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Responding to ENCODE “Skeptics”

Recently, the ENCODE Project Consortium reported that 80 percent of the human genome consists of functional elements, major indicators of design. But some skeptics assert (loudly) that the results of the ENCODE project have been overhyped and misconstrued. In this article, I respond to the most salient points made by the ENCODE “skeptics.” The human genome displays a much greater degree of design than evolutionary biologists could ever imagine.

“I think that the formulation of [DNA’s] structure by Watson and Crick may turn out to be the greatest developments in the field of molecular genetics in recent years.” 
—Linus Pauling

I am always excited when September rolls around because it ushers in the start of the football season. Few things are more exciting than a big play on the football field: a running back breaking away from the line of scrimmage for a long gain; a deep pass over the middle; a punt return for a touchdown. But nothing is more anticlimactic than when a big play gets called back.

This September brought excitement for another reason. The ENCODE Project Consortium announced the results of the second phase of a project designed to identify and catalog all the functional elements in the human genome.1 It is remarkable to think that, in the span of 60 years, science has progressed from determining the structure of DNA—the molecule of inheritance—to sequencing and now deciphering the DNA sequences of the human genome. 

As I describe in the short video below and in the September 6, 2012 episode of Science News Flash, the results of the ENCODE project may well be one of the most important scientific achievements in my lifetime, at least in my time as a professional biochemist.

The Big Play

Shortly after the draft sequence of the human genome was published, researchers’ initial estimates determined that only 1 percent of the human genome consisted of functional sequences, with the rest categorized as junk. But now the ENCODE team reports that a staggering 80 percent of the human genome consists of functional elements; and with the third phase of the project underway, that number may well increase.

The ENCODE project’s impact will be far reaching, providing important knowledge about human biology and the etiology of genetic disorders, and guiding the future direction for biomedicine. The ENCODE results also influence the creation/evolution controversy.

Many skeptics and evolutionary biologists claim that the most compelling evidence for human evolution—and, thus, most potent challenge against intelligent design/creationism—is the human genome’s vast amount of junk DNA. And yet, with the results of the ENCODE project, these arguments evaporate. The ENCODE project has radically altered our view of the human genome. It can no longer be considered a vast wasteland of junk, but must be seen as an elegant system that displays sophistication in its architecture and operation, far beyond what most evolutionary biologists ever imagined.

Called Back

Yet, just as creationists and ID proponents were celebrating this victory, some skeptics threw down the red flag, challenging the call on the field. They asserted that the results of the ENCODE project have been overhyped by the media and misconstrued by creationists and intelligent design (ID) adherents. It looked like the play was going to be called back.2
Specifically, the ENCODE “skeptics” claim:

  1. The results of the project have been sensationalized and poorly reported by science journalists.
  2. The discussion of the ENCODE results ignores the fact that nearly 50 percent of the human genome consists of transposable elements and two percent is comprised of pseudogenes, both of which are nonfunctional, junk sequences.
  3. The ENCODE scientists detected biochemical activity for 80 percent of the human genome, but it is incorrect to equate biochemical activity with function.

The Play Stands

However, after careful review, it looks as if the play on the field stands. First off, it’s hard to accept the claim that the popular science reports are hype. The science journalists who reported on the ENCODE results are among the best in the world—and all it takes is a little digging to show that they reported the story accurately. For example, the ENCODE Project Consortium writes in the abstract of the summary/overview article published in Nature (September 6, 2012), “These data enabled us to assign biochemical functions for 80% of the genome, in particular outside the well-studied protein-coding regions.”3

On September 5, ScienceDaily published a news item based on a press release issued by NIH/National Human Genome Institute (NHGRI), in which Eric D. Green, director of NHGRI, is quoted as saying,4

During the early debates about the Human Genome Project, researchers had predicted that only a few percent of the human genome sequence encoded proteins, the workhorses of the cell, and the rest was junk. We now know that this conclusion was wrong.

When it comes to transposable elements and pseudogenes in the human genome, it is highly likely that the 80 percent of the human genome that possesses functional elements overlaps the 50 percent comprised of transposable elements and pseudogenes. A plethora of work indicates that both types of “junk” DNA are actually functional.5 The functional DNA elements identified by the ENCODE project are involved in regulating gene expression. It is interesting to note that one of the functional roles of transposable elements and pseudogenes in the human genome relates to gene regulation.

Skeptics’ final protest—the claim that biochemical activity doesn’t equate to function—is a distinction without a difference, at least when it comes to the ENCODE study. In other words, the final protest fumbles. In some instances, it is true that biochemical activity doesn’t equate to biochemical function. But it is hard to argue that this is the case for the ENCODE project. The project’s investigators carefully and specifically chose assays to detect biochemical activity (transcription, binding of transcription factors, histone binding, sites where modified histones bind, methylation, and three-dimensional interactions between enhancers and genes) with well-established function. Biochemists have known for some time that the biochemical activities cataloged by the ENCODE Consortium are important for gene regulation and gene expression.

It seems that the distinction between biochemical activity and function is a “sleight of hand”—a ploy to detract from what Christian apologists are saying about the significance of ENCODE. The results of the ENCODE project are a “touchdown!” for creationists and ID adherents who have long argued that scientific advance will reveal that so-called junk DNA sequences are functional and, thus, evidence for design.

  1. The ENCODE Project Consortium, “An Integrated Encyclopedia of DNA Elements in the Human Genome,” Nature 489 (September 6, 2012): 57–74.
  2. These articles delineate skeptics’ complaints about the media’s mishandling of the ENCODE results and how creationists/ID proponents have misconstrued the results: Scientific American Blogs, “Junk DNA, Junky PR,” blog entry by Athena Andreadis, September 17, 2012, and Cryptogenomicon, “ENCODE Says What?” (September 8, 2012).
  3. The ENCODE Project Consortium, 57.
  4. NIH/National Human Genome Research Institute, “First Holistic View of How Human Genome Actually Works: ENCODE Study Produces Massive Data Set,” Science News (blog), ScienceDaily, September 5, 2012,
  5. These RTB articles discuss studies representative of the work indicating functionality in so-called junk DNA.