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

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March 14, 2011 Tags: History of Life

Today's entry was written by Kathryn Applegate. You can read more about what we believe here.

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

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.


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.


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Daniel Mann - #54316

March 14th 2011

I’d like to hear from Venter himself on this one. I took the “bush of life” to refer to micro-evolution and a denial of macro?? But only he knows!

In any event, commonalities—structural or genomic—do not necessarily argue in favor of common descent. I use the same 24 letters as Shakespeare had, but this doesn’t argue that my writing descended from his.


Jared - #54329

March 14th 2011

Daniel, your Shakespeare analogy may not have been the best choice, because when it pans out it works against your position. <meta http-equiv=“Content-Type” content=“text/html;charset=UTF-8”>Anyone writing in a romance language can thank the Phoenicians for their letters. While it’s true your writing might not “descend” from Shakespeare’s (and it’s arguable that in part it may have) you and Shakespeare use the same alphabet because both of your writings descended from a common origin. 



Daniel Mann - #54334

March 14th 2011

Jared,

Good point, but you’re taking the analogy further than I wanted. OK, let’s stay with it! Commonality implies a common creator. As the Phoenicians created our common letters, so too did God create the common letters of our DNA.


Tim McNinch - #54338

March 14th 2011

Fair enough. I too believe that God is behind this all. But, the Phoenicians didn’t create English and Spanish and Italian. They created (I’m assuming) Phoenician, and later languages using their alphabet system evolved from there, eventually becoming distinct languages (macro-ev). Yes, probably taking the analogy too far, like you say. But it’s worth considering, and perhaps conceding, the point that commonalities (while not conclusive evidence) do strongly suggest common ancestry.


Tim McNinch - #54333

March 14th 2011

“In any event, commonalities—structural or genomic—do not necessarily argue in favor of common descent. I use the same 24 letters as Shakespeare had, but this doesn’t argue that my writing descended from his.”


Worth clarifying: the case being made in biology is not that all organisms who share commonalities are descended one from another, but that they are related, i.e. they share a common ancestor. The fact that you use the same 24 letters as Shakespeare is actually very strong evidence that your writing and his are related, as indeed they are—both being forms of English.


Tim McNinch - #54335

March 14th 2011

Oops. Overlapping comment. Yes, what Jared said…


Daniel Mann - #54337

March 14th 2011

Tim,

We creationists are very happy with “relatedness.” We are related because we share a common Creator.


Tim McNinch - #54339

March 14th 2011

We certainly do share a common Creator. But biological commonalities suggest that we likely also share common biological ancestry—a hypothesis that seems to have stood up well when pressed for further interdisciplinary evidence.


p.s. you all comment very quickly! I’m assuming I’ve probably missed a few interchanges while typing this

Daniel Mann - #54425

March 15th 2011

Tim,

“Interdisciplinary evidence” might be easy to come by if thousands of people are all working to uncover support for the same theory—there is such an huge imbalance in favor of the resources that are trying to prove evolution—discarding what doesn’t fit, highlighting what does seem to fit.

For example, I’ve read that there are thousands of possible ways to date age. Only those methods that cohere to the theory are retained.


trubble - #54540

March 16th 2011

You read wrongly then. Only the methods that work are retained. Any scientist would love to falsify any of the dating methods, it would be a feather in his/her cap and a boost to his/her career. Scientists are motivated by proving other scientists wrong, it ensures only the accurate theories remain.

Scientists don’t resent creationists attacking EvNS, they resent the terrible arguments used.


John - #54319

March 14th 2011

Daniel wrote:

I’d like to hear from Venter himself on this one. I took the “bush of life” to refer to micro-evolution and a denial of macro??”

That’s a false dichotomy. But even accepting it, it’s as macro as you can get—showing the ratios of the differences between phyla.

“But only he knows!”

No, Daniel, it’s perfectly clear.

“In any event, commonalities—structural or genomic—do not necessarily argue in favor of common descent. I use the same 24 letters as Shakespeare had, but this doesn’t argue that my writing descended from his.”

In any event, pretending that the bush—which is a representation, not an interpretation—of the DIFFERENCES between groups represents nothing more than vague similarity is a standard deception. Are you deceiving or are you the deceived, Daniel?

IOW, how do you explain the differences, specifically the pattern(s) of the differences?

Daniel Mann - #54328

March 14th 2011

Please John,

Be a little more gracious. Creationists also believe in change over time, but we don’t believe that changes due to natural selection and random mut. can account for macro changes, just micro.


Glen Davidson - #54520

March 16th 2011

The trouble is, the evidence for microevolution is not at all different in kind from the evidence for macroevolution.  


Neither do creationists agree on where one ends and the other begins—mainly because there is no evidence that one “ends” at all.

<a href=“http://tinyurl.com/mxaa3p”>Glen Davidson</a>

Tim McNinch - #54340

March 14th 2011

Thanks for clarifying this, Dr. Applegate. This was a helpful article. Just goes to show how essential context is when making any claim about someone else’s remarks.


unapologetic catholic - #54344

March 14th 2011

“But only he knows!”

How do you reconcile your statement that only he knows wth this:

“Do you know, Craig, how far back to the branch point?” Venter replies, without hesitation, “3.5 billion.”

So Venter does see uninterrupted common ancestry for at least 3.5 billion years.  Do you agree with him at all?

Do you agree that the DI misrepresented his views? 

I always like to be gracious.  How do you graciously observe that a person is “quote mining?”




John - #54360

March 14th 2011

Daniel:

“Be a little more gracious.”

Oh, but I am being gracious by giving you the chance to explain whether you are the deceiver or the deceived. How do you explain the mathematical patterns of the differences?

“Creationists also believe in change over time, but we don’t believe that changes due to natural selection and random mut. can account for macro changes, just micro.”

But see, Daniel, this isn’t a matter of belief for me. It’s a conclusion based on the evidence. So when you grossly misrepresent the evidence and evade the simplest questions about it, I don’t see evidence that you have even an iota of belief in your position. If you believed in it, you also would believe that the evidence is consistent with your position; clearly you don’t!

If you disagree with my conclusion, how do you explain the mathematical patterns of the differences? 

DWD - #54405

March 14th 2011

Kathryn, I just watched the whole panel discussion, and your take is absolutely right. Venter is not disagreeing with Dawkins about the uniform nature of the building blocks of life, but about the form in which it has diversified. I found Paul Davies’ comments interesting, in that he raises the question of how we will identify the presence of other forms of life, if we are only testing for DNA/RNA organisms. Would we “see,” for instance, a silicon-based microscopic blob with no DNA/RNA, which might have information-bearing qualities and be capable of reproduction? Truly such life might be invisible to our methods, or even on the gross scale to our senses of sight and touch. Or, speculating way out there, might we even bring such life into being by expecting and looking for it? How much of the imago Dei did God instill in us - can we be creators in this sense, by imagining something and then devising methods to “find” it? Just having fun thinking about extremes here…


Argon - #54447

March 15th 2011

Aside:

1) Mycoplasmas are a derived group (possibly monophyletic) falling within the gram-positive bacteria.

2) ‘Bush of life’ is a reference to the often closely bunched splitting pattern of life. It’s a recognition of the ‘fuzz’ of diversity surrounding lineages that often makes it hard to identify exact ancestors.

AZDave - #54450

March 15th 2011

Venter didn’t really “synthesize an entire bacterial genome” did he?  Those of us who are computer programs would describe his effort as a form of hacking.  Impressive, but not quite what you said.


Regarding Venter-Dawkins, I was in attendance at the recent ASU Origins Debate, and there was obvious tension between the two regarding common descent.  The disagreement was quickly squelched, but there was disagreement.

I don’t have a firm opinion on the matter, but the resistance to debate, and the predilection to tar and feather anyone who would even question common descent suggests to me that there is something rotten here.

Kathryn Applegate - #54482

March 15th 2011

Hi AZDave,

Venter didn’t come up with the sequence of the artifiicial genome de novo; his team just produced it in the lab.  It’s over a million base pairs long and contains almost 1,000 genes.  The feat was overblown in the media (IMHO) as creation of life from scratch, but it does represent a truly amazing technological advance.  My short description of Venter’s scientific creds wasn’t intended to be misleading.  Apologies if it was!

That’s cool you were there at the ASU event.  From the video, tension WAS apparent between Venter and Dawkins.  I just think Dembski’s post was misleading about what was really at issue.  His post made it sound like evolutionary biology was completely falling apart.  The possibility of life with different biochemistry than us doesn’t take away from the many lines of evidence that point to common ancestry in the species we do know about.

No tar and feathers coming from me!  I think honest questioning is extremely important.


conrad - #54617

March 17th 2011

DNA is certainly a flexible clever molecule.

The “tree of life” is a pencil drawing by Darwin in the margin of his notebook.
 There is horizontal gene transfer and there are many other DNA modifications produced by retroviruses and gene-sharing by bacteria.

DWD - #54458

March 15th 2011

#54450

Regarding Venter-Dawkins, I was in attendance at the recent ASU Origins Debate, and there was obvious tension between the two regarding common descent.  The disagreement was quickly squelched, but there was disagreement.

What did you see as the issue between them? Didn’t they agree on the principle of common descent but disagree on how this happens, with Dawkins using the time-honored “tree” metaphor and saying all life came from the one trunk, while Venter is leaving room for a very early split, perhaps even an independently arising source of primitive life?  Though he does go on to say that all life will be DNA/RNA based, even if there are some differences in the bases and protein codes. Guess I would like to better understand the source of the conflict.


AZDave - #54473

March 15th 2011

I did not take detailed notes on the matter - you could be right.  Paul Davies also questioned the validity of the tree of life metaphor during the exchange and I noticed strain in Dawkins body and facial language prior to an incredulous assertion on Dawkins’ part along the lines of how could anyone question the tree of life.  Craig, Paul and Richard were clearly at odds on this point, but the moderator moved the discussion along.  In general, contentious issues regarding evolution dogma were not to be discussed during this so-called “debate.”  I’m sure an email directed to Paul Davies, the most honest of the three, would yield a better summary than what I have provided.




conrad - #54619

March 17th 2011

Well when “life” is understood it still just provides the hardware that spiritual software runs on.

It is the “dust of the earth”

The “breath of life is not necessarily molecular in structure.

conrad - #54620

March 17th 2011

It is quite likely that your soul is not the product of your brain.

Craig Newman - #54639

March 17th 2011

You are changing the goalposts. It is completely about sequencing, not the organic elements. Quit worshiping your penis.


glsi - #64309

August 28th 2011

Dr. Applegate,


Thanks for the link to this fascinating video.  I wonder if they deliberately situated Venter and Dawkins on the opposite ends of the table.

But are you sure this wasn’t a Star Trek convention?  The search for an alternate form of life on Earth seemed to be of utmost importance along with the theme of computers manufacturing themselves and taking over the planet.  What does separate these guys from a paranormal convention?  The suits?

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