Wednesday, February 28, 2007

Darwins Pitbull

Weve got Darwins Bulldog, Darwins Rottweiler... Darwins Pitbull?


Denier Behaving Badly

Oh Dear! It seems I forgot one similarity between Deniers and Creationists! Thankfully, Dear Gos reminded me of a neat similarity: theyre both scared shitless of people who know what theyre talking about.
How do they combine their fear with their arrogance? Why, talking behind peoples backs, of course!

You all might remember that it was a Comment Blocking from 'Intelligently Sequenced' that prompted my ID vs ERVs series. Now it looks like after a friend posted my article on a Skeptics board he frequents, a Denier thought it necessary to respond.

Not on my blog, of course-- that would require confidence in your views and your ability to defend your views. And you know... balls. But thats okay! Ill discuss his 'rebuttal' here anyway!

Like with Creationists, Average Joes think they have to have some sort of extensive training to address the (deadly) silliness of Denialism. Mr. Gos just proved my point for me: Disarm the Crazy by addressing the dishonest tactics. Anybody can do this.

Tactic 1: ARRRRRRRG! Pirating Research!

Gallo himself, in his original 1984 papers on HTLV-III (HIV), could not seem to find HIV in approximately two out of three patients he studied with AIDS or "pre-AIDS" conditions. So how did the other 2/3rds of the patients he studied manage to get AIDS, if they didn't have HIV?

Tactic 2: Dissenters from Darwinism, Dissenters from HIV/AIDS Dogma
I've got an ace to trump your queen: A PhD in mathematical biology who spent 10 years in HIV research, until only last year when she publicly "quit HIV", when she could no longer fight the urge to stand up and shout, "BULLSHIT!". Her name is Rebecca V. Culshaw, PhD, but your friend knows her as "Cunt Culshaw". Your friend is REAL mature -- I can certainly see why you place so much stock in her scientific opinion.

To learn why Dr. "Cunt" Culshaw "quit HIV", why not read the story from her own pen? You can find it at:

Tactic 3: Science supporters cant talk about science

Whoa! This girl's got some pretty impressive credentials! She's a research assistant in the Midwest (that global hub of science) who has been involved in HIV research for a whole 3 years, and she's currently working on Baby's first paper ever! Oooooh, I'm quaking in my denialist boots!

Tactic 4: Good old fashioned temper tantrums

I'll be posting shortly to address the obvious shortcomings in your friend's "article" in that prestigious medical journal,, but for the meantime suffice to say that her comparison between yours truly and a Creationist reveals far more about her than it does about me -- after all, the most she can seem to do is to ridicule my beliefs, apparently being utterly unable to shoot the science down, and this is a favorite tactic of (guess who?) Christian missionaries.

....And that's gonna wrap up this edition of the Heretic's Diatribe. Tune in next time when I trounce "doctor" Smith's "Five Tactics" comedy routine.

Tactic 5: Stick with what 'works'
HIV has never been *proven* to exist
HIV has never been *proven* to cause AIDS
Well, let me ask you something: When you see an immunosuppressed patient whose body is crawling with all sorts of opportunistic infections, bacterial, fungal, and viral, how do you prove that *one* of these is the cause and all the others are effects of the disease?
the existence of such kooks rarely if ever suggests that the US Government is actually telling the truth about a given subject -- it just so happens that more often than not, it is the existence of obvious government lies that attracts the attention of such people.
Since 1999, the #1 killer of AIDS patients is liver failure.

Thanks for the rebuttal, Gos! If someone other than you asks why Culshaw is a Cunt (C-U-N-T. CUNT.) I will happily explain, and if someone other than you wants to understand why everything under #5 is idiotic (I-D-I-O-T-I-C. IDIOTIC.) I will happily oblige. But you were just pwnd by the very list you were 'refuting.' Theres nothing I can say to you to bring you back to reality.

You know more than the entire scientific community, Gos. You and the Creationists.

Tuesday, February 27, 2007

WHOA! You think CREATIONISTS are a train wreck...

Ive been doing HIV research for a while now. Im still very young, and Im more on the 'Basic Science' end of the research spectrum rather than the 'Clinical Science' that would effect laymen, but Im familiar enough with common misconceptions about HIV/AIDS, HIV+ people, etc. that I can help explain things to people who ask. I also try to be fairly active in the Infidel community, so Reggie over at InfidelGuy asked me to do a show with him on HIV sometime. Yay! I love educating the public! Im not sure when this is going to happen exactly, as its a busy time in the lab right now, Ive got several presentations coming up, and Im starting to write my first paper ever (insert 'Psycho' shower scene music here), but Ill keep you all updated!
Reggie has left his traditional InfidelGuy format for 'The Debate Hour', which I can easily turn into a sweet show. Me and another researcher could have a REALLY fun debate over the efforts to create an HIV vaccine, long-term effects of our current treatment strategies, the new circumcision studies, all sorts of science fun!

... But I dont think thats what he has in mind...

Check this shit out!

Damn! Seriously, when Creationists start getting on your nerves and you think that they are hands-down the most self-delusional people on the planet: refer back to that link. I mean DAMN! lol!

Okay, so I need some practice shooting fish in a barrel before Reggies show, so Im going to play with the screeching monkeys.

A little background for the people who havent encountered Deniers before, here is a list of kinds of Deniers:
1. HIV does not exist. End of story.
2. HIV does exist. It is harmless. (many 'explanations' of its harmlessness-- PCR artifact, endogenous, etc)
3. HIV does exist. It was created by humans. (many 'explanations'-- Created by Republicans, accedentally escaped research lab, created to kill black people, etc)
4. AIDS does not exist. End of story.
5. AIDS does exist. Not caused by HIV. (many 'causes'-- poppers, malnutrition, anal sex, variety of diseases, etc).
6. AIDS does exist. Caused by anti-retrovirals.
7. Cure for AIDS is available. Being withheld from community. Cure is not anti-retrovirals.
8. Cure for AIDS is available. Invented by homeopathists/Professional Deniers/etc.

This list is certainly not exhaustive, as The Crazy runs deeper than I can imagine, Im sure. And, Ive yet to meet a Denier that only falls into one category. Yes, this means they must hold +2 contradictory thoughts in their heads at the same time (#2 and #3, #1 and #7, etc). I know this is weird ground for most of you, but honestly, they have the exact same tactics as Creationists. Disarm the Crazy by addressing the dishonest tactics.

Tactic 1: ARRRRRRRG! Pirating Research!
Creationists do not do research to support their views. Deniers do not do research to support their views. Where do they go to get their 'scientific claims', then? Why, real research, of course! Go to PubMed, type in 'HIV', pick a paper, and cut/paste bits together (+5 points if you dont understand the terms you cut/paste) and VOILA! 'Science' to support Denialism!

Bonus-- Why Deniers are worse than Creationists:
They go to Africa where they dont have to bother with that IRB nonsense, and perform their own little 'research' on suffering people. Tell people not to take their meds, give them vitamins and juice and proclaim they are 'cured'! Then the HIV+ 'cured' folks can go back into the community and spread some more HIV around! Arent Deniers SWEET!!!

Tactic 2: Dissenters from Darwinism, Dissenters from HIV/AIDS Dogma
ID Creationists are SO PROUD of their list of Dissenters. Its kinda cute how theyre so proud of such a pathetic list. Its endearing. And the Deniers are sure proud of their list too! Deniers even have BIOLOGISTS on their list! Peter Duesberg, Kary Mullis, etc.

Ho hum. Too bad these Nobel Prize winning Deniers STILL cant do any research to back up their claims. Why doesnt that seem odd to Deniers? The 'best' scientists on the planet cant establish their case. Huh.

Bonus-- Why Deniers are better than Creationists:
They manage to work 'dogma' right into their list of dissenters. ID Creationists had to add it as an afterthought. Even the Crazies compare bad stuff to religion :P

Tactic 3: Science supporters cant talk about science
While Creationists/Deniers are proud of their lists of 'credentials', no one else is allowed to talk about evolution or HIV. No one.
If you are a PhD doing HIV research, youre a 'paid off shill'. If you are just an Average Joe pointing out something stupid a Denier says, or worse, an Average Joe that has an interest in the topic and point out something stupid a Denier has said about science, youre a 'wannabe hack'.
Deniers, like Creationists, have completely insulated themselves from the outside reality.

Tactic 4: Good old fashioned temper tantrums

We're all familiar with Dembskis historical temper tantrum, well, check out the Deniers:

I understand Dr. de Cock does all his circumcisions in an office.

I wonder if he shares the office with proctologist, Dr. Elliott de Finger.

Do you suffer from some emotionalal disturbances that you have not yet dealt with Robster?

I must presume you also did not get enough attention as a child unless it was negative attention. Is this the case. Someone who seeks to provoke a negative response is attention seeking. Do you not even know yourself well enough at this point to see this trait quite clearly?

Please share with us the trauma of your child abandonment issues so we can get to the bottom of what ails you.

You just made another UNPROVEN UNSUBSTANTIATED CLAIM, as if it were true? Have you no self control, or are you still so completely desperate for negative attention? You really should discuss this with a therapist, or at least tell your father how his negative and unloving treatment of you has screwed up your brain.

And one more thing on tenure files -- they are always open to letters from outside commentators, except for that short period when the file is actively under review. So unless Tara is currently actively under review, any letters received by the Dean of her college are placed automatically in her file -- she does have the right to rebut such letters if they displease her, but she can't keep them out. That's just how tenure works. Kinda sucks, huh?

You see how all that addressed HIV, right? *rolleyes*

Tactic 5: Stick with what 'works'
Creationists and Deniers are stuck in the 1980s. Try to bring up siRNA or epigenetics with a Creationist, and they run off mumbling something about the second law of thermodynamics.
Try to bring up differential evolution of HIV subtypes or siglecs, and Deniers run screaming back to Cunt Culshaw. (Yeah, I said cunt!)
They are physically unable to address real research because they dont understand it. They 'understand' Creationist Claims and Denier Lines that they have memorized. Parrots.

God I know there are more, but thats all I can take for now.

Monday, February 26, 2007

Oh! I have father issues!

Well shoot! I thought I was a Daddy's girl, but thanks to the divine revelation received by a Dr. Michael Anderson, I now know that the only reason Im an atheist is that I have "father issues"!

(In order to watch this, you have to open the file in Quicktime or Windows Media Player or something. You arent missing anything if you dont want to watch it. Honestly, I couldnt take it any more after this 'father' shit)

You know how I was complaining about how Im at a major research institution, but there arent any science/educational programs after work? Well somebody at the Uni reads my blog (lol) because they decided to host a Faculty/Staff speaker after work last Thursday. Minor problem, the topic: 'God and Science'


Look, my evo bio professors were both theistic evolutionists. One was my undergrad research adviser, I loved them so much. I would never make the argument that I have a 'scientific' argument against them-- there is a possibility that their god is guiding evolution. I have no idea. But the fact of the matter is, theyre using one set of episteomological rules 6 days a week, and another set of rules on Sunday. Thats just silly. But like I said, I loved and respected these professors for their science, and I could/can care very little of what they do with their free time. Considering I always had my American Atheist Atom and an Evolve Fish on my backpack, my views on this topic certainly werent a secret to them either-- however they never made jabs at my relationship with my parents. Thats just about the stupidest thing a theist could do with me.

After wrinkling his nose at the idea of monotheists considering their god like a father figure (is he really that shocked? patriarchal societies, man in the sky dealing out rules and punishments. FATHER, son, holy spirit? weird), he declares that atheists are atheists because they dont have good father figures:

[lists someone who 'psychoanalyzed', but never met, certain famous atheists]
"It was unanimous! Each one of these people had a serious problem with their father, if they had one at all!"
"Your lack of religion is a projection of your father image."

So he thinks a neat question to ask is, "What kind of father was in the biographical sketch of each person (atheists) life?"

Well, Dr. Snot, let me tell you about my relationship with my father, since youre so concerned about it.

My earliest memory, I think, of my father was him reading me bedtime stories. He would read childrens stories, he would read 'COSMOS', he would just make things up. I could read before most kids my age could say the alphabet, thanks to my father (and certainly my mother and older brother as well).

I remember having the chicken-pox. I got it at play-school when I was 4 (I was 'too young' for play school, but they made an exception for me, and I got chicken-pox from the bastard kids). And while I just wanted to scream and cry from the pain and itches, Dad would put a cold washcloth on a particularly horrible welt I had on my forehead (and Ive got the scar to remind me of it). All the nights I had the flu, or was just throwing up like kids often do, Dad would sleep on the sofa in my room so I wouldnt be alone.

I remember watching 'Star Trek' and 'Star Wars' and all the great sci-fi movies with my Dad. He had a HUGE hand in cultivating my love of the unknown-- to boldly go where no one has gone before.

I remember sitting at the kitchen table, learning all sorts of math tricks. Easier ways to do this-- Faster ways to do that-- Fractions grades before I would officially learn them in school. Technically this made me bored to tears in my math courses throughout school, but the quality time we spent together I think is the important issue here.

And speaking of quality time, you know what, Dr. Snot? Instead of wasting our time in church for hours every Sunday, my Dad and I would... **GASP!!**... SPEND TIME TOGETHER! Yeah, my Dad, though technically Catholic, is for all intents and purposes religiously apathetic, and doesnt give a shit I dont believe in a god of any kind. Im one of the very, very lucky children who had parents that didnt force theism down my throat.

What a terrible father, eh?

Waste all of your life on sky pixies, for all I care Dr. Snot-- but consider yourself very lucky that I decided to go home and play with Arnie Thursday. My dad taught me so many things, however it was my mother who taught me how to be a beautiful bitch to people who fuck with family.

Sunday, February 25, 2007

ID vs ERVs-- Part Four: Doing the Limbo Rock

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.

How low can they go? Just when you think Creationists have hit an all time low... you find out theyve got a crawl-space to hide in.

Holy crap.

I made a discovery last night that made this whole thing even worse.

Okay, one of the first things I tell friends who are first starting to deal with Creationists online is to Google everything the Creationist writes. Average Joe Creationists are fond of copy/pasting large chunks of text written by other people-- pretending they wrote it when they dont understand a word that was written.


Creationist-- "Radioisotope dating is completely inaccurate! The following is a summary of results from a two year study among 8 scientists:
1. Conventional radioisotope dating methods are inconsistent and therefore not reliable.In dating the same rock layer, radioisotope dating showed four different ages.

2. Substantial amounts of helium found in crystals within granite.If the Earth evolved over billions of years, the helium should have already escaped.

3. Radiohalos in rocks caused by the decay of uranium and polonium, which strongly suggests a rapid decay rate, not gradual decay over billions of years.

4. Diamonds thought to be millions/billions of years old by evolutionists contain significant levels of carbon-14. Since carbon-14 decays quickly, none should have been found in the diamonds if the evolutionary age is correct."

Anyone who saw this would immediately begin carefully refuting every point in the hopes that the person who wrote the post held those opinions because he/she knew enough about physics to summarize the research findings, thus would be able to discuss and be persuaded by evidence.

Unfortunately, the Creationist poster didnt write a word of it.

Certainly Evilutionists frequently copy/paste things from TalkOrigins and such, but I have never seen anyone directly copy a rebuttal to a Creationist Claim without directing them to T.O.

So how does this relate to ID vs ERVs? This is a lesson in clicking EVERY link on a UD article. Look at this excerpt from the UD article:
UD-- The research, published in the October issue of Developmental Cell, suggests that retrotransposons may not be just the “junk DNA” once thought, but rather appear to be a large repository of start sites for initiating gene expression. Therefore, more than one third of the mouse and human genomes, previously thought to be nonfunctional, may play some role in the regulation of gene expression and promotion of genetic diversity. Dr. Barbara B. Knowles and colleagues from The Jackson Laboratory in Bar Harbor, Maine, found that distinct retrotransposon types are unexpectedly active in mouse eggs, and others are activated in early embryos. Surprisingly, by acting as alternative promoters, retrotransposon-derived controlling elements drive the coordinated expression of multiple mouse genes. The researchers think that expression of retrotransposons during very early stages may contribute to the reprogramming of the mammalian embryonic genome, a prerequisite for normal development.

In the UD article, it looks like the writer made these summaries himself, so I knocked down the improper terminology and inaccuracies in this particular claim.

Heres the 'Shauer’s Article' that the UD article links to at the very beginning:
The research, published in the October issue of Developmental Cell, suggests that retrotransposons may not be just the "junk DNA" once thought, but rather appear to be a large repository of start sites for initiating gene expression. Therefore, more than one third of the mouse and human genomes, previously thought to be non-functional, may play some role in the regulation of gene expression and promotion of genetic diversity. Dr. Barbara B. Knowles and colleagues from The Jackson Laboratory in Bar Harbor, Maine, found that distinct retrotransposon types are unexpectedly active in mouse eggs, and others are activated in early embryos. Surprisingly, by acting as alternative promoters, retrotransposon-derived controlling elements drive the coordinated expression of multiple mouse genes. The researchers think that expression of retrotransposons during very early stages may contribute to the reprogramming of the mammalian embryonic genome, a prerequisite for normal development.

To the 'Shauers'credit, he put the quote in italics to indicate he did not write it. But thats who he cited. Not the paper, 'Medical News'. And science journalist are so well known for accurately summarizing research data.

Here is the actual paper:
Retrotransposons Regulate Host Genes in Mouse Oocytes and Preimplantation Embryos

Guess how many times Dr. Peaston says 'junk DNA' in her paper.



Common! You know you know the answer!

Fine. How many times does Dr. Peaston say 'junk DNA' in her paper? Zero.

What have we learned today? You can find out if Average Joe Creationist is misrepresenting their 'knowledge' in one click (Google). Professional Creationists are more elaborate, as you have to click three times to find out theyre lying. lol!

Saturday, February 24, 2007

ID vs ERVs-- Part Three: Tandem Repeats of Straw-Men

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.

While typing up this weeks chunk of ID vs ERVs, I realized this whole ordeal wont be nearly as difficult to wade through as I previously anticipated. Kinda like how when you were little and you figured out that King Hippo is a fuckovalot easier to beat if you hit him in the stomach-- if you find a pattern.

This UD article has a big belly too.

The fundamental flaw in this whole idiotic article is that UD makes the inaccurate claim that 'Evilutionists say junk DNA is worthless!', then lists papers published by Evilutionists that establish junk DNA has a function, something Evilutionists dont deny in the first place. UD repeats this pattern over and over and OVER.

Round 1:

T.O.-- In many ways, transposons are very similar to viruses. However, they lack genes for viral coat proteins, cannot cross cellular boundaries, and thus they replicate only in the genome of their host. They can be thought of as intragenomic parasites.…finding the same transposon in the same chromosomal location in two different organisms is strong direct evidence of common ancestry, since they insert fairly randomly and generally cannot be transmitted except by inheritance….

UD-- So is there evidence that Transposons have function?

Time-out Tampa Bay! Oh wait, crap, thats football... Anyway, what in that T.O. quote implied Evilutionists say some transposons havent been co-opted by the host organism into a biological function? Ohh, I see where theyre going with this:
UD-- ...published in the October issue of Developmental Cell, suggests that retrotransposons may not be just the “junk DNA” once thought...

Ohhhh we're back to the fundamental claim about 'junk DNA' that we've established is bull shit.
UD is also showing their parrot colors-- repeating words theyve heard in an attempt to look like theyre knowledgeable on a topic... but using the words improperly. 'Transposon' and 'retrotransposon' are not interchangable terms. All retrotransposons are transposons, not all transposons are retrotransposons.

Round 1 goes to T.O.

Round 2:
T.O.-- …current evidence suggests that only a very few Alu sequences are active sources of transcripts; perhaps transcription from most copies is inhibited by the chromosomal environment of the insertion
Further, the excellent health of individuals who lack particular Alu insertions supports the view that these insertions do not serve any important function in human physiology.

Yet again, nothing wrong with that quoted paragraph from T.O. Nothing. As I wrote before, 1 in 30 people have a novel Alu site, so there are good odds that you and I arent Alu identical... Yet we are both sitting here, typing/reading a computer monitor, no adverse effects from our differential Alu profile.
Let me also emphasize that last point-- Alus do not serve any important function in human physiology.
UD-- Alu can turn a single gene into multiple proteins
They [Alu] affect Micro-RNA processing

Duh. But thats not human physiology. Thats human genetics. Alus change human genetics. DUH. Alus have been a cornerstone of the evolution of human genetics, as I wrote earlier.

Round 2 goes to T.O.

Round 3:
T.O.-- LINEs thus have several properties expected of “selfish” DNA sequences that can spread in the host DNA simply because they encode their own machinery for spreading.

UD-- In other words, they don’t serve a purpose other than to copy themselves, according to Talk Origins.

Thats not the T.O. quoted phrase 'in other words'. T.O. is precisely right. Thats the definition of LINEs (notice T.O. properly says LINEs, not LINES, whatever). Particularly weak round, even by UDs lowered standards.

Round 3 to T.O.

Match to T.O. by T.K.O.

Alas, like King Hippo, even after you beat the shit out of UD, they jump up and scream "Ha Ha Ha! I'm the king! Ha Ha Ha!"

Ugh. More to go, more to come.

Friday, February 23, 2007

Magnets and Miracles

I often say that nothing I do, nothing in modern medicine, would make sense without evolution. What can I say, its true. And its a fact that bothers Creationists. It bothers them because while finch beaks and octopus eyes are difficult things for Average Joe to relate to, everyone has an Aunt Mary that had a heart attack, dealt with Dads therapy after a stroke, worried over little Billys leukemia... I try to make it very clear in my presentations to the public exactly how I use evolution to help them, and why I need public support and quality science education for children. Its amazing how less Creationist Average Joe Creationists get when they realize how evolution relates to them.

So Creationists spend a good deal of time trying to say that medicine would be JUST FINE without evolution. Theres certainly no shortage of Creationist MDs, and they operate JUST FINE. Anyone who says modern medicine is based firmly on evolution is a liar! A point Gas-Bag #2 is all too happy to make in his little speech.

People threw spears before they knew about aerodynamics and gravity. People could use magnets before they understood magnetism. And people could use animals to study features of human anatomy before they knew about evolution. But thats not an argument against evolution being the foundation of modern medicine.

Which is better: Picking heart transplant donors by heart size, or picking a heart transplant donor based on understanding the evolution of the immune system?

Which is better: Testing drugs on humans straight from the chem lab, or using evolution to create transgenic animals to test the drugs on first?

Which is better: Cutting out tumors and praying to Jesus you get better, or combining multiple therapeutic approaches based on evolution to permanently remove tumors?

In Creationists world where medicine is not based on evolution, we are randomly stumbling upon 'right' answers, without ever understanding why theyre right, or how we can make right answers even better. We're missing right answers that are within our technological reach.

Whatever. Creationists can say medicine isnt based on evolution all they want, aint gonna make it true.

Thursday, February 22, 2007

Why are the comments disabled?

If youre masochistic enough to watch these two videos, give me a call. We could have some fun.

Creationist Gas-Bag #1

Creationist Gas-Bag #2

Theyve disabled comments, so feel free to vent here if you need to.

Monday, February 19, 2007


Today we had a visiting MD/PhD give a little presentation on her research, as she is applying for a position within the microbiology/immunology department. She does more of the 'immunology' thing, which doesnt normally interest me, but she did give me a couple things to think about:

1. Dendritic cells can differentiate into osteoblasts. Dendritic cells. Osteoblasts. I wouldnt have thought of that in a billion years. Weird!!

2. Osteoclasts are multinucleated. When she flashed this pic up, you know what I thought:




During the Q&A session afterwards, Boss asks her "So how do those multineucleated cells form? How is the fusion mediated?" And I KNEW when he saw her slide he thought SYYYYYNNNNNNNNNCCCCCCCCYYYYYYYYYYTIAAAAA!!!!!! too. hehehe! One of my best friends has this cabin and little lake like 10 minutes outside of our hometown. We used to go there every day it was warm enough (and many days it wasnt) to go swimming and fishing and such. Well, you could never go fishing without taking her white lab, Legend. Legend LOVED fish heads. Not fish. Fish heads. If you gave him a fish, hed eat the head. Thats it. Any time you caught a fish, you could see his cute puppy mind screaming "FIIIIIIIIIIIIISHHHHHHHH HEEEEEEEEEEEEEEEEEEEADS!"

Glad to see I have the same cognitive processes as a Labrador :P

Sunday, February 18, 2007

Why I hate science reporting: Hype

I dont know if this is necessarily the fault of science journalists, but the field of HIV research is prone to having every new finding blown into a media frenzy of "OMG WE'RE GONNA HAVE A VACCINE NEXT WEEK!!" I say this isnt entirely the fault of science journalists, because I also place a portion of the blame on the world of HIV research itself. So much work has been done, but its always baby, baby steps-- the pressure to deliver something 'revolutionary' is a monkey on the back of every HIV researcher... But 'revolutionary' hasnt happened in ages.

Sometimes in our desperation to give people some good news, irresponsible data gets paraded around like its groundbreaking (eg the CDC touting its *one* male circumcision study without addressing any of the problems it has in common with female circumcision... a practice the CDC explicitly forbids), or a baby-step gets blown out of proportion. The latest HIV Hype fad was "HIVs SILVER BULLET!!!"


Yes, its a good study. However, there is a fundamental problem with the broadly neutralizing antibodies that have been identified for HIV: theyre all weirdos.
How immunizations normally work is that your body has made all these different rearrangements in the hopes of being able to recognize any sort of crap that might get into you over the course of your lifetime. Normally the bits that recognize parts of YOU are selected out before they can do any harm, but when they do slide through, thats how you get some autoimmune diseases. Anyway, the way regular immunizations work, is that say, some dead viruses are injected into you, those bits that recognize bad bits get your immune system primed, and if youre ever exposed to those virus parts again, your body takes care of it without you getting sick. Hurray!
So why cant we do that with HIV? Because HIV is a bastard, thats why. Sure, most people know that HIV is a retrovirus, so it mutates a lot, and that makes it hard to have an effective vaccine. You might be immunized against 'HIV', but when (not if, when) HIV mutates around your bodys defenses, its in. Thats bastardly enough, but then, get this, it has a cloaking device. Seriously. The parts of HIV that make the BEST recognition sites for our immune system hide in essentially a forest of sugar. Your immune system comes around, says, "Hey, thats sugar. Youre cool" and ignores HIV.

We have found antibodies that neutralize HIV. Great, right? Figure out how they work, make a vaccine, yay! Not quite. The antibodies weve found are freaks. Things inverted, weird binding, Frankensteins. Unless all of us have essentially malfunctioning B-cells in our arsenal, we can try to get you and me to make these antibodies, but its not going to happen. So, we could take B-cells out of each of us, get them to express the appropriate sequence, inject them back into us, hope we dont get cancer. Or, we could use these antibodies as therapy. But neither one of these options are any help to Africa. No help to India. I mean, I dont know who this is supposed to help.

Its a great step forward, but we're not getting an HIV vaccine tomorrow, or the day after that...

I think this study is far more groundbreaking.

Thursday, February 15, 2007

Casualties of Faith: Creationist Kids

A side effect of religion, one that bothered me long before Richard Dawkins brought the idea to a larger audience, is the indoctrination of children with religion. Babies are told they are Jewish, and male babies have the scars to remind them of this fact for the rest of their lives. Children are told they are going to be tortured in Hell unless they take their first communion. And the children of Creationists are forever prevented from contributing to the world of science... unless they go through a painful deconversion process where they either deconvert completely, or just to a more reasonable version of their religion.

Or they do what this kid did.

*shrug* Lies to himself. Lied to his research advisers.

The blog world has been abuzz as to what to do with this boy. Its disarming, knowing that a Creationist could slither his way through a PhD program. Like that feeling you get when someone has broken into your apartment. But we know this isnt new-- Behe, Dembski, Wells, it just sucks every time it happens. And like when someone breaks into your apartment, you want to know how they did it, how to prevent it from happening again... and you want to catch the mother fucker and beat his ass. Well, we wouldnt do that to Ross, but many have suggested that his degree be revoked.

No-- he did the work. He lied, he didnt learn a goddamn thing, but he did the work. Fine, give the boy his degree. Now he is a Creationist with a degree in geology. What is he going to do with it? Obviously he thinks the entire scientific community is on the wrong track: evolution is wrong. So is he going to use his education, degree, and passion for the truth to defend his Creationism myth? To right the world of science? No. Alas, hes doing what every other Creationist with Credentials does. Hes going to run like a cockroach back into the kitchen closet from which he came: the radical Christian confines of Liberty University.

And the sad story doesnt end here. Hes going to be an 'example' for other Creationist Kids, like Mr. 99. "Look! You can be a Creationist with Credentials!" Perpetuating the cycle, robbing humanity of these childrens potential. Case in point, a commenter in this post, kansassam.

Kansassams son is trying to get a degree in chemistry/pharmacology. He wants to save the world. His son is a lot like me, except for one thing: his father indoctrinated him with a religion that says scientists are fools, scientists are liars, the only way you can be a True Scientist is to believe this myth.

As I said in that thread, Im using evolution to hopefully create a treatment that would go hand-in-hand with chemo and radiation therapy, keeping cancers from metathesizing, and hopefully easing the side effect profile of standard treatments. There is no way a Creationist could have thought of this experiment. Evolution must be true for this therapy to work. My HIV research? Evolution must be true for it to work. During my undergraduate education, I took several graduate courses in pharmacology-- evolution must be true for new drug design to be accurate.
This child has the ambition and the smarts to save the world, just like I do. But he has been crippled by his father. His potential has been retarded. Anything we get out of this child will be a miracle, and we will all suffer for it.

Radical Christians lament the loss of potential in aborted fertilized eggs, yet they care nothing for the lost potential in their own live, real children.

Dont try this with a pit bull

Weightless puppy:

Maybe it was just me picturing Arnie levitating in the back of an airplane, but I cried I was laughing so hard at this. Im kidding in the title-- Arnie wouldnt go ballistic... youd just never get him in a plane again.

Wednesday, February 14, 2007

Another person CNN could invite

David Mills:

Sure, he doesnt have a nice rack, but hes a sweet gentleman, excellent writer, and Id much rather have him representing atheism in America than Ellen Johnson. Ugh.

Tuesday, February 13, 2007

Westerns. My mortal enemy.

For a chick that has 'Westerns' listed as her favorite movies, its kind of funny that Western Blots are going to be the death of me. Every day for the past few weeks, Ive dutifully gone to work, run my Westerns, and been disappointed. Sure Ive been doing other things, and those other things are going GREAT!

... But the Westerns never work. Like a dark cloud that follows me around the lab. No matter how great everything else is going, BAM, Western looks like shit.

Im going to jinx myself by saying I think I really, really got it to work today. If it works again tomorrow, Ill let myself be happy. But heres a big thank you to Al in the lab next door, who has been helping me trouble-shoot through this whole ordeal. If I would have followed the exact protocol he wrote in the first place, I might not have had this much difficulty :( Gotta learn to trust other peoples protocols.

Edit, 2-14-07: The western blots officially work. Not only do they work, they are PERFECT. Finally. Fuck.

ID vs ERVs-- Part Two: Tandem Repeats

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.

Find the wrong statements:

Richard Dawkins: And there’s lots more DNA that doesn’t even deserve the name pseudogene. It, too, is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, “tandem repeats”, and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself.

This ones not false. Tandem repeats certainly arent pseudogenes. They definitely can screw things up, they can definitely change things.
So why does UD say Dawkins is a liar for this statement? They reference a PLOS study from 2006 that says tandem repeats are methylated. Duh. And that they play a part in siRNA. Again, duh. Um, okay, UD also references a PNAS study from 2006, again saying that tandem repeats play a role in siRNA. Well, I suppose you can say that our genome has co-opted the fact that tandem repeats are often methylated to help regulate protein coding genes, thus they are 'used by the body itself'.
But what Dawkins said is not incorrect. "WAIT!" you readers say again, "You just said the genome uses tandem repeats! Hes wrong!" Why am I saying 'Duh' to this stuff, and Dawkins appears to be oblivious to this information? Because Dawkins made this statement in 1997 or 1998. It is now, hmm, 2007. Unlike Creationism, real biological research moves at the speed of light. 1998 biology is a completely different world from todays biology.
Why the fuck didnt UD point this out? Who, exactly, are the liars again?

Pandas Thumb: Tandem Repeats are a class of repetitive DNA unique in every individual, which is why they are used in DNA forensic evidence, etc. … Talk Origins also has this to say about Tandem Repeats: “scientists view tandem repeat sequences as resulting from accidental DNA duplications.”

Um, okay, thats not incorrect at all. Not one damn thing is incorrect about that statement.

UD: These research finding show that, far from being junk, Tandem Repeats have important functional roles in the genome. More interestingly, the unique copy number in individuals seems not to be caused by random mutations, but rather by a built-in program that occurs during the combination of male and female DNA. While children will tend to inherit Tandem Repeat numbers similar to those of their parents, this variable component makes every child unique. The fact that Tandem Repeats are so well correlated to racial classifications shows that they have a role in determining what each individual looks like. Tandem repeats appear to be the major factor in what determines the size of your nose, the amount of body fat you have, your height, skin color, etc.

Oh, well then! Tandem repeats arent extended by duplications, they occur during a 'program that occurs during the combination of male and female DNA'. How, do you suppose then, that CAG extended in the first place, in Huntingtons patients? Magic? Magic is how you increase CAG repetitions? Not mutation? Magic? Fantastic. Wrong.
Here is my favorite claim, though-- UD goes from 'tandem repeats are associated with DNA methylation and siRNA' to 'tandem repeats are why black people are black.' ROFL! Thats an impressive hop-skip-and-jump! Dont suppose they have anything to back that up? Why didnt they link to it? Same reason why they didnt link to Dawkins' quote? Ummhmm.

Monday, February 12, 2007

The last remnents of John McCains balls

This is what John McCain has been reduced to.

Aaaaaaand lets not forget about this.

What are we supposed to do with you, John? If you would have fought fire with fire in 2000, you would have been president. If I could have voted, I would have voted for you (I hate Lieberman. HATE. HIM.) Now, youre just like every other pussy. Whoring yourself out for GAWD. Pathetic.

Sunday, February 11, 2007

Darwin Day?

Today is Darwin Day. And Im rather irritated.

Since I relocated to Oklahoma, I have been less than impressed with the pro-science activism going on here. A week after I moved, I attended a presentation given by a Creationist at a local church. No members of OESE were present. In my previous Citizens for Science groups, the members always scouted out local Creationist activities. A few weeks later, a HUGE anti-science fair was held at a popular church just north of town. This time I e-mailed OESE and asked if they were planning on attending, or doing any counter programming. They responded to my note with enthusiasm... but the answer was no. Im sitting here, a few blocks away from a major research institution, a major employer for the area, where every damn bit of research requires evolution... and there are no after-work presentations for the public. Im a hop-skip-and-a-jump away from physicists, geologists, astronomers... same thing.

There is no public outreach at all.

And we wonder why Creationism is so big in OK.

I was speaking with a friend yesterday, history/classics major-- not a science guy, and he articulated very, very clearly why activism is necessary. He said, "Im a pro-science person. I know you all know what youre doing. But I would feel very uncomfortable explaining to someone else why evolution is right. I mean we didnt get any evolution in high school-- I just know its something about bird beaks and stuff changing..."

It would be so simple to give little presentations to the public on topics like "How do we know the universe is old?", "What evolution is and what evolution isnt", "Why should you support evolution?" etc. And such presentations were given in the last Citizens for Science group I was in.

But its not happening here. Oh OESE are doing teacher workshops-- thats a terrific idea! But weve got to do more than that. A friends grandmother invited me to give a simple presentation on evolution to her church (it was supposed to be today, for obvious reasons, but had to be postponed). Im hoping their minister likes what I have to say and will recommend me to other churches. I wont be able to reach the congregations that invite the likes of Brad Harrub to speak, but I need to do something.

Happy Darwin Day. *sigh*

Saturday, February 10, 2007

ID vs ERVs-- Part One: Intro

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 have a habit of picking random nobodies from a pool of Creationists and proclaiming they are geniuses so everyone should listen to them (never mind these geniuses STILL cant publish anything to support their views). Dembski (a nobody before ID Creationism) is the Issac Newton of Information Theory. Mr. 99 is a total nobody, but little kids should look up to him as a successful Creationist 'scientist'. So who did they pick as their super cool resource for ERVs? Andras Pellionisz!!


No, its not just you. Hes a nobody, you arent supposed to have heard of him. Ugh. So what does the esteemed Andras Pellionisz do that would make him an expert on ERVs? He is a, and I quote, "DNA researcher". WTF is a "DNA Researcher"? Thats like what a 7 year old would call a molecular biologist. Jesus. Well, this DNA researcher... is an electrical engineer (please try to hide your surprise that an engineer has a fancy for Creationism). He then went on to get degrees in 'Experimental Biology' (WTF?) and physics. Fantastic. Yes, Mr. Pellionisz, I bet youre just a super "DNA Researcher."

So why did UD pick him? A common argument against design is the rather silly 'design' of our genome. Stretches of CGCGCGCGCGCGCGCGC that go on and on forever, gene duplications that mutated into non-functionality, bits and pieced of retrovirus parts, etc. 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'. The term 'junk DNA' cant even be found in my Introductory Genetics or Human Molecular Genetics textbooks.

Heres where ID Creationists come into the picture. Since Creationists dont actually, you know, do anything, they have to leech off real research and pretend it supports their religion. Their hypothesis is that every little base pair is special and designed by their unnamed 'designer' (Not God. **WINK!**). So therefor whenever a bit of 'junk DNA' finds a purpose, AH HA! EVIDENCE AGAINST EVOLUTION! Theyve chosen Nobody #9284577934, Mr. DNA Researcher, because hes all sad no one in the biological world listens to a word he says. Mr. DNA insists that 'junk DNA' isnt really 'junk DNA', but no one, oh NO ONE will listen to him except the ID Creationists! Let me say this loudly, so Mr. DNA can hear:


"WAAAAAAAIT ERV!" you readers might try to say, "Junk DNA really isnt just junk DNA! Hes right! You just said that yourself" NO! Hes NOT! Hes like a dude running around a chemistry department screaming "Atoms arent the smallest unit of matter! Atoms are made of smaller parts! WHY IS NO ONE LISTENING TO ME???" Everyone is 'dismissive' of him because his 'big revelation' is something everyone already knows.

To pull this back to UDs 'argument', 'junk DNA' might have 'function', but that is in no way an argument against evolution or an argument for fairies or gods. And, the original argument that our genome is put together in a ridiculous fashion is absolutely valid. Creationists admit this themselves (I refer readers to 'The Pinto Argument', care of Casey Luskin).

Noncoding DNA is not an argument for ID Creationism in any way/shape/form.

Up next, Part 2: Dawkins and TO are LIARS!! *rolleyes*

Thursday, February 08, 2007

Why CNN should want to invite me to speak on their network about atheism

I have a real beef with stereotypes of atheists perpetuated by news programs, but right now I have a more important issue to deal with. Ladies and gentlemen, Anna Nichole Smith... has died. Yes, the scheduled Paula Zhan show on atheism (to make up for her bull shit show last week? who knows) was postponed to bring viewers ONE HOUR of Anna Nichole coverage. Why?

Look who they had scheduled (and had for the previous atheism show):
Kevin Smith:

Karen Hunter:

Niger Innis:

Roland Martin:

Debbie Schelslewhatever:

Christopher Hitchens:

Richard Dawkins:

*YAAAAWN!* All those people, not one nice rack. Little Debbie comes close, but every woman on the planet can tell thats a padded bra shes wearing.

Know who they should have invited? Me:

Clearly, by CNNs stringent journalistic principles, I am the most newsworthy atheist on the planet. I patiently await my invite.

Tuesday, February 06, 2007

Great Alma Mater News!!!

Wow I had another crappy day in the lab-- but I got great news about my alma mater! As I was online getting the office numbers of the professors who wrote me letters of recommendation for grad school (to send thank-you notes), I noticed the name of our one Creationist biology faculty member was absent from the faculty list!

I never had him for a class because his course list was curiously restrictive (well, that and fuck if Im paying tuition for a Creationist professor): one upper level specific to his PhD, a section of a senior discussion group, and... a few sections of biology for non-majors (the very people who need a sharp, firm, fast understanding of evolution)... *pause for you to bang your head against the keyboard* But friends of mine did sign up for his courses before they knew of his stance. He wasnt just a Creationist. He would open every lecture with a Bible quote. Religion and anti-sex was fused in to all of his presentations. And to top it off, he was a terrible professor. One of my friends took the senior class with him. Senior discussion was just where you and a few other seniors would meet for one hour once a week, the prof made sure you had someplace to go when you graduated, and youd chat about a topic. I took a biotechnology discussion group, my friend took a 'lifes origins' discussion group with Creationist. I asked him how it was going one day in pharmacology. He blinked and said, "As bad as you think it is: Its worse than that."

Well DING-DONG! The Creationist is gone! YAAAAAAAAY! Smarmy thing evidently retired last Spring! Gawd Ive been feeling so embarrassed about my old Uni having a Creationist biology faculty member, and hes been gone for almost a year! WHOOOOOO!!

There were many times in undergrad when I would vent to my research mentor, "WHY is he a biologist? WHY is he a teacher??? WHO HIRED HIM?? **SCREAM!!**", but youll hear no agonized screams from me over who theyve hired to take over his classes: two young ones from WashU! And get this-- A nice homosexual fellow (whom I got to meet while I was still in school) who does HIV research and a young woman who does Alzheimer's research! WHOOOOOOOOOO!!

Basically the one thing that I didnt like about my Uni is gone, and the replacements more than make up for the initial embarrassment! WHOOOOOOOOOOOOOOO!!!

Monday, February 05, 2007

Admitting you have a problem is the first step, right?

Im prejudice. I admit it. Im prejudice against MDs. Its not because Im 'afraid' of doctors, its because at one point I wanted to be a physician myself. I know a huge part of my problem is cognitive dissonance: I made a decision to forgo medical school, so now anytime I see a physician doing something silly I think "SEE! Look at those weirdos! Arent you glad you didnt go through with that MD nonsense?" There are so many physicians that I respect (as I shadowed them and looked up to them for years), but damn, Ive just had a string of silly MDs cross my path lately, and my prejudice against them is getting just awful.

Last Friday I was hauled away from my work to attend a presentation by a visiting big-wig who was supposedly an *expert* on HIV (no one happened to inform my boss or the other micro prof that does HIV research of this fact). His intro lasted at least 10 minutes, given by a local physician, emphasizing what a big-wig this guy was and how great he is for knowing big-wig. Visiting big-wig got to his wigginess by being a physician in San Fransisco when the HIV storm started. Im not exactly sure how noticing something is *wrong* when 20 year old men are getting Kaposis Sarcoma makes you a medical genius worthy of large wigs...

Big-wigs presentation was absolutely terrible. I have no idea what this gentleman does for a living, as he only posted pictures from UNAIDS, NIH, and others research. Anytime he talked about someone elses research, he had to spend 10 minutes explaining about what big-wigs they were, and how that increased the size of his wig. Worst of all, in his exuberance to highlight the research of people he knew, he presented some complete and utter shit. In my annoyance at leaving my bench for a Wikipedia HIV presentation that a high schooler could have created, I didnt bust his balls for it because I just wanted to leave. Unfortunately, Boss knows me as well as I know myself.

When we got back to the lab (paraphrased):
Boss: "Why didnt you bring up your points against the circumcision study?"
Me: "Its not his research. He doesnt know how to defend it."
Boss: "Hes presenting it. You have excellent points, and they have even more impact coming from a female."
Me: *frown*
Boss: *frown*

An important thing I learned in taekwondo was to never disrespect your master, either directly or through your actions. Whats more, your respect towards other masters, your ability to demonstrate your skills-- those reflect positively on your master. Q&As after presentations are similar for mentors and students-- that was an opportunity for me to demonstrate my critical thinking skills. Challenging the big-wig would have reflected well on Boss, and it was silly of me to waste the opportunity just because I was irritated.

So now Im mad at myself, and even madder at the big-wig physician.

Saturday, February 03, 2007

The Roller Coaster Never Stops

This is how scientific research gets you addicted. Last week was terrible. I mean, I actually got drunk last Saturday because I was so upset. And just when I hit the lowest of my low-- BAM! Im up again! I got the Westerns working *rolleyes*. Alpha-tubulin and TBS with the proper pH fixed that problem. But I got another HUGE result:

Arg those dont show up very well. Well, heres a description-- Those are cells that have been infected by an HIV virus whos genome contains either an added GFP or a dsRED gene. When those viruses infect a cell, they take over the cells machinery to make HIV proteins (now including the fluorescent proteins), and more HIV genomes (which will still contain the fluorescent protein gene). So a cell gets infected, it glows. It makes more HIV viruses that go on to infect more cells, which will also glow. Etc etc etc. Blogger has no resolution on the pics, so here is a close up of a red syncytia:

When youre in a low, you know there is a high coming up around the corner. You just dont know when-- so you keep going, just sure that the next experiment you perform will work and be fantastic. When it doesnt work, youre devistated. But man, when it does work, when you figure out what the problem is and the ball starts rolling, when you get beautiful pics that are better than you were hoping for, its worth all the pain :)