Thursday, November 29, 2007

Turn off your Irony Meters before reading this post.

Dont say I didnt warn you.

.....


Irony meters off? Okay!

So like, you know how Dembski took Harvard/XVIVOs animation, screwed around with the narration, and is now pretending he didnt do anything wrong (but hes going to stop)? Lets get into the Tardis and travel back in time to the year 2001-- the before times, when ERV didnt even know what a Creationist was. Robert Pennock published a book called "Intelligent Design Creationism and Its Critics." Included in this book was an article called "Who's Got the Magic?", by a William A. Dembski. Pennock got permission to use this essay from the journal title that carried Dembskis article, Metanexus. Pennock followed Metanexuss rules. Because rules for us commoners are not good enough for Creationists, William Dembski threw a tantrum. *surprise*

"I had never signed over the copyright for "Who's Got the Magic?" to Pennock or anyone else for that matter. Was it therefore our entire exchange that he was planning to add, with copyright permissions requests (that never came) still down the road ? Or was it just his portion of the exchange and a summary of mine that he was planning to add to "the ms"? Was his mention of adding it to "the ms" a reference to the MIT anthology or to some other work? Finally, the one other ID proponent whom I knew to be a contributor to Pennock's anthology ( i.e., Paul Nelson) had been explicitly contacted about being a contributor. I hadn't."

"... I would like to have seen a public apology by Pennock and some notice by MIT Press indicating that my essays appeared without my knowledge."

Yes, in 2002, William Dembski was bitching about Pennock going through the appropriate channels to add Dembskis essay to his anthology legally. He is demanding an apology by Pennock and MIT Press.

For doing what they were supposed to.

*blink*

I told you to turn off your irony meters.

Lets jump back to today. November 29, 2007. From William Dembskis webpage:
"All material on this website is copyright and may be reproduced only for personal use."

"Who's Got the Magic? A response to Robert Pennock's false dichotomy that ID forces one to choose between mechanism and magic. This article first appeared on Metanexus ( http://www.metanexus.net). It was reprinted without permission in Robert Pennock's Intelligent Design Creationism and Its Critics."

"William Dembski's press releases in response to the publication of this book. Integrity is hard won and easily lost. For publishing William Dembski's work without his knowledge or permission, Robert Pennock and MIT Press compromised their integrity."
But Pennock did nothing wrong. And Dembski admitted that in 2002-- "Pennock and MIT Press are legally in the clear". But hes still got that stuff on his page in 2007. The same year he purposefully stole a $$$$ animation from Harvard, smeared poop all over it, and denounced 'Darwinists' for bringing it to the attention of Harvard (more on 'Darwinists' tomorrow, evidently John West was feeling left out).

What the hell?

Ugh.

What is this, example #2985298571983 of Special Rights for Creationists? Poor babies just cant play by the same rules as everyone else on the planet.




(hat tip to Wes! And Mark Perakh!!)

Tuesday, November 27, 2007

If you have set yourself on fire, do not run.

*sigh* Fundamentalist community, let me pass on some advice to you I learned from the atheistic community:


If you have set yourself on fire, do not run.





Okay? Okay?? Please?

Look, D, you had two months to say to Harvard in private emails, "Im sorry, I shouldnt have been using that animation in my paid presentations. I wont use it again. I really do like 'Inner Life', though, and would love to use it in classroom presentations, from the BioVisions site, if that is acceptable."

I sat here, for two months, waiting for that to happen, anything to happen, and it didnt. Two months, on your own terms, you could have written a similar post to yesterdays. I would have given you the benefit of the doubt-- maybe you didnt know the credits werent visible to the audience, and I wouldnt have said a word beyond this, as its Harvards problem, not mine. This would have been a funny joke to those of us involved in dealing with you people, but it would have been a PR non-issue for you.

...

But after you set yourself on fire, you didnt douse it out with a bucket of ice cold reality and accountability. You ran. And youre still running.

Why?

Why not just state "I screwed up. Sorry everyone." and move on? Why the excuses? Why the denial? Why the passive language? Why the vague words and cryptic capitalizations? Why the writes and rewrites of your 'press release'? We know it wasnt written of your own volition, or it would have been done *before* Harvard had to take action. And, your behavior before this, regarding this issue, is not indicative of someone who made an innocent mistake. Its weird.

So what with this frantic running? Is the inability to say "I was wrong" a pathological feature of Creationists? Or are you hiding something? Or is it both? Or is it more?



And now we get Casey weighing in on the issue, according to cre8id at AboveTopSecret.com-- PBS/NOVA online - Intelligent Design on trial:

...to my knowledge, Discovery Institute has neither authorized nor received nor is making use of any presentation that used that animation. We have had nothing to do with creating or selling a DVD of that animation, nor do we have anything to do with placing that presentation on Google Video.
I dont know what he is talking about with that last part, but the first part sounds similar to DIs claims post-Dover ("WE HAD NOTHING TO DO WITH DOVER!"). Maybe Luskin is telling the truth. Maybe this was a magic non-science Creation-friendly narration with convenient edits that AiG or ICR would have killed for... but only Dembski could find it... but he cant tell us where... and he didnt share it with anyone... and its subsequently disappeared from the Internet...

But that simply isnt what Ive been told. Maybe this was all a silly Dembski mistake, blown out of proportion due to his decision to remain silent... But what if we find more videos of more DI fellows, presenting this animation?

*shrug* If youve set yourself on fire, do not run, DI. If youve done it, better admit it to Harvard now, apologize, and move on.

Monday, November 26, 2007

Mr. Turtle, how many days does it take to get a Creationist to admit they plagiarized?

61, 62, 63... Oh I lost count, but *CRUNCH!!* At least 63. Theyre learning!!!

Though this story broke last week, this was something that me and multiple college students noticed at Dembskis presentation. We asked XVOV/Harvard about it ~24 hours later, and they contacted SW Baptist. Dembski had about 63 days to post "Wait wait wait this was a misunderstanding!" but he didnt. Look, the man is arrogant enough to call the entire scientific community idiots (and wont lower himself to our pathetic 'research'), and he was arrogant enough to play chicken with Harvard Law. Harvard won:

From now on, I will no longer use it and instead go back to using a clip from “Unlocking the Mystery of Life.”
Now, lets ignore the fact the original animation was posted on Uncommon Descent, William Dembskis blog, with the narration, and credits, nine months ago. And lets ignore how Dembski magically stumbled upon this Creationist-Pot-O-Gold that no one else can find 'on the Internet'. Lets ignored the closed comments. Lets ignore Dembski/Behes inability to speak my name. Lets ignore what AtBC calls "The Bart Simpson Defense":
I didn't do it, nobody saw me do it, you can't prove anything.
Or alternatively, "The OJ Simpson Defense":
Won't somebody help Dr. Bill find the real culprits?

Creationists are always talking about 'The Evidence'. Well, if any of you can find the credits Dembski posted a 'screen shot' of in the video posted here, I will buy you an EXPELLED T-shirt. I love the 'Big Science Academy' ones, myself, but any one you want! Show me the credits Dembski posted a 'screen shot' of, win a T-shirt.

GO!






When you find it, and youre all proud of yourself for winning a T-shirt, Ive got disappointing news for you.

I know we are all having a good laugh at this, but unfortunately there is a casualty in this particular fight against Creationism: Harvard is getting 'Inner Life of a Cell' pulled from YouTube and GoogleVideo. They said that since it was available on their website, where they could control it, there was no reason to let uncontrollable copies go on those sites, to be raped by Creationists.

But YouTube is the reason we uncovered this plagiarism. Everyone my age, YouTube is a part of our lives. We've seen every variation of "LEAVE BRITNEY ALON!" and every iPhone unboxing video and LEEEEEEEEROY JENKINS a million times. But YouTube is also a great way to spread knowledge, and millions of people who would not have found 'Inner Life of a Cell' on BioVisions site got to see it.

And like a terrorist putting explosives in their shoes, screwing it up for all of us, such are the actions of Creationists... *sigh* Ill try to convince them to keep it on YouTube, in some capacity...

EDIT 7.30 pm, 11/27/07-- Dembski has edited his original press release. He now says that his credits were dim, and compounded with the projector and lighting (and crappy hack job. he missed crappy hack job of the animation), it might not have been visible to the audience. You know, Im going to give him that. There is something very, very faint on that last screen, and maybe, since he was facing forward, he didnt see that we couldnt see it. Im going to swear to Dembskis god right now, that we were staring at a blank black screen when that animation stopped, and Vic Hutchison supports that:
I was at the lecture and looked for credits on Dembksi's film clip. I did not see one. I have also asked about 12 persons who also attended, including one student member of the Trinity church group, and none recalled any credit at the beginning or end of the clip. Others have also posted the comment that they were at the lecture and saw no credit. Since it is unlikely that all missed it, I conclude that the probability that it was not not there is fairly high.
None of my friends noticed the credits. But fine, Dembski 'intended' the final credits to be there. Hes in the same spot either way-- Harvard told him to stop showing it and delete all copies of the file, and are not amused at any of this, blurry credits or no. Dembski knew about the original animations, but chose not to use them. Dembski has alternate animations to use that he does have a license for, but chose to use one that didnt belong to him, altered, instead. Why? How? We may never know.

Tuesday, November 20, 2007

DI Fellows-- EXPELLED for plagiarism

It is one thing to correct Michael Behe (some structure guy) with zero HIV-1 research experience on HIV-1 evolution. But considering the sheer number of DI 'fellows' who are lawyers, and the fact Im just a biology student with zero experience in law... I found it rather strange that I caught something the DI lawyers evidently had no problem with:

Original:


Long Original with Narration:


DI manipulation with *Narration*:


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

Now, I have brought this to the attention of Harvard and XVIVO. I dont know what theyre going to do (theyre Harvard-- they can do whatever they want). I do know that they are not happy campers. IANAL, I am a virologist, but heres why *I* would be upset.

This isnt a case of naive copyright infringement on Dembskis part, ie "Hey! I found this cool video on YouTube, lets use it!" Though Dembski is pictured here, others have reported multiple DI 'fellows' presenting this manipulated animation. The Discovery Institute does not have a license to use this animation, so they downloaded it illegally.

Maybe they think it is 'okay' to use it anyway, because they stripped off Harvard/XVIVOs copyright and credits.

Maybe they think it is 'okay' because they gave the animation a new title ('Inner life of a cell' became 'The cell as an automated city') and an extraordinarily unprofessional new narration (alternate alternate title-- ' Big Gay Al takes a tour of a cell!'). Harvard/XVIVOs narration, all of the science, is whisked away and replaced with a 'surrealistic lilliputian realm'-- 'robots', 'manufacturing', 'circuitry', 'nano moters', 'UPS labels'. Maybe they think it is 'okay' because they turned all of Harvards science into 'MAGIC!'

Hmm. From my point of view, as a virologist and former teaching assistant, this isnt just copyright infringement. This is theft and plagiarism. Taking someone elses work without their consent, manipulating it without their consent, pretending it supports ID Creationists distorted views of reality, and presenting it as DIs work.

*shrug* The DI fellows would be EXPELLED from my university for this.

Monday, November 19, 2007

Gimme a sec...

Sorry, folks, there is a bug going around campus, and Im feeling a little blah-- BUT Im working on something a little different for tomorrow morning, and since Behe and Selma brought it up, Im going to break the dead air by showing off haircut pics.

"Wait, what? Why?" you might say, dear reader. Well dear reader, you probably werent reading my blog last December, and thats when I got my last hair cut.

Yeah.

Its been almost a year since I got my hair cut... the day before I found Arnie (December 2). So it was getting kinda Compound-Mormon-creepy.

I am now about a pound lighter. I think I got at least 8 inches off.

ROFL!!! Gha it was getting creepy!!

Okay, okay, I promise a real post tomorrow-- a really good one if technology cooperates ;) One more good punch in to the Discovery Institute before I get back to **GASP!** real science posts again hehehehehehe!!

Friday, November 16, 2007

Mr. Owl, how many days does it take to get a Creationist to admit he made a mistake?

103, 104, 105... **CRUNCH!** 105.

105 days after I wrote my essay on Vpu, Behe finally admitted I was right:

Yes, I’m perfectly willing to concede that this does appear to be the development of a new viral protein-viral protein binding site, one which I overlooked when writing about HIV.
Well aint that super. But heres the deal. What would have happened if he had said this, and only this, on say, Day 5? We would have laughed "Silly lazy Creationist!" made comments about "What other mistakes did Behe make in 'Edge'?" and probably gone about our business.

But thats not what happened.

First, Behe dispatched the Discovery Institutes PR attack dog, in hopes that would silence DIs followers.

Then, William Dembskis hired anonymous goons were sent to intimidate me.

Then, William Dembski tried to take a dump in my back yard.

Then, Lilo himself let loose not one, but two sexist cry-baby rants against me.

THEN Behe admitted he screwed up.

But please note, Behe is not admitting that he screwed up to *me*. Behe is admitting he screwed up to *Ian*:
And now let’s talk about Dr. Musgrave’s “core argument,” that subsequent to the virus leaping to humans from chimps Vpu developed the ability to act as a viroporin, allowing the leakage of cations which helps release the virus from the cell membrane.
Um, excuse me, that is *my* core argument. While Behe will lower himself to responding to a worthless foot-soldier scientist like Ian... at least Ian already has his PhD and is a man. Admitting a female who wasnt even a graduate student at the time of the essay, bested him, well, thats obviously another reality Behe is unwilling to accept.

Behe is also unwilling to admit that maybe, just *maybe*, he doesnt know jack shit about HIV-1 and how it evolves in patients and populations. Oh he might have 'overlooked' something (implying he 'looked' in the first place, ROFL!), but really, that evolution is just 'pathetic'.

Pathetic pathetic pathetic pathetic pathetic...

There is certainly something 'pathetic' in this exchange, Behe, but it aint HIV.

Tuesday, November 13, 2007

One Major Beef with Judgement Day

It was missing something.

Something important.

And Im really, honestly mad they left it out.

The Civil Discourse.


Never forget the Civil Discourse.





(Tnx Tyler for teh link, for I has lost it)

Yeah you know, but still-- 'Judgement Day' tonight!

I will link to Uncommon Descent for the last time ever, on this occasion, and copy/paste some relevant bits before they delete this wonderful post forever.

Life After Dover, By William Dembski:

As I see it, there are three possible outcomes:

  1. The Dover policy, in which students are informed that the ID textbook Of Pandas and People is in their library, is upheld.
  2. The Dover policy is overturned but the scientific status of ID is left unchallenged.
  3. The Dover policy is not only overturned but ID is ruled as nonscientific.
For what it’s worth, my subjective probabilities are that outcome 1. has about a 20% probability, outcome 2. has about an 70% probability, and outcome 3. has less than a 10% probability.


Relevant post by Dave Scot (again, not his real name) Billys confidant:
Judge John E. Jones on the other hand is a good old boy brought up through the conservative ranks. He was state attorney for D.A.R.E, an Assistant Scout Master with extensively involved with local and national Boy Scouts of America, political buddy of Governor Tom Ridge (who in turn is deep in George W. Bush’s circle of power), and finally was appointed by GW hisself. Senator Rick Santorum is a Pennsylvanian in the same circles (author of the “Santorum Language” that encourages schools to teach the controversy) and last but far from least, George W. Bush hisself drove a stake in the ground saying teach the controversy. Unless Judge Jones wants to cut his career off at the knees he isn’t going to rule against the wishes of his political allies. Of course the ACLU will appeal. This won’t be over until it gets to the Supreme Court. But now we own that too.

All science so far, eh? Those posts need to live forever.

Michael Behe = Sal Cordova... and you know what that means...

So Im in lab, scarfing down some food before I go infect some cells, and checked into Behes Amazon blog for some dessert.

Michael Behe has the intellectual honesty of Sal Cordova.

September 3, 2007: Cordova: Ms. Smith even conceded the following here about the NON-novelty of Vpu...

November 13, 2007: Behe: After sneering a bit at me, Smith began her post by asserting that vpu is a “new” gene (even though it is found in SIVcpz across several primate families, as her own citations show.)

-------------
AUGUST 2, 2007: Me: Vpu, is in fact, a new gene. Of the five major phylogenetic groups of SIV, Vpu is only found in one group-- Chimpanzee SIV (SIVcpz) and its descendants—including HIV-1. It is absent in all of the other major lineages (Sooty Mangabey, African Green Monkey, Sykes Monkey, and L'Hoest Monkey). This means that Vpu is in HIV-1 but not HIV-2.

Niiiiiiiiiice, Behe! More on how everything is 'pathetic'.

Im sorry, why, exactly, am I supposed to be 'civil' to this hack Creationist?

Epic Fail.

As Dear Dembski would say, "This is not a P-A-R-O-D-Y!!!!"

Michael 'Lilo' Behe, supposedly a 55 year old biochemist, has just thrown an epic temper tantrum on his Amazon blog. That is really Behes blog. He really posted this. I, Abbie Smith, a kid from a farm in the middle of nowhere, am on the receiving end of a Creationist move normally reserved for emergency defense only (ie Dawkins attacks):

YOURE MEAAAAAAAAAANNN!!!! SQUEEEEEEEEEE!!! SQUEEEEEEEEEEEEEEEEEE!!!!!!!!!
Behe, we are having a good time making fun of your science, would you like us to start ridiculing your writing as well? Do you know what the word 'disingenuous' means?

What *I* would call disingenuous is saying anything I wrote was 'insulting' while you seem to have no difficulties dismissing the blood, sweat, and tears of thousands of scientists while you contribute nothing beneficial to society (no, I dont consider feces and CO2 'beneficial'). You have no problem stealing the work of those same scientists and misrepresenting it to laymen, pretending it supports your claims. You have no problem writing entire books on topics telling scientists they have no idea what theyre talking about, but you apparently cant even read an HIV-1 review article. You cant even read your own diagrams!

And then shall we delve into your history and your colleagues? Altering 'quotes' unapologetically? Categorically attacking science students who dare to speak out against Creationism? Referring to evilutionists as Nazis and mass murderers? Defaulting to sexism while addressing a critique? All this is no problem. This is all 'civil discourse.'

But calling bullshit on your bullshit claims? Refusing to play your Creationist games?
UNACCEPTABLE! SQUUUUUEEEEEEEEEEEEE!!! YOURE SO MEANNNNNNNNNN!!!!
You want to be able to act like an asshole and you expect everyone to put on plastic smiles and pretend youre a respectable scientist and have 'civil discourse'. We're supposed to treat you like youre an actual HIV-1 researcher, even though you arent. We're supposed to treat you like an actual biochemist, even though you arent.

And Ian is 'disingenuous'.

Mr. Behe, if you are such a delicate flower that you break under the breeze blown by some woman graduate student, perhaps it is best you stay locked up safe in the confines of your Ivory Tower. I must warn you its only going to get harder for you from here on out-- Im afraid neither I nor any of my classmates are under orders from our mentors and professors to be 'civil' to Creationists, HIV Deniers, ALF/PETA, green anarchists, or any form of anti-science hack. In fact, my classmates have all found your original claims and subsequent responses hysterical. Youre now an official class joke.
Professor: "How would you figure out which signal transduction pathways your receptor is involved in?"
Female student: "You could cross-link, and see which proteins are associated with your receptor."
Professor: "Good! Thats one way..."
Male student: "Good answer. FOR A WOMAN!"
Class: *laughs*
Professor: *confused*
Its also now a class game to figure out what the hell "soak your head" means. We're completely lost. Google doesnt even know what that means. But we have found an awesome arcane insult generator! Thou pribbling boil-brained whey-face!



I also want to emphasize one more thing, for the laymen. Note how Behe is completely unwilling to take responsibility for his own actions. He didnt respond to my essay with anything resembling science... and its *my* fault. *I* was 'mean', and that prevented Michael Behe from responding to my essay like a biochemist. If *I* was 'nice', well, then he could have responded. Really, the lack of science in any of Behes posts is *my* fault. Uh huh.

But remember, folks, Ian is disingenuous.

Friday, November 09, 2007

Get off the streets! GET OFF THE STREETS!!


LILO IS OUT OF REHAB!!!!

AAAAAAAAAAAAHAHAHAHAHAHAHA!

FUNNIEST AMAZON POST EVAH!

Holy CRAP! Michael Behe is now officially in the running for 'Most Delusional Sentient Being in the Universe.' And this is exactly why students should engage Creationists. Not only is it a learning experience for the student, it pops a hole in the Creationists bloated egos. Jerry Coyne, Richard Dawkins-- They make Lilo feel important. Some mouthy kid from a corn farm smacks him, and he cant get off on it.

ROFL! AND ITS GONNA TAKE HIM A WHOLE WEEK OF POSTS!!! AAAAAAAAAAHAHAHAHA!

Hey, Behe, unless you just got a time machine and:

  1. Stopped yourself from publishing 'Edge', or
  2. Blew up about 20 HIV-1 research labs 15 years ago
Youre screwed, dude.


I think this pathetic Amazon post also highlights another important thing for laymen to remember about Creationism. You know how another one of their talking points is "More and more scientists are becoming Creationists every day!"?

Um.

Where are the scientists coming to Behes defense against my points? Im not doing this alone-- Ian Musgrave has been awesome. The PT crew has been awesome. My research mentors have been awesome. PIs Ive emailed have been awesome. Virologists and biochemists and other biologists have come out of the woodwork in my comments and other message boards to add more depth to the science behind my essay.

Where are the Creationist scientists backing Behe up? Ones that dont have to quote review articles?

This disparity highlights another fundamental difference between Creationists and Scientists:
Creationism = Arrogance
Science = Teamwork

Thursday, November 08, 2007

Quick Translation for Laymen II

There have been several calls for a “Quick Translation II”*, and thy wish is my command! Luckily someone else already did most of the work for me! :P From a poster over at After the Bar Closes:

Bystander—
As a non-scientist, it has been hard going, but rewarding, educating myself on the whole HIV issue so I can see the holes in Behe's argument. It still boils down to
Behe: X and there are no studies contradicting this
Others: What about all of these studies?
Behe: Insignificant
Others: They are not insignificant because Y and Z.
Behe: Gratuitous Insults
Others: Wanker

What happened:
Behe: HIV cannot do X and there are no studies contradicting this.
Me: What about all of these studies?
Behe: Insignificant.
Me: They are not insignificant.
Behe: Mean girl.
Me: Charlatan.

What I want to emphasize to laymen is that a talking a major talking point of Creationists is that “All they want is some evidence! If anyone could just show them an amino-acid-by-amino-acid evolution of something new, they wouldn’t be Creationists anymore!”

And that’s exactly what I did (and Ian, and other PT contributors). Amino-acid-by-amino-acid differences between the Vpu gene in two major subtypes of HIV-1, and the biological results of those differences. This was not *new* or *secret* information. This was all publicly available (certainly to Behe, with his Ivory Tower access to scientific journals), but Behe made the decision to write about a field he is not at all familiar with, and to kick and scream when people corrected him.

Rather than accepting refutations of his claims or responding to me in a scientific manner, Behe changed his song. He declared that the changes I pointed out were ‘insignificant,’ carefully omitting the fact that both of the subtypes I discussed formed new molecular machinery (a viroporin), and one of the subtypes evolved a special amino acid sequence that allowed it to be targeted to the cell surface to preferentially make viroporins compared to Vpus other function. Behe says in ‘Edge’ new changes and new protein-protein interactions don’t exist in HIV. Zero. None. He even has a picture with “0”. Magically, when it is pointed out that his ‘zero’ is not accurate, we learn he didn’t really mean zero. He acknowledges my essay, but the changes I mention are now ‘pathetic’.

Only a Creationist could argue zero doesn’t really mean zero.

But lets look at his new claims more closely. What does he say exactly?
  • That doesn’t seem like a fundamental change to me.
  • As I wrote, there are many more ways to cripple a machine than to build one, so destructive Darwinian processes can appear to accomplish more.
  • She goes on to list several other properties of Vpu, but, while interesting, none at all are what one should call “fundamental” changes.
  • I don’t think that’s biochemically fundamental at all.
  • The question, however, is to what extent the immense variation has produced novel virus systems or machinery? And, as I indicated, the answer is very little.
We’re all very clear now, right? The changes I wrote about are pathetic according to Michael Behe. So if Michael Behe were in a lab performing HIV research (instead of sitting in his Ivory Tower, pooping out a book ever decade as if thats an accomplishment, completely isolated from the real world), he would have looked at the data in the papers I listed and thrown them in the garbage.

Again, I want to make sure I am very clear: Behe just said if he was a scientist, he would have dismissed the changes I listed between a couple of HIV-1 subtypes as ‘pathetic.’

It’s a good thing Behe is safe in his Ivory Tower, away from research labs.

A recently published paper revealed that those ‘pathetic’ changes have a HUGE impact on how fast a person gets AIDS after they have been infected with HIV-1. They made two different HIV-1 viruses—One that used the Vpu gene from a Subtype B virus, and another virus that was identical to the first, except it had a Subtype C Vpu gene instead.

The primates infected with Virus 1 lost all of their CD4+ T-cells (the target of HIV, and the measure of progression to AIDS) in 2 weeks. Primates infected with Virus 2 didn’t lose their CD4+ T-cells until about 4 months later!

So say you found out today you just got infected with HIV-1. Would you rather live for months, or years? Would you find that difference ‘pathetic’?

Additionally, contrary to Behes claims about gum and machines and cripples, these differences were a result of one of the subtypes evolving something new. Something new so it wouldn’t cripple your immune system, but still keep the viral load high! Yeah, those researchers measured how much virus was floating around in those infected primates, and the viral loads were about the same—Not only did this evolution not ‘cripple’ the cell, it didn’t ‘cripple’ the virus either!

So what does this mean from the viruses point of view? If it doesn’t kill you, you stay alive (might not even know youre infected…*sigh*) with lots of virus in your system, and you can spread the virus to other people. If you are a female, you could pass it on to your child… and they might even live to reproductive age to pass it on to their children…

But those pathetic changes go even further! So say you found out today you were infected with one of the ‘slower’ HIV-1s. Um, you still don’t want to die of AIDS or give it to your loved ones, right? The good news is those pathetic changes Behe dismisses provided us with brand new, previously unknown, chinks in HIV-1s armor! A chink we are already familiar with! That pathetic viroporin Behe ignored could be blocked with drugs similar to the ones we use against influenza to potentially decrease viral loads.



I don’t think laymen should have any problems seeing whats going on here. You dont have to know any virology or biochemistry or immunology. Just step back, and take all of this at face value. Once again, ID Creationism is a science stopper. Once again, ID Creationism is very, very wrong when applied to the real world. Once again, an ID Creationist falls flat as a ‘scientist’.

Once again its those ‘mean’ scientists saving the world while the Creationists do nothing.

Dare I say it, but even Lindsay Lohan could see whats going on here.






* Quick Translation I
** Illustrate Guide to Vpu

The Conversion of Antony Flew

Holy crap you guys. You have to read Richard Carrier's take on the Antony Flew ordeal. I found it shocking, and Im not usually shocked at Biblotarian activities anymore.

Every evilution proponent should make themselves aware of this situation, atheist or theist, seeing as it is a point Creationists are bringing up (as AtBC posters would say, 'All science so far!')

Wednesday, November 07, 2007

LOL! Baptists

WHOO!! Theres nothing that turns a bad week good like unexpected interactions with Creationists!! Checked my school e-mail this morning to find out the Baptist students were bringing in a speaker to present the topic "Comparative Immunology and the Quest to Understand our Origins." Unfortunately I read this email in class, and appeared to randomly burst out in giddy laughter, but luckily I already warned this prof I was going to be a bit off today, and I think he just thinks I REALLY like EGF receptors...

I was so excited because any time you see the words 'Baptist' and 'origins' together, you know youre in for a real Creationist treat. Though they have no Pope, the official Baptist stance is that 'Evilution is a Lie.' So I Googled the dude, Donald Ewert, and look where I found him:


So after class, a classmate and I told our mentors we were going to 'an immunology seminar' and trotted off to see how everything we had been learning in class was a lie. OMG you guys, I dont think Ive ever laughed this hard for an entire hour. Few opening observations:
  • They provided lunch. Normally there are lots of vegetarians in the research world, so usually these things have pizza/wraps/something where they could get a veggie alternative. NOT THE BAPTISTS! The knew I was an outsider from the get-go cause I wouldnt eat their ham and roast beef sandwiches from Arbys. So for lunch I had Wal-Mart cookies. I had to take almost an entire sleeve because they were all melted together. Note to self: Never expect decent food from Baptists again.
  • As I was waiting in line for my Wal-Mart cookies, I noticed the girl in front of me had a keychain on her backpack "BIG BANG THEORY: GOD SAID BANG! AND IT WAS BIG!" I know my dear readers have as dirty of a mind as I do, so go ahead and go there.
  • It was like "Romper Room" in reverse. "I dont see Curtis! I dont see Kristen! I dont see Sushma!" There was no one there from our department except me and my friend. I dont think there was even anyone from the Graduate College-- though the school is huge, everyone was in scrubs/white jackets, so they were med/dental/nursing students. Ugh.
  • Dude almost had to use my Macbook (with all my Behe shit on the desktop) because his animations werent Windows compatible. Alas, I didnt have a DIV-VGA cord, so no help from me, and no animations for the presentation.
And then the presentation. The presentation, you guys... HYSTERICAL!
  • He became interested in this topic because of the Dover Trial. He is an expert because he has 'read books for several months.'
  • The Dover Trial was in 2003.
  • Those devious prosecutors did a literature dump on poor Behe! Behe didnt have time to read those papers! Why would Behe be familiar with any of those publications?
  • Since there are no 'intermediates' alive, we cant test evolution.
  • Phylogenetic trees are a fraud. You can make them do anything.
  • Quote mines.
  • Evilutionists think V-D-J came about when a bacteria infected the germ line of a shark. Note: this wasnt a momentary mis-speak-- this guy didnt know the difference between bacteria and retroviruses.
  • Throws Judge Jones under the bus.
  • Galileo Gambit
  • Andrew Antony Flew Gambit. Seriously, that was his closer. Came out of left field.
I was in pain the entire hour from Wal-Mart cookies and laughing at this guys presentation. It was SOOO bad! Not just the usual Creationist gambits, it was extraordinarily dumb! You probably could have gotten one of those Baptist spawn in scrubs to give that exact same presentation. LOL!! Good times with Baptists!

Tuesday, November 06, 2007

Slight Delay...

Hey folks!

I hoped to have a "Quick Translation II" up for you all tonight, but its not gonna happen. *little bit* of obnoxious real-life drama today.

1. So Ive been butting my head up against this damn experiment for the past 3 months. Couldnt get it to work, couldnt get it to work, couldnt get it to work, no friggen idea why. Realized today the commercial buffer we used has azide in it for some reason. Azide. Azide kills cells. I was screaming and stomping through the lab for basically the entire afternoon.

2. I spent the morning at the dentist. Nothing bad! I was getting sealants put on my teeth-- theyre cheaper than fillings and no drill involved! Yay! Stop cavities before they start! Well, I just love my dentist here, and he did a great job. But then the hygienist started bitching about how she was trained how to do this, and how she used to do everything at her last job, so Dentist was like, "Um, fine. You do these last three and Im gonna go get a donut." Okay, no big whoop! But then they hygienist put in the last three. It seemed to go fine, but then she got this hook and started scraping on one of my teeth. Hard. "What are you doing...???" "Well, I got some of the sealant on this tooth... **CHUNK!**" Okaaay... Nothing hurt, so I went with it. When she was done, I shut my mouth and I was like "WHOA! This does not feel right. This hurts." And she said, "Youll get used to it."
So as the day went on, the teeth she filled started hurting more and more. I left work early, came home, couldnt even focus to write a little post. So I took some Tylenol PM, and started getting ready for bed.
I cant floss. The dumb bitch got sealant in between my teeth! Got a mirror, she just coated the left side of my mouth with sealant!! WHAT THE HELL?!?! And it hurts. It feels like Butterfingers are packed into/between my teeth! I am so pissed off. Im going to try to go to sleep. Very sorry, "Quick Translation II" hopefully tomorrow :(

Sunday, November 04, 2007

Hello again, Michael Behe!

Hello again, Michael Behe*! Im glad you found the time to reply to my essay, as your response provided me with yet another opportunity to write about really cool research that you are blissfully (arrogantly?) unaware of, and yet another opportunity to expose the fact you are a charlatan to the entire planet! Yay!

For instance, though your hackneyed attempts at personal insults might have offended Arnie**, I see them as a great opportunity to highlight the arrogance of Creationists like yourself. One defining characteristics of Creationists is that no matter what their educational background, their highest attained degree is treated as a carte blanche for authority in any topic under the sun. For example, when I recently attended a presentation by William Dembski, I found out that a PhD in a field of mathematics automatically makes one an authority in microbiology, quantum mechanics, and even architecture. Hence no one should be surprised at your arrogance, claiming you know more about HIV-1 evolution than everyone in the HIV research community, even the people whos papers you chose to cite (more on that later).

Yet despite this fixation on ‘credentials’ you found it appropriate to misrepresent *my* qualifications to write about HIV evolution. I’ve been involved in researching HIV-1 evolution in various capacities since 2003—from undergraduate research assistant, to laboratory technician, to current graduate student in the field of retroviral evolution. Though you, Behe, hump your credentials on the legs of every book you write and presentation you give, you curiously made the decision to exclude all of *my* research experience and chose to refer to me as some ‘woman.’ ‘Woman’. Powerful observation, Michael Behe.

Alas, noticing that I am indeed a woman appears to be the crown jewel of your observational capabilities, and nicely explains why you yourself are not involved in the research world in any meaningful capacity. For instance, you, as an ‘ID scientist,’ proclaimed that the amino acid similarities between HIV-1 Vpu and SIVcpz Vpu is “not a fundamental change.” While I only mentioned their ~37% AA similarity as part of an intro, Behe, if you had taken a few moments to think about this topic as a competent scientist, you would have thought “Hmm. The gene that codes for env, the target of the immune system, is ~59.5% similar between HIV-1 and SIVcpz. Env should be changing the most, but it is out-mutated by Vpu! I wonder why! Whats going on? How are these changes effecting the functioning of the virus? What are the physiological and epidemiological implications of these changes?”

But your ability to ask questions and use PubMed has atrophied, Behe. Your only recourse to my essay was Creationism. You made the decision to ignore everything I said about Vpus differential evolution between subtypes and pubjack a review like a Creationist. As I mentioned before, Cristian Apetrei’s paper in no way, shape, or form supports the claims made in ‘Edge of Evolution’ about HIV-1. The authors point out that we haven’t figured out the physiological and epidemiological significance of inter-subtype differences, and you made the decision to distort their critique of HIV research into ‘HIV hasn’t evolved.’

Alas, a problem with using arguments from ignorance as a positive argument like this, Behe, as you also do with Intelligent Design, is that gaps are ultimately filled, and you are left with your pants around your ankles:

Modulation of the severe CD4(+) T-cell loss caused by a pathogenic simian-human immunodeficiency virus by replacement of the subtype B vpu with the vpu from a subtype C HIV-1 clinical isolate.

Sarah Hill (just some woman), shares one of my concerns with the epidemiology of HIV-1—Subtype C HIV-1 is a less fit virus in all of the systems we have used to study HIV in vitro… but it has overtaken all the other subtypes to compose ~50% of HIV-1 infections in the real world! Why? How?? I think it might have something to do with evolution in env and differential transmissibility. Hill’s lab thinks it might have something to do with Vpu. Unlike Intelligent Design ‘scientists’ who unquestioningly dismiss potentially significant data as ‘pathetic’, Hill looked at the variation between Vpus and wondered, “Where is this gene going? What is it doing in humans?” Then she did something that ID 'scientists' really wont understand... she designed... an experiment! To figure out if anything interesting is going on, she used a classic animal model to study the pathogenesis of HIV. They used a standard SHIV containing a Subtype B Vpu to infect pig-tailed macaques, as well as multiple SHIV alternates—ones with the Subtype B Vpu cut out, and Subtype C Vpus pasted in! A lot like what I do!

Contrary to the claims made on your Amazon blog, Behe, their results were anything but ‘insignificant’:

In our studies presented here, we have concentrated on the contribution of the subtype C Vpu in the pathogenic SHIV/macaque model system. We hypothesized that if a SHIV expressing a Vpu protein from another subtype of HIV-1 (in this case, subtype C) still resulted in severe CD4+ T-cell loss, it would suggest that the divergent sequence of this Vpu (particularly the carboxyl terminus) was not a factor in disease progression. Our results presented here indicate that a SHIV constructed with the Vpu from a subtype C Vpu (SHIVSCVpu) significantly differed in the rate of CD4+ T-cell loss compared to parental pathogenic SHIVKU-1bMC33.

Translation: If Behe is right, the changes in Vpu are ‘pathetic’, they would have seen no difference between the monkeys that got the Subtype B SHIV or the Subtype C SHIV. Behe is not right.

I cant post the figures here, but there *was* a significant difference between the animals that got different SHIVs. The Subtype B infected animals had no CD4+ T-cells by week 2. It took the Subtype C infected animals ~4 months to show the same CD4+ numbers. Slower you progress to AIDS, the more time the virus has to spread to new hosts. What does this data mean to you, Behe? Do you understand how this relates to SIV? Do you understand what this might mean for the evolution of HIV-1 in humans? Do you know what this might mean for potential anti-retrovirals?


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


So whats your deal, Behe? You stepped waaay too far out on a limb with ‘Edge of Evolution’ and left a gaping hole for any HIV researcher to catch. The rather baffling claims you’ve made subsequently have done nothing to support ID Creationism as *science*—Amino acid similarity = Structural similarity, viral protein-protein interactions with cellular proteins or other viral proteins ‘are like chewing gum’ so they ‘don’t count’, ignoring Vpu forming viroporins, pubjacking others’ publications, sexist and other unprofessional comments-- basically acting like a common gutter Creationist. Why? Youre doing this in the name of ‘Intelligent Design’, and the Discovery Institute doesn’t even like you.

So whats your deal? Is it just for the money? You’ve got a litter of kids, and I admit I would find the $20K you get for selling out rather tempting in todays funding climate. Do you just like how you get treated by your followers? Or do you like how you get treated by your opponents, in a Mel Gibson sort of way? Or is your involvement in this whole thing a crazy idea that got out of hand, and you don’t really mean any of it, you don’t really believe any of it, and youre throwing softballs to grad students because you want to get ‘caught’ and give up the whole charade?

*shrug* Or maybe you do mean it. If that is the case, youve seen how I respond. Think very carefully about whether it is in your best interest to continue making claims about HIV-1 in the future. If you are planning on making more incredible claims about HIV, I would appreciate it if you at least made future statements more challenging.






* For some reason, Behe thinks he is Lindsay Lohans character in 'Mean Girls.' Me and the Pandas Thumb contributors are The Plastics. I have no idea what possessed Behe to make this analogy, but far be it from me not to respect Behes wishes. You know Im starting to think analogies arent Behes forte...

** Arnie really is a loyal pup. It doesnt help Behe didnt even acknowledge him in his blog post. Behe probably should apologize to him.

Saturday, November 03, 2007

Using animals in research

Mark wants to know:

If you do science and use animals in research explain on your blog and link back here.
Alrighty. Mark has already emphasized my main point—antibodies. We cannot make synthetic antibodies. We cannot model an antibody on a computer, push a button, and get a gallon of monoclonal antibodies to HIV-1 Subtype B gp120 out the end of a garden hose. We have to use mice, rats, rabbits, goats, donkeys, etc to generate antibodies. We have to.

But we have figured out ways to limit the mice we need to kill for antibodies. For instance, rather than keeping warehouses of mice to generate your antibody, you can stretch the good you get from one mouse’s sacrifice by creating ‘hybridomas.’ If you fuse a cell from a mouse spleen with a cell from an immortal cell line, you can create a cell line to make antibodies for you! Just grow the cells in a flask, collect the supernatant, and purify the antibodies! I use an OKT3 cell line all the time for anti-CD3 antibodies! You can even freeze some cells, FedEx em to a friend, and they can grow the EXACT antibody youve been using in your experiments! You know, Im saying this, assuming that animal rights fundamentalists are like anti-abortion advocates, and don’t give a crap about me killing cells…

Personally, antibodies are my main use of animals in my research thus far.

If we win a grant Bossman is submitting, we are going to be using mice to study the epigenetic control of endogenous retroviruses. We’re not just jumping into killing mice. We first just did some basic experiments using cell lines. Chromatin immunoprecipitation assays, radio labeling proteins, mutating stuff and trying the experiments again, etc. We got really good data. So we need to use mice to figure out how what we see in cell lines translates to physiology. We think disregulation of ERVs causes or perpetuates cancer.

“OMG U R SO DUMB!” an animal rights fundie might scream. “MICE IZ R NOT PEOPLZ!”

Yup, mice iz r not peoplz. Sometimes this is worse for the research than with others (ie infecting mice with HIV-1? have to take your results with BIG grains of salt), but luckily I think findings we make with our particular project will be very applicable in humans. And, we can do things with mice we cannot do with people. For instance, it is unethical to create an experimental group of people, whom we deprive of a particular nutrient connected with this epigenetic system to see if they get cancer. We cannot deprive groups of cancer patients of this nutrient to see if they metastasize more frequently or die faster. We cannot deprive pregnant mothers of this nutrient to see if they abort their babies, or if the babies live, to see what kind of mental/physical deformities they have. We cant take children away from their mothers and give them breast milk from different mothers that have been deprived of this nutrient. We cant use clonal colonies of people, nor can we sequence the entire genome of every human in our trials to make sure everyone has the same ERVs in the same locations.

We can do all of these things with mice. Im going to do my best to make sure not one mouse dies in vain. That I learn something from every mouse I have to kill, and that all the mice I kill die painlessly.

“BUT IZ NOT WURTH IT!” says the animal rights fundie.

What we’re hoping to find with our research: evidence that a new kind of epigenetic modification is important for controlling the activity of endogenous retroviruses, and can be studied to improve the lifespan and quality of life of everyone on this planet.

I think iz wurth it.