Saturday, June 09, 2007

One Last Behe-Bile Post, I Swear!

I am so burnt out on fitness landscapes, but the UD-crew have finally, FINALLY gotten together a review of Marks review of Behes book. Its what we all already predicted, but I feel I need to quote this as even more evidence that I am psychic. Im going to get that Randi prize.

Davie was floored by magnans summary, which isnt surprising because he didnt know how to respond to Mark at all (outside of crying for his mother).

But here is my submission to the Randi Foundation:

ME: Okay, Ive gotta admit, Ive been royally confused at UDs response to Mark Chu-Carrolls review of Behes new book. That they would attack his 'credibility' and pretend thats a rebuttal of his arguments isnt confusing. Whats confusing is that theyre unimpressed with his mathematics credentials. Not his biology credentials. Math.
UD: Though not a biologist I found it interesting to try to evaluate some of his arguments. After all, he isn’t a biologist either but that doesn’t seem to have held him back.



Ahem. Also funny:
UD: The Edge of Evolution is quite evidently directed at nonscientist readers and is simplified accordingly, unfortunately glossing over the fine points. So Chu pounces on every relatively simplified description of evolutionary theory as an indication of Behe’s supposed ignorance and stupidity.
Well maybe you should have fr*med your argument better.


Okay, okay, the meat of the 'rebuttal'. First, as a disclaimer, I want to say it really is awesome when non-biologists take it upon themselves to learn about biology. I LOVE it! Thats one of the main reasons I blog-- to practice translating jargony sciency talk into nice practical terms laymen can understand, without dumbing it down. I really appreciate when physicists do that for me. I appreciate it when astronomers do that for me. I always appreciate someone taking the time to explain complex ideas to me, and I know they appreciate me trying to learn.
And, I absolutely commend magnan for sticking his/her neck out to defend his/her views, as he/she understands them. Good for him/her-- thats a great way to learn.

What I find despicable is that a random poster at UD, not a mathematician, not a biologist, has to defend Professional Creationists. Dembski could only caterwaul. Behe is being awkwardly silent against universal negative reviews of his book. So they let a UD commenter give it a go, and he/she naturally doesnt fare so well.

Lets add 'cowards' to the list of reasons why Professional Creationists are dross*, if its not already there.

*sigh* So it is with no pleasure I take the pawn in this game, but it is necessary.
Recombination mainly reshuffles alleles (different mutated versions of genes) during reproduction of sex cells in eukaryotic organisms.
Recombination doesnt only recombine alleles. You can chop out entire segments of chromosomes. You can duplicate huge chunks of chromosomes.
And once again, HIV is an excellent example against this statement: HIV can recombine 'sexually'. If you are infected with two kinds of HIV, Subtype A and Subtype G, some of your cells can get infected with both subtypes. HIV packages 2 copies of RNA/virus, so as the new viruses are budding off, some will get packaged with 1 A RNA and 1 G RNA. When that virus infects another cell, Reverse Transcriptase can hop back and forth between the RNA strands, creating a Subtype AG HIV.

And thats what happened.

Behe’s prime statistical example of the limits of Darwinian evolution with only random variation is the malaria parasite, and this is a protozoan eukaryote (plasmodium) in which meiotic recombination continually occurs. This example gives every advantage to random variations from all types of mutations and recombinational events in a huge population over millions of generations, but the limitations still applied.
And I gave an example of bacterial anti-biotic resistance, which doesnt even include recombination, with only one dimension, with more necessary mutations, that debunks Behes 'IMPOSSIBLE' claim.

Chu goes into a long diatribe over Behe’s use of the “fitness landscape” concept in his argument. It seems to me these criticisms are obfuscations and irrelevant to Behe’s thesis. However many dimensions of different interacting fitness functions, and however this “landscape” changes with time for a species, for any particular reproductive fitness function the species can still be trapped at a local maximum, unable to get across the “valley” to the next, higher peak without an extremely improbable giant leap.
No, magnan, read my post. Its not irrelevant. A 2D/3D/4D graph gives you a false impression of what peaks are actually high and what valleys really are 'impossible.' And you cannot under any circumstances ignore how landscapes change over time.
You cant ignore the fact that the fitness landscape in a recently HIV+ person is entirely different from the landscape after they are late into AIDS! An impossible valley at 3 months infection is an easy hop late in infection.
Behe is completely wrong about fitness landscapes, and he shouldnt have brought them up in the first place.

The reason for this is that the physical genetic loci coding for different fitness functions or factors are generally uncorrelated with each other. Usually they are not even in the same gene. No matter how many other varied genetic changes affect the phenotype in varied ways, certain specific mutational or other genetic changes are needed to make the jump from phenotype structure A to elaborated structure B in time T as evidenced by the fossil record. The probability of this occurring by accumulation of small random changes or by one giant (random) leap is a function of the total complexity of that particular genetic change, the likely presence of steps that are too deleterious to reproductive fitness to spread and fix in the population, and the number of generations. This is regardless of abstract models like the “fitness landscape”.
This is gobbledy gook, and if I was allowed to post at UD I would ask for a clarification. But I cant, so... Can anyone translate?
Im thinking he/she is trying to say the very opposite of what fitness landscapes tell us.
Fitness landscapes tell us that 'bad' mutations at a gene/biochemical level can be pulled along across a valley by other 'good' mutations because its the overall phenotype of the organism that is selected for. Not one individual variation of a gene. Its called network compensation.
It appears as if magnan is trying to say the phenotype doesnt matter, the mutations are impossible. And something about fossils. I dont know.

The malaria parasite drug resistance example (in addition to others) demonstrates these limitations in the living world, regardless of abstract models.
Fitness landscapes arent 'abstract models'. Our technology now allows for empirical testing of fitness landscapes 'in the living world'. Behe should know this.

*sigh* And thats it. Thats the best rebuttal ID Creationists can come up with.

One last funny:
This is just a rhetorical ploy and carefully avoids trying to apply it to explain any particular evolutionary development sequence.
Wait, wait, wait-- so, Mark is supposed to be a biologist AND a mathematician before he can critique Behe? If hes a mathematician, you win, if hes a biologist, we lose.
Look, this is science, magnan. We work in teams. No one can know everything. Mark took care of some math, some more of us took care of the biology, more people took care of more math, more people took care of even more biology... Have you seen the list?
We're a team.
We dont leave our friends and supporters by themselves and expect them to defend us while we suck our thumbs in our closets, like what UD did to you.

* Word of the day: Dross!


Dustin said...

HIV can swap genes? There's a subtle difference between that and irony, but the appropriate word for it is probably French or German, is 15 letters long, and comes from a literary movement that I've never heard of.

So I'll call it ironic.

Ian said...

So I took a look at the book at was worse than I had expected. He did talk about HIV, and I was curious about one statement: "Yet, through all that, there have been no significant basic biochemical changes in the virus at all". It took me a moment to figure that out ( much "biochemistry" is there in a virus?), but then I read the next paragraph and he asked why it was that some mutant hadn't found a better receptor, and mutated its way into another means of entering the cell. While it's been a long time since I've paid much attention to HIV, iirc, isn't its way into the cell one of its strong points? If so, why would anyone expect that finding an alternative pathway into the cell would provide an advantage? Sure, it would be an advantage in the case of people who are resistant to infection (something Behe talks about), BUT...there is no replication inside a resistant host, so there is no option for selection.

Dustin said...

isn't its way into the cell one of its strong points?

Once, while arguing with Kent Hovind in front of a church, he said to me "You can always kill a fly with a sledgehammer, and evolution can't fix that, so evolution is wrong".

It seems Behe thinks the same way. Lets hope he doesn't pay his taxes, either.

Dustin said...

Dude! I just had a bitchin' idea, inspired by the Blogosphere Behe War of 2007. Rather than calling something a "brouhaha", we'll call it a "Beheehee".

ERV said...

Oh. My. God.

BeheBile: "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."

Ian, Dustin, I will be addressing this in a new post. Oh. My. God.