March 18, 2010 | David F. Coppedge

“Synthetic Evolution” – Is it Really Intelligent Design?

Some Cambridge scientists engineered a four-character genetic code and made some proteins with it.  They guided the process at every step, but claim that they “evolved” this code.  Is that a fair use of language?  This strange admixture of concepts is found in today’s issue of Nature.1  The confusion began right in the title: “Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome.”

  1. …orthogonal pairs have been evolved to incorporate a range of unnatural amino acids…
  2. Here we synthetically evolve an orthogonal ribosome (ribo-Q1) that efficiently decodes a series of quadruplet codons….
  3. Because the synthetase�tRNA pairs used have been evolved to incorporate numerous unnatural amino acids it will be possible to encode more than 200 unnatural amino acid combinations using this approach.
  4. ….this work provides foundational technologies for the encoded synthesis and synthetic evolution of unnatural polymers in cells.
  5. Natural ribosomes are very inefficient at, and unevolvable for quadruplet decoding, which would enhance misreading of the proteome.
  6. …orthogonal ribosomes … may, in principle, be evolved to efficiently decode quadruplet codons on the orthogonal message….
  7. To discover evolved orthogonal ribosomes that enhance quadruplet decoding we first created 11 saturation mutagenesis libraries in the 16S ribosomal RNA of ribo-X (an orthogonal ribosome previously evolved for efficient amber codon decoding on an orthogonal message)….
  8. We used ribo-X as a starting point for library generation because we hoped to discover evolved orthogonal ribosomes that gain the ability to efficiently decode quadruplet codons while maintaining the ability to efficiently decode amber codons on the orthogonal mRNA….
  9. To explicitly compare the fidelity of triplet decoding and quadruplet decoding for the evolved orthogonal ribosomes and the progenitor ribosome we used two independent methods….
  10. ….which is derived from the … pair, by a series of generally applicable directed evolution steps….
  11. …it will be interesting to investigate the enhancement of protein function that may be accessed by combining the encoding of these cross-links with directed evolution methods.

What’s notable in this paper was not only the flagrant use of evolve as an active method that the scientists used to investigate function for the purpose of enhancing protein synthesis, but also their use of the stem word “natural.”  They spoke of unnatural amino acids (those not found in wild-type living cells), and described their attempts to achieve of “synthetic evolution of unnatural polymers in cells.”  They spoke of the “inefficiency with which natural ribosomes decode quadruplet codons” but then praised their fidelity with their triplet system: “Natural ribosomes decode triplet codons with high fidelity (error frequencies ranging from 10-2 to 10-4 errors per codon have been reported).”
    Another mixing of unguided and designed concepts appears in their use of synthetic.  They spoke of “synthetic evolution” (their lab work) but also used and altered the “natural” molecular machines that bind amino acids to transfer-RNA, the tRNA synthetases.  Consider also how the concept of coding was used: they wished to achieve “synthetic genetic code expansion” They shifted seamlessly between the natural genetic code and their expanded, synthesized quadruplet code.  With all this mixture of terms synthesizing and evolving natural and unnatural codes, the reader is left wondering what “evolved” on its own, if anything, and what was intelligently designed.


1.  Neuman, Wang, Davis, Garcia-Alai, Chin, “Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome,” Nature 464, 441-444 (18 March 2010); doi:10.1038/nature08817.

Answer: everything was intelligently designed, both the natural and unnatural codes and functions.  This paper was one of the best examples in recent memory of Truman’s Law: “If you can’t convince them, confuse them.”  Using evolve as a synonym for design is a clever way to blow smoke using equivocation.  Words mean things.  This has nothing to do with evolution in the way Darwin used it, and in the way the debate rages today.  It has everything to do with intelligently designing codes to synthesize things they would not naturally do (that is, without the intervention of a human mind).  These human designers did not “evolve” anything, and they did not rule out intelligent design in the “natural” systems.  If they really wanted to talk about evolution, they should have left the lab and let “nature” take its course.  “Synthetic evolution” is as sophoxymoronic (02/02/2008 commentary) as holy atheism.

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