Pharyngula

Saturday, December 31, 2005

Did I miss a blogosphere memo?

What's with all the stories about toilet science this morning?




Posted by PZ Myers on 12/31 at 09:58 AMprintx
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Friday, December 30, 2005

A signature of a radiation in metazoan evolution

How real is the Cambrian explosion? In a sense, it wasn't an explosion at all in any commonly understood meaning of the term—it was a relatively rapid apparent diversification of animal phyla over the course of at least tens of millions of years, at a rate that is compatible with unexceptional rates of evolution. Even at the most 'explosive' rate that can be inferred from the observations, this is not an event that challenges evolutionary theory, nor should it give comfort to creationists of any stripe.

However, there are controversies here. One camp holds that the rapid divergence of the metazoan phyla in the Cambrian is real: the different phyla all arose sometime around the boundary, 543 million years ago, and then evolved into the various forms we see now. This interpretation is supported by the fossil record, in which the first recognizable representatives of the phyla are found from roughly the same period.

Another interpretation is that the Cambrian explosion is only apparent: that the divergence occurred well before 543 million years ago, and that there was a long period of undetectable evolution. The major groups of animals separated 600 or perhaps even as much as 700 million years ago, flourished as small wormlike forms that would have fossilized poorly, and what the Cambrian represents is an emergence of larger forms with hard body parts that fossilized well. Some of the molecular data supports an early divergence, and there are known pre-Cambrian trace fossils and fossils—the phosphatized embryos of the Doushantuo formation, about 600 million years old, are a good example.

There are also other ambiguities to be resolved. The relationships of many animal phyla are confusing, and who branched from whom remains to be resolved. In the diagram below, the dashed lines in the tree are the problem: do they branch exactly as shown? How deep in time do those branches go?

metazoan radiation
The fossil record and evolution of 9 of the 35 currently recognized metazoan phyla suggest that most animal phyla diverged/arose at the beginning of the Cambrian (C) period. The thick lines represent the known ranges of fossils from their first appearance in the fossil record. Thin lines represent the inferred metazoan phylogeny based on fossil data. Dashed lines represent an amalgam of three conservative estimates of the inferred metazoan phylogeny.

Rokas, Krüger, and Carroll have taken an ambitious molecular approach to answer those questions. What they have done is examine 50 genes in each of 17 different species spanning 9 phyla, making a special effort to collect new data from phyla underrepresented in previous work: Porifera, Cnidaria, Platyhelminthes, Mollusca, Annelida, and Priapulida. The goal was to obtain sufficient data to resolve those branches in the animal family tree.

Their results are the kind that are most challenging to present: they were abstract and negative. Despite all their data, an alignment of 12,060 amino acids in proteins from all those phyla, the relationships of many of the taxa remain murky. The diagram below summarizes the tree they found. The numbers at the branches are the results of maximum likelihood/maximum parsimony analyses (big numbers are better, reflecting greater certainty in the validity of the branch point), while branches without numbers were not resolvable statistically.

metazoan radiation
The lack of resolution in phylogenetic relationships among major metazoan phyla. Values above internodes correspond to support values from ML and MP analyses, respectively. Only internodes with significant support in at least one of the two analyses (ML and MP) or internodes present in majority-rule consensus trees of both analyses are drawn. Analyses were also performed by Bayesian inference. Although certain analyses provided strong support for particular clades, analyses of different subsets of taxa produced significantly different and conflicting results.

Hmmm. All that work, and the branching is still blurry. The investigators evaluated a number of possible problems to see if they were the source of the difficulty. For instance, long branch attraction is a common problem, so they reanalyzed the data, excluding some of the long branched taxa to see if it sharpened up the results. It didn't help.

They speculated that there could be a few "rogue" taxa, whose position in the tree was problematic, so they threw the least stable groups out of the analysis to see if that helped. It didn't.

They didn't think that missing data from some taxa would affect the results, but they reanalyzed, excluding the two phyla with the most incomplete data sets. They were right, it didn't improve their analyses. They tried multiple other approaches to figure out why exactly they couldn't discriminate many of the branch points.

Maybe it's simply a shortcoming of their methods: they don't have the capability to resolve events that occurred several hundred million years ago. To address that, they used their same techniques on a completely different kingdom, the fungi, in which we don't know of any major threshold event comparable to the Cambrian explosion. Those results are diagrammed below; metazoa are in the top half of the tree, while fungal taxa are in the bottom half. The key point is that in most cases, it worked! They could see the relationships of the various fungal taxa with a high degree of statistical significance.

metazoan radiation
The contrast in phylogenetic resolution between the clades of Metazoa and Fungi. Values above internodes are as in Fig. 1. Eleven out of 13 internodes in the fungal clade are significantly supported by both optimality criteria (ML and MP), whereas only 4 out of 14 internodes in the metazoan clade are significant. Analyses were also performed by Bayesian inference.

One possibility is that, unlike fungal history, the speciation events that produced the metazoan phyla were so tightly compressed that they can't be resolved at this distant remove—in other words, that the Cambrian explosion represented a real burst of macroevolutionary branchiness that occurred in a narrow window of time. They tested this hypothesis with a simulation of another known rapid adaptive radiation, the emergence of the mammalian orders. The mammals diverged 107 million years ago over a span of 42 million years, so the window of time is comparable to that of the Cambrian explosion, only much more recent. They then simulated an additional 500 million years of molecular evolution to produce a data set that could be analyzed, and found again that the passage of that much time would obscure the relationships between the orders.

What they propose, then, is that the lack of resolution is data, and represents a positive signature of an adaptive radiation. They come down on the side of the reality of the Cambrian explosion—it is comparable to other situations in which a lineage rapidly diversifies as it exploits a novel or otherwise empty environment.

An accompanying Perspectives article by Jermiin et al. raises some objections to the analyses that were out of my depth, but in particular mentions that some of the assumptions of homogeneity in rate and site of change in genes are unrealistic, and calls for further detailed study of how genes change over time—they are less pessimistic about the resolvability of the branches, and think there is room for improvement in the study. They suggest that it's a step in the right direction of reconciling paleontological and molecular data, and hint that there are 26 more phyla that haven't yet had a similarly rigorous examination yet…there is much work to be done!


Jermiin LS, Poladian L, Charleston MA (2005) Is the "Big Bang" in animal evolution real? Science 310:1910-1911.

Rokas A, Krüger D, Carroll SB (2005) Animal evolution and the molecular signature of radiations compressed in time. Science 310:1933-1938.


Posted by PZ Myers on 12/30 at 02:19 PMprintx
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Thursday, December 29, 2005

Nüsslein-Volhard and Wieschaus retrospective

In the late 1970s, I was an undergraduate working in a fly development lab, and I heard rumors from the people working there about this wild and crazy experiment going on at EMBL—they were ripping through the whole fly genome, trying to put together the big picture of patterning in early embryos.

A little later, I was in grad school, and this amazing paper came out in Nature. I read it, but I have to admit…I wasn't entirely aware of the significance. Lots of mutants, lots of genes, but I was focused on Mauthner neurons and growth cones and synaptic remodeling and cytoskeleton, so I set it aside.

Yet later, my graduate research had taken a slight turn; I'd discovered that spinal motoneurons were identifiable and segmentally repeated, and I got interested in segmentation again, and rediscovered that lovely paper, and the incredible bloom of new work that had followed from it. It was one of the factors that decided me on going back to insects for my post-doctoral work.

It kind of snuck up on me. I can't claim to have predicted the revolution the work of Nüsslein-Volhard and Wieschaus would cause in my field, but now with hindsight it's clear and dramatic. This was the threshold event that changed the way we look at development, genetics, and evolution.

The Nature Genetics blog, Free Association, has a brief look back on the seminal work of Nüsslein-Volhard and Wieschaus, published 25 years ago last October. It's amazing stuff, and if you want to understand where the new metamorphosis of modern biology came from, this was the seed.


Posted by PZ Myers on 12/29 at 07:36 PMprintx
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Wednesday, December 28, 2005

Hubba hubba

Look at this splendid animal; you've got to admit that it is just beautiful.


Posted by PZ Myers on 12/28 at 08:08 PMprintx
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Monday, December 26, 2005

EO Wilson on liberal arts colleges

Andre Brown sent along a quote from E.O. Wilson I like very much.

I went to the University of Alabama and they pretty much let me do what I wanted to do. I got into the Department of Biology and had some very good, attentive professors. It was the late '40s and they paid close attention to me. I was a gangly 17-year-old when I first went and graduated at 19. They were used to dealing almost entirely with preparing students to go on to medical school. Here they had an authentic embryonic biologist, so I got all sorts of special attention, including my own lab space when I was a freshman—it was great.

I'm not sure you could reproduce that experience today. Science has changed a lot. For parents thinking of encouraging their children to become scientists, and especially biologists and naturalists—if the student has that inclination to start with—I would recommend liberal arts colleges, not major research institutes. Go to a major research university after you've had four years of a liberal arts college that believes in generalized training in biology, including natural history, with heavy emphasis on ecology. In the last several years I've visited a number of really outstanding ones and the difference between them and major research universities, including my own Harvard, is striking, in terms of what it can mean to an individual student.

Most science education takes a boot camp approach or is set up to train acolytes. That's because most scientists are journeymen—they're not masters. That is to say, they're well-versed and if it's a major research university they probably have some accomplishments on a narrow segment of scientific research, but basically they think like journeymen and are there to train journeymen. They don't think particularly laterally about what their field means. There are, of course, in every university and college striking exceptions, but most scientists are recognized for and advanced by the discoveries they make. The gold and silver of science is original discovery. They know they have to be involved in making an original discovery, and to do that you move along a very narrow front.

There's time enough to specialize and dig deep into a field in graduate school. An undergraduate education should emphasize breadth of knowledge and a recognition of the big ideas, not giving a fine focus on one tight little problem.

I think his emphasis on ecology is a product of his personal biases, though. If you ask me, you should emphasize developmental and molecular biology.


Posted by PZ Myers on 12/26 at 05:55 AMprintx
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Saturday, December 24, 2005

So that's what draws you readers in

According to AOL, the #1 biggest science story of the year was the live giant squid sighting.


Posted by PZ Myers on 12/24 at 10:40 AMprintx
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Friday, December 23, 2005

Maynard Smith speaks

Take a look at this fascinating interview with John Maynard Smith—he talks about all kinds of things in evolutionary theory, but he also talks about religion. It will confirm some people's impression of evolution that he specifically cites Darwin's Origin as the book that made him apostate. "I think it was an enormous relief to escape from religion," he says.

I've been writing too much about this lately, but I think that's right. While someone can continue to believe in a god or gods and still do science, evolution makes religion superfluous, and once you've got a rational alternative, why stick with unsupported beliefs in remarkably silly superstitions? Evolution is anti-religious in the sense that it removes the rationale for religion.

(via UberKuh)


Posted by PZ Myers on 12/23 at 12:17 PMprintx
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Thursday, December 22, 2005

Breakthrough of the Year: Evolution!

Science has announced their choice for the most important, the most fundamental, the most revolutionary scientific breakthrough of 2005…and their choice is evolution.

You're saying "Hold it! That was a breakthrough 146 years ago, not today!" Haven't you been listening to what I've been saying, though? We're seeing big advances in evolutionary biology. We're on the edge of a Renaissance in the discipline, if we're not already in the middle of it.

I think the announcement is open to non-subscribers, but here's the beginning, just in case it's not.

The big breakthrough, of course, was the one Charles Darwin made a century and a half ago. By recognizing how natural selection shapes the diversity of life, he transformed how biologists view the world. But like all pivotal discoveries, Darwin's was a beginning. In the years since the 1859 publication of The Origin of Species, thousands of researchers have sketched life's transitions and explored aspects of evolution Darwin never knew.

Today evolution is the foundation of all biology, so basic and all-pervasive that scientists sometimes take its importance for granted. At some level every discovery in biology and medicine rests on it, in much the same way that all terrestrial vertebrates can trace their ancestry back to the first bold fishes to explore land. Each year, researchers worldwide discover enough extraordinary findings tied to evolutionary thinking to fill a book many times as thick as all of Darwin's works put together. This year's volume might start with a proposed rearrangement of the microbes at the base of the tree of life and end with the discovery of 190-million-year-old dinosaur embryos.

Amid this outpouring of results, 2005 stands out as a banner year for uncovering the intricacies of how evolution actually proceeds. Concrete genome data allowed researchers to start pinning down the molecular modifications that drive evolutionary change in organisms from viruses to primates. Painstaking field observations shed new light on how populations diverge to form new species--the mystery of mysteries that baffled Darwin himself. Ironically, also this year some segments of American society fought to dilute the teaching of even the basic facts of evolution. With all this in mind, Science has decided to put Darwin in the spotlight by saluting several dramatic discoveries, each of which reveals the laws of evolution in action.

They single out the chimp genome sequence, new discoveries in human evolution, new ideas and evidence in speciation, and the evolution of the flu virus as highlights.

There's also a video presentation online. It seems to be busy, busy, busy right now and I've only been able to watch half of it—it's talking heads, but still, several good summaries of the significance.


Posted by PZ Myers on 12/22 at 04:05 PMprintx
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A possible link between reindeer, daylight deficiency, and artifact delivery

reindeer

I have a theory, which is mine, that there is an entity or intelligence (which I will not name, since that would be unscientific) which resides in the Arctic and makes midwinter use of reindeer in a complex specified task. This theory of mine guides my research, which may not be mine, but as long as it can be interpreted to support my theory of an Arctic Artificer, I can appropriate it as mine, which is just as good.

My theory predicts that there is a peak of artificer activity in late December. The hypothesis that reindeer activity generates a polar distribution force for the delivery of artifacts generated by the Arctic Artificer is consistent with a large body of evidence. It also makes testable predictions. For example:

  1. It predicts that reindeer ought to begin to spread out their levels of activity throughout the day and night in midwinter, to be better prepared to handle the complex specified task, which requires 24 hours or more of sustained activity. Reindeer activity could be monitored to test this prediction.
  2. It predicts that reindeer activity should be correlated with late December deliveries of artifacts to households around the world.
  3. It predicts that the polar distribution force is regulated, at least in part, by solar radiation. It might be possible to observe the incidence of solar radiation in the arctic, and to block the effects of reduced solar radiation with some really bright lights.

If the hypothesis is corroborated by these and other experimental tests, it might facilitate the delivery of artifacts, and/or the early detection of the appearance of the Arctic Artificer. Which would make my theory really important, and ha-ha-nanny-boo to those who deny the existence of an artifact production center somewhere near the North Pole.

I am pleased to report that there is a paper in the prestigious journal Nature which has evaluated my prediction A, and even though the authors had no idea that they were testing Arctic Artificer Theory, I can stretch this tenuous link to a tiny and irrelevant prediction which could also be interpreted to support many other alternatives as support for my grand theory, which is mine and reflects the glory of the Artificer, blessed be his unnamed name. (Oh, and if you can't guess what I'm talking about here, here's a clue.)

But seriously, there really are observations of circadian activity in arctic reindeer that suggest something interesting is going on in reindeer brains in midwinter and midsummer. It doesn't really support any claims of toyshops at the North Pole, but you knew that already.

Here's the real story. We exhibit circadian rhythms in many processes: sleep-wake cycles, temperature variations, hormone rhythms, blood pressure, and behavior. We have an internal clock that is ticking along at about a day, and even if you deprive us of all external cues, for instance by putting us in a cave and removing all signals from the outside world, we still cycle along rhythmically. The rhythm is the rate of our internal clocks, though, which are slightly different from the actual cycle of the sun. One way we feel this difference between what our body's clock is saying and what the world around us is saying when we experience jet lag.

Arctic animals experience an interesting natural version of the experiment of putting a person in a cave: in midwinter the sun sets and doesn't come back up for days, weeks, or months (depending on how far north you are), and likewise the sun stays above the horizon for prolonged periods of time in the summer. Animals from temperate latitudes, when deprived of solar cues, continue to exhibit a circadian rhythm, exhibiting elevated activity during the time that roughly corresponds to "day", and lowered activity during their "night". What about arctic animals?

They seem to shut off their clocks, and their activity becomes arrhythmic.

Here are some of the data to show this. It was collected the hard way, with investigators going out every day at all hours over the course of a year in the Arctic, logging all the behavior of reindeer. The white bars represent periods of alert activity, while the black bars are periods of rest. In the subspecies farther south (the left actogram), you can see a daily rhythm, mostly white during the daylight hours and black in night hours, in Fall, Spring, and Winter. In the more northerly subspecies, what you see is mostly noise (although there is a rhythm in there in Fall and Spring), indicating a lack of a regular clock.

reindeer
Sample actograms showing patterns of activity over one year in sub-adult reindeer in c, northern Norway (R. t. tarandus, 70° N; n=1), and d, Svalbard (R. t. platyrhynchus, 78° N; n=1). Data, recorded continuously using small activity-loggers, are presented as double-plot actograms in which each row represents two consecutive days; time of day is indicated. Bouts of activity (black bars) are interspersed with bouts of inactivity (white spaces). Grey region, data missing. Lines indicating the beginning and end of civil twilight (when light intensity is 10 lux, orange) and sunrise and sunset (yellow) are superimposed on each actogram. Rhythmicity in the actograms was determined by F-periodogram analysis

Why would they do this? What is the advantage of abandoning rhythmic activity patterns in the long arctic day or night?

Reduced circadian organization may enhance animals' responsiveness and speed of phase adaptation to the light/dark cycle, as proposed for migrating birds and mammals emerging from hibernation. And for herbivores in polar regions, there can be little selective advantage in maintaining strong internal clocks in an effectively non-rhythmic environment.

I think what that means is that while they don't get the advantage of a prolonged period of rest, they are more rapidly responsive at all hours—unlike us, most of whom are an unresponsive and lethargic mess if we are awakened at 3AM, because our internal clocks have shut us down into a state of minimal activity.

Or, I suppose, it could be that the reindeer are just primed and on high alert, ready to answer Santa's call at any hour.


van Oort BEH, Tyler NJC, Gerkema MP, Folkow L, Blix AS, Stokkan K-A (2005) Circadian organization in reindeer. Nature 438:1095-1096.


Posted by PZ Myers on 12/22 at 01:04 PMprintx
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Panderichthys rhombolepis

Echoed on the Panda's Thumb

Panderichthys is a widely recognized transitional form in tetrapod evolution (you know, one of those transitional fossils we're so often told don't exist). A description of a specimen with a well-preserved pelvic girdle has just been described in Nature, and it tells us some more about the history of tetrapod locomotion.

Panderichthys is an interesting animal—it definitely looks more like a fish than a salamander, but its fins are stout and bony, and other characteristics of its skeleton clearly ally it with the tetrapods. In the shift from an aquatic to a fully terrestrial life, the limbs and their supporting pectoral and pelvic girdles had to undergo major changes. In fish, the pectoral girdles are coupled to the skull, while the pelvic girdles are small and 'floating' in the musculature. To bear the animal's weight, the pectoral girdles lost their connection to the skull, and both became thicker, stronger, and more closely bound to the axial skeleton. The fins themselves had to change from a fan of slender fin-rays to more solid load-bearing digits. In Panderichthys, we see a mixture of these changes in process.

The fossil isn't the prettiest specimen you'll see, but it's virtue is that poorly described parts of the animals are in relatively good shape and have been exposed and described. Panderichthys contained a mix of primitive and derived characters, the kind of intermediate hodge-podge we'd expect in a transitional form.

Panderichthys
a, Outline of the body of Panderichthys. Grey shading indicates preserved portions of Panderichthys rhombolepis specimen GIT 434-1. Redrawn from ref. 14. b, Panderichthys rhombolepis specimen GIT 434-1 with head (h) and body (b) outlined. The pelvic girdle and fin are shaded in orange. c, Pelvic girdle and fin. The matrix is distinguished from the fossil by an overlay of grey shading. d, Specimen drawing. F, femur; Fi, fibula; Fre, fibulare; Int, intermedium (proximal end of the); Pel, pelvic girdle; T, tibia. Vertical hatching indicates broken bone; grey shading indicates matrix; circles indicate thin dermal bone covering. e, Reconstruction of the pelvic fin. Thick outline indicates preserved margin, thin outline indicates inferred margin, dotted lines indicate uncertain margin. Solid black scale bars, 10 mm.

In particular, the hindlimb has been found to be significantly more primitive than the forelimb—while the forelimb is large and robust and capable of propping the animal up and pushing it along on the substrate, the hindlimb is relatively small and unimpressive, a glorified and lumpy fish fin. In the figure below, the fore- and hind-limbs of an even more primitive fish, Eusthenopteron, are compared with Panderichthys (in the middle) and Acanthostega. While the Panderichthys limbs have a more robust central axis than the branchy, fan-like Eusthenopteron fins, they aren't as obviously leg-like as those of Acanthostega.

Panderichthys
Pectoral (a, c, e) and pelvic fins (b, d, f) of Eusthenopteron (a, b), Panderichthys (c, d) and Acanthostega (e, f) all in ventral view. F, femur; Fi, fibula; Fre, fibulare; H, humerus; Int, intermedium; R, radius; T, tibia; U, ulna; Ure, ulnare. Thick outline indicates preserved margin; thin outline indicates inferred margin; dotted lines indicate uncertain margin. Scale bars, 10 mm.

What's it all mean? In our adaptation to terrestrial life, it suggests it was done forelimbs first. The earliest tetrapod ancestors humped their way along, using the hindlimbs to anchor themselves, arching and extending their backs forward, then hauling themselves further forward with their front legs. Hindlimbs expanded later to contribute more to movement.

Because the paired fin morphology of Panderichthys is defined substantially by a combination of primitive characters shared with osteolepiforms (mostly in the pelvic fin) and derived characters shared with tetrapods (many pectoral fin characteristics) rather than autapomorphies, at least part of the tetrapod stem lineage around the Panderichthys node must have displayed a combination of tetrapod-like pectoral fins with less limb-like pelvic fins. This suggests that the general locomotory pattern of Panderichthys characterized part of the tetrapod stem lineage between osteolepiforms and tetrapods. The evolution of tetrapod locomotion therefore seems to have passed through a 'front-wheel drive' stage powered by body undulation and pelvic fins as anchors, demonstrated by Panderichthys, before shifting to a 'rear-wheel drive' leg-powered walk in the interval between Panderichthys and Acanthostega.

In case you have trouble keeping the names of all those antique tetrapods straight—they aren't quite as popular as dinosaurs, unfortunately—here's an illustration by Carl Dennis Buell. I wish every cladogram were this well done; this is the kind of first rate scientific illustration that Edward Tufte ought to highlight. You can not only see the lineage relationships, but you also see the temporal extent of the known fossils and illustrations of their form, making it easy to see how the transformation of fish into amphibians is represented in the fossil record.

Panderichthys
Illustration by Carl Buell, from Carl Zimmer's At the Water's Edge (amzn/b&n/abe/pwll)

Boisvert C (2005) The pelvic fin and girdle of Panderichthys and the origin of tetrapod locomotion. Nature 438(7071):1145-1148.


Posted by PZ Myers on 12/22 at 09:48 AMprintx
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Tuesday, December 20, 2005

The Mooney show

DarkSyde has used his bully pulpit on the Daily Kos to interview the new media darling, Chris Mooney (soon to be at a multiplex near you!)


Posted by PZ Myers on 12/20 at 09:01 AMprintx
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Dr Scrooge

Doesn't this look fun? It's a play!

Characters:

Dr. Scrooge
Young Scrooge
Teen Scrooge
Scrooge’s mother
Dr. Jacob Marley
Graduate Student Bob Cratchett
Bob Cratchett’s wife
Tiny Tina
The Spirit of Christmas Past, a Developmental Biologist
The Spirit of Christmas Present, a Biochemist
The Spirit of Christmas Future, an Evolutionary Biologist
Faculty member #1
Faculty member #2
A boy

You can get the whole script for a A Bio-Christmas Carol, and if your lab is big enough, put on a show!


Posted by PZ Myers on 12/20 at 07:54 AMprintx
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Sunday, December 18, 2005

Biotech Game of Life

Many of you will be familiar with that family board game, Life, where you roll dice and move around a board and get indoctrinated into the ideals of capitalism (Life is all about ending up with the biggest bankroll). The Science Creative Quarterly has a new version, The Biotech Game of Life, that models the cutthroat world of drug development. You don't get the little cars with the pink and blue pegs, but it does include a pdf sheet of million dollar bills. If you've got a very nerdy, geeky family, you might be able to get into it over the holidays.


Posted by PZ Myers on 12/18 at 08:41 AMprintx
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Saturday, December 17, 2005

The deplorable Hwang Woo-Suk

I've been following the Hwang Woo-Suk spectacle with fascinated disgust. I wrote about their papers a few times way back when, and I was both excited by the possibilities and upset at the way the US had abandoned all leadership in this field. Now it's all falling apart because one of the principal authors seems to have faked substantial amounts of the data, calling the whole project (and all of the affiliated investigators) into question.

It's not entirely surprising. South Korea was throwing lots of money into this research; stem cells have awesome potential, and this was clearly viewed as a source of future biomedical breakthroughs and international prestige. Big buckets of money and a government that wanted certain highly desirable results is a recipe for exploitation, and they seem to have found the man to take advantage of it all.

But I don't need to say much, since bioethics.net has an excellent summary. Here's the long-term worry:

The key questions in the public discussion of the Korean matter seem likely to involve a billion versions of: "Will ethical lapses in this lab damage stem cell research elsewhere?"

Answer: yup. And no amount of late-in-the-day standards creation will change that. People are going to ask whether the mechanisms whereby stem cell money is doled out have to be made much more rigorous. And yet again, the U.S. government will be zero help, since our rule for how to fund stem cell research is based on the altogether stupid idea that some tiny collection of embryonic stem cells in Wisconsin are ok in terms of ethics and money, but anything made after August 9, 2001 is evil and not to be funded.

The flaws run both ways. It is a bad idea to have a research program dedicated to getting a specific end result that accommodates an ideological end. In South Korea, we have science running pell-mell for lucrative and sensational advances in human stem cell research; in the US, we have ideologues running in the opposite direction, convinced that human stem cell research is evil. We have a gap in the middle where we should have a majority of the work directed at simply figuring out what's going on in a small slice of biological reality.

The case of Hwang Woo-Suk may ultimately be helpful if the message taken is that cheating at the science will be caught out, and the culprits will see their respect and reputation demolished. It's a disaster if it is interpreted to mean that their must be greater security and less openness to prevent people from being caught.

I mostly agree with bioethics.net:

There are those who hold that the key issues here involve the money, lack of regulation, conflicts of interest, and misconceptions held by donors, government and the people of Korea about what this research could do - misconceptions that led to giving one man too much lattitude. And there are those who believe that the evils of detroying embryos could only lead to such an outcome, a 'greater evil'. We've made our argument - whatever the cause and whatever the sin there is only one way for the problem to be fixed and that is US funding of stem cell research with concomitant ethical standards the world is forced to either meet or forgo the US market for its drugs and devices.

I'd like to see the US promote a rational strategy for stem cell research (although I doubt that that is possible with the current administration), but I don't think it is the only solution. There is the EU, after all. The US could spiral off into the outer darkness, and there still are other countries that could take the lead in principled research. I admit that abandoning the US to medieval backwardness isn't exactly a desirable solution, but hey, if it's what the majority wills…


Posted by PZ Myers on 12/17 at 09:51 AMprintx
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Friday, December 16, 2005

A few recent papers…

The issue of Nature Reviews Genetics from which I pulled the Homeobox genesis article actually contains a whole series of articles focusing on evolution of the body plan. Here's a brief taste of the good stuff found in the journal:


Garcia-Fernàndez J (2005) The genesis and evolution of homeobox gene clusters. Nature Reviews Genetics 6:881-892.

The crucial function of homeobox genes in patterning the body has been appreciated for decades. This article pulls together existing data to explain how the current clustered organization of Hox genes, and that of the related ParaHox and NK clusters, came about, the forces that preserve gene clustering and the contribution of Hox, ParaHox and NK genes to the major evolutionary transitions in animal body plan.


Pearson JC, Lemons D, McGinnis W (2005) Modulating Hox gene functions during animal body patterning. Nature Reviews Genetics 6:893-904.

The function of Hox proteins in axial patterning and morphological evolution ultimately depends on the effects of these proteins on downstream targets. This article reviews four important lines of research into Hox function - including work to identify the nature of Hox targets and define the structure of target enhancers, and the recent realization that Hox gene expression might be modulated by conserved microRNAs.


Peel AD, Chipman AD, Akam M (2005) Arthropod segmentation: beyond the Drosophila paradigm. Nature Reviews Genetics 6:905-916.

Genetic studies of Drosophila melanogaster have laid the foundations of our understanding of axial development. But just how universal is this fly model? The growing number of experimental methods that have become available for other arthropods is revealing a surprising diversity of pattering mechanisms, and allows us to formulate a model of how segmentation mechanisms might have evolved.


Martindale MQ (2005) The evolution of metazoan axial properties. Nature Reviews Genetics 6:917-927.

Multicellular animals come in many shapes and forms but they owe their body organization to the emergence of three design features - the anterior-posterior and dorso-ventral axes, and the three germ layers. Morphological and, more recently, molecular analyses on four basal metazoan taxa have begun to reveal how such features emerged and evolved, although a consensus model will depend on a stronger phylogenetic framework and a broader sampling of informative taxa.


Keep that all in mind next time a creationist tries to tell you that evolution is superfluous, or that Intelligent Design has a research plan.


Posted by PZ Myers on 12/16 at 05:07 PMprintx
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