Thursday, August 30, 2007

SHIV vs HIV vs SIV: Creationists know everything

... Except how to read.

Towards the end of The Great UD Adventure, Sally decided he knew more about HIV and the HIV research world than me. Granted, lots of people do know a hellovalot more about HIV research than me.

But Sal is not one of those people.

So like I did before, lets use Creationist Behavior as a learning opportunity!

I’m having problems accepting that viropoin capability was novel after emergence in humans in light of this paper:

Scrambling of the amino acids within the transmembrane domain of Vpu results in a simian-human immunodeficiency virus (SHIVTM) that is less pathogenic for pig-tailed macaques.

To date, no studies have been performed to assess the role of this domain in virus pathogenesis in a macaque model of disease. Using a pathogenic molecular clone of simian human immunodeficiency virus (SHIVKU-1bMC33), we have generated a novel virus in which the transmembrane domain of the Vpu protein was scrambled but maintained hydrophobic in nature (SHIVTM), which presumably would disrupt any ion channel TM properties of this protein

Thus, these results show for the first time that the TM domain of Vpu contributes to the pathogenicity of SHIVKU-1bMC33 in pig-tailed macaques.

This paper would appear to weaken the claim that even if “Viroporin capabilities have not been found with SIVcpz Vpu”, that they emerged brand spanking new in humans.

Thus, this would appear not to be an appropriate counter example to Behe’s claims. The fact that one may not see a function in one strain does not imply that it emerged brand new in another strain. It is entirely possible this was a loss of fucntion, and with respect to the issue of this viroporin capability, it was a loss of function (if at all).

Speaking of which, were there even studies done on SIVcpz regarding scrambling of the TM domain? Can’t very well find them if one doesn’t even look for them.

Now, dont laugh at him. Reading is really hard for some people. Maybe he didnt notice the title of the paper he cited:

Scrambling of the amino acids within the transmembrane domain of Vpu results in a simian-human immunodeficiency virus (SHIVTM) that is less pathogenic for pig-tailed macaques.

Thats less pathogenic, folks. Screwing with Vpu makes SHIVs less pathogenic.

Maybe Sal doesnt know what a SHIV is. Hmm... That cant be possible, because the authors of that cited paper define their SHIV right in the intro:
The simian-human immunodeficiency virus (SHIV) is a chimeric virus that contains the tat, rev, vpu, and env genes in a genetic background of SIVmac239.
The tat, rev, VPU, and env genes are from HIV-1. The remaining proteins come from SIVmac. Creating these chimeras is one way we can study AIDS in non-human primates. For instance, pig-tailed macaques cannot be infected with HIV-1, but if you exchange a few HIV genes with SIVmac genes, you can infect them and study AIDS at an organismal level!

And lo and behold, thats exactly what the authors did.
Our laboratory has been using a pathogenic simian-human immunodeficiency virus (SHIV)/macaque model to examine the role of Vpu in disease. Using the pathogenic molecular clone SHIVKU1bMC33, we previously showed that an intact Vpu contributed to the CD4+ T cell loss that occurs during infection with the pathogenic SHIV and that disease in macaques only occurred if compensating amino acid substitutions occurred in the Env and Nef proteins. In order to study the role the TM plays in vivo to enhance pathogenesis, we constructed a mutant SHIV virus (SHIVTM) in which the TM domain of the Vpu protein was scrambled but kept hydrophobic as previously described. In this study, we have analyzed the in vitro replication of this virus and its ability to cause CD4+ T cell loss and disease in macaques. Our results indicate that SHIVTM was not as pathogenic to pig–tailed macaques as the parental SHIVKU1bMC33, indicating that the TM domain contributes in part to the rapid CD4+ T cell loss and disease onset caused by SHIVKU1bMC33.
If you screw up the transmembrane region of HIV-1 Vpu, you get a less pathogenic virus that cant kill CD4 cells as efficiently. Thats what I said. So in addition to no experimental evidence for viroporin formation (see my essay references), this group found no genetic or biochemical reason to expect viroporin capabilities in SIVcpz. Thats also what I said.

*shrug*

You could have read my essay 100 times in the amount of time it took you to find that paper, Sal. Read. Read slowly. And then think reaaaal hard about whether you want to ask an HIV researcher a question, or whether you want to tell that HIV researcher you know more about her specialty than her. Save you some embarrassment in the future.

14 comments:

Salvador T. Cordova said...

You missed the fact that I said at UD:

"I am still unsure of the SHIVTM paper,"

So thank you for clearing that up. I was hoping to get info on that data point from you. Very kind of you to help me out.

I did ask however this question,

"Did Vpu pre-exist in the HIV strain prior entry into humans?"

I'm afraid I missed your response. You kept saying that was my premise, is it not yours?

olegt said...

Sal,

This has become a farce. Abbie is banned from posting at UD but you still let her speak by copying and pasting her responses from this blog. Be a man and restore her posting priviliges at UD. You are a moderator there, after all.

Besides, I am sure you will feel better on home turf and finally deliver the promised coup de grace in front of a sympathetic live audience.

We'll be watching intently.

ERV said...

lol! No, thank you Oleg, but after they wouldnt allow me to post without 'moderation' I wasnt planning on posting/visiting there any more anyway (I copy/pasted the thread just before I found out I was banned this morning).

*shrug* Its the internet. Sal can copy paste me just like anyone else.

quantok said...

Over at UD contributor 'bornagain' is bigging up Sal's slaying of the foul-mouthed Darwinist in Skirts with his 4-point list of biochemical congruences of SIV/HIV.

The claim is that Sal gleaned from peer-reviewed papers (which ERV cited) information that actually refutes her claims of the appearance of new biochemical mechanisms for Vpu since entering humans. The implication is that HIV is a 'degrading' genome not an evolving one, since all its major properties are already present in SIV.

Here are the devastating truths ERV would like to cover up:

1. Vpu pre-existed HIV entry into humans

Which is what ERV's Musgrave phylogeny diagram showed.

2. CD4 degradation capability existed before HIV entry into humans.

And ERV told us that in her first post: "The feature both Vpus have in common, CD4 degradation, is carried out in completely different ways. HIV-1 Vpu requires two casein kinase II sites. You could almost call it irreducibly complex-- If you dont have both CKII sites, CD4 isn't degraded. Yet some SIVcpz Vpus have only one CKII site, and instead utilize a simple string of negatively charged amino acids in place of the second site 11. Different ways of performing similar tricks with totally different amino acids. I think that's biochemically significant as well."

Same capapbility; novel method.


3. viral release regulation via Vpu existed before HIV entry into humans.

I'm stumped by this vague claim. Does he mean the regulatory method is identical in SIV and HIV? That there's no novel bichemical functions?

What about this in ERV's original post on Behe: "It turns out that one of the biochemical differences is that Subtype B Vpus have a Golgi retention signal in the second alpha-helix of the cytoplasmic domain 13. This means that Subtypes B Vpu prefers (if you will excuse me personifying a virus) to be in the Golgi, helping degrade CD4, while Subtype C Vpu prefers to be in the plasma membrane, assisting with the release of new viruses."

4. possibly even ion channel capability existed before HIV entry into humans.

Possibly? Not on any evidence in the cited papers it seems. See SHIV vs HIV vs SIV post on ERV.


What am I missing here? Why has UD declared victory?

What this seems to amount to is a rehash of the "it's still a virus" denial. Phrase the properties of an organism in suitably vague terms and it will always seem as though nothing new has emerged.

I admit I can barely tell a virus from a vibraphone but I can read: and none of the claims being made over at UD (the coup de grace, no less) are substantiated by the abstracts of the cited papers, and which ERV has honestly summarised.

The Factician said...

If HIV evolved, how come there are still monkeys? No, wait, if HIV evolved, how come there are still viruses? No, no, no. It's if HIV evolved, how come it doesn't have a brain and opposable thumb yet?

Salvador T. Cordova said...

Olegt wrote: "This has become a farce. Abbie is banned from posting at UD but you still let her speak by copying and pasting her responses from this blog. Be a man and restore her posting priviliges at UD. You are a moderator there, after all."

Olegt,

My moderator privileges are not as high as DaveScots. I do not have the authority to over-ride DaveScot. My privilege level there is not as high as his.

I must appear here at Abbie's blog to discuss my case because I can not do so over there.

Everyone here is free to take shots at me and ridicule me here. I certainly can't be accused of hiding since I am here at ERV home advantage.

She now can ban me, and the discussion will cease.

I accept the disadvantage of being here where I'm outnumbered 20 to 1.

That said, I opened with a simple question,

"Did Vpu pre-exist in the HIV strain prior entry into humans?"

I don't think it is much to ask to have it answered by Ms. Smith. I would expect you would want to hear the answer from Ms. Smith.

It's not that hard a question. And there will only be a few followups and we'll be done with the matter.

If she wants to drag this on she can choose to not answer.

regards,
Salvador

The Factician said...

My moderator privileges are not as high as DaveScots. I do not have the authority to over-ride DaveScot. My privilege level there is not as high as his.

Meaning DaveScot is a grand poobah, and you are a lesser poobah? Do you guys have a secret handshake? What are your titles, exactly? You actually do name the intelligent designer at your secret meetings, right? Is it Zeus? Come on, I want it to be Zeus...

ERV said...

If she wants to drag this on...
Why dont you start with reading my fucking post from a month ago that explained that clearly. Then why dont you read the proceeding posts that reiterated my answers to that question. Then why dont you read the comments that I wrote for you answering that question. Then you can read the posts OTHER people wrote answering that question by TELLING YOU EXACTLY where I wrote comments AND posts for you before.

Are you retarded?

Salvador T. Cordova said...

Ms Smith asks "Are you retarded?"


Apparently so, that's why I just wanted to make sure that you are indeed answering "YES" because you kept accusing me that it was "my premise" that Vpu pre-existed in HIV prior to entry into humans.

So is it your premise as well that Vpu pre-existed in HIV prior to entry into humans?

For the sake of retarded individuals like myself and the mentally impaired readers who do not quite have the ability to appreciate your literary flourishes, a simple "YES" will clarify the matter greatly.

Thank you in advance.


regards,
Salvador

Torbjörn Larsson said...

Using hybrid virus as example of common traits, hilarious!

As regards Cordova's insistence, hmpf, a yes is a yes even if not repeated.

But, I can cut and paste earlier comments with the best of creationists, thus answering quantok ("Why has UD declared victory?") in the process:

Salvador Cordova:


The first question I posed was, "did HIV-1 have Vpu when it entered humans?"


This is already answered in full in ERV's original post.

"“Sure it’s new in chimpanzees, but its not *new* in HIV-1!” Sorry, you’ll find no escape with that limp-wristed, ad hoc parry. SIVcpz Vpu and HIV-1 Vpu act in different ways, biochemically,"

So Behe claims no functional change in HIV, while ERV describes a lot of finds pertaining to before and after SIV evolved into HIV.

I know this as the last defense of the unable, to repeat an already answered question in varied forms. Pretending not getting an answer serves them as well when they want to claim that science has not the answer they don't want to hear.

I don't expect any new or *new* new questions. Yawn.

Chris Noble said...

I accept the disadvantage of being here where I'm outnumbered 20 to 1.

It seems that you real disadvantage is holding a position that is not supported by the evidence.

Smokey said...

Sal wrote:
"My moderator privileges are not as high as DaveScots. I do not have the authority to over-ride DaveScot. My privilege level there is not as high as his."

Then given that everyone is aware of Dave's intellectual cowardice that leads him to ban anyone with any real knowledge of biology, it was highly unethical of you to invite Ms. Smith to post at UD. It's like inviting someone to stay at your mom's house when she's widely known for not tolerating house guests.

"I must appear here at Abbie's blog to discuss my case because I can not do so over there."

That's nobody's fault but yours.

"Everyone here is free to take shots at me and ridicule me here. I certainly can't be accused of hiding since I am here at ERV home advantage."

We'll accuse you of hiding when you run away, as you did when you were challenged to apply Dembski's Explanatory Filter, which in the 9 years of its existence, has yet to be used to explain anything.

"She now can ban me, and the discussion will cease."

Why would she want to do that? She's kicking your sorry ass up into your throat, Sal!

ERV said...

lol! Its about sex, smokey! They get off on this. BDSM. And when I stopped beating Sal for a second, just to see how he would act-- did you catch his response? Priceless!

Zachriel said...

factician: "If HIV evolved, how come there are still monkeys? No, wait, if HIV evolved, how come there are still viruses? No, no, no. It's if HIV evolved, how come it doesn't have a brain and opposable thumb yet?"

SIV evolved into HIV. That's only a single letter substitution.

Microevolution.