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The "Software" of Life Argument for an Intelligent Designer, part four

Another excerpt from my new book What Your Atheist Professor Doesn't Know (But Should):

Genetics and Epigenetics
Genetics and Epigenetics
Photo by Andrew Burton/Getty Images

As astonishing as this is, there’s more. There are overlapping codes, and codes within codes within codes (three layers of encryption). Some codes extend epigenetically (beyond the genes), and some rely on combinations of genes being switched on and off. Consider this quote in New Scientist:

A single gene can potentially code for tens of thousands of different proteins... It's the way in which genes are switched on and off, though, that has turned out to be really mind-boggling, with layer after layer of complexity emerging. (~Le Page, "Genome at 10," New Scientist, 6/16/10).

Arguably the most prominent atheist of the 20th century, Antony Flew (Professor of Philosophy, author, and debater) announced in 2004 that he had become convinced that there is no way these things could have evolved by chance, due to their stunning information content. As he put it:

It now seems to me that the findings of more than fifty years of DNA research have provided materials for a new and enormously powerful argument to design. (4)

In a bit of news breaking just recently, a joint scientific project called “ENCODE” has determined that a staggering 80% of what was previously considered “junk” DNA actually has purpose. From a materialist viewpoint, this increase in specified complexity dramatically increases the difficulty of arguing against an Intelligent Designer. Here Dr. Fazale Rana of RTB discusses the implications:

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:

The results of the project have been sensationalized and poorly reported by science journalists.

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.

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.