Wednesday, August 03, 2005

We Must, We Must, Develop Robust

The President recently made some offhand remarks supportive of introducing intelligent design into high school curricula. Although some educators and scientists were upset, I doubt if his comments were calculated for political advantage. He didn’t make much of an issue of the matter, and his own science advisors are on the record that ID is not a credible scientific theory. In a very general way, I suppose, evincing skepticism about evolution is a way of demonstrating solidarity with your base, but surely nobody has any reason to doubt Bush’s bona fides as a member of the culture of ignorance. Creationism is a default position. You don’t have to take a course or read a book to be wrong about these things. It’s as natural as breathing. Living things may have developed without effort and forethought, but it requires effort and thought to arrive at understand how they could have developed without such inputs. The truth is located on an upper floor, and there is no elevator in the building.

Some of the heavy lifting involved in actually figuring things out is on display in Andreas Wagner’s new book Robustness and Evolvability in Living Systems. Wagner’s aim is to examine how living things manage to persist, reproduce, and evolve despite the noisiness of their environment. Or to use Wagner’s own words, “Why is an organism not a molecular house of cards?” Stuart Kauffman wrote an influential book some years ago called the Origins of Order. Wagner’s book is about the durability of order, an equally challenging problem. Mutations are inevitable in genetic systems and even a top of the line Xerox machine eventually fails to reproduce a visible image as it copies copies of copies. Even during the life of a given organism, random thermal motions constantly perturb the intricate network of chemical processes that make up metabolism. So how do you have a picnic during a tornado? And why doesn’t the sheer complexity of a single cell, let alone a multi-cellular organism, make life simply impossible? According to Murphy’s Law what can go wrong will go wrong. There are vastly more things to go wrong in a cat than in a can opener, but the cats are still here. Indeed, contrary to what one might think, reliability actually seems to increase with complexity.

Wagner addresses two main questions. He examines the mechanisms that make living systems robust on the genetic, metabolic, and developmental levels; but he also looks at possible explanations of how these systems became robust. Quite a lot is known about the first problem. For example, computer simulations show that the genetic code is optimized for robustness in the sense that random mutations tend to code for chemically similar amino acids more often in the existing code than in all or almost all of the zillions of alternative possibilities. Which means, in turn, that a large proportion of the proteins derived from mutated genes will have the same general chemical properties as the originals and retain or enhance their functionality despite the changes. The chemical pathways of the cell also show a high degree of resiliency that allows metabolism to continue even when one or more enzymes fails, and developmental pathways can be drastically reorganized without obviously changing the morphology of the adult organisms—I was particularly impressed with Wagner’s account of how the embryology of insects in the hymenopteran suborder Apocrita differ depending on their lifestyles, with yolky, Drosophila-style eggs for the free living and ecotoparasitic forms and tiny, yolk-poor eggs for endoparasites. Evidently ontogeny doesn’t always recapitulate phylogeny as revolutionary alterations of developmental processes can occur without altering the end product very much.

How life came to be so tough in the face of noise and mutation is a separate and less clear-cut question. Wagner supplies some suggestions. There is some evidence that living things can and have evolved in the direction of greater robustness, but it isn’t always obvious that straightforward natural selection can account for the trend. For one thing, robustness can be too much of a good thing at some levels. For example, proteins are more stable if they reliably fold into the same shape despite thermal noise, but enzymes often have to be able to change their conformations in order to catalyze chemical changes. There are trade-offs. It is also unclear whether genetic systems can become more robust under individual natural selection, because the inclusive fitness of individuals is not increased by mutations that make future generations less sensitive to mutations. In that case, however, it may well be that the same mutations that increase the robustness of metabolic processes to thermal noise have the more-or-less automatic side effect of increasing the resistance of the genome to unfavorable mutations. Thus the same heat shock protein that protects proteins from folding improperly at high temperatures buffers the effect of mutations as well—knock out the now-celebrated Hsp90 and you and your fruit flies will manifest a host of abnormalities.

Wagner ends his book with a brief look at man-made systems. The telephone grid is like a living body by virtue of its enormous scale and intricacy but also because it is remarkably reliable (~99.999%). As Wagner points out, the great majority of service interruptions occur not because of the failure of individual parts—such failures occur at a rate comparable to the genetic mutation rate in living things, mostly without obvious consequences—but simply because the phone companies decided it wasn’t worth the money to build a big enough system to withstand the occasional overload. In other words, the fragility of the system is planned. Its robustness is not. It is a side effect of the way the system evolved. During the long, piecemeal process of its development, defects and failures continually occurred and were responded to with various ad hoc expediencies. As a result, the grid, like the genetic, metabolic, and developmental systems of living things, looks like a crazy guilt or, if you’re old enough to catch the reference, like a Rube Goldberg contraption. Nevertheless, it works in the sublunary world better than any rationally designed system whose elegant structure is likely to be hopelessly brittle.

By the way, although Wagener doesn’t say a word on the topic and should not be blamed for my homily, his take on robustness suggests a veritable Argument from Non-Design to an infidel like me. To put things simply: We know that living things were not designed. After all, they work. Which brings us back to George Bush’s recent comments.

Monday, August 01, 2005

Admission of Failure is not an Option

If nothing counts as losing, victory is inevitable. On a less flexible scoring system, Iraq sure looks like a failure. What we’ve bought at the cost of 300 billion and thousands of lives is a wrecked nation stuck in a civil war. Under the circumstances, the most favorable outcome would be a country divided between a pro-Iranian Islamic republic in the South and a Kurdish ethnic state in the North. Even in that case, a more or less permanent insurgency would probably smolder in the middle subsidized on the cheap by irritated Sunnis in adjoining areas.

The right wing, seconded by many a pundit from America’s mindless middle, cheerfully responds to the endless train wreck with rhetorical maneuvers patterned on theological apologetics. It isn’t that they examine the facts on the ground and conclude that things are going well. They begin with the conclusion and track back, just as defenders of Christianity or Islam seldom argue for the truth of the faith from the evidence but beg the question from the get go. Since assessing the situation might yield unacceptible results, both the theologians and the political commentators content themselves with the not very challenging task of explaining how a predestined conclusion can be represented as consistent with the acknowledged facts of the case. Such explanations are always possible: “True, no living things more elaborate than Lepidoptera survive in the poisoned wastes of post-war Mesopotamia, but the outcome is as good as anyone could have reasonably expected, and we can thank the President that Manhattan remains markedly less radioactive than Bagdad.” Consistency is a very cheap commodity and worth its price.

To judge by the polls, the American public is not buying the optimism of the right these days; but it is not clear that what the people think matters much as long as the levers of power are in the hands of true believers. Which means that we are at the mercy of a group of people who have decided that it is unmanly and unpatriotic to learn from their own mistakes. Since political stupidities have real costs, however, this principle can only be implemented by cupping your hands around your ears and repeating “la-la-la, I can’t hear you!” Unfortunately, denial is like running up the balances on your credit cards. Only God almighty can afford to be complacent forever.