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.

My ulterior motive

In case you’re wondering why I’m experimenting with video, there actually is an ulterior motive, and it’s the same one that got me into blogging in the first place: teaching. I’m teaching science at an undergraduate institution, and contrary to many people’s expectations, a bachelor’s degree does not confer a deep understanding of science, and it can’t. Students come out of high school with an ability to read and do basic math (at least the ones we admit to college!), and have wildly varying abilities in writing, analysis, and thinking. I think the undergraduate university’s role is more to deepen the student’s abilities in those general skills, and also to provide a broad knowledge base in a discipline of their choosing. We’re preparing students to go off and do science, if that’s what they want to do. I’ve done my job if my students go to graduate school competent and confident, ready to get to work and explore the natural world. Or if they choose not to follow a science career, they’re open to read and think about the world in a scientific way.

So there are a couple of things I do in my upper level lab courses. I take a hands-off approach: I teach students how to use the tools in my lab, give them a general idea of what would be cool to do or see, and turn them loose. If I see a combination of frustration (“I can’t get it to work! How do I get it to work?”) and play (“What if we do this?”), it’s a success. I have them blogging because it’s a sneaky way to get them to think about the subject of the class outside of class, and also to get them to blend their interests — which usually aren’t identical to mine! — with what I’m teaching.

And then there are presentations. Communicating your work is an important part of doing science, too. I try to get them to do that with the blogging, but also our university promotes a capstone experience, our senior seminars. Before a student can graduate, they have to do a one hour talk on some subject in their discipline, and it’s a big deal/ordeal to the students, and also a big deal/ordeal for us faculty in one of the largest majors on campus. Their quality varies all over the place, even though many of my colleagues and I do incorporate requirements for giving in-class presentations in our upper level courses, and we have a preparatory course on writing that includes giving presentations. There’s a limitation on doing that in class, though: you’ve got 20 students, you can’t chew up multiple class hours getting them all to do rehearsals and rehearsals under your supervision. We usually get an abstract and a promise and a conversation with them to help explain the data, and then boom, they do their talk to the class. It’s one shot and they’re done. That’s not the way to learn.

So I’ve had this idea…this is a generation that’s comfortable with their camera phones, that whiles away hours on facebook and youtube. What if I tried to combine that with doing presentations? What if, in one of my lab courses, I made the final project to be producing a short youtube video explaining some piece of data that they’d gotten in the lab? Put a micrograph or a chart or a time-lapse video on the screen and explain it with a voice-over, or stand in front of a camera while discussing some fine point of theory, or make a how-to video on how to use the microscope. It’s something they could tweak until it looks good, I’d be able to review work in progress fairly easily, and then what they put up for final evaluation might be a little more polished. This would be a useful skill for the future. I’m also rather impressed with how Casey Dunn has his students make creature features.

One catch: to have the students do it, I have to be able to do it. So in my spare time (hah!), I’ve been tinkering with ideas. I got some clamp lamps to play with lighting, I’ve got some cheap and simple backdrops to play with, I read Steve Stockman’s How to Shoot Video That Doesn’t Suck (which has a lot of damn good basic practical advice), and I’ve been doing some experimenting, most of which will never see the light of day. I’m learning stuff, which is always fun.

And it’s useful stuff, too. For instance, I’m a words and typing sort of guy, so my approach so far has been to write a script and then wrap video and images around it. That doesn’t work so well. I’m slowly learning that in this medium you start with video and images and wrap words around them. And that’s exactly what we do routinely in a science talk! You’ve got these chunks of data in the form of images and numbers, and what you do in a presentation is show them and add your verbal explanation on top. Man, I ought to know this stuff already. I just have to adapt.

So this summer you might be seeing more of my unphotogenic face in videos as I clumsily try to get some basic skills in this medium. The payoff, though, is that in a year or so I’ll be able to teach my students how to do it better, and then we’ll get a fine new crop of video stars who are comfortable explaining science in front of a camera.

But don’t worry, you don’t have to suffer through my struggles, just don’t watch me.

If only I were a little more unscrupulous (or gullible) …I’d go to CMBF

I would love to visit China. I’d especially love to be invited to go there and have all my expenses covered. So when I got an official-looking invitation to a conference there a while back, I had a few milliseconds of enthusiasm, until I read a little deeper and my excitement got replaced with bafflement. I just turned away from it, but they keep begging me to attend. Here’s the latest letter from the China Medicinal Biotech Forum:

Dear Dr. Paul Myers,

This is redacted, the program coordinator ofthe 6th CMBF-2013. On behalf of the organizing committee of CMBF-2013, I sent you a formal Invitation Letter several weeks ago, which is regarding inviting you to participate in our forum as the Chair/Speaker of Session 7-2: Genetic and Cell Engineering Technologies for Biological Therapy. But we haven’t received any reply from you. In case of missing this grant event, I am writing again to extend to you our sincere invitation. Since we have learnt that you are making valuable contributions to Paul Myers…, your unique and inspirational message will definitely highlight the forum.

The 6th CMBF will be held on September 25-27, 2013 in Shenzhen, China. And it is hosted by CMBA, which was established in 1993 and consisted by 200 enterprise members and over 2000 professional individuals. It is on attachment to Ministry of Health of the People’s Republic of China, which is an executive agency of the state that plays the role of providing information, raising health awareness and education, ensuring the accessibility of health services, and monitoring the quality of health services provided to citizens and visitors in the mainland of the People’s Republic of China. It also cooperates and keeps in touch with other health ministries and departments, including those of the special administrative regions and the World Health Organization (WHO).

We have hosted CMBF for five times in Beijing, Shanghai, Qingdao and Dalian respectively. Each time was in every way extremely successful in spite of the preceding worldwide political and health problems. The strong attendance was a testimony to fact that the CMBF conference is well recognized as the most important international convention on China Medical Biotechnology.

The primary goal of this event is to provide a forum for the exchange of current information about new and emerging scientific knowledge, to discuss implications for future research and the application of new medicinal biotechnology, and to create opportunities for the collaboration and matchmaking between academia and industry. CMBF-2013 will focus on the following topics: Basic Research of Medical Biotechnology, Monoclonal Antibody, Regenerative Medicine & Stem Cell, Bone Tissue Bank, Nanomedicine, Biomaterials, Novel Technologies for Biotherapeutics, Clinical Application Medical Biotechnology (Part I)-Biological Diagnostics, Clinical Application Medical Biotechnology ( Part II)-Therapy, Dietary Fiber.

For more information regarding CMBF-2013, please visit our conference website at http://www.medbioforum.org/.

We look forward to your active support and participation.

Sincerely Yours,

Weird. I’m not a biotechnology or biomedicine researcher. I do not do “Genetic and Cell Engineering Technologies for Biological Therapy”, but they’re asking me to chair a session on the topic? I think it’s very nice that they’ve noticed I am “making valuable contributions to Paul Myers…”, which is true, but I think that only qualifies me to chair a session titled “Paul Myers”. Even if I were confident that this were a legitimate research conference, I’d turn them down.

But I did dig around trying to find out more about them. They’ve had quite a few meetings, and they’ve had some prestigious attendees, including Nobelists. Maybe somebody on their administrative team is a master of SEO, because all I could find with a casual search (sorry, I’m not going, so I wasn’t going to dig deeper) were links to the group itself and to Chinese sources. The topics sound reasonable and legit, but far more applied than anything that would interest me.

But now I’m curious. There are a couple of possibilities here.

One is that it’s a great big scam. I’d agree, and then find myself paying for travel expenses that would never be reimbursed. If that’s the case, we should spread the word.

Another is that it’s a real conference for an obscure organization that has a great deal of Chinese government money thrown at it. They’re honestly reaching out to make connections with US researchers, but they don’t really know who’s who.

Another very remote possibility is that somebody there knows who I am, actually thinks I have a “unique and inspirational message”, and is trying to shoehorn me into a session that is unfortunately a poor fit. I can do a general rah-rah biology talk, but I’m not at all qualified to go into the details of stem cell research and biotechnology.

Anyone have prior experience with this group? If nothing else, promoting a little more second-party information about them on the web would be helpful.