Wednesday, September 28, 2011

evolution and DRY

Reality may be unintuitive. One instance among many is the evolutionary march that yields complexity from chaos, harmony from cacophony, solution from error. At the timescale of a human life, and applied to everyday objects, such a progression is nonsense. In information-theoretic thinking, the introduction of greater randomness to existent information only degrades it with greater uncertainty or "noise", necessitating a communication code that can compensate by adding greater message redundancy. In thermodynamic thinking, the much larger number of disordered states overwhelm the small number of ordered states. Two gases in one box will mix simply because that's far more probable on average than all the undirected gas particles staying apart in the original groupings. In parental thinking, miscellaneous household items won't land in specific designated positions if children drop the items at randomly-chosen times and locations (a four-dimensional vector governed by a stochastic variable).

Clearly, accurate metaphors for biological evolution are lacking. Humans are justifiably amazed by the notion of entire populations of intricate organisms changing for many millions of years. And the changes are related to numerous shifts in myriad factors, including habitat and competition. It's problematic to transplant prior assumptions into that expansively complicated picture.

But a metaphor from software development might be helpful for contemplating the stunning results achieved by the unpremeditated mechanisms of evolution. No matter the particular need served by the software, a solemn rule of development is "don't repeat yourself", which is abbreviated to "DRY". The intent of the rule certainly isn't the naive claim that no repetition ever happens. To the contrary, the rule is about handling repetition correctly. Following DRY is typing a "chunk" of software just once and then somehow rerunning that solitary chunk on different data whenever necessary. The alternative to DRY is duplication. Duplication is often cheaper at the time of initial development, although it's costlier thereafter: two or more chunks are naturally laborious compared to one.

Besides the long-term savings in maintenance work, aggressive DRY has a second effect. The software is divided into chunks. These divisions and subdivisions are easier to read, understand, and analyze. Organization and interconnections take the place of a flat sequence. Appearances suggest conscientious craftsmanship, independent of any knowledge of the software's developers.

Hence, a DRY-compliant outcome has a tendency to look artificially arranged. Evolution could fall in that category. Obviously, unlike in software development DRY can't be a conscious guideline. Instead, inherent constraints "encourage" DRY to occur. Since normally DNA is strongly resistant to massive change, perhaps outright duplication of a gene across separate strand locations is improbable. Reuse of the original gene in a new context accomplishes an identical adjustment in the organism. The DRY-like modifications of the DNA trigger matching DRY-like modifications to the creature. It appears to be the product of a history that's less chaotic than it really is. Thus phenomena that human brains find comprehensible or beautiful, like symmetry or hierarchical containment, arise from frugal genes. So do displeasing phenomena, like unsightly remnants of a contemporary body part's surprising past. DRY pushes for tweaking existing genes and transforming an existing appendage of little value, rather than partial duplication of existing genes and adding more appendages.

Insistent objectors could aver that the DRY metaphor violates the common sense of the conceptual chasm between thoughtful human software developers and thoughtless genetic mutations and transcriptions. The computer programming languages of typical software are specifically designed to enable smaller chunks. Languages incorporate syntax and semantics. How can that be comparable to the simple streams of codons in DNA? Reuse can't happen without a structure to support it. Pronouns are literally meaningless without basic grammar.

Odd as it seems, the genetic code indeed has a grammar. The fundamental building blocks of grammar are symbols that modify the interpretation of other symbols. Here, "interpretation" is the translation of nucleic acids into working cell proteins. Over time, discoveries have shown how subtle the translation can be. It's affected potentially by a host of activity. Genes definitely can adjust the expression of other genes, which is why geneticists hesitate to assign premature importance to single genes. Some of the "words" in this haphazard language are likely grammatical in impact on protein replication, akin to "and", "or", "not". Some might serve both independent and regulatory functions. Incomplete human understanding doesn't cast doubt on the existence or the capacity of evolution's code. It could very well be able to encode the reuse of sections in accordance with DRY-like conservatism. Just as replacing one word in a sentence might have drastic overall implications, replacing a minimal quantity of genes might have drastic overall consequences that give off the impression of evolution acting smart or informative or experienced.

1 comment:

  1. That is very close to the idea as to how the 'rapid' evolutionary changes needed by the punctuated equilibrium theory happen , just changing the handful genes that control the rate of expression of whole complexes of genes can rapidly produce large numbers of variations .