Saturday, February 25, 2006

Thursday, February 23, 2006

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.

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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Friday, February 17, 2006

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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Wednesday, February 15, 2006

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 now online at kete were, with a curious in-flight theme to it.
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Tuesday, February 14, 2006

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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Sunday, February 12, 2006

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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Thursday, February 09, 2006

Funky new tyrannosauroid

This week's Nature reports a new tyrannosauroid sporting a rather impressive crest.

This animal appears to be the most primitve member of the tyrannosaur lineage. Tyrannosaurs are but one of a larger group of meat-eating dinosaurs (theropods), and are along a major branch that eventually led to birds. The thought of T. rex as a relative of birds is a rather striking conclusion when you think of it. But these early, primitive tyrannosaurs help us reconstruct what the ancestors of the whole lineage might have been like. Indeed, the ancestors of much larger tyrannosaurs were quite a bit smaller.

The important thing to note is that this new tyrannosauroid, Guanlong wucaii is not an ancestor of animals like T. rex. At least, it isn't interpreted that way. It is its own unique branch along the base of that family's tree. Certainly, it's rather extravagant crest sets it apart as something quite unique on its own. But it doesn't preclude it from special relationships to other groups. It can be thought of, in a sense, as a side branch. When we have a number of such primitive 'side branches', we can use features common to all of them, but unique to the group, to reconstruct attributes that may have belonged to the anestor and were subsequently inherited by all (or most) of its descendents.

Scientists can see that Guanlong belongs to the tyrannosaur linage because it has a number of features that are unique to tyrannosaurs: the very front teeth in the upper jaw are "D"-shaped in cross-section with serrations along the "corners" of the D; and the way the bones along the top of the snout , the nasal bones and the frontal bones, fuse to each other -- just like T. rex and all its closest kin, but quite unlike all other theropods. However, Guanlong is what we might call "primitive" in other respects of its anatomy. That is, it is lacking a number of other characters unique to tyrannosaurs. For instance, you might have heard the scornful tone of an annoyed six-year-old who sees an ill-informed reconstruction of T. rex with three fingers. Of course, most dino-buffs or otherwise observant folks will know that tyrannosaurs normally only have two fingers. For most theropods, three fingers is the norm and two is the unique property of tyrannosaurs. Guanlong was quite clearly still has hands doing things the 'old fashioned way'. And thus, it was not descended from the common ancestor of those two-fingered tyrannosaurs.

Check out Carl Zimmer's post on this subject -- especially if I just confused you!

Xu, X. et al. 2006. A basal tyrannosauroid dinosaur from the Late Jurassic of China. Nature 439: 715-718.
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Wednesday, February 08, 2006

Attention Montrealers: Darwin Day at the Redpath Museum

I get a lot of visitors from Montreal, and I used to study there, so I should plug the Darwin Day event at my Alma Mater:

The Redpath Museum at McGill University is hosting a special Darwin Day event on February 12th and 13th (the website has an apparent typo - see the flyer).

Looks like it should be fun, it's a shame I'll miss it. On the bill is a lecture by Brian Alters, a McGill professor of education who testified at the Dover trial and made a critical breakdown of the "disclaimer" that was being read in the Dover public schools. He's a very dynamic speaker and gives very entertaining talks - I highly recommend it.

You should also check out Hans Larsson's talk on evolution and the fossil record -- a topic pretty near and dear to me. It's good to see that Hans has gotten aboard the public education thing. Two years ago, he might have dismissed the creationists with a wave of his hand. Now, I think it's becoming glaringly obvious that we've done this for far too long. We've thought that responding to them would simply lend them credibility. Well, it's too late. They've already got that credibility, unfortunately.

What scientists have to realize is that it's not the creationists' phony attempt at a scientific challenge that's a problem. We're not worried that they could actually upset the theory of evolution. Hell, they don't even understand it -- they wouldn't know what actual evidence against evolution would look like if it jumped up and bit 'em in the ass! Also, this is not like responding to that crank who thinks crop circles are flying saucer landing pads. This is much worse. Unlike the UFO cranks, we're talking about a very large, vocal, and politically mobilized segment of society. Many of them think that accepting evolution is the wellspring of moral decay, suicide, and even things like communism. Before you laugh and think I'm joking, think again. They truly believe this. Evolution stands for the root of all things they fear and fear is one of the most powerful agents of mobilization. This is a coordinated wholesale attack on the establishment of science with evolutionary theory as only its first in a long hit-list of targets. These are very large, very well-funded, and very vocal groups who have developed an extraordinarily effective campaign of obfuscation and deceit. State legislatures in the US have had bills before them that would limit the free expression of a scientific idea! Think about that before you just wave your hand and dismiss these people as just another sad bunch of cranks. Never underestimate a crank that votes.
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NY Times tells it like it is

Well, every once in a while, it's nice to see a journalist who will call a blatant falsehood when they see it. It's doubly nice when it's about misrepresentations of evolution:

The Utah bill's main sponsor, State Senator D. Chris Buttars, a Republican from the Salt Lake City suburbs, said he was not surprised by the debate it had inspired. He said ordinary voters were deeply concerned about the teaching of evolution.

"I got tired of people calling me and saying, 'Why is my kid coming home from high school and saying his biology teacher told him he evolved from a chimpanzee?' " Mr. Buttars said.

Evolutionary theory does not say that humans evolved from chimpanzees or from any existing species, but rather that common ancestors gave rise to multiple species and that natural selection — in which the creatures best adapted to an environment pass their genes to the next generation — was the means by which divergence occurred over time. All modern biology is based on the theory, and within the scientific community, at least, there is no controversy about it.

No relativism, no pandering to 'the other view', no references to 'intelligent design' as a 'scientific view'. Just plain tellin' it like it is.

(via onegoodmove and Leiter Reports)
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Tuesday, February 07, 2006

No it's not that Eden...

...but it sure is better than anything that Bronze-Age scribe could dream up!

A group of scientists has surveyed a remote region of Indonesia, the Foja Mountains and discovered a vast collection new plant and animal species. Some of these animals are downright beautiful! Check out this story and some great pictures.
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Behe responds to Kitzmiller decision

Behe's got a bee in his bonnet over the Kitzmiller vs. Dover ruling. The judge's 139-page ruling was one of the most damming pieces of prose that has ever been written against the intelligent design movement (for me this was because it was written by somebody outside the controversy and with no scientific credentials at all). Behe's own testimony served up quite an embarassment for him. So I guess he's decided to come back and try to save face.

Behe begins by contrasting an un-defined "restricted sociological view of science" (which is what he is apparently equating with mainstream science) with this view:

"On the other hand, like myself most of the public takes a broader view: “science” is an unrestricted search for the truth about nature based on reasoning from physical evidence. By those lights, intelligent design is indeed science." [emphasis added]

Really? I'm glad to see that Professor Behe has finally decided to stop focusing on the supernatural. I guess this means intelligent design isn't science or that there is a physical god out there that we can poke a stick at?

I'd be tempted to think of this as just a slip-up, but I'm more tempted to think that it's really a fabrication of his own nebulous and downright absurd definition of science, which we all know includes astrology as science:

Q[Eric Rothschild] Under that same definition astrology is a scientific theory under your definition, correct?

A [Behe] Under my definition, a scientific theory is a proposed explanation which focuses or points to physical, observable data and logical inferences. There are many things throughout the history of science which we now think to be incorrect which nonetheless would fit that -- which would fit that definition. Yes, astrology is in fact one, and so is the ether theory of the propagation of light, and many other -- many other theories as well.

My theory of sedimentary deposition points to the thousands of layers of sediment as evidence that giant men with shovels were throwing dirt around thousands of years ago. It is a completely secular theory and makes no reference to any gods or supernatural factors. It is, quite simply, nonsense. But it sure as hell points to some physical evidence for support.

Science isn't about making up nonsense and then pointing to a bunch of selected observations that might, if all other things are ignored, support your pet theory. I'm sorry but "pointing to" is not a valid method of scientific inference. It is, in fact, a recipe for self-deception.

Next Behe tries to hoodwink us with a nifty bait-and-switch. Watch it happen when ID is interposed with the Big Bang:

ID It does [not violate the centuries-old ground rules of science by invoking and permitting supernatural causation]. The Court’s opinion ignores, both here and elsewhere, the distinction between an implication of a theory and the theory itself. As I testified, when it was first proposed the Big Bang theory struck many scientists as pointing to a supernatural cause. Yet it clearly is a scientific theory, because it is based entirely on physical data and logical inferences. The same is true of intelligent design.
The 'theory' of ID is no theory at all. There is no framework of causative explanation from which we can deduce testable hypotheses. We just say 'Goddidit' and get on with it. The whole theory says that a supernatural being went to work either creating all things or tinkering with things along the way. That's all it says. That's all it's got to say. It's not an implication of the theory, it's the bloody rotten meat and overboiled potatoes.

I certainly do not exclude [the possibility that a precursor to the bacterial flagellum functioned not as a rotary motor, but in some other way, for example as a secretory system] merely by definition. In fact in Darwin’s Black Box I specifically considered those kinds of cases. However, I classified those as indirect routes. Indirect routes, I argued, were quite implausible...

..University of Rochester evolutionary biologist H. Alan Orr agrees

Well, if he agrees, then it must mean that implausibility=impossibility. Of course, that's just logical after all, isn't it? I wouldn't even agree with Orr that it's implausible (provided Behe even has that quote in context). Orr himself is using an analogy to a car, which is a false analogy -- cars and cells are nothing alike. Secondly, Behe assumes that a structure that is co-opted for a new function must be taken out of its old role. However, try a gene duplication or two.

Again, repeatedly, the Court’s opinion ignores the distinction between an implication of a theory and the theory itself. If I think it is implausible that the cause of the Big Bang was natural, as I do, that does not make the Big Bang Theory a religious one, because the theory is based on physical, observable data and logical inferences. The same is true for ID.
Again, if you don't think the Big Bang could have a natural cause, then you still haven't even started a case. What if I were to argue against the germ theory of disease because I don't think that an organism can be so small that it can be measured on the micron scale? What the hell is a micron? I can't imagine an organism that is microns long! I guess that means they don't exist. We should infer the next best explanation for illness, then: curses!.

The Court’s reasoning in section E-4 is premised on: a cramped view of science; the conflation of intelligent design with creationism; an incapacity to distinguish the implications of a theory from the theory itself; a failure to differentiate evolution from Darwinism; and strawman arguments against ID.

What Behe appears to be confusing with a straw man is the fact that we can 'undress' the scientifi air of his canard and treat it for what it is. To help him out, here is what a straw man is: "a characterization of an argument that unfairly creates a much weaker case and is then attacked".

Unfortunately, the case for intelligent design is the inductive statement a property known as 'irreducible complexity' can be (and has been) uncovered. Irriducible complexity points that some structures can't have parts removed or else they stop working. Therefore, we can't 'ratchet' our way up to them from a primordial beginning because the intermediates are non-functional. When a person claims to have discovered such a system, they are claiming that they know: 1) there are no other possible uses for the subcomponents of that system; 2) there are no other possible organizations for an organism that could, in turn, employ a simpler version of a system; 3) they have shown that the components of that system are and have always been entirely unique in the realm of biological diversity and those very components have had to come up from scratch.

What this amounts to saying is that if I start with a naïve and downright dishonest conception of evolutionary theory, I can show that some things cannot be produced by the evolutionary processes that I characterize. Who's talking about straw men? The entire ID movement is based on a straw man! Namely, this is the idea that complex, integrated systems can evolve through the assembly of simpler, un-related functional systems. Of course, Behe has dismissed these as 'implausible' for reasons that are unspecified, or at least seem to make further presumptions about the necessary course of evolution.

The reality is that most complex biological systems, from Behe's butt propellor to the development of an entire animal, most of the components can be shown to be 're-used' parts. So, it doesn't matter how 'implausible' Behe thinks this phenomenon is, the diversity of organisms clearly shows that it's how they're made.

And away we go again with PZ's favourite analogies to machines:

the cell is run by amazingly complex, functional machinery that in any other context would immediately be recognized as designed

Let's parse this little nugget of un-thinking, shall we?

He loves his 'machinery' analogy. So long as he calls thing machines and we accept, by definition, that machines are objects of intelligent design, then our cellular machines must also be designed, no? Eh? Eh? Eh? It's a good argument, eh?

What the hell does it mean to say "in any other context [this] would be immediately recognized as designed"? What are the other contexts? What this is basically saying is: if the cell were not the cell we recognize it as today, it would be recognized as a designed object. Since I wish to call it a machine and I wish to liken its parts to a machine and make it something it is not, I can fabricate a fantasy that the cell is an object built by a ghost and then try to foist this on the public (and particularly young people) as science.

Luckily for Behe, he can always claim some degree of internal consistency in his arguments. Afterall, he never cited logic as a criterion in his 'definition' of science.
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Who'd have thought that the blogosphere has an irreducibly complex metabolism?

Check out the metabolism of the science blogosphere over at Moment of Science. Brilliant stuff.

I can just see the analogies pouring out of the Discovery Institute now. "You see, metabolism is like the blogosphere and the blogosphere is the product of intelligence". Or even Michael Behe claiming that enzymes are "quite literally, little molecular blogs".
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