I'm a graduate student studying the molecular and biochemical evolution of HIV within patients and within populations. I also study epigenetic control of ERVs.
Though only a handful of ERV readers are from Oklahoma, I know all of you are familiar with the handiwork of Senator Randy Brogdon.
He was the fellow who recently tried to get Creationism taught in Oklahoma public schools (FAIL).
Dude is a fucking IDiot (and just plain old idiot) who hates science:
I am also disgusted with the yearlong one-sided celebration of Darwinism that OU is sponsoring on their campus.
Disgusted? Really? Not 'disappointed', or 'dismayed', or 'intrigued, so Im going to check it out', but disgusted? Fantastic.
So what happens when you combine:
1. Anti-science
2. New found hatred of the US federal government
3. Xenophobia/racism
4. Infantile inability to delay immediate gratification for long-term goals
???
Attacks on university professors performing federally funded research!
(link-- might not work, video #1 isnt embedding, and is occasionally disappearing, way to go 'News 6')
Professor Santiago Elena, one of the profs who presented at the Viral Evolution conference I went to last fall, is featured in a nifty video about watching evilution in action!
Evolution of Life: Evolution before our eyes
Just like I use evilution in the lab to understand the population dynamics of HIV-1 to create an HIV-1 vaccine, Dr. Elena uses evolution to understand how viruses evolve and adapt in plants, which will help us protect our crops.
Evolution isnt just about retarded monkey-fish-frogs. Understanding it has a direct impact on your quality of life.
Vpu has kinda been my accessory protein of choice here at ERV, but its not the only one with a super cool evolutionary history and super cool evolutionary implications.
Another particularly fun one is Nef.
This eeeeeeeety bitty HIV-1 protein (27 kDa) has a lot on its plate. Contrary to the 'expert' opinion of Michel Behe, who thinks viral proteins just 'gum up the works', Nef has several exceedingly specific functions--
Down-regulating CD4 from the host cell plasma membrane-- This is basically 'pissing on the fire hydrant'. HIV-1 requires CD4 on the surface of susceptible cells to initiate infection. HIV-1 doesnt want to share a cell with other HIV-1s, so one of the first things it does is haul all the CD4 receptors off the cell surface via clathrin coated pits (animation).
Down regulating MHC Class I from the host cell plasma membrane-- A simple Creationist might think that both CD4 and MHC are pulled off of the plasma membrane the same way. Since Nef just 'gums up the works', gumming up one surface receptor should gum up any surface receptor. This is soooooo not the case. MHC Class I molecules are essential components of a normal cell plasma membrane. They send up flags that say 'Everything is fine here! So dont kill me, k?' Viruses like to take down these flags, because they also can signal 'HEY! Im infected here! Better tell me to kill myself!' Viruses dont want that, so they take down the flags. Minor problem-- If no MHC Class I flags are there, another immune cell notices they are missing, and kills the cell. What Nef does, is specifically targets HLA-A and B, but leaves HLA-C and E alone, effectively keeping other immune cells from knowing anything is wrong with the infected cell. These are very very very specific interactions! Teeeeeeeeny tiny viral protein knows the difference between HLA-A and HLA-C. Thats nuts. Also, it takes these receptors off the surface an entirely different way than the CD4-- Its clathrin independent.
Your immune system doesnt technically 'kill' infected cells. It tells them to commit suicide (apoptosis). Infected cells do not want to die. They want to produce progeny virus, and kill the cell in the process. Thus Nef also has the capability to inhibit a couple of the ways your immune system tries to induce apoptosis, FAS and TNF. EEEEEEEEETY BITTY protein, all those functions.
At one point, Nef had the potential to be our savior. Between 1981 and 1984, eight people in Australia were infected with HIV-1 via blood transfusions from the same donor. This donor happened to have a mutation, where none of their viruses contained Nef. HIV-1, no nef. While this was during the height of the HIV-1 epidemic, people dying left and right, these eight patients were doing real damn good. Better than good. They were fine! None of them were progressing to AIDS, even without antiretrovirals! Scientists had hope that this meant we could make a live attenuated vaccine with delta-nef HIV-1!
Unfortunately, these patients never cleared the virus. And, three of them eventually progressed to AIDS (but responded to anti-retrovirals!) (one died from unrelated causes). Theres no way we could use that for a vaccine. *sigh*
Nef also turned into our nightmare. Know how HIV-1 always has the 'same genes that act the same way', according to Perfesser Behe? Nothing real exciting, he says? Yeah, this one time, back in the late 80's, we accidentally evolved an acutely lethal SIV.
Yes, you read that right. Acutely lethal SIV. As in, it kills you <13 days after youre infected. Not 10 years, less than 13 days.
Yeah.
Yeah.
Oops.
Scientists were passing SIV from sooty mangabeys in pig-tailed macaques. Its a stock-standard way of generating a live attenuated vaccine. Take the pathogen out of its native host, passage it in a non-native host, return the attenuated virus to the original host. The original host can usually fight it off better than the virus you started with.
Yeah, this didnt work with SIV. The 'new' SIV, 'smPBj'* had altered cell tropism, caused super friggen hyperactivated immune systems, and the monkeys basically shat their guts out and died.
All because Nef evolved a new function.
One amino acid mutation turned Nef into an ITAM, and all kinds of hell broke loose.
Happily, this variant of SIV is not found in nature, nor would we expect it to survive in nature (if you are pooping out your guts, you arent having sex to pass on the virus), but the artificial conditions we used in the lab allowed this variant to thrive.
Vpu aint the only cool eeeeeeeety bitty HIV-1 protein to have a fun evolutionary history :)
So a question I get rather frequently is "Why the hell did you decide to go to grad school in Oklahoma??"
Some might assume I only put up with 'Oklahoma crap' because I 'had to', which is certainly not the case.
The University of Oklahoma is actually a really great place to work (when I was a technician), and its been a great place to go to school! My professors are demanding, yet supportive. Knock on their door wanting their opinion/help on X/Y/Z, and they drop everything to help (though its probably better to email first to set up an official meeting-- just manners :) ) I have also seen the way my professors interact with one another, and its nice! Theyre always collaborating on something, happily letting other labs borrow a reagent or use an expensive piece of equipment.
The standard of living in Oklahoma also helps :) The $1600 a month I get as a student takes care of my car, a nice apartment (no roommates) walking distance to work, tons of Arnie goodies, tons of Abbie goodies, and I still put money in savings every month.
Do not underestimate the value of not being stressed about money during grad school.
Anyway, I was happy to see my Oklahoma decision 'vindicated' (as the CFS people would say) by The Scientist. University of Oklahoma Health Sciences Center campus is #4 on their 'Best Places to Work in Academia' list. The institution that hosted the viral evolution conference I went to last fall? The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, middle of nowhere. Theyre #9!
I dont know if I can think of anyone who gets everything wrong, so consistently.
Okay, sure he gets the Creationism thing wrong. Whatevs.
He also makes unwise financial decisions. Who doesnt, these days?
No, get this, dude cant even pick a charity without fucking up! A charity to help stop puppy mills! HE FUCKS IT UP!
1. The 'rescuers' in this video might support HSUS, but they are not some super-special HSUS anti-puppy-mill swat team (despite the fact they are coated head-to-toe in HSUS paraphernalia, except for one lady in uniform). Those rescuers? Theyre normal animal control officers of some city (note their badges). Normal animal control officers who do shit that I physically couldnt do without bawling my eyes out, every day. Part of their job, paid for by our tax dollars, is shutting down puppy mills.
2. Assuming those are HSUS swat team officers with made up badges and uniforms-- Where, exactly, are they taking those rescued puppies? To HSUSs well funded, clean, state-of-the-art animal shelters, manned 24 hours a day by trained veterinarians? Nope. HSUS operates no shelters, and only donates <1% of their hundreds of millions of dollars in income to actual shelters.
3. HSUS doesnt 'rescue' anyone, animal control officers do. HSUS doesnt take care of any pet once its 'rescued', animal control officers and local humane society shelters do. But HSUS gets to put out press releases and YouTube videos with Ben Stein, pretending they are the heroes. "WE SAVE PUPPEHS! SEND MONEY!" Money they can now spend on pursuing their PETA/ALF, anti-pet goals.
Ben Stein, you are quite possibly one of the dumbest people on Planet Earth.
1. Biofortified assured me that the interview with Pollan will be 'educational'. I dont think I can put into words how much I, personally, want to see Pollan grilled by some real scientists. Definitely worth a bit of obnoxious registering to vote.
2. Do you really want some anti-science, anti-GMO assholes getting $1500 to miseducate the public? Bleh its like the Discovery Institute winning $1500 to teach kids about SCIENCE! God... Im going to puke just thinking about that... Again, totally worth the obnoxious registering to vote for a pro-science group.
3. One of Biofortifieds contributors is a new SciBlogger, Pamela, at Tomorrows Table. I also suggested Anastasia and Karl to the SciBlog overlords MONTHS ago. *FROWNY FACE* *kicks overlords in the crotch*
4. If those reasons dont convince you, I can only say,
5. If you are still feeling a bit anti-science and queasy over GMOs, check out the rational comments made by the Biofortified contributors at the contest website, and contrast that with the sheer level of CRAZY coming from their anti-all-GMO rivals. Its comparable to the level of stupid/insanity we get from anti-vaxers, for real. Bleg.
Biofortified deserves the win-- take a minute to vote!
Let me preface this post by stating that I am not an MD. I dont care, particularly, about whether CFS is a 'real' disease or psychosomatic or a catch-all category for people MDs dont know how to treat. Sorry. So if you want to bitch about CFS, pro or con, dont do it in this post.
What I care about is retroviruses.
The behavior of this retrovirus in humans does not make sense as a causative agent for CF or prostate cancer.
I'm a graduate student studying the molecular and biochemical evolution of HIV within patients and within populations. I also study epigenetic control of ERVs.
