It was the week before classes, and all through the house…

The faculty were melting down. It’s going to be a busy week — I have syllabi to finalize and multiple meetings to attend and cranky fish to fuss over (Morris has toxic water everywhere, full of minerals, and we’re dependent on the RO system to clean up the crap…and they’re shutting it down and flushing it with chlorine this week. What? Yikes!). And then I have other things I’m stuck with.

Tomorrow evening at 7:30 I’m doing a book event on KFAI radio. There goes my afternoon and most of the evening.

This weekend we have our Bridge to Biology program — a huge number of our incoming first year students in biology get taken out to the Lake Itasca Field Station, where we try to lose them in snipe hunts get them enthused about science and biology. I’ll be out there with a microscope and cameras and embryos (I hope, if the RO system doesn’t poison everything).

Oh, yeah, I’m preparing all my class stuff. I’m teaching cell biology and cancer biology this term. Any students reading this? You can get a jump on everything by reading the first couple of chapters of Life by Sadava et al., we shall be marching through the first third of this book in the cell biology class. In cancer biology, we’re going to focus on The Emperor of All Maladies by Mukherjee for the first few weeks, so read that whole thing now. Then once you all know what horrible things cancer does to people, we’ll dive into the mechanisms. You’re fortunate, too: last time I taught this, we used Weinberg’s Cancer Biology text, which is really aimed more at graduate level work; this time around we’re using Hesketh’s Introduction to Cancer Biology. The first two words in the title will make it a less daunting exploration, I hope.

News from the world of fish drudgery

I’ve been away from my office and computer all day doing manual labor. Our little fish facility had a problem: the tanks all drain into these custom built trays (we made them from sheet plastic with PVC angle rods glued and caulked around the edges), which then drain into the reservoir tank. It turns out they leak, not much, just a few drops an hour, but when you multiply that by two dozen tanks and 24 hours 7 days a week, it adds up. The custodians complained.

That constitutes a full scale emergency, you know. As every scientist learns early in their careers, the two groups of people you cannot ever piss off are 1) the department secretaries, and 2) the custodians.

So I bought a bunch of solid strong trays (Christian trays, no less) and a pile of bulkhead fittings, and have spent most of the day with a hole saw punching tidy precise holes in their bottoms and clamping on watertight fittings and adding vinyl tubing for precision delivery of waste water, and then ripping out old trays and putting in the new ones.

Now I’m all damp and sweaty. But now water goes in, and water goes out, and I can account for every last drop, so we’re all good.

Also, by the way, we’re getting steady production of about 50 eggs a day, and I’ve got about a hundred larvae I’m nursemaiding every day, with more on the way. We’re struggling with the science side of things now that the production side seems to be working smoothly.


Embryos at last!

Oh, look: The first embryos from our new and improved fish system!


We only got a handful today, but you can see why. Those are about 3½ hours old, so we collected too late and the little babies’ mommies and daddies had spent the previous few hours assiduously poking around in the marbles sheltering the eggs, and had sucked up their little brothers and sisters in a cannibal feast, as they like to do. We’ll be adjusting our schedules, as developmental biologists often have to do, to do much earlier collections starting tomorrow.

The parents look happy and comfortable, perhaps a little plump after their breakfast of caviar and shrimp, so we expect more tomorrow. Right now we’re raising these little guys at a couple of different temperatures to calibrate our staging adjustments.


I got up early this morning and rushed over to the lab to suck on tanks — danios lay demersal eggs that sink to the bottom of the tank, and you can just siphon them up — and…nothing but fish poop. I have a sad face. It was probably overly optimistic since we only have a few adults yet and they’ve just been plunked into the system, but I had hopes. They look so happy! (Zebrafish visibly respond to stress by going pale, and as soon as these guys hit the tanks their little stripes were vividly dark blue).

Water quality is good, but now I’m channelling my grandmother and starting to fuss over their diet. They need to eat and get fat and good rich fatty food is just the ticket. We’ve got the brine shrimp hatchery bubbling and those should be ready tomorrow, and I’m going to be giving them a range of tropical fish foods. We will plump these little creatures up so they can give me more than just feces to look at in the morning.

We’ve also ordered a couple of defined wild type lines — at $20/pair, so we expect thoroughbreds — so the colony population should climb soon, which will help. Then, observations and experiments and breeding and colony expansion.

You asked, I deliver the fish porn

Since everyone insisted, here’s a photo of our incipient zebrafish system, built by my student Josh.


What it is is a set of ordinary plastic shelving with some custom built plastic trays to catch water overflow, and then an array of simple 2-3 liter tanks (the smallest size Kritter Keepers, if you must know — you can get them for about $2 each). There is a 110 liter reservoir tank down below, with an immersible pump that can generate a flow of about 1900 gallons/hour, currently greatly throttled down since we only have a few tanks in place. Water is pumped out of the reservoir to two places: 1) towards the ceiling, where the PVC plumbing splits — with valves, we can select to have the water pumped right out to the sink nearby, or to a bypass line that just has the water going up and back down, or in normal operation, to a line that has a big hunk of 3″ PVC pipe packed with bioballs and charcoal for filtering, and 2) to a big bucket of sand for additional filtration. Water is just flowing all over the place here.

Most importantly, the main outflow line is tapped in 3 spots to some irrigation hose leading to six of these nifty little widgets that provide a trickle of water out nine smaller drip lines, which lead to the fish tanks. It’s amazing what you can find in hydroponics gear. If ever Minnesota legalizes marijuana, I could also cycle fish water (mmm, rich & tasty fish poop) into racks of plants and pay for all this stuff.

Here’s a quick and dirty diagram if that explanation doesn’t help. Not that the cartoon will necessarily help, either. Blue circles are valves. Arrows indicate the direction of water flow.


It’s been running for a couple of weeks solid with no problems (I wish I could say the same for the backup system we set up yesterday, which blew gaskets all over the place and made a mess overnight), so we’ve actually put a few fish in there. With any luck, we’ll have embryos this week!

Next phase begins!

We think our fish facility is complete now. We have run it through the fishless cycling process. Now I have to drive 60 miles to get some cheap pet store danios to give it the live test, so I’m going to be offline for a bit.

Once those are thriving and we’re totally confident that everything is going to work, we’ll be ordering a bunch of defined strains and raising those up…and doing our preliminary baseline analyses on the embryos. It’s progress! Science marches on!

World conquest…slightly delayed

When we fired up all cylinders on our majestic fish apparatus today, we discovered…leaks. Nothing tremendous, no sprays of water under pressure all over the place, just a couple of slow, steady, trickling drips. We demand perfection since this will be running 24 hours a day for months on end. So joins are being resealed and retested. Damn science. Damn engineering. Damn plumbing.

Have no fear, we’re just pushing back teleostageddon a few days. But the Daniocalypse will happen! We cannot be stopped now! The device is nearly complete!

We are go for fishiness

We are now testing the capabilities of our fully armed and operational homebrew fish facility in the lab. Pumps are humming, water is flowing, we are evaluating all joins for leakage, and it’s looking good. Tomorrow we put in a small bank of tanks and start the water cycle. Next week, fish!

That is all.

For the ambitious budding cancer biologist

I’m teaching cancer biology in the fall, and if you want to get a head start over the summer, here are the texts we’re going to be using:

Biol 4103: Cancer Biology

Introduction to Cancer Biology, by Robin Heskith
Cambridge University Press, 1st ed.
ISBN 978-1107601482

The Emperor of All Maladies: A Biography of Cancer, by Siddhartha Mukherjee
Scribner, reprint ed.
ISBN 978-1439170915

Last time around, I used Weinberg’s The Biology of Cancer, which is an excellent, in-depth text, but was really heavy going for an undergraduate course — it’s more of a graduate/MD level reference book. The Heskith book is very good, giving more substantial introductions to the difficult concepts, and also as a bonus, is one third the price. Just having general chapters on cell signaling in normal cells, for instance, will be a big help in bringing students up to speed.

For you outside observers, sorry, but this class won’t be going the supplementary blogging route. I’ve got some other cunning schemes I’m going to try on the students instead.

The first day of the rest of my summer!


It’s going to be a good season, I can tell already. It’s finals week, so I’ll still have an abrupt pile of grading to do on Thursday, but otherwise, my teaching obligations are done for the semester. Now I’m trapped, trapped I tell you, in Morris for almost (I do have two quick trips to Europe planned) the entire summer with a collection of administrative responsibilities, but the good part of that is that I have ambitious plans for what I’ll be doing in the lab. I’m also going to be living the good life.

So this morning I slept in to 7:00. I know, it’s slothful of me, but I have the freedom to indulge myself a little bit now and then. After I got up, I took a nice brisk walk downtown, did some shopping, stocked up on some fresh vegetables, and once I got home, chopped them up and set them to soak in a tasty marinade. I’ll roast them up for dinner tonight.

Then I started reading up an accumulated mass of papers that’ll give me some implementation ideas for the work I have planned.

I’ll have a student working with me, and we’ve got a couple of projects in the works.

  1. There’s some boring scut work to be done: lab cleanup, clearing out old reagents from the refrigerator, making up new stock solutions. Don’t be disillusioned, but part of the research life is janitorial…so much dishwashing.

  2. My grand plan requires an expansion of my fish colony to include multiple genetic strains, so we’re going to be scrubbing tanks, sterilizing surfaces, setting up new tanks with boring feeder fish to get the nitrogen cycle going and condition the water, getting the brine shrimp hatchery (live fish food!) thriving, all that sort of stuff that qualifies you to be a clerk in a pet store.

  3. Once all the tanks are bubbling away happily, we’re getting some new strains from the zebrafish stock center. Then it’s a few months of nursing them along, collecting eggs, propagating new generations and raising them to adulthood to get the whole colony self-sustaining, and to prepare for crosses to produce hybrid strains. After all this, my student will be well-trained to be a hobbyist aquarist.

  4. Concurrently, we’ll be doing some real science on the embryos we get, analyzing their behavior quantitatively to identify consistent differences between strains, and also in response to different environmental stresses. This is going to require a bit of computer work and — oh, no! — basic math to develop image analysis protocols. That’s what I’ve been reading about; I’ve done some of this in the past on an obsolete software system, so I’m going to have to piece together some custom bits to make it all work. I’ve been reading about Fourier analysis and power spectra all morning, and I’m kinda jazzed. Math! Computers! Embryos! Science!

  5. The dream is that once we’ve found some subtle differences between different strains, we can start doing crosses to dissect out and isolate the genetic components, if any, of the behavior. That’s going to take a couple of generations of crosses, which means that if I’m lucky we’ll get those results next year, or at worst, the year after. Behavioral Genetics! Yay! Long generation times! Boo!

It’s step #4 that’ll give us some quick quantitative results, I hope, and maybe something presentable at a meeting or even publishable. It’s all going to be preliminary and descriptive, but that’s what you need to do to establish a foundation for experiments.

Unfortunately for you, I won’t be blogging about any of the details of the work this summer — I’ve been scooped before when I foolishly posted protocols on the web, and especially when you have a very small lab with limited humanpower to throw at a problem, that costs. But I might just occasionally say a few general things about the kinds of analyses we’re doing.

Or I could talk about the moldy stuff we throw out of the refrigerator. That’s probably safe.