Oh, boy. Jonathan Wells explains why some of us reject the outrageous interpretations made from the ENCODE work claiming 80%+ functionality of the genome. It was really an effort to get past this sentence.

Some historical context might help.

Bwahahahahaha! First sentence, he makes a joke. Wells is a creationist clown notorious for his tortured abuse of the history of science. He doesn’t have a merely whiggish view of history — it’s more of a Burke&Hareish perspective, where if History isn’t conveniently dead to permit him to commit ghoulish atrocities on it, he’s willing to take a cosh to it’s skull and batter it into extinction. When Wells announces that he’s going to provide “historical context”, brace yourself for a graceless exercise in ugly alternative histories.

After James Watson and Francis Crick discovered the molecular structure of DNA in 1953, Crick announced that they had found "the secret of life," a popular formulation of which became "DNA makes RNA makes protein makes us."

What? I don’t even…OK, second sentence is wrong. That looks like a mangled version of the Central Dogma of molecular biology, with a weird appendage tacked on to claim that it “makes us”. Crick did not discover the secret of life. What the Central Dogma is about is the irreversibility of information flow: nucleotide sequence specifies the order of amino acids in a protein, but there is no mechanism to translate a sequence of amino acids back into a sequence of nucleotides in RNA/DNA. It’s an important concept, but not the secret of life.

But biologists discovered that about 98% of our DNA does not code for protein, and in 1972 Susumu Ohno and David Comings independently used the term "junk" to refer to non-protein-coding DNA (though neither man excluded the possibility that some of it might turn out to be functional).

More garbage. NO. No one equated non-protein-coding DNA with junk. Unless it was a creationist. In 1972, we knew about lots of non-coding DNA that wasn’t just functional, it was essential — genes for tRNAs and regulatory sequences, for instance. The term “Junk DNA” was initally coined to describe pseudogenes — gene duplicates that had been rendered nonfunctional by mutation. We knew that gene duplication was common, but that successful gene duplications, that is events that resulted in a copy with novel functions that would be maintained by natural selection, were going to be rare. So Ohno expected large quantities of such relics to be found in the genome.

Why didn’t biologists simply call non-protein-coding sequences "DNA of unknown function" rather than "junk DNA?" For some, it was because "junk DNA" seemed more suited to the defense of Darwinism and survival of the fittest.

No, because the term was initially applied to a specific class of sequences that were recognized as failed duplications. They weren’t of unknown function…they were the debris left over from unsuccessful natural experiments.

Now we know of other mechanisms that produce repetitive, non-functional sequences. There are transposable elements that have no purpose but to replicate themselves over and over in the genome, there are viral insertions, for instance. We know how they get there, and it’s not because their existence confers greater fitness on the bearer, or because they make active contributions to the phenotype. They’re just splatters of DNA.

The term “Junk DNA” is perfectly reasonable to apply to such mostly-useless sequences. I think the only legitimate argument against the term is that we have so many different classes of the material that more specific labels would be more useful…but the argument that these sequences are functional is a nonstarter.

In 1976, Richard Dawkins wrote in The Selfish Gene that "the true ‘purpose’ of DNA is to survive, no more and no less. The simplest way to explain the surplus [i.e., non-protein-coding] DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA."

Hey, Wells gets something mostly right! Yes, that’s correct, and it’s the explanation born out by observations of things such as LINEs and SINEs, which code for enzymes (or sequences recognized by such enzymes) that insert copies of themselves back into the genome. This isn’t just a supposition, we know how this works.

He gets the motivation behind the dispute completely wrong, however. We aren’t calling some sequences “junk” because we don’t know what they do: to the contrary, it’s because we know where those sequences come from and what they do. It’s also not because, somehow, it is a Darwinian prerequisite that “junk” exist in the genome. Again, to the contrary, there was initially resistance to the idea of junk because of a Darwinian bias towards seeing adaptedness in everything. The idea of non-functional DNA sequences that don’t contribute significantly to the phenotype emerged from observations of what we actually found when we started taking apart the components of the genome.

That’s why a lot of us are irritated with the ENCODE interpretation that the whole genome is ‘functional’. It’s not because of a philosophical predisposition, or because we apply the label by default to sequences we don’t understand, but because that conclusion rides roughshod over a lot of well-established evidence.

Oh. Right. In addition to history, evidence is another of those esoteric concepts that Jonathan Wells can’t comprehend.