“Frack” should be the new obscenity

Read this article on fracking and you’ll agree with me. The oil companies have reached new despicable lows in their efforts to poison the air and water.

Like any good little privileged American, my first thought was…is this going on in my back yard? And the answer is no, it’s not, there is no fracking going on in Minnesota. However, we are one of the prime suppliers of industrial silica sand used in fracking, and we’ve got lots of mining going on in the southeastern part of the state. So we’re just enablers of fracking.

All that sand is going next door to allow lots of fracking in North Dakota, though. Sorry, neighbor. I do find it ironic that a state known for its regressive/conservative social policies is happily making a big chunk of its territory uninhabitable, though.

What I taught today: toroids!

Hox 11/13 expression in an echinoderm blastula

It was the last day of classes for us. I brought donuts.

Dammit, I just realized I missed a golden opportunity. I should have talked to them about Thrive and Pivar and Fleury and Andrulis. Crackpot fringe developmental biologists all seem to have a thing for donuts.

Rats. Well, I’ll just send all my students an email and tell them they have to come back. They don’t even realize the importance of our little snack together.

Animal-rights activists are the danger to animals

It is possible to have a conscientious opposition to research on animals, and every university has channels by which activists can register their dissent, and by which they can also influence ethical decisions made by institutional animal research review committees. There is a right way and a wrong way to protest. And the wrong way is charge into a lab, disrupt experiments in progress, and “liberate” highly inbred, specialized animals that are dependent on laboratory care for their health and survival. Protesters in Milan chose the wrong way.

Activists occupied an animal facility at the University of Milan, Italy, at the weekend, releasing mice and rabbits and mixing up cage labels to confuse experimental protocols. Researchers at the university say that it will take years to recover their work.

Many of the animals at the facility are genetic models for psychiatric disorders such as autism and schizophrenia.

I don’t even understand the mindset here. Where are you going to release lab animals to? They may require special diets and care, they most likely have been raised in a very specific environment and have no ability to cope with a different place, and they may have genetic diseases that make them completely unable to compete with wild forms. Years ago at the University of Oregon, ALF pulled a stunt like this; they released lab-bred animals along the side of I5. The only animals to benefit in the area were the red-tailed hawks who saw a sudden bounty of terrified white rodents.

And further, scrambling the data for research into human neurological disorders accomplishes nothing other than slowing research. Why? This is nothing but hatred of science.

There’s not much one can do in the face of determined stupidity other than to show a united front. Sign the Call for Solidarity with the scientists in Milan.

What I taught in the development lab today

After our disastrous chick lab — it turns out that getting fertilized chicken eggs shipped to remote Morris, Minnesota during a blizzard is a formula for generating dead embryos — the final developmental biology lab for the semester is an easy one. I lectured the students on structuralism and how there are more to cells then genes (there’s also cytoplasm and membranes and environment) earlier today. This afternnon I’ve given them recipes for soap bubble solution and told them to play. They’re supposedly making little model multicellular organisms by chaining soap bubbles together, and observing how the membranes follow rules of organization just like the ones we see in living tissue.

In case you’re wondering what the recipe is so you can do it too, here’s my bubble soap formula:

  • 5ml Dawn dishwashing soap

  • 100ml DI water

  • 1ml glycerine

It gets better as it ages — there are perfumes and a small amount of alcohol solvent in the dishwashing liquid which evaporate off with time. The students are playing with concentrations, and if you’re making it up fresh and don’t want to wait until tomorrow, you can increase the concentrations of soap and glycerine.

The more glycerine you add, the more long-lasting the bubbles are…and unfortunately, the heavier they are. If you want bubbles that will waft gently on the breeze, you’ll want less glycerine. It’s a very forgiving recipe, just play.

I’ve also provided the students with a couple of books: the classic Soap Bubbles: Their Colors and Forces Which Mold Them by C.V. Boys, and The Science of Soap Films and Soap Bubbles by Cyril Isenberg. They’re more about math and physics, but they have some nice illustrations. These are projects you can do at home with cheap ingredients bought at the grocery store, so those of you with kids might try playing with it this summer. There are simple rules about the angles of intersection between bubbles — if you’re mathematically inclined, take pictures and use a protractor and see if you can work them out. There’s also some really cool stuff going on with colors, since the bubbles have a gradient of thickness from top to bottom and you get wonderful colors caused by refraction and reflection and phase shifts across the membrane.

OK, if you don’t have kids, you have my permission to play with soap bubbles, too. Tell everyone who looks at you funny that you’re doing Science!

Bad laws for science and all growing things

Now it’s getting personal. When the Republicans were just dedicated to making the poor poorer and the rich richer, I could shrug it off. When they kept arguing for the righteousness of bombing foreigners (well, Democrats do that too), I could console myself that they weren’t bombing me, yet.

But now they’re aiming to destroy science in the US, and I have to complain.

The legislation, being worked up by Representative Lamar Smith (R-TX), represents the latest-and bluntest-attack on NSF by congressional Republicans seeking to halt what they believe is frivolous and wasteful research being funded in the social sciences. Last month Senator Tom Coburn (R-OK) successfully attached language to a 2013 spending bill that prohibits NSF from funding any political science research for the rest of the fiscal year unless its director certifies that it pertains to economic development or national security. Smith’s draft bill, called the "High Quality Research Act," would apply similar language to NSF’s entire research portfolio across all the disciplines it supports.

Oh, the “High Quality Research Act”…given the Republican’s fondness for giving their bills the most misleading names possible, we already know this intends the opposite.

What they intend to do is write patriotism into the funding of science. Our work most promote AMERICA, and also must be of utmost importance, where importance is to be defined by Texas a-holes in shitkickers and big ol’ cowboy hats, who probably don’t care much for them fruit flies.

1) "…in the interests of the United States to advance the national health, prosperity, or welfare, and to secure the national defense by promoting the progress of science;

2) "… the finest quality, is groundbreaking, and answers questions or solves problems that are of utmost importance to society at large; and

3) "…not duplicative of other research projects being funded by the Foundation or other Federal science agencies."

If the Republicans really want to start a brain drain, pass that bill. Great way to poison science.

Oh, and yeah, I also hate what they’ve done to both domestic and foreign policy. Is there anything Republicans do that is less than soul-destroying evil?

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.

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.

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.

[Read more…]

It’s another exam day!

I’ve been terrible about updating everyone about my class the last few weeks — we’re coming up on the end of the semester, so I’ve been going a little bit mad. We’ve been focusing on vertebrate development lately, and right now we’ve got a few dozen fertilized chicken eggs sitting in an incubator and developing embryos. Maybe. It is always a real pain to get these things delivered to remote Morris, Minnesota — I delayed this part of the lab to the very end of the semester, hoping the sun would emerge and warm the hemisphere enough that when UPS took their sweet time getting them to me, they wouldn’t freeze in the back of the truck. As usual, though, next day delivery turned into two day delivery, and we haven’t seen Spring yet. So we’ll soon know whether they survived their harrowing journey through the frigid Northlands, and if they haven’t, I’ll have to throw up my hands and cry.

Or I could torture my students to ease my frustration. Yeah, that’s the ticket. So it’s exam day.

Developmental Biology Exam #3

This is a take-home exam. You are free and even encouraged to discuss these questions with your fellow students, but please write your answers independently — I want to hear your voice in your essays. Also note that you are UMM students, and so I have the highest expectations for the quality of your writing, and I will be grading you on grammar and spelling and clarity of expression as well as the content of your essays and your understanding of the concepts.

Answer two of the following three questions, 500-1000 words each. Do not retype the questions into your essay; if I can’t tell which one you’re answering from the story you’re telling, you’re doing it wrong. Include a word count in the top right corner of each of the two essays, and your name in the top left corner of each page. This assignment is due in class on Monday, and there will be a penalty for late submissions.

Question 1: One of Sarah Palin’s notorious gaffes was her dismissal of “fruit fly research” — she thought it was absurd that the government actually funded science on flies. How would you explain to a congressman that basic research is important? I’m going to put two constraints on your answer: 1) It has to be comprehensible to Michele Bachmann, and 2) don’t take the shortcut of promising that which you may not deliver. That is, no “maybe it will cure cancer!” claims, but focus instead on why we should appreciate deeper knowledge of biology.

Question 2: There is an interesting tension in evo devo: on the one hand, we like to talk about the universality of molecular mechanisms, but on the other hand, we’re also very interested in the differences, both in phenotype and genetics. This is an old debate in evolutionary theory, too, so it’s not unique to development, but how do you reconcile unity and diversity simultaneously?

Question 3: When I told you about axis specification in Drosophila, the story was relatively straightforward: maternal factors switch on a chain of zygotic genes that set up the pattern. When I told you about the same process in vertebrates, though, I didn’t give you the same level of detail—I gave you buckets of transcription factors and said they had various roles. Dig deeper. Pick ONE of these vertebrate dorsalizing factors out of the bucket and tell me more about it: noggin, chordin, frizbee, goosecoid, pintallavis.