Science Made Cool

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.

 

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. 

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

 

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.

Great Blue Herons, Up Close and Personal

Last spring the Cornell Lab of Ornithology set up webcams which let people watch the campus' red tailed hawk pair ("Ezra" and "Big Red") raise their chicks on streaming video. This year, they've added a camera for the Great Blue Heron nest outside the Lab's offices at Sapsucker Woods. To date, the female has laid five eggs -- and they should start hatching out gangly fluffy babies in a week or two. 

Man Bites Shark (Infographic)

A paper on the shark fishery coming out in the next issue of Marine Policy estimates that we're catching 100 million sharks each year, largely to supply the Asian hunger for shark fin soup. 100 million is a really big number -- it's understandably hard to translate it into your run of the mill everyday experience. So Joe Chernov and Robin Richards (AKA Ripetungi) made a graphic to help you with that.

To be fair, the issue here is not the sheer mind-boggling enormity of the shark catch: I expect that it's dwarfed by the worldwide catch of herring or sardines. The problem is that sharks are large apex predators who take a long time to grow to maturity and reproduce very slowly. Most shark species make babies using some flavor of vivipary -- instead of spawning, their babies develop inside their moms. In some species pregnancy lasts more than a year. So sharks are classic "K strategists" when it comes to reproduction: instead of tossing millions of fry into the sea, they invest heavily in a few babies. 

Worldwide indiscriminate fishing of animals that have only a few babies at a time once every year or two? Doesn't take long to eat those puppies into extinction.

H/T to Kyle Hill for alerting me to the graphic.

As Seen On TV!

HBO has just announced that they're doing a TV movie about the rivalry between fossil-hunters Edward Drinker Cope and Othniel Charles Marsh. You'll never guess what it's called.

Actually, you will: BONE WARS!

Wired has the story here. It's to be a comedy, featuring James Gandolfini (as, I'm guessing, Marsh) and Steve Carell (presumably as Cope).

I wonder if anybody at HBO is a fan of a certain card game?