Francis Collins does Teshuva

In Genesis and Genes, I mentioned Francis Collins a few times. Recently, important remarks of his have come to light, which I’d like to discuss. Below, I quote the relevant section from Genesis and Genes and then discuss Collins’ statement. In this section of Genesis and Genes, I conduct a conversation with Jonathan, a fictitious character who embodies many individuals with whom I have spoken and corresponded over the past few years. For the purpose of this post, I have omitted the endnotes that appear in the book.

 

YB: Because he [Francis Collins] has written on the subject of junk DNA.

Jonathan: Junk DNA? I thought the T-shirt said, I know I’m important because God don’t make no junk.

YB: Good point, but not a sentiment shared by evolutionary biologists.

Jonathan: So what is junk DNA?

YB: Here’s the basic story. In the 1970s geneticists discovered that only a tiny percentage of our DNA codes for proteins.

Jonathan: What does “code for proteins” mean?

YB: It means “contains the instructions for manufacturing proteins.” Some DNA contains the encoded information necessary to make the crucial workhorses of the cell – proteins. But most DNA does not have that function.

Jonathan: OK. So what’s the story?

YB: The term junk DNA appears to have been coined by the biologist Susumu Ohno of the City of Hope National Medical Center in Los Angeles. In 1972, he published an article wondering why there is “so much ‘junk DNA’ in our genome.” In 1980, two papers appeared back-to-back in the journal Nature. Both argued that much genetic material has no function, and the second article explicitly argued that much DNA in higher organisms is little better than junk. Two biologists wrote to Nature to express disagreement. Thomas Cavalier-Smith considered it “premature” to dismiss non-protein-coding DNA as junk, and Gabriel Dover wrote that “we should not abandon all hope of arriving at an understanding of the manner in which some [DNA] sequences might affect the biology of organisms in completely novel and somewhat unconventional ways.” But the majority of biologists accepted the notion of junk DNA. The suggestion was that most of our DNA is functionless junk that accumulated in our cells as a by-product of merciless evolutionary processes. This became the dominant view among biologists, and the term junk DNA pervaded the literature – both professional and popular. But that view has turned out to be spectacularly wrong. Since 1990 – and especially after completion of the Human Genome Project in 2003 – many hundreds of articles have appeared in the scientific literature documenting the various functions of non-coding DNA, and more are being published almost every week. Far from consisting mainly of junk, our genome is increasingly revealing itself to be a multidimensional, integrated system in which “junk” DNA performs a wide variety of functions.

Jonathan: Sounds familiar by now.

YB: Yes. We’ve seen how, so often, the glow of evolutionary dawn doesn’t last until noon.

Jonathan: How was junk DNA used to argue for evolution?

YB: Initially, the functions of these stretches of DNA were not understood. It seemed as if they did nothing. So many biologists said that junk DNA just accumulates in the genome like, well, like junk in a junkyard. In retrospect, it’s rather like cavemen coming upon an IPod and declaring that it’s only moderately useful for throwing at peaches high up in the trees.

Jonathan: Can you give me an example of a typical statement along these lines?

YB: I could give dozens of examples. Here is one, from the evolution-populariser Richard Dawkins. It’s a paragraph from an article he wrote in the journal The Skeptic in 1998:

Genomes are littered with nonfunctional pseudogenes, faulty duplicates of functional genes that do nothing, while their functional cousins (the word doesn’t even need scare quotes) get on with their business in a different part of the same genome. And there’s lots more DNA that doesn’t even deserve the name pseudogene. It, too, is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, “tandem repeats”, and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself.

Dawkins, like numerous evolution junkies, believes that there is no explanation for this apparently-superfluous material in our genomes, other than the admission that they are the residue of an evolutionary process:

Once again, creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.

In one of his most recent books (published in 2009), The Greatest Show on Earth, Dawkins observed that “the greater part… of the genome might as well not be there, for all the difference it makes,” and that this fact is “useful for… embarrassing creationists.” Similarly, in Why Evolution Is True (also published in 2009), Jerry Coyne of the University of Chicago states that it is a “prediction” of neo-Darwinian theory that we will find the genome littered with useless “vestigial genes”. This sort of claim permeated the literature for decades.

Jonathan: But why is it relevant to Collins?

YB: Because atheists like Dawkins and Coyne were not the only people to make the point. Believers like Collins also used the junk DNA argument to argue for evolution.

Jonathan: Really?

YB: Yes. Collins has written a number of best-selling books promoting theistic evolution. In 2006, he published The Language of God. He wrote that

Mammalian genomes are littered with such AREs [ancient repetitive elements] with roughly 45 percent of the human genome made up of such genetic flotsam and jetsam.

Notice that Collins makes a spectacular claim. He says that almost half of the human genome is flotsam and jetsam. And this convinced Collins of the reality of evolution, because he, like Dawkins, could not fathom why God would insert so much of this useless material into the human genome:

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.

 

Jonathan: It seems like a decent argument.

YB: It’s a terrible argument, for a number of reasons, but I’ll focus only on one.

Jonathan: What’s that?

YB: Things changed. We know now that many features of the human genome that were thought to be junk in fact have important functions. It’s fascinating to track how, over the years, the terminology changed.

Jonathan: What do you mean?

YB: In older publications, it was always junk DNA, or, as Collins puts it, flotsam and jetsam, or some other pejorative sobriquet.  As perceptions changed and biologists realised that they might ultimately be humiliated when junk DNA was discovered to be anything but, they changed tack. If you track the evolution of the terminology – excuse the pun – you will see how the prevalence of junk DNA diminishes in favour of non-coding DNA. This is in recognition of the fact that these regions of DNA, even though they do not code for proteins, nevertheless have other, very important, functions.

Jonathan: Has Collins seen the light?

YB: Yes and no.

Jonathan: What do you mean?

YB: Well, Collins published another book, The Language of Life, in 2010, in which he takes a far more cautious stance vis-á-vis DNA. Gone are the strident declarations about how junk DNA constitutes incontrovertible proof of universal common descent.

Jonathan: What does he say?

YB: Read for yourself:

The discoveries of the past decade, little known to most of the public, have completely overturned much of what used to be taught in high school biology. If you thought the DNA molecule comprised thousands of genes but far more “junk DNA”, think again. [Emphasis added].

Jonathan: Mm…

YB: Mm indeed. Furthermore, Collins now has the chutzpah to scold others who dismissively refer to long stretches of non-coding DNA as gene deserts:

It appears there are also long “spacer” segments of DNA that lie between genes and that don’t code for protein. In some instances, these regions extend across hundreds of thousands or even millions of base pairs, in which case they are referred to rather dismissively as “gene deserts.” These regions are not just filler, however. They contain many of the signals that are needed to instruct a nearby gene about whether it should be on or off at a given developmental time in a given tissue. Furthermore, we are learning that there may be thousands of genes hanging out in these so-called deserts that don’t code for protein at all. They are copied into RNA, but those RNA molecules are never translated – instead, they serve some other important functions.

Other than die-hard materialists such as Richard Dawkins, plenty of scientists are coming to see that the junk DNA paradigm must be ditched. For example, Richard Sternberg and James Shapiro, both of whom are prominent biologists, write that one day, we will think of what used to be called junk DNA as a critical component of truly expert cellular control regimes. In the end, it is clear that Collins’ 2010 book is a significant retreat on the claim that junk DNA dominates our genome. He explicitly admits that non-coding DNA has other functions:

It turns out that only about 1.5 percent of the human genome is involved in coding for protein. But that doesn’t mean the rest is “junk DNA.” A number of exciting new discoveries about the human genome should remind us not to become complacent in our understanding of this marvellous instruction book. For instance, it has recently become clear that there is a whole family of RNA molecules that do not code for protein. These so-called non-coding RNAs are capable of carrying out a host of important functions, including modifying the efficiency by which other RNAs are translated. In addition, our understanding of how genes are regulated is undergoing dramatic revision, as the signals embedded in the DNA molecule and the proteins that bind to them are rapidly being elucidated. The complexity of this network of regulatory information is truly mind-blowing, and has given rise to a whole new branch of biomedical research, sometimes referred to as “systems biology.” [Emphasis added].

 

Jonathan: But still, doesn’t Collins deserve credit for absorbing the new evidence and adjusting his view accordingly?

YB: He deserves very little credit. First of all, in his later book, The Language of Life, he doesn’t tell his readers about what he wrote just four years earlier, in The Language of God. They would have no inkling that the solemn words of rebuke for those who speak of “gene deserts” were written by someone who himself completely botched the junk DNA argument. Secondly, he goes on to argue for universal common descent on the basis of – wait for it – junk DNA.

Jonathan: No!

YB: Yes. His latest book is The Language of Science and Faith, co-written with Karl Giberson and published in 2011. Collins and Giberson look at the vitamin C GULO “pseudogene” found in humans and other primates (as well as some non-primate species), and they contend that it is “not remotely plausible” that “God inserted a piece of broken DNA into our genomes.” They conclude that this “has established conclusively that the data fits a model of evolution from a common ancestor”. So even though Collins himself was forced to retreat from his early tirades about junk DNA by the accumulating evidence that that genetic material actually performs highly-sophisticated tasks that were earlier missed by biologists, he continues to belt out the broken record message of “broken DNA”. This is bound to rebound on Collins. There is a cascade of research these days that’s uncovering more and more crucial functions for genetic material previously dismissed as “junk”. Collins is painting himself into a corner by citing one example – what he considers to be a broken gene – even though his view from just a few years back (that about half the human genome is junk DNA) has proved to be spectacularly wrong.

Jonathan: Can you give me an example of research that is finding surprising functions for non-coding DNA?

YB: Sure. We won’t go into the technicalities, but here is the synopsis of a recent research article from the journal RNA. This is a run-of-the-mill scientific journal whose editors, contributors and readers overwhelmingly subscribe to the evolutionary scenario:

Pseudogenes have long been labeled as “junk” DNA, failed copies of genes that arise during the evolution of genomes. However, recent results are challenging this moniker; indeed, some pseudogenes appear to harbor the potential to regulate their protein-coding cousins. Far from being silent relics, many pseudogenes are transcribed into RNA, some exhibiting a tissue-specific pattern of activation… In another remarkable discovery, it has been shown that pseudogenes are capable of regulating tumor suppressors and oncogenes… The finding that pseudogenes are often deregulated during cancer progression warrants further investigation into the true extent of pseudogene function. In this review, we describe the ways in which pseudogenes exert their effect on coding genes and explore the role of pseudogenes in the increasingly complex web of noncoding RNA that contributes to normal cellular regulation.

 

Jonathan: This is really shocking! If so many functions have been discovered for sections of the genome that were previously not understood, how can anyone continue to argue for universal common descent on the basis of non-coding DNA?!

YB: I agree. When you, as a non-scientist, are trying to form an opinion about evolution, don’t be intimidated by the fact that opinions are expressed by acknowledged experts in their fields. As we have seen in this book, the logic presented is often shoddy and the integrity questionable. [END of QUOTATION]

Now, however, comes news of Collins conceding defeat on this front. Here is what Marvin Olasky writes [https://world.wng.org/2016/06/admission_of_function]:

July 11 is the 10th anniversary of the publication of theistic evolutionist Francis Collins’ The Language of God, which became a New York Times bestseller largely because of Collins’ reputation as director of the National Human Genome Research Institute. That book, in turn, helped Collins gain new fans and a nomination from Barack Obama to head the National Institutes of Health.

Confirmed by the Senate, Collins has been in that position ever since, and I’m glad he’s there. But his book, and a talk about it I heard Collins give in New York, also displayed what Collins now admits was arrogance. Collins claimed on page 136 that huge chunks of our genome are “littered” with ancient repetitive elements (AREs), so that “roughly 45 percent of the human genome [is] made up of such genetic flotsam and jetsam.” In his talk he claimed the existence of “junk DNA” was proof that man and mice had a common ancestor, because God would not have created man with useless genes.

Last year, though, speaking at the J.P. Morgan Healthcare Conference in San Francisco, Collins threw in the towel: “In terms of junk DNA, we don’t use that term anymore because I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome, as if we knew enough to say it wasn’t functional. … Most of the genome that we used to think was there for spacer turns out to be doing stuff.” [END of QUOTATION].

There are a number of lessons to be drawn from this:

  1. Collins deserves at least some credit for conceding defeat and, more importantly, for ascribing his past mistakes to “hubris”. I pointed out again and again in Genesis and Genes that science is done by people. Laymen often stand in awe of scientists, imagining them to be super-heroes who are totally objective, operating without any conditioning, biases or worldviews. The reality is, alas, completely different. Scientists are ordinary individuals (albeit often highly-intelligent and possessing an aptitude for mathematics) who receive no training other than in their narrow, technical fields. The vast majority of scientists have never taken a course in the psychology of research. They know as little as the man in the street does about the history and philosophy of science, and are therefore often pathetically unaware of their own weaknesses as individuals and of historical failures in their respective fields. The admission by Collins that he has retracted from his previous position, and that he was blinded by hubris, is as refreshing as it is rare. One can hardly imagine someone like, say, Richard Dawkins making the same admission.

  1. SCIENCE CAN BE WRONG. It is astonishing how difficult it is to get ordinary members of the public to appreciate this elementary fact of the history of science. Don’t confuse Nature with Science. Nature is what it is, and Science is the attempt by humans to understand Nature. Like all human endeavours, Science is fallible.

  1. Decades of fruitful research were lost because students were taught the dogma of junk DNA and thus discouraged from investigating the properties and functions of these sections of the genome.

  1. Don’t be fooled by peremptory pronouncements. Over the past half-century, scientists insisted that we know that most of the human genome is junk. It is common in these situations for dissenters to be ridiculed and frozen out of research grants. Especially when it comes to fields that have bearing on profound philosophical questions, one should treat absolute statements by scientists with a sack of salt. There is much more that we don’t know about nature than we do
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