Fragments of a shipboard talk

Since it has been a long time since I contributed any content to Pharyngula…here’s something. I was asked to give a brief talk on the ship, so I’ve tossed my written draft below the fold. With these short talks I like to write the story first, but when I get up on the stage and actually perform it, I don’t bring notes or anything like that, so what is actually said follows the structure of what I wrote, and some of the wording comes through, but it tends to be rather different. Probably a lot different —I know I extemporized a fair bit on the last half. This is all you get until I’ve had a good night’s sleep, though.

[Read more…]

Looking for the lizard guts story?

Another bit of distortion from Ray Comfort: he claims now that I was asked to present the very best evidence for evolution, and that all I could come up with was some “little infolding of the gut”. If you’ve come here from Comfort’s ignorance zone, here are the details of the evolution of lizards of the genus Podarcis.

What Comfort cannot comprehend is that there is no one absolute make-or-break piece of evidence for evolution — evolution is a conclusion from the totality of the evidence. There are thousands of cases that demonstrate that the principles of evolution work and are useful for understanding the natural world; there are no cases where creationism has improved our understanding.

Evolve: Guts

Last week, we watched Evolve: Eyes on the History Channel; tonight, shall we watch the next episode, Evolve: Guts, together? Tune in shortly!

A disgusting beginning: competitive eaters? Bleh. It’s a basic introduction to mammalian digestive physiology — I can tell we’re going to get lots of Big Vertebrate biology again.

They show a cool machine called Cloaca that simulates human digestion, with vats containing chemicals to act as the various chambers. They don’t bother to explain why this machine was built, but it is kind of weirdly interesting.

Once again, they openly say that the complexity of the digestive system evolved — that’s rather refreshing.

Yay! They go back to microorganisms 700 million years ago…for 30 seconds. Then we move on to Ediacaran organisms. The evidence shows that they weren’t photosynthetic, but were some kind of animal that had to have fed somehow, and probably were passive absorbers of drifting nutrients. They suggest that they were replaced by Cambrian organisms that had guts.

Jellyfish just have a sac, not a tube. Cambrian creatures had a more elaborate feeding system, allowing for sophisticated mobile predators, and we see an arms race. Nice animations of Anomalocaris all over the place!

Zip to the modern day: submersibles discover exotic deep sea worms that live on dead whale bones. They have no mouth or gut, so how do they eat bone? They were drilling in and bringing bacteria with them that broke down the bone, and then the worms absorbed the bacteria.

Hey, they mention bacteria, and talk about how digestive enzymes secreted by bacteria are predecessors, and are necessary for the extraction of food in our own guts.

They also mention fish and specialization of regions in the gut tube! More fish, please! But no, we’re going to go straight to tetrapods now, and the promise before the break is dinosaurs. Oh, well.

I’m really pining for more about the actual evolution of guts — and something about development. How can they talk about epithelial tubes without talking about development? Jumping to dinosaurs skips all the interesting stuff. Guts are done by the time you’ve got dinosaurs.

OK, dinosaurs. Yeah, yeah. They discuss gizzard stones and the relationship of dinosaurs to birds. Were dinosaurs warm-blooded? Their digestion was less croc-like and more bird like, determined by analyzing dinosaur coprolites, including T. rex droppings, which contain fragments of fossilized bone. They contain large quantities of bone, which suggests a croc-like eating pattern. But they also contains fragments of fossilized muscle tissue, which suggests that food passed through rapidly, like a bird. So it was a glutton that also had to eat frequently.

The K/T event meant that these big consumers all starved to death. The lead-in to the next section is all about snakes and mammals.

Snakes! Theyre going to talk about the evolution of feeding strategies (why not use cichlids, though? They’d be better). Oh…because you can show movies of snakes swallowing mice whole.

Nifty x-rays of poor mice dissolving in a snake’s gut.

Discussion of the ability of the snake to shut down its gut between meals. Microvilli lining the intestine actually contract while fasting, and increase in length when feeding.

20 million years ago, there was a widespread increase in grasslands that represented a new opportunity … but was hard to eat because much of it was bound up in cellulose. Ruminants evolved fermentation chambers. They show a surgically fistulated cow that allows researchers to get their hands right into a gut. They use bacteria to help break down tough plant material.

These adaptations promote the growth of herbivores…which leads to the evolution of predators.

Now it’s on to humans, of course. They suggest that maybe the key innovation in our ancestors wasn’t our brain, but guts: big-toothed, small-brained apes evolved into small-toothed, big-brained humans. A switch in diet to more meat, and the use of tools to ‘pre-digest’ food allowed us to have smaller guts. Cooking was another huge change that greatly improved the quality of the diet.

They measure the energy required by snakes to digest raw vs. cooked meat. Cooking reduces the cost of digestion by 12.5%. Human guts evolved to be more efficient, liberating more energy for the evolution of the brain.

OK, much like last week’s episode, this show’s strengths are also its weaknesses. The emphasis on charismatic megafauna may be great for catching the attention of casual viewers, but it leaves out all the important events in the evolution of these structures, and ends up emphasizing late refinements and details. Somehow, we need to get a documentary that brings up more molecules and development and the all-important teeny-tiny creatures, where the major innovations first appeared.

But still, I’m most impressed to see a television show that unapologetically discusses evolution as the only credible explanation for the appearance of these features.

TV reminder

Tonight, at 9 Central/10 Eastern, it’s time for the second episode in the History Channel’s series on evolution: Evolve – Guts.

It doesn’t just take willpower to survive. It takes guts–in the form of a digestive system that turns food into fuel. Look closely at the role guts have played in shaping some of Earth’s most successful animals: tyrannosaurs, snakes, cows, humans and others. Take a 575-million year journey that begins with the planet’s first multi-cellular organisms and ends at our dinner tables. Watch as live-action natural history sequences, CGI, epic docudrama, and experimental science help to illustrate our and our fellow species’ eternal struggle for survival on earth.

I think I’d rather hear more about the digestive systems of protists, Trichoplax, sponges, and cnidarians than T. rex again, but shall we watch it together as we did last week?

Evolving snake fangs

Blogging on Peer-Reviewed Research
i-3c3ae12d88b9d206fc84149b28a6cf52-fang_embryo.jpg
Ontogenetic allometry in the fang in the front-fanged Causus rhombeatus (Viperidae) displaces the fang along the upper jaw. Scale bars, 1 mm. We note the change in relative size of the upper jaw subregions: i, anterior; ii, fang; iii, posterior. d.a.o., days after oviposition.

I keep saying this to everyone: if you want to understand the origin of novel morphological features in multicellular organisms, you have to look at their development. “Everything is the way it is because of how it got that way,” as D’Arcy Thompson said, so comprehending the ontogeny of form is absolutely critical to understanding what processes were sculpted by evolution. Now here’s a lovely piece of work that uses snake embryology to come to some interesting conclusions about how venomous fangs evolved.

Basal snakes, animals like boas, lack venom and specialized fangs altogether; they have relatively simple rows of small sharp teeth. Elapid snakes, like cobras and mambas and coral snakes, are at the other extreme, with prominent fangs at the front of their jaws that act like injection needles to deliver poisons. Then there are the Viperidae, rattlesnakes and pit vipers and copperheads, that also have front fangs, but phylogenetically belong to a distinct lineage from the elapids. And finally there are other snakes like the grass snake that have enlarged fangs at the back of their jaws. It’s a bit confusing: did all of these lineages independently evolve fangs and venom glands, or are there common underpinnings to all of these arrangements?

[Read more…]

Evolve: Eyes

The warm-up act for this program was a dinosaur program called “Jurassic Fight Club”, which was loaded with CGI and lots of gratuitous razzle-dazzle — but I thought it was a hoot. It also had enthusiasatic scientists talking about how they figured out what had happened (although it does bug me that they treated some speculative stuff in the narrative as if it were factual). Most of the show was taken up with glitzy animations, but it was balanced with at least some discussion of the process of science, so I’ll give it a thumbs up.

Now to settle in for the story of the evolution of eyes…

Oooh: “the sparks of evolution are tiny, random changes called mutations”. I’m pleased that it jumps right in without compromise. It also promptly pushes the timeline back to 600 million years, and describes work done on jellyfish eyes. They show some very cool behavioral studies of how jellies respond to different wavelengths of light, illustrating why even simple animals would find light-sensing organs beneficial.

Teaser before the first commercial: trilobites. It looks they’re trying for a chronological approach.

The commercials are really annoying: Kinoki foot pad quackery and bigfoot. Bleh.

Now we get a quick summary of the Cambrian explosion — I saw an anomalocaris swim by. The first fossil eyes are from the Cambrian; compound eyes on arthropods. Modern insects are shown, explained as not descendants of trilobites, but probably share the same genes Good acknowledgment of the successful utility of dragonfly eyes.

Dang. Too little time spent on invertebrates — they’re already switching gears to focus on vertebrates.

Pikaia! Cool. Kinda nice that they’re setting up the vertebrate eye as an icon of evolution, and a kind of machine — good dig at ID. There’s also a nice simple animation of how an eye patch could form an eye cup, then an eye with a lens.

Yeah, they already leap into those sexy, glitzy dinosaurs. A little more time should be spent on those unsexy hagfish and lampreys, more interesting as transitional forms, but OK, most people wouldn’t find them as interesting as I would. They show Kent Stevens (UO! Yay!) work on identifying visual fields from dinosaur fossils, and discuss binocularity.

T. rex makes for good visuals, but is it really the best animal for discussing the evolution of vertebrate eyes? The innovations were all in place before the dinosaurs came on the scene!

Next lead-in: we’re about to learn about mammals and night vision.

Primitive mammals were largely nocturnal. So what are the special adaptations in the mammalian eye for night vision? Lots of isolated eyes in jars; the answer from comparative anatomy is that the size of the cornea is important. Cool: tarsiers have eyes that are bigger than their brains.

Another strategy: the tapetum, a reflective layer at the back of the eye. Nifty dissection of a big cat’s eye to show the structure.

Looks like the last 15 minutes of the program will be about human vision…

We lucky humans have color vision. Mammals radiated into numerous niches after the great extinction at the K/T boundary, and primates moved into the trees. Why did natural selection favor improved color vision in primates? Monkeys are shown to favor the youngest, tenderest leaves…which have color differences from old leaves.

Primates also have binocularity for better depth perception, an adaptation for living in trees. This gives them a narrower field of view, unfortunately. Birds of prey targeted these animals with limited vision, which made group living more advantageous for primates. They suggest that this would promote more social behavior and intelligence.

Summary: Not bad. The title is a bit of a misnomer, though, since only a little bit of it was about the evolution of eyes. A program more true to its title would have spent much more time on invertebrates, would have said more about the molecular underpinnings of vision, and would have concentrated on hagfish, lampreys, and teleosts among the vertebrates.

I know…dinosaurs and people are much more popular creatures, so the show compromised on the science for the sake of visual appeal. That’s an unfortunate reality of the conventions of TV programming, but it would have been nice to see them break out of that straitjacket, especially since the early part of the show on jellyfish was arresting and cool, showing that it can be done.

It was unabashedly pro-evolution, too, not giving a second to the silly stories we get from creationists. That’s a real plus, too.

Snake segmentation

Blogging on Peer-Reviewed Research

Life has two contradictory properties that any theory explaining its origin must encompass: similarities everywhere, and differences separating species. So far, the only theory that covers both beautifully and explains how one is the consequence of the other is evolution. Common descent unites all life on earth, while evolution itself is about constant change; similarities are rooted in our shared ancestry, while differences arise as lineages diverge.

Now here’s a new example of both phenomena: the development of segmentation in snakes. We humans have 33 vertebrae, zebrafish have 30-33, chickens have 55, mice have 65, and snakes have up to 300 — there’s about a ten-fold range right there. There are big obvious morphological and functional differences, too: snakes are sinuous slitherers notable for their flexibility, fish use their spines as springs for side-to-side motion, chickens fuse the skeleton into a bony box, and humans are upright bipeds with backaches. Yet underlying all that diversity is a common thread, that segmented vertebral column.

i-44c0b44c78c71955b53b0a7f004b7ea4-snakeseg.jpg
(Click for larger image)
Vertebral formula and somitogenesis in the corn snake.
a, Alizarin staining of a corn snake showing 296 vertebrae, including 3
cervical, 219 thoracic, 4 cloacal (distinguishable by their forked
lymphapophyses) and 70 caudal. b, Time course of corn snake development
after egg laying (118-somite embryo on the far left) until the end of
somitogenesis (~315 somites).

The similarities are a result of common descent. The differences, it turns out, arise from subtle changes in developmental timing.

[Read more…]

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.