Junk DNA Redux

Rusty has posted another response on Junk DNA. It's a few days old but I'm just now getting around to answering it. If you're following along, you'll find Rusty's original post here and my response here. The basic assertion up for dispute is Rusty's test for creationism:

Further research will reveal function for so-called Junk-DNA sequences. Although considered by evolutionists to be a closed case, the Creation Model predicts that currently held scientific opinion on this issue will eventually concede that function is inherent in the Junk-DNA sequence. The failure of this test would be a devastating, if not killer, blow to the Creation Model.

I pointed out in response to this that approximately 98% of the human genome is currently believed to be "junk DNA" and I explained that those parts of the genome are made up primarily of 3 things - pseudogenes, transposable elements and repetitive sequences. Rusty begins his latest with this:

Before I respond I should clarify that I am not a scientist. The intent of my posts on science related topics is not to provide a detailed analysis of the scientific data but, rather, to provide a summary analysis of current discoveries in the scientific realm.

And I should point out that I'm not a scientist either. Like Rusty, I am simply an educated amateur who has been studying this informally. But this is something I take very seriously. I think it's important to deal with the evidence as it is. One of the reasons why I pursued this particular argument is because I wanted to make the point that organizations like Reason to Believe have a tendency to play fast and loose with the evidence and to gloss over a lot of important detail. On Junk DNA specifically, Reasons has a tendency to seize on any article they can find in the scientific literature that suggests any function at all for even the tiniest sequence of junk DNA so they can say, in essence, "Ah ha! You see, those scientists don't know so much after all. They were wrong, junk DNA does have function." But there are some things that they don't tell you that are very important - like the fact that those few articles that they've managed to find involve small sequences out of a VAST amount. To pretend that this is a "trend" and that it's standing previous thoughts on junk DNA on its head is just silly. Moreover, as Paul Myers points out, the LINE sequence that was found to have "function" wasn't really function, it was simply an adaptation of functional DNA to the presence of a junk DNA sequence.

They also don't tell you that by comparing pseudogene sequences between species you can build a phylogenetic "tree" that mirrors the one based on comparative anatomy and paleontology. And because pseudogenes are non-coding, it can't be because a creator just used similar genetic material to perform similar functions. And this is not speculation - we've observed how pseudogenes are created through gene duplication and we've observed how the amino acid substitutions build up in the non-functional duplicate over the generations. We can see the telltale signs of pseudogene creation and then identify the same telltale signs in the genomes of a wide variety of species. By tracing these homologies in pseudogenes we can trace phylogeny. These things are important to know if you want the whole picture on evolution and junk DNA. The average reader of Reasons to Believe's website or literature doesn't know that. They just know that a "real scientist" (and never mind that they may be way outside their own expertise) who says he's standing up for their faith in the face of atheistic science that seeks to destroy the bible and faith in God has told them that the junk DNA problem is well on its way to being solved and the scientists are finding out they're wrong.

Rusty continues:

Note that I did not state that there should be 100% function in the DNA code with no regards to potential errors in the code. Am I back-pedaling? No, and heres why. Ed must surely understand that we live in a world with certain laws of physics and that one of the results of those laws of physics is that systems will break-down. Mutations are a part of the natural order we exist in. I would no more expect function in a broken piece of DNA code than I would expect function in a broken piece of code for MS Word. However, if analysis is done on a pure genome (i.e., no errors in coding) then yes, I would expect 100% functionality.

The problem here is that it ignores the fact that pseudogene sequences can be traced between genomes and it results in a secondary phylogenetic tree that is identical to the one based on comparative anatomy, which is why it is such powerful evidence for common descent. Even if we stick to the same genome, I'm not sure I understand what Rusty's prediction really posits if not 100% functionality. What % of junk DNA would he be willing to accept and still maintain that each species was designed by God?

He continues:

Ed has presented a good deal of evidence that posits that the supposed Junk-DNA sequences evolved and mutated into the functionality we see today. Thats nice, but if pressed I could find evidence to the contrary. What ends up happening is that I find scientists who disagree with the conclusions of the scientists that Ed references.

This sounds dangerously close to relativism to me. He seems to imply that the mere fact that you may find 2 scientists who disagree on an issue means there is no means to figure out which one is right and which is wrong. I don't think a person who cares about the truth should be satisfied with that. I can produce an astronomer who thinks the earth is the center of the universe; that doesn't mean that geocentricity and heliocentricity are equally valid and it's just a coin toss as to which one you want to believe. It should also be noted here that the one qualified molecular biologist in the ID movement would not himself deny any of this. Michael Behe accepts common descent, and while he also likes to trumpet that some junk DNA may not in fact be functionless, I highly doubt he would deny that the phylogenetic trees based on pseudogenes are evidence of common descent. I could be wrong, but that would certainly seem to fit with his previous statements on the subject. Don Lindsay gives a perfect example of how tracing the same pseudogene shows evidence of common ancestry here.

Rusty continues:

Evolutionists love to accuse Creationists of appealing to a God who can do whatever He wants, thereby allowing any evidence to be evidence for Creation. Yet here is an example of the evolutionists (in general - not Ed specifically) pulling the old switch-a-roo. Junk-DNA?... Sure! Its what wed expect from evolution through chance mutations. vs. You found some function?... Sure! Its what wed expect from evolution since we observe mutations occurring real-time.

What we end up with is the use of self-referential logic. Essentially it is stated that we know that mutations can evolve functional Junk-DNA because we see mutations occurring in DNA sequences.

This is simply nonsense. There is no bait and switch here because we know how to identify those sequences that have been adapted to have function in one species, again by tracing the same gene at the same spot in the genome between species. And again, we've observed this in the lab in microbes. It's not just a guess that it can happen, it's confirmed to happen. And again, remember that we're talking about a minute portion of junk DNA - a few sequences out of tens of thousands of genes that don't code. We can also identify which genes truly have function and which don't by removing or suppressing a gene sequence and seeing what changes. But here we come again to the difference in testability between evolution and creationism. If those pseudogene homologies did not show what they show - a phylogenetic tree that matches the nested heirarchies predicted by evolution from paleontology and comparative anatomy - evolution would be dead. Creationism, on the other hand, can explain anything. And remember that we're not talking about tracing a single pseudogene here. We're talking about tracing hundreds of them in different places in the genome among hundreds of species and finding the same thing every single time. This is very powerful evidence that MUST be the way it is if evolution is true, but could be pretty much any way for creationism.