TDI Web Log

Our paper Enzyme Induction paper has finally been published!  Woohoo!

Things come in threes. I’m beginning to think that this “law of threes” might be a good gauge for when one should actually speak. Perhaps I’ll try it one day … just keep my mouth shut until there are 3 similar things about which to talk.

Anyway, I recently hosted a poster at the Engineering in Medicine and Biology Conference (EMBC) entitled: Using an In Silico Liver to Evaluate a Hepatic Enzyme Induction Mechanism. I won’t attempt to explain the contents, here (thank the gods, eh?); but the gist of it was that all models, including in silico (a.k.a. computational), in situ, in vitro, in vivo, indeed ALL ways of interacting with anything, involve what we’re calling a “phenomenal manifold” (a.k.a. an “aspect” as in Aspect-Oriented Programming). Basically, whenever a subject interacts with an object, the interaction is always mediated by some layer … a membrane. The subject cannot reach directly inside the object and manipulate or observe anything she might want to. Such interaction is always distorted, governed, or transduced through this layer. Granted, sometimes the layer can be very transparent so that it seems as if you’re touching the object directly. But in other cases, there are highly nonlinear or unpredictable effects when the subject manipulates the object or the data from observation can be very cryptic or misleading.

Why is this important? Well, in the context of using computational models to understand an extant system, the phenomenal manifold must be explicitly included in the experimental method. Otherwise, the results will not be repeatable and the effort can’t be considered “science”.

That’s the first of the three. The second is that one of us just got their hands on a high powered microscope and his family has been spending quite a bit of time staring at pond water animals through it. This sparked an argument between me and him about the telos of these animals’ motion. I suggested that it was primarily (say 70%) random, probably even Brownian (an aggregate of collisions with much smaller forces). He countered that their movements seem very purposeful, that they very clearly swim from place to place.

Now, I ran this by a few people, including biologists, and they all agree with him. The consensus seems to be that the motions of these animals do have telos and I am wrong. However, I maintain my skepticism primarily because this has the same texture as a mistake I’ve seen people make over and over again, never learning the lesson. We humans always ascribe telos. It is the fallacy of anthropocentrism. Besides, I can imagine many random, including Brownian-style, mechanisms that might generate seemingly purposeful behavior. So, as long as my imagined proto-hypothetical mechanisms are not falsified, my skepticism is appropriate and it’s just sloppy thinking to jump to the conclusion that the motions must be purposeful.

So that’s 2. And I was waiting for my partner to post some pictures or video about this locomotion to launch into the argument, here. But then the third thing came rattling down the pipe. I finally got caught up on my e-mail and, lo’ and behold, I find this post on Panda’s Thumb, wherein we find the telos-obsessed Intelligent Design people misquoting John von Neumann regarding the disturbing randomness at the heart of evolution. It’s useful to requote an excerpt of the quote used by Douglas to show that Berlinski misrepresented von Neuman.

Yet many efficient (?) and purposive (??) media, e.g., language, or the national economy, also look statistically controlled, when viewed from a suitably limited aspect.

In the course of my duties as a biological modeler (whatever that may mean to you, my dear reader; were you to exist, of course) I am sporadically called upon to wax explanatory on the relation between generators (abbreviated and unitized as “gene” in some domains) and phenomena. The path from generators to phenomena is called the “forward map” and, perhaps obviously, the path from the phenomena back to its causes, the generators, is called the “inverse map”. It is largely the subject of plectics ¹ (a.k.a. complexity theory) to discover, use, and make repeatable, methods for accurately following these two paths. A primary premise of the computationalist approach to plectics is that the forward map is not so straightforward. I.e. beyond a certain degree of simplicity, it is not clear what phenomena will emerge from the generators. And this premise is emphasized because it is so often forgotten. It is the reason Chaos theory, fractals, and games like chess are so maddeningly interesting.

Similarly, the cyberneticists have an emphatic premise: that complexity comes about through feedback loops. Again, beyond a certain degree of simplicity, it is not clear which part of a system is the cause and which is the effect. Phenomena are exacerbated with positive feedback and dampened with negative feedback.

Both emphases are appropriate and the fact that we even have a distinction between computationalists and cyberneticists is an example of specialization gone mad. ² Both require the notion of loopiness and the somewhat occult nature of both the forward and inverse maps. But the loopiness is often a more difficult concept to grasp.

This article challenges the notion that a complex forward map is sufficient to realize or explain a complex system, especially one so full of occult paths and loopiness (including trans-hierarchy) as multi-cellular life. And I am very happy that such an article has made it into the mainstream news.

1. Murray Gell-Mann tried to install “plectics” in the vernacular, but failed. I buy Murray’s argument and try to use “plectics” whenever I can.

2. Not that I would advocate for huge box stores like Wal*Mart where you can buy diapers, car batteries, and bread all in the same trip or anything. In fact, such lack of specialty disgusts me. But there is something to say for, e.g., the general practitioner or renaissance man (sorry, I just can’t replace “man” with “person” in that phrase) who can think holistically … synergistically … about a subject without her (that should make up for the gender bias) prejudices kicking in to keep her from escaping her current thought rut.