What I taught today: a send-off with an assignment

Today was the last day I lecture at my developmental biology students. We have one more lab and one final class hour which will be all about assessment, but this was my last chance to pontificate at them…so I told them about all the things I didn’t teach them, and gave them a reading list for the summer. (I know, there’s no way they’re going to take these to the beach, but maybe when they move on in their careers they’ll remember that little reference in their notes and look it up.)

So here are the books I told them to go read.

We’ve been all up in the evo-devo house this semester, so I urged them to read the antidote, just to get some perspective. This is the great big book all the grown-up developmental biologists read and admire and regard as gloriously wrong in many ways, but still an important reminder that physical and chemical properties of whole cells and organisms matter — it’s not all genes. And of course that legendary book is On Growth and Form by D’Arcy Wentworth Thompson. I tell all my students that if ever they want to get serious about developmental biology, they must read Thompson.

For the more modern gang who like computers and math and logic puzzles, I point them at At Home in the Universe: The Search for the Laws of Self-Organization and Complexity and The Origins of Order: Self-Organization and Selection in Evolution by Stuart A. Kauffman. He’d really benefit from more time in a wet lab, but still, there’s some very provocative stuff in those books about how complexity can spontaneously arise. I also gave them a bit of an introduction to NK network theory.

There is always a philosopher or two in the class, so for them I suggest that they read The Ontogeny of Information: Developmental Systems and Evolution by Susan Oyama. Developmental Systems Theory suffers for its lack of applicability — it really is a little too abstract for most scientists — but I love it for its more holistic approach to development.

For the hardcore biologists, the ones who are ready to read a book where every page makes them think very hard, I suggest Developmental Plasticity and Evolution by Mary Jane West-Eberhard. It’s quite possibly the most brilliant book I’ve ever read, but it’s dense and challenging. Intentionally challenging: she really does question a lot of the dogma of evolutionary and developmental biology, and forces you to realize there are a lot of wide-open, intensely interesting questions out there.

And finally, I brought up a book I seriously think about making the class text every year, Ecological Developmental Biology by Scott F. Gilbert and David Epel. The course as it is now is a fairly traditional modern molecular genetics and development class, with a solid overlay of evolutionary biology. The Gilbert and Epel book integrates all that with ecology — and I firmly believe that the well-rounded biologist of the type a liberal arts university tries to generate ought to have a balanced conceptual understanding of ecology, development, and evolution.

That’s the short list. It’s too bad I don’t have total control of my students’ lives, or I’d have them studying ten or twenty books over the summer. Or they probably think it’s a good thing I don’t.

Best response to the Aquatic Ape nonsense yet

Mockery is good. Behold the #spaceape hypothesis: humans clearly evolved in outer space!

#SPACEAPE

Basic Arguments of the Space Ape Theory:

1. we have evolved big brains relative to our bodies because we don’t need our bodies to move around in space.

2. we don’t have much body hair because what would be the point of a few more follicles worth in 2.73 Kelvin (-270 Celsius)?

3. sinuses, far from being evolutionary spandrels, are little miniature internal space helmets.

4. our outsize eyes clearly show our relation to other species in space.

It’s taking off on Twitter, too. Next time someone brings up the soggy monkey story, I’m just going to reply with “Space Ape!”

Still waiting for the ID revolution

Hey, boys and girls, does anyone remember the IDEA clubs? IDEA was short for Intelligent Design and Evolution Awareness, and the plan was that they’d form all these advocacy groups at universities all over the country, and from there, take over the world! It was going to be a REVOLUTION…one driven by dishonest, conservative Christians who wanted to roll back the progressive agenda and install a devout theocracy in its place.

joinrevolution_sm

The IDEA club is where Casey Luskin got his reputation as a diligent little gerbil for the cause. He was one of the founders of the model organization at UC San Diego, which is highlighted on the main IDEA Center club page. Amusingly, it’s a dead link now.

Likewise, if you read the various blurbs on that site, there are ever-shifting numbers of these clubs around: they claim a high of 35 worldwide, and have a pull-down menu listing them all, but you will click in vain — it doesn’t work, and the links go nowhere. Elsewhere, they say they’ve got 25 active clubs, but at the bottom of the page there are a collection of links to them…they’ve got 10. All of them lead to empty placeholder pages on the IDEA center site, except one, which futilely tries to take you to a defunct Geocities site.

It’s a dismal and empty virtual ghost town. Visit it and listen carefully and you might hear the sad sighs of creationists long gone, and maybe occasionally the cackling, triumphant laughter of a rational human being passing by to gaze on the fading works of intelligent design, and gloat.

Meanwhile, the Secular Student Alliance has been booming, with 378 groups. The links actually work on their page.

Make the comparison. It’s clear where the momentum lies.

The mysterious Tatsuya Ishida

oppressed

He’s an invisible webcomic artist — here’s one of the rare interviews with the guy, and a review of his work. I’ve been following him for many years, and one of the interesting things you can see as he matured is that he’s gone from drawing pimp ninjas and geisha sluts to developing a very feminist sensibility.

Look at his latest, for instance — no words at all, but he still gets across regret at what patriarchal culture has done.

There’s been a striking transformation going on. I’d really like to hear in his own words what’s going on through his head…but his art seems to be doing a fine job of communicating.

Pre-emptive announcement

I’m going to be at Women in Secularism in a few weeks, which I expect to be great. However, certain nuisances are talking about approaching the people they’ve been harassing online for years, and trying to harass them in real life, getting them to be grist for their podcast mill. Ophelia has made a clear declaration:

Ok this is specifically for Vacula: do not approach me at WiS2. Stay away from me.

That goes for me, too. If you’ve been nattering away on twitter & podcasts & blogs about how evil I am, how useless feminism is, and how much you hate freethoughtblogs in general, we have no grounds for any conversation, so stay the hell away from me. I won’t bother you, you won’t bother me.

I won’t be exchanging a single word with Vacula, or any of his fellow travelers.

I think there’ll be more than enough intelligent, interesting people to have conversations with at this meeting, the dross can just stay away.

Oh, no, not the Aquatic Ape Hypothesis again!

I think BAHFest — the festival of Bad Ad Hoc Hypotheses — has been made entirely redundant. It’s an event to mock the absurdly adaptationist hypotheses put forward by some scientists, and it’s intended to be extravagantly ridiculous. But then, you look at some ideas that are inexplicably popular among scientists, and you realize…it’s a little too close to reality.

I’m speaking of the Aquatic Ape Hypothesis.

The Guardian is running yet another article on the goofy idea that we evolved from swimming apes, and that all of the unique features of our species are a product of adaptations to an aquatic lifestyle. It’s complete nonsense: there is no evidence of long-term residence of our species in the water, and the proponents tend to invent the most outrageous panglossian explanations, fitting data to the hypotheses instead of the other way around. At least this story has one new contrivance I’d never heard before. Take it away, Rhys Evans!

“Humans have particularly large sinuses, spaces in the skull between our cheeks, noses and foreheads,” he added. “But why do we have empty spaces in our heads? It makes no sense until we consider the evolutionary perspective. Then it becomes clear: our sinuses acted as buoyancy aids that helped keep our heads above water.”

<stunned silence>

But…but…but every mammal, as far as I know, has a head full of sinuses! Have you ever taken a mouse skull apart? They’re amazingly spongy. Here are some sections through a mouse skull to show you what I mean:

mousesinuses-3
Coronal sections. There is a distinct osteomeatal complex within the nose that drains the true maxillary sinus as well as ethmoids. The true maxillary sinus is located lateral to the osteomeatal complex, and unlike the other sinuses, is lined by submucosal glands. This true maxillary sinus has a single ostium. Each nasal passage is separated by nasal septum. The posterior septum is deficient along its inferior aspect, and the two nasal passageways communicate freely just anterior to nasopharynx.

Isn’t that just beautiful? It’s fairly typical, too: mammals have these elaborate spaces to lighten the skull, humidify inspired air, and in some provide expanded surface area for olfaction — but I suspect the slight contribution of sinuses to those functions means that they’re actually a consequence of conserved developmental programs to build the skull. They’re there as a byproduct of developmental processes in which a scaffold is assembled first, and then thickens and fills in over time. The density of the skull is relatively easily regulated by modifying the timing of its development.

Just because they’re pretty, here’s another image of mouse skulls:

mousesinuses-4
Plates 1 and 2 display three-dimensional computed tomography (CT) reconstructions of mouse skull in axial and lateral-oblique views. Plates A to F display coronal fine cut CT scan images, confirming our histologic planes of section.

So, did mice have an aquatic ancestor? Doesn’t this hypothesis imply that every mammal descended from an aquatic ancestor? (I shouldn’t ask that: my experience with AAH fanatics is that they joyfully answer “yes” to the question.)

I also wonder if these people ever go swimming. Somehow, my sinuses don’t seem to work very effectively as water wings.

Michael Crawford offers a familiar absurdity: the nutritional argument from docosahexaenoic acid (DHA). DHA is one of those omega-3 fatty acids that is used to build brains, and it’s found in high concentration in lots of seafood. The true zealots consider this indisputable proof that we evolved by eating lots of clams.

“It boosts brain growth in mammals. That is why a dolphin has a much bigger brain than a zebra, though they have roughly the same body sizes. The dolphin has a diet rich in DHA. The crucial point is that without a high DHA diet from seafood we could not have developed our big brains. We got smart from eating fish and living in water.

“More to the point, we now face a world in which sources of DHA – our fish stocks – are threatened. That has crucial consequences for our species. Without plentiful DHA, we face a future of increased mental illness and intellectual deterioration. We need to face up to that urgently. That is the real lesson of the aquatic ape theory.”

An experiment: let’s feed zebras bucketloads of DHA, and watch their brains expand to 3-5 pound blobs that give them advanced communications abilities!

Oh, wait. It won’t work. There’s such a thing as neuroplasticity, but brains aren’t quite that flexible. I’m willing to believe that increased availability of the building blocks of brains might remove a constraint on growth, but not that it’s causal, as Crawford claims. Even feeding many generations of zebras DHA isn’t going to affect brain size much at all…and there’s no evidence that terrestrial herbivores are in any way limited by the availability of DHA.

For one thing, they synthesize it. We humans synthesize it, too. We also get it from the herbivores we eat, and certain plants are rich in the precursors to DHA. Vegans have to pay attention to get their DHA requirements met, but it’s not particularly difficult, and you don’t see lifelong vegetarians walking around with itty-bitty pinheads.

There are good reasons to be deeply concerned about declining fish stocks, but preserving a resource vital to the formation of our brains isn’t one of them. There are many people around the world who don’t eat seafood — there are entire ethnic groups who haven’t touched the stuff for generations. There are big-brained primate species that virtually never eat fish. How do they survive? How do they avoid “mental illness and intellectual deterioration”? They get it from other dietary sources.

Mammals in general are larger brained than other animals, are we to use that as an argument that all mammals went through an aquatic stage in their evolution…oh, wait. I did it again. The True Believers will just say “YES!” to that.

Fortunately for Matt Yglesias, Lindsay Beyerstein only leaves him in a metaphorical smoking crater.

A couple of commenters here have persisted in defending Matthew Yglesias’ odious bleat that life is cheaper in Bangladesh because it ought to be because reasons, and that any anger we Westerners might feel about the horrendous loss of life in the recent factory collapse ought more helpfully be directed to buying clothes made in those collapsing sweatshops so that eventually the people making a few hundred dollars a year will have flat screen televisions just like us.

Yglesias is doubling down. In a followup post, he stands by his conclusion that poor countries need to have less stringent workplace safety standards, and adds, as a prelude to accusing his critics of “poisoning the atmosphere,” [see update at end of post]

I’m not really sure what Americans can constructively do to get better enforcement of building codes in Bangladesh

As it turns out, Lindsay Beyerstein has a possible answer:

A group of Bangladeshi and international trade unionists put forward a bold plan to make the garment industry in Bangladesh safer. A surcharge of 10 cents per garment over 5 years would raise $600 million a year, enough to radically transform the infrastructure of the garment industry in Bangladesh. Walmart and the Gap rejected the proposal in 2011.

So that’s pretty handy: All America has to do to make sweatshops in Bangladesh safer is to stop fucking obstructing their being made safer. It’s win-win!

Oh, and a protip to Yglesias: If you persist in discussing the worker safety aspects of US investment in South Asia, you might want to consider not using “poisoning the atmosphere” as a way to tone-troll your critics. We have a 30th Anniversary coming up late next year that will turn that phrase a bit unfortunate.

Updated: in comments, nialscorva correctly points out that I misread Yglesias’ reference to “poisoning the atmosphere.”  My bad. Leaving the post as it was for transparency’s sake.

Bruce Alberts, failure

This is not a very exciting video, but I might just inflict it on my cell biology students in the fall. We got a fair amount of flak from students last time around who were frustrated when labs didn’t work like a recipe from a cookbook — yet that’s how science usually proceeds, with lots of tinkering and frustration and repetition.

I also like his point about how teaching is important for science (although the students won’t really care about that.) I don’t think I really got the breadth of my discipline until I had to master it in order to teach it — there’s nothing quite like the panic behind “I’ve got to lecture for an hour on vesicle transport tomorrow!” to focus the mind wonderfully on a subject you might have found of only passing interest previously.

(via Sandwalk.)

Musings from the mind of a mouse

Casey Luskin is such a great gift to the scientific community. The public spokesman for the Discovery Institute has a law degree and a Masters degree (in Science! Earth Science, that is) and thinks he is qualified to analyze papers in genetics and molecular biology, fields in which he hasn’t the slightest smattering of background, and he keeps falling flat on his face. It’s hilarious! The Discovery Institute is so hard up for competent talent, though, that they keep letting him make a spectacle of his ignorance.

I really, really hope Luskin lives a long time and keeps his job as a frontman for Intelligent Design creationism. He just makes me so happy.

His latest tirade is inspired by the New York Times, which ran an article on highlights from the coelacanth genome. Luskin doesn’t think very deeply, so he keeps making these arguments that he thinks are terribly damaging to evolution because he doesn’t comprehend the significance of what he’s saying. For instance, he sneers at the fact that we keep finding conserved elements in the genome, because as we all know, there are lots of conserved elements.

Hox genes are known to be widely conserved among vertebrates, so the fact that homology was found between Hox-gene-associated DNA across these organisms isn’t very surprising.

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