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com Pharyngula Email Print Algorithmic Inelegance Complexity in living things is a product of the lack of direction in evolutionary processes, of the accumulation of fortuitous accidents, rather than the product of design. by P !yers " Posted #anuary $, %&&' &()*+ A! ,ruit flies sho- ho- general and global patterning mechanisms can be shaped by evolution into particular, specific, and local control. Illustration by Alison .chroeer !any years ago, I -rote soft-are to supplement my income, and I kno- -ell the satisfaction of -riting code, seeing it execute, and seeing functionality unfold on the computer screen. /here0s something deeply appealing about making logic manifest and producing tools that do intense computational -ork for you at the click of a button1 there can also be something deeply obsessive about being able to hone soft-are to make it more elegant and efficient and, to the programmer0s eye, more beautiful. /he designers of soft-are usually aspire to economy of code, clarity in its operation, and po-erful algorithms that, -ith mathematical and logical beauty, do the -ork of generating a sophisticated result. 2e tend to look do-n on the 3kludge,3 the clumsy addition to fix a problem, or the brute force approach of -orking case by case to force a desired result 4although, to be sure, I0ve seen enough code to kno- that the a-k-ard hack is ubi5uitous6. 7o- I0m a full8time developmental biologist, and unsurprisingly, I see similar expectations in myself and in my colleagues. 2e don0t have the po-er to design embryos, but -e do analyze the 3code39the genetic instructions and the operation of the developmental programs that take the egg from embryo to adult. 2e look for algorithmic elegance and simple procedures that lead to the impressive complexity of form, and sometimes -e see it1 there is often a kernel of clean, simple molecular interactions that lay do-n a frame-ork for the organism. :o-ever, -hat -e more often see is the action of the invisible hand of evolution) the evidence of random accidents that have been incorporated into the code, of elaborations built of bricolage, a collage of bits and pieces assembled into a larger structure. ;ife is a collection of kludges taped together by chance and filtered by selection for functionality1 it all -orks magnificently -ell, but if you look under the hood you are simultaneously appalled by the sheer inelegance of the molecular gemisch and impressed -ith the accumulation of complexity. ,or instance, the segmentation of animals in development is a lovely example of the formation of a simple pattern9the body is built of repeating, nearly identical elements, stacked one after the other. .cientists anticipated that perhaps the rules for building the same thing over and over -ould involve only a fe- genes -orking together to create a repeating spatial pattern, and that -e could see this as an emergent property of regularities and rules. In vertebrates, -hich seem to retain the primitive pattern of segmentation to a relatively greater degree than many other animals, -e see a set of clock8like rules in operation. /he cyclic production of a fe- genes, like analogues of a gene named hairy, produces a pattern of stripes of activation of genes in the 7otch path-ay that set up the boundaries of each segment. /his is a clean solution1 a fe- genes -ith oscillating levels of expression over time set aside pieces of the embryo, one by one, that make each segment. <f course, even in these 3simple3 vertebrates, -e also find layers and layers of genes, -ith narro- and specialized functions, carrying out overlapping and complementary roles9it0s much more complicated than can be summarized in a simple paragraph. .imply put, evolution has encrusted the process -ith many elaborations.

In flies, those paradigmatic models of genetics and development, that process of elaboration has been carried to an extreme. Any algorithmic elegance in the ancestral arthropod has been lost in favor of detailed, segment8by8segment hard-iring of the specification of the body plan. If a fly -ere soft-are, it0s soft-are that has been patched and patched, and patches have been put on patches, until almost all vestiges of the original code have been obscured in the t-eaks. It0s the antithesis of planning and design 9it0s ad hoc co8option and opportunistic incorporation of chance enhancements. It0s evolution. :o- can evolution lead to increasing complexity and specialization of the developmental circuitry= Consider the ancestral mechanism for making segments) A molecular clock ebbs and flo-s, ticking off a ne- partition -ith each cycle. /his mechanism converts time into a pattern in space. In development, time is often at a premium, though) In some lineages, the evolutionary pressure is on accelerating the rate of development to increase the rate of reproduction. /he clock can be ad>usted to run faster and faster, but there are limits) Increasing the rate can increase errors, as -ell, negating the advantages of speed -ith failures in successful completion in development. !olecules and cells can only respond so fast to fluctuations in the levels of regulatory genes -ithout the -hole process smearing into incoherence. !utations that create shortcuts, that set up parts of the pattern independent of the clock, can become highly advantageous. Imagine that an organism has a generic, clocklike mechanism that partitions off identical segments, one after the other, to make a pattern like this) head, A, A, A, A... tail, -here 3A3 represents a particular regulatory gene that defines the form of a single segment, and each A is turned on se5uentially over time from the front to the back. A duplication event 4a very common process in genetics6 produces a copy of the A gene, -hich initially does nothing more than add a little redundancy to the process. ?ut the ne- copy of A 4let0s call it ?6 can evolve independently of the original and ac5uire ne- functions, such as activation in an ad>acent region -hen A is s-itched on9that is, every time A is activated, so is ?, at essentially the same time. 7o- our animal can build segments t-ice as fast) head, A8?, A8?... tail. Evolution can optimize this still further. /he regulatory circuitry for A or ? can ac5uire, by chance, sensitivity to other conditions in the animal, such as the concentration of some other gene product, or the absence of a particular gene product, or the activity of a gene in an ad>acent tissue. If that regulatory change s-itches on one of the segmental genes in a place -here the clocklike circuit -ould have activated it any-ay, it0s all to the good) It makes the segmental pattern more robust. Any addition to the circuit that happens to flick gene A or ? on in the appropriate place can persist and eventually take over the >ob of the clock, at least in that one location. As more and more dedicated regulatory elements accumulate, the original elegant algorithm becomes superfluous and can fade a-ay9selection can favor genetic path-ays that establish the pattern 5uickly rather than se5uentially, and the organism is re-arded -ith faster development built on a frame-ork of dedicated special purpose patches defining each segment. /his is precisely -hat -e see in the fruit fly. It doesn0t build its segments se5uentially at all) instead, gene products interact in complex -ays, -ith broad bands of segmental genes refining themselves rapidly by early interactions to establish a pattern of segmental stripes almost all at once. 2hen the individual segmental genes are examined, they are found to each have stacks of logical s-itches to turn them on in dedicated patterns in specific places in the animal9each stripe is specified by a hard8coded set of regulatory elements. /he complexity of developmental regulation isn0t a product of design at all, and it0s the antithesis of -hat human designers -ould consider good planning or an elegant algorithm. It is, ho-ever, exactly

-hat you0d expect as the result of cobbling together fortuitous accidents, stringing together helpful scraps into an outcome that may not be pretty, but it -orks. /hat0s all evolution needs from developmental processes) something that -orks -ell enough, no matter ho- a-k-ard or needlessly complex it may seem. @ Previous Page all of A 7ext B Algorithmic Inelegance, -ritten by P !yers, posted on #anuary $, %&&' &()*+ A!, is in the category Pharyngula. *& blog reactions Advertisement About seedmagazine.com " Advertise -ith .eed " Contact Cs " Privacy Policy " /erms D Conditions E Copyright %&&+8%&&$ .eed !edia Froup, ;;C