Dueling Scientists and the Tree of Life:  Analyzing the ID Response

"The BioLogos Forum" frequently features essays from The BioLogos Foundation's leaders and Senior Fellows. Please note the views expressed here are those of the author, not necessarily of The BioLogos Foundation. You can read more about what we believe here.

Today's entry was written by Kathryn Applegate. Kathryn Applegate is Program Director at The BioLogos Foundation. She received her PhD in computational cell biology at The Scripps Research Institute in La Jolla, Calif. At Scripps, she developed computer vision software tools for analyzing the cell's infrastructure, the cytoskeleton.

Last week I came across a blog post by Intelligent Design leader Bill Dembski, provocatively titled Craig Venter denies common descent — Dawkins incredulous. Now J. Craig Venter is a world leader in genomics, well known for having led the private-sector effort to sequence the human genome, and more recently for synthesizing an entire bacterial genome in the laboratory. If he denied common descent, it would be a huge deal in the scientific community. Surprised by the headline, I clicked over to read the story. Below is Dembski’s entire post:

Interesting story at Evolution News & Views [the Discovery Institute blog] about an exchange between Craig Venter (of human genome fame) and Richard Dawkins (of neo-atheist fame). Venter denies common descent, Dawkins can’t believe that he would even question it. For the exchange, which also includes Paul Davies, go here (start at the 9 minute mark). Origin-of-life researchers such as Ford Doolittle and Carl Woese have questioned for some time whether there even is a tree of life. Venter is now following in their train.

What’s significant is not so much whether Venter is right (I think he is), but what his dissent from Darwinian orthodoxy suggests about the disarray in the study of biological origins. If common descent is up for grabs, what isn’t? Imagine physics in the century after Newton questioning whether there even is such a force as gravity or suggesting that really it decomposes into several different types of gravitational forces.

Venter’s flight from orthodoxy is even more drastic. Common descent is the sanctum sanctorum of evolutionary biology. If scientists of Venter’s stature are now desecrating it, what’s next?

With just a few remarks, Dembski masterfully calls into question the most basic principle in evolutionary biology. As I said earlier, a disagreement over common descent between leading biologists like Venter and Dawkins would be major news. But this panel discussion happened back in February, and we haven’t seen it in the scientific journals. We haven’t seen it in the newspapers. Why? Because Dembski’s claim is patently false. His blog is so misleading it made me wonder if he actually watched the video.

The truth of the matter is that the brief exchange between Venter and Dawkins was not about common descent, but about the best metaphor for the connectedness of life—whether it is more like a tree or a bush. As we shall see, the context makes this clear.

Now, if Dembski didn’t watch the video, I could understand his confusion because his source for the story, an unsigned post on the Discovery Institute’s blog, is also misleading. The article, colorfully entitled Venter vs. Dawkins on the Tree of Life -- and Another Dawkins Whopper, is apparently part of a series aimed at chronicling how Dawkins is deceiving the public about evolution. The whopper in this case is Dawkins’ insistence that all life forms (“with one or two exceptions too minor to undermine the generalization”) use an identical genetic code.

The universality of the genetic code is often given as evidence for common ancestry, but as the author points out, the code isn’t technically universal. There are at least 17 documented cases where the code varies a little bit from the standard. “’One or two’ is therefore a Whopper,” the author writes. “As in, just not true” [emphasis in the original]. While the author doesn’t say so directly, the implication is clear: no universal code, no universal common ancestry. Whether the existence of variant codes throws a wrench into the argument for common ancestry is a good question. The answer is no, but we will get to that later.

As supporting evidence for Dawkins’ insistence on universality, the author points to the video mentioned by Dembski. It shows a star-studded panel of scientists (if one can use such a term for scientists!) participating in a discussion on a big question: “What is Life?” Topics range from artificial intelligence to panspermia (the idea that life was seeded on Earth from another planet) to synthetic biology. Here I quote at length from the Discovery Institute blog so you can get a sense of the argument:

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?"

The article then breaks to explain how the Mycoplasma and human genetic codes differ slightly before continuing the discussion about Venter, Dawkins, and Davies:

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."

…

"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.

The way this is written, we can only assume Venter’s smile indicates that he disagrees with Dawkins that all life is related. But the actual story is (as usual) much more nuanced. If you listen to Venter’s whole response to Davies (starting at 9:39), he says:

Well, I think the tree of life is an artifact of some early scientific studies that aren’t really holding up so the tree, you know—there may be a bush of life…[laugher, joking]…So there is not a tree of life. In fact from our deep sequencing of organisms in the ocean, out of now, we have about 60 million unique gene sets, we’ve found 12 that look like a very, very deep branching, perhaps fourth domain of life that obviously is extremely rare that it only shows up out of those few sequences. But it’s still DNA-based…we’re going to find the same molecules and the same base systems wherever we look.

Much of the panel discussion centers on the genuine scientific question as to whether there may be another kind of life form out there, either on Earth or elsewhere in the universe, that doesn’t depend on the molecules used by every form of life we know about so far—namely DNA, RNA, and proteins. Venter is clear that all life forms we’ve found so far are DNA- or RNA-based, but he thinks the bush is a better metaphor for the connectedness of life than the tree. Dawkins puts more emphasis on the vertical relationship between species, while Venter, because of his interest in microbial genomes, puts more emphasis on the horizontal swapping of DNA that can happen frequently between microbes. Thus they put the emphasis in different places, but both agree that all the life forms we know about so far are connected by common descent.

Later in the discussion Venter’s acceptance of common descent becomes crystal clear. Around the 17:15 mark, Lawrence Krauss begins to make the case against there being a second form of non-DNA-based life. He says, “Even in the kind of life you’re talking about, that lives in acid levels that would dissolve us, is from the same tree of life. And life seems to have occupied every niche on the planet it could have, the kind of life we have, and therefore I suspect that even if there was another life form, it would have been crowded out by now” (18:20).

Paul Davies disagrees with him, saying that one form of life need not eliminate another: “You’re right that life as we know it is spread into a wide geographical parameter space, but it doesn’t fill it up totally…The archaea and the bacteria have coexisted peacefully for what, 2.5 billion years, 3 billion? I don’t know. Do you know, Craig, how far back to the branch point?” Venter replies, without hesitation, “3.5 billion.”

The “branch point,” for those who aren’t familiar with thinking about trees or bushes of life, represents the last common ancestor between the two major domains of life in question, the archaea and the bacteria. I think this settles the question as to whether or not Venter accepts or denies common descent.

Now, lest I seem too eager to defend these two atheist scientists, I want to point out that I, like Venter, think that Dawkins is too dismissive of alternate genetic codes. We stand to learn a great deal about the history of life by examining the rare cases where life plays by different rules.

To understand why the almost-universal code is so suggestive of common ancestry, an important distinction needs to be made: the genetic code is not the DNA “letters” or bases themselves (A, C, G, and T) or even their sequence, which is expected to be highly similar between related organisms. The code refers to the way groups of DNA bases specify for particular amino acids within a protein. The linear sequence of DNA bases controls the linear sequence of amino acids within a protein. However, instead of one base specifying (or “coding for”) one amino acid, it takes three (e.g. AGG codes for Arginine, AGC for Serine). Since there are four DNA bases, there are 64 triplet “codons” (4x4x4=64), or groups of three bases. Interestingly, since there are only 20 amino acids, some codons are synonyms; they code for the same amino acid (e.g. AGA and AGG both code for Arginine). The reverse is not true, however—each codon codes for only one amino acid.

Why does AGA code for Arginine and not Serine? Nobody knows exactly. It is far from clear whether there are chemical or thermodynamic reasons why the codons correspond to the particular amino acids they do. This pairing could not have been predicted by looking at their chemical structures. They should be interchangeable, like Legos, though there are some clues that the pairings are not entirely random. There are literally billions and billions of possible genetic codes—ways to pair up the 64 codons with the 20 amino acids—but in almost every organism on the planet, the code is identical. Whether you look in animals, plants, fungi, bacteria, archaea, or viruses, the result is the same.

Until the early 1980s, it was thought that the code was “frozen” into place during the early development of life, but we now know the code itself is actually evolving. The 17 alternate codes mentioned earlier so far are not drastically different from the standard—they each vary in only a small handful of the 64 codons. In many cases, it is even understood mechanistically how the variations came about (Osawa et al. 1992. and Jukes and Osawa 1993).

This is why Dawkins does not see them as a threat to the common ancestor idea. To him, they make sense in light of the evolutionary process. Nevertheless he is technically incorrect, as the Discovery Institute blog argues, that small changes in the code necessarily spell immediate disaster for an organism. The existence of a few minor variations on a theme proves otherwise. This is the substance of Venter’s disagreement with Dawkins in the video. Venter doesn’t want us to forget that variants exist. He thinks they might give us important clues about the nature of life itself.

The Discovery Institute has spun this story in a very unhelpful direction. Dr. Dembski, perhaps misled by the post he referenced, has now grossly misrepresented the position of a leading biologist and called into question the enormous body of evidence for common ancestry. We urge him to watch the entire video and post a clarification on his blog if he believes he is in error.