An ID Take on the Genetic Code
by BradfordMike Gene authored The Universal Genetic Code Seen From an ID Perspective. In commenting on the fact that bacteria and eukaryotes share the same genetic code Mike quotes from a paper published in Science.
For example, in 1991, evolutionary biologists Laurence Hurst of the University of Bath in England and David Haig of Harvard University showed that of all the possible codes made from the four bases and the 20 amino acids, the natural code is among the best at minimizing the effect of mutations. They found that single-base changes in a codon are likely to substitute a chemically similar amino acid and therefore make only minimal changes to the final protein.
Now Hurst's graduate student Stephen Freeland at Cambridge University in England has taken the analysis a step farther by taking into account the kinds of mistakes that are most likely to occur. First, the bases fall into two size classes, and mutations that swap bases of similar size are more common than mutations that switch base sizes. Second, during protein synthesis the first and third members of a codon are much more likely to be misread than the second one. When those mistake frequencies are factored in, the natural code looks even better: Only one of a million randomly generated codes was more error-proof.
Vogel, G. 1998. Tracking the History of the Genetic Code. Science 281: 329
Those one in a million odds speak eloquently. Mike also notes a less often mentioned advantage of a common code- making possible horizontal gene transfers.
There is an additional reason to design a "universal code" that follows from any attempt to design life with the ability to evolve. Put simply, if each organism had its own unique code, this would serve as a serious obstacle for the horizontal flow of genetic information. It is now clear that bacterial have made extensive use of horizontal transfer. Successful gene products can be "shared" with very different bacteria such that the recipients receive all the benefits of genes pruned by selection without having to evolve them. This allows bacteria, as a global community of cells, to more successfully and rapidly adapt to various environmental stresses. We need only consider how powerful this mechanism of sharing is when we consider how quickly bacteria are adapting to extreme selection pressures caused by the massive, global use of antibiotics.
Summing things up:
Thus, there are two very good (and obvious) reasons for a designer to have employed the same code in bacteria and eukaryotes: 1) The code is extremely good at preventing deleterious amino acid substitutions and; 2) the shared code allows for the lateral transfer of genetic material and facilitates symbiotic unions. That Miller thought ID incapable of explaining the code, and Pace thought the shared code proved the common descent of bacteria and eukaryotes, only shows how an a priori commitment to non-teleological explanations creates a large intellectual blind spot.
October 5th, 2008 at 10:23 am
Fitness was determined with regards to random codes given the *historical* constraints imposed due to the evolution of the genetic code from the affinity of codons and amino acids (stereochemistry). As this chemical affinity is largely irrelevant to the modern transcription mechanism, an intelligent designer would not be so constrained and could use other code assignments.
If we consider the entire panoply of code assignments available to an intelligent designer, then we have a quite different result.
Fitting very well with the evolutionary hypothesis.
Comment by Zachriel — October 5, 2008 @ 10:23 am
October 5th, 2008 at 10:57 am
You're assuming the conclusion you favor. The affinity of amino acids and codons no more explains the code than the affinity of ink to paper explains language.
Comment by Bradford — October 5, 2008 @ 10:57 am
October 5th, 2008 at 11:39 am
It was *your* cite that assumed stereochemistry as part of its working hypothesis. The newer cite to Novozhilov et al. did not make this assumption, but considered that any code would be available. According to the study, once the code was sufficiently optimized, it became frozen as other considerations became more important to selective advantage.
hypothesis, a tentative assumption made in order to draw out and test its logical or empirical consequences.
The hypothesis is that transcription evolved from a more primitive system where the codons directly coded for amino acids. Stereochemical affinity is an important *prediction* of this hypothesis (Woese, 1967).
Comment by Zachriel — October 5, 2008 @ 11:39 am
October 5th, 2008 at 12:03 pm
These claims are easily made in the absence of suitable selection criteria.
Comment by Bradford — October 5, 2008 @ 12:03 pm
October 5th, 2008 at 12:19 pm
Easy? Just a lucky guess?
In 1967, Woese predicted there would be a statistically relevant stereochemical affinity between codons and their associated amino acids even though they are chemically decoupled in modern transcription. The prediction follows from a hypothesis about the evolution of the genetic code, and would be unexpected otherwise.
Comment by Zachriel — October 5, 2008 @ 12:19 pm
October 5th, 2008 at 12:28 pm
The prediction would also flow naturally from the strong suspicion or knowledge that proteins regulate gene expression; something suspected before Woese.
Comment by Bradford — October 5, 2008 @ 12:28 pm
October 5th, 2008 at 2:24 pm
From Zachriel's article:
Assuming the study is correct, we have two explanations for our standard code:
(1) It evolved that way from random codes.
(2) It was designed that way to balance robustness to translation errors with the deleterious effects on evolution.
Given that we have no evidence of precursors to our standard code, (2) seems more likely.
Comment by Bilbo — October 5, 2008 @ 2:24 pm
October 5th, 2008 at 5:22 pm
If it was *poofed* into the optimal code, then there would be no evolution, so no deleterious effects of evolution. It's only because it is evolving from a less than optimal code with balancing selection that this becomes an issue. The code evolves until it is good enough, then stability in the code becomes paramount as other aspects of cell evolution, which depend on the code, provide the driving force of evolution.
The assignment of codons to amino acids is not random, but provides evidence of its origin. We have evidence of stereochemical affinity between codons and amino acids; evolution from singlet to doublet to triplet codes; amino acids added over deep time; selection for error minimization; and partial optimization of the code towards a local maximum that froze as the cell became more complex and dependent on the code. The data is still tentative, but it certainly wouldn't be correct to say there is "no evidence" of precursors.
Comment by Zachriel — October 5, 2008 @ 5:22 pm
October 5th, 2008 at 5:47 pm
As a former translator let me explain to any baffled by poofed that Zachriel is referring to a deliberate optimization of the code. That might mean there was no evolution of the code but that could be exactly what was needed to allow for cellular evolution.
Comment by Bradford — October 5, 2008 @ 5:47 pm
October 5th, 2008 at 9:42 pm
Oh, good. Maybe you can translate what you just said. I thought we were talking about "deliberate optimization of the code".
Comment by Zachriel — October 5, 2008 @ 9:42 pm
October 5th, 2008 at 10:12 pm
Then why not use plain English phrases like that instead of the disdainful poofs which no doubt earn brownie points with the gallery?
Comment by Bradford — October 5, 2008 @ 10:12 pm
October 6th, 2008 at 7:34 am
So we are talking about "deliberate optimization of the code"?
(I used *poof* to indicate the code was created by an unknown mechanism in a moment of time. *Poof* is quite a bit shorter than "deliberately created by an unknown mechanism in a moment of time", and relays the same essential meaning.
Power Over Original Function, POOF!)I note that my objection is still on the table.
If the code was
deliberately created by an unknown mechanism in a moment of time, then there would be no evolution, so no deleterious effects of evolution.Comment by Zachriel — October 6, 2008 @ 7:34 am
October 6th, 2008 at 1:50 pm
Zachriel, if I understand the latest paper you have referred to, they assume that there was no physico/chemico relationship between amino acids and their codons, but that the code originated randomly. Please correct me if my assumption is mistaken.
Comment by Bilbo — October 6, 2008 @ 1:50 pm
October 6th, 2008 at 6:19 pm
[...] commenter chunkdz sparked this exchange about the genetic code, a subject which was recently cited at Telic [...]
Pingback by Chunkdz Comes Out Smokin - Telic Thoughts — October 6, 2008 @ 6:19 pm
October 7th, 2008 at 7:34 am
They do make that assumption, but the hypotheses are not exclusive. The standard code is "relatively unremarkable" in that you can start with most any random beginning and reach a similar level of partial optimization—despite the ruggedness of the landscape. But early evolution of the code could still be characterized by weak stereochemical associations followed by strong selection. The result would be similar.
Comment by Zachriel — October 7, 2008 @ 7:34 am
October 7th, 2008 at 1:39 pm
And the earlier papers that Mike Gene cited in support of the Genetic Code being optimal: Did they assume that there was a strong physico/chemical affinity between amino acids and codons?
Comment by Bilbo — October 7, 2008 @ 1:39 pm
October 7th, 2008 at 2:08 pm
The researchers assumed that stereochemical affinity formed the historical seed for later optimization. Historical contingency helps determine which fitness peak will be climbed.
Freeland, Knight, Landweber and Hurst, Early Fixation of an Optimal Genetic Code, Molecular Biology and Evolution 2000: "The arrangement of amino acid assignments to the codons of the standard genetic code appears to be a direct product of natural selection for a system that minimizes the phenotypic impact of genetic error."
Comment by Zachriel — October 7, 2008 @ 2:08 pm