Thursday, July 26, 2007

You SHOULD debate Creationists! Maybe.

I meant to write a post on this earlier, but the Great Puppy Adventure came up, and I never got around to it. Luckily, PZ just brought it up again. Heres the deal: I think you SHOULD debate Creationists... IF you are a student.

It is an excellent learning opportunity. Oh god, not for learning Creationist Claims-- That will make you go retarded. I mean a learning opportunity for your own studies. A challenge to synthesize information youre learning in all of your classes, not just lame memorization for tests. And then you have to turn around and be able to present that information to your friends!

A student can safely disarm the problems a PhD would have debating a Creationist, with the added advantage of not having anything to lose. Students can mess up all they want-- theyre still learning! But a Professional Creationist cannot lose one point debating a kid-- theyre supposed to be the professionals. Puts a lot of pressure on the Creationist.

For instance:

It pits oratory against science in a venue where you'll be judged on your rhetoric.
I think here a student would have an advantage (especially on a college campus).

  • Creationists are old white men with the humor of old white men. Attempts to appeal to younger audience members looks forced and pathetic.
  • A debate between a grown man and a student makes the old man look even more pathetic.
  • Student bumbles some words, messes up a little, its okay. Professional Creationist bumbles, messes up, again, is pathetic.
  • Student wins a point, makes the Professional Creationist look even more pathetic.
  • Student learns how to give a better presentation.

It gives publicity to creationists.

"Cranky Old Man picks on local Student"
"Professional Creationist Whomped by local Student"
I dont mind either of those headlines!

Creationists can generate more lies more quickly than you can refute.
Good time to win points with rhetoric-- Student can ask his/her classmates (in the audience) which arguments they find most convincing and address only those.
Those are the claims that matter.

Debates artificially give equal time to two sides, falsely elevating creationist trivia to equality with scientific substance.

Again-- Old Man vs Student throws this off balance. If anything, it degrades the Creationist appropriately. Creationism can be refuted by a high school/undergrad/grad student, so a kid deals with it.

The debates are often used to recruit members to fundamentalist Christian organizations.

They use barbecues to recruit people too, but Im not going to stop grilling. But once again, a Professional agreeing to debate a student does not put Creationism or its proponents in a good light.

I dont think kids have anything to lose by debating a Creationist. I say they should go for it.

Tuesday, July 24, 2007

Evolution and Infectious Diseases

The National Academy of Sciences has a sweet online resource up on Evolution and Infectious Diseases! Including pages, videos, and games for E/C hot topics: antibacterial resistance, HIV, and malaria!

I have a few problems with the HIV video-- all the viral components just sorta 'appear' at the right spot, but its an understandable simplification. But they did great on some little things, like they got reverse transcription right! So I am happy :)

(Hat tip to NCSE)

Monday, July 23, 2007


Well-- All is silent on the ID front. This is good news for you all, bad news for them.

Im working on a 'Game Over' post for Dear Behe. We're talking a cliche 'Go Directly to Jail. Do Not Pass Go. Do Not Collect $200." post. Were talking "In the end, there can be only one, and that 'one' is totally not you, Dude" post. Its iron tight-- Behe made a fatal mistake in that WORLD quote, and well, I want to be Darwins pit bull, so Im going in for the kill.

That means Im actually trying on it, citing sources properly, and trying not to type like a 14 year old gamer. I really want the Panda Overlords to let me post it over there. Next week Im taking a vacation to *home* home, and that post is going to be my project (unless Behe repents between now and then).

So a few fun things-- Speaking of Darwins Pit Bull, Chad Orzel has the cutest friggen pup EVER!

Dawkins has a new documentary coming out. Cant wait to download the torrent :P

Im Deanna Troi:

Your results:
You are Deanna Troi

>Deanna Troi
James T. Kirk (Captain)
Jean-Luc Picard
Beverly Crusher
Will Riker
Geordi LaForge
Leonard McCoy (Bones)
Mr. Sulu
Mr. Scott
An Expendable Character (Redshirt)
You are a caring and loving individual.
You understand people's emotions and
you are able to comfort and counsel them. ">">
Click here to take the Star Trek Personality Test

Im like PZ, except worse. Probably because Im in Generation ME!

You are 85% Rational, 28% Extroverted, 0% Brutal, and 100% Arrogant.

You are the Haughty Intellectual. You are a very rational person, emphasizing logic over emotion, and you are also rather arrogant and self-aggrandizing. You probably think of yourself as an intellectual, and you would like everyone to know it. Not only that, but you also tend to look down on others, thinking yourself better than them. You could possibly have an unhealthy obsession with yourself as well, thus causing everyone to hate you for being such an elitist twat. On top of all that, you are also introverted and gentle. This means that you are just a quiet thinker who wants fame and recognition, in all likelihood. Like so many countless pseudo-intellectuals swarming around vacuous internet forums to discuss worthless political issues, your kind is a scourge upon humanity, blathering and blathering on and on about all kinds of boring crap. If your personality could be sculpted, the resulting piece would be Rodin's "The Thinker"--although I am absolutely positive that you are not nearly as muscular or naked as that statue. Rather lacking in emotion, introspective, gentle, and arrogant, you are most certainly a Haughty Intellectual! And, most likely, you will never achieve the recognition or fame you so desire! But no worries!

To put it less negatively:

1. You are more RATIONAL than intuitive.

2. You are more INTROVERTED than extroverted.

3. You are more GENTLE than brutal.

4. You are more ARROGANT than humble.

Sunday, July 22, 2007

ID vs ERVs-- Part Fourteen: Harun Yomama

With all the press Harun Yahya has been getting recently with their 'Atlas of Creation', I thought now would be an appropriate time to write a post on Islamic Creationists view of endogenous retroviruses.

Minor problem.

Tried "endogenous retrovirus", "ERV", "retroelement", "transposon", "mobile element", "LINE", "SINE", "Alu"... BINGO!

In fact, one of the best-known pseudogene groups, Alu, had always been regarded as functionless and was only recently proved to serve a purpose after all.
**YAWN!** So Alus arent ERVs, but the same logic applies. One, Alus are associated with disease, not just 'good' magic deity things, and two, Harunalakkahikki hasnt addressed the principle of Alus and evolution.

Alu sequences in primates form a fossil record that is relatively easy to decipher because Alu sequence insertion events have a characteristic signature that is both easy to read and faithfully recorded in the genome from generation to generation. The study of Alu sequences thus reveals details of ancestry because individuals will only share a particular Alu sequence insertion if they have a common sexual ancestor.

Hmmm. This is pretty anti-climactic. Ah well, you can head over to Taner Edis's page to learn more about Islamic Creationism!

Thursday, July 19, 2007

Micheal Behe: Im calling you out.

Yeah, I know he doesnt read this blog. I know ID Creationists (Creationists in general) appear not to know this blog exists, if my troll traffic is any indication.

But I cannot ignore Behes continually baffling assertions about HIV.

Hes doing it again.

WORLD: You write that "HIV has killed millions of people, fended off the human immune system, and become resistant to whatever drug humanity could throw at it. Yet through all that, there have been no significant basic biochemical changes in the virus at all." Why is that significant in the debate over Darwin?

BEHE: Like malaria, HIV is a microbe that occurs in astronomical numbers. What's more, its mutation rate is 10,000 times greater than that of most other organisms. So in just the past few decades HIV has actually undergone more of certain kinds of mutations than all cells have endured since the beginning of the world. Yet all those mutations, while medically important, have changed the functioning virus very little. It still has the same number of genes that work in the same way. There is no new molecular machinery. If we see that Darwin's mechanism can only do so little even when given its best opportunities, we can decisively conclude that random mutation did not build the machinery of life.

Behe, here are my questions:
  • What do you want HIV to do?
  • What would constitute a 'change in functioning'?
  • What would constitute 'new molecular machinery'?
I have offered counter examples to both of the latter, limp-wristed statements.

And though Ive sworn off low hanging fruit-- If a professional respected Creationist like Behe wants to give me an easy target, Ill happily snatch it:
Yet all those mutations, while medically important, have changed the functioning virus very little. It still has the same number of genes that work in the same way.
Lets pretend HIV is 'hasnt changed'-- Behe just said 'If humans evolved from monkeys, why there still be monkeys?' 'If HIV mutates so much, how come it aint evolved into a cat yet?'

Ahh its Creationism, not HIV, that hasnt evolved any new tricks in the past 30 years.

Wednesday, July 18, 2007

I have the best readers :)

I woke up this morning to emails and messages from awesome readers who wanted me to know Michael Vick is being indited. A week ago I was too furious for words, as people were reporting that 'indictment was unlikely.' Now Ive got a little hope that the puppies he abused, tortured, and killed will receive some justice. Will any punishment he faces be enough for me? No. Im not sure what would satisfy me-- I picture Arnie in those rings, those fights you all are seeing on the news now. I see the massive scars on his legs and wonder how much pain he was in...

But my hopes are still slim. People simply dont give a rats ass about pit bulls.

Tuesday, July 17, 2007

I get e-mail-- Tard Edition

In honor of Razib's hysterical IslamoCreationistTrollBot invasion, I thought you all might enjoy some of the emails I got when I had the little ones on PetFinder.

From Stone Wang--

My name is Stone,I saw your classified advert Pet on petfinder classified website and i'm interested in Adoption of your pet.

From diana john--
Good Day
My Name is Diana Jackson I'M FROM {New york } from South Ozone Park City USA .This is jUST TO GET YOU INFORM that am interested in buying your pet that you place on advert on the internet YOU PLAcE THAT YOU NEED TO GET IT SOLD WELL i want to know if the pet is in good condition becasuse i want to buy IT for my daugther SHE JUst LOST HER FORMER PET and she's not happy at home she felt lonely all the times and THAT not good enough I KNOW SHE NEED SOMETHING TO KEEP HER COMPANY SO I DECIDED TO get her a pet so that she can be happy again i want to know tha final asking price , including MORE pictures OF THE PET if available ,you dont have be get worried about the shipping because i have a shipping company from (Picayune MS) that always do pick up for me ,i hope this transaction is ok by you and i want to hear from you as soon as you receive this message so will be willing to hear Good respond from you soon.Thanks and have a blessed Day
Best Regards
Mrs Diana

From jame bobby--
i want to have your pet to my lovely home.........
Hello Dear Sir / Madam,

Good to meet you, My name is jame, I saw your posted ads in for adoption of your pet online and immediately I got so fascinated about having the pet. I am an honest, caring man with the utmost fear of God. Having the pet is like owning a fortune and the thought of it makes my vein leap for joy because i really Love pets.

I will like you to foward to me the Last cost Price so as i can make payment sent to you as soon as possible.I will have a Reputable Pet Pick-up Company come for the Pick-Up as soon as the Payment is Cleared from the Bank. I will email you the Pet Pick-up Company's Email address when you got the payment for the pet.

Payment would be in-terms of MONEY ORDER or CERTIFIED CHECK. So I will prefer you email me back as soon as possible with your details to make the payment. Thanks


You cant use ERVs to support common descent. Not every organism has them.

Index to Common Creationist Claims about ERVs

On the one hand, Creationists accept the fact ERVs point to common descent. On the other hand, ERVs pointing towards common descent is unacceptable to Creationists. Thus the Siamese twin of "Common Descent is an Illusion" is born-- "You cant use ERVs to support common descent. Not every organism has them."

The claim I am referring to specifically states that ERVs do not exist outside of mammals. This is not true. ERVs have been found in marsupials, zebra fish, birds, snakes, toads ... Every vertebrate weve looked at has had ERVs.

Evolution only predicts that organisms susceptible to retroviral infection would have ERVs, and those ERVs would form a pattern of descent with modification. Thus far that prediction has held up.

Evolution didnt predict ERVs, so ERVs arent evidence for evolution.

Index to Common Creationist Claims about ERVs

This is probably the most pathetic Creationist Claim about ERVs. No, I did not make it up. Its right there in TrueOrigins 'Critique of +29 Evidences of Macroevolution '.

Evolution does not even predict the existence of ERVs, much less that they will be found at the same location in two or more species. After all, evolutionary theory was considered robust prior to the discovery of ERVs.
Evilution as Darwin knew it did not predict ERVs, specifically. Mostly because DNA, RNA, retroviruses, sequencing, etc etc etc werent discovered yet. Yes, the theory of evolution worked just fine before any of those things were discovered.

Whats important is that their discoveries supported natural selection and descent with modification, thus influenced modern evilutionary theory in a positive fashion (science, unlike dogma, is not static. this is a good thing).

Over and over and over, ERVs can be traced back to create a phylogenetic tree. ERVs and their components descend with modification over time. Sometimes these modifications lead to junk, sometimes they are coopted by their host, sometimes they become such an integral part of the host that it is almost impossible to tell the DNA is exogenous.

ERVs themselves werent predicted by Darwin, but what they do and how they behave was. Descent. Modification.

Saturday, July 14, 2007

Cute Puppies: A Resolution

To quote The Simpsons:

Homer: Marge, Im confused. Is this a happy ending, or a sad ending?
Marge: Its an ending. Thats enough.
The little ones still dont have homes. But the good people at BlueHAWK ** no-kill shelter have offered to take them in. There they are going to get fixed, get checked head-to-toe by a vet, get all their shots, get microchipped, and whoever wants to adopt them has to go through a screening process so the pups are NEVER picked up under similar circumstances again.

So, its not a 'happy ending' (loving home with a college kid who loves to run, or with a mom with two kids that love to play ball...), not a 'sad ending' (one group last night told me to take the brindle on a run at the park, give him a cheese burger, and put him down), but its an ending.

They will find a place. And theyll be taken care of in the mean time, surrounded by other playful dogs. Not a bad deal for two puppies who were starving and dying of thirst in 95 degree weather this time last week.

And it is a happy ending, on my end. I learned a valuable lesson, one that luckily didnt end traumatically, and Ive found a great organization I can volunteer for. Im going to help check out the homes of potential adoptors in the OKC area (make sure they have a fence, house isnt a dog-hazard-pig-sty, etc) and Ill help with adoption days at PetSmart! YAY!

So what little sanity I had this time last week has been crammed back into my head, and we will now return to our regular scheduled programming!


** If any of you folks have an extra $5 lying around (dont we all?), if you scroll down to the bottom of their page they have a PayPal donation button. I need to find a local computer genius to help them with their site layout.

Updated 9.45 PM, 7-14-07-- Blue is meeting a family tomorrow!!!!! FIVE kids to play with! PLEASE dont screw this up Blue-girl! PLEEEEEASE! I checked out mom/dads myspace and they ROCK! ('religion: other' WHOOOO! hehehe!) PLEASE be good, Blue! I want you to have a HOME!!!

Friday, July 13, 2007

Cute Puppies: The Saga Continues

Friday the 13th didnt totally suck for the little ones. Im at least getting help now.

The blue girl (we now call Sammy) has gotten some putative offers, but theyve fallen through in that either the people live in an area where pit mixes are banned, or the parents have been known to chain their dogs.

The brindle boy (whos name is Brutus), has stolen Arnies, the girl whos been helping me, and my heart. He is a DEAR. He knows how to work his eyes to get attention. We all want to keep him, but theres no way I can get another dog, and girl from work already has two...

But Ive found some rescue groups that are actually helping. Theyre helping find potential owners. Theyre doing background checks. One even offered to have their vet check the pups out (I realized I didnt even know if they had heart-worms-- mosquitoes have been unbelievable this year). Though I swear to David Bowie, if these damn dogs have heart-worms I will spontaneously explode.

Oh, and Ive been so stressed about this, my mono has come back. I thought relapses were an old-wives tale.

*sigh* But at least Im getting help. And Ive learned a valuable lesson: I cant do this on my own. This is, hands down, one of the stupidest things Ive ever done. I dont even have a friggen yard! So I have vowed, after I find these two a home, to volunteer with a local rescue center as an outlet for my 'save the puppies' urge, and to never do anything like this again until I have a yard/garage/anything.

Finding them a home has completely consumed my thoughts/actions lately. I promise to get back to science soon... sooner I find them a place, sooner I get back to science posts... just sayin... hehehehe!

Thursday, July 12, 2007

A step in the right direction!

Some of you might know that Im wanting to start a club this fall along the lines of 'Oklahoma Students for Science Education' (eh havent decided on a name) to help graduate/medical/nursing students learn how to present science/evolution/their research to laypeople. We got a new microbiology professor/student adviser this year, and I walked in on her, the retiring adviser, and a professor discussing how disgusted they were that people they graduated with (these are middle-aged ladies), PhDs in microbiology, could know nothing about evolution.

This will sound odd, but that was music to my ears!

I didnt want to interrupt, but I ventured that I was hoping to start a club in the fall, to which one professor bellowed "HAHA! An Intelligent Design club! HAHAHA!" hehehe So I think OSSE will be a well received idea, and I might be able to convince this new lady to be the academic adviser of my club! YAY!

Wednesday, July 11, 2007


I wonder if they offer this to non-Christians? Can any one find more details? Can I say I worship at the gym? Im an atheist, I worship myself, right? Does this cover travel to work for evilutionists? We worship Darwin? Hmmmmmmmmmm, the possibilities!

  • If the insured is involved in an auto accident while driving directly to or from a church service or other scheduled worship activity, the deductible is waived.
  • Medical limits are doubled if the insured is involved in an accident while driving non-family members directly to or from a church service or other scheduled worship activity.
  • Church tithing or donations (up to $750) are paid if the insured suffers a loss of income from a disability caused by any accident at the insured's residence.

Pit Bull vs Shark

Pit Bull won.

hehe Now where the hell am I supposed to get a replacement stuffed Mako Shark??

Lab lesson of the Day: Dont talk to the media

They (an AP article) just 'paraphrased' my boss and his collaborator as saying:

  • We're going to have an HIV vaccine, ready to go, in 4 years (not 'we' the scientific community as a whole, 'we' as in our labs)
  • Natural Killer cells make antibodies
  • We didnt understand the immune system until 5 years ago
To paraphrase them again, "dumbing down something thats dumbed down gives you something thats just wrong."

And who loves it when that happens? Creationists, Deniers, the Usual Suspects.

This is why I love science blogs-- its like a conversation. If I dont simplify a topic well enough, you can ask for more help understanding a topic. If you think a post is cool, you can ask for more details. If I say something that is flat out wrong (Natural Killer cells generate antibodies!) you can say "Whoa whoa ERV! Think youve got a typo, there! Or youre on crack."

Ugh, well, I better go back to work. I gotta solve the problem of HIV vaccines in 4 years :P Go read Taras posts on scientists communicating with journalists.

Monday, July 09, 2007

Oooooh have I got a dog story for you all.

As I mentioned before, Sunday I found two starving pups. One is a boxer, one is a great dane.

The boxer had tags, so I was like "Sweet! Get him home, itll be easy to find baby Dane a home, YAY!"

Oh no. Nothing is ever that easy. Called the vet this morning "Oh yeah! Is that a striped boxer? 2 years old? His name is Scrappy! Heres his owners phone number!"
Me "YAY!"
Call the dude "Uuuuuuuh.... That aint my dog."
Me: "Umm... Well, he fits the description from the vet."
Him: "That aint my dog. My dogs in the backyard."
Me: "......."
Him: "Umm, can I get my tags back?"
Me: *click*

Stupid bastard dumped his dog and was too stupid to take off the tags. I would turn him in to animal control, but Id have to give them the puppy, and theyd put him down as a 'surrendered pet.' *sigh*

So I put a message up on the campus message board "FREE Great Dane Puppy" "FREE Boxer Puppy".
Someone called back immediately interested in the boxer for her sons (9 and 13 years old- perfect!).
30 minutes later, someone called from Dallas wanting the Dane, and others at work wanted the Dane too.


*sigh* The woman interested in the boxer didnt show up this afternoon after work like she said she would. Called the Dallas lady back, she cant pick up the Dane until the end of July-- I cant keep them that long, cause Ive got Arnie Puppy already.


On the bright side, a local no-kill shelter Free to Live and a local Boxer rescue group have been great. If I cant find a place for them soon, they have somewhere to go.

Im so sad... Ive got to stop doing this to myself. But then I see this:

Sunday, July 08, 2007

Creationist Research Abstracts

Sorry, didnt get to write as much as I planned today... I found two more starved puppies this morning... yeah you know how I deal with that...

hehehe I think it will be okay-- I spent the afternoon sobbing to shelters, and I think I found their veterinarians :) Lesson of the day: put tags on your puppies!! Even if its just your vets Rabies shot tag, even if theyre just playing in the back yard. Jesus the Great Dane puppy I found must have cost a fortune. *sigh*

Though I have had time to play on the internet a bit, searching for Creationist Claims about ERVs, and I think I found yet another reason why Creationists dont publish their own research papers (outside of not, you know, doing any research in the first place):


A review of the structure, function, and role of viruses in ecology is presented. It is concluded that viruses are non-living entities, similar to seeds and spores whose functions include carrying genes from one plant or animal to another. Viruses are a part of a system that helps to produce the variety that is critical for life and, importantly, they carry resistance to disease from one organism to another. Most viruses live in their host without causing problems. Pathogenesis is evidence of something gone wrong, a mutation or the accidental movement of genes, and not evidence of a system deliberately designed to cause human disease and suffering.
Even though Im in a bad mood because of the starved pups, and Im no expert on scientific writing myself, I literally laughed out loud hard when I read that abstract. For a while. Arnie jumped off the bed because my laughing was shaking it and nausing him out.

If a middle school student at a science camp turned in that abstract I would be pretty proud of them. But that was written by an adult-- supposedly with scientific training.

"It is concluded..."


heeeeeeeeeeeeeeeeeeeeheheheheheheheheheeeee! AWESOME!

Saturday, July 07, 2007

ERVs are a 'vaccine code'.

Index to Common Creationist Claims about ERVs

This is a specific 'ERVs are functional' subclaim-- That ERVs are somehow 'built in vaccines' placed into genomes by the Designer. Ive seen the following paper used as evidence to support this claim:

Late viral interference induced by transdominant Gag of an endogenous retrovirus

This claim also suffers from the same misapplication of inductive reasoning as its parent claim. A part of an ERV can be a helpful defense against a related exogenous virus means ALL ERVs are 'vaccines'. Yes, parts of endogenous retroviruses that are still active can interfere with infection with related exogenous retroviruses-- Both of those papers involve a virus that has exogenous and endogenous versions (enJSRV vs JSRV). This paper (and related papers) do not hypothsize that every ERV has an antiviral function.

With good reason.

Any ERV proteins that are expressed as your immune system is developing are recognized as 'self'. If a T-cell or a B-cell recognizes this viral protein as 'self', it is killed. Sometimes this can lead to an enhanced infection from exogenous retroviruses, even bacteria, because entire branches of your immune system are killed off!

ERVs are not specially designed 'vaccines.'

I shouldnt breathe right now...

... Im afraid fire will come out.

1. I went to see Sicko. I didnt learn anything new, except that things havent changed since I was a pre-med, and my 'respect' for physicians in the US somehow got even lower. That being said, everyone should go see it. Now. Look, go see Sicko, then go see Harry Potter to cheer yourself back up again.

2. This asshole. So, he could have had a child-porn ring run out of one of his homes, but if he said 'DEEEEERP! I didnt know about it!" he wouldnt have been indited? Why do I find that hard to believe? Why am I not shocked no one gives a shit about 'mean dogs' getting tortured and killed?

3. This asshole. I know I joke about CNN inviting me on one of their programs, but I can wholeheartedly assure them that me + Creationist talking about 'morality' would be a good show. You know how Dawkins kinda tweaked on Haggard during 'Root of All Evil' when Haggard said 'evilution is random'? 'Evilution leads to immorality' is my tweak issue. Its like Marty McFly and 'chicken'.

Friday, July 06, 2007

Mom wants me to marry a doctor...

And Im totally cool with that.
Home on the Strange

New season of 'Dr. Who' starts tonight on SciFi... and my computer (ie my TV) is still in pieces (though they did finally ship the new motherboard). I do have another TV, a rickety one from 1985-ish, but its so old it doesnt get digital channels (anything above Basic Cable).

Sooooo I have to wait another week to catch the re-run. Boo.

HIV: Keeps getting more impossible-er

Im going to pretend to act shocked that no one, including Behe, cares to elaborate on his claims that HIV has evolved ' no protein binding sites — neither short linear peptide motifs nor any other — developed in a hundred billion billion (10 20) malarial cells. Or in HIV.' Or his original 'there have been no significant basic biochemical changes in the virus {HIV} at all.'

I gave one example to the contrary, HIVs vif gene, which figured out (sorry, personifying a virus) how to hijack humans anti-retroviral APOBEC protein for HIVs advantage.

Due to the loose language of his claim, the vif example does leave Behe wiggle room. How about something that goes above and beyond The Blessed Malaria argument? How about a 5 amino acid insertion (not just mutation from one amino acid to another) that changes a vital HIV structure? An insertion that alters a dTTP binding site?

Uh oh!!

Evolution of a novel 5-amino-acid insertion in the β3–β4 loop of HIV-1 reverse transcriptase

Reverse Transcriptase (RT) is the HIV protein that turns its RNA genome into DNA so it can be inserted into your genome. It is the target for anti-retrovirals like AZT. Now, mutations in RT to compensate for the presence of RT-inhibitors are common, and the most 'popular' mutations are well documented. Change an amino acid here, change an amino acid there, HIV becomes resistant to one drug or another (yes, weve even characterized mutational pathways to resistance, much to Behes dismay).

This particular insertion is completely novel to us, and the researchers wanted to know what kind of impact it had on viral fitness and resistance to RT-inhibitors. When they generated a virus identical to the ones with the insertion, but missing the insertion, the one with the insertion was only 3 times as resistant to RT-inhibitors. It doesnt appear to be that big of a deal... until you add a high concentration of RT-inhibitors. Suddenly, 3 times more fit becomes a huge advantage.

And of course, HIV kept evolving in this patient after the insertion. Completely new (seriously, havent seen these before) mutational pathways stepped up to increase the fitness of the RT resistant HIV even further. In ~10 days, HIV viruses with the 5 aa insertion went from making up 5% of the patients quasispecies to 20% of the quasispecies.

In sample 4A only 1 out of the 20 clones (5%) contained the insertion, while sample 4B revealed that 20% of the viral population harboured the insertion (4/20 clones). {Sample 4a collected at ~Day 235, 4B ~Day 245. ERV}
Oh dear. Not only did this real world HIV example exhibit a 'significant biochemical change', it did another Creationist Impossibility: virus went down a fitness valley (drug resistant HIV is usually less fit than wild type HIV, this example was no exception) to reach a higher fitness peak (drug resistant and a higher replicative capacity)*.

I bet theyre wrong, though. Im sure Behe is right.

* Now you and I know that in a real fitness landscape, down isnt always down and up isnt always up, and time is always a dimension, but we're talking about Creationist World and Creationist Fitness Landscapes. This is only a Creationist Impossibility, not an Evilutionary Impossibility.

Thursday, July 05, 2007

Non-functional/Harmful ERVs are _________.

Index to Common Creationist Claims about ERVs

If you know the appropriate response to 'ERVs are functional' you will undoubtedly see its Siamese Twin Creationist Claim: 'Non-functional/Harmful ERVs are _________.'

The blank can be a variety of things.

  • The result of The Fall.
  • The result of The Flood.
  • They used to be useful, but arent needed anymore.
  • They have some hidden use that scientists havent found yet (such as a 'built in vaccine'- which will be covered later).
  • They are tricks embedded by their god to test His Creation.
  • The ever useful 'we cannot know the Designers thoughts'.
  • Conserved non-functional DNA is evidence for a Young Earth, etc.
This Creationist Claim is always in response to the 'ERVs are functional' refutation. Ignoring the philosophical and logical problems with 'answers' like "ERVs are a test!" these claims are ad hoc non-answers-- They do not address the discord between ERVs and Special Creation (common descent, domesticating exogenous genes, etc.), or why this discord does not exist between ERVs and evilution.

If you encounter a ________ youre not sure how to address, please leave a comment!

Wednesday, July 04, 2007

Happiness is a long run

Blogging for a common 'good'

I consider TR Gregory a teammate-in-blogging for a common good: scientific literacy. Now he wants some help with something a little different. I think I (and you all) can help him out there too!

Gregory doesnt know this, but I have personal reasons for wanting to help his parents out: My patients are from Zambia.

IRB/HIPPA/etc prevents me from 'tracking down' any of the children I am studying, but Ive personified one patient in particular: Hes about 9-10 years old, infected with HIV in the womb, and hes still doing okay. At least, he was the last time I got to hear anything about it. He is very unusual, as most children infected in the womb die shortly after birth. His plasma samples might help cure millions of children not as lucky, and he'll never know it, and Ill never know him.

This has always bothered me. But theres nothing I can really do.

BUT maybe hes one of the kids that will benefit from Gregorys parents program. Ill see what I can do with campus (we always have surplus equipment strewn about the hallways) and with my classmates (Im going to try to start a student science education group this fall).

I, as usual, also have a pro-atheist reason for trying to help his parents project:

The Livingstone Performing Arts Foundation (LiPAF) mission is to create and perform traditional and original works of music, song and dance which reflect the history, culture, languages and ethnic background of Zambia.
I. Hate. Missionaries.

Hate. Them.

Its not just the evil lies they tell regarding condoms and such-- theyre committing cultural genocide. They dont even know the names of the gods they are killing.

"WAIT, ERV!" you readers might exclaim. "I thought you hated allllll gods! Youre just against Christianity! I KNEW IT!"
Well, most of you readers are smarter than that, but some readers might think this. I am not against cultural mythology, against honoring your heritage. I like my Jewish heritage. I like my British heritage. I like my Russian heritage. I cant imagine what it would feel like to have your heritage killed off-- to never know your ancestors myths. And, as Im sure some of you noticed in my Blogger profile, I list Ancient Greek Mythology as my favorite literature-- I dont have to believe in the gods to love the stories.

How many of you can name a Zambian deity? How many of you can tell me a Zambian myth?

If the missionaries win there, you will never hear their stories either. His parents might help save the best story you havent heard yet.

I cant promise Ill help personally tomorrow-- but thank you, Gregory, for putting this project on my radar :)

ERVs are functional.

Index to Common Creationist Claims about ERVs

As a defense against the argument that 'junk DNA', including nonfunctional ERVs, is evidence against their choice* of 'Designer', Creationists insist that ERVs are functional.

There is a very big difference between a functional ERV, and a functional component of an ERV. Creationists do not understand this (specific example here)

Yes, we have found a retroviral env that has been co-opted by mammals. Yes, somewhere around 100 human proteins might have evolved from co-opted gag proteins. Yes, we can find retroviral transcripts floating about cells, sometimes. But these are not examples of ERV functionality. They examples of evolution in action-- the host organism salvaging ERV parts for its own use.

Complete ERVs are recombined, mutated, and methylated into junk. When they regain some semblance of functionality, they cause disease! Which is no surprise, as exogenous retroviruses like HIV and HTLV cause AIDS, leukaemia, lymphomas, and various other autoimmune diseases.

ERVs specific to humans, called HERVs, have been tied to multiple cancers, including germ-cell tumors, breast cancer, seminomas, melanoma, ovarian cancer... And autoimmune diseases like multiple sclerosis, rheumatoid arthritis, psoriasis, and lupus (please see this source for more information).

These are just the human-specific ERVs. We have lots more.

DISCLAIMER-- Currently, ERV->disease research is very new, as are the methods we use for studying why they become active (epigenetics). 'Functional' ERVs might be the cause of disease, the effect of disease, or both (the effect, but perpetuates the disease, what I think is going on with ERVs and cancer).

But one thing is certain thus far-- You do not want ERVs to be functional.

* This argument is inappropriate when discussing 'design' with polytheists, deists, or those who believe in a malicious deity. I believe it is also incompatible with theistic evolution. This stance only applies to Creationists.

Monday, July 02, 2007

Creationists Predicted ERV Functionality.

Index to Common Creationist Claims about ERVs

There will be several more posts on ERV 'junk'/'function'/etc, however a main Common Creationist Claim about ERVs is that they predicted ERV functionality before Evilutionists. Evilutionists refused to study ERVs because they are 'junk.'

Parts of ERVs are functional. For instance, the env gene of specific endogenous retroviruses has been co-opted by mammals to form placentas (I elaborate here). Also, endogenous viruses carry genes with them called LTRs. This is how an exogenous virus like HIV uses an LTR-- but when the virus becomes endogenous, the LTR can act as a promoter for endogenous genes, either up or downstream. This paper has a humorous, but accurate name for this: "domesticated long terminal repeats".

Evilutionists did this research, not Creationists. Evilutionists predicted functionality in non-coding regions, not Creationists (see MarkHs post at Denialismblog). ERVs and host co-opting and pirating ERV parts is a prediction made by evilution, not Creationism.

Sunday, July 01, 2007

Retroviral Insertion is not Random. Common Descent is an Illusion.

Index to Common Creationist Claims about ERVs

Ive always said, if Darwin and Wallace decided to open a resort and spa in Cuba instead of going into science, if every fossil was still hidden-- The second we found ERVs, common descent would have smacked us in the head like a sack full of doorknobs.

You can play connect-the-dots with ERVs to draw phylogenetic tress, like they did here (okay, a little more complex than connect-the-dots hehe!)

So the logical claim from Creationists is that this apparent common descent isnt real. Retroviruses (and mobile elements) could have inserted themselves in chimpanzees and humans independently, and we cant prove otherwise.

Here are two papers that Ive seen Creationists use in support of this claim.

You can probably figure out from the paper titles why Creationists latched onto these two. 'Site Preferences'? 'Hot Spots'? Insertion isnt random, therefor apparent common descent is an illusion!

Unfortunately if they had, you know, read the papers they referenced, they would know that the papers do not support that conclusion, and do not contradict the usage of mobile elements as phylogenetic markers.

The first paper simply states that some retroviruses like to insert in genes, some like to insert near promoters of genes, and some like to insert in the middle of no where. The specific insertion sites, what base pairs on on the left, which ones are on the right, is random. Thats exactly what they looked for in that papers methods.
Look at Figure 1: All those blue lollipops are places they found where HIV inserted itself.

Theres a lot more than one lollipop in that figure. The Creationist Claim is wrong.

The second paper gives them a quote to pirate, and while the statement is true, its not true in the way Creationists want it to be.
The presence of a retrotransposon at a single locus in multiple taxa remains an extremely powerful phylogenetic marker, but caution is required before concluding that the existence of a particular SINE at a particular locus in multiple individuals is indicative of common ancestry.
These researchers found two independent SINE insertions in deer mice. They could tell the insertions apart. So their caution was for geneticists making phylogenetic trees-- look closely at your SINEs to make sure they are really related, and not independent events. Something they should be doing anyway, but its nice to know that you might find independent insertions while you are double checking it.

Their conclusion is that retroelements are just dandy for phylogenetic analysis. Again, this Creationist Claim is wrong.

Index to Common Creationist Claims about ERVs

Sure Ive had a lot of *fun* with the ID vs ERV series, but I think it would be more helpful to have a Talk Origins-esque list of Common Creationists claims regarding endogenous retroviruses. Every time I write/find a new one, Ill link the post here.

A nice, reasonable, sane post on Fr*ming

TR Gregory at Genomicron has a fantastic post on fr*ming up! Kind of a relief to read it.

But he didnt address my problem with fr*ming either ;)