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.

Earth Day: Atheism+Environmentalism

We’ve started the hangout on Google+. Stop by if you’re interested.

And…here’s the result.

This is the brief introduction I gave, to try and focus the discussion:

For a long time, I’ve been saying that atheism is a heck of a lot more than just disbelieving in gods: we arrive at that conclusion by various means, so the history matters, and recognition of the consequent reality matters — it has implications. I am an advocate for increasing the depth and meaning of atheism, for broadening it and increasing its relevance to more people. In that sense, I’m kind of an ur-atheism-plusser.

But actually, I think we all are. Atheism has always meant more than just disbelief. Probably the narrowest interpreter of atheism on freethoughtblogs is Edwin Kagin, who has openly said that he thinks the only issue that ought to matter to atheists is separation of church and state. But even that is adding extra meaning to the word, and it’s also a terribly narrow meaning, that really only applies to constitutional issues in the United States. The New Atheists (and Old Atheists, too), blithely fold Science into atheism, with scarcely any complaint from other atheists. There seem to be some affiliated issues that atheists, even atheists who still dumbly assert that atheism just means an absence of god-belief, are happy to unthinkingly accept as natural parts of atheism.

And then there are others. All you have to do is look at the angry loons who have freaked out over Atheism Plus. You want atheists to care about equality, and ethics, and social justice? NNNNOOOOOO! How dare you add stuff that isn’t in my minimalist understanding of atheism to my obligations as a human being? I want to be selfish and self-centered and Darwinian!

Now I’m curious to see what would happen if we say that environmentalism is a natural part of atheism, too. Will there be a freak out again? Will the Libertarians finally go away? Or will a majority happily recognize it as a necessary component of an ethic that tries to build a sustainable society on a world that is not propped up by magic?

So you’re all here to agree or argue with me, to consider the ramifications, to suggest where we’re going to hit a brick wall. And maybe we can also talk about why religion is a poor foundation for a responsible stewardship of the planet.