junk DNA

A biology educator recently wrote me asking how we test intelligent design using the scientific method, how ID is falsifiable, and how ID explains patterns we observe in nature. These are very common questions that we receive all the time from teachers, students, and interested members of the public, and they’re usually legitimate, sincere, and thoughtful questions. In this case, they certainly appeared to be such, and below I post a slightly modified version of my response to the teacher, withholding any information about the teacher to protect his/her identity: We help many educators to better understand the debate over evolution. Contact us for more information!

I have long questioned the assumption that most genomic DNA sequences are “nonsensical” or “junk.” And given the data that have emerged over the past seven or so years, a functionalist view of genome has robust empirical support. It is for this reason that I think many of the arguments presented by the Biologos Foundation are “wrong on many counts,” to borrow a phrase from Darrel Falk.

Here is an example. While reading the “critique” of Steve Meyer’s book, Signature in the Cell, by Francisco Ayala, a number struck me that I know to be incorrect. The integer that I am referring to is “25,000” and it is claimed to be the known tally of genes in our chromosomes:

The human genome includes about twenty-five thousand genes and lots of other (mostly short) switch sequences…

Now, the problem with such a statement is this: While there are ~25,000 protein-coding genes in our DNA, the number of RNA-coding genes is predicted to be much higher, >450,000.¹ Some of the latter range in length from being quite short–only 20 or so genetic letters–to being millions of letters long. Since 2004 we have learned that over 90% of our DNA is transcribed into RNA sequences at some developmental stage, in different cell and tissue types.^{2, 3, 4} (Our brain cells are unusually rich in these non-translated RNAs.) These RNAs are then processed into regulatory and structural sequences of all sizes.^{2, 3, 4}

A recent article in ScienceDaily titled “ Introns Nonsense DNA May Be More Important to Evolution of Genomes Than Thought,” actually demonstrates nothing like Darwinian evolution. Introns are stretches of DNA within genes in Eukaryotes that do not code for proteins. But they aren’t functionless and can play important roles in splicing together proteins. According to the ScienceDaily article: “The scientists also found what appear to be “hot spots” for intron insertion — areas of the genome where repeated insertions are more likely to occur. This implies the occurrence of convergent genetic evolution of introns at specific locations, or as the article repeatedly puts it, “parallel intron gains.” The study’s principal investigator, Michael Lynch, was clear about the implications: Michael Read More ›

Download the Complete “Truth or Dare” with Dr. Ken Miller Lecture GuidePermission Granted to Copy and Distribute for Educational Use. Links to our 7-Part Series Responding to Ken Miller: • Part 1: Science and Religion: Is Evolution “Random and Undirected”?• Part 2: Misrepresenting the Definition of Intelligent Design• Part 3 (This Article): Confusing Evidence for Common Ancestry With Evidence for Darwinian Evolution• Part 4: The Name-Dropping Approach to Transitional Fossils• Part 5: Spinning Tales About the Bacterial Flagellum• Part 6: Misrepresenting Michael Behe’s Arguments for Irreducible Complexity of the Blood Clotting Cascade• Part 7: Ken Miller and the Evolution of the Immune System: “Not Good Enough”? Update 8/7/13: Since this response to Ken Miller was posted, even stronger evidence of Read More ›

Evolutionists have long sought mechanisms for the origin of reproductive barriers between populations, mechanisms which are thought to be key to the formation of new species. A recent article in ScienceDaily finds that “Junk DNA” might be the “mechanism that prevents two species from reproducing.” Basically, so-called “junk”-DNA is involved in helping to package chromosomes in the cell. If two species have different “junk” DNA, then this prevents the proteins in the egg from properly packaging the chromosomes donated by the sperm. The organism does not develop properly. As the article, titled “Junk DNA Mechanism That Prevents Two Species From Reproducing Discovered,” explains: during early development, the proteins required for cell division come from the mother. The researchers speculate that Read More ›

Originally, proponents of neo-Darwinian evolution lauded “junk” DNA as functionless genetic garbage that showed life is the result of blind and random mutational events. Then “junk” DNA was disproved by the discovery that the vast majority of DNA is being transcribed into RNA. Did the failure of this Darwinian assumption cause evolutionists to terminate their love affair with biological “junk”? Of course not. They just shifted their argument back, claiming that the cell is full of “junk RNA”–DNA that is being transcribed into RNA but still does nothing in the cell. Earlier this year we reported on a Nature paper suggesting function for “junk” RNA. Now a Science Daily NewsArticle is confirming that finding. Aptly titled “No Such Thing As Read More ›

Update 8/7/13: Since this response to Ken Miller was posted, even stronger evidence of function for the beta-globin pseudogene has been reported in the scientific literature, further refuting Miller’s argument. See Dover Revisited: With Beta-Globin Pseudogene Now Found to Be Functional, an Icon of the “Junk DNA” Argument Bites the Dust. In his book Only a Theory, one of Dr. Kenneth Miller’s main response to Michael Behe’s arguments for the irreducible complexity of the blood clotting cascade is that sequence similarities between various blood clotting factors demonstrates that they share a common ancestry. Indeed, in his response to me on the irreducible complexity of the blood clotting cascade, Miller again conflates evidence for common ancestry with evidence for Darwinian evolution. Read More ›

As someone who has studied the concept of “junk DNA” for over twenty years, I am dismayed by two statements that appear repeatedly on various blog sites discussing evolution. No, I am not referring to arguments of the form “the onion has six times more DNA than do mammals; therefore, there is no deity,” that are invariably followed by terms of disparagement hurled at anyone who even marginally departs from the Darwinian perspective. Rather, my consternation stems from a half-truth and a false fact that are recycled ad nauseum by those who apparently believe that, despite all the genomic and transcriptomic data that have been obtained only in this decade — data that have overturned a number of trenchant assumptions–a certain hypothesis published in 1980 is outside the purview of serious questioning.

The half-truth is the oft-read comment that goes something like this: “No one ever asserted that junk DNA is without function…it was long suspected that these sequences have important roles in the cells.” Now, to be fair, it is correct to say that models for, say, repetitive DNA-based operations in metazoan development, have been proposed since the 1960s.¹ It is also true that the evolutionary process of exaptation — the accidental acquisition of a function — has been used to explain how the odd transposon here or there along a chromosome can regulate a locus. Nonspecific effects of “extra” DNA on the cell have also been suggested for around three decades, if not longer. That said, the junk DNA hypothesis that one commonly reads as being an unassailable observation, as an incontrovertible empirical conclusion, presents as a clear prediction that the vast majority of non-gene sequences are devoid of any precise specificational role in ontogeny. Allow me to explain.

In the media, it’s not unusual for an interviewer and interviewee to hold similar views on whatever subject they are discussing. Radio show hosts and podcasters, for example, commonly interview friendly guests. But imagine if Paul Allen interviewed Bill Gates on the merits of Microsoft, and then published the interview as an independent journalistic article in Wired magazine. Not only would it would read like a paid advertisement, but critics would begin wondering if Wired was in business to promote Microsoft products. The Microsoft example is of course fictional, but something like it happened recently when Karl Giberson (executive vice president of the BioLogos Foundation) interviewed Francis Collins (the president of BioLogos), and then published the interview in Christianity Today‘s Read More ›

This is the final installment of three posts responding to Stephen Barr. The first post can be found here, and the second post can be found here.

The Collins/Barr Approach: A God Who Misleads?

Stephen Barr identifies himself with the position of Francis Collins who argues that although evolution looks like “a random and undirected process,” it nevertheless could have been guided by God. “Evolution could appear to us to be driven by chance, but from God’s perspective the outcome would be entirely specified.” [Collins, The Language of God, p. 205.]

Barr takes me to task for highlighting Collins’ use of the word “could” because I implied that “Collins is not sure whether God did in fact know beforehand. Anyone who has read Collins’s book, however, should realize that Collins absolutely and unequivocally holds the belief that God knows all events from all eternity.” Really? In the same book that Collins says that God “could” have known and specified the outcome of evolution, he also claims that much of our DNA is basically junk that certainly was not the product of God’s intentional design. In particular, Collins goes on at length about “Ancient Repetitive Elements,” which he disparages as “genetic flotsam and jetsam” that make up “roughly 45 percent of the human genome.” Collins concedes that “some might argue that these are actually functional elements placed there by the Creator for a good reason, and our discounting of them as ‘junk DNA’ just betrays our current level of ignorance. And indeed, some small fraction of them may play important regulatory roles. But certain examples severely strain the credulity of that explanation.” [Language of God, p. 156, emphasis added] In other words, Collins rejects as credulous the idea that such DNA were planned by God for a reason. So much for the idea that God knew and specified the outcomes of evolution from eternity.