Tuesday, February 26, 2008

How a 'just so' story turns into just 'so?'-- HIV and the failures of Intelligent Design

August 2, 2007, over six months ago, I wrote an essay on the evolution of a cool new gene/protein in HIV-1 called 'Vpu'. To quickly summarize, Vpu first emerged in chimpanzees version of HIV, SIV. After chimpanzees transmitted SIV to humans, Vpu acquired new properties to deal with the environment of a new host. As time progressed, HIV-1 split into multiple subtypes, and the Vpus of different subtypes started to evolve different characteristics as well. Thus SIVcpz Vpu, HIVSubtype B Vpu, and HIVSubtype C Vpu are genetically and biochemically distinct proteins.

Quite the opposite of Behes claims about HIV-1 in 'Edge of Evolution', "the story of Vpu is turning into a beautiful example of how evolution works in the real world, the continual evolutionary struggle between host and disease producing a novel function, formation of an active ion channel, from a simple protein. It also nicely illustrates and how scientists use evolution to explore our universe and produce improvements in medical practice." (to quote an email from Ian Musgrave)

This didnt happen a billion years ago. It didnt take a billion years to occur. This is real evolution happening in real time with real consequences.

While that was enough to put Behes ridiculous claims about the evolution of HIV-1 to rest, there is still more to Vpus story. Six months ago, science only had a 'just so story' explanation for Vpu:

So theoretically, ion channel formation evolved in HIV-1 when it infected humans to overcome a species specific and cell specific host factor.
Why did Vpu evolve the way it did? Well, it had to overcome something in human cells. There was something about human cells that were different from chimpanzee cells that HIV-1 needed to evolve around. Whats that something? Um... something. But thats what happened! Thats why Vpu forms a viroporin!

It was one of those 'just so stories' that Creationists love to dismiss.

But that was six months ago. And, you see, scientists arent like 'Creationist' scientists. They dont see a black box, declare a deity made the box, and take the rest of the week off. Scientists see problems and demand answers. Several weeks ago, a paper was published in Nature that turned Vpus 'just so story' into just another 'so?' story for evolution:

Tetherin inhibits retrovirus release and is antagonized by HIV-1 Vpu

Human cells possess an antiviral activity that inhibits the release of retrovirus particles, and other enveloped virus particles, and is antagonized by the HIV-1 accessory protein, Vpu. This antiviral activity can be constitutively expressed or induced by interferon-alpha and it consists of protein-based tethers, which we term 'tetherins', that cause retention of fully formed virions on infected cell surfaces. Using deductive constraints and gene expression analyses, we identify CD317 (also called BST2 or HM1.24), a membrane protein of previously unknown function, as a tetherin. Specifically, CD317 expression correlated with, and induced, a requirement for Vpu during HIV-1 and murine leukaemia virus particle release. Furthermore, in cells where HIV-1 virion release requires Vpu expression, depletion of CD317 abolished this requirement. CD317 caused retention of virions on cell surfaces and, after endocytosis, in CD317-positive compartments. Vpu co-localized with CD317 and inhibited these effects. Inhibition of Vpu function and consequent mobilization of tetherin's antiviral activity is a potential therapeutic strategy in HIV/AIDS.
These researchers used Vpus 'just so story' to discover a new component of the human innate immune system. When most people think of their immune system, they think of antibodies. But there are lots of ways your body can defend itself against viruses without the adaptive immune system. It can be something as simple as your skin (keeps em out!), or something really general like Toll-Like Receptor 3, or pH changes within a cell. So because there are a lot of ways the innate immune system can help get rid of viruses, and there is a very distinct pattern of need/no need for Vpu in different cell lines, these authors thought 'maybe' Vpu was countering one of those innate mechanisms. Here is their initial logic:
1. Some kinds of cells cant be infected well unless you use an HIV that has Vpu.
2. Other kinds of cells dont care if Vpu is there or not-- they produce lots of viruses.
3. Whats different about the protein expression in these two cells?
They used a microarray to identify proteins that were upregulated in cell #1, and not expressed very much in cell #2. This gave them a list of putative proteins that could be interfering with HIV-1 particle release. Then they asked:
4. Vpu seems to act at the cell membrane, where viruses are budding off. That means that the putative protein should be either in the cell membrane, or secreted.
So they kicked everyone off the list that wasnt a membrane bound protein or secreted. This left them with one possibility-- 'CD317'. So then they asked:
5. The cells from #2 dont express CD317. If we make them express CD317, do they act like cells from #1?
6. The cells from #1 express CD317. If we knock down its expression with siRNA, do they act like cells from #2?
The answers to both of those questions is 'YES!!!'

They renamed CD317 'tetherin' and concluded that tetherin is a component of the innate immune system activated by interferon-alpha which interferes with the release of HIV-1 viruses in certain human cells, BUT this inhibition can be overcome by HIV-1 Vpu.

On top of Vpu down-regulating CD4.

On top of Vpu forming super sweet viroporins.

Now its important to note that tetherin is joining lot of other innate anti-viral systems like APOBEC3G (found using the HIV-1 protein Vif) and TRIM5alpha. Its also important to stress that like the APOBEC and TRIM, tetherin isnt a feature unique to humans-- lots of organisms have APOBEC proteins, lots of mammals have TRIM proteins. But, each species particular set of variants, each species restriction abilities, are unique. Comparing different species APOBECs and TRIMs has turned into a fruitful avenue of research.

The publishers at NATURE hope for the same with tetherin-- From a Nature News and Views on this paper:
Because the amino-acid sequence of tetherin differs considerably among mammals, some HIV-1-related animal viruses might find it difficult to overcome human tetherin, preventing them from becoming human viruses. Conversely, it is worth investigating whether tetherin contributes to the inability of HIV-1 to efficiently escape from most rodent cells, which has hampered efforts to develop small-animal models of HIV-1 infection. Even in human cells, Vpu might not always be able to overcome the powerful effect of tetherin, as the release of infectious Vpu-positive HIV-1 can be inhibited with high doses of interferon-alpha. Thus, an understanding of how tetherin works, and how Vpu fends it off, could lead to strategies to limit the spread of HIV-1 and other viruses that target humans.
In six months, evolutions 'just so story' led to new drug targets for new HIV/AIDS therapies, and a brand new avenue of research for immunologists and virologists all over the world (tetherins role in influenza, ebola, EBV, herpes, whoo!!!!).

... But what would have happened in Bizarro World? What would have happened if Intelligent Design Creationists were in charge of the NIH? What if someone like Michael Behe were controlling who got money for research?
Six months ago (well, four months, took him a while) Behe would have thrown everything known about HIV-1 Vpu into the garbage can. My original essay and all of the information it contained was 'pathetic', 'unimpressive', and 'meaningless.' Why would you continue to waste money studying the evolution of HIV-1, when it doesnt evolve in a 'meaningful way'?

This study, this study that discovered a brand new branch of innate immunity, this study that could potentially help us treat all kinds of viral infections, would have never happened in Bizarro World.

What has Behe been doing the past six months? How has he contributed to the HIV research community? The medical community? The scientific community? Its not fair to single Behe out in Bizarro World-- What about Dembski? Wells? West? Am I missing anyone? What have they done in the past six months to help stop AIDS, cancer, influenza, MSRA, anything??

Rather than being an icon for the failure of evolution, HIV-1 is an icon for the complete and utter failure of Creationism.

54 comments:

Chris G said...

That was truly a thing of beauty. Thank you.

waldteufel said...

Amen.

Art said...

Wow, Abbie! Great post, and one that even I could follow.

If ever we let the IDiots be in charge of science, we would have a science fettered not just by non-science, but by active anti-science.

No foxes guarding the hen house, please.

-- HalfMooner

slybird said...

Wow, that was wonderful, atnd a true thing of beauty as noted above.

When all is dark and I'm feeling extra cynical and dejected at the state of the world, it is bloggers like you who make me feel that maybe things'll work out well after all.

Thank you.

~ Nick

jfatz said...

The funny thing is that when you use a host of terms I don't recognize and barely process, you make me even MORE randy than your regular Behe-bashing! ;-)

Amazing, ERV. Instant classic. ^_^

Don Smith,FCD said...

Excellent Post!

You are absolutely right about the religiously motivated. I mean, look at the track record: 1000+ years of suppressing any evidence that didn't agree with the catholic church. 900 years and counting for islam.

I guess the fundamentalists are feeling left out. "When do we get to suppress something?"

Anonymous said...

Abbie, my wife is going to kill me for saying this, but I LOVE YOU!

Corey Smith said...

This is what life is about

Jacob Wintersmith said...

Yet another demonstration that "creation scientists" have no real interest in the natural world but are merely looking for an excuse to believe what they want to believe.

A couple weeks ago I found myself talking to a creationist engineering student in a cafe. He told me that life couldn't possibly have existed on earth for billions of years because stars burn out on a much shorter timescale. When I asked why he thought the astrophysics community had its head so many orders of magnitude up its arse, he became vague and evasive.

Anyone who actually had the slightest interest in how stars work would have set about trying to demonstrate that everyone has been wrong about stellar lifetimes -- and win a free trip to Stockholm if they succeeded. Needless to say, my creationist was not engaged in any such research program. He had stopped thinking about stars the moment he arrived at "...and hence the Bible is right".

Stephen Wells said...

The work described here is amazing, and your description of it is beautifully clear. The idea of a therapy which stops new virions being released from infected cells must be applicable across so many viral illnesses.

Perfectly Candide said...

Well considering the the Discovery Institute crowd is very sympathetic to HIV denial, I would really say they have done nothing to help.

Has Behe done anything besides being associated with

Perfectly Candide said...

Whoops sorry about that.

What has Behe done besides be associated with HIV deniers?

Tim said...

Thanks Abbie.
This is was I was looking for.

Take care.

Tim said...

Don't get me wrong though.
You still bray quite abit and let your emotions cloud your ability to just give the facts. Misrepresent the positions of others and motivate through derision.... dishonest things from someone who claims they value honesty.

S_A_Wells said...

Tim, the term "concern troll" was invented specifically for people like you.

Abbie's position has been vindicated. The creationists have been exposed as the science-blocking, ignorance-worshiping fools that they are. I think Abbie is justified in taking a moment for a happy victory dance on the smoldering ruins.

-DG said...

Great post Abbie, educational as always. This post even got linked to Fark.com, which frequently gets stories linked concerning evolution and creationism.

You are probably going to see a big spike in readership if you haven't already!

Tim said...

Tim, the term "concern troll" was invented specifically for people like you.

Abbie's position has been vindicated. The creationists have been exposed as the science-blocking, ignorance-worshiping fools that they are. I think Abbie is justified in taking a moment for a happy victory dance on the smoldering ruins.


So there is no edge to the capabilities of evolution?

SAWells said...

There are very definite edges to the capacity of evolution, as evidenced by the fact of extinction. If all the members of a species are living in one spot and a whacking great comet falls out of the sky on them, they are not going to get the chance to evolve into something comet-proof :)

Analogy: Behe writes a book claiming that cars are propelled by tiny horses living in the engine, and can travel no faster than the tiny horses run. Abbie and other point out that this is not the case. You pop up asking "so cars have no maximum speed?"

scripto said...

Wish Professor Behe had shown up on the Infidel Guy with you. It seems like he has some explaining to do. Maybe next year.

jfatz said...

So there is no edge to the capabilities of evolution?

There are some, fundamentally, but anything specific and fascinating will be discovered by biologists.

Certainly there's no "Edge" to THAT book (nor much in the way of logic)--hence the proper lambasting.

King Aardvark said...

Seriously kickass.

Cutting-edge science and a quick kick in the nuts to ID. What more can I ask for?

mugwump said...

Abbie: you are awesome.

Tim: u r full of fail.

Anonymous said...

"mugwump said...

Abbie: you are awesome.

Tim: you fail."

This

Tim said...

Analogy: Behe writes a book claiming that cars are propelled by tiny horses living in the engine, and can travel no faster than the tiny horses run. Abbie and other point out that this is not the case. You pop up asking "so cars have no maximum speed?"

I guess when you really only have to worry about one person, me, who disagrees with you... you can do all of the sloppy, lazy reasoning in the world. You'll still be met with pats on the back.

Certainly there's no "Edge" to THAT book (nor much in the way of logic)--hence the proper lambasting.

This blog is laughable. And the majority of you who comment offer nothing.
Are you all the 'free-thinkers' I hear so much about? Most of you just post to say "yeah!!! I agree completely!!!". The only thing that really differs is how you're going to insult me or anyone who disagrees with you.

"Amen", "Wow, Abbie, Great post", "wow, that was wonderful and a true thing of beauty", "Amazing, ERV. Instant classic", "Abbie, my wife is going to kill me for saying this, but I LOVE YOU!", "Great post Abbie, educational as always", "Seriously kickass", "Abbie: you are awesome"...
It's like seals barking for a fish.

Abbie, you should be thanking me. Not only am I boosting your comment section activity.... look at the mindless lot that are praising your every move. Hell, toss another black and white glamour shot of you delicately holding a glass of kool-aid for them all to see.

You can't handle someone disagreeing with you. It gets you worked up. It makes you lash out, get all emotional. If you aren't acting pompous, you're intentionally exaggerating other peoples claims and positions to invalidate everything they say. To tarnish their character.

You mock my morality, but what do you have Abbie? A mean streak and a worshipping flock?

Tim said...

Falwell is an ass. His family is a bunch of little assholes. Im glad Falwells dead, and I wish he took his poor little family with him.

Wow Abbie. You are a disgusting person.
Good thing you have me on your blog... someone has to hold that mirror up to your face.

Albatrossity said...

I see Tim the Concern Troll is still here, admonishing you for meanness and in the same paragraph calling you "pompous" and your commenters "seals barking for a fish". Too amusing.

That is an excellent paper; I downloaded it a week or so ago when you first linked to it. It will be interesting to see if anyone undertakes experiments to pin down exactly the region(s) of CD317 that interact with Vpu, and how (exactly) these two proteins interact. I'm also interested to know if the ion channel activity of the Vpu is important here, or just the membrane localization.

I'm sure that Behe's students are hard at work back in Lehigh, hoping to figure this out and get a paper in Nature...

Bill said...

Fish? Somebody's giving out fish?

Pick me! Pick me!

Timmy barked: You can't handle someone disagreeing with you.

I hear a lot of barking but I don't hear any counter-arguments from barky Timmy on HIV evolution.

Got anything sciency to say, Timmy, or are you just pouting 'cause you're not going to get any fish?

Joe Genes said...

Hey Abbie

Could you please make an entry on your blog as to how your cool research with epigenetics will help generate new organs for people and help cure cancer and stuff. Like you shortly mentioned here...[URL="http://endogenousretrovirus.blogspot.com/2008/02/im-officially-impossible.html"]
I'm officially 'impossible'[/URL]. Could you also please show a few of your peer-reviewed articles if you don't mind. I don't think you want people to think you are a pseudo-scientific douchebag that tries to look smart.

I am also curious on your opinion about where those very first exogenous retroviral vectors came from that caused the first ERV's. Somehow Cdesign Proponentsists feels this is important to their lame arse arguments.
Cretinists are also giving rational people a hard time about all this stuff about why unrelated ERV envelope genes regulate something about the placenta. Apparently this is a crucial process. Please make another bullsh*t buster article about this...

Thank you:)

scripto said...

I am also curious on your opinion about where those very first exogenous retroviral vectors came from that caused the first ERV's.

Joe and I would like an answer by Friday. When you're finished with that I'd personally like to know what came before the Big Bang.

Douche, Mr. Gene, doo shay

michaelf said...

Great post Abbie!

Tim,
Do you go through every blog and complain when someone is mean or blindly agrees with the author? Must keep you pretty busy... do you have a day job?

Here's an analogy for you:
A scientist is standing on the shore looking out at the horizon. He/she says that looks like the edge of the earth. Let's get in a boat and go see what it looks like. They find that it is not really an edge, but look there is another in the distance. He/she keeps going until no more edges appear.

A creationist is standing on the same shore looking out at the same horizon. He/she says that looks like the edge of the earth. Let's not go near it because we might fall off.

When the scientist comes back and says the edge wasn't really an edge, the creationist either doesn't believe him or her or if he/she does says but did you explore every edge?

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

Has Behe done anything besides being associated with
7:35 AM
Perfectly Candide said...

Whoops sorry about that.


No, you got it exactly right.

@ Joe Gene:

Could you please make an entry on your blog as to how your cool research with epigenetics will help generate new organs for people and help cure cancer and stuff. Like you shortly mentioned here...

You repeat yourself without noticing that ERV describes some medical applications of science on viruses - you fail.

Oh, and you don't get that science is a collective effort, where no one can exactly predict which result will be a basis for another, and assumes ERV meant that she would do it personally - you fail doubly.

And it is so easy to google how viruses connects with organ transplants and cancer, it just makes you seem like an ignorant troll. Is that what you want?

ERV said...

Torbjörn-- Well, I wont write about the specific ERV stuff Im doing because its not 'my' research. The stuff we are working on now is for another first author-- Its not my story to accidentally squeal ;)

However, I do have good news on the ERV front-- You know how science research funding SUCKS in the US right now? One of our ERV ideas got an RO1!! Were not gonna go drinking until the check is in the mail, but still! The lab will stay open long enough for me to get my degree!!! And Im generating some preliminary data that could lead to another grant that I would be first author on... HIV and epigenetics!!! LOL!

Im working on writing the red/green HIV stuff right now... headache... Its really friggen funny, though-- Ill spend HOURS, DAYS writing a section. Show it to Bossman. He crosses out everything and rattles off a perfect replacement off the top of his head. AAAAAAARG LOL!

Id also like to remind everyone that my email is listed on my profile, and I happily read all post suggestions people send my way-- No need to spam the comments section ;)

Danny Boy said...

"Troll" nothing, Abbie.
Just someone who thinks your behavior is disgusting.

You said:
"In addition to that, my university knows about my blog."

That's
"In addition to that, my university knows about my blog."

and

"I wanted them to be aware of my blog and aware of my posts just in case a nutjob e-mailed my higher-ups about me.

A nutjob who thinks that:

"Try to bring up differential evolution of HIV subtypes or siglecs, and Deniers run screaming back to Cunt Culshaw. (Yeah, I said cunt!)"

Is in poor taste.

and...

"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."

and...

"Ted Haggard is just a meth snorting hypocritical fag. (and I hope he shoots himself in the head)"

and....

"You Sal Cordova. You cottage cheese dripping pussy"

and...

"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."

He's not an actual biochemist? Sure about that?

You said:

"In addition to that, I actually want my peers and my superiors to respect me. If I lie to them, I fully expect them to turn their backs on me. I would rather die than lose their trust."

He's not an actual biochemist?

"In addition to that, my university knows about my blog."

They know about all of this?!

Dang! Those wacky OU Sooners are pretty laid back. Dr. John West must be one lenient guy.

Bill said...

Not a grad student are you Danny.

We would have eaten you for lunch and spit out your bones at Purdue. You think ERV is "mean?"

You, Danny Boy, are totally clueless.

Try giving a talk to a chemistry department symposium on black body radiation for which you aren't totally prepared. You could only HOPE that someone as nice as ERV would be chewing on your ribs.

While you'll always be a nitwit serving fries for a living, Danny Boy, I'll promise to be in the audience in Stockholm when ERV gives her acceptance speech.

Danny Boy said...

That's a defense for Abbie, Bill?

You're not doing very well. You criticize me for not knowing what you know. Not knowing if I even know it or not.
You preface this with an insult that I'm clueless.

From the guy (Bill), who randomly hopped off topic, couldn't modestly describe my position (mean?), claimed I don't know things that he has no idea whether or not I know, wants me to imagine myself giving an unprepared presentation on black body radiation (what the?!) and assumes I'm just some nitwit who will ALWAYS be serving fries for a living (again... not knowing what I actually do for a living, but assumes it must be fry serving).

Oh, and he said something about eating me up spitting my bones at Purdue (LOL... where do you find these people?)... and something about Abbie chewing on my ribs.


Bill, are you certain I'm the clueless one here?

I'll promise to be in the audience in Stockholm when ERV gives her acceptance speech.

Uhhh, GREAT!!! Thanks for that random promise of yours.
Wait, let me get this straight. I'm clueless?!?!?!
Bill, it appears you haven't a clue to be without.

Jay said...

I was [i]almost[/i] with Danny Boy until I read "You Sal Cordova. You cottage cheese dripping pussy"

Hahaha. Classic insult. Who could help but laugh?

Danny Boy, are you familiar with hyperbole and blue humor? They may not be appropriate for a research paper, but on a personal blog, they are not really worth getting in a tizzy.

Now personally, I try to avoid hateful speech. But you know what? Sticks and stones.

Danny Boy said...

Danny Boy, are you familiar with hyperbole and blue humor? They may not be appropriate for a research paper, but on a personal blog, they are not really worth getting in a tizzy.

I understand what you're saying. I still find the behavior disgusting. I think there's a difference between 'blue' humor and calling someone a "cunt", saying someone isn't "an actual biochemist", wishing a whole family dead, hoping another guy shoots himself.

Even if they want to do this I'm not saying they can't. Simply they shouldn't. There is a difference.
Also, Abbie's the one also saying this:

In addition to that, my university knows about my blog

and

In addition to that, I actually want my peers and my superiors to respect me. If I lie to them, I fully expect them to turn their backs on me. I would rather die than lose their trust.

Remember, she wigged out when Sal suggested she is being dishonest (that was what her posted tirade was in response to).
Maybe the folk at OU (the folk who appear to be aware of this blog) are cool with the 'blue' humor. But what about,

We're supposed to treat you like an actual biochemist, even though you arent

Same Abbie lambasting Sal for his supposed lack of honesty and his potential (exaggerated) injuring of her career with his comments.

What am I missing?

spurge said...

danny boy said

"I understand what you're saying. I still find the behavior disgusting."

Then stop reading the blog.

Problem solved.

Unless you are just a troll?

ERV said...

What am I missing?
The fact that those quotes are all explained in their associated posts and its obvious to even the most casual observer that you are a low level troll? The fact my readers arent retarded and caught you writing identical posts on other female science blogs?

Man where did my HIV Denier trolls go? They were actually clever/funny.

Danny Boy said...

The fact that those quotes are all explained in their associated posts and its obvious to even the most casual observer that you are a low level troll?

Abbie, you must mean that the context of the whole post justifies the way you act, what you say, and those apparent inconsistencies. Wrong, it doesn't.

The fact my readers arent retarded and caught you writing identical posts on other female science blogs?

Yeah, 'caught' me using the same name, "Tim", on a blog that was linked from this blog. There was nothing to catch Abbie, because there was no attempt on my part of trying to be clandestine about it.
Here you go again, trying to make a nothing into a something.
You don't need real estate that bad, do you Abbie?

Man where did my HIV Denier trolls go? They were actually clever/funny.

Sorry Abbie, neither attempting to be clever nor funny for you.
And, if all of what you say is truly your idea of 'good hearted fooling around'.... there would be a large disconnect between my sense of humor and yours.

But back to the point, Abbie. Is your university cool with all of this?
What was the context that makes your comment about Dr. Behe not actually being a biochemist, either funny or somehow not exactly what you said.

ERV said...

Time Warp Tard strikes again.

Weve had conversations on this topic ad nauseum via Casey Luskin months ago. I have no idea why you think youre clever bringing up his exact comments again as if theyre novel.

Haggard fed into a culture of hate that homosexuals had to live in, while Haggard was he himself a homosexual. Children blew their brains out and hung themselves in their bedrooms because of Haggard. Real human beings *die* because of the anti-information Culshaw pukes up.

And you think its 'disgusting' to call BS on their BS.

You do not care in the slightest about any of the quotes you listed, because you left identical messages on someone elses message board (someone else who happens to be an intelligent female, coincidence Im sure).

Please format all future posts in the form of dada poetry, so at least your time-warp tard will be fun to read. See?
Dada Tim-
Attempting of cool this. What not
of and all Dr. Behe
attempting said? Behe of what
to for all would large.
Sorry said. Of you your
nor is my point.

Barklikeadog said...

Tim, what's your actual problem with Abbie calling Behe on his bad science? So you have the superior moral high ground because you don't use bad words & can divert the real argument because Abbie & her readers do. Behe and his ilk aren't providing anything useful to society except some Monty Python type amusement; except their serious. They really think they are right. OK if there is a God. it still didn't set things up to work like Behe & his bad science shows. One way or another it doesn't matter. Believe what you want but the real evidence is there. We can only do stuff about the material world we live in; the stuff that has impact on real bodies, lives & families. That's what Abbie & her lab & others like 'em are doing. I'm nowhere near her level but I still try to lead the next generation onto a better and better understanding & skill than me & my predicessors. I want them to show me up. Abbie is doing that to the likes of Behe & more power & money to her for it. I & mine will be the beneficiaries of it, so will your decendents regardless of the BS you feed them. Go make me a sandwich & can I have some fries with that?

michaelf said...

Behe gave up being a biochemist and a scientist when he identified blackboxes and edges that he could not explore. He declared "god working here" claiming they were off limits to scientific study while scientists were busy studying the very same "supposed" boxes and edges. He has renounced science for religion.

Joe Genes said...

Epic fail Torbjörn

I was specifically asking how HER research is going to help generate new organs for people and help cure cancer and stuff, but thank you for trying. I see you also saw she did not want to answer a straightforward answer. Good on you for doing the right thing mate. I do know how ERVs relate to cancer and was hoping she might say something interesting about HER research. Waiting...
And yes, science is a collective effort, but you are not exactly going into it blindly, you must have some sort of idea what the implications of your research is going to be right? Or are they hoping blindly that their research might somehow, for some unforeseen reason become useful in helping to grow organs and fight cancer?

Scripto, at least you are thinking about it or have an opinion right?

ERV
Do you actually have a story to accidentally squeal? I can understand that you don't want to divulge the specifics of your bossman's research. So aren't you helping with your bossman's work, and not doing your own original research? Care to accidentally squeal how some of your preliminary data will help fight cancer and grow new organs and lead to your "first-author" work?

Now how about those placental envelope genes? Sheesh, some help would be nice.

Thanks.

Joe Genes said...

Oops, "answer a straightforward question"... my bad.

ERV said...

Once again, I have an email if you have questions for me or have suggestions for a post. I have no commenting policy, but this entire comment thread is just crap from trolls.

Joe, I am not the first author on the ERV/cancer project. I am helping another lab with procedures that they cannot do themselves (they are cancer people, not virologists, we have different skill sets). That publication is in press at PNAS, and I will certainly link to it when its published. The project Bossman just won a grant for wont start for months, and I cant talk about it until the PNAS paper is out (we are doing the animal models for said paper). My HIV epigenetics work is preliminary work for another grant, and Im not getting scooped for a troll.

I thank you for your interest, and I hope you check back often so you dont miss the post you are interested in in the future. If you have papers you have found on PubMed regarding epigenetics, cancer, cell differentiation, or virology, please email me your questions and Ill see if I can do a post on those topics for you. Im sure many people have the same questions as you.

Darren said...

Can I have your babies?

Torbjörn said...

ERV, cool that you and your lab is successful. That will mean more insightful blogging! (So I'm an egoist. But as everyone thinks of themselves, no one else thinks of me. :-P)

He crosses out everything and rattles off a perfect replacement off the top of his head. AAAAAAARG LOL!

Been there, done that. A good Bossman knows to infect his slaves with the area's common memes. If you are lucky it may be a persistent condition, so you can rely on those writing skills to pop up when your own falters.

I was specifically asking how HER research is going to help generate new organs for people and help cure cancer and stuff, but thank you for trying.

You were, and I simply explained why it was a mistake. Yes, I know I shouldn't try, as it is now obvious that you are trolling. And rather ineffectively so, as you pound on an inconsequential point that no one cares about as soon as they know you are willingly ignorant and so won't need help.

Okay, I could stop there. But these seemingly rhetorical questions have genuine answers:

but you are not exactly going into it blindly, you must have some sort of idea what the implications of your research is going to be right?

Not really - that is why it is called learning. In most science areas you can either concentrate on a phenomena that is interesting but have unexplained features (i.e. there is a theory to work out, but you have little or no clue if and how it will turn out) or on a method you developed for your tool kit for use (i.e. you have little or no clue which phenomena will yield information from it). Many scientists cycles between these two methods according to which happens to yield most results at the time, or just for kicks (as having fun is essential for good work).

Or are they hoping blindly that their research might somehow, for some unforeseen reason become useful in helping to grow organs and fight cancer?

AFAIK much or all of biology could for unforeseen reason become useful in some area for fighting disabilities. But here there are known ties between the study object and some diseases, as noted.

Martin Wagner said...

So lessee, Abbie's basically got Danny Boy, who thinks he's scoring some stupendous moral victory because he just won't stop wagging his finger at her for using unladylike naughty words, and Tim, who thinks Abbie's all mean and that anyone who applauds her science writings must be some kind of sycophant, which they must be, because no one ever says those things about him! And meanwhile, none of them are pointing to any actual scientific errors in Abbie's writing.

The trolls are really reaching these days, it seems.

Mauricio Monsalve Moreno said...

Good post. Clean logic despite it is an opinion.

A thing that most creationists share is lack of logic. After reading many comments, I really desire that creationists were able to write using formal logic. Then, a simple mechanic and determinist operation (made by a computer or a person) would prove they are mistaken. You know, it is very easy to spot where they are mistaken, but somehow they neglect this fact...

minimalist said...

And meanwhile, none of them are pointing to any actual scientific errors in Abbie's writing.

The trolls are really reaching these days, it seems.


The tard-trolls are just smart enough to recognize when they're outgunned. Nothing like a good long post containing substantive technical information about real scientific benchwork to make them all go "BUHHH?"

So instead they scrabble for little moral victories. Never mind that Abbie's never savaged a creotard that didn't thoroughly deserve it for amply-documented reasons.

Really, when your worldview is built around reaching the "correct" conclusion, you have to take your victories where you can. If creationism isn't correct because there's absolutely no evidence for it, then it has to be correct because Abbie is SQUEEEEEEEEEE SO MEEEEEEEEEAAAANNN!

No, it's not logical, but trolls never are.

tgibbs said...

So aren't you helping with your bossman's work, and not doing your own original research? Care to accidentally squeal how some of your preliminary data will help fight cancer and grow new organs and lead to your "first-author" work?

Do you really think graduate students get to do completely original work? Who do you think pays for it? Any project that a graduate student might start working on is funded from a grant written by their mentor, so while there are plenty of opportunities for a graduate student to exercise originality in a good lab, it must be in the context of the aims of their advisor's grant. If they are very successful, they may eventually obtain their own fellowship support, but that is in the context of a training relationship with their mentor. In the biological sciences, the researcher who actually carries out the research is normally listed as first author on publications, while the mentor who established that research direction and supervised and trained the student typically chooses to list himself last.

Anonymous said...

I just gave up an argument with a creationist on youtube about entropy and the 2LoT when he told me Adam and Eve were at zero entropy and the 2LoT did not exist before original sin. Sigh. It is out there people and it is real. You are a light in the darkness young lady. You have a real knack for laying the information out in a way anyone can understand witha little effort. Keep up the great work. You have no idea how important your work is.