New Paper Argues that Variant Genetic Codes Are Best Explained by Common Design
A popular argument for a universal common ancestor is the near-universality of the conventional genetic code. Critics of common descent often point to deviations from the standard code as evidence against it. A recent paper published in the journal BIO-Complexity, by Winston Ewert, reviews the character and distribution of genetic code variants and the implications these have for common ancestry, and “develops a framework for understanding codes within a common design framework, based crucially on the premise that some genetic code variants are designed and others are the result of mutations to translation machinery.” Ewert explains that,
Upon first investigation, evolutionary theory appears to have a compelling account of the character and distribution of variant codes. Evolutionary theory suggests that if genetic code evolution is possible it should be very rare. This would explain why most genomes follow the standard code and why the exceptions only vary in a few codons. It would also explain the following details about the variant codes. Most variations are found in mitochondria, whose very small genomes would make code evolution easier. Many variations are also found in highly reduced genomes, such as those of endosymbiotic bacteria. No variations are found in the nuclear genomes of complex multicellular organisms like plants and animals. The distribution of many codes can be easily explained by identifying certain points on the tree of life where codons were reassigned and then inherited by all of their descendants.
EWERT W (2024) ON THE ORIGIN OF THE CODES: THE CHARACTER AND DISTRIBUTION OF VARIANT GENETIC CODES IS BETTER EXPLAINED BY COMMON DESIGN THAN EVOLUTIONARY THEORY. BIO-COMPLEXITY 2024 (1):1-25.
Three Tenets
The paper proposes “a framework that seeks to explain the character and distribution of variant genetic codes within a common design framework.” Ewert’s framework has three tenets: First, “the canonical genetic code has been well optimized and is thus an ideal choice for most genomes.” There are multiple optimized parameters and thus “A designer must identify the best trade-offs to select the ideal genetic code.” The second tenet of Ewert’s framework is that a minor variation on the standard code is better suited to some organisms, since those organisms may acquire an advantage by a different set of trade-offs with respect to genetic code optimization. The third tenet is that the translation machinery has been damaged by mutations in some organisms, and that this has resulted in their misinterpreting the code they were initially designed to employ. These are examples of genetic code variants that have evolved naturally.
Five Criteria
Ewert offers five criteria that may be used to distinguish genetic codes that are evolved from those that are designed. First, evolved codes are expected to be found in taxonomic groups below the family level, whereas those that are designed are predicted to be above the level of family. Second, evolved codes should be readily “explicable in terms of some simple mutation to the translation machinery of the cell.” Third, it is predicted that codes that are evolved will be limited to the genomes of endosymbionts. Fourth, it is expected that codes that are evolved utilize a small number of codons so that the variation does not cause the organism too much harm. Fifth, it is predicted that evolved codes will fall into a simple nested hierarchical (phylogenetic) distribution. By contrast,
[D]esigned codons are found in high-level taxa of at least genus-level but typically higher. They involve many reassignments that are difficult to explain with any sort of simple mutation. They are found in free-living organisms. They sometimes reassign codons that are expected to be rare. They are often distributed in a complex fashion that does not fit phylogenetic expectations.
EWERT W (2024) ON THE ORIGIN OF THE CODES: THE CHARACTER AND DISTRIBUTION OF VARIANT GENETIC CODES IS BETTER EXPLAINED BY COMMON DESIGN THAN EVOLUTIONARY THEORY. BIO-COMPLEXITY 2024 (1):1-25.
It has been conventionally thought that evolution provides a good explanation for the character and distribution of genetic code variants — in particular, the near-universality of the standard code; the prevalence of variant codes in simple genomes such as those of mitochondria; and the phylogenetic distribution of variant codes. Ewert notes that, in light of evolutionary theory, it would in fact be expected that there would be variant codes found at the higher taxonomic levels, which would be consistent with the genetic code still being variable at the time of the last common ancestor. However, “What we observe instead are modifications of the standard code. They are not associated with the high-level taxa…”
Furthermore, though we should expect on evolutionary theory that it would be exponentially harder to reassign a code as the number of genes increases, “variant codes are found in nuclear genomes that are not particularly small. They are found in ciliates, which have comparable numbers of genes to the human genome. Additionally, we find them in some multicellular green algae. In fact, we find more code variation in eukaryotic nuclear genomes than in bacterial genomes, despite eukaryotes having much larger genomes.” Thus, Ewert concludes, “despite the initial impression, evolutionary theory does not account well for the kinds of genomes with variant codes.”
Invoking “Inexplicable Events”
Finally, though evolutionary theory would predict that the distribution of variant codes would be consistent with the standard phylogeny, Ewert observes that, “In many cases, the distribution of a code is complex, defying evolutionary explanations. Codes recur in closely related groups in a way not explained by common descent. Evolutionary theory has to invoke inexplicable events such as reversions to the standard code.”
Thus, Ewert concludes, “Initially, evolutionary theory appeared to have some explanatory power. However, upon closer inspection, the features of the variant codes that seemed well explained by evolutionary theory turned out to either be inaccurate or to not follow from evolutionary theory.” Instead, he argues that the character and distribution of variant codes is often better explained under a framework of common design.
The paper is well worth a careful read. It can be accessed here.
