I'm a graduate student studying the molecular and biochemical evolution of HIV within patients and within populations. I also study epigenetic control of ERVs.
Yay! Going to get some new addition to 'Creationist Claims about ERVs', via this bucket of fail from Answers in Genesis:
The Natural History of Retroviruses-- Exogenization vs EndogenizationYou know, good for the YECs. Sure, that statement is demonstrably wrong, but you know what? At least they made a firm, testable prediction, and not the weird 'you will meet a tall dark man' predictions ID Creationists have been making since the failure of 'Darwins Black Box'.The best alternative explanation is that orthologous ERVs were created to occupy similar genomic loci in separate species by a single designer to carry out similar physiological functions.
If ERVs were created in the cell in the beginning, at least some exogenous retroviruses may have been derived from endogenous viruses when viral particles were released from the cell by budding--exogenization. While the ability to exit the host cell and transmit between individuals is designed, uncontrolled infection and deregulated insertion of retroviruses have caused much havoc in the post-Fall world.
Good on you, YECs.
But heres why theyre wrong.
Viruses, including retroviruses, including endogenous retroviruses, dont speak the same language as humans. Sure they use A, T/U, C, G nucleotides in codons, coding for amino acids that make proteins.
But viruses and humans dont speak this language with the same accent. Its called codon bias, or codon-pair bias.
Several codons can code for the same amino acid. For instance, GCU, GCC, GCA, GCG all code for Alanine. So, in the human genome, you would expect ~25% of all the Alanines to use GCU, ~25% to use GCC, ~25% to use GCA, and ~25% to use GCG, right? Nope. For some reason, the human genome prefers GCC over GCG. Four times as many Alanines are coded by GCC as GCG. Humans have a GCC 'accent'.
Viruses have their own codon 'accents' as well. And even though the differences should, theoretically, mean nothing (an Alanine is an Alanine is an Alanine), one way we can attenuate viruses to make better vaccines is to force them to use codons they dont like.
Thus one of the ways we know ERVs are a later addition to the human genome, and didnt originate in the human genome, is that retroviruses have a different codon 'accent' than humans. They dont fit. For example, if you were listening to a recording of Martin Luther King Jrs. 'I have a dream' speech, when suddenly you are accosted by ABBAs 'Dancing Queen, which would you think is more likely?
a-- ABBA was a later addition to MLKs speech when someone accidentally recorded over the original speech.Obviously, A. 'Dancing Queen', while in English, the same language MLK was speaking, has a different accent, different cadence, different tone, than MLKs speech. We know one didnt come from the other. They were two independent recordings mushed together.b-- ABBA stole 'Dancing Queen' from MLKs 'I have a dream' speech.
Human genome is like 'I have a dream'.
ERVs are like ABBA.
*wince*
Boy I did not think out this analogy before I started typing...
Life Science
Comments
"Boy I did not think out this analogy before I started typing..."
Ha! It was brilliant! :-)
Pdiff
Posted by: pdiff | October 6, 2009 11:08 AM
I like ABBA! :-(
Posted by: Naked Bunny with a Whip | October 6, 2009 11:24 AM
On the topic of off-the-cuff analogies, I totally came up with this one during a talk on different selection schemes:
"Positive selection schemes like phosphomannose isomerase are where a teacher encourages the more ambitious students to apply themselves. Negative selection schemes like antiobiotic-resistance are where the teacher executes the slackers."
I shall have to steal your King/ABBA visualization, though.
Posted by: Cody | October 6, 2009 11:24 AM
Mamma mia, there you go again.
By the way there is a flaw in your argument.
You make the assumption that the prefall function of the endogenous sequence was to produce protein. If it wasn't but was in fact some other imaginary function (say regulating the old age resistance genes in 900 year old garden of Eden inhabitants) then there is no need for codon bias!
Hey this creation science is great. You can make up all sorts of rubbish to get out of any awkward corner and never be wrong!
Posted by: Sigmund | October 6, 2009 11:28 AM
California Science Center about to be embarrassed
It's curious how the Creationists simultaneously hate science and try to pretend that they are science.
Posted by: Bayesian Bouffant, FCD | October 6, 2009 12:02 PM
Wait a second......
Abba and "I have a dream"?
http://www.youtube.com/watch?v=qFHbwikzNds
Posted by: Sigmund | October 6, 2009 12:13 PM
AAAAAAAAAAHAHAHAHAHAHA! You suck, Sigmund!
Posted by: ERV | October 6, 2009 12:20 PM
Noooooo! That damned ABBA song has started playing in my mind. It's like a viral infection!
Posted by: DrA | October 6, 2009 12:24 PM
"...and didnt didnt originate in the human genome..."
Ha! I have caught you! If they didn't didn't originate in the human genome, then that means that they DID originate in the human genome! I win! I have caught you in your silly materialistic, atheistic quest to... to do whatever it is that a materialist atheist does!
Posted by: sksfreund | October 6, 2009 1:51 PM
Okay, thats it, Sigmund, sksfreund, BANNED! ALL OF YOU ARE BANNED!
THERE WILL BE NO QUESTIONING OF ERV ON ERV, and ESPECIALLY NO PROOF-READING!!!
*throws a table*
LOL!
Posted by: ERV | October 6, 2009 2:08 PM
Seriously, do these people worship Rube Goldberg, or what?
Posted by: Optimus Primate | October 6, 2009 2:51 PM
What an education you can get on these threads. Alanine accents. Sounds like furniture or, as Dave Barry would say, a good name for a rock band.
Any studies to determine if the human accent/bias, has a tolerance? And if so, how far from some theoretical mean can you go before there's a 'problem'?
Posted by: MikeMa | October 6, 2009 3:36 PM
Thus is demonstrated the power of a single-codon mutation.
Posted by: D. C. Sessions | October 6, 2009 3:58 PM
Table Dancing Queen:
Weegee-ah you go girl! Thats the spirit. Its all in the charts.
Posted by: Rrr | October 6, 2009 4:31 PM
. . . What's wrong with ABBA?
But, I like the accent explanation. Makes things make sense.
Posted by: Seabhag | October 6, 2009 4:37 PM
Abby,
Isn't there is a consensus now that homologous proteins *do* have an effect, in that they take a different amount of time for the Ribosome to process the codon, giving the protein WIP a chance to fold differently?
Perhaps virii somehow take advantage of this delayed processing behavior to fold their proteins, and that's why changing the homologs causes attenuated viruses? Or maybe changing the timing of the various proteins causes an unbalanced number to be produced, limiting reproduction?
Posted by: Richard Hendricks | October 6, 2009 5:21 PM
I would subscribe to the time travelling MLK theory stealing off Abba.
http://www.youtube.com/watch?v=I0F4iXEzOqY
Posted by: BathTub | October 6, 2009 6:32 PM
Henceforth you shall be known as ABBA Smith.
Posted by: Brian | October 6, 2009 9:58 PM
that AAAS abstract on attenuating polio viruses was interesting, but i don't have access to the full text. did they go into any details on why or how this technique weakens a virus? because i'm a know-nothing about genetics and can't figure out any reason why it should, but i'd love to learn.
Posted by: Nomen Nescio | October 7, 2009 12:44 AM
YOU ARE ALL NOW HEARING THE SONG "THE FINAL COUNTDOWN" IN YOUR HEADS!
Posted by: Paul Lundgren | October 7, 2009 1:14 AM
Nomen,
They don't directly talk about why and how, instead they reference this free paper
http://nar.oxfordjournals.org/cgi/content/full/34/3/1015?ijkey=932d2cb000280d13176649305df2186443458d93
Posted by: Richard Hendricks | October 7, 2009 11:31 AM
Paul Lundgren is History's Greatest Monster. His work in disseminating toxic earworms has sent literally handfuls of people into irrevocable madness.
*hums "The Final Countdown"* Damn you, Paul Lundgren, Damn you!
Posted by: stogoe | October 7, 2009 1:17 PM
Geezerhood to the rescue, Squirt! I wouldn't recognize it if I heard it.
Posted by: D. C. Sessions | October 7, 2009 2:41 PM
If ERV's were created before the fall then they should be in "the most limited number of mutations incarnation" within the semi divine bodies of the Elohim and giants of the old testament.
Although I don't know where you would find an Elohim I understand most of the National Basketball Association proffers genetic samples.*
So get thee Abbie, to the Ritz Carlton with luminol!
*Even when hotel management begs them not to do so.
Posted by: Prometheus | October 7, 2009 2:56 PM
Love the post, ERV! Some great literature out there about the effects of codon bias.
One known effect is that silent mutations may not be so silent. If you use an infrequent codon, you can delay translation long enough to promote a folding variation! (some cool data goes with this, too)....
The idea of the same polypeptide having different functions through different fold isoforms because of folding kinetics is pretty swanky.
/geek
Posted by: Jason | October 7, 2009 3:33 PM
Nice of you to give the IDiots a little credit for making a prediction.
Now, if only they could wrap their little minds around that pesky part of doing science....
...admitting they are wrong when the data doesn't fit the hypothesis.
Posted by: FastLane | October 7, 2009 3:50 PM
In my defense, ABBA Smith was the one who brought much-maligned Swedish bands into the analogy, I just took it to a lower level.
Just be glad I didn't expand my knowledge of hair metal by throwing out "Wait" by White Lion. Or "Unskinny Bop" by Poison.
(Did I mention "Let's get rocked" by Def Leppard?)
Posted by: Paul Lundgren | October 8, 2009 12:55 PM
Are you refuting the claim that:
1) ERVs were part of the original genome or
2) ERVs were initially beneficial viruses which became incorporated into the genome early on after creation?
These two are similar but not exactly the same so just wondering...
Posted by: carl | October 15, 2009 3:46 PM
Carl. Both claims are wrong, even on the aig nutjobs' terms:
1) because if ervs were part of the genome before the fall, they'd have no deleterious effect as there was no illness. Then the tards would have to argue for a materialist link between humans eating fruit and ervs altered genetic function.
2) just asserts that the creation wasn't perfect and needed tweaking. Do they think their god fucked up creation v1.0 and made virii to patch it?
In real terms, well, read the OP bits about codon accents.
Posted by: eddie | October 17, 2009 10:45 PM
LOVE the "codon bias as accent" analogy! I am totally going to use that!
Posted by: Cath@VWXYNot? | November 2, 2009 3:29 PM