The Intelligent Design-Darwinism debate just changed, radically

[Dear readers: this post was written as the first post on the ENCODE story, with my post from yesterday as a follow-up. Yesterday's post went up prematurely. This post gives much of the background for the remarkable events playing out now in the ID-Darwinism debate]

By the early 1970's, it was evident that the vast majority of DNA-- as much as 99%-- did not code for proteins. This non-coding DNA was first called "junk DNA" in 1972 by Sasumu Ohno, a pioneer in molecular evolution and evolutionary biology. It soon became clear that there were portions of the genome that were did not code for proteins but which were still functional-- serving a regulatory or structural function. Yet most biologists believed that the functional portions of the genome-- coding and non-coding-- were only a tiny fraction of the total DNA.

Most of the DNA, according to the hypothesis, was non-functional junk. The junk DNA hypothesis was this: during evolution, portions of the genome became non-functional (or were never functional to begin with). Because these "junk" regions of DNA did not code for protein or have other functions, they did not affect the organism's phenotype and were not subject to natural selection. Because they were not subject to natural selection, this DNA "junk" was not removed by natural selection. It accumulated in the genome, a silent witness to eons of random mutation insulated from natural selection.

With haste Darwinists seized on junk DNA as powerful evidence for Darwin's theory. They argued that junk DNA was inconsistent with intelligent agency. An intelligent designer wouldn't pack the genome with non-functional DNA. Furthermore, Darwinists used "junk DNA" conserved across species as evidence for common descent. Why would a designer create different species with identical junk DNA?

Casey Luskin of the Discovery Institute quotes several of Darwinism's most rabid defenders:

Richard Dawkins in 1976:

"The amount of DNA in organisms is more than is strictly necessary for building them: A large fraction of the DNA is never translated into protein. From the point of view of the individual organism this seems paradoxical. If the "purpose" of DNA is to supervise the building of bodies, it is surprising to find a large quantity of DNA which does no such thing. Biologists are racking their brains trying to think what useful task this apparently surplus DNA is doing. But from the point of view of the selfish genes themselves, there is no paradox. 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. (The Selfish Gene, p. 47)"

Brown University biologist Kenneth R. Miller in 1994:

"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. . . . In fact, the genome resembles nothing so much as a hodgepodge of borrowed, copied, mutated, and discarded sequences and commands that has been cobbled together by millions of years of trial and error against the relentless test of survival. It works, and it works brilliantly; not because of intelligent design, but because of the great blind power of natural selection. ("Life's Grand Design," Technology Review,February/March 1994)"

Skeptic Magazine publisher Michael Shermer in 2006:

"We have to wonder why the Intelligent Designer added to our genome junk DNA, repeated copies of useless DNA, orphan genes, gene fragments, tandem repeats, and pseudo­genes, none of which are involved directly in the making of a human being. In fact, of the entire human genome, it appears that only a tiny percentage is actively involved in useful protein production. Rather than being intelligently designed, the human genome looks more and more like a mosaic of mutations, fragment copies, borrowed sequences, and discarded strings of DNA that were jerry-built over millions of years of evolution. (Why Darwin Matters,pp. 74–75)"

University of Chicago geneticist Jerry A. Coyne in 2009:

"Perfect design would truly be the sign of a skilled and intelligent designer. Imperfect design is the mark of evolution." Based on neo-Darwinian theory, "we expect to find, in the genomes of many species, silenced, or 'dead,' genes: genes that once were useful but are no longer intact or expressed." These are called "pseudogenes." According to Coyne, "the evolutionary prediction that we'll find pseudogenes has been fulfilled—amply." Indeed, "our genome—and that of other species—are truly well populated graveyards of dead genes" (Why Evolution Is True, pp. 67, 81)."

Biochemist Larry Moran in 2011 on the percentages of DNA in the genome that are "junk":

"I believe that 90% of the human genome consists of junk DNA (DNA with no known function)"

Total Essential/Functional (so far) = 8.7%
Total Junk (so far) = 65%
Unknown (probably mostly junk) = 26.3%

 Scientists who work from a design perspective knew better.

ID scientists have predicted for years that "junk DNA" is a myth-- that the genome is an elegantly designed biological system, and what we have traditionally understood as "junk" is merely DNA the function of which we have not yet uncovered. There is clear divergence between the scientific predictions of intelligent design-- junk DNA is DNA whose function we have yet to discover-- and the scientific predictions of Darwinism-- junk DNA functionless and is evidence for phenotypically silent random mutations that have accumulated over eons of evolution. This is a clear test of both theories, a test chosen by Darwinists, who have used "junk DNA" to advance Darwinism for four decades.

Here's Darwinophile Larry Moran excoriating Casey Luskin for Luskin's predictions that much of "junk DNA" would be shown to be functional:

Intelligent Design Creationists can't abide junk DNA. Its very existence refutes the idea that living things are designed by some intelligent being. This is why the IDiots go out of their way to make up stories "disproving" junk DNA. 

The latest attempt is by Casey Luskin [Nature Paper Shows "Junk-RNA" Going the Same Direction as "Junk-DNA"]. Having failed to explain why half of the human genome is composed of defective transposons, he now pins his hope on the idea that most of the genome is transcribed. Luskin seems particularly upset by my statement that most of these transcripts are junk [Junk RNA]... 

In other words, most of the transcripts are probably transcriptional noise, or junk, just as I said. This is the consensus opinion among informed molecular biologists. 

This is a point of view that creationists share with many scientists who haven't studied the subject. They assume that the only reason for labeling most of our DNA junk is because we don't know what it does. That's just not true. There's plenty of good evidence that most of our genome can't be functional. We know a lot about the part that consists of transposons and defective transposons, for example [Junk in Your Genome: SINES and Junk in your Genome: LINEs]. That's 44% of our genome.

Intelligent Design proponents have consistently predicted that "junk DNA" was really functional DNA whose function had not yet been discovered. ID scientist Jonathan Wells, in his 2011 book The Myth of Junk DNA, observed:

[ID proponent Richard Sternberg] argues that intelligent design suggests the following hypothesis: The organization of DNA strings along the genome is optimized for the establishment of multidimensional codes at all scales, and each species has a unique and elaborately ordered arrangement of chromosome regions that maximizes the information the genome can carry. The hypothesis is scientific, because it entails two predictions that can be empirically falsified: The first is that the genome of one species cannot be transformed into the genome of another species by random re-arrangements, since this would compromise the formatting, indexing, and punctuation of DNA files. The second is that any observed chromosome changes that result in normal fitness will be those that maintain genomic optimization...

Wells concludes:

Scientists make progress by testing hypotheses against the evidence. But when scientists ignore the evidence and cling to a hypothesis for philosophical or theological reasons, the hypothesis becomes a myth. Junk DNA is such a myth, and it's time to leave it behind—along with other discarded myths from the past.

As recent discoveries have demonstrated, we are just beginning to unravel the mysteries of the genome. Indeed, the same can be said of living organisms in general. But assuming that any feature of an organism has no function discourages further investigation. In this respect, the myth of junk DNA has been a science-stopper.

Not any more. For scientists willing to follow the evidence wherever it leads, these are exciting times.

Does "junk DNA" really have no function, vindicating the Darwinist prediction, or does it have function not yet completely understood, as predicted by scientists working from the design perspective?

The evidence is in, and in the September 6, 2012 issue of Nature and in two other leading biology journals, it is an avalanche. An avalanche for Intelligent Design, that is.

 From Uncommon Descent:

In a spectacular vindication of [the ID] hypothesis [that "junk DNA" is functional], six papers have been released in Nature, in addition to a further 24 papers in Genome Research and Genome Biology, plus six review articles inThe Journal of Biological Chemistry.

The lead publication of the finding (“An Integrated Encyclopaedia of DNA Elements in the Human Genome“) was released in Nature. The abstract reports,

“The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.” [emphasis added]

They further report that, 

“[E]ven using the most conservative estimates, the fraction of bases likely to be involved in direct gene regulation, even though incomplete, is significantly higher than that ascribed to protein- coding exons (1.2%), raising the possibility that more information in the human genome may be important for gene regulation than for biochemical function. Many of the regulatory elements are not constrained across mammalian evolution, which so far has been one of the most reliable indications of an important biochemical event for the organism. Thus, our data provide orthologous indicators for suggesting possible functional elements.”

As this Nature press release states, 

“Collectively, the papers describe 1,640 data sets generated across 147 different cell types. Among the many important results there is one that stands out above them all: more than 80% of the human genome’s components have now been assigned at least one biochemical function.” [emphasis added]

The overview paper in Nature is here.

This is a catastrophe for Darwinism. C-a-t-a-s-t-r-o-p-h-e. Darwinists have been riding the "junk DNA" trolley for decades, confidently asserting that the presence in the genome of worthless non-functional DNA was incontrovertible evidence against design and for Darwin's theory of random mutation and natural selection. Junk DNA was tangible evidence for the "random" in "random mutation and natural selection". It has been a centerpiece of the Darwinist argument for decades.

It is now in dust. ID scientists were right all along. The inference to intelligent design in biology predicted what Darwinism denied: the most important revolution in molecular genetics since the discovery of the genetic code.

So the inference that "shit happened and survivors survived" has held back molecular genetics research in a very serious way-- why devote precious research money and time to "junk"-- and has impaired critical medical genetic research in such diseases as cancer and diabetes for decades.

Darwinism is worse than ideologically-motivated gibberish. It's not just worthless to science. It is actually an impediment to science. It stops science. By insisting on randomness as the origin of biological novelty, it leads researchers away from studying living systems as elegantly integrated systems replete with purpose-- which, as the Nature research shows so clearly, is the true perspective.