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Venter vs. Dawkins on the Tree of Life — and Another Dawkins Whopper

Another Dawkins Whopper: The Universality of the Genetic Code
Since at least the publication of The Blind Watchmaker (1986), Richard Dawkins has claimed that the genetic code is universal across all organisms on earth. This is “near-conclusive proof,” he writes, that every living thing on this planet “descended from a single common ancestor” (1986, p. 270) at the root of Darwin’s universal tree of life.
More recently, Dawkins repeated the claim in his bestseller The Greatest Show On Earth (2009, p. 409):

…the genetic code is universal, all but identical across animals, plants, fungi, bacteria, archaea and viruses. The 64-word dictionary, by which three letter DNA words are translated into 20 amino acids and one punctuation mark, which means ‘start reading here’ or ‘stop reading here,’ is the same 64-word dictionary wherever you look in the living kingdoms (with one or two exceptions too minor to undermine the generalization).

We’ll come back to that last bit, which we emphasized, in a moment. But first, let’s look at the reason Dawkins gives for why the code must be universal:

The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation…this would spell disaster. (2009, p. 409-10)

OK. Keep Dawkins’ claim of universality in mind, along with his argument for why the code must be universal, and then go here.
Simple counting question: does “one or two” equal 17? That’s the number of known variant genetic codes compiled by the National Center for Biotechnology Information (NCBI). By any measure, Dawkins is off by an order of magnitude.
“One or two” is therefore a Whopper. As in, just not true.
“One, Two, or Seventeen, Who Cares — These Are Only Minor Differences!”
This, we imagine, is how Dawkins would object to the NCBI compilation of variant codes. Thus, it’s instructive to watch a fascinating exchange between Dawkins and genome guru J. Craig Venter, which occurred last month during a science forum held at Arizona State University.
The question for discussion at the forum was “What is life?” Most of the panelists agreed that all organisms on Earth represent a single kind of life — a sample of one — because all organisms have descended from a last universal common ancestor (LUCA). This “sample of one” problem is strong motivation, panelist and NASA scientist Chris McKay argued, for exploring Mars and other planets (or their moons) in our solar system, to try to find a second example of life, unrelated to Earth organisms.
Venter disagreed — in a remarkable way (start at the 9:00 minute mark). “I’m not so sanguine as some of my colleagues here,” he said, “that there’s only one life form on this planet. We have a lot of different types of metabolism, different organisms. I wouldn’t call you [Venter said, turning to physicist Paul Davies, on his right] the same life form as the one we have that lives in pH 12 base, that would dissolve your skin if we dropped you in it.”
“Well, I’ve got the same genetic code,” said Davies. “We’ll have a common ancestor.”
“You don’t have the same genetic code,” replied Venter. “In fact, the Mycoplasmas [a group of bacteria Venter and his team have used to engineer synthetic chromosomes] use a different genetic code that would not work in your cells. So there are a lot of variations on the theme…”
Here Davies, a bit alarmed, interrupts Venter: “But you’re not saying it [i.e., Mycoplasma] belongs to a different tree of life from me, are you?”
There Isn’t a Tree of Life
Before we get to Venter’s next (really striking) statement, here’s a quick visual summary of why the Mycoplasma code wouldn’t work with human genes:
Mycoplasma for Venter post.JPG
In human cells, the codon UGA codes for “stop,” meaning the end of an open reading frame (i.e., section of DNA coding for a protein). When the ribosome, the molecular machine that constructs proteins, encounters UGA in the messenger RNA of a human cell, it ceases translation.
Not so in Mycoplasma, where UGA codes for the amino acid tryptophan. On encountering UGA in an mRNA strand, the Mycoplasma ribosome would insert a tryptophan (in the protein the ribosome is assembling) and keep chugging right along with translation, through the following codons, until it met a Mycoplasma stop codon. Human and Mycoplasma cells do not read their DNA in the same way.
This is why Venter says the Mycoplasma code “would not work in your cells.” Indeed, this can be tested by expressing exogenous genes (with the so-called ‘universal’ code) in Mycoplasma to see if functional products would emerge from ribosomes.
So how did Venter answer Davies? Roll the video:
“The tree of life is an artifact of some early scientific studies that aren’t really holding up…So there is not a tree of life.”
Dawkins is Flabbergasted
Fast forward to 11:23, when moderator Roger Bingham turns the microphone over to Dawkins:
“I’m intrigued,” replies Dawkins, “at Craig saying that the tree of life is a fiction. I mean…the DNA code of all creatures that have ever been looked at is all but identical.”
WHOPPER. Venter just told the forum that Mycoplasma read their DNA using a different coding convention than other organisms (for “stop” and tryptophan). But Dawkins is undaunted:
“Surely that means,” he asks Venter, “that they’re all related? Doesn’t it?”
As nearly as we can tell from the video, Venter only smiles.

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