Time to Give It Up [Intelligent Design and Irreducible Complexity]

Seed Magazine ^ | 4/10/06 | Britt Peterson

[LibWhacker]

New research chips away at the "irreducible complexity" argument behind intelligent design.

Lehigh biochemistry professor Michael Behe and his cronies in the intelligent design community have attempted to poke holes in evolutionary theory using an idea dubbed "irreducible complexity"—the notion that complex systems with interdependent parts could not have evolved through Darwinian trial and error and must be the work of a creator, since the absence of any single part makes the whole system void. However, a paper published in the April 7th issue of Science provides the first experimental proof that "irreducible complexity" is a misnomer, and that even the most complex systems come into being through Darwinian natural selection.

"We weren't motivated by irreducible complexity," said Joe Thornton, an evolutionary biologist at the University of Oregon and a co-author of the paper. "How complexity evolved is a longstanding issue in evolutionary biology per se, and it's once we saw our results that we realized the implications for the social debate."

Thornton's team has been studying one example of a complex system in which each part defines the function of the other: the partnerships between hormones and the proteins on cell walls, or receptors, that bind them. The researchers looked specifically at the hormone aldosterone, which controls behavior and kidney function, and its receptor.

"[This pairing] is a great model for the problem of the evolution of complexity," said Thornton. "How do these multi-part systems—where the function of one part depends on the other part—evolve?"

Thornton and his co-investigators used computational methods to deduce the gene structure of a long-gone ancestor of aldosterone's receptor. They then synthesized the receptor in the lab. After recovering the ancient receptor—which they estimate to be a 450-million-year-old receptor that would have been present in the ancestor of all jawed vertebrates—Thornton's team tested modern day hormones that would activate it. Although aldosterone did not evolve until many millions of years after the extinction of the ancient hormone receptor, Thornton found that it and the ancient receptor were compatible.

This cross-generational partnership is made possible, Thornton explained, by the similarity in form between aldosterone and the ancient hormone that once partnered with the receptor.

"The story is basically that a new hormone evolved later and exploited a receptor that had a different function previously to take part in a new partnership," said Thornton.

The principal at work in the evolution of complex systems is molecular exploitation: when an individual component casts around for other materials that might work together with it, even though those elements might have evolved as parts of other systems.

"Evolution assembles these complex systems by exploiting parts that are already present for other purposes, drawing them into new complexes and giving them new functions through very subtle changes in their sequences and in their structures," Thornton said.

While the mutually dependent parts do not evolve to be perfectly complementary to one another, after molecular exploitation, they cleave together and create an illusion of irreducible complexity.

"Such studies solidly refute all parts of the intelligent design argument," wrote Christoph Adami, of the Keck Graduate Institute of Applied Life Sciences, in an introduction to the Science paper. "Those 'alternate' ideas, unlike the hypotheses investigated in these papers, remain thoroughly untested. Consequently, whatever debate remains must be characterized as purely political."

[Antonello]

eat the poppy leaves and see if you get an effect you will not ..the amounts are not significant to effect any defense.

The article didn't say the effect was for humans - it is for the benefit of the poppies. And I'm not the one to argue with over those findings anyway. Take it up with the researchers that published the paper.

[aMorePerfectUnion]

Again, perhaps if you read the article before commenting this would actually make sense to you.

best, ampu

[Antoninus]

"Lehigh biochemistry professor Michael Behe and his cronies"

Oh please. Can we stop this nonsense?

If the ToE case is so strong (and I believe it is), there's no need to belittle, demean and attack those who raise questions.

Attack their arguments, not them personally.

[dread78645]

"Lehigh biochemistry professor Michael Behe and his cronies"

Oh please. Can we stop this nonsense?

Look up the definition for 'crony' ...

[Tokra]

Well, just show me macro-evolution in a lab and I'll sign right up...what's that? You can't? Oh... "

I'll be happy to educate you. Tuition is $20K a semester. I'll get back to you when your check clears.

I'll do it for $19K a semester!

[donh]

Again, perhaps if you read the article before commenting this would actually make sense to you.

Again, perhaps pimping for an editorial by promoting it to an "article", doesn't make it anything other than a dispeptic diatribe. And pompous, dismissive gesturing somewhere else doesn't make you any less the author of the disdaneful characterization of science as a hotbed mindless establishment orthodoxy being constantly rescued by brave outsiders. At best, one can consider this inobservant.

[js1138]

I was surprised that not a single person read and commented on Dr. Lindzen's article in today's WSJ.

First of all, at least 317 people read the article on FR. Second, it seems rather disingenuous for a professor at MIT to be saying that people lose their jobs for saying what he is saying. Has he lost his job? I'm sure climate critics are disappointed that their policy recommendations are not being accepted, but that is politics, not science.

If it were not for the public policy aspect, climate science would not be perceived as unusually contentious.

[aMorePerfectUnion]

Does this mean you also read the editorial essay in todays WSJ?

[aMorePerfectUnion]

js,
I wasn't aware that anyone even posted the WSJ editorial on FR today. Could you provide a link? You do know I'm referring to a different article than the one at the top of this thread?

ampu

ps - tenured profs don't lose their jobs - which was one of the points in the editorial... that few are senior enough to withstand - aw , just read it.

[Stultis]

It is the presuppositions that are built into the program that I question. Once those are hardwired, no one questions them... they just look at the output and say it was "computer generated" and scientific.

Going at least by the history of the discipline, this is simply not true, regardless of what may (or may not) happen in climate science.

Look at the various programs that have been used to deduce phylogenies from genetic sequence data. My Lord, the debate went on and on and on (and still does) about rooting trees, seeding trees, what constitutes a least probability tree and the probability of it being found, the relation between the models and what actually happens in evolution, etc, etc. Every aspect of these programs has been examined in the most excruciating detail, and continues to be.

The inference of ancestral sequences is a closely related problem. To arrogantly and sweepingly assert it isn't/won't receive the same treatment is bigoted and unjustified.

Besides, just a quick glance at the literature indicates (unsurprisingly, at least to anyone who follows science) that the presuppositions involved in infering ancestral sequences are being examined. Here's just one example. It's not chosen for any particular reason, just the first one I happened to google up:

Ancestral sequence alignment under optimal conditions
BMC Bioinformatics 2005, 6:273
http://www.biomedcentral.com/1471-2105/6/273

Abstract (full text available at link)

Background

Multiple genome alignment is an important problem in bioinformatics. An important subproblem used by many multiple alignment approaches is that of aligning two multiple alignments. Many popular alignment algorithms for DNA use the sum-of-pairs heuristic, where the score of a multiple alignment is the sum of its induced pairwise alignment scores. However, the biological meaning of the sum-of-pairs of pairs heuristic is not obvious. Additionally, many algorithms based on the sum-of-pairs heuristic are complicated and slow, compared to pairwise alignment algorithms.

An alternative approach to aligning alignments is to first infer ancestral sequences for each alignment, and then align the two ancestral sequences. In addition to being fast, this method has a clear biological basis that takes into account the evolution implied by an underlying phylogenetic tree.

In this study we explore the accuracy of aligning alignments by ancestral sequence alignment. We examine the use of both maximum likelihood and parsimony to infer ancestral sequences. Additionally, we investigate the effect on accuracy of allowing ambiguity in our ancestral sequences.

Results

We use synthetic sequence data that we generate by simulating evolution on a phylogenetic tree. We use two different types of phylogenetic trees: trees with a period of rapid growth followed by a period of slow growth, and trees with a period of slow growth followed by a period of rapid growth.

We examine the alignment accuracy of four ancestral sequence reconstruction and alignment methods: parsimony, maximum likelihood, ambiguous parsimony, and ambiguous maximum likelihood. Additionally, we compare against the alignment accuracy of two sum-of-pairs algorithms: ClustalW and the heuristic of Ma, Zhang, and Wang.

Conclusion

We find that allowing ambiguity in ancestral sequences does not lead to better multiple alignments. Regardless of whether we use parsimony or maximum likelihood, the success of aligning ancestral sequences containing ambiguity is very sensitive to the choice of gap open cost. Surprisingly, we find that using maximum likelihood to infer ancestral sequences results in less accurate alignments than when using parsimony to infer ancestral sequences. Finally, we find that the sum-of-pairs methods produce better alignments than all of the ancestral alignment methods.

[donh]

Does this mean you also read the editorial essay in todays WSJ?

It is your expressed opinion to which I objected. I'm not your circus monkey, quit trying to think of busywork for me to do before you will deign to defend your balony-ridden argument.

[donh]

Does this mean you also read the editorial essay in todays WSJ?

Oh, and by the way, trying to patronize people because they haven't read an ancillary article you couldn't be bothered to post a navigable url to, or relevant piece of, isn't going to win you a lot of admirers here.

[Stultis]

Reconstructing ancestral genes is a standard procedure.

Good point. I kind of implicitly went along with aMPU's (wildly false) suggestion that there is something new about inferring genetic sequences, or that this hadn't already been thoroughly examined. I should have noted that inferring ancestral sequences is (sometimes, depending on the specific method being used) an incidental step in other procedures such as inferring phylogenies or aligning sequences.

Correct me if I ere. I'm not terribly educated on the topic. Most of what I know I got from reading Kimura's book on "The Neutral Theory of Molecular Evolution". It discussed the various methods of inferring phylogenies and the like in a good bit of detail, but it's dated by now I'm sure, and years since I read it.

[Virginia-American]

...I would imagine that opiates are alkaloids which act as a natural insecticide of sorts...

Not only opium and nicotine, but a huge number of drugs and drug precursors: think of a mouse nibbling on a bit of digitalis, or LSD, or ...

[Virginia-American]

[skulls]

your use of jigsaw puzzle pieces resulted in fakes more times than not.

Please document this claim.

[Coyoteman]

your use of jigsaw puzzle pieces resulted in fakes more times than not.

Please document this claim.

Give him time to search out the creo sites.

In the meantime, here is one of the those "fakes" for all to enjoy. This is Mrs. Ples, one of my favorites; we spent hours with her in grad school. (The cast we had looked much better than this photograph.)

---

Fossil: Sts 5 Site: Sterkfontein Cave, South Africa (1)

Discovered By: R. Broom & J. Robinson 1947 (1)

Estimated Age of Fossil: 2.5 mya * determined by Stratigraphic, floral & faunal data (1, 4)

Species Name: Australopithecus africanus (1, 2)

Gender: Male (based on CAT scan of wisdom teeth roots) (1, 30) Female (original interpretation) (4)

Cranial Capacity: 485 cc (2, 4)

Information: No tools found in same layer (4)

Interpretation: Erect posture (based on forward facing foramen magnum) (8)

Nickname: Mrs. Ples (1)

See original source for notes:
http://www.mos.org/evolution/fossils/fossilview.php?fid=24

[aMorePerfectUnion]

Thank you for a reasoned and reasonable post.

best,
ampu

[aMorePerfectUnion]

Don,
I asked a serious question. If you don't want to participate in the referred article, that's fine. I am not trying to patronize anyone or make admirors either. I was in pursuit of an actual discussion. I'm not sure why you are so antagonistic. If I offended you, you have my sincere apology. If this has been a particularly difficult day for you, you have my empathy.

best,
ampu

[aMorePerfectUnion]

Don,
I asked a serious question. If you don't want to participate in the referred article, that's fine. I am not trying to patronize anyone or make admirors either. I was in pursuit of an actual discussion. I'm not sure why you are so antagonistic. If I offended you, you have my sincere apology. If this has been a particularly difficult day for you, you have my empathy.

best,
ampu

[Ichneumon]

Well, just show me macro-evolution in a lab and I'll sign right up...

...he says, and then a few sentences later in the same post warns that he's "not buying", which sounds like "I don't care what evidence there is, I've decided in advance to reject it."

what's that? You can't? Oh...

What's that, you *presume* the answer in advance? Ah, I hear the sound of a mind slamming shut.

Hint: There are many more ways to demonstrate the validity of a process beyond "showing it to you in a lab".

Hint #2: We can't recreate the Hawaiian Islands in a lab, either, but we can still verify the processes by which they formed, beyond any reasonable doubt.

This "show it to me in a lab" canard is a frequent cheap excuse for "I'll believe what I want to believe, whatever the evidence overwhelmingly indicates" based on either a) a complete ignorance of how science validates things, or b) a purposely dishonest attempt to ask for something the questioner knows is unworkable EVEN IF THE PROPOSITION IS TRUE and verifiable by other methods.

*Note: feel free to attack me Darwin-bots, but I'm not buying

Funny, *you're* the first one to issue an attack on this thread (e.g. "Darwin-bots").

And I have no interest in attacking you. I feel sorry for you.

(and the usual disclaimer: I am not pro-creationism.)

So your mind is equally closed in every direction?