On modularity, and intelligibility of artifacts not designed by humans (1)
The problem with modules (1) (wonkish)
Let’s start by recalling this scene from 3017, in which Sally Fowler and Rod Blaine discuss an alien spacecraft.
“Most of the probe’s internal equipment was junk, fused and melted clutters of plastic blocks, remains of integrated circuitry, odd strips of conducting and semiconducting materials jumbled together in no rational order. There was no trace of the shroud lines, no gear for reeling them in, no apertures in the thirty-two projections at one end of the probe. If the shrouds were all one molecule it might explain why they were missing; they would have come apart, changed chemically, when Blaine’s cannon cut them. But how had they controlled the sail? Could the shrouds somehow be made to contract and relax, like a muscle?
An odd idea, but some of the intact mechanisms were just as odd. There was no standardization of parts in the probe. Two widgets intended to do almost the same job could be subtly different or wildly different. Braces and mountings seemed hand carved. The probe was as much a sculpture as a machine.
Blaine read that, shook his head, and called Sally. Presently she joined him in his cabin.
“Yes, I wrote that,” she said. “It seems to be true. Every nut and bolt in that probe was designed separately […] But that’s not all. You know how redundancy works?”
“In machines? Two gilkickies to do one job. In case one fails.”
“Well, it seems that the Moties work it both ways.”
She shrugged. “We had to call them something. The Mote engineers made two widgets do one job, all right, but the second widget does two other jobs, and some of the supports are also bimetallic thermostats and thermoelectric generators all in one. Rod, I barely understand the words. Modules: human engineers work in modules, don’t they?”
“For a complicated job, of course they do.”
“The Moties don’t. It’s all one piece, everything working on everything else.”
Larry Niven and Jerry Pournelle, The Mote in God’s Eye, Pocket Books, Simon and Schuster, New York, New York (1974)
If the biggest cliche in systems biology is that biological systems are robust, the second biggest is probably that they are comprised of modules.
To start, I need to acknowledge that Sally was right. To build systems, human engineers do work in modules, be those built of mechanical parts, electronic circuitry, or lines of code.
For researchers who wish to underatand biological function, or who wish to design and engineer new functions, it becomes a valid question to ask in which cases the concept of modules is relevant to understanding.
Some of the current belief that biological function arises from the assembled actions of modules arises from influential paper. This paper (“From molecular to modular cell biology”, by Lee Hartwell, John Hopfield, Stan Leibler, and Andrew Murray, 1999) stated “We argue here for the recognition of functional ‘modules’ as a critical level of biological organization. Modules are composed of many types of molecule. They have discrete functions that arise from interactions among their components (proteins, DNA, RNA and small molecules), but these functions cannot easily be predicted by studying the properties of the isolated components. We believe that general ‘design principles’ — profoundly shaped by the constraints of evolution — govern the structure and function of modules.”
In subsequent posts, I will advance the argument that this belief in modularity has not worked out very well. In specific I will argue that, just as with robustness, at the level of the cell, many assertions that processes and phenomena in biology are modular are not not, for reasonable meanings of the word module, true. I will also argue that, at the level of the cell, operation based on that belief has not led to greatly increased understanding, and in fact might have kept human researchers from describing biological systems more accurately. And finally, I will assert that operation based the belief that cellular systems are modular has not led to an improved ability to engineer these systems.
For all three arguments, part of the reason will be that biological systems were evolved. As opposed to being designed and built by humans. Or even by other sentient beings.
Hartwell, L. H., Hopfield, J. J., Leibler, S. and Murray, A. W. (1999). From molecular to modular cell biology 402(6761 supp), C47-C52