A friend writes to mention this page (2016) at National Center for Biotechnology Information:
The following genetic codes are described here:
- 1. The Standard Code
- 2. The Vertebrate Mitochondrial Code
- 3. The Yeast Mitochondrial Code
- 4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code
- 5. The Invertebrate Mitochondrial Code
- 6. The Ciliate, Dasycladacean and Hexamita Nuclear Code
- 9. The Echinoderm and Flatworm Mitochondrial Code
- 10. The Euplotid Nuclear Code
- 11. The Bacterial, Archaeal and Plant Plastid Code
- 12. The Alternative Yeast Nuclear Code
- 13. The Ascidian Mitochondrial Code
- 14. The Alternative Flatworm Mitochondrial Code
- 16. Chlorophycean Mitochondrial Code
- 21. Trematode Mitochondrial Code
- 22. Scenedesmus obliquus Mitochondrial Code
- 23. Thraustochytrium Mitochondrial Code
- 24. Pterobranchia Mitochondrial Code
- 25. Candidate Division SR1 and Gracilibacteria Code
- 26. Pachysolen tannophilus Nuclear Code
- 27. Karyorelict Nuclear
- 28. Condylostoma Nuclear
- 29. Mesodinium Nuclear
- 30. Peritrich Nuclear
- 31. Blastocrithidia Nuclear
Hmmm. Wasn’t a universal code one of the predictions of universal common descent (UCD)? And it was supposed to be really hard to change. It’s a good thing that life forms aren’t really machines (though the functions of some parts can conveniently be explained that way).
Here are some local discussions of the subject:
Dobzhansky believed that the common ancestry of all living things could be seen in the universality of the genetic code. This was the basis of his claim that “all organisms, no matter how diverse in other respects, conserve the basic features of the primordiallife.”9 But we now know that the genetic code is not universal. Thomas Fox reported in 1985 that “some ‘real’ exceptions have come to light” in bacteria and single-celled organisms, “and the notion of universality will have to be discarded.” 10 The number of exceptions has grown since then; a 1995 review noted that “a relatively high incidence of non-universal codes has been discovered … widely distributed in various groups of organisms.” 11 The non-universality of the genetic code suggests that living things may well have had multiple origins. – Jonathan Wells and Paul Nelson, Rhetoric and Public Affairs, November 1998
From a 2001 discussion of the PBS Evolution series,
2. Variant genetic codes are not analogous to the differences between dialects of the same language.
In his press release, Miller writes: “As evolutionary biologists were quick to realize, slight differences in the genetic code are similar to differences between the dialects of a single spoken language. The differences in spelling and word meanings between the American, Canadian, and British dialects of English reflect a common origin. Exactly the same is true for the universal language of DNA.”
This is — at best — a wildly inaccurate analogy. From context and other clues, English speakers can discern that the words “center” and “centre,” or “color” and “colour,” refer to the same object. Meaning is preserved by context, and the reader moves along without a hitch.
But a gene sequence from a ciliated protozoan such as Tetrahymena (for instance), with the codons UAA and UAG in its open reading frame (ORF), cannot be interpreted correctly by the translation machinery of other eukaryotes having the so-called “universal” code. In Tetrahymena, UAA and UAG code for glutamine. In the universal code, these are stop codons. Thus the translation machinery of most other eukaryotes, when reading the Tetrahymena gene, would stop at UAA or UAG. Instead of inserting glutamine into the growing polypeptide chain, and continuing to translate the mRNA, release factors would bind to the codons, and the ribosomes would halt protein synthesis. The resulting protein would be truncated in length, and very possibly non-functional. Unlike variant spellings of “center,” therefore, context cannot preserve meaning. With the codons UAA and UAG, no shared context exists.
Knight et al. present a much better analogy for code changes:
– From Explore Evolution (Steve Meyer, Paul Nelson, Ralph Seelke, Jonathan Moneymaker, and Scott Minnich, 2007): “Another widely used argument for Universal Common Descent has recently come under fire. Biologists have long thought that the genetic code is basically the same in all living organ isms-that is, genes “code for” the same protein in almost identical ways in almost all living things. As our SOS discussion illustrated (See pages 54-55}, it is difficult to see how the codon-amino acid assignments could change without killing the host organism. That’s why evolutionary biologists have argued that the code we have today is the same as the code in the first living organism and why a universal genetic code points to a universal common ancestor. But is the genetic code universal? It turns out that it’s not.12 Since 1985 molecular biologists have discovered at least 18 different genetic codes in various species.13 Many of these are significantly different from the standard code.14 For example, the standard code has three different mRNA stop codons: UGA, UAA, and UAG . (A “stop codon” tells the cell to stop building-the protein is complete.) However, some variant codes have only one stop codon, UGA. The other “universal” stop codons now code for the amino acid glutamine. It’s very hard to see how an organism could have survived a transformation from the standard code to this one. Changing to this new code would cause the cell to produce useless strings of extra amino acids when it should have stopped protein production.”
– From Theistic Evolution (2017): “Perhaps the most common argument for universal common ancestry encountered by students in college-level biology textbooks is the universality of the genetic code- the claim that all life uses the same nucleotide triplets to encode the same amino acids. 5° However, the genetic code is not universal; many variants in the genetic code are known among various organisms. note 51 [51 For a list of known variants to the standard genetic code, see Andrzej (Anjay) Elzanowski and Jim Ostell, “The Genetic Codes,” Taxonomy Browser, National Center for Biotechnology Information (NCB!), accessed October 25, 2016, https://www.ncbi.nlm.nih.govfraxonomyltaxonomyhome.htmllindex.cgi?chapter=cgencodes. See also Robin D. Knight, Stephen J. Freeland and Laura F. Landweber, “Rewiring the Keyboard: Evolvability of the Genetic Code,” Nature Reviews Genetics 2 (January 2001): 49- 58.]”
But, in a world of genomic plasticity, genetic fundamentalism will probably continue to rule. It is easier to teach and undergirds claims for Darwinian mechanisms as the source of most or all variations in life forms.
See also: Mechanics as well as genetics is needed for viable embryo development