A Programmer Unimpressed with Biological "Design"

This Salon article, How I decoded the human genome, contains a comment from someone with a lot of experience in computer programming:

quote:

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Kent spoke to me in nerdspeak, with geekoid locutions such as the use of "build" as a noun: "That's the most recent build of the genome. Build 31." I was used to hearing biologists talking about the elegance of DNA with what might be called reverence. By contrast Kent spoke of DNA as if it were the most convoluted, ill-documented, haphazardly maintained spaghetti code -- not God's most sublime handiwork, but some hack's kludge riddled with countless generations of side effects, and "parasites on parasites."

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"It's a massive system to reverse-engineer," he said. "DNA is machine code. Genes are assembler, proteins are higher-level languages like C, cells are like processes ... the analogy breaks down at the margins but offers useful insights." It was nearly impossible to tell the working code from cruft, Kent said. "That's why a lot of people say, 'The genome is junk.'" But that's what he found interesting: a high-quality programmer's code is always self-evident, but legacy assembler handed down from generation to generation of bricoleurs (I'm paraphrasing again) provides a real challenge for people who like puzzles.

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Gastropodlike U-shaped guts are known from elsehwere, likeCrinoids
Lophophorates (brachiopods, bryozoans, phoronids)There are other examples of such kludgy designs.Amniote early embryos have gill bars, gill pouches, and a fishlike circulation (heart - ventral aorta - gill arches - dorsal aortas). Several of these structures are then used for other purposes; the remainder is resorbed. Birds and mammals resorb one of a pair of arches, the systemic arches; birds resorb the left one and mammals the right one.Some land vertebrates have extra digits with little or no functionality.
(per-foot, not per-animal):
* Dogs and cats have four functional digits and one dewclaw.
* Cows, pigs, etc. have two extra digits, one on each side of their two functional digits.
* Horses are sometimes born with extra digits on each side of their one functional digit.And extinct equines form a nice intermediate state -- they grow all three digits, though in the later ones, the side digits are much smaller than the middle one.Plants alternate between a haploid gametophyte stage and a diploid sporophyte stage. These are distinct individuals among the more primitive plants, but among seed plants, the gametophytes are microscopic and typically only a few cells. Nearly all of a seed plant is sporophyte. It is as if seed plants were trying to converge on the animal situation of only the gametes being haploid, but could not quite make it.[This message has been edited by lpetrich, 02-27-2004]