Essay:Complaint regarding "Self-organisation in dynamical systems: a limiting result"

A major philosophy of science journal just accepted an Intelligent Design article, so Uncommon Descent got all pleased. The article is available online but not yet in print. I basically just got frustrated and threw together an impulsive e-mail to one of the journal editors. Below is the majority of that response, complete with typos, mistakes, and raw LaTeX. Additional thoughts welcome.

Draft of article Published version

(Most of) my response
It has come to my attention that Synthese has accepted (and made available online) an article of Richard Johns', "Self-organisation in dynamical systems: a limiting result". Being only a master's student in physics myself, I'm not in any particular way qualified to judge the philosophic or epistemic value of that work. However, I do have two linked concerns about the paper's mathematical and scientific assertions, which appear to be relatively straightforward and key to the article.

In fact, my first concern is just that; the article clearly proposes to demonstrate "that standard evolutionary theories of the origin of higher organisms are incomplete." In the form of the proposed "random equivalence" theorem, Johns states that "producing a given object with complexity n in a dynamical system is no easier than producing a given n-bit string in a completely random system" and goes on to suggest that abiogenesis and evolution via natural selection could not have produced life as we know it. These are not statements simply about methodology or epistemology, but rather statements about the theory of evolution that, if correct, would be of immediate import to evolutionary biologists. It seems odd that the paper was submitted to Synthese and not to a journal focused on theory of biology or mathematics. I think that one reason for this is Johns' involvement with the Intelligent Design community, which of course is not on friendly terms with most evolutionary biologists. That Richard Johns is supporting Intelligent Design may or may not be of interest to Synthese. However, it seems to me that the fact that he is using this publication to legitimate a hypothesis that cannot hold its own in mainstream biology, this fact should be of at least some concern. Such papers are often used to bolster the appearance that ID proponents are doing "real science" (which perhaps can be true, but does not guarantee the value of their results).

My second and more serious concern with the article is that some of the mathematical proofs provided therein are irrelevant to the conclusions that Johns draws from them. Having some experience with the tools he uses through work in quantum information and correlation, I find his proofs fairly transparent (as he notes himself, he is not a mathematician). It is fairly clear that this work has no direct bearing on evolution. For one, Johns' measures such as salience are invented ad hoc for this paper; there's little reason to agree with the interpretations he applies to them except a superficial plausibility. For another., section 10 involves an odd degree of hand-waving.

The biggest problem, however, is his use of the "random equivalence" theorem. I will acknowledge that the RE theorem holds for Johns' given definition of |\Pi *|, his odd definition of complexity, and one "given string" (or "target"). In fact, I think that it could be derived in an even more straightforward way, such that it would seem a step short of tautological.

But he is not describing anything remotely related to evolution, because evolution is not described by the search for one specific target. Rather, there is a large range of living things that can exist in many different environments, and the potential forms that life can take are different based on which environment they inhabit. By suggesting that evolution is somehow like adjusting the initial conditions (/Pi) to fit a given target, Johns' is taking the wrong approach entirely; the set of survivable organisms (the range of "targets") is in fact dependent on the environment and initial conditions, and a given starting organism will adapt to those conditions, as a result taking on one of any number of forms which individually would have seemed unlikely given the starting conditions. The type of retrospective determinism Johns' advocates was memorably described by Richard Feynman:

“You know, the most amazing thing happened to me tonight. I was coming here, on the way to the lecture, and I came in through the parking lot. And you won’t believe what happened. I saw a car with the license plate ARW 357. Can you imagine? Of all the millions of license plates in the state, what was the chance that I would see that particular one tonight? Amazing!”

With this sort of reasoning, anything can be made to seem unlikely.

There are yet further problems; Johns' "irregularity" is fairly strange. He seems to assume that local interactions cannot produce long-range order; this is not correct in some systems. Additionally, it is clear that living organisms are "regular" in some ways. Certain types of sequence tend to pop up in many different genes because they are particularly useful or the result of common copying errors. In a more banal way, every copy of a given gene is mostly identical to other copies of that gene, and even sequences that may appear very different may in fact be identical in the proteins they produce. To say in spite of this that the genome is "highly irregular" is not a trivial statement. Within the cell itself, there are multiple copies of various structures, machinery and organelles. Surely this is "regularity" on some level, at least in the way Johns seems to use it (to describe the local appearance of an object). And reproduction must count as producing regularity. Yet Johns gives a vague, hand-waving treatment of why we should think of organisms as being not too regular.

Johns' treatment of resources is fairly strange as well, because he does not work with the total time and space necessary to produce an organism, but with the number of products or attempts ("r") which is a function of both. Because his "strings" can overlap arbitrarily, a million-bit string can have two "attempts" with only a million and one bits.

I have some degree of frustration, which is not merely regarding advocates of bad science seeking legitimation through philosophy journals, nor merely regarding the main inadequacy of this paper (which could really be countered with a single paragraph and the Feynman quote). What is most frustrating is the sheer amount of oblivious sloppiness in the paper. It is surely plausible to someone who is checking it merely for consistency or is unfamiliar in the field, but one can't help but be baffled that such a very troubled amateur treatment could be given the green light, much less when it makes such grandiose claims as that it "rules out just about any naturalistic theory of the origin of life" (from Johns' blog), and by implication would be a scientific proof of a supernatural Creator.

I hope that you can give me some kind of reassurance, at the least as to why this paper was accepted by your journal despite (what I perceive as) glaring flaws. Of course you are not in any way answerable to me, but I would hope that you do have something to say in defense of that decision, or at least that the publication is better served by my pointing this issue out.