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.
Look, I like weird people. Goth kids. Sci-fi geeks. Language nerds.
Weird people are far more interesting than, say, the 'normal' people that get cast for shows like 'The Bachelor': Generic Human #231975, Generic Human #576930, Generic Human #750193, bleh.
But theres a whole different level of weird, and that level is 'Creationist'.
Example: Remember that guy, that Creationist that branded kids in his Ohio classroom? Had a whole system of weird signals and words and stuff he was brainwashing kids with?
The caller purportedly told Freshwater that the school had discarded some documents in a dumpster at the high school and that the documents contained information that would exonerate him. Sometime during the night of the 4th or morning of the 5th, Freshwater, his lawyer R. Kelly Hamilton, and his pastor Don Matolyak are said to have gone through one or more school dumpsters, removing some documents and taking them to Matolyak's church, Trinity Assembly of God, to go through them.
The materials were not in a dumpster at the high school, but were by a trash can in an area near it, in an "old black computer bag" inside a plastic bag. On top of the bag was a letter addressed to Freshwater. The police report does not contain the contents of that letter. The bag contained a 3"-4" stack of papers and a "large number of photographs of items from John's room." It also contained three stopwatches, a whistle, and $45 in cash.
OH OF COURSE!
The famous 'three stopwatches, a whistle, and $45 cash' ruling, which states that it is perfectly legal to teach Creationism as science in public school classrooms! DUH!
Well, this changes everything. If there had been two stopwatches and two whistles, with a $50 Target gift-card, Freshwater would have been shit-outta-luck.
But three stopwatches, a whistle, and $45 cash? This changes everything. This completely exonerates Freshwater.
Im sure you all can figure out from that one sentence in that abstract why this is disappointing, but let me give you the back story.
Way back in the 1990s, scientists noticed that HIV-1 and HSV-2 were able to form this awful, unholy alliance. Proteins made by HSV-2 could increase transcription of HIV-1 (you make more HIV-1 viruses). Even if you arent showing any HSV symptoms (you have HSV but dont get outbreaks), if you are also infected with HIV-1, you have more HIV-1 viruses in your blood and genitals.
More viruses, better your odds for transmitting to someone else.
If you do have outbreaks, open sores... well, that pops up your risks for transmitting HIV-1 even higher.
Happily, a drug we use to treat herpes has been around for a million years, acyclovir. It works great, its super cheap, AND, in people who are infected with HIV-1 too? They have lower HIV-1 viral loads than dual infected people who arent on acyclovir!
Lower viral loads, fewer outbreaks, lower your chances of transmitting HIV-1 to your partner, right?
Eh. Wrong, at least according to this paper.
Even though patients taking acyclovir only (no antiretrovirals) had lower HIV-1 titers and fewer HSV-2 outbreaks, they still transmitted to their partners at the same rate as patients who got placebo instead of acyclovir.
So I repeat: Well crap.
This could have been a pretty easy/cheap way to stop a few new HIV-1 infections.
Its not news that I like vampire fiction. Grew up with Lestat, eh, its my fluff hobby.
One of my favorite vampires is Andre, from the Sookie Stackhouse mysteries. Dunno why-- hes not in the books a lot, but there was something about him that caught my fancy. (spoilers ahead) I got (and still am) real mad at Sookie for getting him killed. See, Andre did something particularly vampirish in the service of his Queen (his maker and love for eternity). This pissed Sookie off. Why, I dont know. The few things we know about Andre is that he is a VAMPIRE and he will do ANYTHING for his queen. Thats what he DOES. Thats his THING. Why anyone would be shocked at his behavior is beyond me.
Chris is acting the same way he always acts. How can this be shocking?
May 6, 2009: Some outspoken scientists may have actually increased the polarization on this issue. For example, calling those against vaccines "scientifically illiterate"--or, as CDC vaccine expert Stephen Cochi reportedly put it to one journalist, "junk scientists and charlatans"--may just lead to a further circling of the wagons.
Now, at the time I thought this was real goddamned funny cause Orac says stuff a LOT worse than the guy from the CDC that Mooneytits threw under the bus.
I thought it was especially funny cause ORAC is quoted favorably in the same goddamned article:
... I think it's definitely a response to the science, which has consistently shown no correlation," says David Gorski, a cancer surgeon funded by the National Institutes of Health who in his spare time blogs at Respectful Insolence, a top medical blog known for its provaccine stance....
... "I don't think they woke up that this was a serious problem until maybe 2008," David Gorski says about the growing antivaccine sentiment. George Washington University's Hotez notes that "the office of the surgeon general, the secretary of Health and Human Services, and the head of the CDC have not been very vocal on this issue."...
And, Orac pointed people to the article from his blog:
I will, however, refer you to some good reading on the topic. Chris Mooney has written an excellent article for Discover entitled Why Does the Vaccine/Autism Controversy Live On? You might even recognize one or more of the people he interviewed.
Well, Orac was 'under the weather' at the time. Maybe he didnt read the 'excellent' article before he plugged it.
My superpower is, I can predict what Creationists are going to do before they do it. I wonder if that power extends to people like Mooneytits:
My conclusion was obvious, if Mooneytits would do that to PZ, he would do it to any of us.
Wonder how Orac is going to be 'framed' in Mooneytits next bestseller?? *sits on edge of seat*
THERE IS ONLY ONE BLOG ON THE LIST WHERE THERE IS ONE PRIMARY AUTHOR WHO IS A WOOMYN. ITS AN ART BLOG.
THE OTHER '20%' ARE WOOMYN IN GROUPS. BECAUSE APPARENTLY SCIENCE IS LIKE GOING TO THE BATHROOM BY YOURSELF: ITS JUST TOO SCARY, SO WOOMYN HAVE TO DO IT IN GROUPS. OR ALTERNATIVELY, WE HAVE TO HAVE A BIG, STRONG MAN AS A CO-BLOGGER TO PROTECT US FROM EVIL SCARY STALKER SEXIST COMMENTORS.
SO NOT ONLY IS THIS LIST A REPRESENTATION OF HOW SEXIST THE SELECTION COMMITTEE WAS, BUT ALSO A REPRESENTATION OF HOW SCARY IT IS TO BE A WOOMYN SCIENCE BLOGGER!
Im sure this very serious post will be met with a chorus of support from The Usual Suspects. Oh wait, no it wont, cause The Colgate Twins are on the list (for their posts on kissing pussys, no doubt).
Also note that this post is for lulz only. *HIGH-FIVE!* to my fellow SciBlings and thanks to the list makers for pointing me towards some neat blogs I didnt know existed :)
Researchers took a dozen cat/dog vaccines from manufacturers in Japan and Britain, and looked for a specific cat endogenous retrovirus, RD-114. Why this cat ERV? Cause the viruses in these vaccines are passaged in cat cell lines to attenuate them. Cat cell lines that contain and can produce ERV RD-114. Whats RD-114? Welp, um, its distinct-from-but-related-to feline leukemia virus.
Well, no. MLV and FeLV are equally genetically distant from RED-114, that is, theyre all gammaretroviruses, and clearly genetically related, but they are not 'the same virus' any more than MLV and PERVs are 'the same virus'.
And these are cat/dog vaccines that use cat cell-lines for production. While this is important information for maintaining the heath of our dogs/large cats in zoos/etc (its shouldnt have an effect on domestic cats, as they all already have this ERV), this has a minimal impact on humans. I am unaware of any human vaccines that use cat cell-lines.
...the current methods used for screening human vaccines for retroviral contaminants include extremely sensitive PCR-based RT assays (not required for veterinary vaccines) that are much more sensitive than conventional RT assays. Thus, contamination of human vaccines with XMRV, would not pass undetected with the currently available technology although this may not be necessarily true for vaccines produced in previous decades.
And, as we will see, their 'finding an infectious ERV in pet vaccines' isnt as AAAAAAAHHHHHHHSCARY as Im sure some will make it sound:
Some of you got real damn close to the 'answers' I was thinking of, but you all missed a great big one (which I think will make sense to you after I bring it up hehe!)
1-- Lets say youve isolated white blood cells from CFS patients. You treat these cells with chemicals that interfere with normal DNA/histone methylation.
What do you think will happen?
Do you think that is a good diagnostic test for retroviral infection?
The Reno groups decision to use this as a diagnostic test is absolutely baffling. The idiomatic definition of 'epigenetics', histone and DNA modifications, probably evolved as a method of controlling pirate DNA. Pirate DNA like endogenous retroviruses.
Put 'ERV methylation' into PubMed. 'LTR methylation'. You screw this up, you get particle production.
Treat cells with a chemical that messes up methylation... and you get retroviral particle production... XMRV or not.
2-- Magic Johnson was diagnosed 'early' and got on antiretrovirals. Do you think there is any chance Magic Johnson will develop AIDS?
Maybe he will, maybe he wont. I would not say "Magic Johnson will not develop AIDS" in a million years.
Heres what happens with HIV-1 infected individuals:
Lets say you are diagnosed early. Get on HAART, viral load goes down, CD4+ T-cells stay up, YAY!
Well, there are always drug resistant variants present in the patients quasispecies.
Drug resistance comes at a fitness cost.
So, there are still HIV-1 viruses replicating in the patient. They might be real shitty, replicating real slow and awkward like, but theyre still going.
Some people are very very very unlucky, and in those few crappy replication cycles, the virus stumbles upon a secondary compensatory mutation. A mutation that allows it to be drug resistant AND able to replicate at a normal rate.
Some people are very very very lucky, and in those few crappy replication cycles, the virus just keeps banging its head against a wall.
The latter is like Magic Johnson. But there is no guarantee, with anyone who takes their antiretrovirals religiously, that they wont be unlucky tomorrow.
With todays technology, with todays antiretrovirals, we can extend the lives and improve the quality of life of people with HIV-1. But we cannot say they will 'never' develop AIDS.
3-- Lets say you isolate a retrovirus from a sample from 1984. The sequence from that virus is not significantly different from sequences you are isolating from patients 25 years later. In other words, this 'retrovirus' is not acting as a quasispecies.
What are possible explanations for this?
If the virus does not mutate, why could the British group not find MLV sequences we know are conserved?
If this virus does not mutate, why would the PI looking for this virus be worried about PCR giving 'false negatives'?
They have to. They cannot help it. Its a side-effect of an error-prone reverse transcriptase and inter- intra-strand recombination. Even if it finds the most perfectest sequence EVAH!, it cannot keep it.
And that most perfectest sequence in Patient #1 might be awful in Patient #2, and Patient #3. Every individual is a different environment...
Certainly there are regions of a retrovirus that are functionally constrained-- if they do not have sequence ABC, then the proper structure doesnt form, and viruses are non-infectious, therefore, sequence ABC is always there, but in a region like env? There is genetic plasticity, there is functional plasticity, there is selective pressure by everyones individual antibody repertoire! You cant stop the virus from mutating! If the virus stops mutating, the Red Queen race between us/retrovirus stops, and the virus is gone. I am not currently aware of any instance of anyone or any organism being 'cured' of a retrovirus ever.
But, quote Mikovits, "XMRV doesnt act as a quasispecies."
I just dont see how this is possible.
4-- Lets say we just discovered a new virus in humans. While most laboratories are being conservative/cautious about their statements and approach to this discovery, another lab is verbally, though not scientifically, 'connecting' this virus to CFS, breast cancer, chronic lyme disease, autism, and a cadre of other 'medical mysteries'. Furthermore, the PhDs in these labs are giving medical advice like 'take supplements X, Y, Z and immune modulators' and suggesting 'detox'. They are also heavily emphasizing 'early detection' of this new virus to prevent this list of diseases, and why, they have a test for sale right here.
Do you think that is the most scientific approach to this new virus?
What advice would you give this group of scientists?
This is example #918356125 of how unprofessional the Reno group is. There has been nothing published connecting XMRV to autism. Nothing. There has been nothing published connecting XMRV to chronic Lyme disease. There has been nothing published connecting XMRV to breast cancer. So when youre talking to the general public, you say general things like "Lots of other labs are trying to see if there is a connection between XMRV and their disease of interest. None of this, including XMRV-->CFS, has proven to be causal yet. This is currently a neat phenomena in CFS that might turn out to be something real fantastic! But right now, everything is preliminary."
Standing up in front of a group of laymen saying "THEYVE CONNECTED XMRV TO AUTISM AND BREAST CANCER AND LIEK EVERYTING!" screams insecurity and immaturity.
And a PhD, in any field, giving medical advice? Thats down right irresponsible.
Look, my epigenetic research, I just tell people "You know what? I eat my broccoli, LOL!"
I do not tell people failing chemo "OMFG YOU NEED TO TAKE X, Y, Z SUPPLEMENTS AND DETOX WARBLEGARBLE!"
I have no doubt CFS is a real disease. PhDs are not medical physicians qualified to treat diseases. End of story.
Furthermore, Ive heard it through the grapevine that a nice, normal diagnostic test for XMRV is in the works. It looks for anti-XMRV antibodies. Awesome!
Its not from the Reno group.
It will be for research purposes only, at this point, to study the epidemiology of this virus.
There is also lots of nice, normal basic science, basic virology being done on XMRV.
Not from the Reno group.
There is going to be lots of information coming though the pipeline on XMRV. Maybe it causes CFS, maybe it doesnt. Maybe it causes certain kinds of leukemia, maybe it doesnt. Maybe it causes certain kinds of prostate cancer, maybe it doesnt.
This information is going to come out through hard work done by normal scientists doing normal scientist things.
Not by PR releases accusing other labs of fraud.
Not by doing confusing, scary, and misleading conferences for prostate cancer patients.
2-- If you are a dude, especially a young dude with dreams of 22-inch guns, John Barban has figured out The Secret (**SPOILER** Its steroids).
3-- Peter and Travis of Obesity Panacea have some basic tips for beginners, like What Not To Wear, and Who Not To Be.
Heres a few things I want to add:
You know how people always say "Oh, dont be embarrassed! Everybodys been a beginner, nobodys watching you anyway, just do your own thing!"
Thats not entirely true.
I watch everyone in the weight room.
Not that I care how much they are lifting, its that I am perpetually paranoid that someone is going to kill themselves. Especially people who are benching a lot of weight without a spotter... and they were real shaky on that last rep, but theyre doing another... It bothers me. So honestly, while I am mostly focused on my own workout, I am subconsciously (and sometimes consciously) watching other people. But I am not judging them-- Im just a worrier.
Which brings me to my second point-- the clankers/screamers. I 'grew up' in a powerlifting gym. Humongous guys lifting African elephants covered in chains and shit. One of the gym rules was 'dont drop your weights', and everyone had a spotter, so even lifting approximately half the weight of Mars, the gym was reasonably quiet. So loud screams/clanks/plates slamming to the ground meant Something Bad Happened. I havent been in that gym in years, but the imprinting has been done. When I hear really loud noises in the gym, I assume someone is in trouble/is hurt. But they arent. Douche bags who are shrugging half the weight I deadlift just slam their weights down for attention.
THAT PISSES ME OFF. IT STARTLES ME AND I THINK SOMEONE IS HURT. DONT. DO. IT.
The only other thing I wanted to mention was, just be nice. Its common sense.
Share-- If you are using The One Power-rack in the gym, dont only use it for shrugs or bicep-curls and super-set with 5 other exercises. If someone is doing that (maybe the gym wasnt as full when they started- I do that on Saturday mornings when no one is around *shrug*), just ask nicely to work in. Normal people get the idea that theyre hogging, and let you work in, or move along.
Be sanitary-- In my perfect world, I can work out in a sports bra and shorts. *shrug* I just think clothes are restrictive when Im lifting. But I would never do that in a million years, and it has nothing to do with modesty-- I got sick a few years ago, and as a side-effect of that illness, I got a golf ball sized StaphA abscess in my arm. StaphA that I, no doubt, picked up at the gym. So, if youve been running on a treadmill for 45 minutes, then come over to bench, put down a towel. Wipe off the bench with spray/alcohol wipes after you use it (your gym should provide these for you). Hell, wipe it off before you use it too. I do step-ups on benches, and though I only wear these shoes at the gym (they arent muddy), I wipe down the benches afterward, cause no one wants to sit in gym floor grime.
Clean up after yourself-- No one wants to trip over the dumb bells you left on the floor. No one wants to work up a sweat taking your plates off the barbell or leg-press. No one wants to get a cardio workout hunting down a second 10 lb plate cause you hid them all on one machine doing some weird pyramid sets. Put things back where you found them. Its just nice.
I think its funny that even people who HATE Richard Dawkins, I mean, the people who would run the man down with their car and eat the corpse raw, or even just the hundreds (thousands?) of douche bags who wrote 'reviews' or 'rebuttals' of 'The God Delusion' without actually reading it-- Their lives have been positively influenced by Dawkins.
The word meme originated with Dawkins' 1976 book The Selfish Gene.
Dawkins used the term to refer to any cultural entity that an observer might consider a replicator. He hypothesised that one could view many cultural entities as replicators, and pointed to melodies, fashions and learned skills as examples. Memes generally replicate through exposure to humans, who have evolved as efficient copiers of information and behaviour. Because humans do not always copy memes perfectly, and because they may refine, combine or otherwise modify them with other memes to create new memes, they can change over time. Dawkins likened the process by which memes survive and change through the evolution of culture to the natural selection of genes in biological evolution.
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.
