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Atheists with vaginas.

Fri, 20 Nov 2009 20:00:47 -0500

I am so pissed off. I didnt get out of the lab until quarter till 6 tonight, so there was no friggen way I could get down to OU to see Barker (feed/potty Arnie, feed/potty me, 15 mph on I-35... I would have gotten there by the time his presentation was over. Why the hell is it that on Friday nights I have loose, whatever plans, I can sneak out early at 4, but the Friday I want to leave early, I end up being wrapped up in BL-3 till 5 fourty-fucking-five???? RAAAAAGE!!!)

So I was all hyped up for some quality atheist entertainment, and Im at home instead.

...

So Im going to bitch about w00mynz in atheism.

------------

PZ is awesome.

He gave me (and other female atheists) plugs on Pharyngula, and irl/online interviews when we were nobodies (I HAS BLAG I R FAMOOSE NAU!!!), and he hasnt even been properly certified by SciBlogs REAL Feminists^(TM)*!

My first link from PZ was on my debate with Lenny Horowitz.

Please note he made no mention of 'Guys shes a girl we need to support her!!'

He didnt say anything about my gender.

Just my arguments and a general 'Hurrah!' for support.

*thumbs-up*

While later he and I a conversation on bloggingheads-- We both threw back lots of ideas for things to talk about, and PZ was very adamant about giving me an opportunity to talk about being a woman in science.

Well, the thing is, I probably have a very different view of that than most people (not just women), so I didnt really want to, but PZ kicks ass and wanted to give me the opportunity.

*thumbs-up*

I would be crushed if I found out PZ didnt really like (or even listen to) my debate, but felt the need to link to more female bloggers, and I was good enough.

I would be crushed if I found out PZ didnt really want to talk to me on blogging heads cause we could clear the air on epigenetics, or he wanted to lol about our antics with Creationists, but just scanned his blog-roll for some female, cause he felt 'man guilt'.

So when atheist/skeptical groups are looking for speakers, I want them to say 'Oh Ive heard Abbie gives really good presentations on Creationism... maybe she will give a speech about being a scientist in a Red State!' or 'Weve never had anyone talk about HIV Denial, Abbie would be informative and funny!'

I would even be happy if they said 'Abbie is hot! Lets get her to perform a Rock Band concert for scholarships to AAI!'

*wince* I would rather be run over by a bus than be picked randomly off a list of 'FEMALE ATHEISTS' to fill a guilty diversity quota. "Um... I guess Abbie can talk about Creationism... we have 900 other people talking on it... whove been doing it longer... and were at Dover... but... um... shes got a vagina... soooo...."

I dont think this is what PZ means in his post at all, but I think it could be an easy knee-jerk reaction for organizers of these events-- "AAAH! We need more women!! Name more women!! Who? Ill Google her! Good enough-- whats another one???", so Im saying it straight up:

You want me for my expertise/perspective/body, fine.

Dont ask me just because Im female.

That would make me feel stupid, useless, and used.

Note-- WOOMYNZ opinions offered on ERV might differ from your local WOOMYNZ, so please consult and react accordingly.

* WHITE D00D!!! WHIIIIITE D0000000DE!!! D0000000000000DE!! *collapses in a pile of shoes, puke, and delusions*

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Turning 'crazy' into learnin-- XMRV from contaminated vaccines?

Thu, 19 Nov 2009 21:00:48 -0500

I hate how the 'new' Technorati doesnt let you see everyone whos linked to you. Sometimes, smaller blogs with less traffic write a neat post and link to me, but I dont 'see' the post unless I happen to catch one of their readers clicking to me on SiteMeter.

*FROWNY FACE AT TECHNORATI*

I just happened to catch an interesting post at this blag, Shiningthelights Blog. Dude might be nuts, I dunno. But I do like a Q they brought up (a month ago, *FROWNY FACE AT TECHNORATI*):

Is a mouse leukemia virus contaminating vaccine reagents the cause of Chronic Fatigue Syndrome?

Now, this Q might be coming from a place of deep distrust of all vaccines or the government or whatever-- I dunno. Doesnt matter. Can you answer that Q? Then its a good learnin opportunity, even if it comes from a place of crazy.

Do I think XMRV came from a contaminated cell line? It was one of my posts that got referenced, Oops: Contaminated cell-lines from the NIH.

No.

But thats partially because I think XMRV has shit (or is one of many components, almost shit) to do with Chronic Fatigue.

Its also because there are a gazillion cell lines with +gazillion uses-- And TZM-bls have nothing to do with vaccines. Like I said in that post, problems with that cell line are restricted to people using them as indicator cells for HIV-1 infection. Thats it. Thats all we use those cells for.

But still, how do we know? Can we be certain XMRV wasnt introduced to the population via vaccines?

Well, first we can wipe all the bacterial vaccines off the list (diphtheria, tetanus, pneumococcal, haemophilus influenzae type b, pertussis). Bacterial vaccines arent anywhere near cell lines.

Then we can knock out anything grown in yeast (HPV, Hepatitis B).

And measles, mumps, and influenza are grown in eggs.

Polio is a sturdy little mo-fo. The stuff we have to do to it to 'kill it' would blow the brains out of a wussy, fragile, enveloped retrovirus like XMRV (I just have to use a teeny tiny bit of formaldehyde to kill HIV-1 in the lab).

The people who have CFS now are too old to have gotten the chicken-pox or rotavirus vaccine, so Im not looking them up.

So... we are left with Rubella and Hepatitis A. They are the only ones attenuated/grown in human cells... but theyre lyophilized, and have formaldehyde... Thatll pretty much kill XMRV.

I guess technically, that evil 'formaldehyde' is actually kinda protecting you from wayward/undetected/undiscovered viruses in vaccines...

Even ignoring that the epidemiology of XMRV in vaccines-->CFS doesnt make sense, Im not concerned that vaccines meant for human use have XMRV in them.

*shrug*

But it was a good question!

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An open invitation to Bill Maher

Wed, 18 Nov 2009 22:00:25 -0500

Hi Bill!

I think Ive figured out why youve been... unresponsive... to the Skeptical communitys efforts to educate you on vaccines.

All the people addressing you have been cranky old men.

Apparently you dont swing that way.

I hearby offer to give you a personal crash-course in immunology, virology, and why scientists are so 'into' vaccines.

In my bikini.

Skeptic community gets you to quit spouting anti-vaccine BS on TV (and 'Twitter'), you get an out for admitting youre wrong ('34D! Id believe anything she said!') and can put this topic behind you.

Call my people.

Yours in Christ,
Abbie

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Virus helps save the American Chestnut tree

Mon, 16 Nov 2009 08:33:49 -0500

100 years ago, American Chestnut trees grew up and down the East coast. Great wood, nommy nuts, awesome! Unfortunately, an epidemic of an Asian fungus, Cryphonectria parasitica, basically wiped them out.

Asian Chestnut trees are resistant to the Asian fungus, so theoretically we could 'save' the American chestnut industry by planting Asian trees here... but they dont have the same beneficial features of the American species.

How can we save the American Chestnut?

Solution 1 (in progress)-- Keep crossing Asian Chestnut trees with American chestnut trees until you get a tree with American characteristics and Asian fungus resistance (or take a shortcut and make a GMO).

Solution 2-- While Solution 1 is going, give currently surviving American Chestnut trees a therapeutic vaccine. Therapeutic vaccines dont prevent infection like the vaccines you are familiar with (like MMR, which prevents measles/mumps/rubella), they are given post-exposure to limit pathogenesis.

American Chestnut trees with Asian fungal lesions are given a 'vaccine' in the form of more fungus... but this fungus is infected with a fungal virus, hypoviridae. The virus goes on to infect all of the fungus infecting the tree, weakening the fungus so the trees immune system can kill it off!

Fleas on the backs of fleas!

You cant use virus/fungus as a prophylactic vaccine, as plants dont have an adaptive immune system like we do (they dont 'remember' pathogens theyve seen before). But this therapeutic 'vaccination' strategy can keep the American Chestnut population alive long enough for the breeders to find a permanent solution!

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Dan Barker at OU!

Sun, 15 Nov 2009 12:49:05 -0500

Dan Barker of the Freedom From Religion Foundation is going to be speaking at OU this Friday!

November 20
6:30 pm
Dale Hall

I-35 is Hell in the evening rush hour (last time I went to Norman we were going 15 mph. on an interstate. RAAAAAAGE!!), plus its a Friday, so all you OKCers make sure you leave early enough to get there on time!

Dan is going to be speaking on 'How to be good without God'.

Know what will be funny? If CFI cancels their invitation cause they insist Dans speech be pre-approved, and he wont change stuff they dont like, and then he shows up anyway, and we all beat-up/mace Annie Gaylor...

Too bad that wont happen, cause OUs CFI is made up of some fun, open-minded kids, and its not a troupe of morons.

lol!

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Modified virus lets blind kids see (and some adults too)

Fri, 13 Nov 2009 12:00:31 -0500

A long time ago, in a galaxy far far away, 'visionary' scientists like Francis Collins thought 'genetic diseases' were coming to an end. Because they believed in 'OGOD', 'one gene, one disease' (lol, *blink*), they were sure identifying 'disease' genes would... somehow... give us the ability to cure said diseases.

Unfortunately, even ignoring the technical issues weve had with gene therapy, OGOD isnt exactly how genetic diseases work. Yes, some are caused by one dysfunctional gene, like X-linked ALD I wrote about earlier, but many more are caused by a constellation of genes, environmental stressors on those genes, infectious agents colliding with malfunctioning genes at just the right time...

I dont want you all to get the impression that treating/curing genetic diseases is going to be as 'easy' as the previous post made it out to be.

This is the case with a form of blindness-- Lebers congenital amaurosis (LCA). People born with this disease progressively go blind in infancy-childhood. There are numerous forms of LCA caused by a combination of 13 genes. Where do you start when youre trying to treat a multifactorial disease? Take small steps. Simplify it.

Researchers knew 6% of all LCA cases are caused by a defective RPE65 gene. Without this enzyme, you cant metabolize Vitamin A (EAT YOUR CARROTS!), you go blind.

So they started there:

Age-dependent effects of RPE65 gene therapy for Leber's congenital amaurosis: a phase 1 dose-escalation trial.

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Three viruses join forces to treat X-linked adrenoleukodystrophy

Tue, 10 Nov 2009 20:49:18 -0500

X-linked adrenoleukodystrophy (X-linked ALD) is a demyelination disease in little boys. The kids are usually dead before they hit adolescence.

The demyelination mechanism is not the same as the demyelination disease you all have heard of, MS. With X-linked ALD, the kids dont have a functional ABCD1 gene. This means they cant break down very-long-chain fatty acids (VLCFAs) and they end up accumulating in the brain and screwing with the cells in charge of keeping up myelination, oligodendrocytes and microglia. Screw those guys up, screw up your myelin, screw up signal transduction in your brain and CNS.

X-linked ALD can be treated with allogeneic hematopoietic cell transplantation. You all can tell from the Wikipedia page, this isnt something you want to do unless you literally have no other options--

Hematopoietic stem cell transplantation remains a risky procedure with many possible complications; it has traditionally been reserved for patients with life-threatening diseases. While occasionally used experimentally in nonmalignant and nonhematologic indications such as severe disabling auto-immune disease and cardiovascular disease, the risk of fatal complications appears too high to gain wider acceptance.

Know what might be a better option, especially for kids who cant find transplant matches?

Retroviral gene therapy.

Hematopoietic Stem Cell Gene Therapy with a Lentiviral Vector in X-Linked Adrenoleukodystrophy

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Ongoing witch-hunt against Oklahoma scientists

Fri, 06 Nov 2009 10:30:49 -0500

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')

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Viral evilution in the lab-- 'Evolution before our eyes'

Wed, 04 Nov 2009 12:00:13 -0500

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.

Hat Tip to Teh Evilutionary Biologist!

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Nef: Savior and Satan

Tue, 03 Nov 2009 21:00:03 -0500

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.

Inhibiting apoptosis-- 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.

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 :)

* An acutely lethal SIV, and its name makes my mind scream "ITS PEANUT BUTTER JELLY TIME! PEANUT BUTTER JELLY TIME!!!!"

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Darwinathon: 12 hours of pure, unadulterated EVILUTION!

Sun, 01 Nov 2009 12:30:32 -0500

Im going to be speaking about one of the many ways I use evilution in the lab-- HIV-1 vaccine design!

If youre around OU tomorrow, come check out as many talks as you can!

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Why Oklahoma?

Wed, 28 Oct 2009 19:15:02 -0500

Im not gonna lie.

We got a lot of shit to put up with in Oklahoma.

Batshit insane politicians trying to ban scientists from the state, make federally funded research illegal, hold up HIV/AIDS funding for personal religious reasons, post medical identifiers of women who have abortions online... yeah, theyre just pretty much insane.

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.

Its very cooperative.

Which I love.

I dont want to worry about people putting sodium azide in my coffee, aright?

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!

So... thats why Oklahoma. :P

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Ben Stein literally cant get anything right.

Tue, 27 Oct 2009 20:30:09 -0500

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.

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Vote for Biofortified!

Mon, 26 Oct 2009 12:00:34 -0500

Biofortified, the PandasThumb of crop engineering, is in a contest.

A contest to win an interview with Michael Pollan and grant money for educating the public about GMOs!

GO VOTE FOR THEM NAAAAAAAAAAAAAAU!

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,

DOO EEEEEET FOR THE PAPAYAS!!!!

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!

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XMRV and chronic fatigue syndrome and prostate cancer: blink

Fri, 23 Oct 2009 12:00:18 -0500

Okaaaaaay...

*squint*

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.

It does not make sense.

Thus I think its an effect, not a cause.

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erv

Atheists with vaginas.

Turning 'crazy' into learnin-- XMRV from contaminated vaccines?

An open invitation to Bill Maher

Virus helps save the American Chestnut tree

Dan Barker at OU!

Modified virus lets blind kids see (and some adults too)

Three viruses join forces to treat X-linked adrenoleukodystrophy

Ongoing witch-hunt against Oklahoma scientists

Viral evilution in the lab-- 'Evolution before our eyes'

Nef: Savior and Satan

Darwinathon: 12 hours of pure, unadulterated EVILUTION!

Why Oklahoma?

Ben Stein literally cant get *anything* right.

Vote for Biofortified!

XMRV and chronic fatigue syndrome and prostate cancer: *blink*

Ben Stein literally cant get anything right.

XMRV and chronic fatigue syndrome and prostate cancer: blink