Putting Intentions into Cell Biochemistry: An Artificial Intelligence Perspective
An intriguing article in the Journal of Theoretical Biology I came across this afternoon. The abstract:
The living cell exists by virtue of thousands of nonlinearly interacting processes. This complexity greatly impedes its understanding. The standard approach to the calculation of the behaviour of the living cell, or part thereof, integrates all the rate equations of the individual processes. If successful extremely intensive calculations often lead the calculation of coherent, apparently simple, cellular "decisions" taken in response to a signal: the complexity of the behavior of the cell is often smaller than it might have been. The "decisions" correspond to the activation of entire functional units of molecular processes, rather than individual ones. The limited complexity of signal and response suggests that there might be a simpler way to model at least some important aspects of cell function. In the field of Artificial Intelligence, such simpler modelling methods for complex systems have been developed. In this paper, it is shown how the Artificial Intelligence description method for deliberative agents functioning on the basis of beliefs, desires and intentions as known in Artificial Intelligence, can be used successfully to describe essential aspects of cellular regulation. This is demonstrated for catabolite repression and substrate induction phenomena in the bacterium Escherichia coli. The method becomes highly efficient when the computation is automated in a Prolog implementation. By defining in a qualitative way the food supply of the bacterium, the make-up of its catabolic pathways is readily calculated for cases that are sufficiently complex to make the traditional human reasoning tedious and error prone.
Shapiro seems to suggest that some application of this sort of thinking may be useful for analysis of IC systems. I am only beginning to think about this, and will probably not be finished till at least next week. So perhaps a disclaimer is in order: This post does not imply, suggest or otherwise make any insidious claims about evolution, intelligent design, or any other theory of origins.
But that needn’t thwart discussion– reach whichever conclusions you like on your own.
Really? That’s not what I saw in Shapiro’s comments. About 3/4ths the way down, in the section “A 21st Century View of Genome Reformatting in Evolution,” Shapiro says:
It sounds like he’s expecting obejctors of evolutionary theory to seize upon this work as “proof” of the sudden emergence of complex genomic systems encoding sophisticated multicomponent adaptive features, but that this problem will be countered by “application of lessons from the fields of artificial intellligence, self-adapting complex systems, and molecular cell biology.”Comment by Dan — March 31, 2006 @ 4:55 pm
We’re both referring to the same part of Shapiro’s essay, and I think drawing the same conclusions from it. Maybe I didn’t phrase it very clearly the first time round. It seems to me he is saying the ‘problems’ evolution faces from IC systems can be made tractable (’solved’) by applications from the fields of molecular cell biology, self-adapting complex systems, and artificial intelligence (the article in question being an example of this).
Or am I reading him wrong?
Comment by Freawaru — March 31, 2006 @ 5:08 pm
Ok - no, it would see we are in agreement. It is potentially fascinating how those other fields might be impacting the understandings of molecular evolution and genomics in the coming decades, isn’t it? ;-)
Comment by Dan — March 31, 2006 @ 5:25 pm
Yes, very much so.
Comment by Freawaru — April 1, 2006 @ 2:09 am
Many people misunderstand what IC indicates. Many ID objectors think that the Irreducible Complexity of X means that X cannot have evolved. That is not so. What it means is that X cannot have evolved through Darwinistic (that is, blind) mechanisms.
A paper I’m currently reading, though not specifically mentioning IC by name, does sum up what IC means very well:
“A genome’s ability to grow and to explore new organizational structures would be severely constrained, if its options were limited to simple point mutation…most organisms tolerate only relatively low levels of point mutation in a gneeration. Instead they have evolved _mechanisms that generate multiple sequence changes in a single step_, allowing them to bypass unselected neutral, and negatively selected, sequences that may lie on point mutation pathways between the current sequence and a more optimal sequence. Indeed, where genomic sequences have been available to provide a window into the evolution of a new gene, the series of steps revealed has been complex.” [Chance Favors the Prepared Genome]
_That_ is what IC is all about. When you take into account the fact that for such processes to work, they must be using some sort of an intelligent process to guide the steps, and, as Dembski pointed out, the existance of informationally-guided search must originate with an intelligent designer somewhere in causal history, you get the notion of Intelligent Design (see Dembski’s Searching Large Spaces, or http://www.4truth.net/site/apps/nl/content3.asp?c=hiKXLbPNLrF&b=784461&ct=1742245 ).
Anyway, since you all were talking IC, I thought I’d point out a popular misconception.
Comment by Jonathan Bartlett — April 10, 2006 @ 8:26 pm