Intellectuals Who Doubt Darwin

WACO, Texas -- At one time, the debate over Darwin's theory existed as a cartoon in the modern imagination. Thanks to popular portrayals of the Scopes Trial, secularists regularly reviewed the happy image of Clarence Darrow goading William Jennings Bryan into agreeing to be examined as an expert witness on the Bible and then taking him apart on the stand. Because of the legal nature of the proceedings that made evolution such a permanent part of the tapestry of American pop culture, it is fitting that this same section of the tapestry began to unravel due to the sharp tugs of another prominent legal mind, Phillip Johnson.

The publication of his book, Darwin on Trial, now appears to have marked a new milestone in the debate over origins. Prior to Johnson's book, the critics of evolution tended to occupy marginalized sectarian positions and focused largely on contrasting Darwin's ideas with literalist readings of the Genesis account. Johnson's work was different. Here we had a doubter of Darwin willing to come out of the closet, even though his credentials were solid gold establishment in nature. He had attended the finest schools, clerked for Supreme Court Chief Justice Earl Warren, taught law as a professor at highly ranked Berkeley, and authored widely-used texts on criminal law. Just as Darrow cross-examined the Bible and Bryan's understanding of it, Johnson cross-examined Darwin and got noticed in the process. He spent much of the last decade debating the issue with various Darwinian bulldogs and holding up his end pretty well.

PHILLIP JOHNSON, AND a number of others, raised enough doubts about the dominant theory to cause a number of intellectuals to take a hard look, particularly at the gap between what can be proven and what is simply asserted to be true. Since that time, authors with more technical backgrounds, like mathematician/philosopher William Dembski and biochemist Michael Behe, have published books providing even more powerful critiques of the neo-Darwinian synthesis based on intelligent design theory. Behe's work has been particularly disturbing to evolution advocates because he seems to have proven that organic machines at the molecular level are irreducibly complex and therefore could not have been the products of natural selection because there never would have been any intermediate working mechanism to select. Now, the two team up as Dembski edits and Behe contributes to a bracing collection of controversial writings titled Uncommon Dissent: Intellectuals Who Find Darwinism Unconvincing.

Dembski displays the intellectual doggedness of the group of contributors when he uses his introductory essay to ruthlessly track down and scrutinize the footnotes offered by those who would refute Behe's case. Reference after reference claiming to have decisively defeated Behe turns out to be inadequate to the task. What passes for refutation is instead a collection of question-begging and "just-so stories." Right away, Dembski sets the tone for the book. Nothing will be uncontested. The pro-evolution community will be made to fight for every inch of intellectual real estate without relying on the aura of prestige or the lack of competent critics to bolster their case.

The best way to read the book is by beginning at the end and perusing the profiles of the contributors. There, the reader will be able to select essays from representatives of a variety of disciplines, including mathematics, philosophy, biochemistry, biophysics, chemistry, genetics, law, and medicine. The most enjoyable in terms of sheer brio are the essays by Dembski, Behe, Frank Tipler, Cornelius Hunter, and David Berlinski. Tipler's essay on the process of getting published in a peer-reviewed journal is particularly relevant and rewarding because it deals with one of the biggest strikes against Intelligent Design. ID theorists have had a notoriously difficult time getting their work published in professional journals. Tipler, a professor of mathematical physics at Tulane, crankily and enjoyably explains why.

TOP HONORS, HOWEVER, go to David Berlinski's essay, "The Deniable Darwin," which originally appeared in Commentary. The essay is rhetorically devastating. Berlinski is particularly strong in taking apart Richard Dawkins' celebrated computer simulation of monkeys re-creating a Shakespearean sentence and thereby "proving" the ability of natural selection to generate complex information. The mathematician and logician skillfully points out that Dawkins rigged the game by including the very intelligence in his simulation he disavows as a cause of ordered biological complexity. It's clear that Berlinski hits a sore spot when one reads the letters Commentary received in response to the article. Esteemed Darwinists like Dawkins and Daniel Dennett respond with a mixture of near-hysterical outrage and ridicule. Berlinski's responses are also included. At no point does he seem the slightest bit cowed or overwhelmed by the personalities arrayed against him.

For the reader, the result is simply one of the most rewarding reading experiences available. Berlinski and his critics engage in a tremendous intellectual bloodletting, with Berlinski returning fire magnificently. In a particularly amusing segment, Berlinski, constantly accused of misperception, writes, "For reasons that are obscure to me, both [Mr. Gross] and Daniel Dennett carelessly assume that they are in a position to instruct me on a point of usage in German, my first language." Though his foes repeatedly accuse Berlinski of being a "creationist," the tag has little chance of sticking to a man arguing for little more than agnosticism on the question of origins and who disavows any religious principles aside from the possible exception of hoping to "have a good time all the time." One suspects that the portion of the book occupied by the Berlinski essay and subsequent exchanges will gain wide currency.

For far too long, the apologists for Darwin have relied on a strategy of portraying challengers as simple-minded religious zealots. The publication of Uncommon Dissent and many more books like it, will severely undermine the success of such portrayals. During the past decade, it has become far too obvious that there are such things as intellectuals who doubt Darwin and that their ranks are growing. The dull repetition of polemical charges in place of open inquiry, debate, and exchange may continue, but with fewer and fewer honest souls ready to listen.

Hunter Baker is a Ph.D. student at Baylor University and contributes to the Reform Club.

Let me respond to your post #320 first, before I move on to #321.

I was trying to be careful not to misrepresent your position on the necessity of including an explanation for the origins of life within a scientific evaluation of the Theory of Evolution, and I accept your statement that this was not your intention. I would like to explain briefly why I did this, so that you can appreciate the dilemma I was trying to resolve. You stated that biosemiosis was not the cause of the rise of information in biological systems it was the effect. And you then went on to point me to a link on the quest for the cause, which was the "Origins of Life" competition. Coming on the heels of your raising the question "what is life" as a shortcoming of behavioralistic models -- a point I will contest later -- and then proceeding to mention that successful communication was missing from those models I could not decide whether you meant to argue that a definition of life should contain mention of its origins, or possibly that the Theory of Evolution failed to include an explanation of life's origins, or whether you included the link reference as a side note for further discussion about what is missing from biosemiotics. I now consider the dilemma resolved after your last post.

Now, let us turn to the "randomness pillar" of the Theory of Evolution. I believe this is a misnomer, unless you insist that the Theory of Evolution can only be viewed as the entirety of Darwin's original formulation. Evolution explains the origin of species, natural selection is the engine of evolutionary change Darwin first proposed and which, as I have pointed out repeatedly in this thread, is a point of significant debate among evolutionary biologists and theoreticians because many now reject natural selection's reliance upon random mutations. So before we go any further, let me give you a link to pop up that makes the association of random mutations with natural selection clear, from which I quote the following excerpts and please pay particular attention to the last paragraph:

". . . The mechanism of evolutionary change was natural selection. This was the most important and revolutionary part of Darwin's theory, and it deserves to be considered in greater detail. . . .

. . . Natural Selection Requires. . .

For natural selection to occur, two requirements are essential:

1. There must be heritable variation for some trait. Examples: beak size, color pattern, thickness of skin, fleetness.
2. There must be differential survival and reproduction associated with the possession of that trait.

Unless both these requirements are met, adaptation by natural selection cannot occur. . . .

. . . When we incorporate genetics into our story, it becomes more obvious why the generation of new variations is a chance process. Variants do not arise because they are needed. They arise by random processes governed by the laws of genetics. For today, the central point is the chance occurrence of variation, some of which is adaptive, and the weeding out by natural selection of the best adapted varieties. . . ."

Now the above becomes important in viewing the new formulation you have proposed:

autonomous self-organizing biological complexity + natural selection > species

Though you have attacked the Theory of Evolution for its inclusion of the "randomness pillar" you have persisted randomness in using natural selection as the engine of evolutionary change in your alternative model. This was why I suggested an alternative formulation using Rocha's paper in which he differentiated biological agents by the distinction of "syntactic autonomy":

". . . I propose that until a private syntax (syntactic autonomy) is discovered by self-organizing agents, these agents exist in dynamically coherence or situation with their environments that include other agents. At this stage there are no significant or interesting types of closure or autonomy. When syntactic autonomy is enabled, then, because of description-based selected self-organization, open-ended evolution is established. . . ."

Now I am still turning it over in my own head as to whether Rocha sees "open ended evolution" as the prevailing type, I even considered that he might be trying to suggest that it is likely the only type. But even though his emphasis is upon explaining the concept and the means by which it can be achieved, he at least holds out the possibility that two types of evolution can exist. He begins his paper by mentioning "we need first to understand the nature of distinguishable systems capable of evolving." And later, when discussing the disputes over natural selection he differentiates between biological agents "capable of semantic emergence in a selective environment" which indicates he does see them capable of evolving, and others that are "capable of a full situated semiosis" within "open ended evolution." This was why I suggested that you consider two types of models for evolutionary development as an alternative to your own, which persists randomness. Rocha uses the terms "Disabled" and "Enabled" to distunguish organizing agents, though he sees both as "self-organizing," based upon their ability to participate in the closure of semiotic systems. Rocha never states that "Disabled" agents evolve through natural selection, but since he did not discount the idea of natural selection entirely and he clearly argued that semiosis was something different, I believe the alternatives I suggested would be preferable.

Now; to deal with communication and behavioralist evolutionary models. You initially objected to the difference between "that which is physically alive from that which is physically not alive . . . being described by behavior" and you argued that communication was the key. But behavioralist or semiotic models exist because they enable communication, as Rocha pointed out in part 4 of his paper:

". . . The introduction of a syntactic code allows the kind of recombination of dynamic descriptions used for construction of organisms which leads to open-ended evolution when included in a self-replication scheme as specified by Von Neumann. It furthermore allows the communication of these descriptions to systems which possess the same semiotic code. . . ."

Without communication, syntactic autonomy is impossible. But this is not to say that communication is an unresolved problem in semiotic systems, quite the contrary. See Mouton de Gruyter's "Explaining and Understanding Life" article from the journal Semiotica for a discussion that includes references to Shannon.

Finally; on the rise of biological information and the Theory of Intelligent Design you wrote:

". . . In the absence of a plausible materialistic explanation, the very existence of information in biological systems points directly to Intelligent Design. . . ."

I view this as an unscientific statement. I could accept it if it were reformulated as:

"With materialistic explanations for the existence of information in biological systems now disproven, the very existence of that information points directly to Intelligent Design."

But the fact of the matter is that exobiologists are working to provide the materialistic explanation of which you speak. They have made some progress in explaining the chemical synthesis of RNA as has been pointed out in other posts earlier in this thread. Until exobiologists disprove all materialistic explanations, they remain a possibility, especially in light of the progress they have made up until this point.

". . . At any rate, the recent peer-reviewed article by an Intelligent Design theorist concentrates on two points: the rise of information and geometry in biological systems. . . ."

I took a look at the article and I found some of its points to be highly questionable, so I googled a search on it and I found that the Council of the Biological Society of Washington has issued a statement of repudiation of the article, stating that its publication was a mistake and explaining that one of the reasons it happened was that the article did not go through the normal peer review process. I'll post their statement here:

"The paper by Stephen C. Meyer, "The origin of biological information and the higher taxonomic categories," in vol. 117, no. 2, pp. 213-239 of the Proceedings of the Biological Society of Washington, was published at the discretion of the former editor, Richard v. Sternberg. Contrary to typical editorial practices, the paper was published without review by any associate editor; Sternberg handled the entire review process. The Council, which includes officers, elected councilors, and past presidents, and the associate editors would have deemed the paper inappropriate for the pages of the Proceedings because the subject matter represents such a significant departure from the nearly purely systematic content for which this journal has been known throughout its 122-year history. For the same reason, the journal will not publish a rebuttal to the thesis of the paper, the superiority of intelligent design (ID) over evolution as an explanation of the emergence of Cambrian body-plan diversity. The Council endorses a resolution on ID published by the American Association for the Advancement of Science (http://www.aaas.org/news/releases/2002/1106id2.shtml), which observes that there is no credible scientific evidence supporting ID as a testable hypothesis to explain the origin of organic diversity. Accordingly, the Meyer paper does not meet the scientific standards of the Proceedings.

We have reviewed and revised editorial policies to ensure that the goals of the Society, as reflected in its journal, are clearly understood by all. Through a web presence (http://www.biolsocwash.org) and improvements in the journal, the Society hopes not only to continue but to increase its service to the world community of systematic biologists.

That paper does not meet peer review standards, as even the society which published it regrets its error.

Thank you so much for your replies! I’ve decided to respond to them in reverse order in order to get the simplest responses out-of-the-way first (LOL!)

It has been a pleasure discussing all of this with you primarily because you have refrained from posting third party rebuttals and have instead been asserting your own exhaustive reasoning with source information for background and context. Therefore, I found your last post at 324 disappointing.

It is the nature of peer review to sanction theory which is not “politically correct”. This has lead to a number of tragic results which Lurkers can read about here: Refereed Journals: Do they ensure quality or enforce orthodoxy?

In sum, Nobel prize winners whose papers were rejected include Rosalyn Yalow, Gunter Blobel, Mitchell Feigenbaum. Stephen Hawking’s paper on black holes was also rejected. And, by the way, none of Einstein’s ground breaking papers went through a “peer review” process. Personally, I think it is doubtful any university professor in his day would have accepted Einstein’s theories for publication.

Darwin was not subjected to peer review – neither was Newton or Galileo. Ergo, the quality of the science is not determined by whether it not it survived a peer-review.

In Einstein’s case, the editor was the one who decided whether to publish. That is what happened with this article from the Intelligent Design theorist - the publisher’s remorse for breach of orthodox notwithstanding (emphasis mine):

The Council endorses a resolution on ID published by the American Association for the Advancement of Science (http://www.aaas.org/news/releases/2002/1106id2.shtml), which observes that there is no credible scientific evidence supporting ID as a testable hypothesis to explain the origin of organic diversity. Accordingly, the Meyer paper does not meet the scientific standards of the Proceedings.

For all these reasons, I dismiss both their official response and your quoting it as authority.

But the fact of the matter is that exobiologists are working to provide the materialistic explanation of which you speak. They have made some progress in explaining the chemical synthesis of RNA as has been pointed out in other posts earlier in this thread. Until exobiologists disprove all materialistic explanations, they remain a possibility, especially in light of the progress they have made up until this point.

Exobiology deals with extraterrestrial life. Cosmic ancestry, or panspermia, in arguing against the “theory of evolution” uses rationale which is often indistinguishable from the Intelligent Design arguments. Lurkers might wish to compare the arguments: panspermia to intelligent design. Francis Crick in his book Life Itself - and elsewhere - sounded like any other Intelligent Design theorist in his panspermia speculations.

Notwithstanding all of the above, my original statement would not require a plausible theory for the rise of information in biological systems to have an extraterrestrial materialistic causation. In the realm of terrestrial theory, models which suggest a mechanism like a finite state machine (e.g. Rocha) are being considered for the RNA world scenario. Even so, this would only broach biological autonomy and symbolization – the question of “successful communication” remains unanswered.

All of that brings me to your first post! Whew…

Somehow we have managed to get into a side bar discussion of biosemiosis. The issue that I raised originally focused on self-organizing complexity – which in application to evolution would be biological and autonomous and of course, requires biosemiosis - hence all the emphasis on symbolization.

I raised self-organizing complexity as a separate issue from “natural selection” – though one of the strongest proponents of cellular automata, Stephen Wolfram, goes a step further and suggests that it answers the entire evolution model. In his book, A New Kind of Science, Wolfram says:

[I]n the end, therefore, what I conclude is that many of the most obvious features of complexity in biological organisms arise in a sense not because of natural selection, but rather in spite of it.

But I do not go as far as Wolfram. IMHO, natural selection still plays a part because not all body plans and variations are created equal – some will survive in the environment, others will not. But the true “engine” of biological innovation is not in random mutations but rather in “autonomous biological self-organizing complexity.”

Now, let us turn to the "randomness pillar" of the Theory of Evolution. I believe this is a misnomer, unless you insist that the Theory of Evolution can only be viewed as the entirety of Darwin's original formulation. The problem stems from the definition of the “theory of evolution”. As long as people construe the theory as Darwin proposed it – random mutation + natural selection – it is in error based on what we know today about regulatory control genes (eyeness, etc.) The theory needs to be reformulated and hopefully, renamed. Euclid’s geometry became “dated” as did Newtonian gravity. The same has happened to Darwin.

IMHO, the far majority of contention over evolution would subside if only the randomness pillar were disavowed. After all, the primary difference between Intelligent Design and Evolution is that one is directed and the other happenstance.

Though you have attacked the Theory of Evolution for its inclusion of the "randomness pillar" you have persisted randomness in using natural selection as the engine of evolutionary change in your alternative model. This was why I suggested an alternative formulation using Rocha's paper in which he differentiated biological agents by the distinction of "syntactic autonomy":

". . . I propose that until a private syntax (syntactic autonomy) is discovered by self-organizing agents, these agents exist in dynamically coherence or situation with their environments that include other agents. At this stage there are no significant or interesting types of closure or autonomy. When syntactic autonomy is enabled, then, because of description-based selected self-organization, open-ended evolution is established. . . ."

Natural selection is not the engine of evolutionary change in my alternative model, rather “autonomous biological self-organizing complexity” is the engine. In Rocha’s work I do not see where syntactical autonomy speaks against natural selection at all. Autonomy is necessary to formulate the symbolization for semiosis. At the end of his paper, for an RNA world, he speculates on something like a “finite state machine” changing states between autonomous and non-autonomous to bootstrap a self-organizing mechanism. Without autonomy, there can be no self to organize.

Now; to deal with communication and behavioralist evolutionary models. You initially objected to the difference between "that which is physically alive from that which is physically not alive . . . being described by behavior" and you argued that communication was the key. But behavioralist or semiotic models exist because they enable communication, as Rocha pointed out in part 4 of his paper:

". . . The introduction of a syntactic code allows the kind of recombination of dynamic descriptions used for construction of organisms which leads to open-ended evolution when included in a self-replication scheme as specified by Von Neumann. It furthermore allows the communication of these descriptions to systems which possess the same semiotic code. . . ."

Your statement that “behavioralist or semiotic models exist because they enable communications” is not clear. Semiosis is the process whereby connections are made between symbols. It can be compared to a circuitboard or software. As Rocha says, it “allows the communications”. But it is not the communication itself. A circuitboard or software is dead as a doornail without electricity – and DNA, semiosis capability, chemicals are dead as a doornail without communication.

By examining the semiosis, the symbolization, the autonomy, the changing of states – Rocha and other researchers are proposing the mechanism (or software if you will) for self-organizing complexity in biological systems.

Perhaps we can clear the air a bit by agreeing at least to this: that DNA and biosemiosis is evidence that communication has successfully occurred in biological life.

Or in the computer metaphor - the database and software stored on your hard drive is evidence that the electricity to your computer has been successfully turned on.

I only have a couple of minutes to respond before I have to leave, so I'll take everything up to the "side bar discussion of biosemiosis" as you describe it, and I know a few things I would like to say about that as well, but I want to have some free time, of which I've spent quite a bit these past few days on this thread.

First of all, your disappointment about my post 324 quoting the official statement of the society which published the paper you referenced. You cited that paper as a "recent peer-reviewed article," which I took to mean that you believed it had some authoritative backing as legitimate scientific scholarship. And in earlier posts you have gone to great lengths to make certain that I did not misunderstand any theoretical points you have raised as metaphysical, but rather scientific, and I always commented as to whether the scholarly works you referenced met that test, which they had done up until that last citation. But that paper does not meet it and I regard your resort to calling peer review a "politcally correct" type of scholarly activity as disingenous. Peer review exists for a reason and in the case of that paper it should have rejected it because the author asserts that which cannot be disproved, namely Intelligent Design. He spends a great deal of time pointing out problems with a list of work on the Cambrian Explosion, but at no time does he offer anything in contrast that can be scientifically tested, that is to say disproven using recognized scientific method. These are his conclusions:

"An experience-based analysis of the causal powers of various explanatory hypotheses suggests purposive or intelligent design as a causally adequate--and perhaps the most causally adequate--explanation for the origin of the complex specified information required to build the Cambrian animals and the novel forms they represent. For this reason, recent scientific interest in the design hypothesis is unlikely to abate as biologists continue to wrestle with the problem of the origination of biological form and the higher taxa."

Now to go directly to the point about "the quality of science" you raise in your last response I defy you or anyone else to point out one single thing within the above quoted conclusions about how "purposive or intelligent design" is "a causally adequate explanation for the origin of the complex specified information required to build the Cambrian animals and the novel forms they represent" that can be tested scientifically. There simply is none and as scientific scholarship it is woefully deficient. Now you may wish to point to other great scholars who have had seminal works rejected by peer review, and I can come up with my own list to match it, but in this instance the process of peer review was not used and an incredibly deficient work of scholarship was published when it should have been rejected. Again, I did not raise the issue of peer review with this article Alamo-Girl, you did and I ask you to acknowledge that fact. I felt I was perfectly empowered to address it for that reason.

Now if you want to take his paper apart bit by bit I invite you to put up your critique of it and I'll respond in kind. I'll even give you the following observations to begin with. Meyer falsely claims there are no transitional fossils for the Cambrian period, he cites at least one paper on taxonomic sampling for the Middle and Late Paleozoic and applies it as evidence for the Cambrian, he relies heavily on another Intelligent Design theoretician (Dembski) which makes Intelligent Design believable because Intelligent Design advocates say it is (begging the question), he asserts that scientists and mathematicians have questioned mutation and selection as capable of generating "information in the form of novel genes and proteins" without telling us who these scientists and mathematicians are -- all the while ignoring the fact that it is quite easily-observed in the lab, in nature, and in a wealth of scientific literature that compares genomes, and more and more. You have my ultimate assessment of its invalidity just stated.

Now, on to Exobiology. This is how you describe it:

"Exobiology deals with extraterrestrial life. Cosmic ancestry, or panspermia, in arguing against the “theory of evolution” uses rationale which is often indistinguishable from the Intelligent Design arguments."

I invite you to review my post #166 in this thread where I introduced Exobiology. It is far different from the take you have just given and I believe there is a significant amount of genuinely scientific scholarship undertaken within it to justify my holding it out as truly scientific. You can try to take on the validity of the work and I'll address that in turn as well.

That's as far as I can go tonight. I'll get on to biosemiosis, the random nature of natural selection, successful communication and the rest tomorrow when I have some more time. Got to go now.

Thank you for your replies and links!

PatrickHenry: But given the publishing record of ID, bashing the peer-review system is really all they've got to say for themselves -- other then doing the ol' razzle-dazzle before befuddled schoolboard members.

That old razzle-dazzle is my objection here. Sometimes evolution threads look like the card game "battle" as each side trumps the other with yet another third party article. Some have compiled exhaustive lists of play and trump links which help newcomers get past the 'boilerplate' so that new discussion can commence. But for an oldtimer like me on these threads, the subject gets stale fast when posters play "battle". Conversely, the discussion here has been based on independent thinking and I find that quite delightful.

BTW, the school board meetings also strike me as a game of "battle". Each side throws rational alternative views on the table and ultimately both sides complain that the other's theory is a fabrication and is not falsifiable. Boasts of "explanatory power" and accusations of "just so" stories go back and forth. A case in point:

DrJacques:Now to go directly to the point about "the quality of science" you raise in your last response I defy you or anyone else to point out one single thing within the above quoted conclusions about how "purposive or intelligent design" is "a causally adequate explanation for the origin of the complex specified information required to build the Cambrian animals and the novel forms they represent" that can be tested scientifically. There simply is none and as scientific scholarship it is woefully deficient.

Both sides are blinded to its applicability to their own theory, but this is the same objection raised by Sir Carl Popper in Science as Falsification:

I found that those of my friends who were admirers of Marx, Freud, and Adler, were impressed by a number of points common to these theories, and especially by their apparent explanatory power. These theories appear to be able to explain practically everything that happened within the fields to which they referred. The study of any of them seemed to have the effect of an intellectual conversion or revelation, open your eyes to a new truth hidden from those not yet initiated. Once your eyes were thus opened you saw confirmed instances everywhere: the world was full of verifications of the theory. Whatever happened always confirmed it. Thus its truth appeared manifest; and unbelievers were clearly people who did not want to see the manifest truth; who refuse to see it, either because it was against their class interest, or because of their repressions which were still "un-analyzed" and crying aloud for treatment.

The most characteristic element in this situation seemed to me the incessant stream of confirmations, of observations which "verified" the theories in question; and this point was constantly emphasize by their adherents. A Marxist could not open a newspaper without finding on every page confirming evidence for his interpretation of history; not only in the news, but also in its presentation — which revealed the class bias of the paper — and especially of course what the paper did not say. The Freudian analysts emphasized that their theories were constantly verified by their "clinical observations." …

But back to peer review and the article and publisher statement.

I did not know when I posted the link to the article that it was reviewed only by the editor. Nor did I know that the publisher issued a statement claiming it went against their "standards". I do, however, have a long-standing distaste for intellectual gatekeepers with an ideological bone to pick. Ideology does not belong in science - either in the work product or the keeping of journalistic gates.

The article reads to me as an essay summarizing the state-of-the-art in competing theories, not as a presentation of empirical test results, predictions, etc. If anyone wishes to discuss the theories on that basis, or as they are summarized, that is fine with me and I'll be glad to participate (unless it devolves into a game of 'battle').

I wrote: "Exobiology deals with extraterrestrial life. Cosmic ancestry, or panspermia, in arguing against the “theory of evolution” uses rationale which is often indistinguishable from the Intelligent Design arguments."

You replied: I invite you to review my post #166 in this thread where I introduced Exobiology. It is far different from the take you have just given and I believe there is a significant amount of genuinely scientific scholarship undertaken within it to justify my holding it out as truly scientific. You can try to take on the validity of the work and I'll address that in turn as well.

There is nothing in your post at 166 which alters the definition of "exobiology". It is the branch of biology which addresses extraterrestrial life. It is serious government-funded, NASA sponsored, research. Crick, who found DNA, was a strong supporter of cosmic ancestry, aka panspermia.

Pointing out that the arguments in support of panspermia are often indistinguishable from the arguments in support of Intelligent Design is not an attack the validity of exobiology. Personally, I believe all of these lines of inquiry are valid, of keen interest to the public, and thus deserve equal consideration for public funding.

To the contrary, IMHO, the most effective "attack" on the theory of evolution (the Darwin formulation of random mutation + natural selection > species) is not coming from Intelligent Design or Cosmic Ancestry. Rather, it is coming from the mathematicians and physicists who have been brought to the table by the biologists in this information age. It is coming through the back door, not the front door.

Of all the disciplines, mathematics is the most epistemologically zealous. Information theory is a branch of mathematics. As persistent as mathematicians tend to be, I predict they will stay engaged in the quest until they have solved at least three of the challenges:

1. What is life? or the Pearson challenge, and

2. How did biological complexity emerge? or the von Neumann challenge, and

3. Applicability of randomness in biological systems? or the Chaitin/Wolfram challenge.

All of these are moving together towards a model which identifies information (Shannon, successful communication) as that which distinguishes life from non-life, complexity arising from the iteration of autonomous rules (von Neumann, cellular automata, self-organizing complexity) and randomness as an illusion of self-organizing complexity.

We haven’t spent any time discussing the last point, but essentially it amounts to the strict definition of randomness and complexity. To simplify the concept, if a string of numbers can be produced by a simple algorithm it is not considered very complex (Kolmogorov). A string may have the characteristic of randomness and yet be the effect of a cause (Chaitin’s Omega) – which raises the possibility that apparent randomness is an illusion, a selection from a string from a prior cause (Wolfram). Hence, it may be possible to determine an underlying algorithm which gives rise to apparent complexity and/or randomness (Solomonoff induction).

". . . BTW, the school board meetings also strike me as a game of "battle". Each side throws rational alternative views on the table and ultimately both sides complain that the other's theory is a fabrication and is not falsifiable. Boasts of "explanatory power" and accusations of "just so" stories go back and forth. A case in point:

DrJacques:Now to go directly to the point about "the quality of science" you raise in your last response I defy you or anyone else to point out one single thing within the above quoted conclusions about how "purposive or intelligent design" is "a causally adequate explanation for the origin of the complex specified information required to build the Cambrian animals and the novel forms they represent" that can be tested scientifically. There simply is none and as scientific scholarship it is woefully deficient.

Both sides are blinded to its applicability to their own theory . . ." . . .

I reject your contention that there is any equality of argument as presented by "each side" of the evolutionary debate and that "both sides" are blinded" to the applicability of their own theory. Proponents of the Theory of Evolution have a solid body of evidence upon which to base their claims and anyone who wishes to contest their hypotheses, arguments, and conclusions, can go directly to that evidence and observe, test, and compare new results if they want to challenge them. And that body of evidence is enormous. The evidence of Geologic Time provides a framework -- see my post #91 in this thread for more, the concurrence of the fossil record within distinct strata dated by geologic periods (stratigraphy) is consistent, morphologies and taxonomy can be argued from observation and comparative analysis of skeletal remains, evolutionary biologists and geneticists now work with DNA sequences and find evidence of common genes that cut across biological phyla, researchers working to find a cure for AIDS are making new discoveries about retroviruses that both begin with studies undertaken by evolutionary biologists and inform them further about new directions in their research, and on top of all of this is a mountain of field work in microbiological, botanical, and zoological studies that has tested various aspects of the Theory of Evolution.

What do its opponents have to offer in contrast? Though they are not an amorphous group who argue consistently in the same fashion the list of their objections include a misapplication of epistemological theory that argues "nothing is proven" whenever "absolute proof" is an impossibility in inductive reasoning (the basis of scientific method), which only seeks generalizations as its goal, a denial of the fossil record, a denial of Geologic Time, a denial of nuclear physics when contesting the ability to date rocks, a denial of the genetic findings of DNA and RNA sequences showing shared genetic traits across phyla, and, when all else fails, the postulation of the "Great Evolutionist Conspiracy" that includes almost the entirety of the scientific community including field researchers, the medical community, professional journals, independent theoreticians, government agencies, technically skilled professionals working in the private sector, academia, public school teachers, book publishers, and others who are supposedly all working in concert because anything that undermines the Theory of Evolution challenges their world-view, even though no group composed of such diverse backgrounds could possibly have such a unified world-view. This is the context in which I view the above-cited quote, we're now back to the "Evolutionist Conspiracy" again in which those who are asking for scientific proof and calling for observation of recognized standards within science need not be heeded because the very fact that they call upon authoritative sources as the basis for argument informs one and all that they cannot be trusted. I'll step outside of my usual restraint and respond in the vernacular here. B______t!

Now some brief comments on your last post. Exobiology does treat the possibility of extraterrestrial life, but that is now a scientifically-based pursuit since the discovery of the Murchison Meteorite revealed the presence of organic compounds which have also incidentally been discovered in gaseous clouds in space. And as for panspermia, I certainly don't believe in the version Hoyle argued.

Now, I want to comment on Semiosis and its relevance to this discussion, which you seem to suggest is a sidebar. It is not, because Semiotics is the branch of evolutionary biology that is moving the discipline away from a reliance upon pure "randomness," which you continue to suggest is a major failing of evolutionary theory. What I am seeing is that you argue that mathematicians are asking questions that put the logic of randomness under fire, evolutionary theorists are ignoring the questions, and the Theory of Evolution must therefore be called into doubt as a result. I am responding that randomness is for many trained observers a recognizable problem in evolutionary theory, scientists doing field research have called it into question by raising problems with natural selection, and theoretical constructs for evolutionary development are being reexamined, e.g. Pattee, Rocha, and Josslyn, that propose alternative models in which natural selection is at the very least undermined significantly. But it appears to me that you are attempting to hang on to what I consider to be a central misconception, namely; that there is no challenge to randomness. Perhaps, given your repeated insistence that the work of mathematicians is being ignored, what you really mean to say is that evolutionary theorists refuse to reject randomness on the grounds of mathematical probabilities. That last point is true and for good reason. It makes no sense in the world of science that the results of observation (induction) should be discarded in favor of probabilistic inference (deduction) because probabilistic inference has no direct relationship to causality (which is a central point of Shannon's communication theory by the way). The place of randomness in evolutionary theory is related to natural selection, for which I even provided a quote from a scientific source, which you also seem to ignore.

Now; mathematicians may be more "espistimelogically zealous" in proposing theoretical constructs that can be applied to the study of evolution, though certainly no less zealous than Pattee, but their propositions for reexamining randomness do not carry the weight of the field research produced by evolutionary biologists to undermine natural selection, since the latter must put theory into practice.

Let me deal with Shannon and information directly now. Shannon's propositions fall within statistical analysis and probability theory, something with which I am thoroughly familiar from my own professional background. The relevance of probability theory to models of evolutionary development is that they inform evolutionary scientists of logical constructs which, depending upon the context of theories, either should be incorporated into their work, or at the very least accounted for in some way. When Shannon talks about "successful communication" he refers to a message that begins as information is then sent and received and afterwards is transformed back into information that is either exactly or approximately the same as its original. When applied to systems theory in general it can be used to establish a statistical correlation between the behavior of two systems, from which we may hypothesize a causal influence of one system acting upon the other in some fashion, but only at risk because "successful communication" is not a theory of causal influence, it is pure probability. It is also relevant to "Shannon Entropy," which refers to the number of placeholders (or bits) needed to represent the message. Dembski and other Intelligent Design theorists rely upon Shannon entropy to establish probability models to explain "complexity" which they believe indicates that a deterministic model, such as evolution, is statistically impossible. First of all, that is false. Complexity is not the same thing as the probability of an event occuring and the probability of life processes becoming so complex as to be statistically impossible is not represented in communication models either. But Intelligent Design theorists want to believe it is because they wish to move the debate from scientific observation and testing (induction) to deductive mathematics (intuition) because they know they cannot win if their proposals are to be validated against empirical data, which is something that cannot be done with Intelligent Design.

With that in mind I come to your last assertion about where evolutionary theory is heading:

". . . All of these are moving together towards a model which identifies information (Shannon, successful communication) as that which distinguishes life from non-life, complexity arising from the iteration of autonomous rules (von Neumann, cellular automata, self-organizing complexity) and randomness as an illusion of self-organizing complexity. . . ."

Only in the dreams of Intelligent Design advocates is the debate over the Theory of Evolution moving towards a probabilistic information model that denies randomness has been addressed in evolutionary theory and dismisses real world scientific observation, seeking only to negate its results with mathematical formulae. While I am only an outside observer, my restatement of where evolutionary theory is going would look something like the following:

Evolutionary theory will have to be modernized so as to accomodate the scientific revolutions in systems theory that is the result of quantum mechanics, in genetics and microbiology that suggests a semantics of genetic translation and expression, in geology to incorporate the evidence of real-world catastrophes, in mathematics to accomodate chaos theory and the morphology of structures, and in evolutionary field studies that have undermined the previously-held inviolability of natural selection.

While I have probably left something out I am certain that I am much closer to where evolutionary theory is really going.

Thank you for yet another original, exhaustive reply!

However, many of your statements presume positions which neither I nor the sources upon which I have relied have taken. Thus, they are arguments which I cannot further discuss. Here are some examples:

1. Intelligent Design advocates do not propose that the theory of evolution is, as you say, ”moving towards a probabilistic information model that denies randomness has been addressed in evolution theory and dismisses real world scientific observations”. Neither do I. For one thing, randomness is a pillar of the Darwin formulation: random mutations + natural selection > species. And for another, nowhere have I (or to my knowledge, any Intelligent Design theorists) – dismissed real world scientific observations. To enter that arena of dispute, you’d be talking to Young Earth Creationists who dispute the age of the universe, geological evidence, dating methods, etc.

Speaking only for myself, I assert that the theory of evolution as Darwin originally proposed it, relies on randomness in mutations which is not supported by the evidence, e.g. eyeness developing concurrently across many phyla. I will say it again. No matter how you chose to phrase it, the emergence of functional complexity across phyla (with eyeness as a prime example) – indicates that regulatory control genes are largely immutable and thus, the biological innovations which we call “species” is primarily the result of autonomous biological self-organizing complexity working together with natural selection.

2. You said ” When Shannon talks about "successful communication" he refers to a message that begins as information is then sent and received and afterwards is transformed back into information that is either exactly or approximately the same as its original.” The message is not information. Information is the decrease in uncertainty in the receiver.

Shannon’s formulation, is more accurately defined as follows:

Glossary for Molecular Information Theory and the Delila System

information: Information is measured as the decrease in uncertainty of a receiver or molecular machine in going from the before state to the after state.

"In spite of this dependence on the coordinate system the entropy concept is as important in the continuous case as the discrete case. This is due to the fact that the derived concepts of information rate and channel capacity depend on the difference of two entropies and this difference does not depend on the coordinate frame, each of the two terms being changed by the same amount."

--- Claude Shannon, A Mathematical Theory of Communication, Part III, section 20, number 3

3. You said: ” But it appears to me that you are attempting to hang on to what I consider to be a central misconception, namely; that there is no challenge to randomness. Perhaps, given your repeated insistence that the work of mathematicians is being ignored, what you really mean to say is that evolutionary theorists refuse to reject randomness on the grounds of mathematical probabilities. That last point is true and for good reason.” I have been saying all along that the randomness pillar of the Darwin formulation is being challenged. The Weiss article alone is evidence that it is not being ignored.

4. You said: ” Now; mathematicians may be more "espistimelogically zealous" in proposing theoretical constructs that can be applied to the study of evolution, though certainly no less zealous than Pattee, but their propositions for reexamining randomness do not carry the weight of the field research produced by evolutionary biologists to undermine natural selection, since the latter must put theory into practice.” But the mathematicians (including H.H. Pattee as a physicist and therefore deeply rooted in math) do not seek to undermine natural selection – with the one notable exception of Stephen Wolfram.

The collective research centers on the von Neumann challenge, that complexity in biological systems arose from simple rules by iteration (cellular automata). This does not dispute the natural selection side of the Darwin formulation, though it does diminish the random mutation side of the equation: random mutation + natural selection > species

Taken together, in your statements which I have excerpted above, you are evidently suggesting that physical evidence gathered in field work trumps the mathematicians. But there is no dispute between biological self-organizing complexity and the fossil evidence.

5. You said: ” Complexity is not the same thing as the probability of an event occuring and the probability of life processes becoming so complex as to be statistically impossible is not represented in communication models either. But Intelligent Design theorists want to believe it is because they wish to move the debate from scientific observation and testing (induction) to deductive mathematics (intuition) because they know they cannot win if their proposals are to be validated against empirical data, which is something that cannot be done with Intelligent Design.”

However, I defined complexity rather strictly using the Kolmogorov construction, which is the most precise construct and is widely accepted among mathematicians. Also, deduction in mathematics is not intuition. Of all the disciplines, mathematics goes through strict “proofs” of its theories – whereas other disciplines rely on empirical tests and observations. Finally, Solomonoff induction is mathematics.

Concerning the Murchison meteorite, the latest information I’ve found is research identifying diamino acids in the Murchison meteorite. The panspermiasts are particularly interested in the Murchison meteorite. A reaction though in 2000 was that the Murchison meteorite was infested with earth bacteria and thus, was a false lead. For more on contamination of samples: imaging of biological contamination of meteorites.

You seem to be cross-pollinating between Young Earth Creationism and Intelligent Design. In the following excerpt, the items emphasized are peculiar to YEC:

What do its opponents have to offer in contrast? Though they are not an amorphous group who argue consistently in the same fashion the list of their objections include a misapplication of epistemological theory that argues "nothing is proven" whenever "absolute proof" is an impossibility in inductive reasoning (the basis of scientific method), which only seeks generalizations as its goal, a denial of the fossil record, a denial of Geologic Time, a denial of nuclear physics when contesting the ability to date rocks, a denial of the genetic findings of DNA and RNA sequences showing shared genetic traits across phyla, and, when all else fails, the postulation of the "Great Evolutionist Conspiracy" that includes almost the entirety of the scientific community including field researchers, the medical community, professional journals, independent theoreticians, government agencies, technically skilled professionals working in the private sector, academia, public school teachers, book publishers, and others who are supposedly all working in concert because anything that undermines the Theory of Evolution challenges their world-view, even though no group composed of such diverse backgrounds could possibly have such a unified world-view. This is the context in which I view the above-cited quote, we're now back to the "Evolutionist Conspiracy" again in which those who are asking for scientific proof and calling for observation of recognized standards within science need not be heeded because the very fact that they call upon authoritative sources as the basis for argument informs one and all that they cannot be trusted. I'll step outside of my usual restraint and respond in the vernacular here. B______t!

I am not a Young Earth Creationist per se. Relativity and the expansion rate of the universe clearly indicates that approximately 15 billion years from our space/time coordinates is equal to 6 equivalent days from the space/time coordinates of inception.

Age of the Universe

(In case you want to know, this exponential rate of expansion has a specific number averaged at 10 to the 12th power. That is in fact the temperature of quark confinement, when matter freezes out of the energy: 10.9 times 10 to the 12th power Kelvin degrees divided by (or the ratio to) the temperature of the universe today, 2.73 degrees. That's the initial ratio which changes exponentially as the universe expands.)

Therefore, considering your above paragraph and since I am not a Young Earth Creationist and do not subscribe to that line of reasoning, I have arrived at the point where I see no further good purpose to be served by our discussion. It has been quite engaging though and I do thank you very much for your research and for sharing your original thoughts!

Well I see your point in ending the discussion, but there are items in your response I cannot leave unaddressed.

"1. Intelligent Design advocates do not propose that the theory of evolution is, as you say, ”moving towards a probabilistic information model that denies randomness has been addressed in evolution theory and dismisses real world scientific observations”. Neither do I."

Behe and Dembski both present probabilistic models to explain complexity which argue that it is statistically unreasonable to assert the evolution of early higher-order life forms from simpler life.

"For one thing, randomness is a pillar of the Darwin formulation: random mutations + natural selection > species. "

Yes, of course it is. But you yourself cited Rocha whose "Syntactic Autonomy" called natural selection into question, I cited the study on grasses, and I've pointed out how other evolutionary theorists are calling natural selection into question. That is the state of at least one branch of evolutionary theory right now. And you cannot have natural selection without persisting randomness, which you have done while complaining that the "randomness pillar" is a central problem.

"And for another, nowhere have I (or to my knowledge, any Intelligent Design theorists) – dismissed real world scientific observations."

Stephen C. Meyer states that there are no transitional fossils leading up to the Cambrian Explosion, even though there are. I take that to be dismissal. But beyond that, the value of presenting hypotheses which can be tested in the real world is dismissed by Intelligent Design theorists, as I pointed out.

"No matter how you chose to phrase it, the emergence of functional complexity across phyla (with eyeness as a prime example) – indicates that regulatory control genes are largely immutable and thus, the biological innovations which we call “species” is primarily the result of autonomous biological self-organizing complexity working together with natural selection."

I see nothing in Weiss's article which argues that "functional complexity" emerged across phyla. He uses the terms "functional similarity" and "functional value." The word "complexity" is not even in his article at all. View the article as HTML and use the Edit -> Find tool to see for yourself. And he says the following about mutations and eyes:

". . . Such mechanisms may not be so difficult to induce rapidly in a new evolutionary context, as shown within species by the occurrence of sponta-neous ectopic wings, antennae, legs, eyes, nipples, teeth, or hair. This may just require the mutational production of short regulatory gene enhancer sequences in the DNA upstream of a gene that then becomes recruited. . . ."

At no point does Weiss say that regulatory genes are largely immutable. In fact in two different spots in the paper, the above citation and one a few sentences later he is pointing out "enhancer sequences" for regulatory genes. I do not see that Weiss's article makes the argument you claim. He does present what he himself calls "plausible scenarios" for the the evolution of eyes that he believes remain problematic because they appear to be post hoc reasoning, but that is as far as he goes.

"2. You said ” When Shannon talks about "successful communication" he refers to a message that begins as information is then sent and received and afterwards is transformed back into information that is either exactly or approximately the same as its original.” The message is not information. Information is the decrease in uncertainty in the receiver."

You wrote in the above that "the message is not information." That is correct, but that is also not what I stated. Read it again, just as you quoted me above. I wrote that after the message is sent and received it "afterwards is transformed back into information."

"3. You said: ” But it appears to me that you are attempting to hang on to what I consider to be a central misconception, namely; that there is no challenge to randomness. Perhaps, given your repeated insistence that the work of mathematicians is being ignored, what you really mean to say is that evolutionary theorists refuse to reject randomness on the grounds of mathematical probabilities. That last point is true and for good reason.” I have been saying all along that the randomness pillar of the Darwin formulation is being challenged. The Weiss article alone is evidence that it is not being ignored."

Ok, I take you at your word that you recognize it is being challenged. But in your post #322 you stated that mathematicians "will stay engaged in the quest until they have solved . . . Applicability of randomness in biological systems . . ." For that reason I took your position in the aforementioned quote to mean that you believed mathematicians would have to solve the applicability of randomness in biological systems, which would be a mathematical solution.

"But the mathematicians (including H.H. Pattee as a physicist and therefore deeply rooted in math) do not seek to undermine natural selection – with the one notable exception of Stephen Wolfram."

First; Pattee does undermine natural selection by promoting a semiotic model, which, in the works of others, includes "syntactic autonomy," the basis for a new engine of evolutionary change, semiosis. Second; and I repeat, natural selection is the means by which randomness is persisted in the Darwinian model. If mathematicians are working to solve the problem of "applicability of randomness in biological systems" then they are working on a theoretical alternative to natural selection. Natural selection is not just the passing on of a heritable trait through biological success, if you will go back to my post #322 and read the quote I gave you from a linked source you will see that ". . . variants do not arise because they are needed. They arise by random processes governed by the laws of genetics." That is natural selection as it is still used today.

On Von Neumann and complexity, I have no problem with what you posted, nor do I think your response contradicted me.

"Also, deduction in mathematics is not intuition. Of all the disciplines, mathematics goes through strict “proofs” of its theories – whereas other disciplines rely on empirical tests and observations. Finally, Solomonoff induction is mathematics."

Let's start at the end. Yes, Solomonoff induction and Quantitative Theory -- my background is in Quantitative Analysis -- are mathematics, to be sure. But deduction is dependent upon intuition in the same way that induction is dependent upon experience. Put another way, there are two methodologies of reasoning; Deductive and Inductive. Deductive reasoning can also be called "Intuitive" and Inductive reasoning can also be called "Empirical," i.e. "that which comes from experience." Deductive reasoning emphasizes Logic(which defines the rules for establishing the "mathematical proofs" you mention), whose rules of inference are understood by intuition. Inductive reasoning emphasizes experimentation, which occurs in the realm of experience.

Regarding Young Earth Creationism, I do not regard you as a Young Earth Creationist and never have.

I can tell by your suggestion that the discussion should end here that you realize it has become strained. It was never my intention to argue in a rough manner. But I definitely took offense to being slammed for posting the news of the scholarly rejection of the Meyer article, which I still believe says a lot about its lack of credibility. And I did not appreciate being lumped in as one in a school board battle being blinded as to the applicability of proof to evolutionary theory and then told that authority within the scientific community was reason enough to question it.

But in spite of all of this, if I have given offense for whatever reason, I offer an apology because I try to pride myself on a reliance upon rational argumentation. I wish you well Alamo-Girl.

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