Thursday, October 18, 2007

He isn't pubjacking! He's commandeering a publication!

No, this is not my official 'response' to Behe. But I thought this was significant enough for its own post. The second prophesy has been fulfilled!

*sigh* So lets hear it, Behe, what's your excuse for missing this? Go ahead—run off to PubMed and find a paper to pubjack. I'm not going anywhere.
I sincerely hoped Mr. Behe wouldnt stoop to the level of a low-life-YEC or a two-bit-online-hack... but alas... the Creationist within him is stronger than the 'biochemist.'

So whos the author of the pubjacked lucky paper? Cristian Apetrei of Tulane, and his article "HIV Genetic Diversity: Biological and Public Health Consequences" :

Butler at al (HIV Genetic Diversity: Biological and Public Health Consequences, Current HIV Research, 2007, 23-45) remark under the subheading “Biological Consquences of HIV Diversity”:

With such breadth of genetic diversity among HIVs, one might expect significant biological differences between the clades. Although interesting variations can be seen, much of the data concerning biological implications of HIV diversity is contradictory.

Plenty of differences do exist, and some are “interesting”, but not all that great.

Hmmm. Now that statement looks funny. I mean it lacks the tell-tale "..." that usually mark Creationist quote-mines, but something just looks fishy about Behes choice of quote. Hmmm. Wonder what comes right after the portion Behe chose to quote?
The long terminal repeat region (LTR) of the HIV genome regulates transcription and viral replication, acting as a promoter responsive to the viral Tat protein. Although all subtypes share the same LTR function, they differ with respect to LTR sequence structure, basal activity and response to cytokines and transcription factors [95]. The majority of HIV-1 group M subtypes contain two nuclear factor binding sites (NF-kB). A minority of subtype C contain an extra NF-kB that may promote replication in the presence of TNF-and chronic immune activation [135]. CRF01_AE, in contrast, has one NF-kB site, but contains a different transcription factor binding site that may allow it to replicate in a wide variety of cells. Indeed, when compared with other subtypes, CRF01_AE encodes a highly potent LTR region [2, 135, 257]. Although there are clear differences in LTR sequences and basal replication capacity among subtypes, the influence of these molecular level changes on specific subtype epidemics and the global spread of the virus remain uncertain.
You know, that kinda looks like my essay, except looking at LTRs instead of Vpu. And they dont stop with one example! They go on to describe several more genetic differences between HIV-1 subtypes and what researchers think those differences mean biochemically... but like a true Creationist, Behe ignores all of that information and attaches his suckers to the fact that the authors admit "We dont know everything." They lament the fact that our understanding of how these biochemical differences translate into the real world is lacking. Sometimes we think a difference means one thing, sometimes we think it means something else. And Behe uses that honesty to imply the authors agree with him-- HIV hasnt evolved.

But the authors of this paper in no way support Behes bizarre claims about HIV-1 evolution (or lack thereof).

And wouldnt you know it, but what this paper is talking about is exactly what I research every day. I see changes in a very small region of env between subtypes, and over the course of time in the same patients. Im already know the biochemical effects of these changes-- Im trying to figure out the physiological and epidemiological impact of the changes. Im hoping that I can figure out a genetic determinate of transmission, narrowing down the epitopes a potential vaccine would need to contain. Everybody is trying to figure this kind of thing out now in the HIV research world.

If Michael 'LiLo' Behe is right, we are all wasting our time. Micheal Behe, the world-wide expert on HIV evolution, who 'refutes' a short essay containing a dozen primary research articles from a first year grad student, with a quote mine from a review*.

Im going to have to take a play from the Masked Mans book, Mr. Behe, and suggest that if you are going to write chapters on what HIV-1 can and cannot do, you get a little more familiar with the literature. Until then, Mr. Behe, I think you need to focus on reading and comprehending review articles. Then, you can graduate to reading big-boy articles-- primary literature with 'immunoprecipitations' and 'Western blots.' Once youve mastered those, come to the grown-ups table, and we can talk about HIV.




* Certainly Dr. Apetreis review is excellent, but clearly not sharp enough to get through the thick skull of a Creationist.

40 comments:

Anonymous said...

Such anger and bitterness. I get the impression that you are not really enjoying life. Your profile photo displays a kind of haunted despair. 24 year-olds should be happier than this. Perhaps it is because you don't know God. He reveals Himself to those who have a true desire to know Him. Maybe you should give it a try. You might be pleasantly surprised. It's one of the more interesting experiments one can do. But without an honest desire and openness, not much is going to happen. And that's a repeatable result.

Anonymous said...

I think that the photo is actually rather "arty".

If by happiness you mean that dreamy oblivious to reality state induced either by valium or religion, then you can keep it, anonymous.

Been there, done that, bought the t-shirt, found that it had no basis in reality. Left it long behind for a state of happy atheism.

Cheers,
KiwiInOz

Sven said...

Anonymous, you should be happier than this. Perhaps it is because you don't know Santa Claus. He reveals himself to those who aren't naughty, but nice. Maybe you should give it a try. You might be pleasantly surprised. It's one of the more interesting experiments one can do.

And he gives presents at Christmas!

Dan said...

Valium rocks, don't compare it to religion. It will take revenge upon you for your blasphemy if you do not repent.

Also, why would you preach at someone making an argument about scientific literature? How is it supposed to be relevant?

Anonymous said...

Anonymous, that haunting stare is 200% solid sex appeal.

You know sex right? That thing that everyone else in college is doing but you?

Poor young Christian... what must you do with all those hormones and all that guilt?

Nigel D said...

Sven, I hope you realise that Santa Claus is actually my Dad. And he doesn't have any reindeer at all.

Anyhoo, thanks again, ERV. I do like your writing style. And it's nice to read some of your summaries of the state of HIV research. A few years ago, I attended a virology conference, and I have to confess that at least half of the talks I attended went right over my head. Mind you, I think you have to be fully au fait with the literature to follow a talk where the speaker is fitting 60+ slides of dense text and data into 40 minutes, using two projectors simultaneously and speaking pretty darned quickly, too.

Torbjörn Larsson said...
This comment has been removed by the author.
Torbjörn Larsson said...

And that's a repeatable result.

I read that as "repeatable insult" the first time.

It may or may not have been the preaching... who am I kidding. Of course it was the preaching!

And, boys and girls and Arnie, now we know why creationism will never be a science. Or even as sympathetic as dear Mr. Claus.

the speaker is fitting 60+ slides of dense text and data into 40 minutes, using two projectors simultaneously and speaking pretty darned quickly

That's what a virus or two can do to you.

Rich Hughes said...

anonymous:

So anonymous and preachy. How can you be so socially dysfunctional? Probably too much god.

dustin said...

So, I was going to flame anonymous there, but this:

Anonymous, that haunting stare is 200% solid sex appeal.

You know sex right? That thing that everyone else in college is doing but you?


Is Extra Large Grade A Fuckoff. I can't do better.

dustin said...

Every time you talk about the Masked Man, I imagine Dembski in a crudely rendered anime style with Masked Man being introduced by a frenetic narrator as, "Littledoes SpeedDembskiknowthe Mysterious Masked Man isactuallyhis longlostbrother!"

Behe is ChimChim.

PsychoAtheist said...

Can anonymous (the first poster) say 'projection'?

It seems that without a supernatural babysitter in your life you would be abjectly miserable because obviously without that you would have no friends, no family, no social life, no hopes, no desires and absolutely no desire to get out of bed in the morning. Or maybe, just maybe, life is worth living on its own accord.

So, how about you ditch the celestial overlord and enjoy the life that you have? It's the only one that you have and as someone much more erudite than I once stated "This is not a dress rehearsal".

386sx said...

But without an honest desire and openness, not much is going to happen.

It isn't very honest if someone pretends to believe something for the heck of it just to see what it's like. That and the Pascal's wager thing isn't very honest either.

I once knew someone who pretended they could look at a picture and imagine they know everything there is to know about whatever it is they wanted to pretend like they know. That's called projection and it was kind of a sad thing to witness. They must have been a very very sad person. :_(

And that's a repeatable result.

Yes it is!! If I knew what you were talking about. Many thnaks.

MajorMath said...

"Such anger and bitterness."

Proselytizers seem to love opening with this phrase (palmistry and astrology aficionados prefer "You are misunderstood" as an opener.)

I like the joie de vivre ERV brings in taking on these cheap charlatans.

So, reach into your goodie (or Goddie) bag and try again.

guthrie said...

I liked the post, except one small thing annoyed me.
That was the "Im", without the '.
Please could you spell them "I'm" next time.

J-Dog said...

I contend that "Anonymous" is either Behe, Sal or Dembksi.
OK Creos - Prove me wrong.

Oh - and the new pic is HAWT!

J-Dog said...

I just realized that Behe's plaid shirt picture at his infamous Amazon blog site reminded me of something that should be shared with the class:

BEHE (Wearing plaid shirt):
I'm a lumberjack, and I'm okay.
I sleep all night and I work all day.

UD-ERS:
He's a lumberjack, and he's okay.
He sleeps all night and he works all day.

BEHE:
I cut down trees. I eat my lunch.
I go to the lavatory.
On Wednesdays I go shoppin'
And have buttered scones for tea.

UD-ERS
He cuts down trees. He eats his lunch.
He goes to the lavatory.
On Wednesdays he goes shopping
And has buttered scones for tea.

He's a lumberjack, and he's okay.
He sleeps all night and he works all day.

BEHE:
I cut down trees. I skip and jump.
I like to press wild flowers.
I put on women's clothing
And hang around in bars.

UD-ERS:
He cuts down trees. He skips and jumps.
He likes to press wild flowers.
He puts on women's clothing
And hangs around in bars?!

He's a lumberjack, and he's okay.
He sleeps all night and he works all day.

BEHE:
I cut down trees. I wear high heels,
Suspendies, and a bra.
I wish I'd been a girlie,
Just like my dear Papa.

UD-ERS:
He cuts down trees. He wears high heels,
Suspendies, and a bra?!

[talking]
What's this? Wants to be a girlie?! Oh, My!
And I thought you were so rugged! Poofter!...

[singing]
He's a lumberjack, and he's okay.
He sleeps all night and he works all day.

He's a lumberjack, and he's okaaaaay.
He sleeps all night and he works all day.

Thank you again Oh Mighty Monty Python!

Forthekids said...

"Sometimes we think a difference means one thing, sometimes we think it means something else. And Behe uses that honesty to imply the authors agree with him-- HIV hasnt evolved.

But the authors of this paper in no way support Behes bizarre claims about HIV-1 evolution (or lack thereof)."

Um....no, Behe doesn't imply that the authors agree with him. This is the typical Darwinist view of "quote mining".

If an ID proponent points out that scientists sometimes think a difference means one thing, and sometimes they think it means something else, or sometimes they just don't freaking know for sure what they think....then it's still up for discussion.

Dan said...

When you quote someone, they don't have to be people who would support your conclusion.

However, their quote, in context, should at least support your POINT.

If the quote you're quoting doesn't support the point you're making with it when in context, you're quote mining.

Behe's point was that HIV does not show complexity and evolution. The immediate context right after the quote he uses to assert this directly contradicts it, so he's quote mining.

Here's a handy example for you:

"Behe doesn't imply that the authors agree with him."

From your own mouth, Behe admits no one who has ever written agrees with him. Why do we even put up with someone who admits nobody agrees with him? He must do it just to annoy.

where are the answers? said...
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waldteufel said...

Looks like our poster child for a brain on creationism, now posting as "where are the answers?" is babbling again.

One reads his/her/its posts hoping for at least a cogent sentence, but none is forthcoming.

Perhaps he/she/it is lacking the cerebral synaptic connections required for lucidity.

txjak said...

ERV, I'm sure Behe thinks that he's "washed his hands" of you now. He's probably going to be too busy to continue to be bothered by (i.e., be embarrassed by) a "mere" grad student. His response was probably drafted by the DI attack mouse.

I like your blog, but I have one nit to pick. "Im" looks to me like lol speak for I am. Is that intentional (i.e., apostrophes are passe) or am I being too A-R to expect to see apostrophes used in contractions? OTOH, it might be a means to track quote miners. :-)

Sven, it is interesting to think of treating Santa Claus as another god, ala FSM. Good one.

Anonymous said...

I really like this blog,but the comments suffer sometimes from the fact that most of the commenters want to get their hands on Abbie lol......Just a thought guys :-)

Rich Hughes said...

The place for quotemines:

http://www.talkorigins.org/faqs/quotes/mine/project.html

Reverted said...

Not only does "anonymous" seem too timid to post under an actual name, but the content is so generically sheep-like that it could be posted by virtually any "fundie". So, perhaps posting anonymously is actually a MORE appropriate approach because it can indirectly represent an entire flock, rather than a single sheep (since it lacks explicit attribution). Praise Jesus!

No, wait... actually, now I'm reminded of a tshirthell.com t-shirt I saw quite some time back: "If Jesus comes back, we'll kill him again." LOL

Anyway, I'm enjoying your blogs, ERV. Thanks for yet another good one.

I just find it sad (? pathetic? ironic?) that creationists claim honesty is a noble and good thing---even going so far as to claim it, and morals in general, are founded upon Christianity---while consistently "lying for Jesus" in their ridiculous writings. It speaks volumes that the term "quote mining" even needed to arise at all, in order to succinctly describe their widely prevalent tactics.

fnxtr said...

Uh-oh, Neal's off his meds again.

Xeno said...

I like that photo. It reminds me of Sinead O'Connor.

Also, anonymous, who wants to 'learn' about god when there is such a fascinating world/universe to discover out there.

ERV said...

Anon-- I have some wonderful wine right now. Im enjoying life very much, thank you. And thanks for pointing out, once again, how this is a 'sex' issue. You would have never made that comment on a mans blog. Piss off.

txjack-- One wonders why he bothered with this as all. Hes just made himself look even worse.

Xeno-- Holy crap. That wasnt on purpose. ROFL!

who the fuck cares what my name is, it is TRUTH THAT COUNTS, YOU STUPID FUCKS said...
This comment has been removed by a blog administrator.
monado said...

"where are the answers?," you want "its," not "it's," for a possessive. And you're foaming at the mouth. Such anger and bitterness! Obviously, you've never looked at the evidence with your own eyes.

Even your precious Behe admits there's common descent. He's just looking for some mathematical proof that on some level angels are pushing molecules around to make things happen. He makes way-out assumptions to cook his results. Unfortunately, his maths are strained and incompetent, as many others have pointed out. He reads research and misses the point of most of it, just extracting one little thing that he can use. It's sort of like quote-mining.

Until you can see new evidence and change your mind, you're a not a scientific person, and you're talking like a creationist. "Chemicals to ecosystems" implies that the theory of evolution includes a theory of abiogenesis. It doesn't.... that's just creationists moving the goalposts and asking it to explain everything--kind of like asking a map of London to get you to Hong Kong.

A scientist tries to disprove his theory. A scientist looks for the other explanations that might produce the same results, weighs them, argues them, and occasionally changes his or her mind. Quote-mining and appeals to authority are not science.

The history of science is full of raging debates. Sometimes it takes twenty years to change a concensus. But at 150 years, evolution is just getting more and more confirmed with different lines of evidence coming together and gaps being filled in both in fossils and in molecular evidence. Go look at some fossils. And take your meds.

who cares? it the ideas that count!!!!!! said...
This comment has been removed by a blog administrator.
Anonymous said...

"And all those exclamation marks, you notice? Five? A sure sign of someone who wears his underpants on his head."

Terry Pratchett - Maskerade

Torbjörn Larsson said...

most of the commenters want to get their hands on Abbie

Um, no, my hands are otherwise occupied ... oh, you know what I mean.

Seriously though, you seem to be projecting a lot. Take a cold shower, if blogging here is all you get.

macro-evolutionary psuedo-scientists

Great, another impotent... speller, I guess. And ranter.

Look, "chemicals to ecosystems" isn't what evolutionary biology describes. It describes how existing populations behave.

And I'm glad you mention religion, so both you and us are clear on that you aren't discussing science.

Btw, your meds is on another table.

snaxalotl said...

such anger and bitterness. yet unlike most young people ranting about the world, you are knowledgeable, on target, effective in your attack, and even respectably measured for someone facing up to such nitwits. You sound like someone on the path to a rewarding career, respect, fulfillment, happiness, and speaking engagements as an anti-horseshit expert

fnxtr said...

Indeed. Neal/Lean/Wherearetheanswers/w.t.f.c.w.m.n.i...
is a model of coherence and restraint. Well done, sir or madam.

Thought Provoker said...

There are just some quotes too precious to ignore.

"...PLEASE, admit that and put your effort in to the appropriate forum..."

Abbie, you really should show some respect for the person who made the effort to put up this nice looking site. After all, if you wanted present you personal views, you should start your own blog.

...err ...um ...

Nevermind ;-)

truth machine said...

"it the ideas that count"

Yes, the ideas of Behe that his citation undermines, rather than supports as he falsely claims. But his dishonesty counts too, as you would acknowledge if you weren't dishonest as well.

truth machine said...

But without an honest desire and openness, not much is going to happen.

Tell that to Behe, who has closed his mind to science.

truth machine said...

And that's a repeatable result.

So is flipping a coin and having it come up heads.

VFXJoshGemmell said...

"Go tweak someones clit by all means if thats what you really think is what you should do."

Hey, that's actually good advice!