A blurb about prediction in historical science

Let's call this 'Part I' of a series I'll finish on Thursday.

The origin of tetrapods is one of the most important and remarkable events in the history of animal life. It is, after all, part of the story of our own origins. According to the fossil record, this event appears to have taken place in the Late Devonian period, between 375 and 365 million years ago. This event gave rise to the lineages that ultimately became humans, dinosaurs, birds, whales, and any other vertebrate that makes a living on land (or had an ancestor that did).

That is to say, the earliest tetrapods we have are known (from complete remains, anyway) from the very latest Devonain, a stage called the Famennian (see the diagram below). We already know that some very fish-like tetrapods called 'elpistostegalians' have been discovered in the earliest part of the Late Devonian, an interval called the Frasnian. Somewhere in the intervening Frasnian and Famennian rocks should be more tetrapods or elpistostegalians.

The diagram below shows some of the most completely known forms surrounding the origin of tetrapods and their distribution in time. The large pink band shows the approximately 10-million-year interval where very few fossils are known. Admittedly, the gap is somewhat exaggerated, there are some fragmentary animals known from this interval.

Modified from Carroll, 1997 Patterns and Processes of Vertebrate Evolution

One can see quite easily that finding more intermediates will involve finding more fossils in Late Devonian rocks. For instance, in the early part of the Frasnian, the elpistostegalian Panderichthys is present and is already very tetrapod-like, but still recognizably a 'fish'. Presumably, more tetrapod-like fishes will be found in rocks of similar date. A prediction is furnished.

To try to bear out this prediction, two intrepid palaeontologists set their sights on some new rock outcrops. Instead of going back to localities that have already been known and worked for decades, Ted Daeschler and Neil Shubin set their sites on a massive band of Devonian rocks in the Canadian Arctic.

An article dating back to 1999 quotes Shubin:

"A place like this that’s so vast and so clearly in the right time period is a great opportunity for us."

Daeschler adds:

"the earliest of the limbed animals. Or at the other end, fish that are just beginning to develop limblike structures."

As you can see, before Shubin and Daeschler ever set foot in the arctic, they already knew where they were going to look. All the following parameters need to be correct and established independently in order to make the prediction: the age of the rocks, the type of sediment, and the estimation of when the even took place. Then you should be able predict where you will find the fossils you want. In this case, the scientists knew from previous work (done by geologists, independently of they) that there was a huge section of the righ age and type of rocks in the Canadian Arctic.

I'm telling this story for a number of reasons. One, is that it's because I found this article some time ago, but that the results of six years of work in the arctic have not yet come to light. The artcile was written seven years ago when this expedition was being planned and the first year of several years work by Shubin and Daeschler. It's now quite dated and written quite some time before the authors ever went up. It provides perfect evidence for a 'case study' of how palaeontologists work. I'm often asked how palaeontologists know where to dig to find fossils, and this article helps give some insight as to how palaeontologists plan their expeditions.

The key is that the object of the Daeschler and Shubin mission is very rare. To pinpoint where one might find such rare fossils, a lot of things have to go right: the age of the rock formation needs to be known (and correct). The type of environment it was deposited in needs to be correct. Marine-type sediments very rarely have tetrapods or their nearest relatives. Thirdly, your prediction based on the evolutionary sequence seen in the rest of the fossil record has to be accurate. In essence, multiple independent lines of historical evidence are being put to the test. Each one converges to pinpoint where the right fossils of the right type and age will be found.

I'll leave the reader with those thoughts to contemplate and investigate. I'll finish this up later this week.
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Centipede eats mouse

In the tradition of the Octopus eats shark video that was so wildly popular, I give you Centipede eats mouse. Believe me, this video is not pleasant if you are faint of heart -- the audio captures exactly how unpleasant the mouse is finding this...

Edit: By the way, the centipede is Scolopendra

(Via Pharyngula)
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My last exam...

I've just finished what is my last (written) exam ever. If all goes well, I should never have to write another. There is, however, that little thing called my defense, however.
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Randi speaks!

James "The Amazing" Randi, stage magician and investigator (=debunker) of claims of the paranormal, has recently undergone a major bypass operation. He has been recovering for the past few weeks, and friends have been filling in his weekly commentaries. According to the JREF website (Randi's outreach organization), he has been making considerable progress.

Randi has left an audio message for all his readers. He sounds a little weak, but it's good to hear that he will be back to kick some 'paranormal' butt soon!

I wish him well, soon!
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Good Math, Bad Math

There's a new blog about math, this one that tackles the particularly bad math of creationists. It should be informative, and the author writes in a very clear style (no equations, if you're not into that). Check out Good Math, Bad Math.

(Via Pharyngula)
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Juravenator and the complex pattern of feather evolution

I normally like to post news here, but since this is a science and natural history blog (plus, apparently, random ramblings about other things) I'll post something that isn't very novel: a new theropod dinosaur published in Nature this week. The big news about Juravenator starki is what it doesn't have: for once, Nature is running an article about a dinosaur that doesn't have feathers.

Type specimen of Juravenator starki from the Late Jurassic of Germany. From Göhlich and Chiappe 2006

Ultraviolet and normal light photographs of the tail, showing patch of scales. From Göhlich and Chiappe 2006

The reason this is of interest to some palaeontologist is the fact that the authors' analysis suggested that it "should" have had feathers. That is, it was a type of theropod dinosaur that nested in the tree where feathers are predicted for the common ancestor.

Phylogeny showing the relationships of Juravenator with other theropod dinosaurs. From Göhlich and Chiappe 2006

Birds have scales and feathers needn't always cover the remainder of the body. The preservation of feathers in Juravenator's nearest relative known to have feathers, Sinosauropteryx is apparently limited to a mindline "mane" of filaments, an may not necessarily have covered the bodies. Whether or not this was the true condition in life could, potentially, be disputed. However, it follows from the enormous diversity of theropod dinosaurs that their feather distributions (both within and among taxa) were considerably more varied than previously though.

Tyrannosaurs are known to have patches of scaly skin, but recent discoveries show that their ancestors probably had feather-like structures. Thus, at some point, feathers must have been either incompletely covering the animal or lost and gained over varying degrees. Moreover, it appears that estimates of feather covering in dromaeosaurs were dramatically underestimated It would appear that our interpretation of feather evolution paints, perhaps too conservatively rather broad coating of feathers on just about anything descended from the common ancestor of all coelurosaurian dinosaurs.

Xing Xu, who has described many of the Chinese feathered dinosaurs, wrote a News and Views piece which raised some interesting cautions about these results: For one, we don't know that Juravenator did not have feathers. All we know is that parts of its body had scales. Fossilization is biased against feather preservation and those few records we have are remarkably rare. The specimen is apparently a juvenile and may, in fact, create a false signal pulling the animal to a particular part of the tree. Normally, this would be the other way around: juvenile characters tend to make you look more 'primitive'. However, Juravenator clumps with a group of small theropod dinosaurs which may share character similarities simply related to the fact that they're small, and not any real common ancestry. It's possible that this animal is more primitive, but unites with these other animals due to bias.

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Göhlich, U.B. & Chiappe, L.M. 2006. A new carnivorous dinosaur from the Late Jurassic Solnhofen archipelago. Nature 440: 329–332.

Xu, X. 2006. Palaeontology: Scales, feathers and dinosaurs Nature 440: 287-288.
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Will they be controlled by a collective overmind?

I'm still not sure if this is some kind of joke. I don't suppose that trying to engineer a battalion of cyber-insects is entirely out of the question.

The article has some anecdotes of past attempts at animal-based warfare:

WWII: Attach a bomb to a cat and drop it from a dive-bomber on to Nazi ships. The cat, hating water, will "wrangle" itself on to enemy ship's deck. In tests cats became unconscious in mid-air

It looks like the U.S. military's Tierekrieg strategies have a poor track record.

EDIT: Predictably, there's some great commentary over at Pharyngula.
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I bet they won't be calling Randi

The Catholic Church, that harbinger of critical thought and objective reasoning, is said to be "investigating an alleged miracle that, if proven true, could be crucial in naming John Paul II a saint." Oh, how our mortal intellects can only guess at what truth will be discovered.

According to the article:

John Paul... has been credited with curing a French nun of Parkinson's disease.

Conveniently, however

The woman's name, age and place of residence have not been disclosed.

No surprises. If you read the article you'll see that we're fed the same old B.S. that we see from the Peter Popoff's and Oral Roberts's. We've got the anecdotal evidence from 'honest people', the claim that 'science can't explain it', and the media failing to pass any critical judgement. The big difference is that it's the Catholic Church, so it's dressed up in white robes, rubies, and over a thousand years of gullible credulity so that a billion people are going to believe it simply because they will have been told to.

Rest assured, the hard-nosed team conducting the investigation has no interest in pursuading you of "miracles" or "saints":

Msgr. Slawomir Oder, a Pole who is leading the case for John Paul's sainthood, said he is asking the French bishop in whose jurisdiction the alleged miracle took place to start investigating what happened.

Of course, the candidate saint performs these miracles after they die. But, of course, if a miracle happens after a pope dies, then I mean, c'mon, who else could have done it, right? I mean, the miracle practically proves itself, let's not beat around the bush here.

Here is the rigorous water-tight methodology that will be used to objectively ascertain whether or not a miracle had in fact occurred:

All of the testimony gathered will be sent to the Vatican. After that, a team of experts appointed by the Vatican's Congregation for the Causes of Saints will determine whether a miracle happened.

Something tells me that they won't be calling in James Randi to conduct the "investigation". After all, we know what he might find out, and wouldn't that upset this little pageant? Randi's still has his unclaimed million-dollar prize for anybody who can prove their claimed miracle. And, I'm guessing, with all those collection plates that get passed around on Sundays, the Catholic Church could really use a million bucks, right?
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More Tommy

There's some more interesting stuff and links about Tommy Douglas over at Chandrasutra. Check it out!
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Tommy Douglas: The Greatest Canadian

Attention Canadians! Be sure to tune in to CBC's Prairie Giant: The Tommy Douglas Story tonight at 8PM E.T. Douglas is the man responsible for bringing us health care in Canada (in the same capacity that King Ralph may well bring it down). Douglas is also the founding father of the NDP a socially conscious left-wing party in Canada.

Tonight is apparently the second part of the series, meaning that I missed plugging part one. I obviously can't view it over here in Sweden, but I'd appreciate hearing from anyone who's seen the series. Please post a review in the comments section here -- I would be most grateful!
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Spreading the word: arsonists' attack on Holocaust History Project

Arsonists have attempted to burn down an office for the Holocaust History Project (THHP), an organization that publishes and distributes educational material about the holocaust. See Orac's post for details and a press release. THHP has been a vocal opponent of holocaust denial efforts, making it a prime target for radical anti-semetist movements--the likely perpetrators of these attacks. The attacks targeted a distribution

If so, then the attacks are an effort to silence THHP and further an anti-semetic agenda. In response, bloggers have been linking to the site and raising awareness about the attacks that have escaped considerable media attention.

I'm deeply ashamed of my delay in posting this and sorry that I missed this post earlier in the week. Please, spread the word and visit the THHP website.
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When it doesn't contradict your previously conceived view...

Sorry I haven't been posting much recently. I've been up to my eyeballs in a full-time course balanced with my research responsibilities (=major overtime!). I still haven't got much time to write anything substantial these days, but I can't resist pointing out when creationists are caught with their pants down.

I love how blatantly creationists are willing to accept facts when they are (seemingly) not contradictory to their worldview, even when accepting that same fact is contrary to arguments they've already made against evolution. Creationists have been quite adamant in their disputation of feathered dinosaurs. Groups like the multi-million-dollar organization Answers in Genesis have gotten a lot of mileage out of the "Archaeoraptor" incident, despite the fact that it is irrelevant to the question of dinosaurs with feathers. "Archaeoraptor" was a dinosaur rear-end stuck on a bird's upper torso. However, both taxa involved are known to have feathers. What's funny is how much effort they've expended in trying to dispute the feathers and other lame efforts to try to explain them away as plant matter or accidentally associated bird feathers.

Generally speaking, these creationist articles refrain from publishing any pictures of the actual fossils. They prefer instead to lure in unsuspecting children with images of the big, colourful, and goofy-looking dinosaur models and then abuse their minds with the senseless tripe in the articles.

However, AiG has published this twadle about a recently described Jurassic fossil mammal from China, Castorocauda. Here, we see no question of the preservation of integumentary structures (i.e. hair, in this case).

The fossil is in good enough shape to preserve hair

What? What about all those fantastic theories about ginko leaves or wildly improbable chance association of bird feathers and dinosaur bones? Isn't this another prime example of evil-atheist-evolutionist-commie-paleo brainwashing? Oh wait! There's nothing about the presence of hair on a mammal fossil that challenges AiG's preconceived view of the world, so might as well let it slide. Just because we know that mammals have hair, it doesn't mean that we can just go making such wild-ass conclusions about this grubby-looking fuzz around a mammal fossil! C'mon, guys (and they are all guys), you could at least be consistent in your challenges to the preservation of keratinized structures!

How does AiG fit Castorocauda into their worldview? Why, by fitting facts to fairy-tales, of course!

One interesting question in the creation model is where these mammaliaform organisms fit ecologically into the pre-Flood world. Modern groups of placental mammals are not found among the dinosaurs—only mammaliaforms and some marsupials. This suggests that placental mammals may not have lived with dinosaurs [i.e., shared the same habitat] before the Flood—only mammaliaform animals and some marsupials. The destruction of that entire ecosystem might explain why not only the dinosaurs, but also the mammaliaform animals, are not found on the earth today.

Yes, the fact that several thousand species of modern mammal are known from (or around) all continents and that dinosaur fossils are known from all continents (even Antarctica) sure sounds like a good indication that they would not have lived together in the pre-flood world. You mean to say that with dinosaurs roaming the entire planet not one happened to cross into the general neighborhood of a wildebeest, or a buffalo, or a kangaroo, or a cat, or a bear, or a squirrel, or a cow, or a sheep, or a pig, or a...

Too bad creationists are serious. You can't write comedy like this.
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Octopus eats shark

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The Bearded Man Conundrum

Over at the Panda's Thumb there is a rather lively discussion about who is the bearded man in the picture.

The picture purports to be from and signed by Charles Darwin. While it is a man with a white beard (not nearly as impressive as Darwin's), the picture sure doesn't look like him!

Anyway, I'm somewhat interested in knowing what comes out of this, so I thought I should spread it around a bit more.
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Old icons will die hard

It would be grossly inappropriate for a blog called The Lancelet to avoid discussing some of the interesting findings reported in today's issue of Nature. The new study, puts an interesting twist on our deep ancestry. In what is almost prototypical for science, it seriously challenges the common sense perceptions that have led us to our traditional classification. That is, science is almost at odds with how our subjective impressions tell us things ought to be. In this case, the authors have challenged a prevailing idea of how vertebrates are related to our neares invertebrate relatives.

Lancelets, or Branchiostoma, or amphioxus, (seen in the header of this site) are almost iconic in their status as the protovertebrate. There is even a song about our kinship with the lancelet. Lancelets have a notochord (a firm rod of tissue that underlies the dorsal hollow nerve chord -- one of the unique features that unites chordates, the group that includes tunicates, lancelets, and vertebrates), an elongate row of gill slits, and segmented muscle blocks.

A debate has raged among biologists as to who is more closely related to vertebrates: lancelets or tunicates. Tunicates (or sea squirts) are sessile animals that live kind of like a sponge, rather than like a fish. As was noticed by the early 19th C. embryologist, Karl Ernst von Baer, they have a free-swimming larval stage that has gill slits and a notochord and looks a lot like a lancelet. The ongoing debate (especially in recent years with the advent of molecular phylogenies) has been who is more closely related to whom: are lancelets more closely related to vertebrates? Are tunicates? Or are tunicates and lancelets closer to each other than either is to vertebrates?

The new study tested tested the interrelationships of the deuterostomes: the branch of the animal family tree that includes vertebrates, the various chordates, and echinoderms (sea stars & co.). The researchers used 146 nuclear genes of 36 different animals and two fungi. Their results were rather unorthodox. They recovered a tree that placed the tunicates as the sister group of the vertebrates. But what was more striking was the placement of lancelets with an echinoderm lineage.



The results, if correct, imply that the last common ancestor of vertebrates and echinoderms was an animal very much like the lancelet and that sessile filter feeders are more closely related to us than is a particularly vertebrate-like swimmer. A common, but fallacious, interpretation of such a phylogeny is that it implies we evolved from a sessile filter-feeder or, in this case, a tunicate. But it makes no such implication, since all the tunicates converge to a single unique node in the tree (the red branches marked "Tunicata"). What the tree actually implies is that their condition evolved along the "trunk" of that cluster of branches. This in itself partly explains why tunicates have a free-swimming, lancelet-like larval stage.

Common sense would make us want to lump lancelets with vertebrates. After all, lancelets look most like fishes. However, the question raised by this analysis is more along the lines of: what if tunicates split from the tree after lancelets split from vertebrates? This is an entirely possible scenario, but one that is not accounted for by a classification that focuses on overall similarity. The way evolution works is not necessarily reflective of the way we think it should work.

The reality is that looking back at evolutionary history from the present can be as biased as observing the solar system from here on earth. Appearances can be deceptive. The reason why we share so much in common with lancelets may not be because we have a special common ancestor with them. Instead, it may in fact be because lancelets haven't changed much since the common ancestor of vertebrates and echinoderms. Instead, it may be that tunicates and echinoderms are the ones that have diverged the greatest. This is certainly what the new result implies.

However, this phylogeny is far from being the last word on the interrelationships of our deepest ancestors. The authors themselves call for the need to test the grouping of lancelets with echinoderms. One of the potential problems here may be that each is represented by a single taxon. In the case of lancelets, we haven't got much choice. However, more echinoderms will be needed. A single, ancient lineage in an analysis can cause problems due to a phenomenon that systematic biologists call "long branch attraction". In simple terms, this just means that the longer and more rapidly evolving your lineage is, the greater the chances that parts of your genetic sequence will happen to match that of another ancient lineage, just by chance. When this happens, two unrelated branches can "snap together" implying recent common ancestry, when there is in fact none.

One of the strengths of this study is that they tried to circumvent this and other potential problems as much as possible. They concentrated on what were considered to be slowly evolving lineages. One of the problems that happens when a gene evolves too quickly is that it changes too much and, consequently, looks a lot less like the ancestral gene would have looked like. The result is that fast-evolving genese amount to a lot of "noisy" data over very long periods of time. The old information gets overprinted by new information and confuses the analysis and also confuses the analysis process.

There will certainly will be a number of researchers who will dispute this analysis. People who know their molecular evolution far better than I do will probably have much to say about it. In the meantime, it serves as a welcome challenge to the prevailing "dogma". This is not the first analysis to cast doubt on the status of lancelets, and certainly won't be the last.

EDIT: Predictably, Carl Zimmer has written another summary with an interesting twist. Check it out.

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Delsuc, F., Brinkmann, H., Chourrout, D., and Philippe, H. 2006. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439: 965-968. link.

Gee, H. 2006. Careful with that amphioxus. Nature 439: 923-924. link.
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The transition from chemical to Darwinian evolution

Well, the lecture by Jack Szostak was excellent. I had no idea how much progress has been made on pre-cellular evolution. Even though I've read a little bit about the subject, I was still blown away by the some of the research that the Szostak lab has done. I want to summarize everything, but I realize that's just not feasible. So I'll concentrate on some highlights.

Two of life's key features are, without a doubt, self-replication and compartmentalization. Without self-replication, life could never sustain itself and it would lack the main pre-requisite for evolution. So, we're looking for a simple self-replicator, first. Compartmentalization is just as important, because without it the molecules of a would-be living thing would simply diffuse into the environment. The work by Jack Szostak and his colleagues concentrated on the origin of these different systems and how they might have eventually been brought together.

We've now got a handle on how some simple nucleic acid (mostly RNA) self-replicators work. But they're pretty slow and have low-fidelity. Part of the problem is the chemistry of RNA itself. The nucleic acids we know today tend to have a large triphosophate group on them, this forms an "arm" that is negatively charged and would tend to repel rather than attract each other. That sort of slows down the whole self-replication thing. However, Szostak gave some very good reasons for looking elsewhere in "chemical space", as he called it. DNA and RNA, for instance, are not the only nucleic acid polymers out there. They've got a number of close cousins that can do the job also: TNA, GmNA, and GNA to name a few. They all have genetic potential and need to be explored. Diversity, here as in everywhere in evolution, is always that which defeats the small probabilities

There are also other permutations of molecules like DNA and RNA that are 100-fold more efficient at sticking themselves together. They might offer better candidates for self-replicating polymers than the versions modern cells use.

In living cells, compartmentalization is accomplished by membranes formed of fatty acids. Vesicles are self-organizing fatty acid membranes similar in organization to that of living cells. All cells are have such membranes, and they are one of the most cruicial aspects of life -- and they can self-assemble! This has been known for quite some time. But what Szostak and colleagues have been doing is to experiment with vesicles formed of simpler fatty acids, something more likely to have been around 4 billion years ago. Out own cell membranes are made of phospholipids that these cells synthesize. The array of available fatty acids for study shows what looks remarkably like a series of transitional forms between simpler fatty acids such as oleaic acid and our own more complex phospholipids.

Clay has been a major player in the study of the origin of life, since it has been found to have the ability to adsorb RNA to its surface. Szostak and colleagues tried to see what would happen to vesicle self-assembly when a piece of montmorillonite clay was added to the mixture. The results were dramatic: the rate of vesicle self-assembly went from a low linear rate to a steep logarithmic growth! What's more is that when clay with RNA adsorbed to it was used, many of the resulting vesicles could be seen to have the RNA inside of them!

One of the most interesting experiments was testing how different sugars would flow into/out of these fatty acid vesicles. Of the five or so sugars that was tested, ribose was -- by some considerable measure -- the most efficiently uptaken. Why is this important? Well, ribose is the R of RNA (ribonucleic acid). Ribose is the sugar out of which nucleic acids are made. This may explain why we use ribose in our own genetic information, since any proto-cell using ribose for its genetic material would've been at a significant competitive advantage.

What's really interesting about all this is that so many of these reactions are spontaneous. That is, they're energetically favrouable, at least under the conditions that were given. So, what's going on is that this isn't just people synthesizing the components of life in the lab, but the observation of the actual processes involved. I can't help but feeling ridiculously optimistic about have spontaneously generating protocells in the tube before I'm a middle-aged man.

I think these highlights just scratch the surface. I want to cover some more about the lecture, so I'll defer that to another post on Saturday or Monday.
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Lecture on early evolution of life

I'm attending a lecture this afternoon at the Ångstom Laboratory entitled: "The Transition from Chemical Evolution to Darwinian Evolution" by Jack W. Szostak. This should be of interest to readers here, so I'll try to post a summary later this afternoon or tomorrow.
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Tangled Bank #47

...is now online at kete were, with a curious in-flight theme to it.
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How to evolve a watch

A brief response to Paley:



The image was produced by Andreas Wallberg of Uppsala University's Department of Systematic Zoology.
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Darwin Day 2006

Charles Darwin was born 197 years ago on this day (as was Abraham Lincoln). This marks Darwin Day at many universities around the globe. Check out the link for any events at a campus in your area.
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