for things like introns and other "junk" DNA--apparently at a cost. An insightful 2003 paper in Science talks about how the evolutionary assumption that repetitive DNA has no function has actually hindered the progress of cellular biology:
Although catchy, the term 'junk DNA' for many years repelled mainstream researchers from studying noncoding DNA. Who, except a small number of genomic clochards, would like to dig through genomic garbage? However, in science as in normal life, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. Because of them, the view of junk DNA, especially repetitive elements, began to change in the early 1990s. Now, more and more biologists regard repetitive elements as a genomic treasure.5
Not only is Falk's argument for common descent misplaced, but by presuming that non-coding DNA had no function, his argument reflects an attitude that may have hindered the progress of biology and medicine to discover the true functions of these types of DNA.
Dr. Falk also argues that pseudogenes have "no function" (p. 188) and that shared genetic features in pseudogenes provide evidence for common ancestry. But again, the more we study "pseudogenes," the more we're finding that they can have function. The 2003 paper in Scientific American explains how evolutionists approach pseudogenes:
As an example of the unappreciated power of RNA, consider pseudogenes. Surveys of human DNA have found in it almost equal numbers of genes and pseudogenes--defective copies of functional genes. For decades, pseudogenes have been written off as molecular fossils, the remains of genes that were broken by mutation and abandoned by evolution.2
And a paper in Annual Review of Genetics from that same year argues that the more we study pseudogenes, the more we're finding function:
Rather, pseudogenes that have been suitably investigated often exhibit functional roles, such as gene expression, gene regulation, generation of genetic (antibody, antigenic, and other) diversity. ... Pseudogenes exhibit evolutionary conservation of gene sequence, reduced nucleotide variability, excess synonymous over nonsynonymous nucleotide polymorphism, and other features that are expected in genes or DNA sequences that have functional roles.6
Consistent with this, studies have found a variety of functions for various pseudogenes.7 Indeed, the very pseudogene Dr. Falk cites -- the Serine hydroxymethyltransferase pseudogene, or SHMT-ps1 -- reportedly shows "a high degree of sequence conservation in SHMT-ps1 among a number of nonhuman primates relative both to the human sequence and to each other."8 Could that potentially imply function? Dr. Falk appears to be too hasty in his assumption that pseudogenes have "no function" and thereby show evidence for common ancestry.
The bottom line is that the "junk" or "gibberish" DNA paradigm is being consistently overturned as time goes on, and we now know that the vast majority of our DNA has function. As one news article said when reporting on the results of the ENCODE project in 2007:
The findings, from a project involving hundreds of scientists in 11 countries and detailed in 29 papers being published today, confirm growing suspicions that the stretches of 'junk DNA' flanking hardworking genes are not junk at all. But the study goes further, indicating for the first time that the vast majority of the 3 billion 'letters' of the human genetic code are busily toiling at an array of previously invisible tasks.9
Dr. Falk's argument for common ancestry based upon the alleged "gibberish" nature of non-coding DNA -- including introns -- is based upon a premise that is being continually refuted by the data, and may even reflect how neo-Darwinism has led many scientists down a blind alley of research.
[1.] Helen Pearson, "Codes and Enigmas," Nature, Vol. 444:259-261 (Nov. 16, 2006).
[2.] W. Wayt Gibbs, "The Unseen Genome, Gems Among the Junk," Scientific American (November, 2003).
[3.] James A. Shapiro, and Richard v. Sternberg, "Why repetitive DNA is essential to genome function," Biol. Rev., Vol. 80:227-250 (2005).
[4.] Richard v. Sternberg, "On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic-Epigenetic System," Annals of the NY Academy of Science, Vol. 981:154-188 (2002).
[5.] Wojciech Makalowski, "Not Junk After All," Science, Vol. 300(5623) (May 23, 2003) (emphasis added).
[6.] Evgeniy S. Balakirev, and Francisco J. Ayala, Pseudogenes, "Are They "Junk" or Functional DNA?," Annual Review of Genetics, Vol. 37:123-51 (2003) (emphasis added).
[7.] For examples of some papers that have found function or pseudogenes, see: D. Zheng and M. B. Gerstein, "The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?," Trends in Genetics, Vol. 23(5):219-224 (2007); S. Hirotsune et al., "An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene," Nature, Vol. 423:91-96 (May 1, 2003); O. H. Tam et al., "Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes," Nature, Vol. 453:534-538 (May 22, 2008); D. Pain et al., "Multiple Retropseudogenes from Pluripotent Cell-specific Gene Expression Indicates a Potential Signature for Novel Gene Identification," The Journal of Biological Chemistry, Vol. 280(8):6265-6268 (February 25, 2005); J. Zhang et al., "NANOGP8 is a retrogene expressed in cancers," FEBS Journal, Vol. 273:1723-1730 (2006).
[8.] Eric J. Devor, , Rebecca M. Dill-Devor, Harry J. Magee, Rafiq Waziri, "Serine hydroxymethyltransferase pseudogene, SHMT-ps1: A unique genetic marker of the order primates," Journal of Experimental Zoology Part A: Comparative Experimental Biology, Vol. 282(1-2):150-156 (1998).
[9.] Rick Weiss, "Intricate Toiling Found In Nooks of DNA Once Believed to Stand Idle," Washington Post (June 14, 2007; A01).