ENCODE, Junk DNA, and Intelligent Design Creationism

andyjones has replied to my earlier posting on ENCODE and junk DNA. You can read his response at: (More) Function, the evolution-free gospel of ENCODE. Here's part of what he says ...

Larry Moran has sort-of replied to my previous blogpost but disappoints with only one substantive point. And even that one point is wrong: ID is not committed to the idea that individual genomes be well-designed; that is just an expectation some of us derive based on belief in a designer which is established on other evidence. ID would still be true if only globular proteins were designed (lookup Axe), or even if only the flagellum was designed (lookup Behe), or even if only the first life form was designed (lookup Meyer – and please read their actual work, not cheap reviews, because reviewers often dont pick up on the salient points – more below). I just say this lest readers get the impression that this is ID’s strongest point, or in any sense a weak point. It is neither.

It's true that there are some IDiots who are distancing themselves from a commitment to junk DNA. There are probably some who claim that they could live with the fact that 90% of our DNA is junk.

But let's not forget that Jonathan Wells is a prominent IDiot and he wrote a book on The Myth of Junk DNA. It sounded very much like Intelligent Design Creationism is staking its reputation on finding function for most of our genome.

Have you heard of someone named Stephen Meyer? He wrote a book called Signature in the Cell and that book seems to be widely admired in the IDiot community. I think it's been mentioned once or twice on the Intelligent Design Creationist blogs. I blogged about what Meyer wrote about junk DNA a few years ago [Stephen Meyer Talks About Junk DNA]. Here's part of what's in that post, quoting from Stephen Meyer's book ....

ID advocates advance a different view of nonprotein-coding DNA. The theory of intelligent design predicts that most of the nonprotein-coding sequences in the genome should perform some biological function, even if they do not direct protein synthesis. ID theorists do not deny that mutational processes might have degraded or "broken" some previously functional DNA, but we predict that the functional DNA (the signal) should dwarf the nonfunctional DNA (the noise), and not the reverse. As William Dembski explained and predicted in 1998: "On an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function." The discovery in recent years that non-protein coding DNA performs a diversity of important biological functions has confirmed this prediction. It also decisively refutes prominent critics of intelligent design—including Shermer Miller and Kitchener—who have continued to argue (each as recently as 2008) that the genome is composed of mostly useless DNA.

Then there's the famous Casey Luskin who is never one to back away from a prediction. Here's what he wrote in Intelligent Design and the Death of the "Junk-DNA" Neo-Darwinian Paradigm.

Intelligent Design has Long Predicted This Day

Proponents of intelligent design have long maintained that Neo-Darwinism's widely held assumption that our cells contain much genetic "junk" is both dangerous to the progress of science and wrong. As I explain here, design theorists recognize that "Intelligent agents typically create functional things," and thus Jonathan Wells has suggested, "From an ID perspective, however, it is extremely unlikely that an organism would expend its resources on preserving and transmitting so much ‘junk'." [4] Design theorists have thus been predicting the death of the junk-DNA paradigm for many years:

I guess these guys (Wells, Meyer, Dembski, and Luskin) don't speak for andyjones but I think it's fair to say that they represent the consensus view of the average IDiot. Let's stop pretending that junk DNA isn't an affront to intelligent design. Junk DNA is a major threat to their position and that's why they're so concerned.

Let's look at a bit more of what andyjones has to say ..

In case you missed it, the interesting thing about ENCODE is the discovery that 80% of the human genome is transcribed.

That was somewhat "interesting" in 2007 when the ENCODE pilot project was published but it wasn't the least bit interesting last September. Scientists have known since the mid-1970s that a large fraction of our genome is complementary to RNA in the cell. We've known for almost as long that most "pervasive" transcription is very likely useless transcription or accidental transcription. This is consistent with a lot of papers showing that RNA polymerase binds at many sites besides functional promoters. It's in most of the textbooks. This explanation became more widely known following publication of the pilot study in 2007. Unfortunately, it's not only the IDiots who ignore it but also many of the ENCODE workers.

Darwinian theories did not predict this.

That's correct. Darwinian theory is focused on natural selection as the most important mechanism of evolution. Strict Darwinists predicted that there would be very little junk in our genome. Most of them still stand by that prediction and that's why there are so many ENCODE workers who are opposed to junk DNA. (The IDiots know this because I've recently been assured that they understand the difference between Darwinism and modern evolutionary theory.)

For anyone who does not have a strong upstream thought-filter*, and has not been brain-washed by the cult, transcription is strongly indicative of function. Thus ENCODE’s headline is on target.

Yes, it's true that most—but not all—functional regions are transcribed and it's true that transcription can be indicative of function, especially if the transcripts are abundant.

On the other hand, regions of the genome that are transcribed very rarely do not turn out to be reliable indicators of function because we have a better explanation. Most of pervasive transcription falls into this very rare category.

It is quite reasonable now to expect that details of actual function will subsequently be found for much of the genome. Therefore we should keep looking for that function.

Scientists have accumulated plenty of evidence that most of our genome is not functional in any meaningful sense of the word. It's unlikely that this evidence will be overturned or discredited in the near future and it's unlikely that we will find functions for any significant portion of our genome. There are some very good scientists who have been looking for decades.

This site (UncommonDescent) has many articles on elements of DNA, previously thought junk, that turned out to be of importance. For examples, pseudogene transcripts regulate those of real genes, and ERV-elements turn out to be important in developing embryos.

It's true that Uncommon Descent has been a bit obsessive about the issue. It almost looks like discrediting junk DNA is a big deal for the IDiots in spite of what andyjones says above. If we add up all of the functional regions of the human genome that have appeared on the blog—or in Jonathan Wells' book— they probably amount to about 0.1% of the genome ... and that's being generous.

As I said, quite reasonably I think, ‘Time will tell’ for all the rest as well.

At the rate they're going (0.1% in ten years) it's going to take about 9000 years to find new functions for the 90% of the genome we think is junk.

Most of the IDiots are going to be raptured long before that ....

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