Genomicus writes:
I'll take a look at that paper, but there are some things that need emphasizing. That the standard genetic code is not at a global optimum for error minimization really isn't bad news from an ID perspective. This is because there are other functions aside from error minimization that would be optimized, and this is indeed the case in the genetic code, as highlighted by Bollenbach et al., 2007:
Yes, that's the answer I was expecting, but it was optimization for error minimization that you mention in the O.P. In fact, the paper suggests that the standard code is frozen some way off even its local fitness peak so far as error correction is concerned. However, the other improved error minimization peaks are so numerous that it would seem unlikely that there aren't those that would achieve better all round balanced function (or more rational design) than the one we've got. The designers had a lot of choice.
Geno writes:
Full optimization of one function may significantly reduce the optimization of another. Thus, a balance would have to be made between various functions.
Correct.
Geno writes:
The genetic code is, nevertheless, at a local optimum for error minimization.
More likely at a local balanced optimum because of the other functions you mentioned, and frozen there (with the few known exceptions) because of the difficulty of traversing valleys to reach other high points (which the front-loaders could have done).
Geno writes:
And the absence of a phylogenetic tree like I describe in my essay, and the fact that this highly optimized genetic code is nearly universal, points to front-loading.
It fits the scenario of an initial random functional code evolving to become optimized, and hitting a local peak on the fitness landscape fairly quickly then getting frozen. The paper suggests that random codes hit their local optimums easily and quickly.
Geno writes:
The prokaryote LUCA could easily have had a thoroughly sub-optimal genetic code. This would, in turn, evolve and be fine-tuned, but many detours and by-ways would be explored, with some less optimal genetic codes branching off, producing a phylogenetic tree of genetic codes. There is no reason why this should not have occurred, under the non-telic model.
The quick and easy arrival at a local balanced optimum would be one very plausible reason, don't you think?
If I'm getting it right, the variations that we do see from the standard code should be rare examples of it traversing slight valleys on the fitness landscape, and hitting other local peaks. They may not be sub-optimal for their circumstances in the balanced sense, even if they are for error correction or other single functions (just like the standard).
Their survival might indicate that a rational seeming option of seeding the planet with organisms containing lots of different codes could have left a number of them with much more radical differences. Different
non-local fitness peaks. But we don't see this.
There's one thing that I will say about our standard code. It will be exactly right for doing what it has done on this particular planet regardless of its objective efficiency, and that's a prediction of both a non-telic view of evolution and a pure front-loading telic view. "Side loading" I.D. views do not predict this, and their claim is that what we see happening on the molecular level is inadequate to produce the variety and complexity of life that we see around us, and therefore the constant intervention of intelligent design is required.
There's quite a gulf between your view and that of the side-loaders.
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