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.

It’s Not Just the Internet. It Never Has Been.

What Emily Finke says:

“Oh, the anonymity of the internet makes people behave badly!”

“If we just used real names, there people wouldn’t be as vicious.”

“Oh, that’s just 20-something guys in internet chatrooms. That’s how they all are.”

On the contrary, the viciousness we see, isn’t just a side effect of the internet. It’s a side effect of our culture.

No, I would go beyond that. It isn’t a side effect of our culture. It *is* our culture.

Why would I ever say this? I mean, everyone knows that those anonymous trolls on reddit would *never* act like that in the real world. It’s the structure of the internet that allows them to be assholes. Everyone knows that if we just avoid the problematic sites, like reddit, or the skeptics movement, or, well, anywhere else online, we wouldn’t have to deal with this.

Bullshit.

People do act like that in the real world.

 

(If you don’t know Emily’s blog, you ought to. She doesn’t post often, but what she does post is really good. This one from last year still gets me.)

Here I Stand; I Can Do No Other

I weigh in on Google Glass at KCET.

The gist:

Some of us come out to the desert to escape the Panopticon that life in the city already is, increasingly. In Los Angeles, Google Glass might be just one more increment of invasion in a landscape already thoroughly colonized by surveillance cameras, red light cameras, random private webcams, smart phone videographers and other such prying eyes. But there are places out here that don’t even have 4G yet. In fact — and you might want to sit down here and swallow that mouthful of coffee — there are some places out here where even the 3G coverage is spotty. We are in the back of beyond here in much of Eastern California.

And we like it that way, mostly.

So by all means, come on out and visit the desert. Bring your recording equipment, whether it’s a shoulder-mounted Steadicam or this latest bit of geek lust from Google sitting on your face. Document your hike. Record that coyote begging for sandwiches. Take video of that gorgeous desert bloom backlit by sunrise. The desert needs all the documentation it can get.

But if you’re talking to me, take that Google Glass off and put it away. If I’m speaking in public — which I do from time to time, offering lectures and poetry readings and such — and see you’re in my audience wearing Google Glass and you haven’t cleared it with me first, I will stop what I’m doing and ask you to put it away or leave. If you’re at an adjacent cafe table facing me and recording in my direction, I will write something derogatory in Sharpie on a sheet of paper and hold it up. I may escalate from there. And I’m not alone.

Read the whole thing.

[Read more…]

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))

Speaking of terribly rude women…

Now Amina has disappeared.

The 19 year old Tunisian Amina who posted a topless photo of herself with the slogan “my body belongs to me, and is not the source of anyone’s honour” has disappeared. Most likely her family have kidnapped her and taken her to an unknown location, (earlier reports mentioned a psychiatric hospital). What’s clear is that they have removed all forms of communication from her so that she can no longer be reached.

Let’s have a discussion now about how impolitely exposing one’s breasts is a disproportionate response to the dudebros. She should have just had a quiet discussion in private with her imam.

Ars Technica weighs in on Adria Richards, and flaunts a double-standard

Here we go again. The Adria Richards story has settled into a couple of common themes, and Ars echoes the conventional wisdom. I’m very disappointed in this lazy editorial.

First, look at this nonsense:

Let’s start by spreading the blame where it’s deserved: on nearly everyone involved. The “Boy’s Club” mentality is thankfully no longer acceptable in tech, but it’s still common—some people have actually described tech to me as “men’s work.”

It’s no longer acceptable, but it’s common? Huh. Somebody didn’t think about what they were writing. We’ll just announce that the problem is nonexistent, while sweeping the reality of the situation aside.

But I’d like to point out something sneakier. Here’s the common message:

“Forking a repo” and “big dongles” must rank somewhere around “0.5: classless brospeak” on the seismic scale of harassing/menacing behavior toward women. While such sexually inappropriate comments are completely unnacceptable in professional settings (to many men as well as women), neither merits firing unless someone had a history of making unwelcome comments.

I think we all agree 100% that no one ought to have been fired over this incident. The major villains here are the two companies that used this event as an excuse to axe a couple of employees.

But notice what else everyone is saying: what the two guys did was trivial and minor, “‘0.5: classless brospeak’ on the seismic scale of harassing/menacing behavior toward women”. Keep that in mind for a moment. That kind of thing has been said a lot.

Yet these two men don’t get all of the blame. One recurring theme on message boards and chat rooms, including our own, is that while Richards had every right to report the behavior of the two men to conference organizers, snapping their photograph and posting it publicly to “Twitter shame” them was a step too far (speaking of a step too far, there are other, more repugnant recurring themes among commenters, too). They’re right; going public was not the only way Richards could get a relatively minor issue addressed. She could have confronted the two men or she could have gone straight to PyCon. Her actions only escalated the situation.

It’s a “relatively minor issue”. OK, let’s go along with that for a moment…let’s say it really was an inconsequential, negligible faux pas by the two guys. But if that’s the case, what is this bullshit?

…snapping their photograph and posting it publicly to “Twitter shame” them was a step too far…

Was it something to be ashamed of, or not? Was it a horrible, embarrassing thing to publicize, or was it a “relatively minor issue”? You don’t get to have it both ways. Either it was too damaging to make public, or it was a slight affront that shouldn’t seriously affect any of the participants — it was a minute impropriety that was perfectly reasonable to mention on a casual, conversational medium like Twitter.

This is what’s really pissing me off right now: the flagrant dishonesty of all these people having the vapors over someone posting a photo on Twitter and saying someone’s behavior was “not cool”. Jesus. Have they ever fucking used Twitter? It’s non-stop chatter — just today I’ve been accused of being a “Nazi” and of being “evil”. Please, Ars Technica, do your tut-tut routine right now over all the naughty people ‘Twitter shaming’ right and left. Please also express your sadness that thousands of tweets are going up right now ‘Twitter shaming’ Adria Richards in far more outrageous terms than “not cool.”

Are people seriously proposing that somehow Twitter should be policed for manners, and we should start wagging our fingers at people who dare to rebuke others via that medium? If so, half my correspondents are going to have to shut up. This is ridiculous. Richards’ comment was minor, was appropriate, and was addressing a real issue in a reasonable way.

And then there’s this:

In a blog post explaining the story in her own words, Richards wrote about how, over the course of the jokes, she moved from “I was going to let it go” to “I realized I had to do something.” The moment of decision came after seeing a picture of a young girl on the main stage who had attended a Young Coders workshop. “She would never have the chance to learn and love programming,” Richards wrote, “because the ass clowns behind me would make it impossible for her to do so.”

Clearly, this is hyperbole. These two guys weren’t going to prevent anybody from doing anything. Suddenly, a couple off-color jokes represented all the serious forces that can hold women back from tech careers. While denouncing bad behavior certainly has its place, proportion is important—and this approach to these jokes simply makes it harder to have a sincere discussion about misogyny and men’s/women’s issues in the workplace.

It’s only hyperbole if you misinterpret it. No, I doubt Richards thought these two guys were going to run up on the stage and slap awards off the podium and denounce the young girl being recognized. Richards was referring to a culture that considers those kinds of off-color remarks reasonable in a professional setting. Remember, “it’s still common”. That is what inhibits women from participating in these opportunities.

We’re living in a world where those off-color jokes are dismissed as “classless brospeak”, not worth making a fuss over, while someone tweeting a picture of someone engaging in “classless brospeak” is a disproportionate response, and “makes it harder to have a sincere discussion about misogyny and men’s/women’s issues in the workplace”.

But unwanted sexual innuendo doesn’t? Both men and women make jokes about sex, of course, and there’s a tricky line to be drawn between what’s appropriate and what isn’t, but one of the things I’m seeing all over the place is that in the conversation about where to draw the line, women are expected to shut up; that when they do speak up, however mildly, and say “not cool” or “guys, don’t do that”, boom, the guyverse explodes and denounces the damned uppity woman in either the most furious and violent terms possible, or with polite little suggestions that maybe they should be quieter next time.

But you know, the latter is almost as bad as the former. It’s the privilege of the majority to use politeness to maintain the status quo, while it’s a necessity for the minority to assert the right to offend.