Altenberg 2008 is over

Massimo Pigliucci has posted the notes, parts 1, 2, and 3, from the Altenberg meeting that was unfortunately over-hyped by the creationist crowd (no blame for that attaches to the organizers of this meeting). It sounds like it was a phenomenally interesting meeting that was full of interesting ideas, but from these notes, it was also clearly a rather speculative meeting — not one that was trying to consolidate a body of solid observations into a coherent explanation, but one that was instead trying to define promising directions for an expansion of evolutionary theory. That’s also the message of the concluding statement of the meeting.

A group of 16 evolutionary biologists and philosophers of science convened at the Konrad Lorenz Institute for Evolution and Cognition Research in Altenberg (Austria) on July 11-13 to discuss the current status of evolutionary theory, and in particular a series of exciting empirical and conceptual advances that have marked the field in recent times.

The new information includes findings from the continuing molecular biology revolution, as well as a large body of empirical knowledge on genetic variation in natural populations, phenotypic plasticity, phylogenetics, species-level stasis and punctuational evolution, and developmental biology, among others.

The new concepts include (but are not limited to): evolvability, developmental plasticity, phenotypic and genetic accommodation, punctuated evolution, phenotypic innovation, facilitated variation, epigenetic inheritance, and multi-level selection.

By incorporating these new results and insights into our understanding of evolution, we believe that the explanatory power of evolutionary theory is greatly expanded within biology and beyond. As is the nature of science, some of the new ideas will stand the test of time, while others will be significantly modified. Nonetheless, there is much justified excitement in evolutionary biology these days. This is a propitious time to engage the scientific community in a vast interdisciplinary effort to further our understanding of how life evolves.

That’s a little soft — there are no grand reformulations of the neo-Darwinian synthesis in there, nor is anyone proposing to overturn our understanding of evolution — but that’s what I expected. It’s saying that there are a lot of exciting ideas and new observations that increase our understanding of the power of evolution, and promise to lead research in interesting new directions.

Unfortunately, one reporter has produced an abominably muddled, utterly worthless and uninformed account of the Altenberg meeting that has been picked up by many crackpots to suggest that evolution is in trouble. This not only ignores a fundamental property of science — that it is always pushing off in new directions — but embarrassingly overinflates the importance of this one meeting. This was a gathering of established scientists with some new proposals. It was not a meeting of the central directorate of the Darwinist cabal to formulate new dogma.

Where one ignorant kook dares to assert her inanity, you know the Discovery Institute will stampede after her. Both Paul Nelson and now Casey Luskin have cited her lunatic distortions favorably. Luskin’s account is egregiously incompetent, as we’ve come to expect — he even thinks Stuart Pivar was an attendee. Pivar is an eccentric New York art collector, heir to a septic tank fortune, who has no training in science and whose “theory” is a nonsensical bit of guesswork that is contradicted by observations anyone can make in a basic developmental biology lab. He was not at the meeting. No one in their right mind would even consider inviting him to such a serious event. Maybe if it was a birthday party and they needed someone to make balloon animals, he’d be a good man to have on hand.

Now we can move beyond the garbled hype of the creationists. Pigliucci lists several concepts up there that have promise for further research, and that may help us understand evolution better. That’s the productive result of the meeting, and the only part that counts. Those concepts are also going to be discussed by many other scientists at many other meetings — even I talked about some of them recently — but don’t let the liars on the creationist side confuse you into thinking that the fact that scientists are talking about new ideas is a sign that evolution is in crisis. Talking about new ideas is normal science.

Someone was awake at GECCO

Hooray, I have evidence that at least one person didn’t fall asleep at my GECCO keynote: here’s a summary. He even managed to pay attention right up to the dramatic conclusion, which I usually keep a secret, but now the beans have been spilled.

Wait…the biology-oriented keynote at last year’s GECCO was a panel with Lewis Wolpert, Steve Jones, and Richard Dawkins? I would have been a lot more nervous if I’d known I was following up that act.

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

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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

Blogging on Peer-Reviewed Research

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.

[Read more…]

Ventastega

Blogging on Peer-Reviewed Research

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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

Blogging on Peer-Reviewed Research

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

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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.

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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 Ai-233f23e2a2ca8059264849e39e1760d2-heart.gif Ki-233f23e2a2ca8059264849e39e1760d2-heart.gif Qi-233f23e2a2ca8059264849e39e1760d2-heart.gif Ji-233f23e2a2ca8059264849e39e1760d2-heart.gif 10i-233f23e2a2ca8059264849e39e1760d2-heart.gif 9i-233f23e2a2ca8059264849e39e1760d2-heart.gif 8i-233f23e2a2ca8059264849e39e1760d2-heart.gif 7i-233f23e2a2ca8059264849e39e1760d2-heart.gif 6i-233f23e2a2ca8059264849e39e1760d2-heart.gif 5i-233f23e2a2ca8059264849e39e1760d2-heart.gif 4i-233f23e2a2ca8059264849e39e1760d2-heart.gif 3i-233f23e2a2ca8059264849e39e1760d2-heart.gif 2i-233f23e2a2ca8059264849e39e1760d2-heart.gif
Hand 2 Ai-94f8cf214b78029e2cd1e9398229dda0-club.gif Ki-94f8cf214b78029e2cd1e9398229dda0-club.gif Qi-94f8cf214b78029e2cd1e9398229dda0-club.gif Ji-94f8cf214b78029e2cd1e9398229dda0-club.gif 10i-94f8cf214b78029e2cd1e9398229dda0-club.gif 9i-94f8cf214b78029e2cd1e9398229dda0-club.gif 8i-94f8cf214b78029e2cd1e9398229dda0-club.gif 7i-94f8cf214b78029e2cd1e9398229dda0-club.gif 6i-94f8cf214b78029e2cd1e9398229dda0-club.gif 5i-94f8cf214b78029e2cd1e9398229dda0-club.gif 4i-94f8cf214b78029e2cd1e9398229dda0-club.gif 3i-94f8cf214b78029e2cd1e9398229dda0-club.gif 2i-94f8cf214b78029e2cd1e9398229dda0-club.gif
Hand 3 Ai-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif Ki-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif Qi-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif Ji-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 10i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 9i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 8i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 7i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 6i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 5i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 4i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 3i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 2i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif
Hand 4 Ai-37cc42c4042ea4372806e327e67b2e42-spade.gif Ki-37cc42c4042ea4372806e327e67b2e42-spade.gif Qi-37cc42c4042ea4372806e327e67b2e42-spade.gif Ji-37cc42c4042ea4372806e327e67b2e42-spade.gif 10i-37cc42c4042ea4372806e327e67b2e42-spade.gif 9i-37cc42c4042ea4372806e327e67b2e42-spade.gif 8i-37cc42c4042ea4372806e327e67b2e42-spade.gif 7i-37cc42c4042ea4372806e327e67b2e42-spade.gif 6i-37cc42c4042ea4372806e327e67b2e42-spade.gif 5i-37cc42c4042ea4372806e327e67b2e42-spade.gif 4i-37cc42c4042ea4372806e327e67b2e42-spade.gif 3i-37cc42c4042ea4372806e327e67b2e42-spade.gif 2i-37cc42c4042ea4372806e327e67b2e42-spade.gif

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.