STATISTICAL ARTIFACT MEANING CODE

Here we avoid methodological debate by using the analytical methods of the original coevolution paper ( 3).

STATISTICAL ARTIFACT MEANING CODE

Indeed the claim that recent literature вЂњhas taken for granted the existence of a correlation between the biosynthetic relationships of amino acids and genetic code organizationвЂќ ( 20) is legitimate the only direct reappraisal of coevolution theory ( 30) demonstrated diminished statistical significance when different methods were used, but has itself been criticized on methodological grounds (refs. 27 and 29), and evolutionary explanations for the expansion process (e.g., refs. 24вЂ“ 26 for overviews), the statistical basis for perceived coevolutionary patterns within the canonical code, the intermediate codes leading to the structure we see today (e.g., refs. These papers address topics including: the mechanism by which codons were ceded from precursor to product amino acids (see refs. More than 100 publications have either built on or espoused the original coevolution model. Specifically, a central tenet of coevolution theory is that a вЂњproductвЂќ amino acid synthesized from a precursor amino acid usurped codons previously assigned to this precursor, such that the sequence of steps by which the code expanded is visible within modern codon assignments (Fig. 4, 20, 22, and 23 for selective reviews), coevolution theory has gained the widest acceptance by proposing an explicit pathway of code evolution that apparently had strong statistical support ( 3, 19, 20). Although the general idea of code expansion originated much earlier ( 1) and has appeared in many forms (see refs. The theory postulates that the earliest genetic code used a small number of prebiotically synthesized amino acids ( 21), and subsequently expanded to its present form by incorporating novel derivatives of these primordial amino acids as metabolic (biosynthetic) pathways evolved. Thus we conclude that coevolution theory cannot adequately explain the structure of the genetic code.ДЄ very different theory, called code coevolution, holds that the organization of the canonical code reflects the historical pathways by which amino acid biosynthesis evolved at the dawn of life ( 3, 12вЂ“ 20). Finally, even this figure rests on post hoc assumptions about primordial codon assignments, without which the probability rises to 62% that chance alone could explain the precursor-product pairings found within the code. A conservative correction for these errors reveals a surprisingly high 23% probability that apparent patterns within the code are caused purely by chance. In addition, the theory neglects important biochemical constraints when calculating the probability that chance could assign precursor-product amino acids to contiguous codons.

We show that the theory's definition of вЂњprecursor-productвЂќ amino acid pairs is unjustified biochemically because it requires the energetically unfavorable reversal of steps in extant metabolic pathways to achieve desired relationships. Here we re-examine the biochemical basis of this theory to test the validity of its statistical support. It further proposes that a comparison of modern codon assignments with the conserved metabolic pathways of amino acid biosynthesis can inform us about this history of code expansion. The most influential form of this idea, вЂњcode coevolutionвЂќ, proposes that the genetic code coevolved with the invention of biosynthetic pathways for new amino acids. It has long been conjectured that the canonical genetic code evolved from a simpler primordial form that encoded fewer amino acids.

Statistical artifact meaning