What I taught today: Nuffin’!

Nothing at all! I gave the students an exam instead! While I got a plane and left ice-bound Morris to fly to Fort Lauderdale, Florida! Bwahahahahahaha!

Sometimes it is so good to be the professor. And if ever you wonder why my students hate me with a seething hot anger, it’s because I’m such an evil bastard.

Here’s what they have to answer.

Developmental Biology Exam #1

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: We’ve discussed a few significant terms so far: preformation, mosaicism, regulation, epigenesis. Explain what they mean and how they differ from each other. Can we say that any one of those terms completely explains the phenomenon of development, or is even a “best” answer? Use specific examples to support your argument.

Question 2: Tell me about the lac repressor in E. coli and Pax6 in Drosophila. One of those is called a “master gene” — what does that mean? Is that a useful concept in developmental genetics, and is there anything unique to a gene in a multicellular animal vs. a single-celled bacterium that justifies applying a special concept to one but not the other?

Question 3: Every cell in your body (with a few exceptions) carries exactly the same genetic sequence, yet those cells express very diverse phenotypes, from neurons to nephrons. The easy question: explain some general mechanisms for how development does that. The hard part: answer it as you would to a smart twelve year old, so no jargon or technical terms allowed, but you must also avoid the peril of being condescending.

Wait…I’m going to have to fly back to Morris on Sunday, and then I’m going to have to read and grade all those essays! Aargh — they’re going to get their revenge!

What I taught yesterday: master genes and maps

On Wednesdays, I try to break away from the lecture format and prompt the students to talk about the science of development. We’re working our way through Sean Carroll’s Endless Forms Most Beautiful, and yesterday we talked about chapters 3 and 4.

Chapter 3 has an overview of basic molecular biology — transcription and translation, that sort of thing — and since these are junior and senior students who’ve already heard that a few times, we skipped right over it and they explained to me what master genes are, with specific examples of homeobox-containing genes like the Hox genes and Pax6. They caught on fast that what we call master genes are actually just transcription factors located high up in a regulatory hierarchy.

I think we also got across a less-than-naive idea of the evolution of Hox genes. There is a recognizable, conserved motif in each of these genes, but the proteins are far more than just their homeodomains, and can exhibit considerable variation — necessary functional variation, because the expression of different Hox genes are going to have distinct morphological consequences.

Chapter 4 has a general theme of maps and geography — what does it mean for a cell to be in a particular position and to have a particular fate? We also get into details. This is a very fly-centric chapter, and we get a picture of early development in the fly and the specific patterning and positional organization in the early embryo of that organism, with an introduction to many genes we’ll be hearing much more about during the course of the term. We also got enough information on vertebrate development that I could ask them to play the compare and contrast game: what’s different and what’s the same in fly and mouse development? I’m trying hard to be the Reese’s Peanut Butter Cup of development in this class: it’s so easy to say, “they’re the same!” and focus on common molecular mechanisms, or to say “they’re different!” and talk about the numerous quite radical innovations between them (especially in the fly, which is a weird, highly fine-tuned machine for rapid robust development). I’m trying to get across that both statements are absolutely true, and they really taste great together.

Friday is their first exam. Next Monday, class will be an overview of nematode development, to prime them for the lab exercises for the next two weeks which will be all about photomicrography of worm development and behavior, and also more details about early fly embryology to get them prepared for a couple of weeks of nothin’ but flies. I also warned them that next Wednesday we’ll be discussing chapter 5 in Carroll, just chapter 5, because I’ve found in the past that that’s usually the brain-clogger chapter, with all its talk of boolean logic and gates and circuits.

How about if we stop pretending religion is an important academic subject at all?

I was asked to promote this petition to stop forced religious indoctrination in Greek schools, and I support it and you should go sign it if you agree.

Greek public schools hold daily Orthodox prayer, schedule regular church visits as well as mandate the taking of a “religious studies” class every year. However, Greek law also allows students to opt out by submitting a simple form signed by their guardian if they are under 18. Unfortunately, many school administrators are either unaware or simply refuse to allow the exemption and ministry officials are not holding them to account.

The latest case is Stavros Kanias, School Principal in the Glika Nera suburb of Athens. Kanias is refusing to allow a middle school student to opt out even stating that his refusal is based on a desire to “follow the law of Christ”. Even though the required form has been submitted it is not being accepted. Many similar cases are often not publicized.

When Greek MP’s have raised the question in parliament, the Education Minister has simply reiterated the procedure and deferred to lower ministry officials.

But I do have one reservation: it doesn’t go far enough. It’s a good idea to give students the ability to opt out of religious instruction, but why is religious instruction in any school any where?

I’ve usually taken a pragmatic perspective on this issue before. We don’t have much choice to but to give way on minor compromises in school curricula, and this is often an easy one: if religion is taught comparatively and objectively, it’s a good tool for breaking dogma. I can’t get too irate at a school offering a “world religions” class, because I know that would be the first step towards atheism for the students (for the same reason, though, I’m suspicious. Our opponents aren’t morons, and they’d know this too — I suspect them of plotting to smuggle orthodoxy into the classroom under cover of objectivity, and for instance, knowing that a local priest of the dominant cult will often offer to teach the course.)

But here’s my major problem. It’s a useless subject. And no, I’m not one of those elitist yahoos who thinks art and philosophy are useless subjects, rejecting anything that isn’t a hard science; I mean, it is literally useless, distracting, and narrow. If right now students were getting an hour a week in a “religious studies” class, I think they’d be far better served by getting an hour a week for anthropology, or philosophy, or poetry…or sure, more math.

I know what the usual argument would be: but every culture has a religion of some sort, it’s a human universal, people find it important and we ought to acknowledge it. So? Every human culture has parasites and diseases, so why don’t we have a mandatory weekly course in parasitology? It would be far more entertaining, interesting, and useful. What wouldn’t be quite so useful, though, is a course taught from the perspective of the malaria parasite, praising its role in shaping human civilizations for thousands of years, which is pretty much equivalent to what kids get in a “religious studies” class right now.

I don’t think religion will ever disappear, but I’ll be satisfied when seminaries and theology departments all shut down everywhere for lack of interest.

Need more paleontological women

The latest issue of Priscum, the newsletter of the Paleontological Society (pdf), has an interesting focus: where are the women in paleontology? They have a problem, in that only 23% of their membership are women, and I hate to say it, but the stereotype of a paleontologist is Roy Chapman Andrews — most people don’t imagine a woman when they hear the word paleontologist (unjustly, I know!)

On the other hand, 37% of the paleontology presentations at the GSA were by women. They’re there, but they aren’t getting far up the ladder of success. They’re not achieving high status positions within the society at the same rate as men, and then there’s this skewed distribution:

genderdisparity

So women are over-represented in the student category, but under-represented in the professional category. The optimistic way to look at that is that there is an opportunity for change, and maybe that wave of current students will move on up and change the distribution ten years from now. More pessimistically, it suggests that there could be barriers that preferentially block the advancement of women in the field; if the distribution doesn’t change in the next decade, that says that there were more frustrated women who left the discipline than men.

So why would women experience greater barriers to advancement? It isn’t about evil men keeping the women down, and I wish we could clear away the resentment some men express when they hear that there are greater obstacles to women’s progress — too often I hear angry responses to accusations of academic sexism taken personally, as if it were a statement of personal criminality. It’s a product of the system, and men and women mostly contribute to it by neglect and an unwillingness to change the status quo.

What I most often see is statements of fact that I don’t disagree with, such as that women on average have lower publication rates than men, but the problem is that these advocates of blaming the inherent properties of women for their failure don’t think it through. Why do women have lower publication rates? Are there structural/cultural/professional properties that conflict and cause problems that men don’t see? And most importantly, if there are, what can we do to correct those institutional biases? Just saying that “women publish less” begs the question.

This article had a very helpful diagram illustrating the contributing factors, taken from a paper discussing a similar problems among evolutionary biologists.

womeninscicycle

Right there in the center is issue of lower publication rates in women, but it looks deeper at consequences and causes. Follow the arrows. I’ve seen similar charts before — it looks a heck of a lot like an extinction vortex, a self-perpetuating cycle of defeat.

Another article in the same newsletter describes the distribution of the leadership of the Paleontological Society. It shows steady improvement in the proportion of women in the society leadership, but still, most of the executive positions have been held by women less than 10% of the time. The more recently the position was created, the higher the proportion of women. I also noticed one outlier: 67% of the Education and Outreach Coordinators (a very new position) have been women. That’s another stereotype, too, that women are better suited to teaching. Look at the diagram above: going into teaching is also one of the factors that hurts research productivity, and as long as research is more highly valued than teaching, and teaching is considered ‘women’s work’, it’s going to skew representation of the sexes.

They have a proposal to correct the imbalance. Notice that it doesn’t involve simply declaring that they have equality of opportunity (which they don’t!) and doing nothing. Correcting these kinds of biases requires active intervention.

Societies are strengthened by incorporating diversity (of gender, of ethnicity, of abilities, of ideas, and of disciplines). As a society, we need to be aware of equity issues and take intentional steps to counteract imbalances. The recommendations below relate to increasing ALL types of diversity. So far, we have data on gender equity, but there are many other types of diversity we should work to improve. This set of recommendations applies to all of them.

Intentional nominations. Think about the excellent female colleagues you have. Now nominate at least one of them for a leadership position (we have several open this year!) or a society award. All Society positions are open nominations, so please share your ideas!

Mentoring. Establish professional relationships with young women in paleontology (students and early career professionals). Spend some extra time at poster sessions meeting some of our student members. Encourage women to submit abstracts for oral presentations. Established women, share your career stories and experiences.

New initiatives. PS Council is dedicated to increasing equity for all types of diversity in our membership. Please share any ideas you may have for initiatives with [the author] or other council members—now and in the future.

Today an egg, tomorrow the world!

Man, you give them a millimeter, they take a centimeter. We had a successful fundraiser for the Kasese Humanist School — they just wanted a chicken coop and a flock of chickens so the kids would start the day with good nutrition. And they got that. Here are these kids, grateful for an egg.

But that isn’t enough. These kids want more. Come on, guys, you’ve got an egg…it’s not enough?

No, it’s not. Now they want to own their school, which is currently on some leased property. So they’ve started another fundraiser to pay for a small plot of land — they need $7000.

I don’t know about this. First they’re getting a whole egg, and next they’re getting a school…I expect some day they’re going to be posting videos of kids graduating and getting diplomas and going off to college…scary stuff.

If you want to encourage that kind of ambition, go ahead, donate a few dollars.

Godless goals, godless progress

Debbie Goddard has a most excellent post on Skepchick (she should write more!), declaring that the atheist movement should care about poverty.

Unless we address the classism and broaden the elitist culture of the atheist movement, the underprivileged students in the Philadelphia public school classrooms that I’m familiar with and in the South Los Angeles classrooms that Sikivu Hutchinson works in will continue to be marginalized and will never have access to the “enlightened” educational opportunities that the movement too often takes for granted.

Some would say it’s not the movement’s responsibility to address poverty and public education. I disagree. This is a movement; we want the world to be a better place than it is now. We want to reduce suffering and foster a just society. If we agree there’s no cosmic justice system and there’s no reward for suffering after we die, we need to effect change here, now, in this life, in this world, for as many people as we can reach. Education is key for change to occur.

You won’t be surprised to learn that I agree completely, and that education is an excellent priority for atheist communities to pursue. She cites the Black Skeptics article I mentioned earlier today, in which they are looking for donations for their First in the Family Humanist Scholarship. It’s a worthy cause, and I donated…you should too, if you can.

Every effort to improve human knowledge is a contribution to atheism, so anything you can do will help; teach a child, donate books to your local library, volunteer at your elementary school. It’s our cunning godless scheme to make the world a better place.

What I taught today: Axis specification

We began today with chocolate. Always a good thing at 8am, I think — so I brought a candy bar to class. Then I told the students that I loved and respected them all equally and that they all had equal potential, but that I was going to mark just one person as special by giving them that candy bar*. So I asked them how I could decide who should get it, telling them right off that dividing it wasn’t an allowed solution, and that yes, this could be an openly unfair process.

There were lots of suggestions: we could do it by random chance. I could throw it into the middle of the room and let them fight over it. We could analyze everyone’s DNA and give it to the most average person…or the most genetically unusual. I could just give it to the first person to raise their hand, or the person closest to me, or the person farthest from me. We could have a competition of some sort, and the winner gets it. I could give it to the person who wants it most, or who needs it most.

The point I was making is that this is a common developmental problem, that you have a potentially uniform set of cells and that somehow one or a few have to be distinguished as different, and carry out a different genetic program than another set of cells. One cop-out is to invoke mosaicism: that is, they aren’t uniform, but inherit different sets of cytoplasmic determinants that make them different from the very beginning, but that even in that case, these determinants aren’t detailed enough to specify every single cell fate in most organisms. Even with an initial prepattern, you’re eventually going to end up with a field of cells, like the dorsal side of the fly wing, and within that uniform field, some cells will have to be programmed to be epithelial, others to be bristles, others to be neurons. And that means that in every organism, even the most classically mosaic, you’ll reach a point where cells have to process information from their environment and regulate to build differential structures.

And with that I went on to talk about some animals that were judged as being mostly mosaic in character: molluscs, tunicates, echinoderms, and nematodes. Even here, these animals all required complex molecular interactions to build their embryos.

For example, I’d earlier used echinoderms as classic examples of regulative development. You can dissociate them at the 4-cell stage and each blastomere can go on to build a complete embryo. But at the 8-cell stage, when the cleavage plane separates an animal half from a vegetal half, that’s no longer true: the top four cells when isolated are animalized, forming only a ciliated ball, while the bottom four cells are vegetalized, only making a static blob with a bit of a skeleton inside. Clever experiments can quantitatively juggle these cells around, removing just the bottom 4 cells (the micromeres) at the 16-cell stage, or assembling composite embryos with different ratios of the different tiers of cells, and get different degrees of development. Even when you’re discussing an organism in which you’d call the pattern of development mosaic, it absolutely depends on ongoing cell:cell signaling at every step, and the final form is a consequence of interactions within the embryo. It’s a mosaic-regulative continuum.

I also described very superficially the work of Davidson and Cameron on specification events in echinoderms. These interactions can be drawn as a kind of genetic circuit diagram, where what you’re seeing is the pattern of genes being switched on and off. We can describe a cell type as the output of mappable gene circuitry, and we can even identify modules of networks of genes associated with a particular kind of cell, and that we can also see a limited number of genes that mediate interactions.

Next week I promised to start going into more detail, when we start talking about early fly development and axis decisions. The next class we’re actually going to switch gears a bit and discuss Sean Carroll’s Endless Forms Most Beautiful.

Slides used in this talk (pdf).

*Yeah, I lied again. I brought enough candy bars for everyone, and after we’d generated a list of ways to share just one, I gave them to everyone. They’ll never trust me again.