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Creationists are WEIRD

Tue, 09 Feb 2010 14:00:45 -0500

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?

Yes, that was weird, but now weve reached a level of weird only Creationists can hope to attain:

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.

And then theres this bit of weird:

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.

O.o
-----

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Swing and a miss: Yet another HIV-1 downer

Tue, 09 Feb 2010 12:00:09 -0500

Acyclovir and Transmission of HIV-1 from Persons Infected with HIV-1 and HSV-2. --Daily acyclovir therapy did not reduce the risk of transmission of HIV-1, despite a reduction in plasma HIV-1 RNA of 0.25 log10 copies per milliliter and a 73% reduction in the occurrence of genital ulcers due to HSV-2.

Well crap.

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.

*sigh*

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IMPORTANT NEWS! Someone says stuff they have said in the past and are acting the same way they always act!

Sat, 06 Feb 2010 16:07:16 -0500

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.

But Sookie got him killed, so, there you go.

Similarly, I am completely baffled at Orac being weirded out by Mooneytits latest 'advice' for combating anti-vaccinations.

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*

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Rule #30: There are no girls on the internet.

Wed, 03 Feb 2010 11:00:32 -0500

The following post should be read in the voice of 'Jakov', from the timeless South Park episode, 'Jakovasaurs'.

*ahem*

THIS IS JUST SO TYPICAL.
TYPICAL WHITE ELITIST D00D DOMINATION OF THE SCIENCES.

EUREKA JUST RELEASED THEIR TOP 30 SCIENCE BLOGS, AND ONLY 20% OF THEM ARE AUTHORED BY WOOMYN.

BUT GET THIS.

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!

HELP, HELP, IM BEING REPRESSED!

[/end scene]

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, there were no virologists on the list.

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 :)

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Infectious ERV particles in cat and dog vaccines

Tue, 02 Feb 2010 14:00:04 -0500

I hesitate to write about this, as Im sure its going to be taken and amplified by Teh Crazy... but I suppose I better just get a head start...

Isolation of an Infectious Endogenous Retrovirus in a Proportion of Live Attenuated Vaccines for Pets

Well shit.

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.

...

FLVISMLVISXMRVWARBLEGARBLEOMFGWEGOTXMRVFROMVACCINES!!!1!eleventy!!

:-/

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.

However, this could have an impact on live attenuated vaccines passaged in mouse 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:

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XMRV and chronic fatigue syndrome: Questions I have

Mon, 01 Feb 2010 21:23:41 -0500

So here are my answers to The Brainstorm Challenge.

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'?

*sigh*

Fish gotta swim.

Birds gotta fly.

And retroviruses gotta act as a quasispecies.

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.

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Im watching you.

Sun, 31 Jan 2010 18:02:30 -0500

For the new year, lots of blogs and blags are posting great intros for beginners.

1-- If you are real new to weight-lifting, please check out Lyle McDonalds 'Beginning Weight Training' series.

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.

Anyone else have any good beginner tips/links?

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MEMES!

Fri, 29 Jan 2010 10:49:29 -0500

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.

How?

MEMES!:

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.

Link just in case you get 'LOADING LOADING LOADING...'

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REPOST: OOPS! They did it again!

Wed, 27 Jan 2010 12:00:58 -0500

This is a repost from the old ERV. A retrotransposed ERV :P

The Proceedings of the National Academy of Science have a special online edition focused on the place of evilution in medicine.

Shorter Michael Egnor:

:-O

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KLZF KRABs with nine zinc fingers...

Tue, 26 Jan 2010 16:00:01 -0500

Okay, you know how I say with ERVs and disease:

Expression of the ERV protein causes the disease

Expression of the ERV is an effect of the disease (a useful biomarker)

Expression of the ERV is an effect that perpetuates the disease

I just read a paper that exemplifies #3!

Regulation of human endogenous retrovirus-K expression in melanomas by CpG methylation.

So, you know how you have KRABs that bind to ERV DNA, and these KRABs recruit epigenetic machinery that silences the ERVs?

Well, these folks looked in various melanoma cell lines, and looked for a specific ERV we see upregulated in people with advanced/aggressive melanoma: HERV-K. HERV-K is a family of young ERVs. Most of them came about after the human/chimpanzee split, and quite a few of them (50-60) are still pretty complete ERVs (LTRs, gag, pol, and env). Not the solo LTRs and shattered genes that make up most other ERV families. So since these guys are young, they still have the ability to cause trouble.

They looked at a bunch of these HERV-Ks, but focused in on this one on chromosome 7p22, HERV-K-108.

Cells that had lower DNA methylation had higher expression of this HERV. And, when these cells were treated with a compound that screws up DNA methylation, HERV-K-108 expression didnt go up (it did go up in cells that previously didnt express this protein).

So, we can be pretty sure that the reason HERV-K transcripts/proteins in melanoma cells is because their epigenetics, specifically their DNA/histone methylation is screwed up.

But did the activities of this HERV-K start the cancer in the first place?

Probably not:

Demethylation is obviously necessary for the expression of HERV-K. As it is unlikely that HERV-K is able to demethylate its proviruses, the loss of methylation must be the result of genetic changes in the cell, e.g., a loss of DNMT1 activity. Therefore, the activation of HERV-K expression ought to be understood as a secondary event.

But wait! Allowing this ERV to be transcribed isnt just a harmless side-effect/biomarker.

HERV-K encodes two proteins, Rec and Np9. These proteins bind to a KRAB, KLZF, and inhibits KLZFs inhibitory function. In other words, KLZF normally recognizes this ERV sequence and KAP-1 (probably) comes in and epigenetically modifies the DNA. BUT, the viral proteins Rec and Np9 bind up KLZF so it cant see the retroviral DNA, thus KAP-1 doesnt know to go there and silence the DNA, thus you get retroviral transcription.

So if the epigenetic profile of a cell breaks down, transcription of this ERV will be self perpetuating-- you make more and more Rec & Np9, thus mess up ERV epigenetics even more.

This causes all kinds of crazy trouble!

The increase in demethylation may enhance expression of HERV-K mRNA as well as Env, Rec and Np9 proteins. As there is preliminary evidence that Rec and Np9 may be involved in tumorigenesis, they may contribute to tumor induction. In addition, the expression of the immunosuppressive Env protein may contribute to tumor progression preventing tumor rejection by the immune system. In this context it is of great interest whether HERV-K proteins are good targets for cancer immunotherapy. Such investigations will help to understand the role of HERV-K proteins, if any, in the development of melanomas.

Probably one of the few cases where having KRABs is a good thing ;)

Oh, and this still doesnt sound like magic, does it? hehehehe!

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XMRV and chronic fatigue syndrome: Brainstorm Challenge!

Sun, 24 Jan 2010 17:05:50 -0500

While listening to Judy Mikovits presentation to CFS patients on Friday, I took a few notes.

Well, I took a few notes in between screaming at my computer, slamming my head into my keyboard, and popping Xanax like they were Skittles.

Ive got a few questions for my regular readers, because I genuinely believe readers of my blog are smarter than Judy Mikovits.

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?

2-- Magic Johnson was diagnosed 'early' and got on antiretrovirals. Do you think there is any chance Magic Johnson will 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'?

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?

Just curious as to what my regular readers would make of this.

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Epigenetics is not magic.

Thu, 21 Jan 2010 20:30:05 -0500

My god, epigenetics is a woo-magnet.

Its not epigenetics fault, its just science.

But the word 'epigenetics' gets put on this ('chambery thing' heh.).

And this.

And this.

And... well, just Google it. Find your own favorite bit of self-help/explain all/magic epigenetic crap.

Attention woo-meisters:
STOP WHORING UP EPIGENETICS. IT IS NOT MAGIC. ITS JUST THAT 'BORING SCIENCE CRAP' YOU HATED IN HIGH SCHOOL.

Its science and its cool because its science.

DEAL WITH IT.

THIS is epigenetics:

KAP1 controls endogenous retroviruses in embryonic stem cells--
Almost half of the mammalian genome is derived from virus-like entities called retroelements, many of them the result of the incorporation of endogenous retroviruses. Didier Trono and colleagues use a combination of genetic, functional and biochemical analyses to demonstrate that KRAB-associated protein 1 (KAP1)-mediated epigenetic regulation is involved in the early embryonic silencing of intracisternal A particles (IAPs), a still active and highly polymorphic subset of endogenous retroviruses. This work establishes a role for the KAP1 co-repressor in the control of endogenous retroelements during early embryonic development.

This paper is awesome. They did so much work, and only 13 authors. Theres no way I could cover it all in a blog post-- but I can give you all the jist of it.

ERVs and ERV-like-thingies, IAPs, are trouble for developing babbies. If these chunks of pirate DNA are hopping and plopping around a genome, they might cause cancer in grown adults (exogenous retroviruses do cause cancer in adults), but they would immediately kill a developing babby.

Well, apparently, one of the ways genomes have evolved to keep some kinds of pirate DNA silent during the crucial process of development is epigenetics. Not 'BIRD SONGS ARE EPIGENETICS! DIIIIRP!', but real 'science' epigenetics-- You have a family of proteins in your genome, KRABs. KRABs are sequence specific, and nestle up next to DNA with their particular sequence. We have a ton of KRABs in our genome (at least 250-ish), and theyve been under strong evolutionary stress over the course of our evolution. For some of them, we know what that stress was: they recognize ERV and IAP sequences. But KRABs themselves have no 'function'. They just recognize sequence.

KAP-1 (aka TRIM28) sees the KRABs. KAP-1 is the opposite of KRABs-- they have a function, but not really any specificity. It dunno where to go. BUT, if it finds a KRAB, it knows just what to do!

KAP-1 trundles over to a KRAB with a chromatin remodeling complex (histone methyltransferases, heterochromatin proteins, histone deacetylases), thus silences the surrounding DNA, thus keeps ERVs/IAPs silent.

They figured out some of the protein players in epigenetic control of ERVs.

**TA-DAH!**

Remember this post the next time you read some feather-brained article on epigenetics. Does what theyre writing, what theyre saying, look like this?

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XMRV and chronic fatigue syndrome: Insanity

Wed, 20 Jan 2010 19:14:21 -0500

This is insanity, people.

Scientific insanity.

Moved right from 'this does not make sense' and 'youre acting like a bitch' to 'this is insane'.

#1-- Lead author of the Reno XMRV-->CFS study is holding a live-streamed press conference at Hotel Mar Monte on Friday.

*blink*

This is insanity. They have no evidence connecting XMRV to CFS in anything but a casual manner, and yet she is giving a presentation/Q&A to CFS patients. Insanity.

Furthermore, the people 'hosting' this talk, ProHealth? What is this? What is this crap? Pages and pages and pages of powders and potions and crap.

Why in gods name would any scientist with any sense of self-worth agree to this event?

I mean, I 'debated' Lenny and his magic tuning forks, but that was for lulz. Im assuming Mikovits is serious about this.

Insanity!

#2-- I am completely baffled by VIPDX super awesome NEW diagnostic test. Okay, old test was PCR. Fine. I mean, sure it had a false positive rate of 1:25, where the false positive rates of HIV-1 tests are 1:250,000 (at worst), but whatever, it 'worked'.

Dudes switched to 'viral culture based tests'.

WHAT?

Viral culture is an old-school way of diagnosing viral illnesses. By 'old-school', I mean 50-60 years ago, and they did it because they did not have technology like 'immunology' and 'PCR'. Today, when you go to the doctor to get tested for Mono or flu or HIV-1 or herpes, they use todays technology-- usually immunology (cheaper) but sometimes PCR (more accurate, but also more expensive).

Example-- How we do HIV-1 testing.
1. You are PCR positive right after you get infected. ONLY the viral RNA (and DNA) is there.
2. Next, you are ELISA positive. The RNA/DNA is there, and its making proteins.
3. Finally, you are Western Blot positive. Viral RNA/DNA/proteins are there, and you are making antibodies to HIV-1.

Sure PCR(1) is 'the best', but its more expensive (especially Real-Time), so today you can just do a quick HIV-1 test to look for antibodies(3).

The only people who do viral culture for HIV-1 are research labs. They arent doing it for diagnostic purposes, they are doing it to isolate single viruses (well, their genomes) for us to study in the lab.

On no planet is viral culture 'better for diagnosis' of HIV-1 than PCR/ELISA/WB.

Though technically, once viral culture did give me an advantage over PCR-- I infected a cell line that was labeled 'uninfectible' with HIV-1. I got about 50 infected cells out of a several billion cells, which is WAY below my detection threshold for PCR, and the threshold of every other HIV-1 researcher that had used this cell line. The only reason I know those 50 cells were infected was because my HIV-1 makes cells glow green when they are infected.

But, unless these patients are infected with viruses that contain EGFP, I really cannot imagine how viral culture is 'better' than PCR.

Furthermore, MLV is notorious for contaminating cell lines. Its not just TZM-bls, you can go to PubMed and find a number of papers that suggest routinely checking cell lines for MLV, like we regularly check for mycoplasma.

Its insane that theyre switching from PCR to culture.

Furthermore, gf01 kindly left some test results in a comment here:

Only one was postive for XMRV with both the PCR and culture test.

Seven more were positive with only the culture test.

Seven were negative for both.

We already know that 1:25 PCR results are going to be false positive, yet more patient samples were culture positive than PCR positive, which can only make sense if your friggen cell line is contaminated with Plain Jane MLV.

*blink*

This is insanity.

This is pure insanity.

Im out until someone from another lab publishes.

ADDED 1-22-10: After listening to most of this presentation and Q&A, I have lost all faith in the Reno research group. I will elucidate why later when my blood pressure goes down and I take half a bottle of Xanax.

Read the comments on this post...

LINEs dont do RT like ERVs, HIV, or HBV!

Mon, 18 Jan 2010 13:30:14 -0500

The only creatures that existed in the RNA World that still exist today, are viruses.

They are the only creatures that still use RNA to store their genome-- they never upgraded to V2.0, DNA.

In fact the creatures that might have written V2.0, retroviruses, are still around today too. They carry their genomes as RNA, but convert it to DNA via reverse transcription in order to take advantage of their hosts.

Ive written a bit about reverse transcription before... its kind of a mess to describe... however every retrovirus, from simple retroviruses like Avian Leukosis Virus (only gag, pol, and env) to wildly complex HIV-1 (gag, pol, env, vif, vpu, vpr, tat, rev, nef) to ERVs, they all do reverse transcription the 'same' way: Happens in the cytoplasm, tRNA primer starts reverse transcription, RT hops around a few times, badda-bing, badda-boom, dsDNA moves from the cytoplasm into the nucleus for integration.

Hepatitis B, a DNA virus, has evolved a different way to do things-- instead of using a tRNA primer to start reverse transcription, it uses the same RNA structure it uses to package its genome into virions to initiate reverse transcription. This might be a new thing, or it might be a very old, leftover thing. But its totally different from the way retroviruses do it.

And then we have non-LTR retrotransposons like LINEs and SINEs. They make up most of that "half your genome is retroviral" thing you hear me say all the time. Chunks of DNA in your genome that proliferate like bunnies. I have LINEs you dont have. You have SINEs I dont have. Aaaand sometimes that leads to trouble (genetic diseases, yay...).

Even though LINEs code for reverse transcriptase proteins (which SINEs steal), 'just like' retroviruses, their reveres transcription process is nothing like that of the retroviruses and ERVs we know and love today. Since its not 'normal' it gets its own name-- Instead of 'reverse transcription', their process is called 'target primed reverse transcription'.

LINEs code for an mRNA, which is taken to the cytoplasm to be translated into a protein. Halfway through (after the RT protein is made), the rest of the RNA curls up (not translated), and the RT&leftover RNA is carried back into the nucleus. There, it finds/makes damaged DNA-- a nick where the leftover RNA can sliiiiide in, and match up with the exposed DNA. A leftover -OH group on that unlucky bit of DNA is used as a primer for reverse transcription. All of the action happens in the nucleus.

The point is, though LINEs/SINEs are retrotransposons, they dont look like anything alive today. What happened to the retroviruses that behaved like LINEs/SINEs? They are extinct, or, at least we havent found one yet. So ironically, the only survivors of their species are 'mistakes' that incorporated into germ-line cells. Nestled in the warm confines of our DNA, being passed on vertically from parent-->offspring for millions and millions and millions of years...

I wonder what they used to look like.

Read the comments on this post...

Steroids!

Sat, 16 Jan 2010 12:22:52 -0500

The 'fitness' news this week has been all about STEROIDS!

Pals went on a grand adventures with an anti-aging wooer (Train Wreck 1, Train Wreck 2, Train Wreck 3-- holy crap!).

Well, dont feel bad, Pal. There is no question in my mind that this guy 'has issues', because I get 'Life Extension' magazine. The guy who lived in my apt before me got it, and he never changed his address. 'Life Extension' is a beautiful glossy magazine that sells pages and pages and pages of snake oil and vitamins. Theyll have an article on how to 'REVERSE mitochondrial damage!!', then 3 pages later, there are full page ads for all the supplements mentioned in their 'article'.

And I know what 'Life Extensions' position on steroids are.

Ive written about it before.

Thus I dont believe, in the slightest, that Dr. Crisler doesnt prescribe HGH for ~~anti-aging~~ "testosterone deficiency" **WINK!**. Partially because of his affiliation with 'LE', but also because he has.

I have serious doubts, independent of Pals observations, that this has anything to do with prescribing hormones for real medical deficiencies.

Then we have Mark McGuire, who recently came out of the steroid-closet.

I dont care if Mark McGuire used steroids. I dont care if anyone uses steroids. Ive stated before, if its perfectly legal for me to go under the knife getting breast implants and a nose job and lipo tomorrow, if I want-- procedures that could kill me and are troublesome to reverse-- why cant someone else do a physician-guided cycle of steroids for cosmetic purposes?

I also dont care if the NFL/MLB/NHL/whatever say its against their rules to use them, and they kick out people who break that rule. Their clubs, their rules.

What pisses me off, is that Mark McGuire denied he used steroids.

Alllll those kids out there, thinking if they work hard enough, if they eat right, if they exercise right, they can look like Mark McGuire.

They cant. Unless they use steroids.

So when they fail, they think its because of their own personal failings. They didnt work hard enough. They dont have 'the right genetics'.

That pisses me off.

Read the comments on this post...

erv

Creationists are *WEIRD*

Swing and a miss: Yet another HIV-1 downer

IMPORTANT NEWS! Someone says stuff they have said in the past and are acting the same way they always act!

Rule #30: There are no girls on the internet.

Infectious ERV particles in cat and dog vaccines

XMRV and chronic fatigue syndrome: Questions I have

Im watching you.

MEMES!

REPOST: OOPS! They did it again!

KLZF KRABs with nine zinc fingers...

XMRV and chronic fatigue syndrome: Brainstorm Challenge!

Epigenetics is not magic.

XMRV and chronic fatigue syndrome: Insanity

LINEs dont do RT like ERVs, HIV, or HBV!

Steroids!

Creationists are WEIRD