"Ultimately selection needs to explain the origin of the mechanisms that account for complexity."

Once again, this quote displays a fundamental misunderstanding of the role of natural selection in evolution. As I stated earlier in this thread, natural selection doesn't explain the origin of anything (including species, Darwin notwithstanding). Natural selection isn't a creative process; rather, it is an outcome. The creative processes that provide the "raw material" for natural selection are those developmental, genetic, and ecological processes I have lumped under the term "engines of variation". These include genetic mutations at the nucleotide, gene, chromosome, and genome levels, sexual and asexual recombination, developmental plasticity, and environment-phenotype interactions, just to name a few major categories. Natural selection "preserves" those variants that the environment does not eliminate, providing a new "starting point" for new variations generation after generation.

However, I do agree with you: the time has come for a paradigm shift. As Will Provine has repeatedly pointed out, the "modern evolutionary synthesis" of the 1930s-60s has long been superceded, and the fundamental assumptions upon which it was based have been seriously questioned. Recent empirical findings have made wholesale revision of the "modern synthesis" necessary, especially with regard to the interactions between genome and environment "“ see M. J. West-Eberhard's Developmental Plasticity and Evolution and L. Margulis & D. Sagan's Acquiring Genomes as just two recent examples of where the "new synthesis" of evolutionary theory is going.

Also, I applaud your comments in other threads vis-a-vis the irrelevance of theism/atheism debates in the ongoing evolution of the theory of evolution. Like Darwin, I myself have never been motivated by either theism or atheism in my own work in evolutionary biology. Rather, I have been repeatedly struck by observations that cry out for explanations, which evolutionary biology in its most recent (i.e. post-modern) form has repeatedly provided. Personally, I would welcome a moratorium on all debates about metaphysics and theology (both pro- and anti-). Perhaps it's time for us all to adopt Newton's point of view: "I feign no hypotheses!" (hypotheses non fingo) Or, as Thought Provoker is fond of repeating, "Let's do science!"

Allen MacNeil writes:

In particular, evo-devo provides a biological explanation for precisely the kind of "self-organization" described in the abstract cited above:

It may not have been clear in the abstract but it appears that the paper of Trevor and Abels was focused on the source of self-organization in a prebiotic setting. It certainly looks like that when this quote (taken from the text) is examined:

The problem with polymerization on clay is the strong tendency to produce highly ordered sequences rather than informational sequences. Montmorillonite aligned monomeric sequences offer no help in explaining the origin of genetic instructions. Bernd M. Rode's group has also been a leader in pursuing spontaneous peptide formation, including homochiral preferences. Homochirality refers to a pure population of the same optical isomer (all right-handed gloves, or all left handed gloves). Most of Rode's group papers have been first-authored by either Plankensteiner [96,97] or Bujdak [21,23]. Bujdak has also worked with clay adsorption [20,22]. Certain amino acids can catalyze peptide bond formation in "Salt-Induced Peptide Formation (SIPF)" reactions. Rode argues that SIPF reactions in connection with adsorption processes on clay minerals is the most likely universal mechanism for initial biopolymerizations in a Peptide World [109]. Certainly Rode and many others are correct that physicodynamic biases exist, especially with clay adsorption. However, the reasoning strikes us as being a nonsequitur in the statement, "Reaction-inherent preferences of certain peptide linkages make the argument of "statistical impossibility" of the evolutionary formation of the "right" peptides and proteins rather insignificant" [109]. In our opinion, physicodynamic bias only reduces through self-ordering tendencies the vast sequence spaces needed for prebiotic molecular evolution. Even if vast sequence spaces had been available in a theoretical primordial soup, no known mechanism exists for the prebiotic selection of prescriptive sequences. Prescriptive sequences require freedom of selection at each successive decision node. This freedom is anti-thetical to the self-ordering "necessity" of physicodynamic bias.

AM: The real paradox, therefore, is that a process that itself is almost certainly not teleological (i.e. evolution by natural selection) can produce entities that just as certainly teleological (i.e. living organisms).

Earlier in this thread I wrote that: Ultimately selection needs to explain the origin of the mechanisms that account for complexity. If natural selection fails at point of origins then a paradigm shift is in order. That point remains relevant to teleology. Mayr could make a strong argument for genetic variation via selection when mechanisms essential to gene expression are in place. Contending that the origin of such mechansms is exclusive of teleology is a very much weaker argument.

The synthesis that will arise out of this thesis/antithesis will almost certainly be different in some respects from what either side currently expects"¦but isn't that what makes science so much fun?

Nice. Quite refreshing to hear from an ID critic with some class, thank you.

Regards.

"I think one of the greatest mysteries in biology at the moment is whether natural selection is the only process capable of generating organismal complexity"

That a prominent scientist should so badly misunderstand the role (and limitations) of natural selection is both distressing and (sadly) not particularly surprising. As I have been pointing out in recent entries in my own blog, the idea that natural selection is "capable of generating organismal complexity" has been an erroneous misinterpretation of how natural selection works since Darwin's publication of the Origin of Species in 1859. Darwin himself preferred the term "natural preservation" over "natural selection," as the latter term suggested an active, designing force at work, whereas the former term clearly indicated that nature simply "preserves" those variants that survive and reproduce more effectively than others.

As John Endler has clearly pointed out in Natural Selection in the Wild (1986, Princeton University Press), natural selection is not a "mechanism" that "does" anything: "…natural selection does not explain the origin of new variants, only the process of changes in their frequency." (Endler, 1986, pg. 245). Stated even more clearly,

"…natural selection is a process resulting from the interactions between variable organisms and environment, and not a mysterious "force" that "acts." The use of "acts," "force," and "intensity" has the same status as phlogiston in thermodynamics; it is descriptive but misrepresents the process, confuses cause and effect, and focuses attention away from causes." (Endler, 1986, pp. 32-33)

Natural selection is therefore a result of three processes, as first described by Darwin:
"¢ Variation
"¢ Inheritance
"¢ Fecundity
which together result in non-random, unequal survival and reproduction of individuals, which results in changes in the phenotypes present in populations of organisms over time.

The real "engine" of evolutionary change is not natural selection, but rather the "engines of variation," which include genetic mutations, but also dozens (possibly hundreds) of other processes that have the effect of producing heritable phenotypic variation. With the advent of evo-devo we are beginning to gain some insight into the properties of such "engines of variation" and their dynamics.

A full understanding of the "engines of variation" and their interactions with the demographic processes that produce natural selection is a long way off. However, it is already very clear that the dynamics of variation depend on a continuous feedback between organisms and their environment, and are not necessarily gradualistic/monotonic processes. Recognition of this fact holds the promise of reconciling such long-disputed controversies as gradualism vs punctuated equilibrium and adaptationism vs drift/neutralism is only one source of the increasing excitement in evolutionary biology today.

In particular, evo-devo provides a biological explanation for precisely the kind of "self-organization" described in the abstract cited above:

"Organization typically contains large quantities of prescriptive information. Prescriptive information either instructs or directly produces nontrivial optimized algorithmic function at its destination. Prescription requires choice contingency rather than chance contingency or necessity. Organization requires prescription, and is abstract, conceptual, formal, and algorithmic. " (Abel & Trevors, 2006)

This description is striking in how clearly it conforms to Ernst Mayr's description of "teleonomic" processes (Mayr, 1974). According to Mayr, "All teleonomic behavior is characterized by two components. It is guided by a 'program' and it depends on the existence of some end point, goal, or terminus which is foreseen in the program that regulates the behavior." (Mayr, 1974, pg. 97). Mayr's "program" is essentially the same as Abel & Trevors's "prescriptive information," which they claim is necessary for organization. Mayr takes pains to point out that the origin and evolution of such programs is not the result of a teleological process, and nothing in Abel & Trevors's analysis suggests otherwise.

The real paradox, therefore, is that a process that itself is almost certainly not teleological (i.e. evolution by natural selection) can produce entities that just as certainly teleological (i.e. living organisms). That both evolutionary biologists and intelligent design proponents are focusing on the "engines of variation" is a healthy sign; healthy for evolutionary biologists because it means they are finally getting at the underlying causes for biological diversity and variation, and healthy for intelligent design proponents because it means that their ideas can finally be tested empirically. The synthesis that will arise out of this thesis/antithesis will almost certainly be different in some respects from what either side currently expects…but isn't that what makes science so much fun?

REFERENCES CITED:

Abel, D. L. & Trevors, J. T. (2006) Self-organization vs. self-ordering events in life-origin models. Physics of Life Reviews, Vol. 3, No. 4, (December 2006), pp. 211-228

Endler, J. (1986) Natural Selection in the Wild. Princeton Univesity Press, 336 pp.

Mayr, E. (1974) Teleological and teleonomic: A new analysis. Boston Studies in the Philosophy of Science, Vol. XIV, pp. 91 -117

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Allen D. MacNeill, Senior Lecturer
The Biology Learning Skills Center
G-24 Stimson Hall, Cornell University
Ithaca, New York 14853
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phone: 607-255-3357 (Allen's office)
email: adm6@cornell.edu
website: http://evolutionlist.blogspot.com/
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"I had at last got a theory by which to work"
-The Autobiography of Charles Darwin
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"I think one of the greatest mysteries in biology at the moment is whether natural selection is the only process capable of generating organismal complexity,"

Massimo

Sounds like someone just came to terms with the substance of Michael Behe's latest book.

You often express an understanding there is no magic bullet, definable edge or mathematical analysis that is going to "prove" your hypothesis.

Hi TP,

Could you be more explicit with your comment regarding a definable edge that is going to "prove" a hypothesis?
I think you're refering to Behe, but I could be wrong.

This is what sets you apart from a lot of other ID Proponents.

You often express an understanding there is no magic bullet, definable edge or mathematical analysis that is going to "prove" your hypothesis.

That has been my position from the start. So one of the things that sets you apart from a lot of other ID critics is that you notice it.

Be careful of the term "self-organization". There is a difference between self-ordering and self-organization. See:

http://dx.doi.org/10.1016/j.plrev.2006.07.003

I have a copy of the paper. If anyone is interested, mail me at johnnyb /\ at /\ eskimo.com.

From the link:

"A classic example outside of biology are hurricanes: These are not random air movements at all, but highly organized atmospheric structures that arise spontaneously given the appropriate environmental conditions," Pigliucci said. "There is increasing evidence that living organisms generate some of their complexity during development in an analogous manner."

So far so good. But look where he goes.

A biological illustration of self-organization is protein-folding. A lengthy necklace of amino acids bends, twists and folds into a three-dimensional protein, whose shape determines the protein's function. A protein made up of just 100 amino acids could take on an endless number (billions upon billions) of shapes. While this shape-shifting takes on the order of seconds to minutes in nature, the fastest computers don't have the muscle yet to pull off the feat.

The protein folding process itself can be described in terms of a self-organization. But the real issue, left unaddressed, is whether the folding is attributable to the nature of the protein itself and whether the nature of the protein is in turn explained by the protein's amino acids and their sequence. If it is then the selection issue needs to be revisited. Ultimately selection needs to explain the origin of the mechanisms that account for complexity. Complexity comes in different shapes and flavors. If natural selection fails at point of origins then a paradigm shift is in order.