What I taught today: Position and Polarity

You really can’t teach a class by lecturing at them…especially not an 8am class. But sometimes there is just such a dense amount of information that I have to get across before the students know what to ask that I have to just tell them some answers. My compromise to deal with this eternal problem is to mix it up; some days are lecture days, others are discussion days. And today was a discussion day.

I’ve been talking at them for the past two weeks, basically working to bring them up to a 1950s understanding of the field of developmental biology, with a glimmering of the molecular answers to come and some of the general concepts, so that they’re equipped to start thinking about the contemporary literature. So I had them read this paper before class:

Kerszberg M, Wolpert L (2007) Specifying Positional Information in the Embryo: Looking Beyond Morphogens. Cell 130(2):205–209.

And then today they got into small groups and tried to explain it to each other. I primed them by suggesting that they try to define the terms positional information, gradient, morphogen, and polarity, and mentioned that I was playing a dirty trick on them, giving them a paper to introduce a basic concept that at the same time was pointing out some of the difficulties and problems of the idea, so I expected them to also do some critical thinking and question the concepts.

So they went at it. It went well; they had some lively conversations going on, which I always worry won’t happen with early morning classes. I find it helpful to ask students to try to poke holes in an idea, rather than just recite by rote what the paper says — it sends them hunting rather than gathering.

Several students noted that having a simple continuum of a molecule begs the question of how that gets translated into many discrete cell types; why does having one concentration of a morphogen make a cell differentiate into a thorax, while a very slightly lower concentration means it differentiates into an abdomen? It’s all well and good to suggest that a couple of overlapping gradients can specify position, like laying out a piece of graph paper with coordinates on it, but it doesn’t explain how that gets translated into position-specific tissues. I was most pleased that several of them, while groping for an answer, related it to the lac operon in E. coli, and brought up the idea of thresholds of gene activation. Yay! That so sets up future discussions about early fly embryogenesis, where that is exactly the answer.

I think they also got the idea that an explanation for general specification of body parts, for example, may not apply for explaining polarity within a body part; we may have to think about some kind of hierarchy of regulation, where we progressively partition the embryo into smaller and smaller units, with different mechanisms at different scales. They might be catching on to the depths of the problems to come.

Another way the paper primed the students was that it very briefly introduces a whole bunch of specific molecules: dpp, bicoid, sonic hedgehog, activin. They got a very general idea of the broad roles these molecules play, all part of my devious grand plan. When we start talking about the details of how animals set up dorsal-ventral polarity, for instance, and dpp/BMP start coming up in more specific contexts, I want them to be familiar old friends — molecules they already knew casually and informally, and now see doing very specific things, and interacting with another set of molecules, which now also joins their circle of pals. Before I’m done with them, they’re all going to regard these developmental signals and regulators as part of their family!

Cafe Scientifique tonight, in Morris!

You Twin Cities folk will have to drive like maniacs to get here in time, but you can do it: I hear the roads are slick as glass so you can just slide all the way here. At 6pm we’re doing another science for the community event, this time with Michael Ceballos talking about biology and biofuels. I’ll be heading over in a little bit to set everything up — I get to be the emcee. It does mean I’ve got a long evening ahead of me, though, and I haven’t had a nap.

csbiofuels

Nitpicky terminology distinction

Minor point that I wanted to clarify for the benefit of all, since a student just brought it up to me.

When we take pictures of stuff we see on the microscope, it’s called photomicrography. We are taking photomicrographs, or photographs of microscopic object.

It is not microphotography. A microphotograph is a teeny-tiny little picture, a small picture of a larger object. You’d need a hand lens to see a microphotograph.

OK? Just a little peeve. You’ll sometimes see people using the two terms interchangeably. They are bad people who must be crushed immediately, their remains scuffed into the dust, and their names obliterated from all stelae and funerary urns.

I do photomicrography, and have never ever done microphotography (which is a real thing, it’s just not what microscopists do.) If you need help remembering the distinction, just remember my initials are PM, and I do PhotoMicrography. So you don’t get pissmisticated when you make a horrible gaffe in front of me.

(The student got it right, by the way, and so I allowed them to live.)

What I’m also going to teach today: a little image processing

My development class also has a lab. The last few weeks have all been teaching them how to get good optics on a research scope, and how to take photomicrographs with my PixeLink camera system. Today I’m going to show them how to appropriately process an image for publication, so they’ll learn a few digital enhancement tricks and a few ethical rules. I lay down a few laws about using image processing on scientific data:

What you must do to your image:

  • You must archive the original data and work with a copy. If I ask to see the original after you’ve enhanced the image up the wazoo, you better be able to show it.

  • You must document every step and every modification you make. You’re going to describe everything either on the image itself or in a figure legend; if this were to be published, you’d probably include it in the Methods section.

  • You must explain the scale and orientation of the image. The scale is usually shown by including a scale bar; orientation may be shown either by including annotations (text describing landmarks in the image) or an explanation in the figure legend, such as that it is a sagittal or horizontal section.

  • You must save the image in a lossless format, such as .png or .psd or .tiff. Do not save it in a lossy format like .jpeg, which can add compression artifacts.

What you may do to your image:

  • You may crop and rotate the image.

  • You may adjust the contrast and brightness for the whole image.

  • You may carry out simple enhancements, like applying a sharpening filter or unsharp masking, to the whole image…but remember, document everything!

  • You may splice multiple images together to produce a photomontage; you can also insert panels with enlarged or otherwise enhanced regions of the image, as long as it is absolutely clear what you’ve done.

What you may not do to your image:

  • You must not carry out selective modifications of portions of the image; you cannot sharpen the cell you care about and then reduce the contrast for other regions, for instance. You should not burn or dodge regions of the image.

  • No pixel operations or retouching: you are not allowed to go into the image and paint your data into existence!

We do a lot of this preliminary basic stuff because I run the course out of my research lab, rather than a student lab. I want to make sure they’re not going to break anything, and also that they know how to do good imaging, a skill they’ll find useful in other courses and in research (years ago when I taught this stuff, we’d also do black&white darkroom work — nobody does that any more, so now it’s all photoshop). The goal is to get them all able to churn out lovely photographic data, so later I can just hand them some nematodes or fruit fly embryos and tell them to do their own experiments and observations, just show me the pretty pictures when they’re done.

It’s a good life, being able to sit back and let students bring me gifts of biological beauty. I think they’ll also be posting some of these to their blogs.

What I taught today: gene regulation and signaling

Today was more context and a bit of a caution for my developmental biology course. I warned them that we’d be primarily talking about animals and plants (and mostly animals at that), but that actually, all of the general processes we’re describing are found in bacteria and other single-celled organisms — that in a lot of ways, microbiology is actually another developmental biology course. Yes, I went there: developmental biologists tend to be imperialists who see all the other sciences as mere subsets of the one true science. Of course, you could also take that as developmental biology being a synthetic discipline that steals bits and pieces from everywhere…

So the primary lessons today were reviews of stuff these students should have gotten in cell and molecular biology, with bits of biochemistry and microbiology thrown in. We talked about genes getting switched on and off, and the example I used was the classic: the lac operon in E. coli. What? You don’t know about it? It’s a beautiful system, in which the bacterium switches on the genes needed for digesting the sugar lactose only when the sugar is available in the environment. I showed this nice little 3 minute video:

Switching genes on and off? That’s development! It gets a little more intricate in multicellular animals, but all of the fundamental logic is right there in E. coli: activators and repressors, positive and negative feedback, the boolean logic of gene regulation. I also mentioned that when we’re reading Carroll’s Endless Forms Most Beautiful, he’s going to make a big deal out of exactly this kind of regulation, but I want them to remember that it’s not unique to butterflies or fruit flies or frogs, it’s a common theme in all kinds of diverse cells.

We then talked about cell signaling. How does a cell know which genes are supposed to be off and on? It interacts with its environment (as in the lac operon) or its neighbors to make decisions about activity. To illustrate that, we went through quorum sensing and biofilms — again, cell signaling is not unique to animal development, it was all worked out in principle in single-celled organisms. I gave them a little foreshadowing and mentioned that we’d be discussing Sonic Hedgehog and Notch and Delta later in the course, classic examples of signaling in multicellular systems, but in bacteria we have things like hapR and AHL signaling.

Finally, I raised the issue of a phenomenon we’ll be talking about on Wednesday: patterning. Why aren’t your arms growing from your hips, why don’t you have fingers on your feet instead of toes, why are your eyes paired and on the front of your head? Because there is positional information in the embryo that can be read by cells and tissues and lead to development of appropriate structures in their proper places. But once more, this is not unique to multicellular animals. A paramecium, for instance, is not a generic blob, but has a definite shape and orientation; it has organelles in predictable places, and is covered with a nearly crystalline lattice of cilia with specific axes of orientation. I showed them choanoflagellates and pointed out that these protists, representing a multicellular precursor, had a specific shape and a collar organ in a specific functional location: how do they know how to do that?

That’s the question we’ll be asking next. I warned them too that I won’t be lecturing at them on Wednesday, so they’d better have their morning coffee. I’m expecting them to read a review paper on positional information in embryos (pdf), and I’m going to make them explain it all to me for a change.

Slides for this talk (pdf)

For Wednesday:

Kerszberg M, Wolpert L (2007) Specifying Positional Information in the Embryo: Looking Beyond Morphogens. Cell 130(2):205–209.

#giantsquid time!

I’ve fired up the television and am tuned to the Discovery Channel. What is this godawful crap about rednecks and moonshine leading in to the documentary on the giant squid? It does not bode well.

Ooh, they’re teasing us with short clips right at the very beginning. Good start. Less “monster” talk would be welcome, and more biology and ecology would be welcome.

Boy, they really threw money at this project: multiple submersibles, multiple film crews, cameras all over the place. Also infrared lighting, which accounts for the appearance of some of the video previews.

I would like to know what the recipe for that gloppy squid lure Steve O’Shea is mixing up. He calls it a squid “aphrodisiac”…and he tasted it. Squid breath!

Ah, the aphrodisiac is squid bits run through a blender, a squid milkshake. Do not try something analogous if you are looking for a human aphrodisiac.

Hmm. They’re kind of setting this up as a conflict between the three scientists involved — Widder, O’Shea, and Kubodera, and portraying O’Shea as ‘controversial’. Really? We’ll see if there’s any real drama or if this is exaggerated and contrived (I suspect the latter).

Real science is often tedious. This show is just giving us the highlights — O’Shea just went on a 7 hour dive in a submersible, we got to see a couple of brief shots of some lovely jellyfish and a couple of small squid (which were nice!)

I guess this is build up. 45 minutes in, we’ve seen all three scientists do a dive, and all three fail. That’s OK, I think they’re illustrating how science is done about as effectively as you can with a television entertainment.

This so reminds me of going fishing, trying different lures semi-randomly to find out what they’re biting.

Oh, wait, they are fishing!

I’ve been watching for an hour and ten minutes, and they finally flash a glimpse of a large squid at us. Need…more…data. Getting a little thin here.

It figures. All the people hanging about underwater in submersibles…nada. Unmanned probe left to record unmonitored for 30 consecutive hours…success!

It is now sinking in that that 30 seconds of a giant squid lunging at a robot probe has been padded out to an hour and a half. It’s spectacular footage, but there really isn’t that much of it.

OK, stop this. Last 15 minutes seem to be solid commercials interlaced with one minute segments of documentary. This is getting ridiculous.

Finally! A giant squid just hangs onto some bait while brightly lit for 23 minutes…and they show us about a minute of it. Why not just drop that fluff and have the last half hour be nothing but continuous footage of the 26 foot long beast hanging there? That’s what I want!

My final assessment: mixed. They got some really, really good video, but apparently they didn’t think it was enough, and so they padded it out way too much. There were some half-assed attempts at the beginning to play up conflict and drama between the researchers, but they didn’t pan out and weren’t at all relevant; the stuff about “monsters” was distracting; the occasional attempts to compare this search to bigfoot, UFOs, and the Loch Ness monster — only real — was just annoying. There was some promising set up of the methodology, but not enough about the biology.

The people who made the show clearly didn’t think just the video footage of the squid was sufficiently engaging. They were wrong. They also clearly felt a need to milk it for every penny of commercial time they could get.

I look forward to when just the raw footage of the squid is released. That’s what I want to see.

An important warning regarding your household recreational drug use

I  try not to abuse my soapbox here by proselytizing too often, given that this is a topic on which hordelings have deeply divided points of view. But sometimes a warning is just far too important not to share.

I’m not moralizing here. What you do with your own body is between you, your conscience, and your connection. But an informed choice is always the best choice. I urge you to pay close attention to this Public Service Announcement.