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Origins Essays: May 2009 Archives

sea lamprey (Wikipedia)

The sea lamprey draws attention mainly for its alienlike appearance, particularly its oval mouth ringed with rows of sharp teeth that allow the parasitic creature to latch onto a fish host. These eel-like creatures are often called “living fossils” because they are thought to have changed little since they arose 450 million to 500 million years ago, as part of a branch of jawless creatures that split off early from the rest of the vertebrate tree. Lampreys and hagfish are the only survivors of that jawless branch, and accumulating evidence indicates that the animals have developed an immune system far different from that of other vertebrates, including people. Today, in Nature, a team led by Max Cooper of Emory University in Atlanta, Georgia, unveils the latest chapter in this emerging evolutionary tale, providing data indicating that the sea lamprey has its own versions of B and T cells, the two cell types central to the so-called adaptive immune response found in people. Whether those lamprey cells are related to our T and B cells, or are an independent invention, remains unclear, but that hasn’t dampened the fascination of immunologists. “I don’t think there’s any question now that there’s a separate adaptive immune system in the lampreys,” says Chris Amemiya of the Benaroya Research Institute at Virginia Mason in Seattle, Washington.

This month’s Origins essay tackled the evolution of the immune system, but it took a decidedly parochial view of the topic, focusing primarily on the microbial defenses wielded by people and other jawed vertebrates. The essay didn’t describe the lamprey story, which first gained prominence several years ago.

Now a Ph.D. student in evolutionary biology, Nicholas J. Matzke was a public information officer at the National Center for Science Education (NCSE) back in 2005. As such, he played a key role in NCSE’s participation in the Kitzmiller v. Dover Area School District trial that pitted intelligent design (ID) proponents against supporters of evolution. In particular, Matzke was central to the trial’s focus on the evolution of the immune system and the cross-examination of ID proponent Michael Behe. He recalls that episode, described in this month’s Origins essay looking at the evolution of the immune system, in an e-mail interview (edited for clarity) with Science's John Travis.

Q: Was it obvious to make the origin of the immune system a focal point of the case? I read that previous online debates with ID proponents led to the choice.

N.M.: Yeah, partially. The fuller story is that for several years, 2001-2004 or so, a number of us "Internet creationism fighters," of which I was one (as a hobby, before I worked at NCSE), would get on various UBB bulletin boards and newsgroups (and blogs starting in about 2004) and debate the ID guys. We were the people associated with TalkOrigins.org, TalkDesign.org, etc. (Later, this group became the Panda's Thumb bloggers.) Anyway, these debates were long and covered just about every topic in more detail than almost anyone could want. After doing this for years, we got a sense of not just where and how the IDists were wrong (since they are wrong on just about everything), but areas where they are spectacularly, obviously, blatantly, embarrassingly wrong. E.g., Behe's irreducible complexity (IC) argument is the favorite ID argument. And it is true that in 1996, some of the biochemical systems Behe used as examples had not received much attention in terms of their evolution. However, the immune system had received lots of attention even in 1996, and much more by 2005, primarily because (1) it is medically crucial, so there are many more researchers/funding/studies on it, and (2) much of immunology going back to the beginning has relied on comparative studies in animals, so there has been an explicit evolutionary context for 100 years in that field.

The amount of work is relevant because the IC argument always goes like this: 1. ID guy: Natural selection can't explain an IC structure because all of the parts would have to come together at once. 2. Evo guy: Here are some systems with only some of the parts but they still have some function, so your argument doesn't work. 3. ID guy: That doesn't explain how these systems arose, we need to see peer-reviewed publications giving detailed, testable explanations. 4. Evo guy: Here is a peer-reviewed publication on the topic. 5. ID guy: It's not detailed enough, I need to see every single mutation and selection event detailed or I will still say that ID was responsible, not evolution.

At this point, the ID guys have (a) given up on their original IC argument and (b) demanded an impossible, ridiculous amount of detail for the evolutionary explanation, while providing no details or tests of their own explanation. It looks ridiculous from the outside, but ID guys, including Behe, made these moves so regularly that it was pretty predictable.

So, in 2002 this began to become obvious when Matt Inlay wrote it up in an essay for talkdesign.org ("Evolving Immunity"). We then jumped Dembski with it in 2002 or 2003 on his own Internet forum at iscid.org and observed the above progression. Then we posted a bunch of references to articles on the topic and challenged Dembski to provide as much detail for the ID explanation. Here was Dembski's response:

"ID is not a mechanistic theory, and it's not ID's task to match your pathetic level of detail in telling mechanistic stories."

A similar episode happened with Behe in 2005.

In spring 2005, Eric Rothschild began preparing for Behe's deposition in the Kitzmiller case, which was happening in May. I gave him all this background and said if we wanted to pick one system to challenge Behe on, it should be the immune system. We poked him a bit on it at the deposition and got the expected replies.

So then, before the trial, I assembled the stack of books (from the UC Berkeley biosciences library) and articles on the evolution of the immune system and made a big exhibit for Eric to use. Eric asked the questions and got the expected replies, so when Behe started making noises about how the science "wasn't detailed enough," Eric started piling books and articles on the stand, and asking Behe if it was good enough for him. The rest is history...

Q.: You have called the Behe cross-examination on immune origins a "turning point" in the trial. Why do you say that?

N.M.: Well, it was kind of the ultimate Behe defeat amongst a long string of defeats during the Behe cross. I think Eric's whole cross was a "turning point" in that Behe's direct testimony was the one big chance the defense had to come back after the plaintiffs had been beating on ID for 3 weeks during the plaintiffs' case.

It was kind of a turning point for the whole ID argument over the last decade or two because it really exposed for all to see that ID was mostly boasting and dissembling, compared to the substance (physical substance, in the case of the immune system exhibit!) of the evolutionary science.

It was very gratifying to have my very obscure hobby turn into a key skill in an internationally recognized court case. It was kind of like the movie Galaxy Quest, where the Trekkie nerd gets told that the spaceship and aliens from the Star Trek-esque TV show are all real, and his nerdy knowledge saves the day.

In our initial Origins essay looking at the origin of life on Earth, Carl Zimmer discussed research on how the key genetic molecule RNA may have arisen from an abiotic broth. Part of the discussion centered on the RNA work of John Sutherland of the University of Manchester in the U.K., some of which is being published today in Nature. Here's the relevant excerpt from our essay:

Step 1: Make RNA
An RNA molecule is a chain of linked nucleotides. Each nucleotide in turn consists of three parts: a base (which functions as a "letter" in a gene's recipe), a sugar molecule, and a cluster of phosphorus and oxygen atoms, which link one sugar to the next. For years, researchers have tried in vain to synthesize RNA by producing sugars and bases, joining them together, and then adding phosphates. "It just doesn't work," says Sutherland.

This failure has led scientists to consider two other hypotheses about how RNA came to be. Cleaves and others think RNA-based life may have evolved from organisms that used a different genetic material—one no longer found in nature. Chemists have been able to use other compounds to build backbones for nucleotides (Science, 17 November 2000, p. 1306). They're now investigating whether these humanmade genetic molecules, called PNA and TNA, could have emerged on their own on the early Earth more easily than RNA. According to this hypothesis, RNA evolved later and replaced the earlier molecule.

But it could also be that RNA wasn't put together the way scientists have thought. "If you want to get from Boston to New York, there is an obvious way to go. But if you can't get there that way, there are other ways you could go," says Sutherland. He and his colleagues have been trying to build RNA from simple organic compounds, such as formaldehyde, that existed on Earth before life began. They find they make better progress toward producing RNA if they combine the components of sugars and the components of bases together instead of separately making complete sugars and bases first. Over the past few years, they have documented almost an entire route from prebiotic molecules to RNA and are preparing to publish even more details of their success. Discovering these new reactions makes Sutherland suspect it wouldn't have been that hard for RNA to emerge directly from an organic soup. "We've got the molecules in our sights," he says.

Sutherland can't say for sure where these reactions took place on the early Earth, but he notes that they work well at the temperatures and pH levels found in ponds. If those ponds dried up temporarily, they would concentrate the nucleotides, making conditions for life even more favorable.

Were these Darwin's warm little ponds? "It might just be that he wasn't too far off," says Sutherland.

Today's New York Times has one of the many newspaper articles discussing the study, and it includes a nice graphic that helps explain the new advance.

—John Travis

April's Origins essay in Science is devoted to the evolution of flowering plants and so, too, is a meeting yesterday and today at the Royal Society in London. The finale of the meeting will be an evening public lecture on 12 May, Web cast live and then available archived, by Sir Peter Crane, a former director of the Royal Botanic Gardens at Kew who is now at the University of Chicago in Illinois.