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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.

Comments

  1. Artor says

    Careful, PZ. Some of those young whippersnappers might tag your house with fluorescent dye.

  2. Johnny Vector says

    I remember in grad school watching Alar Toomre show us the movie he made in, um, the seventies? Which was the first ever numerical simulation of colliding galaxies. It had 500 total mass points, each indicated by a little ‘M’ on one of those green Tektronix storage scopes, photographed onto 16mm film. Two galaxies, a couple minutes of film, and it took 2 weeks of computation (on a computer that filled two relay racks) to render it. A couple years later, when screen savers were all the rage (mid-90’s), I was amused by the colliding galaxies one. Here we had three or four or five galaxies, each with a couple hundred point masses, being rendered in real time using spare cycles on a $2000 machine that fits under your desk.

    Also, now I have the John Henry song in my head. Happily, it’s the Smothers Brothers version.

  3. Sunday Afternoon says

    OK, and a few months of learning how to use the complicated new toys.

    That’s the fun part for me – learning how to do new things with the complicated new toys.

  4. says

    Yeah!? Well in my first job we had to do statistics using an Olivetti electro-mechanical calculator!
    (And we had to put up with smart-alec ‘humourists’ who would set it to divide all the nines by one, and then unplug it so it chundered for about two minutes when the next guy went to use it—Oh! Wait, that was me…oh how we laughed!)

  5. Big Boppa says

    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…..

    Not to mention that you had to do all that AFTER walking 4 miles, uphill, through a snowstorm just to get to the lab.

  6. unclefrogy says

    what you are highlighting by your personal anecdote is fundamental to scientific thinking.
    You are not recoiling from new instrumentation or new capabilities you want to use it because you know that with it we will discover new information. every new technology reveals new information hidden by the difficulty to see it. We just need the something similar to effects of Moore’s law to work itself out a while.
    that eager curiosity seems to be lacking in the pious religious mind though it may be found in other more practical people .
    uncle frogy

  7. mothra says

    When I was a kid: brontosaurs lived in swamps, Iguanodons balanced on their tails, coelosaurs could not be ancestral to birds because they all lacked collar bones, falcons were related to other hawks, vireos were related to warblers and people were building bomb shelters in their back yards.

    Now: Apatosaurs are terrestrial grazing machines, Iguanodons balance with their tails, coelosaurs are ancestral to birds (some have collar bones), falcons are more closely related to parrots, vireos to shrikes and only millitaries and crazies build bomb shelters. Mostly- YAY science.

  8. bryanfeir says

    I remember a comment years ago, by one of the people involved in the Human Genome Project. I can’t recall it exactly, but it boiled down to: “If we lost all the data and samples we’ve been collecting over the last ten years, but got to keep the new technology and techniques we’ve developed, we’d have everything reconstructed within a year and a half.”

    The technology developed while pushing towards a goal can accelerate the progress more than people expect at the time…

  9. epikt says

    Johnny Vector:

    I remember in grad school watching Alar Toomre show us the movie he made in, um, the seventies? Which was the first ever numerical simulation of colliding galaxies.

    Wow. Serious flashback. Toomre was my calculus 1 & 2 professor. I didn’t find out about his galactic models until long after I’d graduated. I still think those were exceptionally cool, even though these days you can run them much faster on your phone.

    I ran into him a few years ago at a class reunion. I told him I really liked that work, and if I’d known about it back then I would probably have pestered him until he let me do my undergrad thesis working for him.

  10. David Marjanović says

    coelosaurs are ancestral to birds (some have collar bones), falcons are more closely related to parrots

    Most theropods, not just coelurosaurs, have turned out to have full-blown wishbones (yes, Coelophysis has a wishbone), and falcons are most closely related to parrots + songbirds.