Anti-Reductionism: An Example?

"There are three good reasons to think that reduction will fail on any likely development of social sciences: (1) multiple realizations of social events are likely; (2) individual actions have indefinitely many social descriptions depending on context; and (3) any workable individualist social theory will in all likelihood presuppose social facts. Each of these claims, if true, rules out reduction as defined here." -- Harold Kincaid (quoted in J. E. King (2012)).

Kincaid is arguing against strong methodological individualism. To help explicate his first reason, I want to consider a different domain, biology, and some literature crossing over between biology and computer science.

I suppose I ought to first state the reductionist theory I want to oppose: The theory of evolution can be reduced to the biochemistry of DNA.

A large body of literature explores the logical structure of reproduction, including reproduction with mutations, independently of consideration of the structure of DNA. I think of Von Neumann's work on celluar automata, which, despite the publication date of the work Burks edited, pre-dates the discovery of the molecular structure of DNA. As I understand it, Von Neumann described a structure in which a part simultaneously functions as a blueprint for the next generation and as a component that is duplicated in reproduction.

Von Neumann described a celluar automaton with many states, but his logic can be implemented in a particular celluar automata with only two states, namely Conway's Game of Life. Plausibility arguments that this celluar automata can be used to form a universal computer were available before Paul Rendell implemented a Turing machine in the game of life. Basically, one can identify mechanisms for implementing a memory and an array of gates (for example, AND, OR, and NOT). The gates apply to bits flowing across a wire, in some sense. Jacob Aron has create another interesting pattern in the game of life relevant to my thesis, namely a self-replicating creature.

Some researchers have also explored the role of mutations in self-replicating automata. As I understand it, they typically assume the existence of an assembly language for a virtual machine. One can imagine small programs being executed in parallel in some sort of common memory. One needs some way of introducing random changes in some of the instructions over time cycles and a way of rewarding successful programs with, say, more energy, in some sense.

The different artificially alive creatures in these simulations do not reside in separate protected memories. They have the capability of overwriting one another and resisting such overwriting. Some have even arranged tournaments, called core wars, in these simulations. In some sense, the literature I am referencing includes some bits of recreational mathematics.

I have never seen much more than what the literature says in the little bit of exploration of the above I have done. I did once write an implementation of Conway's Game of Life in which the rules were configurable. I was able to create crystal-like growth, but nothing as interesting as in the original game.

I have pointed to some work exploring a logic of reproduction above the level of the biochemistry of DNA. DNA is one means of instantiating this logic. I have not pointed out any other non-virtual mechanisms for instantiating this logic. I do not know if mitochondrial DNA differs sufficiently from regular DNA to count. Silicon-based life forms on other planets is a standard trope in science fiction. Apparently, Reaves et al. (2012) show the supposed discovery of arsenic-based life forms in certain California lakes has not worked out. But does this anti-reductionist argument require the actual existence of another instantiation, or merely the demonstration of the possible existence of one?

References

• J. E. King (2102). The Microfoundations Delusion: Metaphor and Dogma in the History of Macroeconomics.
• Lenski, Richard E., Charles Ofra, Robert T. Pennock, and Christoph Adaml (2003). The Evolutionary Origin of Complex Features, Nature, V. 423 (May): pp. 139-144.
• Poundstone, William (1984). The Recursive Universe. William Morrow.
• M. L. Reaves et al. (2012). Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells.
• Thearling, Kurt and Thomas S. Ray. Evolving Multi-Cellular Artificial Life.
• Von Neumann, John (1966). Theory of Self-Reproducing Automata (ed. by A. W. Burks).

Weird Science II

A bit from Avatar reminds me of Ursula K. LeGuin's "Vaster Than Empires and More Slow", a short story republished in her collection The Wind's Twelve Quarters (1975). LeGuin postulates a world in which nodes in tree roots act like synapses. The plant life is one sentience. Maybe even vines and spores partake in it. As before, a cultural work reminds me of some science:

• The longest lived thing is arguably Pando, a grove of aspens in Utah that seems to be one plant, connected at the roots and propagating through runners like strawberries or mrytle.
• Or maybe it is an instance of the fungus Armillaria bulbosa in Oregon.

A Wikipedia article lists other such organisms, for what it's worth. (The references in this post are reminders for me to look up sometime.)

O Brave New World That Has Such Bacteria In It

The BioBricks Foundation (BBF) has Request For Comments (RFCs), just like the Internet Engineering Task Force (IETF). They have a BioBrick language, a graphical language, and are working on an RDF-based framework for a synthetic biology ontology. (The Resource Description Framework (RDF) is a standard for the semantic web.)

BBF is using this this computer science technology and organizational structure to create "standard biological parts" that "encode basic biological functions". The goal is to enable biological engineers to "program living organisms in the same way a computer scientist can program a computer".

(Hat Tip to Michael Specter's New Yorker 28 September 2009 article.)

It's Herd Behavior, Uh Huh, It's Evolution, Baby

Anybody interested in institutional economics should be interested in evolutionary theory, a theory that I can stand to learn more about. The interest in evolution among institutionalists goes back to Veblen. A more-or-less mid twentieth expression of interest can be seen in Ayres's biography of Thomas Huxley, also known as "Charles Darwin's bulldog". Geoffrey Hodgson is a current institutialist interested in evolution. What evolves in economies? I suggest organizational forms, business processes, and technology, at least.

I never saw anything interesting when operating Tierra on my old computer. Perhaps I understand neither the assembly language nor the visualization well-enough. Or perhaps I should have designed experiments and let it operate for more generations. I was never into Core Wars either. John Conway's Game of Life was more my speed. I don't seem to have executables for any of these for my OS X Macintosh.

But I think Thearling and Ray (1994) describe a neat idea. In Tierra, programs composed of machine instructions reproduce, perhaps with mutations. Memory is not protected, and programs can overwrite one another's code. An ability to more successfully protect one's own code and data and overwrite others is selected for.

One can do repeatable experiments with a computer program. Each generation can be saved, and the simulation can be rerun from any point in time, with random number generators restarted with new seeds. Lenski et al (2003) report such experiments with Avida, a computer simulation much like Tierra. In Avida, evolving computer programs collect energy to run their code. Programs that can do advanced logical operators are more fit. Lenski et al show that the evolution of a complex feature may depend on the prior evolutionary history of an organism providing the potential of the last few steps, even if previous mutations do not increase fitness.

I was surprised to find last week not only that repeatable experiments with evolution have been performed on simulations, but that Richard Lenski has been performing such a repeatable experiment on real-world organisms - namely, E. Coli - since 1988. (I must have missed Carl Zimmer's article, of 26 June 2008 in The New York Times, on the Long Term Evolution Experiment (LTEE).) Anyway, Blount, Borland, and Lenski's 2008 article reports on recent results.

In the LTEE, populations of each generation are isolated in a solution containing glucose for the E. Coli to eat. The isolated solution, I guess, acts like the simulated core memory in Tierra. And the E. Coli of any generation and evolutionary history can be frozen and restarted, just as an image of the computer core memory in a simulation run can be saved and reloaded. One run yielded a mutation that seems to have surprised Linski. This mutation allows the E. Coli to thrive on citrate, whatever that is, in the solution even "under oxic conditions". The ability to sample previous generations and look at other isolated population histories starting from the same initial conditions allows Linski and his colleagues to understand something about this mutation even before genetic sequencing. It is not the result of a single gene mutating, but is dependent on prior mutations in the history. These prior mutations may not have increased fitness themselves, but prepared the E. Coli to become dramatically more well-adapted for their specific environment after a couple more mutations. History matters.

References

• Ayres, Clarence (1932) Huxley, W. W. Norton
• Blount, Zachary D., Christina Z. Borland, and Richard E. Lenski (2008) "Historical Contingency and the Evolution of a Key Innovation in an Experimental Population of Escherichia Coli", Proceedings of the National Academy of Sciences V. 105, N. 23 (June 10): 7899-7906
• Hodgson, Geoffrey (2008), "Interview" Revue de la Régulation (January)
• Lenski, Richard E., Charles Ofria, Robert T. Pennock and Christoph Adaml (2003) "The Evolutionary Origin of Complex Features", Nature, V. 423 (8 May): 139-144
• Thearling, Kurt and Thomas S. Ray (1994) "Evolving Multi-celluar Artificial Life, Artificial Life IV, MIT Press