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Trash Be Gone: Why Are Biologists Lashing Out Against Empirically Verified Research Results?

Trash no more.jpg

Editor's note: This is Part 1 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.

Is the vast majority of the human genome useless junk or crucial for cellular function? Scientists are split over this question, with evolutionary biologists principally holding the former viewpoint, and molecular biologists the latter.

In our era of advanced biological research, one would think this an easily resolvable question, but when a powerful evolutionary paradigm is threatened by the findings of molecular biology, don't expect the establishment to quickly concede defeat. Indeed, the entire debate over neo-Darwinian evolution and intelligent design (ID) may turn on the outcome of this question.

Flotsam and Jetsam No More

For those who follow the debate over origins, the demise of junk DNA is old news. My very first Operation ID column, in the Fall 2008 issue of Salvo, recounted how Francis Collins argued in The Language of God that our genome is full of "genetic flotsam and jetsam" (i.e., trash), making it "virtually inescapable"1 that we share common ancestry with mice. But as I explained then, numerous functions had been discovered for noncoding DNA, and more have been found since, forcing a revolution in biological thinking. In a sign of the times, a 2010 Nature article heralded this new era of genomics, noting that "biology's new glimpse at a universe of non-coding DNA--what used to be called 'junk' DNA--has been fascinating and befuddling."2 Many other scientific papers reporting functions for "junk" DNA have made similar remarks.

But no publication shook this debate so much as a 2012 Nature paper that finally put junk DNA to rest--or so it seemed. This bombshell paper presented the results of the ENCODE (Encyclopedia of DNA Elements) Project, a years-long research consortium involving over 400 international scientists studying noncoding DNA in the human genome. Along with 30 other groundbreaking papers, the lead ENCODE article found that the "vast majority" of the human genome shows biochemical function: "These data enabled us to assign biochemical functions for 80 percent of the genome, in particular outside of the well-studied protein-coding regions."3

Ewan Birney, ENCODE's lead analyst, explained in Discover Magazine that since ENCODE studied 147 types of cells, and the human body has a few thousand cell types, "it's likely that 80 percent will go to 100 percent."4 Another senior ENCODE researcher noted that "almost every nucleotide is associated with a function."5 A headline in Science declared, "ENCODE project writes eulogy for junk DNA."6

Bad News for Darwinism

This report was a game-changer in the debate over Darwinian evolution and intelligent design because, since the mid-1990s, ID theorists had been predicting that noncoding DNA would turn out to have function, and ID critics had been arguing that junk DNA drove a stake through the heart of ID.

For example, back in 1994, pro-ID scientist Forrest Mims submitted a letter to Science warning against assuming that "junk" DNA was "useless."7 Science wouldn't print the letter, but that same year, anti-ID biologist Kenneth Miller published an article in a different journal making the opposite conclusion, namely that "the human genome is littered with pseudogenes, gene fragments, 'orphaned' genes, 'junk' DNA, and so many repeated copies of pointless DNA sequences that it cannot be attributed to anything that resembles intelligent design."8

Contrast Miller's assertion with a conclusion of Discover Magazine 18 years later in light of ENCODE's 2012 breakthrough report: "The key point is: It's not 'junk.'"9

Evolutionists Strike Back

Darwin defenders weren't going to take ENCODE's data sitting down. But this time, they found themselves in an unaccustomed position. Many Darwinians take great assurance in knowing they stand in the scientific majority, which enables them to appeal to the consensus and dismiss challengers as "deniers." But in the post-ENCODE world, Darwin defenders have found themselves challenging the consensus of an international body of leading molecular biologists who have discovered that the vast majority of human DNA has biochemical function.

How could they possibly oppose such empirically based conclusions? The same way they always defend their theory: by assuming an evolutionary viewpoint is correct and reinterpreting the data in light of their paradigm--and by personally attacking those who challenge their position.

For instance, multiple initial rebuttals from evolution defenders called ENCODE "hype"10 and castigated researchers and science journalists for acting "irresponsibly" in favorably reporting on its findings.11 In a post titled "The ENCODE Delusion," PZ Myers dismissed ENCODE's central claim that 80 percent of the genome has biochemical functions as "bull****," maintaining that evidence of biochemical activity in DNA and RNA "isn't function. That isn't even close." He called the ENCODE researchers themselves "fundamentally dishonest," and scoffed at Evan Birney, saying, "I don't think Birney has a clue about the -biology."12

Another Darwin-defending biologist, Nick Matzke, allowed that the ENCODE researchers weren't stupid, just ignorant: "I'm beginning to think that certain parts of molecular biology and bioinformatics are populated with people who are very smart, but who got through school with a lot of detailed technical training but without enough broad training in basic comparative [i.e., evolutionary] biology."13 But University of Toronto biochemist and pro-evolution blogger Laurence Moran wouldn't even grant that the ENCODE researchers were intelligent: "I guess I'll just have to be content to point out that many scientists are as stupid as many Intelligent Design Creationists,"14 he ranted.

Moran further lamented that "the creationists are going to love this," and he feared that ENCODE's results were "going to make my life very complicated,"15 since "it's going to take a lot of effort to undo the damage caused by [ENCODE]."16

The vast majority of those defending ENCODE, however, are not pro-ID and have no motive to aid and abet "the creationists." They're driven by the empirical data. For example, University of Chicago geneticist James Shapiro praised ENCODE's results while simultaneously disavowing ID. He found that "the old idea of the genome as a string of genes interspersed with unimportant noncoding DNA is no longer tenable," since "ENCODE revealed that most (and probably just about all) of this noncoding and repetitive DNA contained essential regulatory information."17

Shapiro wrote papers in the mid-2000s predicting function for "junk" DNA, and he explained that his co-author was an ID proponent who held views he didn't share:

In 2005, I published two articles on the functional importance of repetitive DNA with Rick von Sternberg. The major article was entitled "Why repetitive DNA is essential to genome function."

These articles with Rick are important . . . for two reasons. The first is that shortly after we submitted them, Rick became a momentary celebrity of the Intelligent Design movement. Critics have taken my co-authorship with Rick as an excuse for "guilt-by-association" claims that I have some ID or Creationist agenda, an allegation with no basis in anything I have written.

The second reason the two articles with Rick are important is because they were, frankly, prescient, anticipating the recent ENCODE results. Our basic idea was that the genome is a highly sophisticated information storage organelle. Just like electronic data storage devices, the genome must be highly formatted by generic (i.e., repeated) signals that make it possible to access the stored information when and where it will be useful.18

Clearly, some ID critics are embracing ENCODE's results. But most remain steadfastly resistant, most likely because ENCODE threatens to overturn some of the most prominent scientific arguments for an unguided evolutionary origin of the human genome.

What If ENCODE Is Right?

Earlier in 2014, Science reported on the arguments made by another leading evolutionary critic of ENCODE, University of Houston biologist Dan Graur. According to Science, "Graur's atheism inflamed his anger at ENCODE."19 It's not surprising that Graur would become emotional over ENCODE given his blunt framing of the issue in a talk he gave in 2013:

If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome. If, on the other hand, organisms are designed, then all DNA, or as much as possible, is expected to exhibit function. If ENCODE is right, then Evolution is wrong.20

Graur's framing of the issue just might be correct. But to appreciate why ENCODE's critics are wrong, wait for the next installment in this series.

References:

[1.] Francis Collins, The Language of God: A Scientist Presents Evidence for Belief (Free Press, 2006), 136-137.

[2.] Erika Check Hayden, "Life Is Complicated," Nature, 464:664-667 (April 1, 2010) (emphasis added).

[3.] The ENCODE Project Consortium, "An integrated encyclopedia of DNA elements in the human genome," Nature, 489:57-74 (Sept. 6, 2012).

[4.] Ewan Birney, quoted in Ed Yong, "ENCODE: the rough guide to the human genome," Discover Magazine (Sept. 5, 2012): http://tinyurl.com/knr9co7.

[5.] Tom Gingeras, quoted in Yong, ibid.

[6.] Elizabeth Pennisi, "ENCODE Project Writes Eulogy for Junk DNA," Science, 337:1159-1161 (Sept. 7, 2012).

[7.] Forrest Mims, "Rejected Letter to the Editor to Science" (Dec. 1, 1994): forrestmims.org/publications.html.

[8.] Kenneth Miller, "Life's Grand Design," Technology Review, 97(2):24-32 (February/March 1994).

[9.] Yong, note 4.

[10.] Nick Matzke, "ENCODE hype? From now on I'll just reply: #oniontest," Panda's Thumb (Sept. 5, 2012): http://tinyurl.com/nmxeu4t; Laurence Moran, "The ENCODE Data Dump and the Responsibility of Science Journalists," Sandwalk (Sept. 6, 2012): http://tinyurl.com/k7eup3n.

[11.] Moran, ibid.

[12.] PZ Myers, "The ENCODE delusion," Panda's Thumb (Sept. 23, 2012): http://tinyurl.com/moefwye.

[13.] Matzke, note 10.

[14.] Laurence Moran, "Intelligent Design Creationists Choose ENCODE Results as the #1 Evolution Story of 2012," Sandwalk (Jan. 4, 2013): http://tinyurl.com/p8dc6yp.

[15.] Laurence Moran, "ENCODE Leader Says that 80% of Our Genome Is Functional," Sandwalk (Sept. 5, 2012): http://tinyurl.com/m96r5un.

[16.] Moran, note 10.

[17.] James Shapiro, "Bob Dylan, ENCODE and Evolutionary Theory: The Times They Are A-Changin'," Huffington Post (Sept. 12, 2012): http://tinyurl.com/pmxowlu.

[18.] Ibid.

[19.] Yudhit Bhattercharjee, "The Vigilante," Science, 343:1306-1309 (March 21, 2014).

[20.] Dan Graur, "How to Assemble a Human Genome?" (December 2013): http://tinyurl.com/mpmxkyw (emphases in original).

Image: � kessudap / Dollar Photo Club.