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Wednesday, February 28, 2007

Reading List: Investigations

Kauffman, Stuart A. Investigations. New York: Oxford University Press, 2000. ISBN 0-19-512105-8.
Few people have thought as long and as hard about the origin of life and the emergence of complexity in a biosphere as Stuart Kauffman. Medical doctor, geneticist, professor of biochemistry and biophysics, MacArthur Fellow, and member of the faculty of the Santa Fe Institute for a decade, he has sought to discover the principles which might underlie a “general biology”—the laws which would govern any biosphere, whether terrestrial, extraterrestrial, or simulated within a computer, regardless of its physical substrate.

This book, which he describes on occasion as “protoscience”, provides an overview of the principles he suspects, but cannot prove, may underlie all forms of life, and beyond that systems in general which are far from equilibrium such as a modern technological economy and the universe itself. Most of science before the middle of the twentieth century studied complex systems at or near equilibrium; only at such states could the simplifying assumptions of statistical mechanics be applied to render the problem tractable. With computers, however, we can now begin to explore open systems (albeit far smaller than those in nature) which are far from equilibrium, have dynamic flows of energy and material, and do not necessarily evolve toward a state of maximum entropy.

Kauffman believes there may be what amounts to a fourth law of thermodynamics which applies to such systems and, although we don't know enough to state it precisely, he suspects it may be that these open, extremely nonergodic, systems evolve as rapidly as possible to expand and fill their state space and that unlike, say, a gas in a closed volume or the stars in a galaxy, where the complete state space can be specified in advance (that is, the dimensionality of the space, not the precise position and momentum values of every object within it), the state space of a non-equilibrium system cannot be prestated because its very evolution expands the state space. The presence of autonomous agents introduces another level of complexity and creativity, as evolution drives the agents to greater and greater diversity and complexity to better adapt to the ever-shifting fitness landscape.

These are complicated and deep issues, and this is a very difficult book, although appearing, at first glance, to be written for a popular audience. I seriously doubt whether somebody who was not previously acquainted with these topics and thought about them at some length will make it to the end and, even if they do, take much away from the book. Those who are comfortable with the laws of thermodynamics, the genetic code, protein chemistry, catalysis, autocatalytic networks, Carnot cycles, fitness landscapes, hill-climbing strategies, the no-go theorem, error catastrophes, self-organisation, percolation phase transitions in graphs, and other technical issues raised in the arguments must still confront the author's prose style. It seems like Kauffman aspires to be a prose stylist conveying a sense of wonder to his readers along the lines of Carl Sagan and Stephen Jay Gould. Unfortunately, he doesn't pull it off as well, and the reader must wade through numerous paragraphs like the following from pp. 97–98:

Does it always take work to construct constraints? No, as we will soon see. Does it often take work to construct constraints? Yes. In those cases, the work done to construct constraints is, in fact, another coupling of spontaneous and nonspontaneous processes. But this is just what we are suggesting must occur in autonomous agents. In the universe as a whole, exploding from the big bang into this vast diversity, are many of the constraints on the release of energy that have formed due to a linking of spontaneous and nonspontaneous processes? Yes. What might this be about? I'll say it again. The universe is full of sources of energy. Nonequilibrium processes and structures of increasing diversity and complexity arise that constitute sources of energy that measure, detect, and capture those sources of energy, build new structures that constitute constraints on the release of energy, and hence drive nonspontaneous processes to create more such diversifying and novel processes, structures, and energy sources.
I have not cherry-picked this passage; there are hundreds of others like it. Given the complexity of the technical material and the difficulty of the concepts being explained, it seems to me that the straightforward, unaffected Point A to Point B style of explanation which Isaac Asimov employed would work much better. Pardon my audacity, but allow me to rewrite the above paragraph.
Autonomous agents require energy, and the universe is full of sources of energy. But in order to do work, they require energy to be released under constraints. Some constraints are natural, but others are constructed by autonomous agents which must do work to build novel constraints. A new constraint, once built, provides access to new sources of energy, which can be exploited by new agents, contributing to an ever growing diversity and complexity of agents, constraints, and sources of energy.
Which is better? I rewrite; you decide. The tone of the prose is all over the place. In one paragraph he's talking about Tomasina the trilobite (p. 129) and Gertrude the ugly squirrel (p. 131), then the next thing you know it's “Here, the hexamer is simplified to 3'CCCGGG5', and the two complementary trimers are 5'GGG3' + 5'CCC3'. Left to its own devices, this reaction is exergonic and, in the presence of excess trimers compared to the equilibrium ratio of hexamer to trimers, will flow exergonically toward equilibrium by synthesizing the hexamer.” (p. 64). This flipping back and forth between colloquial and scholarly voices leads to a kind of comprehensional kinetosis. There are a few typographical errors, none serious, but I have to share this delightful one-sentence paragraph from p. 254 (ellipsis in the original):
By iteration, we can construct a graph connecting the founder spin network with its 1-Pachner move “descendants,” 2-Pachner move descendints…N-Pachner move descendents.
Good grief—is Oxford University Press outsourcing their copy editing to Slashdot?

For the reasons given above, I found this a difficult read. But it is an important book, bristling with ideas which will get you looking at the big questions in a different way, and speculating, along with the author, that there may be some profound scientific insights which science has overlooked to date sitting right before our eyes—in the biosphere, the economy, and this fantastically complicated universe which seems to have emerged somehow from a near-thermalised big bang. While Kauffman is the first to admit that these are hypotheses and speculations, not science, they are eminently testable by straightforward scientific investigation, and there is every reason to believe that if there are, indeed, general laws that govern these phenomena, we will begin to glimpse them in the next few decades. If you're interested in these matters, this is a book you shouldn't miss, but be aware what you're getting into when you undertake to read it.

Posted at February 28, 2007 00:14