Science Made Cool

Evolution for Third-Graders

It’s early on a Friday morning, and I’m standing in front of a crowd of eight-year-olds holding a fistful of dead crayfish. The mudbugs are a biological supply company purchase sorted into sealed sandwich bags – the subject and substrate for the science project I’ve volunteered to lead today.

The activity I’ve planned is the most basic sort of comparative anatomy: we’re going to dissect crayfish and talk about how their bodies differ from our own. These kids won’t learn about evolution in school for years yet, but I’m hoping to lay some groundwork now that will make it a little less alien when they finally do get to it.

Before we start, I ask if they can think of any other animals that are related to the crayfish. Hands shoot up. Lobsters, crabs, ants and other insects are named. I add a few other arthropods to the list, then drop the bombshell that makes them really pay attention: biologists think that every one of them is also a very very very distant cousin to those crayfish, the relative we shared probably looked a lot like a worm, and over the next hour I want them to think about how both the crayfish and vertebrates like us have solved the same problems while becoming less wormlike. They put on their gloves, I give them some quick instructions on how to use their dissecting scissors and probes, and at last, I hand out the specimens.

There’s a chorus of ‘eeew’s as the kids dump crayfish onto their dissecting trays and the faint smell of preservative fluid wafts out of the bags. It’s followed by 40 minutes of barely controlled chaos.

We count crayfish legs. We look at the eyes and the antennae. We look for the mouth, and talk about what all the little leglike structures that surround it are for. We figure out whether each group has a boy crayfish or a girl crayfish. We cut open the thorax and look for gills, heart, and stomach. We open the stomach and poke the hard gastric teeth with our fingers. The kids are delighted by the very idea of “stomach teeth.” We find the nerve cord running along the belly and the intestine running along the back of the animal – the exact opposite of our own body plan. Some kids ask what’s inside the eyes. Others ask where the crayfish keeps its brain. I try to find something recognizable to point out inside the specimen that one group has poked to paste. At one table, a dark-haired girl has pushed her body as far away from the crayfish as possible, face twisted in disgust, but still cranes her neck around to see what her partners are doing. At another, a girl and a boy keep repeating to one another, “This is the best day ever!”

After we clean up, the kids ask questions – but very few of them are actually about the dissection. Most of them, it turns out, are about me. What other animals have I dissected? What’s the worst thing I ever smelled? How long does it take to get a Ph.D.? What do I do at work all day? Do I have a dog?

I get it, really. I’m probably the first scientist they’ve met in the flesh. All those questions are just proxies to ask: “If I wanted to, could I be a scientist when I grow up, too?” I hope I was able to let them know that even though it takes a lot of hard work, the answer to that question is yes.

 

Cross-posted from The Evolution Institute

A Buried Childhood: Tree-Style

Trees grow in two ways: they get longer, and they get wider. That doesn’t sound too different from the way an animal grows, but unlike animals, trees only grow longer at their margins. The tip of each stem contains a small cluster of undifferentiated cells called the apical meristem: as these cells divide, the undifferentiated cells are pushed forward and new shoot cells are laid down in their wake. The result?  Older cells in a tree’s stem never change position relative to the ground: the part of a 300 foot redwood tree that’s at eye level now was also at eye level when the tree was only 8 feet tall.

So why aren’t trees tall lanky whips of spaghetti-thin twigs? They have another trick, which lets them grow thicker as trunk and branches push out at their tips: the tissues near the outer surface of the stems called secondary meristem. When these tissues divide, they add layers of cells to the outside of the stem, gradually adding girth to the tree, forming rings of new wood over older tissues, and engulfing older branches over time.

Where animals remodel during growth, plants enclose – so every tree contains the shape of its younger self. 

 

The Hidden Life Within: Giuseppe Penone                              (wood: newer wood removed to reveal older developmental stages)                   Photo by Sphilbrick, via Wikipedia 

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.

 

Beautiful Anatomy on Display

Before there was computed tomography, before there was CLARITY, biologists used clearing and staining to study the three-dimensional anatomy of bones, cartilage, and nerves. The technique is actually straightforward, if time-consuming: soak a whole animal (dead, of course) in materials that make its skin and muscles transparent, while applying stains that meld to specific kinds of tissue.

The results are gorgeous.

A skeleton in shades of red and blue is revealed through the ghostly outline of the animal. Intricate details that normal dissection can destroy are visible: tiny bones around the eye, miniscule gill supports, the connections in living levers.

These preparations are usually stored in laboratories and the back rooms of museums – they are, after all, made for research - but two museums have brought them (or more precisely, their images) out to the public as art installations.

Skate: ©2013 Adam Summers

At the American Museum of Natural History, large-format photographs of cleared and stained fish are part of the Picturing Science exhibition, along with examples of infrared and fluorescence photography, at the museum’s Akeley Gallery until May 31, 2014. And until spring of 2014, the Seattle Aquarium is displaying enormous photographic prints of cleared and stained fish that Adam Summers used for his own research on the biomechanics of fish feeding, locomotion, and ventilation. (Adam's also made these images available on greeting cards and a 2014 calendar.)

If you find yourself on either coast before the end of winter, you should check one of these exhibits out. You'll be amazed.

A Quill as Mighty as a Sword

This is my dog.

She’s a sweetheart, but like most bird dogs she’s been bred to be rather – um – inquisitive. And thanks to that curiosity, last week she wound up looking something like this:

Astra met a porcupine. And it did not want to play with her.

Porcupines are one of the largest rodents living near my house in New England, second in size only to the beavers that keep themselves to themselves in the pond down the road. Not that I’ve ever seen a porcupine in the flesh myself – they’re mostly nocturnal, and I don’t go stumbling around our woods at night. But at this time of year, the porcupines are out looking for love. Searching for potential mates in the crisp fall air leaves them awake and active at odd hours, raising the chance that they’ll run into a potential predator (or an exuberant housepet).

Fortunately for them, porcupines have a phenomenal defense mechanism. Their backs are covered with quills -- more than 30,000 of them – long, hollow tubes armed with wicked barbs. One pat with a paw, one playful nip, and your dog looks like a pincushion.

A quill’s anatomy makes it a formidible weapon. Quills are modified hairs, and they’re shed easily when they’re touched. But where your own hair is made of a thin and flexible strand of keratin, a quill arranges its keratin in a tube, making it stiffer by the same principle that makes the tubes in a bicycle frame sturdier than cables containing the same amount of metal. Run your fingers over your head, and you can feel your thinner, more compact hairs bend away. Tubular quills resist bending, and where your hair is pushed away at a touch, a quill is likely to push back.

And pushing back usually means pushing in. The end of a quill doesn’t just have one barb at its tip: it’s covered with tiny overlapping barbs that point backwards like rows of wicked teeth. Those barbs tear into skin like a serrated knife blade, concentrating penetration forces at each tiny point to shred through structural proteins. It sounds violent, but probably makes a cleaner cut than a smooth blunt quill could. But it makes the quills something of a challenge to remove. Pulling a quill backwards spreads out its barbs and anchors them firmly in flesh. And the barbs’ cutting action means that embedded quills can continue to migrate through the quilled animal’s body.

Which is why I didn’t take the time for a real photo of my dog plus quills. We were at the vet 10 minutes after her accident. Our vet had them out in about 15 minutes. And we'll be walking on leash until porcupine mating season is over.

 

References:

Cho et al. 2012. Microstructured barbs on the North American porcupine quill enable easy tissue penetration and difficult removal. PNAS: www.pnas.org/cgi/doi/10.1073/pnas.1216441109

Johnson et al. 2006. Porcupine quill injuries in dogs: A retrospective of 296 cases (1998–2002). Can Vet J. 2006 July; 47(7): 677–682.

Vincent, J. F. V. 2002. Survival of the cheapest. Materials Today 5: 28-41. http://www.sciencedirect.com/science/article/pii/S1369702102012373

 

Three-Dee Anatomy Challenge

There’s really no getting around it – anatomy is a challenging subject. It’s not just the enormous number of names to memorize. You also need to remember the relative locations of scores of organs and muscles and internal spaces and such, which gets even more complicated when you consider that many of the shapes and spatial relations inside an animal can change when muscles contract. In short, doing 3D reconstruction in your head on the fly is really hard.

                        Alligator cloaca, viewed from above (dorsal).

So when I was doing the research for my paper on male alligator reproductive anatomy, I deliberately dissected the pelvic region of each of my specimens from a different direction: I worked on one alligator from the belly upwards, another from its back downwards, and two from the flank inward. Each direction helped me build a better picture of how muscles wrap around the cloacal space and where tendons and ligaments thread through the system and attach to bone. But I still don’t know what all of those structures look like when the phallus is in its “functional” position. I think that some of those muscles squish the cloacal wall into a different shape, but it’ll take a lot more work, some luck, and really good scientific visualization methods to find out for sure.

That’s one reason I’m excited about Mieke Roth’s crowdfunding campaign. Her goal? -- to spend a year dissecting Nile crocodile specimens in John Hutchinson’s lab at the Royal Veterinary College and turning her drawings and notes into a detailed 3D computer reconstruction of this magnificent beast. All of it. Head to tail, skin to gut lining. Her fantastic octopus reconstruction is a testament to her skills, and I for one would love to see her succeed in this larger (much larger!) endeavor -- and not just because she’ll let me help out when she gets to the cloaca.

Detailed anatomical reconstruction of the sort Roth is proposing is fairly rare for large animals: they're far too big to stick inside a microCT scanner (a technique that's given us high-resolution virtual models of the anatomy of small invertebrates), so detailed reconstruction tends to focus on one 'region of interest'. So we have projects like Larry Witmer's fantastic Visible Interactive Alligator giving us a detailed picture of the head, or Colleen Farmer's beautiful 3D reconstructions of alligator lungs, while other areas of the crocodilian body remain something of a mystery. You can help change that. 

Check it out: Ultimate Croc Anatomy: IndieGoGo - by Mieke Roth 

Diane Natters On

Last week I shlepped down to Brooklyn, treated myself to a fabulous sushi supper, and waited nervously for my turn to get up on stage and tell a story. The result is now a podcast on The Story Collider's site: they're calling it "Confronting Death on the Road." Have a listen. And if you want to know more about how I wrote it, head over to Last Word On Nothing, where Ginny Hughes does a fine job of summing it up. 

The Art of Anatomy

Here's another style of data visualization from this year's TEDMED -- Lisa Nilsson makes life sized paper sculptures of anatomical cross sections. It's amazing, intricate work -- she rolls thin strips of paper and squishes them into shapes that mimic 19th century medical art.