Evolution's New Wrinkle?
by JoyProteins With 'Cruise Control' Act Like Adaptive Machines
"The discovery answers an age-old question that has puzzled biologists since the time of Darwin: How can organisms be so exquisitely complex, if evolution is completely random, operating like a 'blind watchmaker'?" said Chakrabarti, an associate research scholar in the Department of Chemistry at Princeton. "Our new theory extends Darwin's model, demonstrating how organisms can subtly direct aspects of their own evolution to create order out of randomness."
The paper presents the first quantitative experimental evidence that evolutionary control strategies in the organisms themselves work to maximize their fitness to the environment they inhabit. Chakrabarti calls this an application of "Control Theory," which is basically an appeal to engineering and… design. He of course denies that the findings support the notion of ID, but ID encompasses the notion that design can be entirely 'natural' if one allows for the actual participation of organisms in their own design and evolution. Something biologists have been notoriously reluctant to do for the last 150 years. Looks like now they're going to have to go ahead and admit what the evidence demonstrates to be true.
It's about time.
November 12th, 2008 at 5:19 pm
Interesting paper. Here's a quote from it:
If I understand it correctly (on browsing the actual paper), they show that the terminal stage of the electron transport chain is optimized (maximal energy production) wrt redox potentials (RPs) of the chain's proteins. Application of optimal control theory (standard calculus of variations) shows that the optimum is a "bang-bang" control, either minimal or maximal RP.
This is nothing new. I having been using the same techniques for many years.
What's perhaps most interesting is the claim that the system's optimality is robust wrt mutations, in the sense that
This doesn't look like a revolution to me. Did I miss something?
PS. It's telling it was published in a physics journal, where no biologist will read it.
Comment by Raevmo — November 12, 2008 @ 5:19 pm
November 12th, 2008 at 6:21 pm
Ding dong the witch is dead… rofl
Comment by willo — November 12, 2008 @ 6:21 pm
November 12th, 2008 at 6:38 pm
Hey Willo, could you be a bit more specific, or don't you mind looking like an idiot?
Comment by Raevmo — November 12, 2008 @ 6:38 pm
November 12th, 2008 at 7:19 pm
Raevmo, I can't find it online anywhere, do you have the paper? If so could you send it to me?
thanks
Comment by Chris Harrison — November 12, 2008 @ 7:19 pm
November 12th, 2008 at 7:21 pm
Raevmo:
Oh, there's all sorts of cool stuff happening at the physical end of biology. There's quite a bit of crossover of physics with biology, and a lot of publications.
Comment by Joy — November 12, 2008 @ 7:21 pm
November 12th, 2008 at 7:47 pm
Heh Raevmo, just having a bit of fun… didn't mean to get under your skin.
Anyway here are a couple of interesting quotes to chew over:
"Evolution is guided by the optimization of fitness meaures that balance functionally beneficial properties."
"The authors sought to identify the underlying cause for this self-correcting behavior in the observed protein chains. Standard evolutionary theory offered no clues”
I'm melting melting… sorry couldn't help myself
Comment by willo — November 12, 2008 @ 7:47 pm
November 12th, 2008 at 9:18 pm
Optimal control of evolutionary dynamics [pdf], uploaded in June.
Comment by Joy — November 12, 2008 @ 9:18 pm
November 12th, 2008 at 11:17 pm
I wonder if anyone predicted a mechanism that would defeat selection in some cases?
A good follow up work might be to look for a similar mechanism involved in shielding certain ultaconserved areas of the genome from selection as well
peace
Comment by fifth monarchy man — November 12, 2008 @ 11:17 pm
November 13th, 2008 at 3:12 pm
From the article:
http://www.sciencedaily.com/releases/2008/11/081111183039.htm
As ID has claimed all along, there is no conceivable way “natural selection” might turn a collection of random accidents into complex, intelligently interacting biological structures.
Poor guys! It must be hard to admit that the only alternative to accidental assembly would be some form of intelligent, purposeful organization.
Biological change is always driven by random mutation and selection, but at certain pivotal junctions in evolutionary history, such random processes can create structures capable of steering evolution toward greater sophistication and complexity.
But hey! They still struggle save their deity: “Natural selection somehow acted upon random accidents to create the complex, intelligent mechanisms which THEN organize complex, purposeful biological systems.”
EAM posits that biological change does not originate in genomes, but in individual living organisms, all of which have some limited ability to reorganize, intelligently and purposefully in response to environmental challenges. Used organs develop and unused ones atrophy. Wounds are sometimes purposefully repaired and disease overcome. Such “mutations” are inherited epigenetically as they develop, and are only incorporated into the genome if persistent over generations.
Whether the organizing intelligence is internal to the system or it emanates from some God, it is still intelligent design. Evangelical materialists are just going to have to swallow that bitter pill.
Comment by Bert — November 13, 2008 @ 3:12 pm
November 13th, 2008 at 3:48 pm
Raevmo,
No, it's telling that it took chemical physics to explain what Darwinism couldn't. And evolutionary biologists better start reading or they'll be left in the dust.
The dynamical systems approach is the future. Biology IS the study of engineering.
This paper is just one example of the stark impotence of the victorian era approach.
Comment by chunkdz — November 13, 2008 @ 3:48 pm
November 13th, 2008 at 5:31 pm
chunkdz:
Did you read the paper? What does it explain according to you? Please back it up with specific quotes from the paper.
The dynamical systems approach has been used extensively in biology for many decades. How would you call the approach used by R.A. Fisher in the early 20th century? Likewise with optimal control theory. Standard tool in evolutionary biology. You should read some of the professional journals like Evolution or Genetics. Or read the book by John Maynard Smith (an engineer): Evolution and the Theory of Games.
What approach would that be?
Comment by Raevmo — November 13, 2008 @ 5:31 pm
November 13th, 2008 at 5:40 pm
Bert:
Ah, so now this paper is evidence against materialism? Two questions for you, Bert: (1) What part of the results cannot be explained by "materialism"? (2) Is optimization evidence of intelligent design?
Comment by Raevmo — November 13, 2008 @ 5:40 pm
November 13th, 2008 at 7:14 pm
Raevmo,
Why would I comment on something I haven't read? I thought that only happened at the Panda's Thumb.
It says optimal control theory explains extremization in redox potentials.
Ummm, you mean like when they said "Optimal control theory explains a striking pattern of extremization in the redox potentials…"?
I didn't say it hasn't been used. I said it is the future. If you don't believe me, just do a journal search for "dynamical-systems-evolutionary-biology" and see if there isn't a trend.
Eugenics.
Same thing as above. I did a pubmed search for "optimal-control-evolutionary-biology." 85 papers. Every one of them within the last 8 years.
That was my point, tuffie. The study of biology IS the study of engineering. Highly advanced engineering. So it is not surprising that these disciplines are blurring together.
Comment by chunkdz — November 13, 2008 @ 7:14 pm
November 13th, 2008 at 7:25 pm
Raevmo:
And the electron transport chain is well known as well as proton transfer across membranes. Not being a biochemist, I can only surmise from the publicly available pre-print that these scientists' "surprise" was to find that the evolution of proteins relied upon the same chemical electrodynamics. Based on protein function, not DNA molecular or chemical peculiarities.
I thought it was interesting that their application of OCT was computer modeled from protein form/function, not demonstrated actual by any in vitro experiments with actual mutant DNA. You guys consider this sort of experiment legitimate, don't you? Isn't that what comprises the realm of genomics?
They could not identify the true underlying mechanism, they just observed the 'bang-bang' optimization – the functional constraint on protein evolution for these proteins.
But I must say I'm impressed that your reaction isn't as knee-jerk as PZ's, who appears to think PRL is some fly-by-night operation and Chakrabarti must be some "weird, isolated crank." That's refreshing.
Comment by Joy — November 13, 2008 @ 7:25 pm
November 13th, 2008 at 8:34 pm
chunkdz:
Oh idunno, because you're an ignorant blowhard?
John Maynard Smith wrote a much-cited review called "optimization theory in evolution" in 1978. From the introduction:
Comment by Raevmo — November 13, 2008 @ 8:34 pm
November 13th, 2008 at 9:35 pm
Raevmo,
Adorable.
But my definition of an ignorant blowhard is someone who reads a research paper that offers real insight, then summarily dismisses it as "nothing new".
He was wise to recognize the trend, but notice that his assumption
is a strict selectionist assumption. I don't believe he anticipated the systems approach whereby systems could evolve to regulate their own evolution, but he sure recognized the need to describe evolution in engineering terms.
The gene centric approach is no longer sufficient to describe what we're seeing in biology.
Comment by chunkdz — November 13, 2008 @ 9:35 pm
November 14th, 2008 at 9:45 am
Bertvan: Hi Raevmo. Anything can be (and has been for the past century) explained by materialism. The question is whether a materialist explanation is the most reasonable one. I suspect there will always be materialists and there will always be people not satisfied with materialist explanations. I'm content to let everyone make their own judgment. If non materialists ever become a majority in the field of biology, I would not favor allowing them to impose their view upon everyone and outlaw materialist explanations.
Bertvan: 'Optimizaion' is just a word. What does the process consist of?
Is it something more than natural selection doing something to random accidents? If so, precisely what? Apparently random mutation and natural selection was the best materialistic explanation Darwin could come up with.
http://30145.myauthorsite.com/
Comment by Bert — November 14, 2008 @ 9:45 am
November 15th, 2008 at 11:15 am
chunkdz:
If you would read my above comments carefully, you might notice that "nothing new" refers to the use of optimal control theory, which has been used for a long time in evolutionary modeling. I like the paper just fine.
That's true. He was in fact one of the pioneers in the application of optimization theory to evolutionary modeling, and the (co)author of many books including Evolution and the Theory of Games, and The Major Transitions in Evolution. He was also a Marxist for a while, a real one, unlike professor Obama. Not to mention a connaisseur of fine Scotch Whiskey. And last but not least a very nice guy.
I think this publication refutes that claim:
Taddei, F., Radman, M., Maynard Smith, J., Toupance, B., Gouyon, P. H. & Godelle, B. (1997) Role of mutator genes in adaptive evolution. Nature 387, 700-702.
That is correct, but who would disagree with that?
Comment by Raevmo — November 15, 2008 @ 11:15 am