Tuesday, September 04, 2007

Viruses are not magic

Add this to the list of Creationist-Denier similarities: Viruses can do anything.

A common Denier Claim is that HIV (or another virus if they completely deny the existence of HIV) works in magical ways.
Example One
Example Two

Creationists now have employed the 'Viruses=Magic' defense in my comments, in an attempt to save Behe:

Here's the link to an article that is looking at the similarity between Vpu and the M2 gene of Type A Influenza. The M2 produced protein of Type A Influenza, in mammalian cells, forms a viroporin. In the article I linked to, they demonstrate that Vpu "also forms
ion channels in planar lipid bilayers". It appears the basic chemistry of the Vpu, like the M2, spontaenously form such an 'ion channel'. It would be easy, I think, to simply suppose that somewhere along the line that SIV picked up the M2 from a chimp that was infected with Type A Influenza. The fact that the 'ion channel' seems to form spontaneously minimizes any supposed complexity that we want to attribute to Vpu on the basis of its forming a viroporin. Again, we might be dealing with just a few a.a. substitutions, and a "mutational powerhouse" like HIV should have no problem finding those a.a.'s.
Ian Musgrave put together a great response so I could ace my test today :)
Here's the link to an article that is looking at the similarity between Vpu and the M2 gene of Type A Influenza.

Functional similarity only in this paper. Vpu and M2 are structurally similar to the extent that "A hydrophobic N-terminal anchor is followed by a very hydrophobic C terminus, with at least 18 charged residues in each case." Klimkait et al. 64 (2): 621. J Virol. (1990). In terms of sequence, there is no significant sequence similarity between M2 and Vpu (sequences and alignments on request).

And it turns out that the conclusion of the paper you cite is that Vpu, while a cation channel, is not a proton channel like M2 (pg 7115):
It would seem, therefore, that Vpu channels are unlikely to be functionally analogous to the M2 and NB channels of the influenza viruses.


It would be easy, I think, to simply suppose that somewhere along the line that SIV picked up the M2 from a chimp that was infected with Type A Influenza.

Easy, but dead wrong. A) SIV Vpu is not a viroporin, the viroporin activity appeared only after HIV had infected humans for some time (remember this timeline. B) SIV Vpu and M2 viroporins share no significant sequence similarity. C) M2 viroporin and HIV-1 Vpu viroporins share no sequence similarity either; it is very unlikely that Vpu is a modified M2 in any form.


The fact that the 'ion channel' seems to form spontaneously minimizes any supposed complexity that we want to attribute to Vpu on the basis of its forming a viroporin.
It’s not complexity per se (but lots of proteins form structures spontaneously, from ion channels to the viron capsids themselves to flagella, the fact that it occurs spontaneously doesn’t mean it’s not complex), but the fact that Vpu has gained an entirely new function. Vpu is not a viroporin in SIV, HIV-1 class O or HIV-1 Class N viruses, it is only a viroporin in HIV-1 class M viruses.

So, during it’s stay in humans, HIV-1 Vpu has gained a new protein-protein binding site that allows it to form a viroporin, it has also gained a binding site that targets it to the Golgi apparatus (this isn’t present in SIV or early HIV-1 strains). Also, in the 60’s Vpu gains a membrane targeting sequence in the HIV-1-M C subgroup.

To summarize, since HIV has infected humans, HIV-1 has gained a minimum of 3 protein-protein binding sites (I’m ignoring a new Casein Kinase II binding site and there is probably also a new ion gating site as well in HIV-1-M C). In the "Edge of Evolution", Behe states a couple of times quite unequivocally, that HIV has developed no new binding sites (eg See page 143 and figure 7.4, page 144 of EoE, where Behe shows HIV having 0 new binding sites). So, Behe is dead wrong about HIV, and that is just looking at one HIV protein, let alone the rest of the HIV proteins. What else is he dead wrong about?

I would like to add a tiny bit more to this from the 'Viruses are not magic' file.
It would be easy, I think, to simply suppose that somewhere along the line that SIV picked up the M2 from a chimp that was infected with Type A Influenza.
Viruses are not magic. They are not a singular entity.
  • Influenza-- Segmented negative strand RNA virus, infects airway epithelial cells through endocytosis, needs RNA dependent RNA polymerase
  • HIV-1-- Double-stranded retrovirus, infects CD+ T-cells (eh, some other immune cells) through membrane fusion, needs reverse transcriptase
Square Peg. Round hole. These guys arent going to be swapping genes. Unless we do it.


5 comments:

Chris Noble said...

It would be easy, I think, to simply suppose that somewhere along the line that SIV picked up the M2 from a chimp that was infected with Type A Influenza.

Sal is right. It is easy to suppose.
It's easy to suppose that the magic man dunnit too.

It also strikes me that both evolution deniers and HIV deniers fail to distinguish between functional homology and sequence similarity

Tyler DiPietro said...

"It also strikes me that both evolution deniers and HIV deniers fail to distinguish between functional homology and sequence similarity"

This is true of a lot of people, really. In my mind it's one of the many problems that come from the overuse of the "computer code" metaphor. It often obscures the true limitations of DNA by giving people the impression that the pairing of nucleotides has some kind of defined syntax; people are surprised to find out that genomic sequence similarity means approximately squat.

Tyler DiPietro said...

That should read "often means approximately squat" above. Don't want to come off as overly broad.

quantok said...

Still trying to get my head around Sal's thought processes.

He reads a specialist scientific paper and decides he can draw a conclusion about the origin of Vpu in HIV that the authors of the papers themselves missed.

Subscribers to UD must be awestruck by the fact that Sal can peer review papers at any level of difficulty and in any subject area, and still find profound scientific truths no one else has spotted.

Surely this must be the finest intellect the universe has seen since the Big Wet Hissy Fit.

ERV said...

Chris-- Its actually a different poster. I didnt put their name on the post because I didnt figure they would ever come back, but they did, and theyre still "...fail(ing) to distinguish between functional homology and sequence similarity".

*head banging keyboard*

quantok-- Creationists know everything. The rest of us are just trying to catch up.