Skepchick is a little late on this one

Skepchick has a quickie up about Dr Ben Carson’s commencement speech at Emory University, and specifically about the vocal opposition to bringing a creationist like Carson to speak. Only thing is, that was the 2012 commencement address — it’s a done deal. Carson did speak last spring, and the good news is…he’s a terrible boring speaker. I really, really hope the Republicans continue to try and make him a nominee.

Here’s his speech. Good if you’re suffering from insomnia, or some terrible medical condition that can only be cured with supplemental platitudes.

As someone who has sat through many commencement speeches, I am unsurprised. Most are entirely forgettable. It’s going to be interesting to see how UMM’s commencement speaker fares next month: it’s Al Franken.

How I spent the last few days

I am sad to say I missed the American Atheists 2013 National Convention — it sounds like it was a blast, but I was booked up with a series of talks out in lovely warm sunny Seattle. Here’s what I’ve been up to.

On Wednesday, I talked to Seattle Atheists on “Moving Atheism Beyond Science”. I argued that modern atheism is built on the twin pillars of anti-religion and science, and not that there’s anything wrong with either of those, but that we have to have a wider foundation. In particular, I defied the recent trend to broaden science to encompass morality — I see that more as a conservative effort to refuse to step out of our comfort zone of science to consider philosophy and ethics — and most of the talk was a review of the ways science has failed to support a moral standard. Science has a definite place of importance, but let’s stop using it as our sole hammer.

Then I attended Norwescon, a science-fiction convention. People give me weird looks when I say I’m going to a con as a scientist/educator — but really, this is another example of stepping out of our comfort zones and reaching out to a different population of people…and SF people are a very receptive audience for science talks. So here are the sessions I was up-front and talking (there were others where I just sat back with the audience, of course).

Evo-Devo: More than a cool band name. This one was cool and right on my interests. I shared the panel with Annie Morton, a local ecologist, Jim Kling, a science journalist, and Dr Ricky, a scientist and also author of a food blog, Science-Based Cuisine. I started off by giving a definition I’d been asked to give on Twitter: Evodevo: Primacy of regulatory mutations in the evolution of form in multicellular organisms. I know, it’s much narrower than the standard definition which emphasizes comparative molecular genetics, but I was trying to summarize the current focus. And then we went back and forth on the details.

The Anthropogenic Extinction event. Somehow, I ended up on a series of depressing panels. I shared this desk with Annie Morton again, and Kurt Cagle. Short summary: we’re doomed. My final statement was that one basic rule is that you don’t shit in your own nest, and now that we’re a global species, we apparently have forgotten it.

Bullies Still Suck: Why We Don’t Just Get Over It. Oh, jeez. The most depressing panel ever. I was on it with Mickey Schulz (Geek Girls Rule!) and Maida “Mac” Cain. I think I was there to represent targets of online bullying, but here’s the deal: it was attended by a large number of SF con nerds and geeks who could give us all lessons on what real bullying is like. I didn’t have to say much at all: the audience spoke out with testimonials about their lives as four-eyed nerds, gay people, trans women, Asperger kids, “sluts” so-called, and rape victims. I think my main job here should have just been to shut up and listen.

It’s the End of the World As We Know It, with Gregory Gadow, Peter Blanton, Russell Campbell, and Dr Ricky. We were supposed to talk about our favorite doomsday scenarios. I don’t have one. I did say I thought all the emphasis in the popular press on big explosions and cosmic collisions and such was egocentrism, that that’s not how most extinctions occur. I gave the example of the Heath Hen, a chicken-like bird that was common on the eastern seaboard at the time of the European colonization, and that gradually was reduced to a single isolated population on Martha’s Vineyard by habitat destruction and hunting, and when it was down to the last few hundred animals in the 19th century, efforts were made to give it a sheltered sanctuary. The population briefly rose to a few thousand individuals before a fire killed many, then a storm killed more, and then a disease spread from turkey farms to kill even more, reducing them to 7 individuals, mostly male, and the last lonely bird died in 1932. That’s what we should expect. No grand spectacular drama, we’re most likely to flicker out with a dismal whimper.

Blinded by Pseudoscience. I wasn’t suppose to be on this one, but Dr. Ricky asked me to get on the stage with Janet Freeman-Daily, Gregory Gadow, and Ro Yoon. We talked a lot about cancer quackery, especially the Burzynski fraud, and tried to deliver some suggestions about how to detect when you’re being lied to: too good to be true promises, demands for money up front, lack of scientific evidence, etc.

Designer Genes. Gregory Gadow was the moderator, and it was largely a discussion between me and Edward Tenner…and we pretty much agreed on everything. I think the theme was unintended consequences: sure, we can and will be able to do amazing things with somatic and germ line gene therapy, but trying to do this with complex systems is likely to have all kinds of unexpected side effects. Correcting single gene defects is one thing, but ‘improving’ the human race is a far more complex problem that isn’t going to be easily accomplished.

Remedial Exobiology, with Annie Morton and Dame Ruth. This one was very well attended and less depressing! At a science fiction convention, there were a lot of authors in the audience who are very interested in the topic of implementing good biology in their stories (sorry, but I said that there were almost no science fiction stories that addressed biology competently, and we also snickered at James Cameron a bit). I tried to be fair and give shortcuts: I said imagination is good, you don’t have to master all of biology, but instead of just starting with bipedal anthropoids and building a new alien on that body plan, at least browse through the available and highly diverse morphologies present in other lineages on this planet, and build on that. One person in the audience also recommended this book, Eighth Day Genesis: A Worldbuilding Codex for Writers and Creatives, as a tool for inspiring science-based creativity.

And now I’m winding down and getting ready to fly home and resume teaching biology in Minnesota again. I encourage all science educators to stretch out and try talking about their favorite topics in different venues: it’s how we expand the relevance of science!

What I taught today: O Cruel Taskmaster!

I’m out of town! Class is canceled today! But still, my cold grip extends across the Cascades, over the Palouse, the Rockies, the Dakota badlands, the old homeland of the American bison, the the great farms of the midwestern heartland, to a small town in western Minnesota, where I crack the whip over a tiny group of hardworking students. They’ve been mastering the basics of timelapse video microscopy in the lab this week, I hope, and will be showing me the fruits of their labors on Monday. I’m also inflicting yet another exam on them over the weekend. Here are the questions they are expected to address.

Developmental Biology Exam #2

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 the claims of evo devo is that mutations in the regulatory regions of genes are more important in the evolution of form in multicellular organisms than mutations in the coding regions of genes. We’ve discussed examples of both kinds of mutations, but that’s a quantitative claim that won’t be settled by dueling anecdotes. Pretend you’ve been given a huge budget by NSF to test the idea, and design an evodevo research program that would resolve the issue for some specific set of species.

Question 2: Every generation seems to describe the role of genes with a metaphor comparing it to some other technology: it’s a factory for making proteins, or it’s a blueprint, or it’s a recipe. Carroll’s book, Endless Forms Most Beautiful, describes the toolbox genes in terms of “genetic circuitry”, “boolean logic”, “switches and logic gates” — he’s clearly using modern computer technology as his metaphor of choice. Summarize how the genome works using this metaphor, as he does. However, also be aware that it is a metaphor, and no metaphor is perfect: tell me how it might mislead us, too.

Question 3: We went over the experiment to test the role of enhancers of the Prx1 locus which showed their role in regulating limb length in bats and mice. Explain it again, going over the details of the experiment, the results, and the interpretation…but without using any scientific jargon. If you do use any jargon (like “locus”, “regulation”, “enhancer”), you must also define it in simple English. Make the story comprehensible to a non-biologist!

Yeah, you don’t have to tell me. I’m evil.

What I taught today: those oddball critters, the vertebrates

We’ve been talking about flies nonstop for the last month — it’s been nothing but developmental genetics and epistasis and gene regulation in weird ol’ Drosophila — so I’m changing things up a bit, starting today. We talked about vertebrates in a general way, giving an overview of major landmarks in embryology, and a little historical perspective.

We take a very bottom-up approach to studying fly development: typically, fly freaks start with genes, modifying and mutating them and then looking at phenotype. Historically, vertebrate embryology goes the other way, starting with variations in the phenotype and inferring mechanisms (this has been changing for the last decade or two; we often start with a gene, sometimes from a fly, and use that as a probe to hook into the genetic mechanisms driving developmental processes). What that means is the 19th and early 20th century literature on embryology is often comparative morphology, looking at different species or different stages and trying to extract the commonalities or differences, or it’s experimental morphology, making modifications (usually not genetic) to the embryo and asking what happens next. Genes were not hot topics of discussion until the last half of the 20th century, and even then it took a few decades for the tools to percolate into the developmental biologists’ armory.

And much of 19th century embryology went lurching down a dead end. We talked about Haeckel, the grand sidetracker of the age. There was a deep desire to integrate development and evolution, but they lacked the necessary bridge of genetics, so Haeckel borrowed one, his theory of ontogenetic recapitulation. A theory that quickly went down in flames in the scientific community (jebus, Karl Ernst von Baer had eviscerated it 50 years before Haeckel resurrected it). We actually spent a fair amount of class time going over arguments for and against, and modern interpretations of phylotypy — it isn’t recapitulation, it’s convergence on a conserved network of global spatial genes that define the rough outlines of the vertebrate body plan.

Finally, I gave them a whirlwind tour of basic developmental stages of a few common vertebrate models: frog, fish, chick, and mouse. We’re going to talk quite a bit about early axis specification events in vertebrates (next week), and gastrulation (probably the week after), so I had to introduce them to the essential terminology and events. I think they can see the fundamental morphological events now — next, β-catenin and nodal and Nieuwkoop centers and all that fun stuff!

(Today’s slides (pdf))

What I taught today: molecular biology of bat wings

Hard to believe, I know, but this class actually hangs together and has a plan. A while back, we talked about the whole cis vs. trans debate, and on Monday we went through another prolonged exercise in epistatic analysis in which the students wondered why we don’t just do genetic engineering and sequence analysis to figure out how things work, so today we reviewed a primary research paper by Chris Cretekos (pdf) that teased apart the role of one regulatory element to one gene, Prx1, in modifying the length of limbs. It’s a cool paper, you should read it. It’s kind of hard to replicate the teaching experience in a blog post, though, because what I did most of the hour was ask questions and coax the students into explaining methods and figures and charts.

I’m afraid that what you’re going to have to do is apply for admission to UMM, register for classes, and take one of my upper level courses. I always have students read papers direct from the scientific literature, and then I torture them with questions until they extract meaning from them. It’s fun!

Although…it would also be cool to have a scientific-paper reading and analysis session at a conference, now wouldn’t it? Especially if it could be done over beer.

What I taught today: farewell to flies (for a while)

A good portion of what I’ve been teaching so far uses Drosophila as a model system — it’s the baseline for modern molecular genetics. Unfortunately, it’s also a really weird animal: highly derived, specialized for rapid, robust development, and as we’ve learned more about it, it seems it has been layering on more and more levels of control of patterning. The ancestral system of establishing the body plan was far simpler, and evolution has worked in its clumsy, chance-driven way to pile up and repurpose molecular patterning mechanisms to reinforce the reliability of development. So I promised the students that this would be the last day I talk about insects for a while…we’ll switch to vertebrates so they can get a better picture of a simpler, primitive system. What we’ll see is many familiar genes from flies, used in some different (but related!) ways in vertebrates.

But today I continued the theme of epistatic interactions from last week. Previously, we’d talked about gap genes — genes that were expressed in a handful of broad stripes in the early embryo, and which were regulated in part by the even broader gradient of bicoid expression. The next level of the hierarchy are the pair rule genes, which are expressed in alternating stripes — 7 pairs of stripes for 14 segments.

First point: notice that we are seeing a hierarchy, a descending pattern of regulatory control, and that the outcome of the hierarchy is increasing complexity. One gene, bicoid sets up a gradient that allows cells to sense position by reading the concentration of the gene; the next step leverages that gradient to create multiple broad domains; and the pair rule genes read concentrations of gap genes and uses the boundaries between them to set up even more, smaller and more precise domains of stripes that establish the animal’s segments.

This is epigenesis made obvious. The 14 stripes of the pair rule genes are not present in the oocyte; they emerge via patterns of interactions between cells and genes. The information present in the embryo, as measured by the precise and reproducible arrays of cells expressing specific genes, increases over time.

So part of the story is hierarchy, where a complex pattern at one stage is dependent on its antecedents. But another part of the story is peer interaction. Cells are inheriting potentials that are established by a cascading sequence of regulatory events, but in addition, genes at the same approximate level of the hierarchy are repressing and activating each other. We can tease those interactions apart by fairly straightforward experiments in which we knock out individual pair rule genes and ask what the effect of the loss has on other pair rule genes. I led the students through a series of epistatic experiments which started out fairly easy. Knock out a pair rule gene that is expressed in odd numbered parasegments, for instance, and it’s complement, the pair rule gene expressed in even parasegments, expands its expression pattern to fill all segments. Sometimes.

Some of the experiments reveal simple relationships: hairy suppresses runt, and runt suppresses hairy. That makes sense. They have mutually exclusive domains, so it’s no surprise that they exclude each other. But then we looked at other pair rule genes which are expressed in patterns slightly out of phase from the hairy/runt pair, and there the relationships start getting complex. Genes like fushi tarazu are downstream from all the others, and their effects are straightforward (their loss doesn’t disrupt the other pair rule genes), but genes like even-skipped have much messier relationships, and the class was stumped to explain the results we get with that deletion.

So I asked them to come up with other experiments to tease apart these interactions. I was somewhat amused: when I think along those lines, I come up with more genetic crosses and analyses of expression patterns — I think about regulatory logic and inferring rules from modifications of the pattern. Students nowadays…they’re so much more direct. They want to go straight to the molecular biology, taking apart the genes, identifying control elements, building reporter constructs to see gene-by-gene effects. I felt so old-fashioned. But we also had to talk about the difficulty of those kinds of experiments, and that often the genetic approach is better for building a general hypothesis that can be fruitfully tested with the molecular approach.

Then we stopped — we’ll come back to flies later, and start looking at some specific subsets of developmental programs. Next, though, we’re going to take a big step backward and look at early events in vertebrates and progress through that phylum until we see how they build segments. I’m hoping the students will see the similarities and differences.

Slides for this talk (pdf)

Sadly, it’s International Women’s Day

It’s that day when we’re supposed to celebrate the accomplishment’s of women. I say “sadly,” because unfortunately there are way too many people out there who would rather sneer at and diminish women’s status in the world.

Case in point: on twitter, I ran across this lovely tweet from one of those repugnant slymepitters.

On #IWD remembered the nearly 0 wimmin – Nobels in science, highbrow art, chess GMs, great standups, but 100s of pop-culture hos #ftbullies

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Yes. Let’s remember those women.

Let’s remember Lise Meitner, Hilde Mangold, Chien-Shiung Wu, Rosalind Franklin, and Jocelyn Bell — who were all well-qualified (men won the prizes for work equivalent to what they did, instead) to win a Nobel but didn’t get one.

Rather than 0 women, perhaps we should remember Marie Curie and Maria Goeppert Mayer, who won Nobels in physics; Irène Joliot-Curie, Dorothy Crowfoot Hodgkin, and Ada E. Yonath in chemistry; Barbara McClintock, Carol W. Greider, Christiane Nüsslein-Volhard, Elizabeth H. Blackburn, Françoise Barré-Sinoussi, Gertrude B. Elion, Gerty Cori, Linda B. Buck, Rita Levi-Montalcini, and Rosalyn Yalow, in physiology or medicine. Clearly women are not intrinsically incapable of scientific work at the highest levels. Of those whose work I’m familiar with in detail, I have to tell you that McClintock blows me away with the stunning brilliance of her abstract reasoning — I know of no other male scientist whose work is at all comparable (that of course is a matter of taste!)

The relatively lower frequency of women recieving Nobels is not something any man should take pride in; what it really indicates is that we’ve been shortchanging half the human population, depriving them of opportunities to excel. Wait — we’ve been doing worse than shortchanging women; we’ve been depriving all of humanity of the potential in those minds. This pattern of discrimination against women has hurt us all.

Let’s not forget also all the people, men and women alike, deprived of opportunities because of their race or class — deprived by the kind of endemic bigotry that would, for instance, denigrate an entire group of people as “pop-culture hos”. And it’s not just science — it was good of our petty MRA to remind us that we’ve also lost their contributions to art and theater and games.

That’s what I think of everytime some bigot crows about the absence of some group of people from some field of endeavor — it’s a reminder of all that we’ve lost to selfish stupidity.

My university in the news!

Now if only it were good news. It seems we’re the victim of bureaucratic excess.

College administrators have found an interesting new way to strike it rich: quitting their jobs. Upon leaving his role as executive vice president of NYU for a job with Citigroup in 2006, Jacob J. Lew (the current Secretary of the Treasury) took a $685,000 bonus from the university. Harold S. Koplewicz, an executive at the NYU Medical Center, got a $1.2 million severance after choosing to leave voluntarily. Given that NYU’s tuition and fees are among the highest in the nation, we’re curious how students who took out hundreds of thousands of dollars in loans feel about their money going towards generous benefits and severance packages for administrators.

At least NYU is a private institution, so tax dollars are not spent to cover its inflated costs. As the New York Times notes, public universities are just as guilty of letting a bloated and inefficient administration drive up tuition costs. The University of Minnesota employs 19,000 administrative officials employees, and administrative personnel account for 24 percent of its total payroll, compared with only 20 percent in 2001. At Purdue, the number of administrative employees grew by 54 percent in the last decade.

Overall, the number of administrators hired by colleges and universities increased 50 percent faster than the number of instructors hired between 2001 and 2011, according to the U.S. Department of Education.

We’ve felt the pain down here in the trenches, too. Our core biology curriculum was disrupted a bit by the reluctance of our administration to hire replacement faculty — they saved a few pennies by bringing in temporary faculty as replacements and deferring filling tenure track lines. The replacements were good people, but when you’ve got students coming up through a curriculum pipeline, you really want stability and continuity at the base.

The good news, though, is that the blockages have been uncorked and we’re finally expanding our biology faculty from 8 to 9 — a big boost at a small college.