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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observers removed from the phenomena they examine and that in fact, they are continuing to project the bias of an outdated language of Physics that was replaced by quantum theory and which still has applicability to the other scientific disciplines, biology in this case.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.)