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.


Tyler DiPietro said...

Excellent work! This is why we read and love you.

Apropos to the topic, I have noticed that the general quality of creationist quote-mining has gone downhill big-time as of late. Often times their cites are so easily corrected that it's laughable. Perhaps they see the writing on the wall and are grasping at straws, or perhaps things have just gotten so much easier where we have an extensive blogosphere of experts who are ready to debunk 24/7.

Hume's Ghost said...

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!

I remember I was hammering on a fence in the backyard when Dad approached. He was carrying a letter or something in his hand, and he looked worried.

I continued to hammer as he came toward me. "Son," he said, "why are you hammering on that fence? It already has plenty of nails in it."

"Oh, I'm not using nails," I replied. "I'm just hammering." With that, I returned to my hammering.

Dad asked me to stop hammering, as he had some news. I did stop hammering, but first I got a couple more hammers in, and this seemed to make Dad mad.

"I said, stop hammering!" he yelled.

I think he felt bad for yelling at me, especially since it looked like he had bad news. "Look," he said, "you can hammer later, but first-"

Well, I didn't even wait to hear the rest. As soon as I heard "You can hammer," that's what I started doing. Hammering away, happy as an old hammer dog.

Dad tried to physically stop me from hammering by inserting a small log of some sort between my hammer and the fence. But I just kept on hammering, 'cause that's the way I am when I get that hammer going. Then, he just grabbed my arm and made me stop.

"I'm afraid I have some news for you," he said.

I swear, what I did next was not hammering. I was just letting the hammer swing lazily at arm's length, and maybe it tapped the fence once or twice, but that's all. That apparently didn't make any difference whatsoever to Dad, because he just grabbed my hammer out of my hand and flung it across the field.

And when I saw my hammer flying helplessly through the air like that, I just couldn't take it. I burst out crying, I admit it. And I ran to the house, as fast as my legs could take me.

"Son, come back!" yelled Dad. "What about your hammer?!"

But I could not have cared less about hammering at that point. I ran into the house and flung myself onto my bed, pounding the bed with my fists. I pounded and pounded, until finally, behind me, I heard a voice. "As long as you're pounding, why not use this?" I turned, and it was Dad, holding a brand-new solid-gold hammer.

I quickly wiped the tears from my eyes and ran to Dad's outstretched arms. But suddenly, he jumped out of the way, and I went sailing through the second-story window behind him.
- Jack Handey, Fuzzy Memories

Creationists are like that boy .... they can selectively hear "you can hammer" and start going on the attack against evolution.

ERV said...

Tyler-- Theyre quoting freely available papers. I dont understand what they think theyre doing.

And I think the science blog network is whats killing them. I dont have to be an expert on geology- someone else has that covered. You dont have to be an expert on astronomy- someone else has that covered.

On the other hand, Behe has to be a mathematician. Dembski has to be a biologist. They dont have each others backs. For gods sake they had to find a non-scientist commenter at UD to defend Behes book! Creationists Ive met in real life seem startled when I refuse to answer their physics questions as Im not a physicist, and neither are they. Team-work-- Lovin the science blogs :)

Hume-- ROFL! So true, with every Creationist Claim on ERVs!

Chris Noble said...

Tyler-- Theyre quoting freely available papers. I dont understand what they think theyre doing.

That's the baffling thing. You don't even have to be an expert in the field to read the paper and catch their misrepresentations.

It seems to me that they can't separate their misinterpretations from the findings of the paper. Children go through a stage where they can't comprehend that other people have a view different from their own. They project their ideas onto everyone.

Besides, they aren't attempting to convince scientists. Their target audience is unlikely to read the papers for themselves.

Torbjörn Larsson said...

That was a humedinger of a story! Since I can't be that funny, let me be boring, ehrm, serious, instead:

It seems to me that they can't separate their misinterpretations from the findings of the paper.

Mark Hoofnagle has posted an exposition about crankery and denialism as the Unified theory of the crank.

As we all know, a crank denialist probably belong to the group of incompetent people, persons who can't understand his/her incompetence, a verified phenomena. And as Mark points out, we also know that such persons can't understand competence either.

So I guess it is not surprising if these persons can't really understand a theory, a method or even a simple rational argument. It may be beyond their capacity to distinguish sanity from lunacy. In a very real sense, they could make shit up (from their own misunderstandings) and expects us to believe it too.

As for how it works out among the public, they will continue blissfully spouting their truthiness come rain or shine. The goal should be to remove their platforms (financially and politically). Science blogs showing which is science and which is crankery is helping.

Hugo said...

That is the explanation i was looking for. Thanks.

Can I post your texts on Youtube and a link to your blog and the
"blue lollypops" picture?

ERV said...

Please do!

Everything I write is open access, just cite me :)

Anonymous said...

HIV integrates randomly. Did the ancient retroviruses integrate randomly? Is there any evidence one way or the other?