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Post-ENCODE Posturing: Rewriting History Won’t Erase Bad Evolutionary Predictions

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Editor’s note: This is Part 4 of a 6-part series on ENCODE that Casey Luskin has been publishing this year in Salvo Magazine. Parts 1, 2, 3, 4, 5, and 6 have already been published. The prelude can be found here.

Even in the face of the ENCODE consortium’s compelling experimental results, many evolutionists still adamantly maintain that the vast majority of the human genome is junk. Some Darwin-defenders have tried hedging their bets by embracing ENCODE’s research. This group seeks to revise history by claiming that evolutionary biology expected all along to find what ENCODE found: mass functionality in our genome.

Others are more forthright. They concede that evolutionary biology was mistaken about junk DNA, and they admit that new models are needed to accommodate ENCODE’s data. In other words, they accept ENCODE’s conclusions, but admit they can’t explain them in evolutionary terms.

In this series, after introducing ENCODE, I have addressed various objections from evolutionists who reject the ENCODE results. In this and two subsequent articles, I will assess two more responses from evolutionists — those who accept ENCODE, but now struggle to comprehend a junkless human genome in the post-ENCODE world.

Junky Predictions
Before going on, it’s important to document what evolutionists were saying prior to 2012 when ENCODE’s breakthrough papers showed that the vast majority of our genome is functional.

In an April 1980 issue, Nature published papers by influential biologists arguing that evolution predicts our genomes should be full of junk DNA. The first article, “Selfish Genes, the Phenotype Paradigm and Genome Evolution,” by W. Ford Doolittle and Carmen Sapienza, maintained that “Natural selection operating within genomes will inevitably result in the appearance of DNAs with no phenotypic expression whose only ‘function’ is survival within genomes.”1

A second paper, “Selfish DNA: the ultimate parasite,” was by Francis Crick, who won the Nobel Prize for determining the structure of DNA, and the eminent origin-of-life theorist Leslie Orgel. They concluded, “Much DNA in higher organisms is little better than junk,” and “it would be folly in such cases to hunt obsessively for” its function.2

Fifteen years later, the junk-DNA paradigm was alive and well, as Scientific American reported:

These regions have traditionally been regarded as useless accumulations of material from millions of years of evolution … In humans, about 97 percent of the genome is junk.3

I could give numerous other examples, but will allow just one more to suffice. In 2007, Columbia University philosopher of science Philip Kitcher published his Oxford University Press book Living with Darwin. Citing the mass of “genomic junk” that “litters the genome,” Kitcher announced, “The most striking feature of the genomic analyses we now have is how much apparently nonfunctional DNA there is.”4 In his view, “From the Darwinian perspective all this is explicable,” but “if you were designing the genomes of organisms, you would certainly not fill them up with junk.”5

Just Kidding — We Anticipated Function!
When ENCODE’s findings were published, many evolutionists reacted harshly to the conclusion that virtually our entire genome is functional. Others, however, realized that it would be sage advice to switch their bets, or simply place new ones alongside the old.

For example, a 2014 paper in Biology & Philosophy initially claimed that “junk DNA seems at odds with the view that the genome is … the work of an intelligent force or designer,” but then argued that a junk-free genome “is compatible with evolution by natural selection,” because “we could expect natural selection to evolve lean genomes.”6 According to this posturing, whether our genome is full of junk or devoid of it, evolution wins.

But first prize for betting on both horses goes to Richard Dawkins. In his 1976 book The Selfish Gene, Dawkins famously argued that “a large fraction”7 of our genomes is useless parasitic DNA, and that Darwinian evolution explains why:

The true “purpose” of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.8

Again in 2004 he railed against “creationists” on the basis of our junk-laden genomes:

[C]reationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.9

As recently as 2009, Dawkins adopted the incredible position that “the greater part (95 per cent in the case of humans) of the genome might as well not be there, for all the difference it makes.”10

In September 2012, however, Dawkins changed his tune dramatically. Just one week after ENCODE’s results were published, in a debate against Britain’s chief rabbi, Dawkins declared that ENCODE’s results are precisely what “Darwinism” (in Dawkins’s own words) predicts:

There are some creationists who are jumping on [ENCODE] because they think it’s awkward for Darwinism. Quite the contrary, of course, it is exactly what a Darwinist would hope for — to find usefulness in the living world.11

He went on to say, “[W]e thought that only a minority of the genome was doing something, namely that minority which actually codes for protein. And now we find that actually the majority of it is doing something.” Under Dawkins’s newly reformed view, “the rest [of the genome] which had previously been written off as junk” is now understood as “the program” that’s “calling into action the protein coding genes.”12

It’s as if Dawkins’s decades of arguing that our genome is full of junk never happened.

History Is Not Easily Rewritten
While some evolutionists try to erase their history of failed predictions, others seek to mitigate their embarrassment by highlighting the occasional suggestion, mined out of the annals of scientific literature, that some rare bits of the junk might end up being functional. For example, University of Guelph evolutionary biologist T. Ryan Gregory is an ENCODE-critic,13 but he has dug up a nice little collection of quotes from evolutionary scientists who purportedly predicted our finding some function for non-coding DNA.14 Presumably he did this just in case ENCODE turned out to be right.

Many of Gregory’s quotes don’t really support his case. They simply show biologists finding experimental evidence of function for noncoding “junk” — just like ENCODE did — not predicting it before the fact on the basis of a scientific model (as intelligent design proponents did). To be sure, many of the biologists who made these discoveries are evolutionists, but they made their discoveries by spending time in the lab studying how the cell works, not on the basis of evolutionary theory.

Gregory, however, makes a stronger argument, as he co-wrote in a scientific paper:

[I]t is simply not true that potential functions for noncoding DNA were ignored until recently. In fact, various early commenters considered the notion that large swaths of the genome were nonfunctional to be “repugnant”, and possible functions were discussed each time a new type of nonprotein-coding sequence was identified…15

The quote about “repugnant” non-functionality comes from a paper that revealed much of our genome is repetitive DNA16 — long cited as “junk.”17 It’s true that those particular authors didn’t think the repetitive DNA was “trivial,” but their paper was published in 1968, before the term “junk” DNA was even coined.18 Indeed, soon thereafter, this paper on repetitive DNA was being cited by another paper in Science that has proven foundational for evolutionary biology in establishing the pro-junk viewpoint. That latter paper (published in 1969) offered the astounding suggestion that “99 percent of mammalian DNA is not true genetic material”19 — i.e., it is junk. In 1972, Susumu Ohno, the Japanese evolutionary biologist who coined the term “junk DNA,” made a similarly striking prediction: “At least 90% of the mammalian genomic DNA appears to represent ‘nonsense’ DNA base sequence of various kinds.”20

Thus, while it’s true that some scientists have proposed various functions for noncoding DNA, evolutionary theorists by and large predicted that the vast majority of the genome would turn out to be functionless.

The typical attitude is canonized in various editions of Douglas Futuyma’s evolutionary biology textbooks, published from the 1970s into the 2000s. His first edition, written just a few years after the concept of junk DNA was conceived, anticipated that repetitive DNA would have no function:

[O]ther features may well be neutral, having no function whatever. The most extreme, still hypothetical, example is that of the highly repetitive short sequences of DNA that may never be transcribed into RNA. These may have a function … but I would not be surprised if they did not.21

Futuyma’s second edition, published in 1986, likewise claimed our genome is full of transposable, repetitive DNA sequences which “do not exist because they serve the organism” but rather are “ignorant DNA” or “selfish DNA … and may be viewed as parasites.”22 The third edition, published in 1998, again stated that these repetitive elements generally “do not provide any adaptive service to the organism” because they are “selfish DNA” or “parasites, much like viruses, of the genome in which they reside.”23 Futuyma’s still heavily promoted this viewpoint in his 2005 textbook, where he wrote:

Because natural selection consists only of differential reproductive success, it results in ‘selfish genes’ and genotypes, some of which have results that are inexplicable by intelligent design. We have seen that genomes are brimming with sequences such as transposable elements that increase their own numbers without benefitting the organism.24

As late as 2009, Futuyma’s textbooks still claimed “In eukaryotes, the vast majority of DNA has no known function, even though as much as 80 percent may be transcribed.”25 While Futuyma often includes caveats allowing that some small portion of this DNA might turn out to be functional, his view is typical of the evolutionary community: it’s mostly junk.

Biologist Richard Sternberg offers a forceful reply to Gregory’s style of argument:

As someone who has studied the concept of “junk DNA” for over twenty years, I am dismayed by … a half-truth and a false fact 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.”26

Sternberg acknowledges that a few evolutionary scientists speculated that some junk might accidentally acquire a useful function. Even Crick and Orgel suggested that “occasionally” this might happen, but they still predicted “most sets of repeated sequences will never be of use.”27 Their view — common among evolutionary theorists — stands in stark contrast to ENCODE’s findings. Sternberg explains:

[T]he view expounded by Orgel and Crick …, and Doolittle and Sapienza … has been considered by many cellular and molecular biologists to be the correct explanation for much of genomic DNA until very recently. So the oft-read claim on the web that the term “junk DNA” never implied developmentally “non-functional DNA” is one that is made either out of ignorance or disingenuousness.28

Indeed, it’s difficult to accept Gregory’s claims that evolutionary biologists by-and-large anticipated function for non-coding DNA when he himself is a prime example of an evolutionary scientist who ardently advocates the view that our genome is overwhelmingly junky. In a March 2015 article in the New York Times, “Is Most of Our DNA Garbage?,” science journalist Carl Zimmer praised Gregory’s research and noted that he “champions an idea first developed in the 1970s but still startling today: that the size of an animal’s or plant’s genome has essentially no relationship to its complexity, because a vast majority of its DNA is — to put it bluntly — junk.” According to Zimmer, “Where some look at all those billions of bases and see a finely tuned machine, others, like Gregory, see a disorganized, glorious mess.”

Zimmer goes on to explain that Gregory not only thinks that there’s much junk DNA in our cells, but also lots of junk RNA:

But to Gregory and others, [the view that most noncoding RNA is crucial] is a blinkered optimism worthy of Dr. Pangloss. They, by contrast, are deeply pessimistic about where this research will lead. Most of the RNA molecules that our cells make will probably not turn out to perform the sort of essential functions that hotair and firre do. Instead, they are nothing more than what happens when RNA-making proteins bump into junk DNA from time to time.

Zimmer concludes by saying Gregory believes the prevalence of junk DNA is strong evidence for evolution:

The blood-drenched slides that pack Gregory’s lab with their giant genomes only make sense, he argues, if we give up thinking about life as always evolving to perfection. To him, junk DNA isn’t a sign of evolution’s failure. It is, instead, evidence of its slow and slovenly triumph.29

Zimmer quotes other evolutionary biologists asserting that most of our genome is junk, which is no surprise since his own evolutionary biology textbook, co-written with biologist Douglas Emlen, promotes the standard view that our genome is full of junk:

Over half of the genome is composed of neither genes, nor vestiges of human genes, nor regulatory regions. Instead, it is made up of parasite-like segments of DNA, known as mobile genetic elements, with the capacity to make new copies of themselves that can then be reinserted into the genome. Some mobile genetic elements originated as viruses that integrated their genes into the genome of their host. The origins of other mobile genetic elements are more mysterious. Once they become established in their host genome, mobile genetic elements can proliferate into thousands of copies and take up large amounts of space.30

However, what I’ve shown above only scratches the surface of a huge body of literature. Again and again, evolutionary biologists have predicted that our genome is primarily useless junk. Occasional caveats from evolutionary scientists, allowing that some small amount of the “junk” might be functional, do not mitigate the widespread, longstanding view that our cells are full of junk DNA. We now know that, on this point, evolutionists were wrong. The “junk DNA” paradigm has conclusively faltered.

We now return to the central question raised my first post: Is the vast majority of the human genome useless junk, or is the vast majority of the human genome crucial for cellular function?

In answering this question, it’s important to clarify what the different camps are, or are not, saying. ID proponents and ENCODE defenders, who take the latter view, aren’t saying the genome must have zero junk. And ENCODE’s evolutionary critics, who take the former view, aren’t saying that all non-coding DNA must be junk. Nonetheless, there’s a titanic difference between the two viewpoints. In fact, if evolutionary scientists hadn’t long-predicted that our genomes would be mostly functionless junk, we wouldn’t be having this conversation.

[1.] W.F. Doolittle and Carmen Sapienza, “Selfish genes, the phenotype paradigm and genome evolution,” Nature, 284:601-603 (April 17, 1980).
[2.] Leslie Orgel and Francis Crick, “Selfish DNA: the ultimate parasite,” Nature, 284:604-706 (April 17, 1980).
[3.] Philip Yam, “Talking Trash,” Scientific American, 272:24 (March, 1995).
[4.] Philip Kitcher, Living With Darwin: Evolution, Design, and the Future of Faith (Oxford University Press, 2007), 129, 62, 58.
[5.] Philip Kitcher, Living With Darwin: Evolution, Design, and the Future of Faith (Oxford University Press, 2007), 58, 57.
[6.] Germain et al., “Junk or functional DNA? ENCODE and the function Controversy,” Biology & Philosophy, 29:807-831 (November, 2014).
[7.] Richard Dawkins, The Selfish Gene (Oxford University Press, 1976), 44-45.
[8.] Richard Dawkins, The Selfish Gene (Oxford University Press, 1976), 44-45.
[9.] Richard Dawkins, A Devil’s Chaplain: Reflections on Hope, Lies, Science, and Love (Mariner Books, 2004), 99.
[10.] Richard Dawkins, The Greatest Show on Earth: The Evidence for Evolution (Free Press, 2009), 333.
[11.] Richard Dawkins, “Jonathan Sacks and Richard Dawkins at BBC RE:Think festival 12 September 2012“: 12:57-13:11.
[12.] Richard Dawkins, “Jonathan Sacks and Richard Dawkins at BBC RE:Think festival 12 September 2012“: 13:18-14:10.
[13.] Alexander Palazzo and T. Ryan Gregory, “The Case for Junk DNA,” PLOS Genetics, 10(5):e1004351 (May 2014).
[14.] See T. Ryan Gregory, “Junk DNA — the quotes of interest series,” Evolver Zone Genomicron (February 18, 2008).
[15.] Alexander Palazzo and T. Ryan Gregory, “The Case for Junk DNA,” PLOS Genetics, 10(5):e1004351 (May 2014).
[16.] R.J. Britten and D.E. Kohne, “Repeated Sequences in DNA,” Science, 161:529-549 (August 9, 1968).
[17.] See Wojciech Makalowski, “Not Junk After All,” Science, 300:1246-1247 (May 23, 2003).
[18.] Susumu Ohno, “So Much ‘Junk’ DNA in our Genome,” Evolution of genetic systems, Brookhaven symposia in biology, no. 23 (New York: Gordon and Breach, 1972).
[19.] Jack Lester King and Thomas Jukes, “Non-Darwinian Evolution,” Science, 164:788-798 (May 16, 1969).
[20.] Susumu Ohno, “An argument for the genetic simplicity of man and other mammals,” Journal of Human Evolution, 1(6):651-662 (1972).
[21.] Douglas J. Futuyma, Evolutionary Biology (Sinauer Associates, Inc., 1979), 434 (emphasis added).
[22.] Douglas J. Futuyma, Evolutionary Biology (Sinauer Associates, Inc., 2nd ed., 1986), 457.
[23.] Douglas J. Futuyma, Evolutionary Biology (Sinauer Associates, Inc., 3rd ed., 1998), 640.
[24.] Douglas J. Futuyma, Evolution (Sinauer Associates, Inc., 2005), 531.
[25.] Douglas J. Futuyma, Evolution (Sinauer Associates, Inc., 2nd ed., 2009), 189-190.
[26.] Richard Sternberg, “How The Junk DNA Hypothesis Has Changed Since 1980,” Evolution News & Views (October 8, 2009).
[27.] Leslie Orgel and Francis Crick, “Selfish DNA: the ultimate parasite,” Nature, 284:604-706 (April 17, 1980).
[28.] Richard Sternberg, “How The Junk DNA Hypothesis Has Changed Since 1980,” Evolution News & Views (October 8, 2009).
[29.] Carl Zimmer, “Is Most of Our DNA Garbage?The New York Times (March 5, 2015).
[30.] Carl Zimmer and Douglas Emlen, Evolution: Making Sense of Life, p. 132 (Roberts and Company Publishers, 2012).

Image: � Minerva Studio / Dollar Photo Club.


Casey Luskin

Associate Director, Center for Science and Culture
Casey Luskin is a geologist and an attorney with graduate degrees in science and law, giving him expertise in both the scientific and legal dimensions of the debate over evolution. He earned his PhD in Geology from the University of Johannesburg, and BS and MS degrees in Earth Sciences from the University of California, San Diego, where he studied evolution extensively at both the graduate and undergraduate levels. His law degree is from the University of San Diego, where he focused his studies on First Amendment law, education law, and environmental law.



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