Pharyngula

Another junk DNA denialist on a tirade

When I decide to take a break from the mad scramble of organizing my classes, I really shouldn’t follow a whim and take a peek at Uncommon Descent. The lead article has this astonishing opening paragraph.

Remember the dark days of vestigal organs? You know, back when there was a list of 180 vestigal organs? Or remember the days of junk DNA – when repetitive DNA, large regions of non-protein-coding DNA, and all sorts of mobile DNA were assumed to be non-functional simply because the investigators had assumed Darwinism rather than design?

I’m half a century old. I remember a lot of things, but I don’t remember those.

There were and are still vestigial organs, and nothing any creationist has ever said has refuted that. They constantly confuse “vestigial” with “non-functional” — the appendix, for instance, is a functional section of epithelium with many of the specialization we associate with other regions of gut epithelium, but it has lost the utility of acting as a fermentation chamber that we see in other mammals, and is greatly reduced in size…therefore, it is a vestigial cecum. The coccyx is a set of fused bones that still has muscles attaching to it, a blood supply, and sensory innervation, but it is a greatly diminished relic of the prominent post-anal tail of other vertebrates…therefore, it is vestigial. I really don’t understand what’s so hard to comprehend about all that; if you want to argue that your coccyx is not a vestigial tail, then please do show me how you can swat flies with it, or extend it caudally to assist in your balance, or attract mates in front of you with its display.

I remember the days when cell biologists were describing satellite DNA and all those other interesting repetitive sequences (OK, actually, it was a little before my time, but the questions were still rumbling about). I remember Arthur Whitely telling us about this stuff and scratching his head and wondering what it did — there was initially no assumption that it was non-functional, and if Darwinian preconceptions fed into the argument at all, it was to suggest that there must be an underlying utility to such ubiquitous elements of the genome. What led to the conclusion (not assumption) of non-function was observations of its nature and experimental work that showed it was highly variable, and changed and deleted without observable consequences to the organism. It also helped that comparative work showed no discernable pattern to the distribution of the stuff. Junk it was, and junk it still is.

This gibbering creationist showed right there in the beginning that he doesn’t know what he’s talking about, and he makes it worse a little farther down.

I’m not big into counting genes, especially as regulatory regions (you know – “Junk DNA”) seem to be as important as the genes themselves.

Regulatory regions have been known since the 1950s. I know regulatory regions; developmental biologists are acutely interested in them, sometimes to the point that they forget that there are functional genes attached to them. And I assure you: regulatory regions have never been classified as junk DNA. Junk DNA and regulatory regions are not synonyms.

What has this clueless ideologue frothing at the mouth is that he has learned a tiny bit about how human DNA sequences are analyzed to find genes. What scientists do is search for sequences called open reading frames (ORFs) that meet a simple criterion: they have to begin with an initiation sequence, the three nucleotides ATG, and they extend until there is a stop codon. Any given 3-nucleotide sequence, though, will appear with a fairly high frequency in a random stretch of DNA, about once every 64 nucleotides, so just finding an ATG and announcing that there is a gene doesn’t work. If every ATG marked the start of a gene, which seems to be the idiot creationist criterion, we’d probably have about 47 million “genes”.

So the genomics people use other criteria. One is length: something that codes for one amino acid before coming to a halt is not likely to be a real gene, but a 300 amino acid sequence is fairly typical. Another is comparative: if an ORF has no homolog in other species, if it seems to be completely new and different from anything in any other genome, it’s probably a random sequence and not a true gene at all.

Our frothing demented creationist is very upset about this criterion, because it applies evolutionary principles to sequence analysis—he says it makes “Darwinism to be the official rule book for analyzing the genome”. This is actually true. Evolution has proven itself to be a very useful tool for analyzing sequences. It works! The ID approach seems to be that there should be many more genes in the genome (47 million?), therefore they want to strip away any refining technique that removes false positives, and want to accept the slackest, loosest, most undiscriminating criteria they can invent.

I will throw the poor guy a bone, though. The concluding paragraph of the press release he is citing is a mess; you can’t use a set of genes filtered by comparative criteria to then declare that the mammalian genome has experienced little innovation. You have to use other information, like expression and function and developmental data that are independent of evolutionary interpretations to do that. A next step is to ask if you can find the ORF sequence in an expression library, for instance, in which you have copies of all the transcribed message RNA for a cell. Unfortunately for the creationist, we do have such information for many genes (but not all; we’re a long way from completion), and that also supports the evolutionary explanation.

I think next time I get an idle moment, I’d rather read Genomicron. Ryan Gregory discusses the same issues, but unlike the poltroons of Uncommon Descent, he actually knows something about the subject.

Comments

  1. #1 David Marjanovi?, OM
    January 23, 2008

    A single three-nucleotide sequence to designate start-of-record?

    Not really. That’s the signal for the point where translation should start. Transcription has different, and longer, starting signals. But you are right that the length is nowhere encoded — nor is there a way the repair machinery could measure it, as far as I can imagine.

    BTW, the whole thing is digital. It just has 4 states (ACGT) instead of 2 (01).

  2. #2 Bjørn Østman
    January 23, 2008

    PZ, I fear there may be some miscommunication going on here:

    The creationists care about vestiges because if an organ (or trait) is of no use, that would support evolution, and falsify creationism, since “why would God give us an organ of no use?” Therefore, when we communicate with these people, we should give examples of vestigial organs that have no current use. If the vestige has a (new) use, then the creationists can just claim that God created it with the that use in mind (e.g. the appendix).

    In other words, for arguments sake, vestiges can be split into two subcategories: 1) those that have acquired a new function, and 2) those that have no function (yet). When communicating with creationists, we should take care to think of the latter only.