Science Made Cool

Why CT?

OK, so I’ve put some alligators through a CT scanner to create three-dimensional models of their cloacas. How exactly is that going to work? 

A CT scanner is an ordinary X-ray machine on steroids. The basics for both machines are the same: stick an object-to-be-imaged between an X-ray source and an X-ray detector, and measure the number of X-rays that make it through the object. X-rays are a form of light and do all the same things as ordinary visible wavelengths when they interact with the stuff of the world: some materials bend them, some reflect them, some absorb them. But because X-rays are much more energetic than visible light, more materials are transparent to them. Most visible light bounces off our skin, but to an X-ray it’s as clear as a windowpane.

But an animal’s body isn’t completely transparent to X-rays – molecules in the muscle, fat, and bone can absorb or bend some of the light as it passes through. When this happens, fewer X-rays make it to the detector, and these X-ray-deficient shadows form pictures of the stuff inside the animal.

 Your run of the mill X-ray machine takes a picture through a single plane. You’ve no doubt experienced this at the dentist: they stick a detector in your mouth, point a X-ray source at your cheek, and bam! Image of your teeth, roots and all.

 CT scanners work on the same principle, but mount the X-ray source and detector in a ring that rotates around the specimen (or person, or whatever) and take many many more pictures in the process. The pictures are fed into a computer program that performs some mathematics I don’t even pretend to understand (this is the “computed tomography” - “CT” - part) and hands back a stack of images that look like a orderly series of planes cut through the specimen. This is a “Z-stack”, and it looks like this:

 This particular one (from Julio Pereira) is a stack of images through a human head and chest. Even though the image is in shades of gray, you can clearly see different kinds of tissue: brain, bone, muscle, lungs – all thanks to differences in gray value. Lighter tones represent denser tissues, so bones appear white and the air-filled lungs look black. (Scanning through this particular stack, you can also see a spot where some metal dental work scatters the X-rays into starbursts.) 

Importing a Z-stack into specialized image segmentation software makes it possible (again, using some complicated math) to use these grayscale differences to define the surfaces of different tissues throughout the stack and create 3-dimensional models that can be virtually dissected. This fish (scanned and reconstructed by Sarah Faulwetter) is one example: starting with a Z-stack from a CT scan, it's possible to make a model of the surface of the fish that has a model of its skeleton embedded inside it.

How I Started My Summer Vacation

I don’t teach during the UMass Amherst summer session, but that doesn’t mean I get to spend three months sunbathing in my backyard. As soon as I turn in my final grades, the frenzy of experiments begins – basically everything I don’t have time for during the school year (because I’m, y’know, teaching) gets crammed into the weeks between May and September. This year, I spent the end of May in Louisiana, where I met up with one of my collaborators to work on a 3D anatomical atlas of the alligator cloaca.

                    Getting ready for his closeup.

This is part of a larger project examining the evolution and function of archosaur reproductive systems: right now, we want to define how the cloacal muscles, blood vessels, and the phallus are oriented relative to one another. And because it's really challenging to define these relationships by dissection alone, we used a modern imaging technique to try to get a more precise picture of the cloaca in situ. In short, we ran 7-foot long American alligators through a CT scanner. 

Why so big? We needed mature animals, and alligators don't become sexually mature until they're more than 6 feet long. (These animals were actually on the small side for adult males, but we were also limited by the size of the table in the CT scanner!) So we were lucky to have the expert help of both the wildlife biologists at the Rockefeller Wildlife Refuge and the vets and technicians at the LSU School of Veterinary Medicine for this part of the project. I was amused to see how excited the students were to see what we were doing -- vets-in-training kept stopping by the imaging suite to watch us work.

Of course, collecting the data is just the first step: we’ll be analyzing the images and building 3D computer models for months to come. But it was a particularly thrilling first step.

 

Teens and Science Game Design at #scienceFTW

The American Museum of Natural History is in the midst of running their first afterschool science card game program for teenagers (called #scienceFTW), and I’ve been delightedly following Barry Joseph’s reports on how it’s going. It’s not just that I’m really proud that they adopted both Bone Wars and Parasites Unleashed for the program – I’m impressed that they’ve gone beyond simply giving kids some science games and passive instruction about “what they’re teaching.” Instead, the teens in the program are learning to analyze game mechanics and graphic design, and think about how those elements can be used to convey information about science.  That experience in critical thinking should be helpful when they start to develop their own deck building games later in the program – they plan to build a pterosaur deck for the ever-versatile Phylo, as well as an original game prototype about museum scientists. And judging from the photos, they’re having a great time. 

Munch, Munch, Munch

My personal fitness plan revolves around trees. We have a wood stove which contributes a not-inconsiderable fraction of our home heating during the winter, and that means I have to spend spring and summer refilling the woodpile. 

Mostly I cut up deadfalls, but occasionally I do cut down trees which look as though they're going to fall down anyway, or which are in places I don't want them to be. (I've tried asking them politely to move, but they ignore me.)

Earlier this summer I took down a medium-sized pine tree, about 40 feet tall, in order to bring more light to part of the yard. I cut off the branches, then sliced the trunk into 16-inch sections so that I could split them and burn them later.

Now, pine wood isn't as dense as, say, maple or oak, so it doesn't burn as hot. It's also full of resins and whatnot, so the result is that burning pine gunks up your flue with soot. My plan was to split the pine wood, but keep it separate from the rest of the woodpile for use as kindling wood or emergency backup fuel. So I stacked the cut segments and turned my attention to a fallen birch on the other side of the lot, because birch burns like plutonium. (And it gives the woodpile a pleasant root-beer scent.)

A couple of weeks later I happened to pass the stack of pine logs, and I noticed something. Two things, really. 

The first was the sawdust. I cut the tree where it lay on the ground, then moved the pieces to the pile. So why was the pile of pine logs covered with sawdust? Not just a little sawdust, great drifts of sawdust. Hmm.

I bent closer and noticed the second thing. The wood was making noise. I could distinctly hear a crunching sound. Like something chewing wood...

My resident scientist did some Googling, and we guess it was some sort of beetle larvae, from one of the many species of beetles which attack pine logs. We could have split one of the logs to examine the larvae in situ, but I was more interested in getting the infested stack as far away from our house (built mostly of pine) as possible. The noise-making logs went into the gully beyond the driveway, where the beetles can reduce them to sawdust.

So the lesson for today is: listen to your wood. It might tell you something worth knowing.

A Meeting With Medusoid

It's not quite artificial life, but it's certainly a step in that direction. As a "proof of concept" for work on artificial hearts and muscle systems, a group of researchers at Caltech (and Harvard) have created what they call a "Medusoid" -- a kind of synthetic jellyfish made of silicone rubber and cultured muscle cells. PhysOrg has the story, including video of the Medusoid swimming around.

Reactions, predictably, are heavy on the "It's ALIVE!" Frankenstein mad doctor electrical zapping hoo-ha. But the real story is that this thing works. It's not very far removed from something that could be implanted in your chest if your heart stops doing its job.

Though if the medical applications don't pan out, this would still be a hell of a fun thing to keep in your aquarium.

Team Einstein Close Enough For A Field Goal

In the ongoing faster-than-light neutrino struggle between the OPERA experiment at CERN and General Relativity, there's been a major development. A new press release from the OPERA team has identified possible equipment issues as the source of the timing error which suggested that neutrinos were moving faster than light.

If you were hoping to see Einstein overthrown, it's bad news. Loose cables don't equal major paradigm shifts.

This, by the way, is exactly how science is supposed to work.

Life Imitates Art

A team of Russian scientists are boring through miles of ice into a twenty million year old lake in Antarctica. They haven't been heard from for a week now.

It's pretty obvious that the Shoggoths have gotten them.

(Note: Lovecraftian humor aside, I hope that nothing actually has happened to these brave researchers, and that they succeed in getting uncontaminated samples from Lake Vostok.)

Update: As of February 13, they're reporting success, and no Shoggoths. (Of course, that's just what they would say if the Thing has replaced them all.)

The Trebuchette: Extremely Easy Hurling

Last April, I posted a link to a Kickstarter campaign that was raising money to produce miniature plywood trebuchets. Of course, I sent them some cash: some for their “trebuchets for schools” effort, and some so I could have my very own tiny siege engine. The kit arrived at Christmastime, but I didn’t get a chance to put it together until this week.

Assembly was remarkably fast: it took me less than 30 minutes. The kit really does just snap together – no glue, no sanding, no prep beyond peeling protective paper off each side of the plywood pieces. The peeling is necessary -- the tolerances of the laser-cut pieces are so tight that the kit’s tabs won’t go through its slots until the paper is removed – but the end result is a model without any wobble or shimmy. The trickiest part was threading the thin string through the tiny holes in the sling, and that’s more of a comment on my middle-aged eyes than anything else.

The kit comes with a pair of superballs as ammo. I used one for the inaugaral throw. Foolishly. Inside the house. I didn’t break anything, but we’re still looking for one of the balls. After that, we switched to crumpled balls of paper and were consistently shooting them 30 feet across the room. Our cat now thinks we bought the treb for her. You can order one for your very own at siegetoys.com.

 

The Information Age Finally Arrives

Back in the 1980s, when personal computers first appeared on the market and people began plugging them into modems to communicate with other computers, there was a lot of excited talk about what this new "Information Age" would bring to us.

Some of the ideas were stupid even at the time: I recall that a selling point for early home computers was that they could be used to organize recipes and compose shopping lists. Organize recipes? I was not aware that disorganized recipes was a problem worth $1000 in 1980s money to solve. Shopping lists had to wait for pocket devices like the iPod or Blackberry, but recipes remain unorganized to this day.

Another big idea for the Information Age was that we would have access to school and college courses, making brick and mortar academies obsolete. That took a while to manage. "Distance Learning" began early on, but those pesky schools and professors did insist on being paid for their work, so most were subscription-based, or part of college tuition. Online encyclopedias and archives also demanded money -- which is why the error-riddled Wikipedia has become the resource of choice for everyone. It may be wrong, but it's free.

Well, now the Information Age has finally realized its potential. You can now take courses at MIT online, for free. So stop reading this, go follow the link, and get educated. Build your own damned flying car.

Team Einstein Intercepts!

Physicists at the Italian Gran Sasso laboratory have released a study indicating that the faster-than-light neutrinos reported by the OPERA experiment at CERN must be measurement error. The study is based on the particle energy of the neutrinos, which pretty much matches what one would expect if they were traveling at normal speeds  (i.e. very close to, but not over the speed of light).

So coach Einstein's team has a first down, and are within scoring distance of the CERN end zone, but the scrappy OPERA players aren't giving up yet. This is still anyone's game.

It's kind of neat to watch the process of science taking place in real time. Result is announced, result is tested, some tests confirm it while others contradict it. The tests are tested, and eventually we'll know the truth. This is how science really works.