Apr 15 2014

Science conspires to make me feel really old now

Virginia Hughes tells us about techniques to look inside the zebrafish brain. The gang at HHMI are using two photon imaging and clever image analysis to get very clear, sharp images of fluorescent neurons.

Oy, that’s pretty. This old codger did some of that stuff, many years ago, but you know what we had to do? Point injections of tracer dyes, followed by serial sectioning and reconstruction. Early on we use injections of horseradish peroxidase into, for instance, the muscle, so that neurons in transit through the lesion site would pick up the enzyme…and then we’d have to fix and process the animals with a series of reagents to visualize the stuff. Then you’d have to section the animal — I think I spent most of my graduate years hunched over either a vibratome or an ultramicrotome. This technique was hit-or-miss, so you’d only get a subset of neurons labeled, and you’d have to do it over and over hundreds or thousands of times to get a good sampling. Later we started using lineage tracer dyes like rhodamine dextran, and later still lipophilic dyes like Di-I, to get fluorescent images that allowed us to skip the tedium of sectioning, but it was still haphazard labeling. If you tried to label everything, you got a glowing blob with no ability to sort out the fibers and cells.

And even then, we used early generation intensified cameras to pick it up! Imagine those grainy images from the night-vision cameras CNN would use during the Gulf War, all stored on VHS tapes. That’s what we had. None of these lasers and all digital storage at high resolution, and computers that automatically optically scan through to produce a 3D image.

It’s like seeing a few years of your work reproduced in an afternoon by some cocky young whippersnapper with a fancy machine, all a bit John Henry.

Being really close to the work sometimes helps, though. Hughes recites a number, that there are 300,000 neurons in the zebrafish brain. I did some of that work, too — I did counts of cells in the spinal cord, which involved doing many sections and counting and measuring cells in each, to get an estimate of average cell volume, and then measuring the dimensions of the organ in question, so you could calculate the number of cells present. I did the spinal cord measurements: there were about 100,000 cells in there. That number is an overestimate of the number of neurons, though, because I know that many of the cells I was counting were neuroblasts and glia and other oddments, and we didn’t have a robust way of distinguishing neuronal elements from others.

Give me a two-photon scope, a big computer, and a collection of molecular probes for various cell types, though, and I’d be happy to re-analyze that data. It would probably take a few days. OK, and a few months of learning how to use the complicated new toys.

Apr 15 2014

Know any philatelic homophobes?

You can blow their minds now. The US has released a commemorative stamp honoring Harvey Milk, which is a great step forward.

But we’ve been totally eclipsed by Finland, which has just created Tom of Finland stamps.

I have to say, though, that Tom of Finland makes me vaguely uncomfortable — not because of the open homosexuality, but because his drawings of men are so objectifying and sexually idealized, and I know that I can not, have not, do not, and never will look anything like them. They are the masculinized version of the airbrushed/photoshopped women’s magazine cover, and I can see how if these kinds of men were as ubiquitous as the plasticized-sexified images of women in advertising, I might feel a bit intimidated.

Apr 15 2014

What will you do with a biology Ph.D.?

This chart of the distribution of the biology workforce is a bit complicated, but somehow dismaying and reassuring at the same time.

As it points out, over half of all biology grad students hope for that tenure-track research position, but only a small fraction will get it. That’s the depressing part. But at the same time, it shows all the alternative career paths: getting a biology Ph.D. does not doom you to becoming a drunken hobo, and not getting a tenure-track position is not a mark of failure.

It’s also a little misleading. “Current non-tenure track academic positions” ought to be relabeled “Serfdom”.

Apr 15 2014

That’s a terrible chart

I wish I’d had this a few weeks ago, when I was telling students how not to present their data. This is a chart illustrating the effects of stand-your-ground-laws on murder in Florida.


I glanced at that and thought, “Whoa, surprise: the stand-your-ground-laws had a pretty dramatic effect in reducing murder. I did not expect that at all.”

And then I was a bit disappointed: “But they really should have set the Y axis at zero. It’s a bit misleading and magnifies the apparent effect, otherwise.”

And then I did a double-take: “They inverted the freaking Y axis!”

That’s right. It doesn’t show a decline, it shows a dramatic spike in murder after the law was passed. The text in the article actually says that clearly, but the chart was actively selling the opposite message. They’ve since added a corrected chart that actually makes the point clearly, instead of obscuring it.


I took away two points. It’s really easy to lie with graphics, and shouldn’t any evidence-based legal system recognize the consequences of passing a bad law and correct itself?

More from a data visualization expert.

Apr 14 2014

Not another lawsuit!

Yet another case of a litigation happy bozo harassing one of our own. This time, it’s a narcissistic neo-Nazi suing Ed Brayton.

Isn’t this fun?

If you’re able to help at all, he has a fundraiser in place. This is yet another silly suit, so it’s going to be open-and-shut, but it’s still a pain in the butt.

Apr 14 2014

Cataclysms on the way!

What are you doing this summer? You might want to change your vacation plans. There is going to be a lunar eclipse tomorrow night, and according to Pastor Hagee, that means disaster. I don’t know what he’s talking about; he’s a minister, he gets loads of tax breaks, so 15 April is no big deal to him.

"I believe that the heavens are God’s billboard, that he has been sending signals to planet Earth," he explained. "God is literally screaming at the world, ‘I’m coming soon.’"

So what’s going to happen?

Hagee predicted that the four eclipses were signaling a "world-shaking event that will happen between April 2014 and October 2015."

A world-shaking event, some time in a span of a year and a half? That’s pretty vague. Could you at least say something like an event that starts with the letter ‘m’, or maybe ‘j’ or ‘t’, on a planet with a name that definitely begins with an ‘e’. Come on, try a little harder.

But this surprises me:

"God sends planet Earth a signal that something big is about to happen! He’s controlling the Sun and the moon right now to send our generation a signal, but the question is, are we getting it?"

He’s controlling the Sun and moon? But these are phenomena that are reliable and mathematically predictable, a pattern determined by the movements of the bodies involved. It’s like announcing that twice today, God will make both the little hand and the big hand on your clock point straight up — it’s a non-power. We don’t need prayer for it to happen, and praying won’t stop it from happening, and it won’t mean anything other than that it is noon and midnight.

I’m gonna go out on a limb here and predict that sometime today, god will make me hungry, and then god will make me find something to eat, and later tonight god will make me sleepy.

Uh-oh, how will I be able to remain an atheist with proof like that?

Apr 14 2014

Murdering people who accuse you of murder always works

And it’s exactly the kind of tactic a murderous deity would endorse!

Apr 14 2014

Mary’s Monday Metazoan MISANDRY


That photo is from a lovely new documentary, with this trailer.

However, I have to call attention to one troubling fact.

“All these lemurs have one thing in common – from the little one to the very largest one – they all have female dominance. The females are the leaders. The females are the ones that make the choices of where they go and what foods they eat and where they’re going to sit,” says Dr. Wright.

We must immediately call for an MRA boycott.

Apr 14 2014

Minnesota was the first!

Maybe it’s not quite as prestigious as First Man on the Moon, but Minnesota has First Beer Delivery by Drone.

I suspect a little cheating. I don’t think that drone could lift a full box of beer. But then, Amazon hasn’t actually made any deliveries with their drones yet, either — at least Minnesotans have their priorities straight.

Apr 14 2014

Years of Living Dangerously

This new documentary on Showtime is pretty good (despite the appearance of Thomas Friedman), and this is the premiere episode.

One of the most interesting aspects of the show is that it emphasizes economic issues. The standard tactic of the climate change denialists is to argue that it’s happening, we can’t do anything about it, and it would hurt our economy to take measures to reduce emissions; but this show focuses strongly on the fact that climate change is doing us economic harm right now.

The denialists are, of course, squinking furiously against it already, but they lie. They lie hard.

By the way, Harrison Ford, one of the sponsors/narrator of the show, has also done an IAmA on Reddit lately — he seems to be a cool and admirable dude.

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