Analogy-nomics

Codex
Genetic codex

It’s hard to find a popular article about genetics that doesn’t contain the word “code”. Scientists use the phrase “genetic code” specifically to mean the rules governing which of 64 codons correspond to which amino acids. But for the public, the term is much broader, implying a kind of computer program. The idea that DNA houses the “software” which runs on the “hardware” of the body is so pervasive, people often forget it’s just a metaphor. The characters in this XKCD comic, for example, discuss DNA as literally code in the computational sense.

 

But it’s not really code. Not any more than, say, the topography of North America is an algorithm with rainfall as input and lakes as output. If we beamed a genome sequence into outer space, a race of super-intelligent aliens (if they existed) would never be able to reconstruct an earthling without a lot of additional information about terrestrial biology. To remind everyone that it’s only an analogy, here are some other equally valid genome metaphors that I like:

 

Music. Score and sequence share a special, almost ineffable kinship. Individual bare notes harmonize into a symphony so much greater than the sum of its parts. I first encountered this idea as a teen reading Gödel, Escher, Bach. One of my favorite expositions on the topic comes from Nathan Pearson as he chats with Ozzy Osbourne about Ozzy’s genome (see from 1:30-4:30). To paraphrase Nathan, both genomes and music show theme and variation. The conserved patterns (theme) are shared among all of us. The unique flourishes (variation) are what make Ozzy, or Crazy Train, so distinct. The same themes are repeated and varied both among different songs/genomes and within the same songs/genomes. Similar sections are usually closely adjacent, but they can also reappear after long intervals, leading to particular mathematical signatures. But, as will be true of all examples in this post, one big difference between the metaphor and reality is size. To play every note of the human genome at a reasonable tempo, a thousand-piece orchestra would need to perform continuously for a month. And our genome is hardly the largest. Don’t even get me started on the lungfishes. Still, the comparison goes deeper. Although music is merely vibrating air molecules, we perceive it as a recurring mounting and releasing of tension. That’s what makes music so satisfying: the stored-up energy of a G major seventh chord resolving into a blissful C major. Homeostasis is restored. We don’t yet completely understand how thousands of genes work together to build and organism, but something similar must be going on. One gene’s product would produce an unbearably intense concentration of hydrogen ions, but another gene restores the balance. When played in full on our instruments of flesh, the composition all comes together.

 

Beads. If DNA is a string of pearls, a genome is the gaudiest jewelry you’ve ever seen. Picture a bead one centimeter in diameter, like you might find on a heavy necklace. Say that’s an individual nucleotide, represented by the letter A, C, G, or T in a DNA sequence. At this scale, most genes are around the length of a large city block, but some are several miles long. A gene is a pleasant stroll, or at most, a morning hike. But genomes are huge. The human genome at this scale would reach 3/4 of the way around the Earth. The genome of a Mexican white pine would reach to the moon, and don’t even get me started on the lungfishes. Of course, a necklace doesn’t do anything. It’s just for admiring, or at best for identifying people. Well, that’s the only practical utility of much of the genome. Some DNA is functional, but far from most. So imagine a stretch of this circumnavigational rosary, perhaps lying across the vast endless red dust of the desolate Australian outback. One pebble-sized bead out there may make all the difference: between dark and light, between male and female, or between alive and dead. But most of them are just bling.

 

Narrative. I love the idea that an organism is a story. Words combine to construct an entire universe in a way that would never be apparent to a reductionist examining the text letter-by-letter. Once you contemplate how literary magic works, the need to assign a metaphysical soul to a body seems a lot less pressing. Yet despite this holism, a change to a single letter in the right place can completely alter the meaning of a novel. Not that this is some simple tale. Although you could feasibly read the human genome in a lifetime, it would require a bit of dedication. Break it into into average-sized “words” of about five letters each, and spend two hours a day reading it at 200 words per minute. It would take you over seventy years. The real problem with this metaphor is that a story is too coherent. A novel has a single author, a unified style. It all makes sense. A genome is an odd compendium of different passages that arose for different reasons, separated by pages and pages of nonsense filler that seems to bear no relation to anything else. The closest book is probably the Bible, actually. The Bible is redundant, inconsistent, and illogical, yet it still works for folks in a way that has ensured its success over millennia. People around the world are in awe of its complexity, endurance, and wisdom, and refuse to accept that it originated naturally. However, the Good Book was not intelligently designed, but resulted from accumulations of change via many small independent forces. I’m trying not to sound like a cynical atheist here. I may not take scripture literally, but I can’t deny it’s beautiful in a way reminiscent of molecular biology. It’s even about the length of a typical bacterial genome. The human genome, meanwhile, is as long as a thousand Bibles. A kilobible, if you will. And don’t even get me started on the lungfishes.

 

An enlightened view of biblical stories doesn’t take them as fact, but sees them as metaphors for life. Likewise, only a genetic fundamentalist would take a genome metaphor literally. That doesn’t mean they’re not useful for understanding. If I had to pick, I’d say the Bible is the best genome metaphor we have. Which is actually too bad, because it has too much baggage for use in the classroom. Our culture is too embedded in it for folks to see it objectively. Like DNA, perhaps. Maybe we should stick with Crazy Train.

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