Friday, May 11, 2007

ID vs ERVs-- Part Ten: The Red Queen Declares "OFF WITH HIS HEAD!"

You all will have to forgive me for totally mixing my 'Alice in Wonderland' and 'Through the Looking Glass' queens, but The Red Queen is the topic of this installment of 'ID vs ERVs'... and well, she whoops Mr. Black Holes ass.

You see, Mr. Black Hole is terribly offended by the very existence of the Dear Queen. Shes a path up Mount Improbable. She is another one of those non-intelligent creative forces that Creationists cannot fathom.

So who is this fiery babe? I hate to say "use common sense", because science rarely works on the level of "common sense", but common sense is a good way to understand the Red Queen. Start with a population of deer. There is a natural variation in how fast each of these deer can run within this population. There is a population of wolves nearby, also with a natural variation in running speed. Faster wolves catch more deer. Faster deer survive generating a population of deer with a natural variation of speed higher than that of the pre-wolf population. Then the wolves get faster, then the deer, etc etc etc. This goes on on a billion different levels. Deer with harder hooves can kick harder-- Wolves with thicker skulls dont get knocked out. Wolves with sharper teeth-- deer with slicker fur. Whatever you can imagine, I bet its wrestling with the Red Queen.

"WAIT!!!" you readers must be thinking. "So why dont we have deer running at the speed of light right now??"

Well the Red Queens sister is The Happy Medium. Lets use HIV as an example for the Happy Medium. HIV is the deer, our immune system is the wolves. HIV needs to evolve at a fantastically high rate to stay one step ahead of our immune system. HOWEVER-- the mutation rate isnt infinitely large. If HIV mutates too much, an infected cell wont produce any infectious progeny. Theyll all be mutant bastards. If it doesnt mutate enough, the immune system catches up. The Happy Medium is where HIV wants to be. But it can never escape the grasp of the Red Queen.

But Creationists dont see the world like you and I. You and I see a process like siRNA, and see an end result of billions years of evolution. Teeny tiny steps, twisting and turning with the Red Queen and the Happy Medium, everything being selfish for itself and accidentally bringing other bits on for the ride. A biological goulash resulting in what we see as siRNA.

Creationists just see the siRNA.

They see the peak of Mount Improbable.

They see magic.

So Im not at all surprised that Mr. Black Hole is completely and totally oblivious to the obvious answer to this 'unanswerable' question:

"One obvious problem with interpreting epigenetic control of REs/TEs as support for the selfish DNA story is the conservation and ubiquity of the phenomenon. Transcriptional and transpositional silencing of TEs are efficient and occur in fungi, plants, and animals. Epigenetic silencing mechanisms can thus be said to be a derived character present in all eukaryotes (a cladistic autapomorphy). It should be noted that the phenomenon is not sequence-specific, as artificial constructs such as transgenes can be inactivated. So in the face of the universality of tight epigenetic regulation of eukaryotic REs/TEs, a valid question, related to the topic of infectious TEs, is: how have any RE/TE families been able to transpose and/or amplify?"
Um. Well, viruses have their own epigenetic profiles. Host cells have epigenetic profiles. They are in a Red Queen race to see whos profile will 'win' (or some other weird messy merge happens). You can change epigenetic profiles through changes in the environment (dietary changes and such). Something that is 'silent' one day can be actively transcribed if, say, you arent getting enough to eat.

Mr. Black Hole doesnt get it. It seems as if he thinks if an ERV is silent NOW it has always been and will always be SILENT. "... How have any RE/TE families been able to transpose and/or amplify?"

His answer:
"A simpler interpretation is that the plesiomorphic epigenetic system determines which sequence will amplify and when, for how long, and at what levels. To put this another way, the multitude of "young" RE/TE families that have amplified in the context of a very conserved epigenetic control system suggests that the latter promotes element "selfishness," not that this system is engaged in an arms race with such sequences."
Post-modernist coagulated word-salad. 'Very conserved epigenetic control system'? What does that mean, 'very conserved'? The 'epigenetic control' of say, your liver cell vs a red blood cell is totally different. The 'epigenetic control' of your liver cell vs a liver cancer cell vs a Hepatitis C infected liver cell is totally different. Epigenetic landscapes change!
Mr. Black Holes data-free answer is that new ERVs have popped up because our epigenetic profiles wanted them to reproduce. Our and the ERVs epigenetic profiles arent competing-- everything happens for pre-programmed 'reason.'

"The crux of the matter is basically this: the currently emerging model of the genome—opposed in all details to the atomistic model—logically entails that selfish DNA as a general phenomenon is an impossibility..."
Selfish DNA is impossible. The Red Queen doesnt exist. Blue isnt a color. Shit tastes like bubble-gum. This paper is a grown man screaming "LALALALALALA VIRUSES ARENT SELFISH! LALALA VIRUSES ARE JUST PINING FOR THE FJORDS!"

What does the Queen have to say to that? "Humph! OFF WITH HIS HEAD! Hes certainly not using it."

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