Arthrodires got penises!

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This is the skull of an arthrodire, an armored placoderm from the Devonian.

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Somehow, 20 foot long predatory fish with a mouth lined with razor-edged bony shears has never made me think of sexy time…until I ran across this comparison image.

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Oh, schwiiing. It really doesn’t take much to get a mammal to associate just about anything with sex. And then, what do you know, the latest Nature has a short article on an interesting fossil: it’s the pelvic region of an arthrodire, Incisoscutum ritchiei, and look what it’s got: an ossified clasper, comparable to the erectile organ of modern sharks. This is a bony rod that would have been the core of an intromittent organ in the living animal, so what we have here is a small relic of the sex life of a big fish from a few hundred million years ago.

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a, Pelvic girdle in dorsal view; b, pelvic girdle restored.

Think about this, you over-sexed apes: what will be left of your manhood 300 million years from now?

Ahlberg P, Trinajstic K, Johanson Z, Long J (2009) Pelvic claspers confirm chondrichthyan-like internal fertilization in arthrodires. Nature 460:888-889.

Gene regulatory networks and conserved noncoding elements

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We miss something important when we just look at the genome as a string of nucleotides with scattered bits that will get translated into proteins — we miss the fact that the genome is a dynamically modified and expressed sequence, with patterns of activity in the living cell that are not readily discerned in a simple series of As, Ts, Gs, and Cs. What we can’t see very well are gene regulatory networks (GRNs), the interlinked sets of genes that are regulated in a coordinated fashion in cells and tissues.

[Read more…]

The future is roaring your way…

Edge hosted an amazing session that described the looming future of biology — this is for the real futurists. It featured George Church and Craig Venter talking about synthetic genomics — how we’re building new organisms right now and with presentiments for radical prospects in the future.

Brace yourself. There are six hours of video there; I’ve only started wading into it, but what I’ve seen so far also looks like a lot of material that will be very useful for inspiring students about the future of their field. There is also a downloadable book (which is a dead link right now, but I’m sure will be fixed soon) if you don’t want to watch the talks…but the talks are pretty darned good. Somehow, I’m going to have to make time to soak these up. Here’s the overview of the six sessions:

  • Dreams & Nightmares
    Overview, safety/security/policy, nanotechnology, molecular manufacturing

  • Smaller than life
    What is life, origins, in vitro synthetic life, mirror life, computing and DNA, computing with DNA

  • Engineering microbes
    Bio-petrochemicals & pharmaceuticals, accelerated lab evolution

  • Engineering humans
    Electronic-biological interfaces, bioengineered personal stem cells, humanized mice, bringing back extinct species

  • The sorceror
    The diversity of life, constructing life, from Darwin to new fuels

  • The near future, big questions
    Terraforming earth, creating extraterrestrials, the singularity, human nature

There goes your weekend.

The evolution of Hedgehog

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PLoS has recently published a highly speculative but very interesting paper on how a particular signaling pathway, the Hedgehog pathway, might have evolved. It’s at a fairly early stage in hypothesis testing, which is one of the things that makes it interesting — usually all you see published is the product of a great deal of data collection and experiment and testing, which means the scientific literature gives a somewhat skewed view of the process of science, letting the outsider mainly see work that has been hammered and polished, while hiding the rougher drafts that would better allow us to see how the story started and was built. It’s informative in particular for those who follow the creationist “literature”, which often crudely apes the products of actual working science, but lacks the sound methodological underpinnings. In particular, creationism completely misses the process of poking at the real world to develop ideas, since they begin with their conclusion.

So take this description as a work in progress — we’re seeing the dynamic of building up a good working model. As usual, it starts on a sound foundation of confirmed, known evidence, makes a reasonably hypothesis on the basis of the facts, and then proposes a series of research avenues with predicted results that would confirm the idea.

[Read more…]

Brian Goodwin, 1931-2009

It’s sad to see that we’ve lost Brian Goodwin, one of the genuinely original (but not always right!) thinkers of our time. There aren’t many left of the old structuralist tradition in biology, the kind of non-genetic purists who tried to analyze development in terms of the fundamental physical and chemical properties of the organism—they’ve been swallowed up and lost in a triumphal molecular biology research program.

Edge has a nice interview with and essay by Goodwin — they’re good places to start. If that whets your appetite, you should also read his book, How the Leopard Changed Its Spots : The Evolution of Complexity(amzn/b&n/abe/pwll), which is aimed at general audiences and is a good overview of why we should look at more than just genes to explain form.

He was an advocate for one view of nature, and I think he missed the mark by neglecting genes as much as he did; we know now that a lot of details of morphology are directly affected in subtle and not-so-subtle ways by the genetics of the organism. But I think we can also make a case that the modern molecular biological approach is also missing a significant element. Every biologist ought to read a little Goodwin, just to leaven their picture of how biology works with his special perspective.

Good TV

I must thank the reader known to me only as CAC for sending me DVDs of the Inside Nature’s Giants programs. I’ve been enjoying the dissections of an elephant and a whale in the evening — most of the organisms I cut into are millimeters long and require very sharp, thin instruments, so it’s interesting to see ones that require hip waders and backhoes.

You should all lobby your local PBS stations and tell them these would be wonderful additions to the lineup! You might also suggest that broadcasting them during the dinner hour might not be recommended.

What caused the Cambrian explosion? MicroRNA!

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No, not really — my title is a bit of a sensationalistic exploitation of the thesis of a paper by Peterson, Dietrich, and McPeek, but I can buy into their idea that microRNAs (miRNAs) may have contributed to the pattern of metazoan phylogenies we see now. It’s actually a thought-provoking concept, especially to someone who favors the evo-devo view of animal evolution. And actually, the question it answers is why we haven’t had thousands of Cambrian explosions.

In case you haven’t been keeping up, miRNAs are a hot topic in molecular genetics: they are short (21-23 nucleotides) pieces of single stranded RNA that are not translated into protein, but have their effect by binding to other strands of messenger RNA (mRNA) to which they complement, effectively down-regulating expression of that messenger. They play an important role in regulating the levels of expression of other genes.

One role for miRNAs seems to be to act as a kind of biological buffer, working to limit the range of effective message that can be operating in the cell at any one time. Some experiments that have knocked out specific miRNAs have had a very interesting effect: the range of expressed phenotypes for the targeted message gene increases. The presence or absence of miRNA doesn’t actually generate a novel phenotype, it simply fine-tunes what other genes do — and without miRNA, some genes become sloppy in their expression.

This talk of buffering expression immediately swivels a developmental biologist’s mind to another term: canalization. Canalization is a process that leads organisms to produce similar phenotypes despite variations in genotype or the environment (within limits, of course). Development is a fairly robust process that overcomes genetic variations and external events to yield a moderately consistent outcome — I can raise fish embryos at 20°C or at 30°C, and despite differences in the overall rate of growth, the resultant adult fish are indistinguishable. This is also true of populations in evolution: stasis is the norm, morphologies don’t swing too widely generation after generation, but still, we can get some rapid (geologically speaking) shifts, as if forms are switching between a couple of stable nodes of attraction.

Where the Cambrian comes into this is that it is the greatest example of a flowering of new forms, which then all began diverging down different evolutionary tracks. The curious thing isn’t their appearance — there is evidence of a diversity of forms before the Cambrian, bacteria had been flourishing for a few billion years, etc., and what happened 500 million years ago is that the forms became visible in the fossil record with the evolution of hard body parts — but that these phyla established body plans that they were then locked into, to varying degrees, right up to the modern day. What the authors are proposing is that miRNAs might be part of the explanation for why these lineages were subsequently channeled into discrete morphological pathways, each distinct from the other as chordates and arthropods and echinoderms and molluscs.

[Read more…]

Why do they hate the manimal?

It’s happening again. The Republicans are tilting at one of their favorite windmills, the mad scientists’ dream of creating an unholy union between beast and human to produce a slave race of soulless monsters. They have introduced legislation to ban human-animal hybrids. And it’s even bipartisan! They’ve got 19 Rethuglicans, like Sam Brownback, the ignoramus from Kansas:

What was once only science fiction is now becoming a reality, and we need to ensure that experimentation and subsequent ramifications do not outpace ethical discussion and societal decisions. History does not look kindly on those who violate the dignity of the human person.

And they’ve also got 1 Dimocrat, Mary Landrieu of Louisiana:

Here in the United States, we simply cannot open the door to the unethical blending of humans and animals, which the British government seems intent on doing. It creates an unnatural species and is a clear line we cannot cross.

One teensy little problem: these clowns do not understand the science. We actually aren’t planning to creating a slave-race of beast-men; the technology isn’t there, for one thing, and for another, that’s really not at all an interesting goal. No one is planning on operating on any human persons, or even violating them; the focus is all on cells and molecules. This is routine stuff. In one hand, you’ve got a dish full of human cells — it doesn’t talk, it can’t sign a consent form even if it had the capacity to understand one — and you want to know what makes them tick. In the other hand, you’ve got a collection of hard-won tools you’ve gathered from work in mice or worms or flies; interesting vectors, genes that act as indicators or switches, ways to basically reach into a cell and toggle states. Scientists have had these for years, and we’ve regularly used these tools to manipulate cells and puzzle out what happens.

Another example: we want to know what genes on different human chromosomes do, but it is highly unethical to do random mutagenesis on human gametes, bring them together, and then raise up the fetus in a volunteer’s womb to find out what interesting ways it might go kablooiee. One technique that has been used is to make mouse-human hybrid cells: use a little ethylene glycol to weaken the cell membranes, push a mouse cell next to a human cell, and presto, they fuse. They then recover and go through cell divisions, and the hybrid cell begins to lose pieces of the unnatural excess of chromosomes it’s got. You can then screen the resultant cells and correlate the presence or absence of gene products with the presence or absence of specific human chromosomes.

I know. It sounds so nefarious.

One more example: scientists have made transgenic pigs carrying five human genes. The idea is to create animals that can be a source for xenografts — transplanted organs — in humans with a reduced level of rejection. These pigs would become illegal under the Brownback bill, because they mingle a blessedly human H-transferase gene with pig cells. This is not to argue that there are no ethical considerations in these kinds of experiments, since there certainly are: we can argue about the ethics of creating species of pigs with the specialized purpose of providing organs for human use (it’s about as great a moral dilemma as raising pigs for meat), and there’s also the concern that hybrid pigs will also be dangerous incubators for training viruses to respond to human epitopes. But the ethical debates aren’t the domain of crude science-fiction versions of the science that these clueless lawmakers think them to be.

I’d like Brownback to answer a simple question. Does putting the human insulin or growth factor gene into E. coli violate the dignity of the human person? If it does, he’s suggesting shutting down a good chunk of the pharmaceutical industry. And Ms Landrieu: what is an “unnatural species”? If they’re unnatural and we can’t cross that line, then we certainly don’t need legislation to enforce it.

I don’t know why she bothered to complain about the British government, unless she’s using just plain old conservative xenophobia to stir up votes. American scientists have been using hybrid cells and have been introducing cross-species genes into cells for a long, long time now.

Auf wiedersehen, Lindau!

Yesterday was my last day in Lindau, I’m sorry to say — it was also the day of the closing ceremonies on the island of Mainau, in case you were wondering why it was so quiet on the blog. I decided to leave all my electronical gear behind at the hotel and venture out for the last session with a stark naked brain.

The day began with a walk down to the harbor to board the Sonnenkönigin, a very impressive ship that can only be inadequately be called a ferry. We were welcomed aboard with a glass of wine or a glass of juice if you felt 8 am was a little early to begin, and tables heaped with food. One thing I’m going to miss a great deal when I get back to Minnesota is good bread — the stuff that is chewy and substantial and has all this flavor. Bread back home is a kind of glorified aerogel, a pale and puffy spongy substance.

We also got some musical entertainment, and a lot of hard sell for the German province of Baden-Württemburg. They can do everything, except speak proper German (really, it’s their motto: “Wir können alles. Außer Hoch-Deutsch.”) They put on a good show with lots of exhibits touting their support for basic research and industry — if nothing else, I’m convinced they value the practical benefits of science enough to heavily recruit mobs of graduate students.

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Mainau is a lovely island in Lake Constance, topped with an old baroque Schloss and filled with gardens and walking paths. We were there for a final panel on sustainability. The panel consisted of four nobelists, Pachauri, Molina, Schrock, and Stocker, one government minister, whose name I’ve probably misspelled since her tag was turned away from me — Quellen-Thielen, I believe — and one annoying crackpot, Bjorn Lomborg, who really didn’t belong up on the stage. Even as insubstantial as he was, though, Lomborg did agree, along with every one else, that climate change and global warming are real phenomena. Here’s a short summary of what they said.

Pachauri: Our big problem is unsustainable growth. It’s inevitable and desirable that third-world economies expand, but the old strategies of exploiting fossil fuels aren’t going to work.

Lomborg: While global warming is real, it’s not a crucial problem, since it will only cost 0.5% of world GDP to cope with it. He’s pro-development, and thinks, for example, that while global warming may increase the incidence of malaria by 3% more, we ought to be focusing on the 100% of malaria cases occurring now rather than trying to reduce the 3%. We need to invest in better technology, but imposing limitations on CO2 emissions now is fruitless.

Molina: We aren’t taking the right path in growing economies — we need to convince the world that building sustainable energy supplies and limiting environmental damage now is the best viable long-term strategy. He had to take a poke at Lomborg, too: putting a dollar value on irreversible changes is inappropriate and misleading. Focusing on one aspect of the problem and calling the cost increases and human losses manageable hides the risks of passing a tipping point. He favors, as an important early step, incorporating the costs of externalities such as CO2 emission into the economy.

Quellen-Thielen (sp?): Germany takes climate change seriously, and the government sets policies and targets for emissions. They also materially support new technologies, like photovoltaics. These actions have not harmed the economy but instead have created new jobs and positioned Germany as a global leader.

This prompted one of the more obnoxious jabs from Lomborg, who literally sneered at German environmental efforts, pointing out that all the photocells Germany has built are already obsolete, and that it was just money thrown down the drain. Throughout, Lomborg took the attitude that direct action now is inefficient, and that we’re better off waiting for new technologies to emerge, at which time the magic of the market will kick in and our problems will go away. Quellen-Thielen reasonably pointed out that their development now means they’ve got a leg up, that they’re obtaining a reasonable fraction of their energy directly from the sun right now, and they are also building the industrial infrastructure to build on new ideas quickly.

Schrock: He was a bit out of place here; I think the presence of Lomborg effectively derailed the whole panel away from a discussion of a diversity of solutions to the global warming and into a wasted defense of the rightness of taking any policy action at all. Schrock clearly wanted to talk about catalysis and the importance of chemistry in generating technical solutions, and advocated more investment in basic as well as applied research — he fears that we could lose the potential for long-term improvements in a frantic search for solutions we can implement right now.

Stocker: he also spoke against the bean-counter on the panel, pointing out that the 2003 heat wave killed thousands, and within 30 years, that kind of event will likely have a frequency of every other year. He thinks global warming is a misnomer: it’s more than just a temperature shift, but it’s going to lead to a sea level rise, changes in the availability of water resources in some of the most heavily populated areas of the world, and is going to trigger resource wars that will be devastating. He pointed out that this really is an anomalous event in our history, that CO2 is 29% higher than at any time in the last 850,000 years. He believes we need a globally binding emissions target set right away.

So it was a mildly interesting discussion, but it could have been so much better — I suspect someone noticed it was hard to find a strong contrarian among Nobel prize winners, and decided to bring in a last-minute alternative view. Unfortunately, Lomborg’s basically an advocate for do-nothingness and did nothing but distract the others from wrestling with more substantial ideas.

After sitting in the sun for this outdoor panel, I got a sunburn and a strong desire to escape, so I spent the time afterwards wandering about in the gardens. Then the best part, getting back on the Sonnenkönigin and being handed a big mug of cold beer as I boarded. I’m beginning to get the impression that all bier in Deutschland ist frei. That can’t be true, but empirically it seems to be the case. Or maybe it’s just Baden-Württemburg’s cunning plan to persuade us that southwestern Germany is paradise.

We had more entertainment on the trip back — Stuart Pivar was aboard, doing tricks with balloons! No, actually it was some other guy who made balloon molecules, as well as strange hats. I guess the guy just looked at me and decided I needed more tentacles.

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Do you want this to be the dominant image of atheism?

He also made a buckyball out of balloons, and guess who ended up wearing that on his head?

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Sir Harold Kroto

And that’s all there was. A great meeting overall, lots of fun, and lots of networking. The majority of the attendees are graduate students who are brought over to hob-nob with the biggest of the big-wigs of science, and most importantly, make international connections with their peers. Any graduate student readers of this post: ask around in your department if anyone knows about nominations for the Lindau meetings. They are definitely worth attending for young people wanting to get involved in this global enterprise called science.

One evening after the talks, when we were hanging about in a gasthof enjoying some good food and beer, the Countess Bettina Bernadotte stopped by our table (Yes! You also get to meet European nobility!), and we all talked a bit about the meetings. She’s the president of the council for the meetings, and puts a tremendous amount of effort and fund-raising to get them off the ground. When asked why she was doing it, the answer was simple: that while she gets no direct personal or material gain from the meetings, as a citizen of the world she feels an obligation to make a contribution to bettering the world’s knowledge, and this is an opportunity to foster a positive benefit to science. The whole meeting is built around giving young investigators connections.

Now I’m on my long, slow way home. It was worth it, and hope I can go again.

Tonight I’m in the city of Friedrichshafen, home of the zeppelin (I asked if there were any connecting flights by zeppelin, but I’m out of luck and will have to take an Airbus tomorrow, instead.) Then I’m off to Frankfurt, Philadelphia, and finally, Minneapolis. All should be smooth this time — I don’t have any too-short layovers on this trip.

Now I’m going to stroll about and use the Fourth of July to celebrate the 90th anniversary of the first transatlantic zeppelin flight — I noticed that there was a big brass band down by the harbor, with fellows in bright green uniforms and tall hats with tassels. It should be fun!