Atlanta GECCO 2008

I’m on my way home, and am actually using a fast internet connection at the airport — I’d forgotten what it was like! I quickly uploaded a few essential files, and my mail software is downloading my email. Unfortunately, I’d need a really fast connection to handle all that — the number of messages pouring in might actually hit 5 digits. If you’re hoping for a reply to anything, you might well be out of luck here.

Atlanta has been very pleasant, with friendly people and good company. I’ll have to come back sometime. The meeting itself was challenging for a mere biologist, but I might have absorbed a few glimmerings. At least it’ll help me dig into the literature a little more.

As for my talk, and since I haven’t had time to put much science here lately, I’m making my GECCO 2008 talk available as a pdf. These presentations are always a little cryptic when handed out without my explanatory overview, but at least in this one I’ve included my presenter notes, which might help a little bit. The first half is an overview of some concepts in evo devo, which includes those little reminders of what I was supposed to say; the last half is a description of two experiments, and I’m afraid my notes are a little thin there — the data in the research always seems self-explanatory to me. Sorry about that, you should have registered for the conference!

Email download complete: it didn’t quite hit 5 digits, only 9865 messages in the last few days. Maybe if I included the spam that gmail filters out for me…

Ack! I couldn’t add this note from the airport because “Your computer was automatically blacklisted (blocked) by the network due to an abnormal amount of activity originating from your connection.” Curse you, Boingo! What good are you if I can’t even download email without you suspecting I’m up to no good?

Mad Scientist contest

There’s a new contest you can enter: Build a Lifeform. A real one.

Yes, it can be done now…or at least, we can insert new capabilities into existing organisms. Before you get too excited, though, most of this work involves directed tweaking of phage or E. coli, which is powerful stuff, but far removed from the dream of building Kelly LeBrock in my garage.

We’re going to need another decade or so before we can do that.

Ice, Mud and Blood

I’m very fond of Chris Turney‘s book, Bones, Rocks, and Stars. It’s a slender, simple description of the many tools scientists use to figure out how old something is, and when arguing with young earth creationists, it’s become the first thing I recommend to them. It’s short and easy to read, and focuses on explaining how dating methods work.

Turney has a new book out: Ice, Mud and Blood: Lessons from Climates Past^{(amzn/b&n/abe/pwll)}. This is the one you’ll be able to hand to climate change denialists, and it’s a winner.

Its virtues are the same as his previous book, the careful documentation of exactly how we know what we know, and less dictation of the conclusions. This is useful, because as we all know, climate is a phenomenon that shows a lot of variability, exhibits patterns in its history, and also has large degrees of uncertainty, phenomena that denialists can seize upon to magnify that uncertainty into a basis for an unwarranted rejection of well-supported hypotheses. So while we can see distinct variations from simple linear uniformity of climate change like the Little Ice Age and the Medieval Warm Period, that doesn’t change the fact that greenhouse gases profoundly influence earth’s temperature, and it’s clear that CO₂ has risen to levels the planet hasn’t seen in at least 650,000 years. The past tells us what we can expect in the future, and it’s grounds for serious concern. Yes, Turner comes down firmly on the side of an anthropogenic cause for the current trend of global warming, and he explains exactly why, step by step.

Where Turner departs from the formula of his last book, though, is that this one, while still fairly short, is much denser and more technical. Anyone can read it — I managed, despite knowing next to nothing about climatology — but it’s not the kind of thing you’ll be able to do in an evening or two of light reading. There are a few places where the level of detail slowed me down to a steady slog rather than a fast flit, but face it, any book that tries to untangle ocean currents, monsoons, El Nino, and past current reversals is going to occasionally demand the same level of studious, focused attention you’d need to clean up a snarled fishing reel. This is a book that is describing some extraordinarily complicated stuff.

If you want just one book, not too thick or too technical, that will give you the intellectual tools to at least understand what the climate change experts are talking about, this is the one. I recommend bringing it to the beach and reading it there — you’ll appreciate the rising tide and the ocean beaches a little more, and perhaps regard them with a little more respectful dread.

Evolving proteins in snakes

We’ve heard the arguments about the relative importance of mutations in cis regulatory regions vs. coding sequences in evolution before — it’s the idea that major transitions in evolution were accomplished more by changes in the timing and pattern of gene expression than by significant changes in the genes themselves. We developmental biologists tend to side with the cis-sies, because timing and pattern are what we’re most interested in. But I have to admit that there are plenty of accounts of functional adaptation in populations that are well-founded in molecular evidence, and the cis regulatory element story is weaker in the practical sense that counts most in science (In large part, I think that’s an artifact of the tools — we have better techniques for examining expressed sequences, while regulatory elements are hidden away in unexpressed regions of the genome. Give it time, the cis proponents will catch up!)

This morning, I was sent a nice paper that describes a pattern of functional change in an important molecule — there is absolutely no development in it. It’s a classic example of an evolutionary arms race, though, so it’s good that I mention this important and dominant side of the discipline of evolutionary biology — I know I leave the impression that all the cool stuff is in evo-devo, but there’s even more exciting biology outside the scope of my tunnel vision. Also, this paper describes a situation and animals with which I am very familiar, and wondered about years ago.

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Ventastega

i-bb62d30eff8c4b9362f8c97ad45335fc-ventastega_recon.jpg

The paleontologists are going too far. This is getting ridiculous. They keep digging up these collections of bones that illuminate tetrapod origins, and they keep making finer and finer distinctions. On one earlier side we have a bunch of tetrapod-like fish — Tiktaalik and Panderichthys, for instance — and on the later side we have fish-like tetrapods, such as Acanthostega and Ichthyostega. Now they’re talking about shades of fishiness or tetrapodiness within those groups! You’d almost think they were documenting a pattern of gradual evolutionary change.

The latest addition is a description of Ventastega curonica, a creature that falls within the domain of the fish-like tetrapods, but is a bit fishier than other forms, so it actually bridges the gap between something like Tiktaalik and Acanthostega. We look forward to the imminent discovery of yet more fossils that bridge the gap between Ventastega and Tiktaalik, and between Ventastega and Acanthostega, and all the intermediates between them.

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Amphioxus and the evolution of the chordate genome

This is an amphioxus, a cephalochordate or lancelet. It’s been stained to increase contrast; in life, they are pale, almost transparent.

It looks rather fish-like, or rather, much like a larval fish, with it’s repeated blocks of muscle arranged along a stream-lined form, and a notochord, or elastic rod that forms a central axis for efficient lateral motion of the tail…and it has a true tail that extends beyond the anus. Look closely at the front end, though: this is no vertebrate.

i-e961343b9bf5b6dfd74823fba6deeafb-amphioxus_closeup.jpg

It’s not much of a head. The notochord extends all the way to the front of the animal (in us vertebrates, it only reaches up as far as the base of the hindbrain); there’s no obvious brain, only the continuation of the spinal cord; there isn’t even a face, just an open hole fringed with tentacles. This animal collects small microorganisms in coastal waters, gulping them down and passing them back to the gill slits, which aren’t actually part of gills, but are components of a branchial net that allows water to filter through while trapping food particles. It’s a good living — they lounge about in large numbers on tropical beaches, sucking down liquids and any passing food, much like American tourists.

These animals have fascinated biologists for well over a century. They seem so primitive, with a mixture of features that are clearly similar to those of modern vertebrates, yet at the same time lacking significant elements. Could they be relics of the ancestral chordate condition? A new paper is out that discusses in detail the structure of the amphioxus genome, which reveals unifying elements that tell us much about the last common ancestor of all chordates.

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Basics: Synteny

Let’s play the most boring card game in the universe!

Here are the rules. We start with a fully sorted deck of 52 cards, and we deal out four hands. We don’t deal in the ordinary way, either: we give the top 13 cards to the first player, then the next 13 to the second, and so forth. (We could also do the usual deal, but it makes the illustration and logic a little more difficult to see. We’ll keep it simple for now.)

This is what the table will look like.

Hand 1	A	K	Q	J	10	9	8	7	6	5	4	3	2
Hand 2	A	K	Q	J	10	9	8	7	6	5	4	3	2
Hand 3	A	K	Q	J	10	9	8	7	6	5	4	3	2
Hand 4	A	K	Q	J	10	9	8	7	6	5	4	3	2

Next, we play the game, whatever it is. It really doesn’t matter, since we know exactly what hand everyone has, right? So don’t worry about the rules for that. What’s important is that next the dealer carefully picks up each hand in reverse order and stacks them, restoring the original arrangement of the deck.

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Hubris, gall, arrogance…inanity

Would you believe that Andy Schlafly, head kook at Conservapædia, wrote a letter to Richard Lenski, demanding release of his data to Schlafly and his crack team of home-schooled children? Schlafly is a creationist and ideologue of the worst sort; he has no qualifications in biology, and only wants the data because he doesn’t believe it, and would no doubt then use his vast powers of incomprehension to garble it.

That isn’t noteworthy, though. We expect creationists to act like indignant idiots when the facts are shown to them. What’s really cool is that Lenski wrote back.

Dear Mr. Schlafly:

I suggest you might want to read our paper itself, which is available for download at most university libraries and is also posted as publication #180 on my website. Here’s a brief summary that addresses your three points.

1) “… your claims, that E. Coli bacteria had an evolutionary beneficial mutation in your study.” We (my group and scientific collaborators) have already published several papers that document beneficial mutations in our long-term experiment. These papers provide exact details on the identity of the mutations, as well as genetic constructions where we have produced genotypes that differ by single mutations, then compete them, demonstrating that the mutations confer an advantage under the environmental conditions of the experiment. See papers # 122, 140, 155, 166, and 178 referenced on my website. In the latest paper, you will see that we make no claim to having identified the genetic basis of the mutations observed in this study. However, we have found a number of mutant clones that have heritable differences in behavior (growth on citrate), and which confer a clear advantage in the environment where they evolved, which contains citrate. Our future work will seek to identify the responsible mutations.

2. “Specifically, we wonder about the data supporting your claim that one of your colonies of E. Coli developed the ability to absorb citrate, something not found in wild E. Coli, at around 31,500 generations.” You will find all the relevant methods and data supporting this claim in our paper. We also establish in our paper, through various phenotypic and genetic markers, that the Cit+ mutant was indeed a descendant of the original strain used in our experiments.

3. “In addition, there is skepticism that 3 new and useful proteins appeared in the colony around generation 20,000.” We make no such claim anywhere in our paper, nor do I think it is correct. Proteins do not “appear out of the blue”, in any case. We do show that what we call a “potentiated” genotype had evolved by generation 20,000 that had a greater propensity to produce Cit+ mutants. We also show that the dynamics of appearance of Cit+ mutants in the potentiated genotypes are highly suggestive of the requirement for two additional mutations to yield the resulting Cit+ trait. Moreover, we found that Cit+ mutants, when they first appeared, were often rather weak at using citrate. At least the main Cit+ line that we studied underwent an additional mutation (or mutations) that refined that ability and led to a large improvement in growth on citrate. All these issues and the supporting methods and data are covered in our paper.

Sincerely,

Richard Lenski

Wow. That was far more polite than they deserve, but good for Dr Lenski. Unfortunately, Schlafly will now use the reply as an opportunity to smugly regard himself as a serious player, and he will also ignore the substance to continue to deny that evolution occurred. But maybe, just maybe, someone in the collection of deprived children subjected to Schlafly’s tutelage will notice that real scientists can give substantial replies to his usual ignorant nonsense.

How Life Began

As I said I would, I’m watching this History Channel documentary about the origin of life. How about a little live-blogging?

8:00. Ugh. It begins with a bunch of tripe from Coyne and Polkinghorne, claiming we need religion to understand the meaning of life. This is a bad, bad start, but I’m hoping it’s nothing but a weasely preliminary that they will then abandon to get to some real science.

There are lots of gimmicky special efects, but OK, let’s get the general audience interested. I’m not too keen on the parade of talking heads, though: they keep trotting out different investigators, letting them say a sentence or two, and then zipping off elsewhere. I know you don’t want some guy sitting and droning at you, but this seems like a poor compromise.

8:15. It’s a quick tour of the complexity of the cell. They’re using this special effects analogy of a “factory of life” where chemistry is going on.

First important element of life: metabolism. Second: life is cellular, with compartments. Third: life can replicate.

Now we get a parts catalog of polymers: lipids, proteins, and nucleic acids.

Very weird: in their factory analogy, they point to something hidden behind a big red curtain and say that that’s where all these bits and pieces come together to make something that’s alive; it seems a bit of a cop-out, a way to pretend there’s something hidden where the viewer can imagine anything they want. Come on, bite the bullet and admit it: life is chemistry, and there is nothing more.

Now we get a fairly lengthy discussion of the idea of emergence. At least they clearly state that emergence is nothing magical, but is just a consequence of the execution of the laws of nature. This is a rather pointless digression, I think.

OK, now we get a timeline of the origin of life: it appeared about 3.8 billion years ago, on a very hostile planet with no oxygen in the air, and just cooling after the last of the great meteor bombardments. This leads naturally into a discussion of extremophiles, with a tour of Mono Lake.

Segue to commercial by mentioning that life will change the environment of the earth.

8:30. Conditions on early life are hostile to us, but chemical energy is abundant. Life would have existed as single-celled forms only, which may have been unrecognizable to us (why are they showing video micrographs of nematodes while they tell us this?)

Stromatolites are introduced, as organisms that grew on chemical energy sources. What are those energy sources?

The camera crew goes spelunking. They’re collecting rock-eating microbes, which the scientists argue is a kind of primitive chemistry that evolved before photosynthesis.

Nice reminder that single-celled life was the only form of life here for 80% of the history of earth, but then they make the mistake of using the past tense in saying they were the dominant form of life on the planet.

Wait…now they’re saying that the ability to reproduce is a property of DNA? That’s kind of cutting off the possibility of an interesting discussion of alternative paths.

Suddenly, boom, they’re talking about Leeuwenhoek. Hang on, this is a bit jumpy. Can we talk more about extremophile chemistry before we start on 17th-18th century microscopy?

Now it’s all about photosynthesis. We’ve moved way, way beyond the period of early abiogenesis already, and they’ve scarcely touched on any of the major theories.

Before the commercial, we get talk about multicellularity and oxygen chemistry. Either they’re going to be jumping about an awful lot and scrambling the story, or we’re not going to get anything about abiogenic chemistry…

8:45. Oops, I had to miss part of this section to run some real-world errands. I come back to see the Burgess Shale and a discussion of the Cambrian explosion. This is long, long after the origin of life!

It’s an excuse to show some computer animations of Anomalocaris, anyway.

George Coyne does a good job now saying that life doesn’t need a designer; Polkinghorne pops up to make excuses for the metaphorical nature of the book of Genesis. Bugger off, Polkinghorne, you bother me, ya twit.

Now we get a summary of the importance of selection and sex. I don’t think we’re going to get a good review of biogenesis anymore — sex is not an important issue in that field.

I am completely baffled. Before the commercial, they say the big question was how human life arose…then they ask, “What was the specific mechanism that caused non-living chemistry into living biology?” Weird. These are very different questions. They seem to be muddling up the origins of life with the origins of the only important form of life, humans.

9:00. We’re back to animals. Come on, animals are peculiar latecomers.

Maybe it’s an excuse to return to a historical survey of ideas about the origin of life. I hope.

Aristotle proposes the idea of spontaneous generation, an idea that hangs on for centuries but is relatively easy to disprove…as Redi and Spallanzani do. This stuff isn’t bad, but it feels like introductory material they should have brought up at the beginning.

Actually, I’m enjoying this part best of all so far. They’re actually talking about the experiments done to disprove spontaneous generation, so it’s a useful summary of how scientists actually do science.

Our closing question: so how did life arise from chemistry? The second half is off to a good start, I think.

9:15. I’ve got to say…the actor playing Charles Darwin looks nothing like him, and that beard looks cheesy and fake.

We get the early concepts: “warm little pond”, “primorial soup”. There the questions are about what kind of chemicals and conditions existed at the beginning of life. They mention Oparin’s ideas about the chemical monomers available, and the idea that these chemicals would accumulate in the oceans. It seems like a very low probability sort of exercise.

The Miller/Urey experiment at last. This is well done, with a very nice illustration of the apparatus and techniques. They get it right, too — it was nice work that showed that the natural chemistry that would produce organic substrates for life was relatively trivial. It also set up unrealistic expectations for how easy it would be to create life.

Closing premise: now there is a race to figure out prebiotic chemistry.

9:30. Let’s consider other sources of organic matter!

Space-borne debris. Complex organic molecules are found in metorites and in space. We get to see scientists extracting organic molecules from ground-up meteorites. Panspermia is mentioned, but they aren’t doing a good job of distinguishing chemicals from life. At least Bob Hazen is razor sharp in pointing out that panspermia is a cop out.

Hazen also clearly explains bottom-up (exploring basic principles about biochemistry to replicate the events at the origin) vs. top-down (working in reverse from extant life backwards to the origin). He also explains that we need a multiplicity of approaches, and the origin may also have been generated from diverse sources.

Hmm. Commercials seem to be coming more frequently as we get close to the end.

9:40. It’s deep-sea vent time, with nice shots of black smokers and squid. Then Bob Hazen shows us how his experiments on the chemistry at high pressure and temperature are done. Cooking a little pyruvate for a while generates substances that form micelles.

Clays! Clays are shown as potential catalytic surfaces that would concentrate organic compounds and promote reactions that form, for instance, RNA. RNA monomers will polymerize in the presence of clays.

Transition: are scientists on the verge of creating artificial life in the lab?

9:50. It’s “3000 years after Aristotle”? What?

Never mind. Now we get pretty crystals growing and changing. This bit is a little fluffy.

All right: Jack Szostak. They describe his efforts to try and create a protocell. Cool video of creating cell membranes — beautiful little droplets bubbling out of an electrode. Some good cautionary statements: if they succeed, this will still only be a model, not a demonstration of how it actually happened 3.8 billion years ago.

They don’t really say much about the mechanisms in the closing minutes, but they do have a nice statement by Neil de Grasse Tyson about how the search is the important thing, even if we don’t get an answer.

Summary: the first hour was a muddle, and not worth watching. If you’re going to catch it later, just watch the second half.

The last half wasn’t bad. It at least talked very briefly about the actual science and how it is done. It was all painfully abbreviated and only touched lightly on the subject, but I think that is simply a limitation of the medium. I imagine it’s a seriously difficult balancing act to try and meet the needs of real nerds (like us!) and the more casual viewer, so I’ll accept the compromise.

Something at the end to lead the interested viewer to more in-depth sources would have been a good idea — they could have at least mentioned Hazen’s Genesis as a plug.

Historical contingency in the evolution of E. coli

While I was traveling last week, an important paper came out on evolution in E. coli, describing the work of Blount, Borland, and Lenski on the appearance of novel traits in an experimental population of bacteria. I thought everyone would have covered this story by the time I got back, but there hasn’t been a lot of information in the blogosphere yet. Some of the stories get the emphasis wrong, claiming that this is all about the rapid acquisition of complex traits, while the creationists are making a complete hash of the story. Carl Zimmer gets it right, of course, and he has the advantage of having just published a book^{(amzn/b&n/abe/pwll)} on the subject, with some excellent discussion of Lenski’s work.

The key phrase is right there at the beginning of the title: historical contingency. This paper is all about how accidents in the genetics of a population can shape its future evolutionary trajectory. It is describing how a new capability that requires some complex novelties can evolve, and it is saying plainly that in this case it is not by the fortuitous simultaneous appearance of a set of mutations, but is conditional on the genetic background of the population. That is, two populations may be roughly equivalent in fitness and phenotype, but the presence of (probably) neutral mutations in one may enable other changes that predispose it to particular patterns of change.

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Pharyngula

Evolution, development, and random biological ejaculations from a godless liberal

Antithetical to good science

The Great Gardening of 2025 - Part 40 - Topping & Trimming Tomatoes

Mentour Pilot rocks Clow UFO Base (Fiction)

Great moments in sports fandom

Abortion Action Nonsense

Hating the artist, hating the art

The Probability Broach: Blood on the highway

Atlanta GECCO 2008

Mad Scientist contest

Ice, Mud and Blood

Evolving proteins in snakes

Ventastega

Amphioxus and the evolution of the chordate genome

Basics: Synteny

Hubris, gall, arrogance…inanity

How Life Began

Historical contingency in the evolution of E. coli

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