Monday, June 04, 2007

Look Ma! No math!

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. And theyre desperately attempting to give Behe some ethos as a mathematician (eg '... there was more math in chemistry than in computer science.')

This is very, very odd to me.

My boss is a biochemist (BS and PhD). Everything I do is related to biochemistry even though I dont consider myself a biochemist. My boss and I use fitness landscapes.

Behe is a biochemist too. So, whats his excuse for screwing this up so badly? From my point of view this has nothing to do with 'math' at all.

If anything, I thought UD would go after Marks lack of biology credentials. I know that Dawkins WEASLE program (see Dysfunctional Analysis and Greedy Greedy Algorithms) and such use genetic algorithms and all sorts of fun math that are well beyond my Calc I capabilities... but if 'easier' biochemical (non-math) examples refute Behes statements, whats the point in damning someones mathematical credentials?

As I pointed out in a comment on PandasThumb, nothing I do regarding fitness landscapes requires high-level math. And its not just me-- let me go over a recent paper in Journal of Virology to give you all another example of how Behe is being extraordinarily silly (or maybe this is his normal level of silliness, meh.) Nothing in this paper goes beyond simple algebra and statistics (except for the math behind phylogenetic tree programs).

Fitness Landscape of Human Immunodeficiency Virus Type 1 Protease Quasispecies

I know all of you can read the abstract, even if you cant see the whole paper, so you know where Im going to go with this... but lets not play Creationist and say a paper supports our views just from what the abstract appears to say.

Okay, an essential protein to HIV is called 'protease'. Protease is an enzyme responsible for maturing new HIV viruses after they bud off of the host cell. If there wasnt a maturation step like this, there would be nothing preventing new viruses from turning around and infecting the host cell again (all the right receptors are right there). So this makes the protease enzyme a great target for anti-HIV drugs. Youve probably heard of 'protease inhibitors' before.

Unfortunately because of the quasispecies nature of HIV, the second you give someone protease inhibitors, HIV finds a way around that hurdle, so PIs cant knock out HIV for good. What makes this even worse is protease can mutate a LOT and still function just fine... or better than the quasispecies consensus sequence. What Creationists say cannot happen: "... rugged HIV-1 protease quasispecies fitness landscape may be formed by a continuous network that can be traversed by single mutational steps without passing through defective or less-adapted proteins."

So without any slights of hand, this is what these researchers are going to do, no intensive math required:

"We determined the fitness of each variant present in the quasispecies in order to establish the relatinships between genotype, phenotype, and fitness and constructed a phylogenetic-fitness landscape map for each quasispecies."
Step 1: Filter out all the dimensions you arent interested in.
First thing these researchers had to do was get the protease gene out of its natural environment. Take it away from the CD4+ and CD8+ T-cells. Away from the antibodies. Away from in vivo. An easy way to do this with retroviruses is to blow up some infected cells, isolate the cellular DNA, put one copy of cellular DNA per well, and PCR out the gene youre interested in. Each infected cell will yield a different protease gene. Now, the sequence you isolate might be a dud. It was 'good enough' to get in, but the reverse transcription process mutated it out of working order. Thats okay, in this case. We want to see the duds (non-functional proteases) too, to determine why they are non-functional.
Now again, we have to strip all the other dimensions of the fitness landscape away, so you put the isolated protease genes in a common background- in this case a bacteriophage.

Step 2: Test the dimension youre interested in.
Infect cells with phages containing different kinds of proteases (note: theyre using E. coli here to use phages, not eukaryotic cells!). The special bactereophages allow the researchers to compare protease activities-- its a model system instead of directly measuring protease activity differences (they go back and make sure their model predicts normal HIV protease activity. it does).

Step 3: Combine your fitness measurements with your phylogenetic tree.
Ill take this down if JViorl wants, but I think its fair use:Bigger the circle, higher sequence frequency. Longer the line, more different the circle is from other circles. The different colors relate to how active each protease sequence is. Translation: You can be real different from the consensus sequence and still work fine.


No math.

Breakdown of what percentage of sequences they found that were 1, 2, 3, 4, 5, 6 base pairs different from the consensus sequence!

Diagrams of protease color coded to show where mutations were occuring, and at what frequency!

Relation of fitness in the bactereophage system back to fitness in HIV!

Relation of replication capacity to protease activity in HIV!

Super cool relation of mutation rates and protease activities back to the disease progression in the patients!

No hard math!


Oh wait, Im supposed to write about why Behe is silly, not why this particular paper is cool.


Okay, let me go back to the four points, and put some relevant text from this paper for a rebuttal. *sigh*

1. Evolution can be modeled in terms of a static, unchanging fitness landscape.
"... although the three analyzed quasispecies shared some traits, such as the presence of several fitness optima, every protease quasispecies formed distinctive individual fitness landscapes...
... even quasispecies N and O (two different patients they looked at, ERV), which had similar amino acid diversities, formed very different fitness landscapes."

2. The fitness landscape is a smooth, surface made up of hills and valleys, where a local minimum or maximum in any dimension is a local minimum or maximum in all dimensions.
"... within each quasispecies, there was a large number of fitness optima... Because fitness optima were frequent, the HIV-1 protease quasispecies complexity does not depend exclusively on the enzymes catalytic efficiency..."

3. The fitness function mapping from a genome to a point of the fitness landscape is monotonically increasing.
4. The fitness function is smoothly continuous, with infinitessimally small changes (single-point base chanages) mapping to infinitessimally small changes in position on the fitness landscape.
...Several single substitutions were lethal and led to the master sequence to drop down the peak. However, at other positions, single substitutions sent the master sequence to a new optimum or peak, suggesting that the master sequence may walk through the quasispecies fitness landscape without being trapped at suboptimal alleles...

No advanced super-hard math tricks that no one can understand except for 'math' PhDs.

What am I missing? Why are the UD-crew going after Mark Chu-Carrolls 'math' credentials?

Edited 8.30 pm 6/4/07-- I realize Behe tries to use math to support his views in the chapter Mark is discussing, but Behe should know, as a biochemist, that his arguments are incorrect. No math should be needed... unless hes trying to intimidate his readers into thinking 'Oooh hard math! He must be right!'


Tyler DiPietro said...

I refrained from defending Mark against the credential-bashing because I don't know much about compiler design (other than the Chomsky-hierarchy, I've had close to zero exposer to the field) but I knew that what they said was likely a crock anyway. Just about every field of computer science is laced with higher math. As the title of my blog suggests, my particular concentration is on Optimization Theory (even more specifically, heuristics and approximation algorithms for NP-hard problems), which requires the typical three semesters of calculus, linear and abstract alegebra, probability, combinatorics and enough hard analysis to grasp asymptotic notation. But I didn't want to venture too far outside my area of expertise and left it to Mark to defend himself, since he's obviously more than capable of doing so. ;)

The reason why they jump to math from science is obvious. As you point out and everyone knows, the science simply does not support them. So they dress it up in fancy pseudo-mathematical terminology to make it look more respectable. It's all going for the "it looks damn scientific ta' me!" effect on their audience.

ERV said...

...I refrained from defending Mark against the credential-bashing...
From my point of view, you and Mark are both overqualified to critique Behe. He should know his claims fail at a very, very simple level of fitness landscapes. He shouldnt have ever made it to the 'hard math' level... Unless he was purposefully making things harder than they are to confuse readers.

The reason why they jump to math from science is obvious. As you point out and everyone knows, the science simply does not support them. So they dress it up in fancy pseudo-mathematical terminology to make it look more respectable. It's all going for the "it looks damn scientific ta' me!" effect on their audience.
If I can play my arrogant card for the month, thats why they havent linked to my post. I mean Im low-hanging-fruit for the UD crowd! Hell I can write the post myself! "Are there any Anti-ID writings that the Pandas Thumb wont endorse? Evidently not." Not even in grad school yet. No math since my freshman year of college. Havent read any of Behes books. Evil Atheist minion of PZ and Dawkins. Im an awesome smear target, if I do say so myself!

But then theyd have to link to a simple explanation of fitness landscapes with real world examples of why Behe is mistaken (and should know better), hopefully (hopefully) written in a way non-scientists can grasp (I swear, if that post isnt clear, ask a question!)

Eh I hope some Average Joe IDists find their way here and learn something...

Chris Noble said...

IDers love abusing analogies. Apparently the genome is a computer program written by the Designer. Who should be best qualified to comment on the subject following this analogy?

If Mark were a supporter of ID they would be bragging about his credentials.

It is a simple pattern that all Denialist/cranks follow. If your allies have credentials no matter how irrelevant than make an appeal to authority. If your critics have credentials then bring out the ad hominems.

Dustin said...

The really stupid thing is that Mark's credentials are perfectly suited to the discussion. Dembski and Marks are over at Baylor having this "searches don't work unless they use the problem specific information" jerk-fest, and Mark makes his living on searches and algorithms.

Real computer science isn't programming, or memorizing the Windows API. Real computer science is picking up where people like Turing and Von Neumann left off, and it's all the theory of computation and its applications. That's not just mathematics, it's closer to the foundations of mathematics than what I do. That's why Chu-Carroll is always talking about things like category theory, logic, and set theory (all things that give me the willies).

Mark makes his living doing the kinds of math that Dembski is always distorting, so Dembski can stuff it in his sweater.

ERV said...

Chris-- Its so disrespectful to laymen.

On one hand, its 'Science/Math/ID whatever is too hard for you normies to understand. You have to have credentials like us to know whats going on. We cant explain anything to you, but dont worry, weve got it covered.' From what I understand, Behe/Dembski are incomprehensible in their presentations to the public. We get bitched at by the Fr*mers, but the Professional IDCs are remarkably jargon-esque for a group of people you 'want to have a beer with.' Have any of the IDers ever sat down and clearly explained their ID concepts to anybody??

Their gobbeldy-gook speak intimidates laymen and discourages them from investigating things for themselves.

On the other hand, you have completely condescending posts that oh-so-easily explain non-science to layman: "HIV is an ERV! Scientists use retroviruses to make GMO corn! Dont you feel smart now?" like we got from AiG and DaveScot.

Simultaneously discouraging independent research and feeding incorrect 'knowledge'. Disgusting.

Dustin-- I want that sweater. I want to wear it at every major public presentation. I want to wear it to my doctoral defense.

It will be mine. Oh yes. It will be mine.

Dustin said...

I don't know about the sweater thing. Dembski cooties are probably drug resistant.

And what the fuck is up with Behe and his fixation on point mutations? I am so sick of hearing "point mutations don't account for [insert thing here]". Obviously, they don't!

We're all carrying around the information to build a chimpanzee's jaw. It didn't have to be removed from our genome piece by piece... it just had to get switched off. Also, it isn't as though genes don't get moved around. Whenever you hear someone babbling about the differences between chimpanzee genetics and human genetics and how it would be impossible to accumulate that much difference in 6 million years, it's because they're simply lining things up and looking at them side by side, deliberately ignoring the fact that translocations have occurred.

Behe is (at least ostensibly) a biochemist. I have a freshman's understanding of biology, and I can see through his crap. How is his failure to recognize that things other than point mutations happen anything less than a deliberate lie?

And just to freak out on Behe some more -- that static selective landscape of his is another carefully selected piece of crap. Again, I'm not a biologist, but it seems to me that a bulk of evolution happens because of the accumulation of a wide range of selectively neutral traits and then the landscape changes, which automatically starts to select for the formerly neutral traits which aren't neutral any more. A static landscape with a population hoping to get beneficial mutations would probably just lead to extinction in most cases, and that's why he's presenting that as the theory of evolution instead.

He's a wanker.

josh said...

dustin said:

"We're all carrying around the information to build a chimpanzee's jaw."

Oooh. No.

You've slipped into that "Great Chain of Being" thought mode. We carry the information to build a human jaw; chimps carry the information to build a chimp jaw. But we diverged nigh on 10 million years ago (less, prolly); who's to say that "jaw construction" is one of those conserved sequences? There's no doubt if you took a chimp mandible and a human mandible and looked at them, they'd be different.

I don't mean to be pedantic, but the creationist nutjobs are always looking for things which appear to represent inconsistencies. It behooves us to speak carefully, lest we give the hooting hordes more hooties.


Chris Noble said...

Its so disrespectful to laymen.

The thing that pisses me off is that IDers and HIV Deniers give two contradictory messages to their lay-audiences.

On the one hand they give overly simplistic analogies and strawman versions of science and tell their lay supporters that they don't have to bother learning the real science because "common" sense is enough to find the flaws in HIV-AIDS/evolution.
Don't listen to those silly scientists with PhDs.

On the other hand they will tell any layperson that can see the flaws in ID or HIV Denialism that they need a PhD before they should dare to criticise Behe/Dembski/Duesberg.

Once you filter out the contradictory messages about credentials then it boils down to "listen to us not them".

Dustin said...

'You've slipped into that "Great Chain of Being" thought mode. We carry the information to build a human jaw; chimps carry the information to build a chimp jaw. But we diverged nigh on 10 million years ago (less, prolly); who's to say that "jaw construction" is one of those conserved sequences?'

I haven't. The structure of a chimpanzee jaw musculature is largely determined by MYH16, which we have, but in humans it carries a small mutation which prevents it from being expressed. AFIK, the human MYH16, being unexpressed, has picked up some drift, but it's still MYH16, and that drift serves to tell us when the gene stopped being expressed.

Behe likes to drag "point mutations" around as though they were the primary engines of evolution. They aren't -- expression has much more to do with it.

ERV said...

OMG you guys, gouge out my eyes if I ever try to read a post at UD again. 'Truth Squad'. *VOMIT*

Dustin-Josh-- I think Josh was worried that Creationists would pick up on the usual 'All the information to make dawgz came from the Dawg Kind on THE ARK!' So thank you for realizing the abuse potential, Josh, and thanks for the MYH16 clarification, Dustin!

Chris-- Bleh. Creationists, HIV Deniers, same damn people. Bleh.

Dustin said...

OMG you guys, gouge out my eyes if I ever try to read a post at UD again.

Whaa? It isn't like the main posts aren't just as bad. Have you seen O'Leary's latest opus? I'll summarize. "OMG U GUISE!!! APEZ NOT HAZ LANGUAGE CUZ TEHY UZE KEEBORD TO ASK 4 TREATS!!!!"

Then she goes all Dr. Zaius on us with: And what a naive thought! - that apes can really help us understand the fundamental riddles of human existence.

Torbjörn Larsson said...

And what the fuck is up with Behe and his fixation on point mutations?

Let us call your observation Behe fixed point theorem. ( As this is a post assuming minimal math, see for obscure reference in case of need.)

If a creationist avoids a known fact, it is because it destroys his argument. In this case Behe is aware that duplications provides the material that scaffolds around his 'IC' imagery.

And he can avoid mentioning it by throwing up Dembski's/YEC's 'no new information' when he needs to explain himself to other creos. By hammering on point mutations as the only mechanism in his strawman of evolution he gets just the right amount of complexity in his life. He he.

(...OMFlyingPastaMonster, this blog has infected me with a joking meme. Must-Go-Read-Some-Serious-Shit-Now.)

Kristjan Wager said...

There are two kinds of computer scientists - the mathematical ones, which Mark certainly belongs to, and the others. Personally I fall into the later group, and only apply math to problems if others have given me the tools for it.

There is a reason why Mark works as a researcher for Google, and I don't.

Compiler theory is heavily based upon math, as are search algorithms. So, for a moron like DaveScot, who as far as I know have no mathematically based patents to his (real) name, to claim that someone like Mark doesn't know math, shows how little he understands computer science. Which is probably why he claimed that Mark has a degree in computer programming (something I actually have, though it's hardly an university degree - just the end result of a 2½ year study)

Cole Miller said...

Hey ERV,

I got here late; I'm catching up on my PT reading at the end of a trip. Nice Behe takedown, and nice blog. I'm an astronomer, but like to keep somewhat informed about biological
issues as well as tracking the good fight of reason versus, well, non-reason. Your explanations are clear and your writing style is lively.

Do you do requests? As a layman, I've always thought that the AIDS cocktail is a good example of how evolutionary principles can lead to therapies. My understanding is that the cocktail
requires the virus to make many modifications simultaneously to avoid getting nuked, lowering the probability for a genetic modification that is successful enough to propagate. Without
that understanding, maybe people would have tried one at a time, leading to resistant HIV. If you agree and are interested, would you mind writing an entry about this?

By the way: keep up the good fight for public outreach. I see it's been frustrating, and I also am irritated by journalists holding forth about not enough scientists communicating.
I suspect that your opportunities will increase with time.

Cole Miller