Wednesday, January 16, 2008

Crazy places you find HIV Deniers

Rants & Raves, the new hangout for infidels on the internet, is my new favorite forum. There is (so far) no moderation, so its a strange combination of logical arguments and references, sprinkled with insults and boobs. I think its wonderful :)

I wasnt aware that it had become so popular until I started noticing the woo-ers coming out of the woodwork. First the anti-vaxer from, now an HIV Denier. If the poster isnt being a poseur, its none other than David Rasnick.

The same David Rasnick who 'collaborated' with Matthias Rath, a professional woo-er who says vitamins can cure AIDS and cancer.

Thats another topic for another post, but what the heck is Rasnick doing on Rants & Raves? Posting on a thread about a new HIV study you might have seen on the news:
Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen.

I dont even have to go through his whole post-- the first sentence could not be made by a virologist with a sound mind:

I was surprised to learn the Harvard study led by Professor Stephen Elledge was conducted in highly aneuploid "HeLa-derived TZM-bl cells". I've worked the past 11 years studying the consequences of aneuploidy and feel I should pass along some of my concerns about the study's experiments and the authors' conclusions.
I cannot, for the life of me, figure out why this dude is 'surprised' at the use of a cell line called 'TZM-bl'. TZMs are standard in HIV research laboratories. To any HIV researcher, why these cells were used by Elledge et al is shockingly obvious. Even to someone unfamiliar with modern HIV research, like an HIV Denier might be, the reason why this cell line was used is described on the first page of the article.

HeLa cells are a cell line derived from a 1951 case of HPV induced cervical cancer (side note: some say they are no longer human). TZMs are special HeLa cells that have basically been genetically engineered for HIV research-- They express CD4 (normally only expressed on T-cells, the target of HIV-1), and the TZMs genome contains two 'reporter genes'. If the TZM is infected with HIV, a protein tat will start transcribing the two reporter genes! One reporter gene you can stain with a dye and see underneath a microscope, like I did in this post. You can also use the other reporter gene by blowing up all your cells and doing a luciferase assay.

So an HIV lab using TZMs should not be surprising to anyone supposedly as familiar with HIV research as Rasnick.

Ignoring all of that, Elledge et al also explained specifically why they used TZMs in their paper and in supporting materials. They needed the reporter genes for their initial controls and in their experimental procedures. Those reporter genes are not in patient donated PBMCs. They also gave other reasons for why TZMs were used, though they were not ideal:
TZM-bl cells were chosen due to limitations in experimental methods using more relevant T and macrophage cell lines. They proved useful for screening because they are easily transfected with siRNA, are hardy enough to survive high throughput manipulations and support a full HIV lifecycle to produce infectious virions.
There are positives and negatives to all cell lines, but there are also positive and negatives to using fresh PBMCs. There are positives and negatives to using animal models or human subjects.

Im going through all of this with my own research-- I started with cell lines, then I moved to using PBMCs. Then Im going to try organotypic cell cultures, then animal models, then hopefully I will have a PhD and pass the project to someone else :) But while I want my research to be as biologically relevant as possible, Im not going to wait until vaccine trials to publish a friggen paper.

Ugh, friggen stupid comment from a stupid friggen Denier.


Anonymous said...

Just read both the relevant RnR thread and your blog post.

I'm not a professional biologist, but I've had enough of a proper science education to know that what you posted makes eminent sense. But then I'm probably fortunate in that respect - as in having had a proper science education. I have the good fortune of living in a country that doesn't allow science classes to be compromised by religious ideology - yet.

DS said...

Nice post. It's a tired old argument when people bring up problems with immortal cell lines. As with any argument there's a morsel of truth there, the cells are certainly messed up and people have to be careful how the results are portrayed. But HeLa cells have been used for generations and are a fantastic tool for basic research. Not having read the paper, I can't vouch for this, but I seriously doubt someone like Elledge would overstep his bounds on this. In any case, it is entirely stupid to act surprised at the use of these cells, they are ubiquitous in biomedical research. And it's even stupider to dismiss an entire body of work because of their use.


Anonymous said...

Just a note that the article you have linked to "no longer human" contains a rather glaring error stating that "It’s a fundamental tenet of evolutionary theory that evolution doesn’t repeat itself."

This is obliviously false, i.e. convergent evolution etc. There is nothing in the theory that makes it impossible or even improbable that evolution will repeat itself.

Chris Noble said...

How dare you criticise the imminent scientist David Rasnick.

His groundbreaking research proved that vitamins can cure AIDS.

Scientifish Evidence

The experimental design used in the trials reveal Rasnick's brilliance.

a) No control group
b) Many patients also on ARVs
c) Deaths not mentioned

Please learn from the master.

trrll said...

"This is obliviously false, i.e. convergent evolution etc. There is nothing in the theory that makes it impossible or even improbable that evolution will repeat itself."

Untrue. Convergent evolution is recognized as convergent precisely because evolution did not repeat itself exactly. Instead, it filled the same niche as another animal but by a different evolutionary route.

The expectation that it is improbable that evolution would repeat itself derives from a huge amount of information about development, genetics, protein structure, and biochemistry, which show that there are typically multiple ways of accomplishing a particular functional, developmental, or regulatory biological end. Each mutation that divides one species from another is a decision, for which there are likely many other possible alternatives that would similarly affect fitness. So for the hundreds or thousands of mutations that distinguish different species, the probability that the exact same sequence of mutations would repeat itself is probably less than expecting a game of poker to repeat itself exactly.

jfatz said...

I can see how you might enjoy the place. ;-)