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.

"The experiments you cite don't seem to include the consideration of randomness."

There are two parts to the Theory of Evolution; the origin of new species, referred to properly as "speciation," and the engine of evolutionary change, which most, but not all, hold to be "natural selection." "Randomness" is only an issue if you discuss natural selection, it is not necessary to proving the origin of new species through evolutionary change. Contrary to what many who contest the Theory of Evolution argue, attacking the random character of mutations only undermines natural selection, it does not weaken the Theory of Evolution as explaining the origin of new species.

That having been stated, both articles can only be said to not include what you describe as the "consideration of randomness" if you insist that the controlled nature of the experiments eliminates randomness. There are two problems with this. One; there is no splicing of mutated genes to create new species done in the various experiments which means that the mutations were induced by controlled external conditions not by direct genetic manipulation. The bacterial splicing in the first article was done to test the ancestral strain's survivability in an environment free of antibiotics but containing the new resistant genes, not to create or test the evolved strains. Two; there can be no such thing as a scientific experiment without controlled conditions because scientific method requires controls to eliminate error. Since you asked for a "collection of experiments" that means you have requested scientific testing under controlled conditions. If you now argue that the controls on these experiments eliminates the consideration of randomness, which they do not since speciation was not the result of gene splicing, then you have asked for that which, by your definition, cannot be provided. But by the rules of scientific method it can and has been given.

Ok, I have briefly examined the two links you have provided. They are true scientific scholarship, though I am not sure at the brief glance I have given them whether they establish exactly what you seem to claim - and I want to make sure I do not misrepresent what you are arguing Alamo-Girl - so allow me to state a couple of points if I may. And I should state that, after a very brief read, I now understand that the term "self organizing" does not imply consciousness as I earlier either led myself to believe or was led to believe.

First; I want to point out something I have stated earlier in this thread, and elsewhere, which is that the engine of evolutionary change, generally accepted to be natural selection, is a subject of real debate among evolutionary scientists. Both of the papers you reference apply to this debate, but either in different ways, or perhaps better stated, to a differing degree in the way they argue for a reexamination of the assumptions evolutionary theorists operate upon, beginning with the very language of communication they share, which the two authors clearly believe leads them to operate upon premises about evolutionary systems that are false.

Pattee's paper (the first link) deals with the way evolutionary scientists reason and challenges their claims to true objectivity in pointing out that they are denying their own subjectivity in acting under the pretense that they are neutral observers removed from the phenomena they examine and that in fact, they are continuing to project the bias of an outdated language of Physics that was replaced by quantum theory and which still has applicability to the other scientific disciplines, biology in this case.

Rocha's paper goes farther to apply this call for a "new symbolic language" to evolutionary systems analysis and more. I think the following quote gets to the heart of this new "syntax" he feels must be applied (I'm removing superscripted footnotes from the text and underlining a portion for later comment):

". . . In evolutionary systems this is at the core of the feud between those who claim that natural selection is the sole explanation for evolution and those who stress that other aspects of evolutionary systems, such as developmental constraints, also play an important role. It is no wonder then that the first group stresses the symbolic description, the gene, as the sole driving force of evolution, while the second group likes to think of the propensities of matter or historical contingencies as being of at least equal importance in evolution. . . ."

To note the underlined text, I would refer you back to what I wrote earlier about the discussion of "entropy" as a possible driving force in the evolutionary development of grasses which at least one evolutionary biologist believes guided the material nature of mutations of newer strains of grasses that evolved from a common parent and which argued against natural selection as the sole driving force in evolution. This gets right to "the propensities of matter," as referenced above, which must interact with energy sources.

Now to backtrack a bit, Rocha will use this new "syntax" to establish an argument for J. Von Neumann's model of "open ended evolution" which refers to "a threshold of complexity after which systems that observe it can for ever more increase in complexity." The key point I want to make about this as it relates to the Theory of Intelligent Design is that consciousness and/or being are not discussed here. The point about "systems that observe" is related to the "expression" of information and the way it is "organized," expression being a term well understood in genetics. Now you are correct to point out that this is as much mathematical in nature as it is biological, because Rocha's work is in fact a treatise on "systems theory" that is applicable to computer models for artificial intelligence among other things, but right after the above quote (see italics) he does make a point that I believe will have significant meaning to evolutionary biologists:

". . . this model clearly does not rely on a distributed but on a local kind of memory. Von Neumann's descriptions entail a symbol system on which construction commands are cast. These descriptions are not distributed over patterns of activation of the components of a self-organizing system, but are instead localized on "inert" structures which can be used at any time -- a sort of random access memory. . . ."

Anyone who has been following some of the most recent developments in genetics and its application to evolutionary biology has seen the term "retrovirus" introduced as an unknown variable and still unresolved problem in evolution. Retroviruses have been shown to exist in DNA, they are essentially "inert" structures within RNA strands, and there has been some theorizing that these viruses may remain dormant until "triggered" by some unknown or not-yet-understood mechanism. I see no discussion of this in Rocha's paper, but I can only imagine that his use of the aformentioned language alludes to this possibility, while at the same time remaining relevant to his larger "systems theory" approach. One of the things that is most interesting about the work on retroviruses and the way they may impact genetic mutations is that they may establish a "pre-encoded design pattern" for mutations to follow, a very controversial proposition but one which has its adherents among evolutionary biologists and geneticists nonetheless. And it is in this area of "pre-encoded design patterns" for mutations that the unique presence of inert structures within DNA that contain retroviruses become "self-regulating" and "autonomous."

What all of this seems to suggest to my brief reading of those two sources, and that was a lot to digest in an hour and a half, is that Pattee and Rocha, the two authors you referenced, have proffered a very substantial argument that there may in fact be a design inherent in evolutionary development, but they have offered nothing that suggests consciousness, or intelligence, as a guiding factor. "Patterned Design," or "Translated Design," or "Semiotic Design," are all terms that may fit their work, but I think "Intelligent Design" may go too far.

Finally, I would like to refer to something you posted earlier as a model for evolution:

autonomous self-organizing biological complexity + natural selection -> species

I would suggest you consider the following two models, based upon Rocha's work (go to his conclusions for this) which distinguishes the models based upon their "discovery" of a "private syntax" for autonomous self-organization:

Model #1:

Disabled syntactic self-organizing agent + natural selection -> species

Model #2:

Enabled syntactic self-organizing agent + semiosis -> species

Semiosis being the translation process by which the original genetic structures are recognized within a pre-encoded design process and new genetic structures are built to replace them.

To sum it all up Alamo-Girl, I see real worth to the sources you have referenced but I come away from them, and again I have only examined them briefly, with the conclusion that they do not fully support "Intelligent Design" as it seems to me you may have done. I hope I have not misstated or misrepresented your position in all of this, but that is what I see. And I also hope you give me credit for a good faith effort to take you seriously, something which is not often done on these Crevo threads.

Thank you so much for your engaging reply, StJacques! I greatly appreciate your stepping through your analysis of the H.H.Pattee and Luis Rocha articles and especially your discussion of the retro-virus.

To sum it all up Alamo-Girl, I see real worth to the sources you have referenced but I come away from them, and again I have only examined them briefly, with the conclusion that they do not fully support "Intelligent Design" as it seems to me you may have done.

Neither Pattee nor Rocha are Intelligent Design theorists. And the concept of autonomous biological self-organizing complexity is not an Intelligent Design theory. Its roots are in von Neumann’s cellular automata which roughly proposes that complex systems, including biological systems, can arise autonomously through iteration of simple rules.

This explanation is a better “fit” for what is observed in nature than the simplistic happenstance of “random mutations”. The biological system of eyeness developing seemingly at the same time across many phyla is a good example. IOW, it is not reasonable to suggest that was the result of concurrent random coincidence of mutation. A more fitting explanation is an autonomous (essentially non-mutable) set of simple rules in a common ancestor which would have similar results concurrently through iteration (cellular automata).

Again, none of this is Intelligent Design theory. But it clearly illustrates that the original formation of ”random mutation + natural selection > species” needs to be brought up to date. I prefer the phrasing “autonomous biological self organizing complexity” because biological autonomy is crucial to the theory.

Although this formulation is not Intelligent Design theory, it is the bringing of mathematicians and physicists to the “evolution” table which has raised issues which point directly to Intelligent Design.

Chief among these, IMHO, is the mathematicians/physicists’ attempt to answer the question, ”what is life?”. Here’s a helpful thought experiment: visualize a dead skin cell and a live skin cell next to each other and meditate on the difference between the two.

To fast forward through a lot of research, the difference is information. Both contain the chemistry and the DNA which is as good dead as alive. In this construct, DNA is the message. Information, defined by Claude Shannon, is roughly a “successful communication”. More specifically, information is a reduction of uncertainty in the receiver, even in "a molecular machine".

The inability to find a plausible materialistic explanation for the rise of information both in biological systems and the universe points to Intelligent Design as clearly as does the beginning of time in all cosmologies (ekpyrotic, cyclic, multi-verse, multi-world, big bang, imaginary time, etc.) – the physical constants in this universe including the "rules" for "autonomous biological self-organizing complexity" - and (my personal favorite) “the unreasonable effectiveness of math” (why pi, Mandelbrot sets, Riemannian geometry being picked off the shelf to explain general relativity, duality in nature, dimensionality, etc.)

". . . The inability to find a plausible materialistic explanation for the rise of information both in biological systems and the universe points to Intelligent Design as clearly as does the beginning of time in all cosmologies (ekpyrotic, cyclic, multi-verse, multi-world, big bang, imaginary time, etc.) – the physical constants in this universe including the "rules" for "autonomous biological self-organizing complexity" - and (my personal favorite) “the unreasonable effectiveness of math” (why pi, Mandelbrot sets, Riemannian geometry being picked off the shelf to explain general relativity, duality in nature, dimensionality, etc.)"

In terms of biological theory, I do not believe that the problems of information and information exchange you cite point to Intelligent Design. And what I believe you are overlooking, to work within the theoretical assumptions of the authors you reference, is "Semiosis," which handles the problems of information and information exchange without inserting "consciousness" or "intelligence" into the mix, but which also uses a descriptive language alike unto itself that is relevant to "genetic expression," the semantics [as a term in language, not biology] of which appear to the average person to indicate intelligence, but is in fact part of the scientific nomenclature relevant to microbiology and evolutionary biology. I would like to recommend a link on Semiosis, which like Rocha's work has some applicability to larger systems theory, for reference here:

Kalevi Kull: On Semiosis, Umwelt, & the Semiosphere

And I want to directly paste in a quote from the above:

". . . a mechanism consisting of a sender, receiver, and transmitter of information does not work as a semiotic mechanism, while not embedded in a semiosphere. Also, biological terminology based on inheritance and reproduction hardly allows any further generalization due to its strong connection to the molecular genetic mechanisms which assume the concrete substances responsible for this process. Therefore, semiotic terminology of text and dialogue, recognition and translation may be much better suited for the description of isomorphisms between biological and cultural phenomena. This may be acceptable for both the language of natural sciences and that of the humanities and arts.

Thus, I define semiosis as a process of translation, which makes a copy of a text, suitable to replace the original text in some situations, but which is also so different from the original text that the original cannot be used (either spatially, or temporally, or due to the differences in text-carrier or language) for the same functions. This translation process (i.e., semiosis) requires two types of recognition processes. First, the translation assumes that parts of the original text are recognized (on the basis of pre- existing memory-text) and as a result new structures are built, whereas a certain isomorphism between the original and the new text is retained. And second, there is a recognition process which starts the translation process, which is required for the existence of the whole process on another level, and which at the same time gives an intentional dimension to any particular semiosis. I also state that the one carrying out the translation (the translator, which includes memory) is itself a text, i.e. the result of some translation process. From this definition it follows that semiosis always requires a previous semiosis which produced the translator. Since the translator already recognizes, i.e. matches with something, the form of which has been stored, i.e. which has previously been matched, it follows that the current translation process is preceded by some previous translation process. Also, the text used for translation is the product of a previous semiosis. . . ."

Semiosis is in fact more "behavioralistic" than "materialistic," but with that understanding in hand it does provide, to use your words, a "plausible explanation for the rise of information both in biological systems and the universe" that you suggested was the inherent problem with evolutionary theory that points to Intelligent Design. I believe the experts you have cited would argue that bio-semotic systems theory suggests otherwise.

"To restrict the practice of science only to the information which is gained through the scientific process is to discredit the art of practicing science. Just ask Einstein. Shucks, Newton would have told you that, centuries ago."

I think you need to review what you have learned of Newton and Einstein. Newton's scientific method was pure induction, which was in fact one of his great contributions to science. I'll paste in the following, reorganized as a bulleted list, from this link on Issac Newton:

". . . Newton presented his methodology as a set of four rules for scientific reasoning. These rules were stated in the Principia and proposed that:

We are to admit no more causes of natural things such as are both true and sufficient to explain their appearances
The same natural effects must be assigned to the same causes
Qualities of bodies are to be esteemed as universal
Propositions deduced from observation of phenomena should be viewed as accurate until other phenomena contradict them. . . .
. . . Newton wrote, 'As in mathematics, so in natural philosophy the investigation of difficult things by the method of analysis ought ever to precede the method of composition. This analysis consists of making experiments and observations, and in drawing general conclusions from them by induction...by this way of analysis we may proceed from compounds to ingredients, and from motions to the forces producing them; and in general from effects to their causes, and from particular causes to more general ones till the argument end in the most general. This is the method of analysis: and the synthesis consists in assuming the causes discovered and established as principles, and by them explaining the phenomena preceding from them, and proving the explanations.'"

Einstein, by comparison, was much more willing to discuss metaphysical concepts than Newton, but he nonetheless was extremely careful never to mix the two. As he saw it, scientific method was a means to understanding objective reality, but that understanding is not the highest end to which humanity aspires. I have a second link to give you a quote from Einstein that makes this clear:

". . . For the scientific method can teach us nothing else beyond how facts are related to, and conditioned by, each other. The aspiration toward such objective knowledge belongs to the highest of which man is capabIe, and you will certainly not suspect me of wishing to belittle the achievements and the heroic efforts of man in this sphere. Yet it is equally clear that knowledge of what is does not open the door directly to what should be. One can have the clearest and most complete knowledge of what is, and yet not be able to deduct from that what should be the goal of our human aspirations. Objective knowledge provides us with powerful instruments for the achievements of certain ends, but the ultimate goal itself and the longing to reach it must come from another source. . . ."

In Einstein's opinion science and metaphysics were not to be mixed, but metaphysics had its own place just the same.

Thank you for your reply!

Semiosis is in fact more "behavioralistic" than "materialistic," but with that understanding in hand it does provide, to use your words, a "plausible explanation for the rise of information both in biological systems and the universe" that you suggested was the inherent problem with evolutionary theory that points to Intelligent Design. I believe the experts you have cited would argue that bio-semotic systems theory suggests otherwise.

The article was quite interesting but obviously it is taking a behavioralistic approach to the definition of ”what is life?” rather than the more epistemologically zealous approach of mathematicians and physicists. The original challenge (quoted by Pattee):

"How, therefore, we must ask, is it possible for us to distinguish the living from the lifeless if we can describe both conceptually by the motion of inorganic corpuscles?" - Karl Pearson The Grammar of Science

Semiosis concerns the ability to establish connections between symbols and, whereas it speaks to the mechanism, translation and therefore effectiveness of communication, it does not speak to the successful communication itself, i.e. the reduction of uncertainty in the receiver (i.e. information, Shannon).

IOW, bio-semiosis is an effect of the rise of information in the universe and in biological systems – it is not the cause of that effect. As a metaphor, biosemiosis is like your computer and software, information (Shannon, successful communication) is like your electrical current and internet connection.

The first person to come up with a plausible cause which is published in a peer-reviewed journal will be able to claim the prize.

BTW, I do not wish to demean the value of biosemiotics for biological research. Symbolization is an important advancement in understanding molecular biology. As your article says:

Biosemiotics, if it is a paradigm for biology, should mean a different approach in all branches of biology. It cannot restrict itself to the re-interpretation of existing knowledge (like a philosophy of biology), with the application of a new terminology. It is a way of thinking, experimenting and describing for both theoretical and empirical biology. For Uexküll, Umweltforschung was, first of all, an experimental science, the detailed physiological description and analysis of functional circles, the investigation of sensors and effectors of organisms together with the codes which connect them both inside and outside the organism. The semiotic approach has raised this problem and makes this work meaningful. However, the problem of what the semiotic approach should mean for experimental biology, is still almost uninvestigated in contemporary biosemiotics.
From the point of view of sociology of science, biosemiotics, according to the impact made by Hoffmeyer, seems to be a child of the cultural movement, related somehow to the values of methodological anarchism and love of symbiosis, holism and critics of neo-Darwinism. However, my belief is that it should be combined with the results of theoretical biology, as we understand it at the end of the 20th century, with the understanding of complex systems, chaos, recursive mathematics etc. When combining all these tools, biosemiotics may indeed build the bridges it has started to build.

Ok, so if I understand you correctly, you believe that the evolutionary model will not be believable until it accounts for the origins of life rather than just explaining the processes of evolution within life. Am I right? If not, I'll wait for further elucidation.

Now; on to your quote from Pearson, which you note Pattee presents as "the original challenge." I would like to suggest that you examine exactly what the challenge is to which Pattee refers. It is not to define life in terms of purpose or normative values, but rather to propose a standard upon which to build an alternative to what he describes as the "reductionist" approach that has come to dominate within biology that uses the pre-quantum theory language of Physics when building biological models and systems. Pattee wants biologists (molecular, evolutionary, etc.) to develop a new symbolic communication that treats life and its processes differently than non-life. And he argues that scientists operating within the outdated epistemological framework of the "reductionist" era of Physics cannot accurately approach the dynamic nature of biological systems since they attempt to reduce them to constituent parts through the "measuring constraints" they impose, and in the process insert their own subjective judgement that natural laws permit them to accurately observe the phenomena from which they wish to draw scientific generalizations. And Pattee argues that this fails to incorporate the dynamic nature of the process of measurement when dealing with life, he says you must have "dynamical laws" as a complement to "natural laws," and is really only accurate in measuring the constraints scientists impose before making their observations. Note the following quote, I'm removing footnote notations again, taken from part 9 of Pattee's treatise:

". . . The most convincing general argument for this irreducible complementarity of dynamical laws and measurement function comes again from von Neumann. He calls the system being measured, S, and the measuring device, M, that must provide the initial conditions for the dynamic laws of S. Since the non-integrable constraint, M, is also a physical system obeying the same laws as S, we may try a unified description by considering the combined physical system (S + M). But then we will need a new measuring device, M', to provide the initial conditions for the larger system (S + M). This leads to an infinite regress; but the main point is that even though any constraint like a measuring device, M, can in principle be described by more detailed universal laws, the fact is that if you choose to do so you will lose the function of M as a measuring device. This demonstrates that laws cannot describe the pragmatic function of measurement even if they can correctly and completely describe the detailed dynamics of the measuring constraints. . . ."

What Pattee is doing here is applying the language of quantum physics to scientific observation of biological phenomena by pointing out that observing life itself changes the rules. It is the same logic Neils Bohr used (and Pattee cites him) when he proved that you could measure the speed of an electron without knowing its location or conversely you could ascertain the location without measuring the speed because the observer acted as a subjective participant choosing to target one or the other and that both could not be known simultaneously, thus contradicting one of the key principles of Newtonian physics, which is that knowledge of all phenomena could be known. In the same way that quantum physics moved science beyond Newtonian "natural law" philosophy, a new dynamic form of reasoning that accounts for life as something distinct from non-life and recognizes the subjective role the observer plays is needed, according to Pattee and Von Neumann. Quite frankly, it's brilliant. But that is the context in which Pattee asks the question "what is life"? Because he views it as a dynamic system whose observable phenomena must be handled within a new context of observation that accounts for the role of the observer. He is not asking the question in reference to the origins of life, he is insisting that life functions under a dynamical system all its own.

And finally; Semiosis and the "rise of information both in biological systems and the universe." I wish I had caught something I now see in this precondition you set because, when discussing the Theory of Evolution, the rise of information in biological systems is relevant while the rise of information in the universe is irrelevant. The first condition is a scientific query. The second is a metaphysical one that can never be proven or disproven and has no place in a scientific discussion of the Theory of Evolution. Semiosis, according to its adherents, is the control mechanism of evolution, explaining how it proceeds from one step to the next. As a control mechanism that starts, runs its course, finishes, and then starts again it is circular in nature but it does explain how the rise of information proceeds from one stage to the next. To view the entirety of the rise of information you need a linear model, which is how Von Neumann presented "open ended evolution." Semiosis does not offer an explanation that begins before the origins of life, as Pattee makes clear in part 10 of his paper:

". . . We speak of the genes controlling protein synthesis, but to accomplish this they must rely on previously synthesized and organized enzymes and RNAs. This additional self-referent condition for being the subject-part of an epistemic cut I have called semantic (or semiotic) closure. This is the molecular chicken-egg closure that makes the origin of life problem so difficult. . . ."

So Semiosis does not explain the origins of the first stage of the creation of information in a biological system but it does explain the dynamics of how that information rises from simple to ever more complex stages. And the joining of the circular model of Semiosis with a linear model is a "Semiotic System" as argued by Cliff Josslyn, another of the Los Alamos scientists building upon Pattee's work, in his paper The Semiotics of Control and Modeling Relations in Complex Systems. See part 6, "Controls and Models as Semiotic Systems."

Now as I stated in the beginning of this post, I'll have to wait and see whether you will argue that the Theory of Evolution fails because it does not offer an explanation for the origins of life. I will point out that I find none of the experts you have referenced presenting this as a shortcoming of the theory, though I imagine this is viewed as a problem in the Theory of Intelligent Design, which I am gradually coming to view at a distance, though I have not read it personally, as unscientific.

Thank you for your reply!

Now as I stated in the beginning of this post, I'll have to wait and see whether you will argue that the Theory of Evolution fails because it does not offer an explanation for the origins of life.

I have made no such claim. In the first place, the origin of life is not part of the theory of biological evolution. And in the second place, my claim from post 264 forward has been that the “theory of evolution” needs to be brought up-to-date. Specifically, I said:

As evidence I assert the randomness pillar in the equation random mutation + natural selection > species stands defeated because regulatory control genes are not mutable.

A better formulation for today might be autonomous self-organizing biological complexity + natural selection> species - but it shouldn't be called the theory of evolution since the first formulation fails.

I offered the seemingly concurrent geological evidence of the evolution of the eye across many phyla as an example of the fatal flaw in the “randomness pillar” of the theory of evolution. Further, I offered information on “autonomous biological self-organizing complexity” to support why it is a better explanation than randomness. Everything I offered is conventional, mainstream science.

Nowhere have I said that the theory of evolution fails because it doesn’t address the origin of biological life.

What I have raised in support of Intelligent Design theory is that information (Shannon, successful communication) is that property which separates that which is physically alive from that which is physically not alive. I objected to the difference being described by behavior (symbolization/semiosis) since there is an underlying physical difference, i.e. information; and I noted that the chemical and DNA constituents are just as good dead as alive. The hard, physical, difference between a dead cell and a live one is information – one successfully communicates with itself and its environment, the other has ceased communicating. The chemicals, the DNA, the semiotic potential remains – but is dead without the successful communication.

The quest for a materialistic explanation of the rise of biological information has nothing to do with the “theory of evolution” – but it has everything to do with abiogenesis/biogenesis. It is among the inquiries of the Chowder Society which is comprised of such formidable scientists as Tom Schneider (Laboratory of Experimental and Computational Biology) and Hubert P. Yockey (physicist, professor and author, Information Theory and Molecular Biology).

In the absence of a plausible materialistic explanation, the very existence of information in biological systems points directly to Intelligent Design. To that I will now add that autonomous biological self-organizing complexity is not directionless or happenstance and thus serves Intelligent Design theory equally as well as Evolution Theory (provided that regulatory control genes are largely immutable).

IMHO, Intelligent Design theory went off-track by using a backward looking approach at molecular evidence in proposing “irreducible complexity”. Evolution theory was formulated by looking backward, but Intelligent Design theory would have been better served (IMHO) by focusing on the rise of functional complexity – and in particular, the rise of functional complexity across phyla. Perhaps it would have been first to propose autonomous biological self-organizing complexity. At any rate, concurrent evolution by autonomous biological self-organizing complexity suggests a high degree of non-mutable regulatory control genes in common ancestors. To Intelligent Design theory, this in combination with the Cambrian Explosion might suggest direction, i.e. intelligent design.

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. Since both deal with origins, neither should be considered as assaults on "the theory of evolution".

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