Literature

Genetic information: Codes and enigmas
There's more than one way to read a stretch of DNA, finds Helen Pearson — and we need to understand them all.
Nature 444, 259-261 (16 November 2006) | doi:10.1038/444259a

Computer buffs interested in cracking codes have developed software routines to prise out hidden information. “We are treating DNA as we used to treat problems in intelligence” [Shepherd] says. “We want to break the code at the most fundamental level.”

This is the first point where an ID perspective will help research. “Breaking the code” cannot be reduced to an exercise in computer science. We need to recognise the biological context for the DNA operation and to treat the whole cell as a complex system. This will lead to a systems engineering methodology for analysis.

A highly significant paragraph is as follows:
“DNA seems well adapted for supporting a number of codes. For a start, only 1-2% of the human genome is occupied with protein-coding sequences, which leaves plenty of intervening DNA to hold other information. But many stretches of DNA in humans and other organisms manage to multitask: a sequence can code for a protein and still manage to guide the position of a nucleosome. This is possible because the triplet code is ‘degenerate’. Several slightly different triplets can code for the same amino acid, and many positions in a protein can be filled by different amino acids – so different sequences can effectively mean the same thing. This allows other signals to be imprinted on top of the first – especially when those other signals are themselves encoded with some slack.”

Multitasking is something we typically associate with intelligence. Getting a code to convey one message is a challenge in itself, but getting the same code to carry several messages is evidence of higher level intelligent agency. ID helps here, allowing the premise that the ‘degenerate’ aspects of the triplet code are actually designed to permit sophisticated encoding.

The writer, however, goes on to make an extraordinary comment on this. “This elegance is surely the handiwork of evolution – and if the way in which that hand had worked to solve these problems were clearer, the simultaneous decoding of all the messages involved might become easier.”

It is extraordinary because of the word “surely”. Why “surely”? Not because of the sophisticated design features! Not because the whole thing is “elegant”! I can only think that the word “surely” is deductive: because “we know” that Darwinism is true. The same rationale is behind this comment that appears earlier in the article: “Biology has probably figured out a way to squeeze every bit of information from that molecule it can”.

There is no empirical base for suggesting that these design features can emerge from evolutionary processes. Our recognition of them as a phenomenon comes only because we have met them before in intelligently designed digital information.

That sentence should read: “This elegance is surely the handiwork of an Intelligent Designer – and if the way in which His hand had worked to solve these problems were clearer, the simultaneous decoding of all the messages involved might become easier.”

One further point on the use of anthropomorphic language. Examples already cited are:
“Biology has probably figured out a way to squeeze every bit of information from that molecule it can”.
“This elegance is surely the handiwork of evolution”
“the way in which that hand had worked to solve these problems”

In each case, we have intelligent agency attributed to the mechanistic processes of evolution. As Dembski’s design filter shows, these mechanisms give us law-like and chance-like characteristics, but these are distinct from design-like characteristics. Although the evolutionary paradigm dies not permit intelligent agency, those within its mould have to resort to anthropomorphisms to develop their ideas. Sad. That's perhaps the biggest "enigma" in this essay.