Arthur Hunt posted Signature in the Cell? at his blog The RNA Underworld. Art attempts to refute Meyer by citing a paper (RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code, J Mol Evol; 69:406–429) authored by Michael Yarus, Jeremy Joseph Widmann and Rob Knight. As Art explains:
Put more plainly, 75% of tested amino acids associate with their anticodon (in some cases, along with their codon) in these studies. This is remarkable, as it is demonstrative of an underlying stereochemical basis for at least some of the genetic code.
Art then proceeds to make a speculative argument based on the study:
Thus, we can discern that the genetic code as we understand it today likely evolved in several steps – a stereochemical era wherein a core set of triplet-amino acid correspondences was first established, followed by subsequent expansion of the assignments of other triplets and recruitment of other amino acids (typified by gutamine and leucine) via other mechanisms.
Let's look at this closely before proceeding. Blogs are not textbooks so we do not expect Art to supply a detailed account of actual protein synthesis but to give you some idea, refresh memories or simply put you on notice that a short one paragraph argument needs some context I'll provide links. First this:
The assembly of biological molecules, including proteins and nucleic acids, requires the generation of appropriate starting materials. We have already considered the assembly of carbohydrates in regard to the Calvin cycle and the pentose phosphate pathway (Chapter 20). The present chapter and the next two examine the assembly of the other important building blocks—namely, amino acids, nucleotides, and lipids.
The availability of appropriate starting materials is a huge point. Protein synthesis depends on the capacity of cells to synthesize basic required biochemicals and make them available as needed. That in turn presumes a cellular state known as homeostasis i.e. a capacity to generate conditions that are hospitable to the realization of cellular functions. Don't presume that such conditions persist in the extra-cellular world of prebiotic earth. If you do so make that assumption clear.
We see Art outline a series of steps describing an evolutionary process: "a core set of triplet-amino acid correspondences was first established." This set will include a variety of amino acids, nucleotides and, at some point, distinct forms of specified RNA. "Recruitment of other amino acids (typified by gutamine and leucine) via other mechanisms" follows. How did these other mechanisms come about and what do the look like? They no doubt evolved but how?
If Art and others wish to dismiss Signature in the Cell with remarks like this:
First, it is true that Yarus’ ideas, and the underlying experiments, are far from a direct and complete demonstration of the origination of the complete RNA decoding system that we see in modern cells. However, the body of work discussed by Yarus et al. constitutes a significant and compelling set of positive experimental support for the hypothesis that the genetic code has an underlying chemical basis. As such, it far outstrips the entire body of positive experimental support (there is none) for Meyer’s claim that there can be no way to explain the genetic code (the Signature in the Cell) in terms of chemistry and physics.
You need to consider the nature of the "significant and compelling set of positive experimental support" and decide for yourselves if it meets this descriptive level.
The level of support necessary is that level needed to establish a viable physical process culminating in a self-replicating cell. More details on biosynthesis follow although it is by no means a comprehensive view of what takes place during protein synthesis. Continuing with the linked source:
In amino acid production, we encounter an important problem in biosynthesis—namely, stereochemical control. Because all amino acids except glycine are chiral, biosynthetic pathways must generate the correct isomer with high fidelity. In each of the 19 pathways for the generation of chiral amino acids, the stereochemistry at the α-carbon atom is established by a transamination reaction that involves pyridoxal phosphate. Almost all the transaminases that catalyze these reactions descend from a common ancestor, illustrating once again that effective solutions to biochemical problems are retained throughout evolution (Figure 24.1).
Don't confuse stereochemical bonding explanations with stereochemical control. The latter entails timely regulatory functions. At this point the precursor cell objection is raised. Bradford, don't you know that protocells were far less complex and did not initially contain these modern cellular features? They subsequently evolved. Fine. Take that as an article of prebiotic faith if you wish but don't confuse it with solid empirical support of the same.
Biosynthetic pathways are often highly regulated such that building blocks are synthesized only when supplies are low. Very often, a high concentration of the final product of a pathway inhibits the activity of enzymes that function early in the pathway. Often present are allosteric enzymes capable of sensing and responding to concentrations of regulatory species. These enzymes are similar in functional properties to aspartate transcarbamylase and its regulators (Section 10.1). Feedback and allosteric mechanisms ensure that all twenty amino acids are maintained in sufficient amounts for protein synthesis and other processes.
Was mention made of enzymes? If anticipated reactions are to proceed we can expect explanations as to how they were catalyzed and where catalytic agents came from. There have been related studies on this and in the comment section you will likely see links to such studies. Bear in mind the conditions required in separate studies and whether complementary outcomes come with mutually exclusive conditions.
In addition to pointing out enormous holes in the much touted positive experimental support, it behooves us to look at a more serious theoretical flaw. A plausible evolutionary process offers a model of a replicating system. Something we can analyze and visualize. More importantly it suggests reasons for supposing that extra-cellular reactions in a prebiotic soup would favor, not only nucleic acids and amino acids of sufficient amount and variety- unencumbered by competing organic chemicals. It requires a natural selection basis consistent with the conditions of that prebiotic world. Significant support? No way.
In his blog piece Art quotes Meyer:
“Polyani argued that, in the case of communications systems, the laws of physics and chemistry do not determine the arrangements of the characters that convey information. The laws of acoustics and the properties of air do not determine which sounds are conveyed by speakers of natural languages. Neither do the chemical properties of ink determine the arrangements of letters on a printed page. Instead, the laws of physics and chemistry allow a vast array of possible sequences of sounds characters, or symbols in any code or language. Which sequence of characters is used to convey a message is not determined by physical law, but by the choice of users of the communications systems in accord with the established conventions of vocabulary and grammar – just as engineers determine the arrangement of the parts of machines in accord with the principles of engineering.
Thus, Polyani concluded, communications systems defy reduction to physics and chemistry for much the same reasons that machines do. Then he took a step that made his work directly relevant to the DNA enigma: he insisted that living things defy reduction to the laws of physics and chemistry because they contain a system of communications – in particular, the DNA molecule and the whole gene-expression system. Polyani argued that, as with other systems of communication, the lower-level laws of physics and chemistry cannot explain the higher-level properties of DNA. DNA base sequencing cannot be explained by lower-level chemical laws or properties any more than the information in a newspaper headline can be explained by the chemical properties of ink.16 Nor can the conventions of the genetic code that determine the assignments between nucleotide triplets and amino acids during translation be explained in this manner. Instead, the genetic code functions as a higher-level constraint distinct from the laws of physics and chemistry, much like a grammatical convention in a human language.”
Art then adds his comment on this:
In other words, Meyer is claiming that the genetic code is arbitrary, that there are no chemical or physical underpinnings to the codon-amino acid correspondence that we see in life. It is because the code is arbitrary, Meyer implies that it must be designed:
I think Art mischaracterizes Meyer's point which is not arbitrariness but rather one of causal adequacy. Meyer had argued that the origin of specified complexity or functionally specified information in DNA must be explained. He also made the point about ink on paper to emphasize that chemical affinity is not the same as a causally adequate chemical pathway to coded systems. Let's stipulate that stereochemical properties describe tRNA. Yes, and…