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".

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.

He [John Maynard Smith, or JMS as he is often referred to] was wise to recognize the trend

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.

is a strict selectionist assumption. I don't believe he anticipated the systems approach whereby systems could evolve to regulate their own evolution

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.

The gene centric approach is no longer sufficient to describe what we're seeing in biology.

That is correct, but who would disagree with that?

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"?

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.

2) Is optimization evidence of intelligent design?

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/

Oh idunno, because you're an ignorant blowhard?

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".

John Maynard Smith wrote a much-cited review called "optimization theory in evolution" in 1978.

He was wise to recognize the trend, but notice that his assumption

It is assumed that evolution has occurred by natural selection…

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.

Why would I comment on something I haven't read?

Oh idunno, because you're an ignorant blowhard?

I did a pubmed search for "optimal-control-evolutionary-biology." 85 papers. Every one of them within the last 8 years.

John Maynard Smith wrote a much-cited review called "optimization theory in evolution" in 1978. From the introduction:

In recent years there has been a growing attempt to use mathematical methods borrowed from engineering and economics in interpreting the diversity of life. It is assumed that evolution has occurred by natural selection, and hence that complex structures and behaviors are to be interpreted in terms of the contribution they make to the survival and reproduction of their possessors–that is, to Darwinian fitness. There is nothing particularly new in this logic, which is also the basis of functional
anatomy, and indeed of much physiology and molecular biology. It was followed
by Darwin himself in his studies of climbing and insectivorous plants, of fertilization mechanisms and devices to ensure cross-pollination.
What is new is the use of mathematical techniques such as control theory,
dynamic programming, and the theory of games

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.

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.

Did you read the paper?

Why would I comment on something I haven't read? I thought that only happened at the Panda's Thumb.

What does it explain according to you?

It says optimal control theory explains extremization in redox potentials.

Please back it up with specific quotes from the paper.

Ummm, you mean like when they said "Optimal control theory explains a striking pattern of extremization in the redox potentials…"?

The dynamical systems approach has been used extensively in biology for many decades.

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.

How would you call the approach used by R.A. Fisher in the early 20th century?

Eugenics.

Likewise with optimal control theory. Standard tool in evolutionary biology.

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.

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.

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.

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.

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?

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.

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 is the future. Biology IS the study of engineering.

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.

This paper is just one example of the stark impotence of the victorian era approach.

What approach would that be?

It's telling it was published in a physics journal, where no biologist will read it.

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.

http://www.sciencedaily.com/releases/2008/11/081111183039.htm

..it would be statistically impossible for this self-creating behavior to be random.

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.

The scientists do not know how the cellular machinery guiding this process may have originated, but they emphatically said it does not buttress the case for intelligent design.

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.