Educating an Intelligent Design Creationist: Evidence for Junk

I'm replying to a post by andyjones (More and more) Function, the evolution-free gospel of ENCODE. That was the fourth post in an exchange between me and him. In response to his latest post, I'm working my way through five issues that Intelligent Design Creationists need to understand. So far, we've covered four of them.

Educating an Intelligent Design Creationist: Introduction
Educating an Intelligent Design Creationist: Pervasive Transcription
Educating an Intelligent Design Creationist: Rare Transcripts
Educating an Intelligent Design Creationist: The Specificity of DNA Binding Proteins
Educating an Intelligent Design Creationist: The Meaning of Darwinism

Intelligent Design Creationists have difficulty understanding the arguments for junk DNA and the evidence that supports those arguments. We try to explain the genetic load argument but it doesn't seem to penetrate. We try to explain that half of our genome is composed of defective transposons and viruses—often fragments of the intact genes. This doesn't phase them. And no matter how many times we describe the "C-value Paradox" and why junk DNA resolves the paradox, that evidence is ignored. We patiently describe the megabase pair deletions of the mouse genome and why this is evidence of junk. We teach them about copy number variation in the human genome and why DNA fingerprinting works. We show them examples of deletions and insertions in the genomes of different individuals telling them that these seem to have no effect as far as we know. We take time to explain modern evolutionary theory and why it is consistent with junk DNA. Finally, we describe our detailed textbook understanding of transcription and DNA binding proteins and they don't listen.

Andyjones says,

The fact that some very good scientists have not found functions for all of the genome does not negate the many functions they have found so far, for many classes of genetic element, including those commonly classed as ‘junk’. And they are still working. Part of the problem is this: if a layperson were to take apart a microchip, would he be able to discern the function of all the parts at the first attempt? Probably not. The problem is not lack of intelligence, but an early lack of understanding of the principles by which the thing is built. As soon as he understands a particular design principle, suddenly huge areas of the chip will be comprehensible to him. I humbly suggest that we have a number of such minor revolutions ahead of us in molecular biology. We are making great strides, but we do not yet understand all the principles of the transcriptome never mind the whole interactome. Perhaps there is more to learn about binding sites for RNAP? Or take pseudogenes: they have already been found to function in some cases as regulators, through their RNA transcripts interacting with real gene RNA transcripts. Then, alternative splicing is only partly understood. Who knows what other mechanisms operate at the RNA level? If you can’t imagine the function yet, it can be pretty hard to find it. But if one asserts there is no function (for example for rare transcripts) like Larry does, it will be even harder to find it.

This is a common theme among the Intelligent Design Creationists and, in fairness, among many molecular biologists. They think that junk DNA is simply an expression of ignorance. They ignore everything we tell them. They think that just because they don't understand something then nobody else does either.

In spite of what our opponents say, we actually have a pretty good understanding of the principles behind how a genome is built. Population genetics tells us that it ain't designed.

When I assert that rare transcripts probably have no function I'm not just talking through my hat and I'm not the only biochemist who says that. When I say that one million little bits and pieces of Alu SINES are very unlikely to have a function, that's not just idle speculation. When the ENCODE workers try to tell me that most of the genome is a huge web of 636,336 regulatory sequences, I can test this claim against the vast amount of information that we already know about genomes and transcriptional regulation and declare that this makes no sense. These are not arguments from ignorance.

Opponents of junk DNA are never going to be credible unless they tell us why the genetic load argument is invalid. They need to explain how their ideas comport with the data on genome size (The Onion Test). They need to explain why the average gene needs 5000 regulatory sites. They need to come up with a reasonable explanation for lack of sequence conservation. They need to tell us why the vast majority of defective transposons evolved a function.

Opponents of junk DNA need to address the arguments and evidence for junk DNA and stop pretending that those arguments don't exist.

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