What I taught today: induction in worms, early development in flies

Today was the due date for the take-home exam, which meant everything started a bit late — apparently there was a flurry of last-minute printing and so students straggled in. But we at last had a quorum and I threw worms and maggots at them.

The lab today involves starting some nematode cultures so I gave them a bit of background on that. They’re small, transparent hermaphrodites that can reproduce prolifically and will be squirming about on their plates this week. They’re models for the genetic control of cell lineage and also for inductive interactions: I gave them the specific example of the development of the vulva, in which a subset of cells in close proximity to a cell called the anchor cell develop into the primary fate of forming the walls of the vulva, cells slightly further away follow a secondary fate, forming supporting cells, and cells yet further away form the hypodermis or skin of the worm. I had them make suggestions for how we could test that the anchor cell was the source of an inductive signal, and yay, they were awake enough at 8am to propose some good simple experiments like ablation (should lead to failure of the vulva to form) or translocation (should induce a vulva in a different location). I also brought up genetic experiments to make mutants in the signal gene, in the receptors, and deeper cell transduction pathways.

All those experiments work in the predicted ways, and I was able to show them an epistasis map of the pathways. Two lessons I wanted to get across were that we can genetically dissect these pathways in model organisms, and that when we do so, we often find that toolkit Sean Carrol talks about exposed. For instance, in the signal transduction pathway for the worm vulva, there are some familiar friends in there — ras and raf, kinases that we’ll see again in cancers. And of course there are big differences: mutations in ras/raf in us can lead to cancer rather than eruptions of multiple worm vulvas all over our bodies, because genes downstream differ in their specific roles.

Then we started on a little basic fly embryology: the formation of a syncytial blastoderm, experiments with ligation and pole plasm manipulation in Euscelis that led to the recognition of likely gradients of morphogens that patterned the embryos. From there, we jumped to the studies of Nusslein-Volhard and Wieschaus that plucked out the genes involved in those interactions and allowed whole new levels of genetic manipulation. As the hour was wrapping up, I gave them an overview of the five early classes of patterning genes: the maternal genes that set up the polarity of the embryo; the gap genes that read the maternal gene gradient and are expressed in wide bands; the pair-rule genes that respond to boundaries in gap gene expression and form alternating stripes; the segment polarity genes that have domains of expression within each stripe; and the selector genes that then specify unique properties on spatial collections of segments.

And that’s what we’ll be discussing in more detail over the next few weeks.

Slides used in this talk

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.