Saturday, March 31, 2007

Why Horowitz Published in Medical Hypotheses

Sorry to you guys who havent gotten to hear the 'debate' yet, but I am going to be focusing on some of his claims for the next few posts :) Sorry for the spoilers :)

So the fellow I 'debated' last night was so upset because when I searched his name in PubMed, nothing came up (search 'Horowitz, Leonard').

Turns out he publishes under Horowitz LG.

He wanted an apology for not being able to find his paper, published in a relatively obscure journal*.

Well folks, Id love to rip up his paper for you, but unfortunately, even at a major medical research institution, I dont have access to this particular journal. Thats certainly telling, in and of itself, but lets take a look at a few details.

1. Who sponsored/supported Horowitzs article?
"Tetrahedron Incorporated, Sandpoint, Idaho, 83864, USA. tetra@tetrahedron.org"

Who publishes Horowitz's books?
"Tetrahedron Incorporated, Sandpoint, Idaho, 83864, USA. tetra@tetrahedron.org"

Thats what we call a conflict of interest, ladies and gentlemen. For someone who was so concerned about pharm companies, this fellow sure doesnt mind using the same tactics.

2. What is the mission statement of 'Medical Hypotheses'?

Medical Hypotheses takes a deliberately different approach to peer review. Most contemporary practice tends to discriminate against radical ideas that conflict with current theory and practice. Medical Hypotheses will publish radical ideas, so long as they are coherent and clearly expressed. Furthermore, traditional peer review can oblige authors to distort their true views to satisfy referees, and so diminish authorial responsibility and accountability. In Medical Hypotheses, the authors' responsibility for the integrity, precision and accuracy of their work is paramount. The editor sees his role as a 'chooser', not a 'changer': choosing to publish what are judged to be the best papers from those submitted.
Translation: "We're a journal for conspiracy theorists to publish in to proclaim they have a published peer reviewed article."

lol Lame, dude! Ill apologize when you publish in Journal of Virology.







*If youll excuse a touch of boasting, turns out this side project Im doing is going to be published before my main project (I think). While Im not going to be the first author, just some schmuck in the middle, its going to be PNAS. The Proceedings of the National Academy of Sciences. Holy Fuck. Um, yeah, Ill take that for my first publication.

Friday, March 30, 2007

Why cant Deniers impress a 23 year old?

Well, just got done doing the show with Reg! He did great moderating, despite the fact we all were being, well, rude. I was hoping it would be a bit more of a challenge, but this guy isnt a Dembski/Behe/etc. He doesnt have the lingo down yet, so everything he said was very superficial and easy to refute.

He tried to gallop, but I wrote all his Qs down :D

And you all will be pleased to hear that he FREAKED OUT when I didnt call him doctor. Thats gotten me in trouble before, and I plan on continuing to do this to people who want to flaunt their irrelevant credentials. Youre a dentist. You are not a scientist. Calling you 'Dr.' in a debate is inappropriate, because theoretically you are getting an unearned advantage with the audience by virtue of an irrelevant credential.

You are Mr. Horowitz when you are trying to talk about HIV.

You are Dr. Horowitz when you are talking about teeth.

Ironically enough, all of my professors INSIST upon being addressed by their first names, and I have been reprimanded for calling profs "Dr. ___" The fact that Horowitz freaked out proves my above point-- he only wanted the title for unearned respect on the debate topic. He NEEDED it.

Anyway, Reg should have the mp3 up in a few days, and Ill post it here!

Thursday, March 29, 2007

Why cant Wooers use PubMed?

I mean, I know PubMed doesnt have the *best* search engine, its no Google, but like, its not THAT hard to maneuver. Why cant Wooers/Deniers/Creationists/etc figure it out? Good god, Horowitz is an "internationally known authority in the overlapping fields of public health, behavioral science, emerging diseases, and natural healing"... and hes baffled by the PubMed search engine?

One

Two

Three

Four



You get the idea. Took me ~5 minutes to find those. Its not hard.

Translation of those papers: They found the exact colonies of chimpanzees where we got HIV-1 Group M and N. They found the exact colony of gorillas where we got HIV-1 Group O. The SIV found in chimpanzees where polio vaccinations were supposedly contaminated with SIV, dont match HIV. HIV didnt come from 'contaminated' vaccines.

Quote IG: "Dr. Horowitz, unequivocally, claims that HIV is man-made. He says he has evidence for his claims."

He might have that 'evidence', but PubMed doesnt. Wonder why...

Wednesday, March 28, 2007

The King David of Woo

Oh youve seen them all-- the anti-vaxers, the terrorism conspiracy theorists, the Creationists, the crystal healers, the nutrition-is-magic-men, the Deniers, homeopathists, the paranoid Big-Brother watchers, the megalomaniacs, the DaVinci Code decipherers, the prophets and fortune tellers, the ghost/Angel/God whisperers, the sciency 'electromagneticstringtheoryquantumsomething' crap pushers...

Anything. Any kind of woo you can think of, I (more like Reggie) has found him... The Kwisatz Haderach of Woo. And Im going to 'debate' him on HIV this Friday.

Dont say I didnt warn you.

Like, if I didnt know better, I would think that was the woo version of The Onion. I mean, I dont even have to say anything. You all can just click on a page and read a sentence or two yourself to see how deep, how concentrated his guys woo runs.

Well Im gonna go get a bottle of water, put on some tunes, and study up on our Dear Doctor Dentist.

Tuesday, March 27, 2007

Lighten up!

When theyre making you mad, all you can do is laugh!






(thanks to duke and cyris!!)

Monday, March 26, 2007

Happy Birthday, Richard Dawkins!

There are no words for how this gentleman has inspired me. I cant even write a limerick for him, like I did for PZ. But as I was lifting tonight, a song popped on my mp3 player with a lyric that ironically seemed an appropriate dedication to Prof. Dawkins:


Franz Ferdinand
"The Fallen"

Some say you're trouble, boy
Just because you like to destroy
All the things that bring the idiots joy
Well, what's wrong with a little destruction?

A new ERV just in time for Easter!

The first lentiviral ERV was found in Oryctolagus cuniculus, the European rabbit! ERVs are about the best we can hope for in terms of viral 'fossils', so finding a lentiviral ERV can help us understand the evolution of lentiviruses.

Because of their absence in our genome, we assumed that lentiviruses were simply 'newer' viruses, evolutionarily--theyre younger, so they havent had as many opportunities to integrate. These authors think their ERV was inserted in the European rabbit genome about 7 million years ago. Our HERVs inserted themselves ~50 million years ago, so even though this RELIK (cute name!) is 'ancient', I would still call it young on an evolutionary timescale.

RELIK is pretty simple for a complex retrovirus (lentiviruses are 'complex', vs a 'simple' betaretrovirus), but it still has lots of tasty bits: gag (matrix, capsid, nucleoproteins), pol (protease, reverse transcriptase, RNaseH, dUTPase, integrase) and env (subunit and transmembrane) of course-- but also tat and rev! Its sequence is also A rich, C poor, characteristic of lentiviruses-- So I believe them.

Oh now before the Deniers start hopping around, they searched 46 mammalian genome libraries. And they only found these guys. And though the RELIKs were relatively 'complete', they were all hopelessly degraded. For example, one chunk had five stop codons, 11 frameshift mutations, and two SINE insertions. You arent going to get a pathogenic ERV out of that.

Saturday, March 24, 2007

Roving Bands of Trolls

Ugh Blogger butchers this image, but I love this cartoon.

Wait, IM the one with father issues?

Okaayy...
Ive got a sweet PNAS article review in the works, but I had to stop to make a post on this insanity.

Oh my fucking god. And these people have the nerve to say I have father issues?? WTF!

Just by sheer coincidence, BF brought this group of nuts up last night in conversation. Now the most recent Creationist Behaving Badly on PZs blog appears to be a participant in this bizarre ritual.

They all have different names-- silver rings, gold rings, whatever, but I swear to god if my Dad tried any of this shit I would have asked to enter foster care. Creepy shit.

It’s like a wedding but with a twist: Young women exchange rings, take vows and enjoy a first dance…with their dads.
No, that doesnt remind me at all of pedophelia.
Seated at a table with four couples, I watch as the gray-haired man next to me reaches into his breast pocket, pulls out a small satin box and flips it open to check out a gold ring he’s about to place on the finger of the woman sitting to his right. Her eyes well up with tears as she is overcome by emotion.

The man’s date? His 25-year-old daughter.
*twitch* Nope. Nothing weird about this at all. Not even a whiff of incest.

Dude, 25??? 25 is certainly a weird time to be taking a chastity pledge with your father, but watch this video. Check out the end-- 10 year old?? 4 year old??? WTF!

"Pastor Fred, I just dont know what to do! Im afraid my 4 year old daughter is going to be a whore!"

Watch the top video. Every Sunday, these kids get on their knees in front of their father and he 'blesses them.'

WHAT? Are these people insane??
While the abstinence movement itself is fairly mainstream—about 10 percent of teen boys and 16 percent of girls in the United States have signed virginity pledges at churches, rallies or programs sponsored by groups such as True Love Waits
Uh huh. Then they all break these pledges, cause sex is a normal human urge/need-- but they dont know how to use condoms so theyre wonderful little baby factories.

They also 'reclaim' their virginities at a later date (because sex is shameful), tell their new partners that theyre virgins, and turn into wonderful little STD factories.

This shit doesnt work.

Oh, and here I am, silly heathen child who missed out on the wedding dress ballets around a cross, who got a frank and honest sex-ed discussion from her parents, who got birth control no questions asked when I wanted it, hmm not preggars and no STDs.

Yes, denying your emotions is the 'healthy' way of addressing sex, and denying physical urges is a great way to build 'healthy' relationships. Thats 'sarcasm', Creepy Mother.

Good god-- my childhood wasnt perfect, but seeing insanity like this reminds me how lucky Ive been.

Friday, March 23, 2007

Alpharetroviruses: Bane of Chickens



Chickens so rarely get honorable places in history. Yet they do have at least one cool honor-- the species in which the first retrovirus was discovered!

Though RT wasnt discovered until the 1970s, way back in 1911, a fellow named Peyton Rous discovered that if he injected a healthy chicken with bits of chicken tumor, the healthy chicken got tumors. The idea that viruses could cause cancer was novel enough to win him a Nobel Prize in 1966! Sweet! Though he didnt know it at the time, Rous was studying alpharetroviruses.

Retroviruses are currently classified by phylogenetic analysis of RT genes. Obviously retroviruses have incredibly variable genomes, but their RTs remain stable enough that this analysis is possible. Theyre currently grouped into seven genuses, one of which is alpharetroviruses. Alphas, and Alpha-ERVs can only be found in birds... including our poor dear chickens.

The archetypical Alpha is Avian Leukosis Virus, the bane of chickens. ALV isnt exactly our buddy either. In the late 80s/early 90s, a subtype A ALV recombined with an endogenous ALV to create a subtype J, which caused a bit of a chicken epidemic. Big problem for chicken farms.

This also effects humans through our vaccine production. Turns out embryonic chickens arent just good for breakfast, theyre great little vaccine factories too! But unlike human ERVs, chicken ALV ERVs can still be pathogenic. There was a 'scare' in the late 1990s when RT activity was detected in MMR vaccines (*cue anti-vaxers* OMFG ALV CAUSES AUTISM!!111!!!1!). It is reasonable to assume alpharetroviruses wont know what to do with a human host, and the CDC explains why nicely:

Several factors, including a natural human resistance to infection with endogenous ALV, may explain the lack of transmission of these viruses to MMR vaccine recipients. However, few or no data are available on the ability of endogenous ALV to replicate in human cells. Resistance to endogenous ALV infection may, for instance, be attributed to the absence of a human cell-surface receptor for the virus as well as to other intracellular blocks for ALV replication. A tumor necrosis factor receptor-related protein, referred to as SEAR, has been recently identified as a receptor for endogenous ALV in turkey cells (22). Plasmid-encoded expression of SEAR in human 293 cells can confer susceptibility to infection by endogenous ALV, suggesting that human cells can support endogenous ALV replication if virus entry is achieved (22). Human serum can lyse ALV by complement activation (23); however, this protective mechanism has not been demonstrated for endogenous ALV and EAV particles.
Translation: We dont have the receptor it needs to get in our cells. Its only got one key, and it doesnt fit any of our locks. Cant get in. However, we do have ways of getting rid of it. Oh, but dont let that SCIENCE nonsense get in the way of a bit of fear mongering!
If portions (genes) of animal viruses are introduced into humans, they have the potentials to interact differently with each individual's immune system and DNA, and cause disease. The presence of an avian leukosis virus (AVL), a retrovirus that infects birds, could be the reason approximately 1 in 1000 children will be diagnosed with leukemia by the age of 19.

Thus the CDC study mentioned above may not have presented an accurate assessment of viral presence, or long-term effects from the numerous ALV-associated offspring viruses. Considering that ALV can for example, easily capture the human erbB oncogene (59), and that erbB as well as the oncogene called myc are strongly associated with common forms of human breast cancer, it seems that the issue of ALV vaccine contamination would deserve a high level of attention

I recently acquired an empty vial of yellow fever vaccine and was startled at what was written on the label. "Avian leukosis free". Is this an admission that it one time the vaccine did contain avian leukosis?

Yellow fever vaccine was known to contain avian leukosis virus.* During World War II, batches of yellow fever vaccines were inadvertently also contaminated with hepatitis B virus. Current measles, mumps, rubella (MMR) vaccines contain low levels of reverse transcriptase, an enzyme associated with retroviruses. Both Salk and Sabin polio vaccines made from rhesus monkeys contained live monkey viruses called SV40, short for the fortieth monkey virus discovered. As Dr. Horowitz documents, polio vaccines may also have contained numerous other monkey viruses, some of which may have provided some building blocks for the emergence of HIV- 1 and human AIDS .

* Editor's note: This is the retrovirus that causes leukemia in chickens.
Chicken embryos (eggs) used in making vaccines against influenza, mumps, measles and yellow fever commonly contain the retrovirus, avian leukosis virus (ALV) which has the amazing ability to mutate into numerous other viruses by incorporating oncogenic gene segments into its own genome.
Some of these segments which can be easily incorporated include human oncogenes strongly associated with common forms of breast cancer. As well, ALV can incorporate itself directly into the human genome.



Yay!

Thursday, March 22, 2007

Welcome Comrades!

Looks like Im not the only one who was... 'inspired'... by the trolls at Aetiology/Respectful Insolance/Pharyngula/etc. Ah those guys over at ScienceBlogs are spawning blog-children left and right!

Big welcome to Denialism.com!!

I already like them:

HIV/AIDS Denialism - seems to feed into some egomania of this particular type of denialist. They frequently make statements about how one day they'll be vindicated, and seen as heroes because they saw the truth first. They also seem to really like inversions, and to feel superior because they believe in something that no one else does. Other conspiracy theorists, such as 9/11 conspiracy theorists, I think are similar. There is an egotistical appeal to possessing "secret" knowledge or holding controversial opinions. Basically, I'm calling them assholes.

My sentiments exactly!

Wednesday, March 21, 2007

Why Arent Creationists Funny?

Billy-Boys Christmas gift to Atheists was not funny.

This 'parody' of Richard Dawkins is not funny. It dosent even look good.


I knew Fundamentalists lost the ability to detect irony, but I guess a malfunctioning laugh box is a prerequisite as well.

Intelligent Design Creationists INSISTING They are Dumber than High Schoolers

Fodder brought to you by the same ID Creationists that led to the ID vs ERVs series.

I was wondering how IDCs were going to react to this asshole getting fired. Wonder no longer!


If the Sisters parents, teachers, and public school administrators
are so '"enlightened," why isn't he aware that creationism and ID
are two quite distinct propositions? That AiG is a creationist
website? That many AiGers are as anti-ID as they are?

What difference does it make whether the teacher used AiG source
material? Isn't what's important whether or not the source
material is scientifically correct, not the source or the content
of AiG's mission statement?

(re above comment)
Well, that's what Dean Kenyon, Nancy Bryson, Caroline
Crocker, etc, etc., and several public high school
biology teachers did, and they all paid the price.

As Richard Lewontin, for one, has honestly acknowledged,
"The primary problem is not to provide the public with
the knowledge of how far it is to the nearest star and
what genes are made of.... Rather, the problem is to get
them to reject irrational and supernatural explanations
of the world, the demons that exist only in their
imaginations, and to accept a social and intellectual
apparatus, Science, as the only begetter of truth.... We
exist [solely] as material beings in a material world,
all of whose phenomena are the consequences of material
relations among material entities.

It's not science or reason that drives Darwinists to
deny God's handiwork...

Anymore, American Christians are resident aliens.



It would have been more interesting and instructive if
the teacher had been able to introduce scientific
facts not linked to any particular organization but
linked to research papers. For example, a teacher
could cite the information rich nature of nucleic
acids in some detail and then let it be known that we
have never observed the formation of a single
information rich nucleic acid except those templated
from already existing information laden NAs in
biological processes involving organisms. (This
includes living organisms known as scientists who with
planning and forethought deliberately manipulate NA
within or extracted from living organisms. For the
purpose of this post viruses are considered
"organisms."). Implications of this are significant
for life's origins.
*blink*

WHO ARE THESE PEOPLE TALKING TO???

These messages were taken from a small IDC only board. Not like there were fence-sitters around to sway. Who are they trying to kid?

"ID isnt Creationism!!"....... Did he not get the Wedge memo?? How??

"Deny Gods handiwork..."......... Did she not get the memo about IDC not being religion? *WINK!*

"Would have been more interesting if the teacher had linked to science..." ...... Do ya not know IDC, or any Creationist for that matter, have not done any research to support their religious views?

These are the Usual Parrot Squawks, but I didnt realize they just sat around squawking at each other.

Tuesday, March 20, 2007

HAAAAHAHA Even YOUNGER kids smarter than UD!

14-18 year old high school kids slam ID Creationist teacher.

And theyve got their parents support.

"I'm here to tell you that I am absolutely outraged to the deepest level of my bones that this curriculum, that this study session, was allowed to be presented to our families and our children without anybody looking over anybody's shoulder, and I would like to know how this occurred and why it occurred and what remedies the board has," said parent Dan Harrison.

And theyve got their school boards support.

By a vote of three to one, with one member abstaining because of a lack of background information, the board terminated the employment of the probationary, part-time teacher.

"I think Mr. Helphinstein wasn't teaching good science... I think his performance was not just a little bit over the line. I think it was a severe contradiction of what we trust teachers to do in the classroom," said board member Jeff Smith.

Good job, all around!

Keep an eye on the comments section-- looks like the Creationists are already weighing in :P Should be entertaining!

Monday, March 19, 2007

hehehehe Another kid smarter than UD

Okay, he might object to me calling him a kid, but he shouldnt. I consider myself a kid (happens when everyone you work with are geniuses 3 times your age, you always feel like a little kid).

Anyway, after UD butchered ERVs, heres an 18 year old kid who 'gets it'. Intelligent Design was 'born' approximately the same year as Chris, ~1989, with 'Of Pandas and People'. Look at what one kid thinking for 18 years can become. Compare that to what ID has done in the past 18 years.

I just think thats kinda ironic.

Sunday, March 18, 2007

"When does Skepticism become Denial?"

Wow hat tip to grisha on Skeptic Talk!

"When does Skepticism become Denial?"
by Steven Novella... M.D.!! No wayyyyyyy! M.D.! An M.D. that talks some sense! Sweet! Oh sorry, thats not the point of this post :P

A few great bits:
Regarding Science vs Pseudoscience

Philosophers of science often speak of the demarcation problem, referring to the difficulty of distinguishing consistently between science and pseudoscience. I am proposing that there are two subsets to this demarcation problem, between appropriately skeptical science and true belief or gullibility at one end, and absolute denial at the other.
At both extremes, gullibility and denial, the core of pseudoscience is the same - namely that pseudoscientists begin with a desired conclusion, and then go through the superficial motions of science to arrive at their predetermined conclusion. Whereas with healthy science inquiry precedes belief or condemnation. For deniers, their dedication to the denial of the offensive belief supercedes fair-minded skepticism. While attempting to portray themselves as skeptics, they are forced to employ a series of pseudoscientific tactics and logical fallacies to maintain their denial.

Regarding HIV Denial
The HIV denial literature reflects a basic distrust of authority and the institutions of medicine. Perhaps it is just the fascination of uncovering a conspiracy, or the psychological secondary gain of being involved in a righteous crusade. The AIDSrealitycheck website, for example, proudly displays the header, “This website is not brought to you by any pharmaceutical company.” At least in some cases there is a more direct secondary gain to HIV denial. Dr. Mohammed Al-Bayati, founder of Toxi-Health International, proclaims that “HIV Does Not Cause AIDS.” (Al-Bayati, 1999) Rather, he claims, it is caused by toxins, which his clinic is uniquely qualified to diagnose and treat.

The HIV deniers behave similarly to the psychiatry deniers. For example, one pro-HIV denial article states that semen samples from HIV positive individuals often contain the same concentration of HIV as does saliva, and yet HIV is allegedly transmitted by semen and not by saliva. (Farber, 1992) This is only partly correct, however. The article leaves out the important fact that intercourse creates small abrasions that allow for the virus to get into the blood stream, whereas the virus cannot penetrate the oral mucosa. In fact, if someone had a cut in their mouth then they could acquire HIV through saliva. Also, the rate of transmission of HIV is much higher in individuals who have other sexually transmitted diseases because they often have open sores which allow easier access to the virus.

Another common representation of the unreasonably far goalpost is the frequent demand by prominent holocaust deniers to be shown “one piece of evidence” which proves the holocaust happened. No one piece of evidence can establish such a complex historical event. Just as no one piece of evidence can establish that organic evolution happened on this planet. Not even the rather straight forward claim that HIV causes AIDS can be established by a single piece of evidence, it must be the result of a chain of evidence.
The HIV deniers have taken a similar stance. The correlation between the HIV virus and AIDS has been established beyond all reasonable doubt. Much is known about how HIV works, and drugs which specifically target retroviruses (the type of virus HIV is) have successfully prolonged survival and decreased opportunistic infections in HIV positive individuals. Yet this is not enough for the HIV deniers. They attack the pieces of the puzzle we don’t yet know, or which can only be inferred but have not yet been definitively proven. Why haven’t we seen the virus actually killing T-cells (the cells of the immune system targeted by HIV)?

Anti-HIV crusader, Dr. Peter Duesberg, has argued that HIV “fails to meet the postulates of Koch and Henle,” (Duesberg 1988) which were designed to establish criteria for demonstrating the link between an infectious agent and a disease. However, the Koch and Henle postulates were developed in 1840 and 1890 respectively, before viruses were even discovered. Biology has evolved far beyond Koch and Henle, whose postulates are no longer definitive.

They have also employed the “show me one piece of evidence” strategy. In fact, one HIV denier is offering a $10,000 prize (sound familiar) for anyone who can reference one article which demonstrates all the key elements necessary to establish HIV as the cause of AIDS. Typically, however, the research necessary to demonstrate such a connection would be spread out over many articles. The request is unfair and is made solely for its dramatic effect.

The HIV denial literature is also replete with similar claims of emerging skepticism. For example, Celia Farber wrote in a pro-HIV denial article, “More and more scientists are beginning to question the hypothesis that HIV single-handedly creates the chaos in the immune system that leads to AIDS.” (Farber, 1992) The article was published in 1992, and ten years later there remains a solid scientific consensus that HIV causes AIDS.

As part of this strategy deniers tend to rally around a figure head, a scientist insider who spearheads the denial movement. HIV deniers have virologist Dr. Peter Duesberg as their champion.
Sweet.

Saturday, March 17, 2007

How much more clueless could Engor be?

And the answer is none. None more clueless.


I mean, Id like to write an 'objection' piece to Engors 'replies'... but whats there? 'We dont need evolution for comparative anatomy!!' Well, I already answered that, a long time ago... And my observations are hardly novel. 'Genetics isnt evolution!!' Well, yeah it is. I already replied to that too.

This is the best Creationists have. Chin up, Creationist Kids! One day you, too, can be laughed at by someone a third your age, just like Engor! His present is the best possible future you have to look forward to, if you want to be a Creationist physician!

Unless, of course, you pay attention in school. Then you might, you know, use evolution to cure a few kinds of cancer or something. No, why would you want to do that when you could be an Engor.

Stupid and depressing.

Friday, March 16, 2007

I can writes GOOD!

The past few weeks Ive been trying my hardest to write the intro for my paper. Im about 99.8% certain my boss already has one written, but hes having me do it to practice, and to get me more familiar with the literature relevant to our research (normally you would do a literature review before you started doing the research, but I kinda jumped into this project after it was already up and running). I knew this draft wasnt perfect, but I thought it was *kinda* good?


ROFL! Not ONE sentence was left unaltered! HAHAHAHAHA!

Boy I sure loved my liberal arts school. I even took like 8 'writing intensive' courses (we only *had* to take three or four). But I guess 'extended metaphors' and 'alliteration' are frowned upon in scientific journals :P

HAHAHAHA!!!

Thursday, March 15, 2007

Skeptics Circle

Head over to Scientia for some Skeptic relief!!

Radioactive Lab Pets: Why ERV Needs A Day Off

Look who I found in the lab today!!!!



A cute little blue fungus! A BLUE fungus! A blue RADIOACTIVE fungus! Isnt he adorable???

Hes got a little blonde girlfriend, but its hard to see her in the yellow radioactive waste. :(

Im not *entirely* sure how theyre surviving in that particular mixture of chemicals...


(yes, I need to go to sleep early tonight... LOL!)

Wednesday, March 14, 2007

Deniers vs ERVs: Round 1, TKO

You know I was comfortable with Deniers going after HIV and Creationists going after ERVs, but over the past couple of weeks Ive learned that Deniers want to get their garlicy lemon-juice fingers into both of my research topics. A reader (far more patient than I) and Chris Noble (also more patient than I) have brought some of their specific claims to my attention, but lets just shut this nonsense down once and for all in one sentence. One sentence. It took me five posts to 'get' the Creationists ERV game. This turned out to be a lot easier.

"Lentiviruses and deltaretroviruses also share the distinction of being the only retroviral genera for which endogenous counterparts have not been identified."
The Evolution, Distribution and Diversity of Endogenous Retroviruses


Okay I lied, two sentences (really its just the same sentence again).
"No delta or lentivirus representatives were found among ERVs."
Use of Endogenous Retroviral Sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy


One of the funny things about viruses is that no matter how you classify them, one in a group will always be vastly different from another in that same group. Try classifying all viruses by their genomes-- but would you rather have a wart (HPV- DNA virus) or Hepatits B (also a DNA virus)? Their replication cycles are vastly different! Well, surely like, viruses with the same name are similar, like HSV-1 and HHV-6? Nope. Both herpes, but they infect totally different cells. Hmm. Well, maybe classify viruses by the types of tissue they infect-- Compare Hepatitis B (double stranded DNA virus) with Hepatitis C (single stranded +RNA virus). Totally different creatures.

So if you dont study retroviruses, you wouldnt know that there are currently seven different kinds of retroviruses: alpha-, beta-, gamma-, delta-, epsilon-, lenti-, spuma-. If you dont study endogenous retroviruses, you would think that theyre all essentially the same thing. They arent. To put this into perspective, when you hear Culshaw/Duesberg/et al talking about how HIV is an ERV, imagine theyre saying that a chimpanzee is really a humpback whale. Theyre both mammals, right? HIV and ERVs are both retroviruses, right?

There are no lentiviral ERVs, thus HIV cannot be an ERV.

Whats particularly troubling to me about this whole scenario is that I didnt know this information 24 hours ago. I mean I figured you could classify ERVs into the seven groups, but I didnt know there were no lentiviral (or delta-) ERVs. I just stumbled upon this info this morning while playing on PubMed (technically I was doing a literature review, but when work is fun, its playing). I didnt put in any weird, unique search terms. This means that 'trained' Professional Deniers are making these asinine comments without even bothering to do a PubMed search before they say anything! Theyre THAT arrogant! Well, theyre either arrogant, or they know damn well what the literature says and they prefer to be Professional Jackasses like Professional Creationists (no, I dont believe Behe, Dembski, etc believe a word they say).

Anyway, next time you hear one of them say something about HIV-->ERV say "Chimpanzee--> Whale." There. Now we can expect Deniers to stop saying shit about ERVs, right?

.... Right?

**faint sounds of a Creationist talking about the second law of thermodynamics**


Shit.

Why I look up to Angelina Jolie

High on the bfs list of 'People I hate' are 'Otherwise heterosexual women who say they would have sex with Angelina Jolie' (its so obvious your just trying to seem 'cool'), so he was concerned when he found 'Angelina Jolie' listed under my 'Heroes' on MySpace. Well, sure shes damn sexy, and I could pull off being her stunt-double in Tomb Raider with minimal PhotoShopping, but thats not why I look up to her.

THIS is why I consider Angelina a hero of mine.

Im continually disappointed in family members who choose to throw The Wedding of the Century or to buy another sports car, while shit, and I mean SHIT is going down all over the planet. Same can be said of 99.9999% of celebrities-- choosing to spend their money on crap, or flying to Italy for a cup of coffee, or refusing to do social work without a camera crew in tow or a court order. Heres a woman whos doing something.

A quote I can relate to, in particular:

"Do you despair?
Certainly, at times. The first two years I just cried constantly like a woman does.

Oh, like anybody does.
Yes, like anybody does, thank you. I couldn't really talk about the situation without being emotional. And I went through a period of just complete lack of hope. Just feeling like it was way too overwhelming and feeling like I wouldn't be able to make a dent. And then I went through a period of anger that smart, articulate people in power have not been able to answer these issues quickly and clearly and define ways of intervention. And that it just keeps going on. About a year ago, I got a lot of books on international law and I tried to study what was going on—just out of a curiosity about what was this bigger picture. I don't want to have to keep going back to camps, five different times, over the next 30 years of my life, [for situations] that there are no solutions for. "

I face despair every day at work- "Whats the point? All these kids are going to die anyway. We're never going to cure HIV infection. We're never going to figure out a vaccine. The problem is too big. Why bother?" But I keep trying anyway because ts the only thing to do.

It cheers me up to see someone else happily jumping into the hopelessness and trying to help anyway :)

Tuesday, March 13, 2007

Im not buying her book. Im not doing it.

Latest ERV readers comment about Rebbecca Culshaws devastating take-down of HIV/AIDS Dogma:

Culshaw claims that "endogenous retroviruses are primarily transmitted perinatally, from mother to child" ( p.45).

*blink*

No way. No friggen way. There is no goddamn way she is serious.
Main Entry: en·dog·e·nous
Pronunciation: en-'dä-j&-n&s
Function: adjective
1 : growing or produced by growth from deep tissue <endogenous plant roots>
2 a : caused by factors inside the organism or system endogenous depression> < endogenous business cycles> b : produced or synthesized within the organism or system endogenous hormone>
- en·dog·e·nous·ly adverb

If ERVs were transmitted perinatally... THEY WOULD BE EXOGENOUS RETROVIRUSES.

Sure she could play the 'Gosh golly, Im not a scientist' card* with some of her other claims, but you just have to have a dictionary to call BS on that sentence! No WAY she can be serious!

For a more sciency answer to that-- Okay, so each ERV is present in every cell of your body. Every cell, with each ERV in the EXACT same location. And Culshaw says that this doesnt happen through germ lines getting infected with RVs (becoming ERVs). No, this happens when infants are infected perinatally with exogenous retroviruses resulting in an effect called endogenous retroviruses. Yeah, her explanation makes a lot more sense. *blink* I dont want to know how she thinks this deep, deep understanding of ERVs relates to HIV. I dont want to know.



*When backed into a corner over idiotic claims they make-- Deniers and Creationists like to revert from "Im smart! Listen to me! EVERYONE IS WRONG BUT MEEEEEE!!!" to "Look at that meanie scientist picking on someone who just wants to learn! Boo hoo hooooo!!!"

Monday, March 12, 2007

DONT TELL DAWKINS

I dont think Dawkins reads my blog*, so this is safe here-- but dont ruin the surprise.


March 10, 2007

Richard

We're going to be creating a birthday present for Richard Dawkins' birthday, March 26th. We would love for you to incorporate your message into the gift!

Please CLICK HERE to enter your birthday message to Richard!

http://richarddawkins.net/bdayMessage

(It's a secret link, unconnected from the regular website)

If you have a creative birthday image or video you'd like to include in the birthday gift, please email it to design@richarddawkins.net with 'RD birthday stuff' in the subject line. Maybe fun or creative images of you with your copy of The God Delusion? Maybe in an interesting setting? Maybe you can get a video of yourself with all your friends at a pub singing happy birthday to Richard Dawkins? Everyone in your class/office/megachurch/whatever? Be creative!

PLEASE DO NOT post this info in the RichardDawkins.net forum or in the comments. We don't want Richard stumbling upon it and seeing it before his birthday! He's not on this mailing list, so I think we're safe here. I'm also going to post some myspace bulletins, I don't think he looks at those. Maybe some of you internet rockstars out there could help us covertly spread the word?

Thanks!

Josh Timonen
www.RichardDawkins.net






*And if Richard Dawkins does read my blog, Im going to go throw up. I cant handle that kind of pressure.

Junk DNA?

I couldnt understand why ID Creationists were suddenly in a rush to claim 'junk DNA is proof for Design'. And they arent stopping. I think I get it now. A few blogs, written by biologists, have debunked similar claims-- And I think we all used different definitions of 'junk DNA':

Me: "A while back we didnt know as much about our genome as we do now, so researchers called these silly bits 'junk DNA'. People used to think that genes that encoded proteins were the only important parts of our genome. However, when it became apparent that too many weird repeats can cause disease (eg Huntington's), ERV bits contribute to the transcription of protein coding genes, and other bits of 'junk' were parts of previously unknown biological processes (eg siRNA), most people stopped using the term 'junk DNA' and started using the term 'noncoding DNA'."

Sandwalk*:
"The genomes of many complex multicellular organisms have vast quantities of DNA that serves no purpose. It's junk."

The Daily Transcript:
"the term junk DNA is commonly used to describe portion of the genome which have no described function"

Evolgen:
"Not useful, but not bad enough to be worth eliminating."

(I know there are more people who have addressed this.)

Hmm. Were all saying similar things, but not the same thing. You know what that means: ID Creationists are going to jump ALL OVER IT. They capitalize on any fuzzy area of science to feed Average Joes confusion. Thats why theyve been so excited about 'junk DNA' recently. Maybe we should just drop it entirely? Like I said in the Intro-- I wasnt technically even taught the term 'junk DNA' in the first place, its arcane-- like 'MT Tropic HIV'. Ugh but then the IDC will just scream 'SEE!! NO JUNK DNA!! CREATIONISM IS RIGHT!!!'

Any ideas?

*Searching for 'junk DNA' on Sandwalk, I noticed Larry Moran found Mr. DNA Researcher before me. Quote Larry: "You're welcome to visit whenever you want. But you're still a kook." ROFL!!!

Saturday, March 10, 2007

OOPS! They did it again!

Hat tip to Pharyngula.

Oops. Dr. Egnor, Mr. Professor of Neurosurgery, doesnt seem to have learned a lesson from Mr. 99. And now hes going to get made fun of by a 23 year old girl, too. Someone get a Ziploc bag for his testicles.

Really, it’s a funny question. Think about it. Would anyone sponsor an essay contest on ‘Why I would want my doctor to study anatomy’ or ‘Why I would want my doctor to study physiology’? Of course not, because we all know that these kinds of science are important to medicine. Is evolutionary biology important? If it is, why do they have to ask the question?Because assholes like you are telling kids that they dont need to know evolution to be a physician. If there were school boards insisting that children shouldnt learn anatomy in school (wouldnt be surprised. just sayin) and neurosurgeons claiming that they never learned muscle or skeletal anatomy and they can operate on brains JUST FINE, then we would consider sponsoring such a contest.
A fantastic reason to sponsor such a contest is to encourage kids to actually pay attention in their bio classes when the teacher/prof is talking about evolution. You know, what you didnt do, Egnor. The surviving pre-med bio majors in my class were loathed to take required courses such as ecology (what does a pre-med care about deer and invasive species?), but if they took their heads out of their own butts for a second they would have realized that they were 'studying' epidemeology, aetiology, etc.

Another reason would be to get these kids to transmit this information to their parents. Like Ive said over and over and over, Average Joe Creationists slide right off that Creationist-Wagon when they realize how evolution is directly connected to their quality of life. Its not just about 'dogs turning into cats'-- its about Mom not having to go on chemo when she gets breast cancer because her genotype matches the cancer that can be treated with radiation alone. Its about inventing new drugs and vaccines to make our lives better. Get high school kids to write about these kinds of real-world benefits, and suddenly Mom and Dad dont mind evolution being in the curriculum anymore. Might even be inclined to start fighting against Creationism.

Gee, why would ID Creationists be upset at a contest like this?

Doctors don’t study evolution. Doctors never study it in medical school, and they never use evolutionary biology in their practice. There are no courses in medical school on evolution. There are no ‘professors of evolution’ in medical schools. There are no departments of evolutionary biology in medical schools.
No, honey, replace 'doctors' in that paragraph with 'you.' Not all doctors are as stupid as you, even I have to admit. Evolution was implied in all of my 'medical' courses in undergrad-- everyone had already taken intro biology courses thick on evolution, so words were used in immunology, virology, pharmacology, etc that implied you already had a firm understanding of the basics. By Egnors logic, I wasnt required to take an advanced evolutionary biology course as a biology major- therefore evolutionary biology isnt used in biology.
You know, this essay is more telling of Egnors pathetic performance as an undergrad, rather than an essay on 'Evolution in Medicine.' I read on Oracs blog that Egnor was a bio-chem major. My apologies to hard working bio-chem majors out there (hell, my boss was one), but from my experience, bio-chem majors were the bio majors that couldnt pass the evolution intensive upper-level biology courses, so they took upper-level chem instead. I know its a cliche stereotype, but Egnors fitting the bill beautifully at this point...

If you needed treatment for a brain tumor, your medical team would include a physicist (who designed the MRI that diagnosed your tumor), a chemist and a pharmacologist (who made the medicine to treat you), an engineer and an anesthesiologist (who designed and used the machine that give you anesthesia), a neurosurgeon (who did the surgery to remove your tumor), a pathologist (who studied the tumor under a microscope and determined what type of tumor it was), and nurses and oncologists (who help you recover and help make sure the tumor doesn’t come back). There would be no evolutionary biologists on your team.
Wait, you include the physicist who designed the MRI, but conveniently forgot to mention the biologists that made the pharmacologists drug design possible? Do you know what 'basic research' is, Egnor? You know, those of us that figure out what genes do, what viruses look like, etc so 'clinical researchers' can figure out how to treat diseases? Wanna show me one basic research paper that doesnt require evolution? I mean do you think clinical researchers and pharmacologists figure this stuff out through magic? What the hell? And what do you think those pharmacologists test their drugs on before they give them to humans? Why do you think animal testing (though it has its limitations) works? Again, magic?
And I take this comment personally, in particular, because as some of you might know, one of my projects (epigenetic control of ERVs) spawned an idea for increasing the efficacy of traditional cancer therapies. Yeah, Egnor, Im using evolution to help treat cancer, including brain tumors. God youre arrogant.

I am a professor of neurosurgery, I work and teach at a medical school, I do brain research, and in 20 years I’ve performed over 4000 brain operations. I never use evolutionary biology in my work.
No, you dont know how youve used evolutionary biology in your work. And you dont care that you dont know. That makes you an arrogant idiot, not someone children should look up to.

Would I be a better surgeon if I assumed that the brain arose by random events?
No, you would be a better surgeon if you actually paid attention in your classes as an undergrad. Kids know stuff you dont know, Mr. Professor of Neurosurgery. Kids. 18 year old kids. Yeah, lets all listen to what you have to say.

Of course not. Doctors are detectives.
No, youre a mechanic. Sorry. PhDs are detectives. PhDs are explorers. PhDs seek out new life and new civilizations. You fix brains. PhDs tell you how to do it. Specifically, PhDs that paid attention in undergrad tell you how to do it.

I do use many kinds of science related to changes in organisms over time. Genetics is very important, as are population biology and microbiology. But evolutionary biology itself, as distinct from these scientific fields, contributes nothing to modern medicine.
Theyre all connected, if not the same damn thing. Genetics means nothing without evolutionary biology. Not a damn thing-- unless hes suggesting we create knock-out human babies to figure out what all of our genes do. And what the hell do ERVs in our genome say about evolution?
Move those goal-posts, Egnor. Good full-body workout.

Without using evolutionary theory, doctors and scientists have discovered vaccines (Jenner, in the 18th century, before Darwin was born), discovered that germs cause infectious diseases (Pasteur, in the 19th century, who ignored Darwin), discovered genes (Mendel, in the 19th century, who was a priest and not a supporter of Darwin’s theory), discovered antibiotics, and unraveled the secrets of the genetic code (the key to these discoveries was the discovery of the apparent design in the DNA double helix). Heart, liver, and kidney transplants, new treatments for cancer and heart disease, and a host of life-saving advances in medicine have been developed without input from evolutionary biologists.
Okay, ignoring the fact that all the people involved with discovering DNA is a double helix were atheistic Evilutionists, Egnor is spouting shit Ive already covered. You should read my blog, Egnor-- save you some shame! Yes, stumbling around and randomly smacking into solutions to our medical problems without understanding why or how those solutions work, nor how to improve upon those random discoveries is SO much better than using evolution. How long would it have taken us to figure out the impact of ERVs on cancer without evolution, Egnor? You want a number on how many mutations it takes to turn a 'monkey' into a 'man'? I want a number, in years, for how far back our technology would be without evolution. When would you have discovered the importance of ERVs and cancer, Egnor? Never? You think the answer might be never? Maybe? Jerk.

No Nobel prize in medicine has ever been awarded for work in evolutionary biology.
Oh now youve moved from asshole/jerk to just plain idiot. What the hell do you think siRNA is, genious? siRNA runs down to almost the root of the Tree of Life. Wow youre smart, Mr. Professor! UGH I get so damn angry when people who have more experience, who Im supposed to learn from, can teach me nothing. Worse than that-- I know things that they are supposed to know. Its pathetic.

Thursday, March 08, 2007

Happy Birthday, PZ!

First blog I started reading.

First person I knew who loathed Creationists as much as I did... And enjoyed mercilessly ripping them limb from limb too (figuratively, of course).

Im sure 99.9% of you already read Pharyngula, but if not, check it out!


There once was a sci-prof from Morris,
Whos blog tended to preach to the chorus.
But with steel-toed boots,

and brass knuckles too,

He hammers creationists for us!




*giggle* If you dont get the steel-toed boots/brass knuckles comment, just ask an IDer hehehehe!

Old Papers

Recently a commenter pointed out that Deniers like-- no, LOVE, using papers from the 1980s to support their assertions. Deniers still in grad school were lamenting the fact that they had to, you know, keep up with other peoples research in order to publish themselves (reading is an unbearable burden when youre intellectually lazy). And it got me wondering, whats the oldest paper Ive referenced? I *think* its this one:

Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1.


I specifically research this region in Subtype C HIV. Its a real neat stretch of DNA-- in Subtype B HIV, V3 is one of the most variable regions of env ('Variable 3' region), but in Subtype C, its one of the most conserved regions! So you can have lots of fun cutting and pasting various bits of this region into different subtype backbones just to see what happens (of course we're learning about how the viruses work too-- but it helps that its ridiculously fun to see what kind of virus pops out at the end of a cut/paste). And its fun to look at the evolution of the V3 loop in Subtype C patients because it doesnt change very much. Little amino acid changes can really screw around with the virus!

The only reason I can have all this fun is that Im standing on the shoulders of giants that got some essential things figured out early on. Though even I have to admit, this paper was kind of hard to read. Like reading 'English' from the 1800s. They use arcane terms like 'MT tropic' and 'T tropic' viruses, but if I squint and just look at the figures, theyre doing things very similar to what I do 16 years later (good god I was 8 when this paper came out). They cut and pasted various bits of 'MT tropic' and 'T tropic' gp120s together to see if they could make an 'MT tropic' virus a 'T tropic' virus. Lo and behold-- they could do it just by switching out the V3 regions!

In 1991, this was a HUGE revelation. This was a SCIENCE paper! Now? Meh, you mention it and get on with your data, its kinda sad. All novelty in science is fleeting. I suppose the authors consolation is that we have moved light-years ahead of where we were when this was published. I would be honored if something I published became a 'Meh' in hundreds of other papers, so I hope they are too.

Wednesday, March 07, 2007

Science as a Foreign Language

I went to a Liberal Arts university for undergrad, which means that I was required to take a lot of fun courses-- two courses in musical theatre, ancient Greek literature, philosophy-- when youre a science major, these classes are a pleasant break from 12 hours of lab work a week.

But when those science courses got tough, it was hard not to resent the extra coursework. I remember during one infuriating study session for a Bio Major Weed-Out Course (we got a crash course on every species on the planet), memorizing words like parenchyma, sclerenchyma, and chlorenchyma and declaring we should get foreign language credit for Bio-II.

Learning biology, learning any science, IS like learning a foreign language!! And even though Ive been in science-world for years, I STILL screw words up all the time! So dont feel bad if you bumble a lot!

Some common ones:

Transcription - Turning DNA into RNA
Translation - Turning mRNA into proteins

Splice - Cutting RNA
Cleave - Cutting Proteins

Transform
- Putting plasmids into bacteria
Transfect - Putting plasmids into eukaryotic cells
Infect - Putting, in my case, viruses on cells

Those are some a little more specific for my field-- what are the major word mix-ups in your alls fields?

Tuesday, March 06, 2007

If this sentence is representative of the book...

I always admired Latin as a written language. Our professor might only ask us to translate a page of Latin into English, but it would take us five pages of English. The Romans were so efficient.

The Romans would be impressed with this sentence from Rebecca Culshaws book that a reader brought to my attention, as it addresses both HIV and ERVs. Culshaw took a page from the Creationist play book and published a pop culture book instead of a journal article, with you know, science. But dont let her PhD in math and direct-to-consumer publication fool you! This chick knows SCIENCE!:

"Furthermore, such apoptosis-inducing proteins as gp120, tat, and nef are present in other retroviruses including human endogenous retroviruses, yet these retroviruses are not thought to induce apoptosis to anywhere near the extent that HIV supposedly does."
OOOOOOOOOOOOOOOOOOOOOOW! How did she do that??? I mean, UD is great at fitting a lot of wrong information into compact language, but theyve had decades and decades to practice! Deniers havent had nearly as long, and look what they can do!

Heres the short reply:
"Well all Staph bacteria secrete toxins, but not all toxins are harmful to humans, therefore Staphylococcus aureus is harmless. Har har har!"

Heres the long reply:

Retroviruses in general just require three genes-- gag, pol, and env (hence my blog subtitle). Other genes like tat, nef, vif, vpr, etc are just accessories for some viruses. Retroviruses in general also have extremely compact genomes, which means to get alllll of the genes it wants, usually there are 'alternate reading frames' and 'alternate splicing patterns' for the same stretch of DNA. Take a look at this pic: (ugh click on it and look at it. thank you blogger.)


See how the boxes are overlapping? You can get more than one protein out of the same stretch of DNA just by starting a base pair later or cutting the proteins up differently. I would not expect ERVs to maintain the sequences necessary to keep the accessory proteins functional. And, a quick PubMed search agrees with me.

'erv env'-- 27 hits
'erv gag'-- 10
'erv pol'-- 20

'erv tat'-- 1 hit, a review (no data) from 1996, doesnt address tats in ERVs
'erv nef'-- 0
'erv vif' --0
'erv vpr'-- 0

As I said, ERVs are a young field, so 27/10/20 vs 0 might not be as impressive as 295876249674234 vs 0, so lets pretend that there are lots of transcribable/translationable tats and nefs in our genomes, we just havent found them yet. Then you have epigenetics to deal with.

There are ways your cells keep certain parts of your DNA from being expressed. You can methylate DNA to keep it from being transcribed, or make modifications to 'histones' to wrap DNA tighter (no transcription) or looser (more transcription). ERVs are wound up TIGHT! Like I said in Part 5 of 'ID vs ERVs', you do NOT want ERVs to become active because of the damage they do! Parts are okay if theyve been co-opted for other uses, but retroviruses are dangerous! Even the envs that are active are only active at very specific times and places when it is safe from an immunological attack.

The reader then brought up an excellent point that I didnt even think of:
Do you know if any HERV has a 'gp120'? ERVs have well-conserved envelope genes, from what I gather, but can they be processed into a gp120 (even assuming that they're transcribed and translated)?

DOH! Of course!

Okay all retroviral envs are cleaved into a transmembrane and subunit piece-- but not all retroviruses cleave into gp120, gp41. gp100, gp135, etc etc etc.



I currently know of no ERV that specifically cleaves into a gp120 SU. gp120-gp41 splicing is not characteristic of all retroviruses in the first place, so when you add in a few million years for an ERV env to mutate, you REALLY would be surprised to find that particular splicing pattern.

What the HELL is Culshaw talking about??

My local library doesnt have this book. Im not buying it... Unless enough people are interested in helping me take it down a la 'Politically Incorrect Guide to Darwinism'. Or maybe one of the Deniers who lurk here will send me a copy?

Monday, March 05, 2007

HPV vaccines in Red States

We all know that the Religious Right/Conservatives/Biblotarians are all up in arms over Gov. Rick Perrys suggestion that all 11-12 year old girls get vaccinated with the HPV vaccine. Before, I was ambivalent about it. I completely agree with mandatory or opt-out vaccination, but even if you grow up in a radical Christian household and you mom doesnt mind risking her daughter getting cervical cancer, you can still be okay. If we ignore the public-health risk of not hitting everyone hard (like we did will small-pox and almost polio), once you turn 18, even if you dont have your own medical insurance, you can find a state or student clinic where you could get the vaccines. Evil Mom doesnt even have to know about it.

But then I tried to get the vaccine.

About a month ago I had my yearly check-up. I figured while I was there and while I had health insurance that covered the vaccine, I should get it. My doc agreed and went to get the vaccine. ~20 minutes later she came back and said they didnt have any. Call back later. Okay, no big whoop! Called back a week later: "Yeah I think we have it in!............ We dont have it. Call back later." Week later: "Yeah I think we have it in!............ We dont have it. Call back later." Week later: "Yeah I think we have it in!............ We dont have it. Call back later." Last week I called them every day, and I finally freaked out* on Thursday "I HAVE BEEN TRYING TO GET THIS VACCINE FOR A MONTH! What is the matter with you people??????" "We dont have it. Call back later."

Today I got a little further: "We have it, but you have to make an appointment with your doctor for a counseling session before you can get it." WHAT??? WHAT THE FUCK??? I sure dont remember having a 'counseling session' before my last tetanus shot, or the series of hepatitis B shots, or my meningitis shot, or flu shots... What the hell is going on here?? Luckily I thought fast on the phone "Actually we already did that at my last appointment. When can I come in?" *silence* "Um, you have to talk to Dr. Physicians nurse. Shell be the one giving you the vaccine."
Then I get forwarded to a voice mail account. Not to a phone, it didnt ring once-- a voice mail account. And since when do nurses make their own appointments?

Oh and wouldnt you know it, no one called me back.

I have no idea whats going on here, but if my experiences are representative of what other women are going through trying to get this vaccine, HPV vaccines need to be mandatory and regulated. Now.



* Totally TMI, but there is a certain gentleman that I wouldnt mind being intimate with, however we agreed that I should get the vaccine first. So Im a *little* pent-up about this delay, ignoring the societal implications of the difficulties Ive been having. Just a *little* pent up. *twitch*

Oh my! Um... Howdy!

As I was going through my morning computer routine today (email, weather, news, blog) I couldnt help but notice my site traffic is like, oh, FIFTY TIMES WHAT IT NORMALLY IS.

LOL!

Thanks to some great bloggers adding me to their blog rolls (Pharyngula, A Blog Around the Clock, Growth Rate), Deniers, IIDB folks checking out the 'ID vs ERV' posts, and something called StumbleUpon.com (I dont know what this is, but thanks to whoever added me!), I got more hits this past weekend than I have in basically every other month combined.

Ask questions, guys and gals, if you have any! Im just a student, so answering your questions helps me learn too! Or just stop to say hi in the comments!

Howdy!

Saturday, March 03, 2007

ID vs ERVs-- Part Five: ERV on ERVs

How does UD do it? How do they fit so much crap into a single post? Uuuuuuuugh! Its going to take me forever to clean this up! But, Im ERV. If anyone is going to clean up a UD ERV crapfest, its me. So Im going to hack at this bit by bit.


ID Creationists want ERVs to be functional very badly. Sure Im biased, but I think ERVs are the bane of ID Creationists existence. All these exogenous bits of DNA randomly integrated themselves into genomes in a pattern that just-so-happens to look like descent with modification. ERVs are damning evidence against any Creationism, but ID Creationists hate them specifically because ERVs beautifully illustrate the ability of evolution to take whatever bits it is given to mutate them into SOMETHING interesting. Takes 'Irreducible Complexity' and unevolvability and throws them right out the window. Evolution is a fucking MacGyver making placentas out of a chunk of retrovirus and a stick of Wrigley's Spearmint Gum!!!

But UD didnt want to talk about that. They want to slander T.O. Ugh, okay, fine-- what horribly horribly wrong things did T.O. say about ERVs, UD?

TO-- Endogenous retroviruses are molecular remnants of a past parasitic viral infection. Occasionally, copies of a retrovirus genome are found in its host's genome, and these retroviral gene copies are called endogenous retroviral sequences.

Essentially all of these endogenous retroviruses contain mutations that would disrupt the function of their genes, as would be expected if they inserted millions of years ago with no selective pressure to maintain the function of the genes.

UD. UD, that phrasing looks awkward. UD, you didnt cut and paste two phrases from different articles and paste them together like thats how they were originally written, did you?
One
Two
Awwwwwwwwww goddammit! Fine fine fine whatever. Theyre both from T.O. *rolleyes* Whats youre 'rebuttal', UD?
UD-- "Human tissues that lack HERV transcription could not be found..."
Yes. Transcripts. Functional ERVs would mean that they could find viral particles circulating within humans. Youre not proving T.O. 'wrong' with that paper.

UD-- "In particular, a class of endogenous retroviruses, known as endogenous retroviruses related to Jaagsiekte sheep retrovirus or enJSRVs, are critical during the early phase of pregnancy when the placenta begins to develop."
Yeah, thats env. Syncytia. Again, thats not a functional ERV. Thats a gene that used to be retroviral that was co-opted by the host organism for a job.

UD-- "Indeed, the LTR is the dominant promoter in the colon, indicating that this ancient retroviral element has a major impact on gene expression"
UD, do you not know the difference between an LTR and an ERV? You would have if you actually READ the T.O. articles you quoted. Its just another part of ERVs, like env is. Its just a part thats been co-opted. ERVs are not functional.

UD actually wrote this next part, as opposed to copy/pasting or pirating:
UD-- Admittedly, most of the scientists involved in the above studies of Endogenous Retroviruses still assume that they were parasites that somehow were incorporated into the genome with functional roles. However, since many of these perform similar functions in different species, one cannot prove common descent based upon the idea that shared retroviruses are shared errors.
What? I understand thats English, I recognize the English words, but does that make sense to anyone? Seems like UD is just getting lazy, "Ive copy/pasted 8 pages of shit, they arent going to notice if I dont make sense! These people are too dumb to know Im bullshitting!"

I have no idea why UD even TRIED to address ERVs. It doesnt take a molecular biologist to figure out what would happen if endogenous retroviruses were functional!

Every cell in your body has the same DNA, its just differentially expressed in different tissues. Whats going to happen if every cell in your body starts making viruses? Retroviruses? Imagine what happened in the SCID study... TIMES 10 TRILLION CELLS. Times the number of ERVs in your DNA (lots.)!!! Ugh do Creationists ever think??

More importantly, what kind of opinion do they have of their followers to treat them like idiots? "Im going to bullshit you because I know youre too dumb to know any better."

I need cheering up

I said it once, Ill say it again: Best band out there today, and they have the audacity to be OUT atheists. Go buy their stuff (or at least watch them on YouTube)

Friday, March 02, 2007

Dawkins was only half right.

Youll have to forgive the fragmented nature of this post, but Im really irritated right now. Irritated and disappointed.

For those of you who dont know the term, 'Neville Chamberlain Atheist' was a phrased coined by Richard Dawkins in 'The God Delusion.' He defined them as a group of atheists that will happily blast Dembski and Behe on their god-science, yet are as equally happy to turn around and blast atheists who point out to theistic evolutionists that they arent being epistemologically consistent.

Dawkins was on the right track, but I think there is a better descriptor for this issue that also explains other problems in the nontheistic community.

I think the main problem with the NCA definition is that cooperating with theistic evolutionists to communicate science to the general public is something that all atheistic scientists do. Certainly there are varying degrees of tolerance for this cooperation, but I dont think it is necessary to make a distinction between levels of tolerance. I mean, I certainly wont waste my time attending a Francis Collins presentation (or this asshole), and I would never hide my displeasure at his philosophical inconsistencies, but the fact of the matter is I really REALLY dont care what other scientists do on their time off. I need help getting evolution taught to kids. I need help explaining to adults how my research, research that requires evolution, relates directly to their quality of life. Whether you go to Star Trek conventions or the Mormon church after I get that help means little to me.

I think Dawkins missed the larger picture. There is, it seems, a subculture in the atheist community where attacking everyone, friend and foe, is in vogue-- the Neville Chamberlain Atheist^2. Extend Dawkins point out from Creationists vs Evolution to Theism vs Atheism, to Silence vs Voice. I think my irritation is best explained through a scene from 'The Last Battle', by C.S. Lewis (yes, militant atheist read C.S. Lewis, eyes didnt boil out of her sockets nor did she convert). At one point in the battle, it seemed the side of Good was lost, but then, over the hills, came the cavalry (literally). The talking horses come pounding over the mountains to save the day!.... And theyre all slaughtered. By the Evil side? No. The dwarfs. What did they have to say for themselves? "We dont want either side to win."

There is a subculture within the atheistic community that doesnt want anyone to 'win'-- they love to blast Creationists and Christian hypocrites as much as I do, but then they turn around and chastise other atheists for having the audacity to speak their mind. Im not sure what their ultimate goal is, and maybe they dont have one. Maybe they just really enjoy bitching (as its far easier than doing anything), and I have a hunch thats the case.

Example A: Theism vs Atheism
There was a LOT of bitching from this subculture when 'The God Delusion' first came out-- but curiously, none of these bawlers appeared to have, you know, READ the book before they started bitching. One of these individuals 'uncovered' that Dawkins signed a petition that wanted to make forcing religion on children illegal and thought himself quite clever. Never mind Dawkins thought that the petition was for school indoctrination only, never mind he was speaking on schools in the UK which are set up differently than were familiar with in the US, never mind that anyone who was passingly familiar with Dawkins would have known precisely what he meant (either by reading TGD, watching 'Root of All Evil', or checking his damn Wiki page). No, "Dawkins wants to make religion illegal!!"

Of course if Dawkins is using atheism to justify child pornography or illegal activities, THAT we should all speak out against. But it was like this subculture was making a mountain out of a molehill just to have the opportunity to BITCH about something.


Example B: Silence vs Voice
Now this subculture has decided that atheists are not allowed to speak their minds without being 'idiots.'

Its no secret that I like David Mills. I like Atheist Universe. I love the fact that hes an Average Joe atheist, like most atheists-- hes not a professor at Oxford or Tufts. Hes just a regular guy with a wife and a kid, and he wrote a book that is understandable by Average Joe Atheists that have no desire to get PhDs in philosophy or physics.
Anyone who knows him, has conversed with him over e-mail, has heard him on a radio interview, or has, you know, READ his book, knows that David is silly. I think you would have to have a sense of humor to be an atheist in West Virginia. But once again, this atheist subculture is too good to actually read the books and know who the atheists are that theyre bashing-- no that would take time away from bitching.

Worst of all in that post, and individual that I respect (despite the fact he is a physician) came in to repeat Dembskis devastatingly clever response to the Blasphemy Challenge: "If youre so tough, why dont you blaspheme against Allah?"

*blink*

HOW MANY RADICAL MUSLIMS DO YOU THINK LIVE IN WEST VIRGINIA??????? ARRRRRRGGGGGG!!!!! FUCK!

Look, Davids video is silly. Its not something I would have made. But Im not going to call him an idiot for posting it, nor am I going to sit here and let some pompous ass act like hes better than David and call him an idiot. I dont care if you paint a picture of the Virgin Mary and shit on it. I dont care if you take your dogs to your old church and let them shit all over their parking lot (as long as you pick it up). I dont care if you act like a stereotypical 'teenage atheist' dress in all black and write songs about fucking Jesus in the ass. I dont care if you jump out of an airplane with 'GOD IS DEAD' written on your parachute. I dont care if you plant a garden of tulips in the shape of a pentagram. I dont care if you put an Evolve Fish on your car and wear an Atheist Atom on your jacket lapel. Im not going to call someone an idiot for expressing their views and frustrations in a way thats appropriate for them, especially when they are doing nothing wrong.

Whatever. I just keep repeating to myself "Atheists have nothing in common except a disbelief in deities. Atheists have nothing in common except a disbelief in deities..."

New Lab Member!

WHOOO!! Boss and the PI next door are teaming together to bring a post-doc into my lab! Theyre collaborating on a super cool project, but my lab is literally me and Boss. Thats it. Needless to say Ive been feeling a bit stressed lately, due to the lack of help and huge projects on our plate right now.

And its not just ANY post-doc-- Its a gentleman that I worked with before during my first internship in college! Hes going to mesh so well with Boss and I, being laid back personally and a hard worker professionally.

On top of it all, we can bring him in due to my impending pay slash (experienced lab assistant--> grad student, ugh) which means that we wont have the $$ to bring in another grad student until after we get another RO1 (not until after my big project is published this summer/fall) which means that I am officially going to be Bosses First Grad Student! WHOOOO!!

Im weirdly possessive about this :P

Im just really glad to see this collaboration get off the ground, too. Combining our labs experience with the evolution of HIV with the other PIs experience with the immune system, we might have a way to figure out how to increase the efficacy of currently manufactured HIV vaccines. Or we might have shit. No way to find out without doing the experiments! Yay!!!

Thursday, March 01, 2007

Last Denier post for a while, I swear!

I kindly thank you readers for putting up with this string of Denier postings-- Im trying to prep for Reggies show, and this blog has been a great outlet for me to solidify my thoughts :)

Im sure all defenders of Evolution are familiar with this next Creationist-Denier similarity I missed (thanks Gos!)-- Cant debate Deniers because theyre parrots, cant CANT debate Deniers because then they WIN!

I consider it my responsibility as a HIV researcher, as a biologist, as a scientist, to educate the general public on those issues. Tax-payers pay for my grants, and since The Man wont let journals be public access, I feel it is also part of my job to explain what I do to the public. If I were addressing the public at large right now, this would be a very different conversation, but currently I am addressing a particular Denier that wants to 'discuss' science. He 'knows' more than the entire scientific community, therefore it is not necessary for me to do any more than explain the protocol used to result in this image. Im sure he will have no trouble explaining the image to other readers, and explaining to me why Im wasting my time/others lives/tax-payers money and how his hypothesis better explains the data.

Chimeric pNL4-3 plasmids were constructed by replacing the C2-V4 region of env with patient sequences sampled at various time-points over +5 years. Cos-1 cells were labeled with S35 24 hours post transfection. Supernatants were collected 24 hours post labeling-- viruses pelleted in the standard manner and IPed with patient sera. Lane 1 Mock, Lane 2 wt, Lanes 5-->Chimeric.*


Okay, Gos, 'discuss science'. Explain this image to everyone, what I think it means, what you think it means, and how the Denier position explains this data.




*Im not telling you what Lanes 3 and 4 are. Thats super secret.