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Junk DNA RoundUp (and Rebuttal): How Neo-Darwinism Creates Junk-Hypotheses, Then Resists Their Demise

Sometimes after explaining how the now-defunct junk-DNA mindset was encouraged and fostered by neo-Darwinian evolution, evolutionists respond by asserting that nonetheless some individuals from their camp explored function for junk-DNA. This, they claim, absolves their neo-Darwinian camp from any charges of science-stopping, and shows that the neo-Darwinian paradigm did not hinder research into junk-DNA. But if a 2003 article in Science is any indication, then it seems that the neo-Darwinian paradigm did indeed impose a taboo on research into function for junk-DNA. As the article stated:

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."

(Wojciech Makalowski, "Not Junk After All," Science, Vol. 300(5623):1246-1247 (May 23, 2003).)

How much clearer could it be? This 2003 article acknowledges that "the term 'junk DNA' for many years repelled mainstream researchers from studying noncoding DNA" and further notes that those biologists who did study function for "junk-DNA" faced "the risk of being ridiculed." (emphases added) In science, where reputation is so important, it's much easier to shift one's research focus to where the money, the momentum, and the praise flow freely -- not where research is "repelled" and "ridiculed."

In fact, even some of the evolutionary biologists who risked "ridicule" to seek function for junk-DNA have lamented how their paradigm has stifled research into junk-DNA. Also in 2003, John Mattick, an evolutionist biologist who is a standout because of his research seeking function for junk-DNA, stated in Scientific American the following striking comment:

"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."

(John S. Mattick quoted in W. Wayt Gibbs, "The Unseen Genome, Gems Among the Junk," Scientific American (November, 2003).)

The largely refuted junk-DNA mindset was born and bred out of the neo-Darwinian paradigm, and if some rogue Darwinian (and non-Darwinian) biologists had the courage to study function for junk-DNA that's great, but it was not because of the neo-Darwinian paradigm but rather in spite of it.

A Prediction about Future Junk Hypotheses
The central dogma, as it's commonly called, of molecular biology entails the fact that the information in DNA is transcribed into RNA, which is then translated to create proteins. In March I recounted how once function was suggested, partly through the discovery of large-scale transcription, for non-coding DNA, evolutionists "pushed the 'junk' back to RNA." As I noted, evolutionists have "effectively argued, 'Sure, we know that most of the genome is being transcribed into RNA, but that doesn't mean that the RNAs have function. Much of the transcriptome might in fact be junk.'" Because evolutionists love the "junk" argument, I predict that now that there is evidence of function for RNA, we're going to see evolutionists push the "junk" back another level and postulate much of the proteome is junk: "junk proteins."

In fact, when I came up with this idea I suspected that perhaps I wasn't the first person to think of it. So I searched for "junk protein" and immediately found that yes, some evolutionists have already proposed this concept. Here's an abstract from one such paper:

It has recently been shown that many proteins are unfolded in their functional state. In addition, a large number of stretches of protein sequences are predicted to be unfolded. It has been argued that the high frequency of occurrence of these predicted unfolded sequences indicates that the majority of these sequences must also be functional. These sequences tend to be of low complexity. It is well established that certain types of low-complexity sequences are genetically unstable, and are prone to expand in the genome. It is possible, therefore, that in addition to these well-characterised functional unfolded proteins, there are a large number of unfolded proteins that are non-functional. Analogous to 'junk DNA' these protein sequences may arise due to physical characteristics of DNA. Their high frequency may reflect, therefore, the high probability of expansion in the genome. Such 'junk proteins' would not be advantageous, and may be mildly deleterious to the cell.

(Simon C Lovell, "Are non-functional, unfolded proteins ('junk proteins') common in the genome?," FEBS Letters, Vol. 554(3):237-239 (November 20, 2003).)

Since the author admits that unfolded proteins can be "unfolded in their functional state," and that their high prevalence is unexpected if they are truly non-functional "junk," it seems that this "junk protein" hypothesis has a lot going against it from the outset. But if history is our guide, then contrary evidence has done little to slow junk-biological molecule hypotheses among our Darwinian friends before.

Discovery Institute fellow Cornelius G. Hunter has also noted the Darwinian love-affair with "junk" and how this will lead to hypotheses about "junk proteins." At his new blog, Darwin's God (Darwins-God.blogspot.com), Hunter recently wrote a post titled "Now It's Junk Protein," where he writes that the assumption of junk "pervades evolutionary thinking, and shows up again and again to be wrong. This week, instead of the usual junk-DNA-turned-marvel, it is junk protein."

So I'll make a little prediction: Based upon current trends, the hypothesis that many proteins are in general always junk is going to go the same way as junk-DNA and junk-RNA: into the junk-pile.

An Interlude: A Quick Rebuttal to the YouTube "challenge's" Response to me
A recent YouTube response to my response to the YouTube "challenge" video makes false charges that I misquoted Francis Collins. To set the record straight, I'd like to show what Dr. Collins wrote, what I said he said, and how there was no misrepresentation whatsoever of Dr. Collins on my part. I include this here because it involves a relevant discussion of "junk" DNA and how the data is continually refuting that viewpoint.

In his book The Language of God, Francis Collins wrote:

"This evidence alone, of course, does not prove a common ancestor; from a creationist perspective, such similarities could simply demonstrate that God used successful design principles over and over again." (The Language of God, pg. 134)
Collins' statement seems pretty clear-cut: though he frames his argument in theological terms, it's clear that he believes that shared functional biological similarity does not demonstrate common descent over common design. Thus, in my response to the YouTube challenge, I quoted Collins as follows, in terms that fit with intelligent design's scientific approach:
Collins writes in The Language of God that genetic similarity "alone does not, of course, prove a common ancestor" because a designer could have "used successful design principles over and over again."

I also stated: "the presence of shared functionally similar sequences between different organisms does not make a good test of discriminating between design and descent. Even leading evolutionists like Francis Collins recognize this point." (emphasis added) The key word there is "functionally similar" -- I'm talking about Collins' view with respect shared functional sequences here, not his views regarding shared non-functional or "junk" DNA. And Collins plainly stated that such shared functional similarity (i.e. "successful design principles" that are "used over and over again") does not refute common design in favor of common descent. That's pretty much all I said about Collins in my post.

So let's again make clear the very limited point on which I was citing Collins: I was only citing him to back my argument that shared functional biological similarity is not evidence of common descent instead of common design. This contravened a claim made in the YouTube challenge video. That's all I was citing Collins to say. In particular, I never claimed Collins argued the genome was intelligently designed, and as you can see, I even noted that Collins is an "evolutionist," and thus it should have been pretty clear that he rejects biological design.

So what's the problem? The video response to my blog post gets quite upset because Collins also says in that same paragraph I quoted above: "The study of genomes leads inexorably to the conclusion that we humans share a common ancestor with other living things," and "As we shall see, however, and as was foreshadowed by the discussion of 'silent' mutations in protein-coding gene regions, the detailed study of genomes has rendered that interpretation virtually untenable--not only about other living things, but also about ourselves." The video implies that because Collins clearly believes the genome was not intelligently designed, I somehow misrepresented his views.

Did I misquote or misrepresent Collins? Again, I never said that Collins didn't believe in common descent, and as I said, I noted that he's an "evolutionist," so it should have been pretty clear he rejects biological design. Moreover, in the quote from Collins above on page 134, he clearly thinks that shared functional similarity (i.e. "successful design principles" that are "used ... over and over again") does not necessarily demonstrate common descent over common design. Since that's all I said about Collins, again I fail to see how there was any misrepresentation of his views.

So why does Collins think the genome was not designed? It's not because of shared functional similarity, but rather he argues against design based upon what he thinks is shared functionless similarity, or functionally unnecessary similarity, particularly shared junk-DNA. Thus if you read on past page 134 in Collins' book, he makes it clear that he thinks the purported shared junk-DNA -- i.e. shared functionless genetic sequences are what demonstrate common ancestry over common design. He calls such junk DNA sequences "genetic flotsam and jetsam" (p. 136) and holds that it's only when we are dealing with shared sequences that are non-functional (i.e. junk) that we uncover a strong argument for common descent:

Even more compelling evidence for a common ancestor comes from the study of what are known as ancient repetitive elements (AREs). ... Mammalian genomes are littered with such AREs, with roughly 45 percent of the human genome made up of such genetic flotsam and jetsam. ... There are AREs throughout the human and mouse genomes that were truncated when they landed, removing any possibility of their functioning. ... Unless one is willing to take the position that God has placed these decapitated AREs in these precise positions to confuse and mislead us, the conclusion of a common ancestor for humans and mice is virtually inescapable. (The Language of God, pp. 135, 136-137)
Collins also makes it clear that if these sequences DID INDEED HAVE function, that would NOT refute their design:
Of course, some might argue that these are actually functional elements placed there by a Creator for a good reason, and our discounting them as 'junk DNA' just betrays our current level of ignorance. (The Language of God, p. 136)
Again, we see that Collins clearly feels if DNA is "actually functional" then one could argue it was "placed there by a Creator for a good reason." Thus he argues against genomic design on the grounds that these are shared features that have no function. Of course Collins frames his argument in theological terms, but clearly he admits that shared functional similarity is not a good argument for common descent over common design. This confirms that I did not misrepresent Collins' views on the limited point for which I was quoting him.

In sum, I never said Collins felt the genome was intelligently designed. All I said was that that he admits that shared functional similarity does not refute design. The original YouTube "challenge" video feels different than Collins because it argued that shared functional similarity does refute design and implies common descent instead of design. Thus, the video claimed that a gene is only designed when it has no known homologues (i.e. it is completely unique). According to the "challenge" video, if two functional proteins are similar, they were not designed, and when we find homology for a functional protein, that somehow refutes intelligent design. I correctly quoted Collins as part of my argument that the video was simply incorrect on this point.

The context of our dialogue over the YouTube video was regarding shared functional similarity (the video discussed protein homology), and not shared functionless similarity. Collins rejects design of the genome for reasons that are different from what we were talking about in the dialogue over the YouTube video, for he rejects design not due to shared functional similarity, but due to shared functionless similarity.

The other video is unwittingly misquoting Collins by implying that the Collins quote that I provided above on page 134 is regarding shared junk-DNA, when it isn't; it's about shared functional DNA. Indeed, I agree with Collins that shared functional similarity is not evidence for descent over design, and that shared functionless similarity can point to common descent over common design. I suggested Collins believed otherwise in my piece.

Regardless of the YouTube video's misguided accusations, there is one major thing wrong with Collins' argument: As discussed below, while Collins is right that shared non-functional "junk"-DNA can indicate common ancestry, he's wrong to presume this repetitive DNA is necessarily non-functional "junk."

A Reality Check for Francis Collins' Argument: Discovery of Function for Repetitive DNA
We have now seen how the eminent evolutionist biologist Francis Collins relies heavily upon the alleged lack of function of repetitive DNA as an argument for common descent. Yet papers are coming out all the time that report function for so-called "junk" repetitive DNA. In "A Reply to Francis Collins's Darwinian Arguments for Common Ancestry of Apes and Humans," Logan Gage and I recount the finding of a variety of functions for repetitive DNA. Below is a summary of two articles from the past few weeks reporting studies that found function or so-called "junk" repetitive DNA:

  • A May 30 news article on Science Daily observes that "tandem repeats" are now thought to have function, even though we used to think they were "useless trash":
    "Scientists used to believe that most of the DNA outside of genes, the so-called non-coding DNA, is useless trash that has sneaked into our genome and refuses to leave. One commonly known example of such 'junk DNA' are the so-called tandem repeats, short stretches of DNA that are repeated head-to-tail. "At first sight, it may seem unlikely that this stutter-DNA has any biological function," says Marcelo Vinces, one of the lead authors on the paper. "On the other hand, it seems hard to believe that nature would foster such a wasteful system."
    Of course we know that neo-Darwinism did not help solve this problem. So what's the function for this repetitive DNA? The article explains:
    The international team of scientists found that stretches of tandem repeats influence the activity of neighboring genes. The repeats determine how tightly the local DNA is wrapped around specific proteins called 'nucleosomes', and this packaging structure dictates to what extent genes can be activated. Interestingly, tandem repeats are very unstable -- the number of repeats changes frequently when the DNA is copied. These changes affect the local DNA packaging, which in turn alters gene activity. In this way, unstable junk DNA allows fast shifts in gene activity, which may allow organisms to tune the activity of genes to match changing environments -- a vital principle for survival in the endless evolutionary race.
    Take the evolutionary narrative gloss away, and we see that junk-DNA helps determine when and where genes are activated.

  • Another recent Science Daily article from May 21 titled, "'Junk' DNA Has Important Role, Researchers Find," found a function or transposons, which of course are another common type of repetitive DNA:
    [R]esearchers from Princeton University and Indiana University who have been studying the genome of a pond organism have found that junk DNA may not be so junky after all. They have discovered that DNA sequences from regions of what had been viewed as the "dispensable genome" are actually performing functions that are central for the organism. They have concluded that the genes spur an almost acrobatic rearrangement of the entire genome that is necessary for the organism to grow.

    It all happens very quickly. Genes called transposons in the single-celled pond-dwelling organism Oxytricha produce cell proteins known as transposases. During development, the transposons appear to first influence hundreds of thousands of DNA pieces to regroup. Then, when no longer needed, the organism cleverly erases the transposases from its genetic material, paring its genome to a slim 5 percent of its original load.

    The article concluded that gene-regulation function of transposons is showing that "selfish DNA" may be in fact beneficial to the organism, and not useless junk:
    The term "junk DNA" was originally coined to refer to a region of DNA that contained no genetic information. Scientists are beginning to find, however, that much of this so-called junk plays important roles in the regulation of gene activity. No one yet knows how extensive that role may be.

    Instead, scientists sometimes refer to these regions as "selfish DNA" if they make no specific contribution to the reproductive success of the host organism. Like a computer virus that copies itself ad nauseum, selfish DNA replicates and passes from parent to offspring for the sole benefit of the DNA itself. The present study suggests that some selfish DNA transposons can instead confer an important role to their hosts, thereby establishing themselves as long-term residents of the genome.

    Transposons and other repetitive elements have long been cited by evolutionists as evidence of junk DNA that has no function. As noted, Francis Collins made heavy use of repetitive DNA in his argument for common descent. Given the trend of discovering function for so-called junk DNA, including repetitive DNA, should we trust this argument? How much more quickly would these discoveries have been made if neo-Darwinism were not the reigning paradigm guiding biological research? I leave you to decide these questions for yourself.