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There are now many variants of the “universal” genetic code


File:DNA simple.svg A friend writes to mention this page (2016) at National Center for Biotechnology Information:

The following genetic codes are described here:

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

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
So not only did we win with the spectacularly unlikely spontaneous formation of life once but.... multiple times? Really? Will our gentle interlocutors reject science and invoke panvitalism? Life just pops out everywhere. It's what NASA believes. The Big Bang and Evolution are the creation stories. Now liquid water provides the baptismal tank from which new life arises. They've got all the religious rites. As Cornelius says: "Religion drives science, and it matters." Latemarch
So, it will be argued that such cannot be used to argue against the evolutionary view. Of course, it ought not to be used to imply its empirical soundness either. But the real issue lies elsewhere: machine language is a complex integrated functionally specific, information-rich system. It needs execution machinery to work, which must be coherent. We thus see that over two dozen times, we have to account for the rise of FSCO/I in the form of these dialects. There is no sound, empirically warranted body of evidence that shows blind chance and mechanical necessity generating such or any other FSCO/I beyond 500 - 1,000 bits of complexity. The pivotal question of invention of such languages in a co-ordinated communication and cybernetic system at molecular scale is being begged. KF kairosfocus
No variants is consistent with the theory of evolution. Many variants is consistent with the theory of evolution. aarceng
Why are there ever so many computer languages, some fairly similar to others? kairosfocus

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