From a public perspective, biology in the oceans, like biology on the land, tends to favor the charismatic megafauna. Stop by your local aquarium and you'll find masses huddled around the seal pool or the shark tank. People will even attempt to interact with the octopodes. Meanwhile, smaller creatures sit on the sidelines. Crabs, starfish, and ray-like skates have some admirers at the touch tanks. But in the world of small things, they're actually quite large. The ocean is full of even tinier organisms—worms and snails, small shelled animals and even stationary colonies of life that look like rocks or lumps of sand.

The ocean is an amazing place, and Bill Grossman can tell you about the things that live there—large, small, or tiny. Grossman is specimen collector for the Marine Biological Laboratory. Essentially, he's part of a system of support staff for scientists. When researchers at MBL need sea creatures to study, it's people like Grossman who go out on the water and find them.

Back in May, I got to take a short trip aboard the R/V Gemma, MBL's specimen collection boat. The videos I brought back can teach you some amazing things about animals you thought you knew well, and introduce you to creatures you probably never noticed before.

The first video, posted above, focuses on three animals: Skate, crabs, and a strange, colony-dwelling life form known as a sand sponge.

Skates, as you'll notice, look a lot like rays—and they are closely related. The key difference between the two is actually alluded to in the video. Grossman explains that researchers at MBL are particularly interested in skates because of the eggs that they lay. These are some amazing eggs. You won't see any in the video, but they're black, crazy looking, hard packets, bracketed between two long spines. In the packet, which is semi-opaque, you can see a bright orange blob—the embryonic skates. Seriously, it's like something out of Aliens.

Rays don't produce those. In fact, they don't lay eggs at all. Baby rays are born alive, just like human babies.

The other thing I want to give you a better look at is the sand sponge. It's not actually a sponge. Nor is it, as it appears, a blob of sand stuck together. Instead, it's a colony of creatures called ascidians, or sea squirts. If I'm understanding correctly, that sandy exterior is actually part of their living tissue.

In this second video, Grossman pulls half of a bivalve shell out of the pile shells, and crabs, and urchins on the Gemma's deck. But it's not bivalves that we're learning about. Instead, that shell, abandoned by its deceased original owner, has become an ecosystem in its own right, home to a variety of worms and snails and other small creatures.

In particular, pay attention to the hydroides. These are little worms that live inside tubes made calcium carbonate. The tubes are white or red, and the worms like to build them on hard surfaces. That includes empty shells, but it's more than that. Hydroides can build their tubes on the undersides of boats. They also build inside intake pipes, meant to bring cooling water to power plants and factories. In those situations, these little worms can become big pests.

Finally, this last video is all about sand collars and starfish. What's a sand collar? It's not an animal, itself. Instead, the collar is a gelled-together mass of eggs produced by the moon snail. These animals have a beautiful, frilly name, but are actually ravenous predators. They eat clams. Lots of clams. Moon snails eat clams like drunk frat boys eat buffalo wings. In fact, back in 2010, a veritable phalanx of moon snails nearly put Maine's human clam diggers out of business.

In all of these little tidbits, there's a key lesson you ought to learn: Amazing things are happening, all the time, at a scale that we don't always pay attention to. If your interest in animals begins and ends with creatures larger than the average Collie dog, you're going to miss out. Here's a challenge for what's left of the Summer. Get down on your hands and knees, and spend some time inspecting all of the life forms that are smaller than a breadbox.

For more information on specimen collection, read this interview with Ed Enos. He's Bill Grossman's boss, and superintendent of MBL's Aquatic Resources Department.

IMAGES:
• Egg case from a skate &mash; Wikipedia user Xtylee, via CC
• Sand sponge — MBL Marine Organism Database
]]> http://boingboing.net/2012/07/20/the-wonder-of-small-things.html/feed 10 http://boingboing.net/2012/07/02/the-beginning-of-life.html http://boingboing.net/2012/07/02/the-beginning-of-life.html#comments Mon, 02 Jul 2012 16:42:12 +0000 Maggie Koerth-Baker http://boingboing.net/?p=168622

Cells divide. One single piece of life tugs itself apart and splits in two. It sounds like a purely destructive process, reminiscent of medieval woodcuts where the hands and feet of some unfortunate thief are tied to horses heading in opposite directions. But that's the macro world. On the micro scale, to split is to live. A dividing cell doesn't just rip itself to pieces. Instead, the cell first makes a copy of its genetic information. When the cell splits, what it's really doing is making a new home for that copy to live in. Make enough copies—and enough copies of the copies—and you eventually end up with a living creature.

Back in May, I took part in the Marine Biological Laboratory Science Journalism Fellowship, a 10-day program that gives journalists hands-on experience in what it means to be a scientist. The program is split into two tracks. As part of the environmental track, I went to the Harvard Forest, where nature is one giant laboratory. But, at the same time, other journalists were busy in a different sort of lab.

Steven Ashley is a contributing editor at Scientific American and writes for a host of other publications. He took part in the fellowship's biomedical track. Ashley and the other journalists fertilized the eggs of sea urchins and other small ocean creatures, and then used specialized biomedical microscopes and cell imaging software to create brilliant photos and mesmerizing movies of cell division and growing animals.

Ashley was kind enough to send me some of those images and movies. In them, you can see the tiny structures and every day processes that form the basis of life.

That's Steven Ashley working the pipettes in the image above. Pipettes are just tools that scientists use to measure out small volumes of liquid and transport that liquid. You know how you can stick a straw into a glass of water and suspend some of the liquid in the straw by crimping the top, and creating a little vacuum seal? Pipettes work a lot like that.

Here's what Ashley had to say about his lab experience:

I worked with fellows Catherine de Lange, Alaina Levine, Euna Lhee, Sue Nelson and Maria Stenzel. Under the direction of Professors David Burgess and Brad Shuster, we took some sea floor creatures and processed them—their eggs and embryos—in the lab for viewing on the microscale.

There was lots of pipetting and waiting for cellular development to happen, followed by the incredible opportunity to operate $100,000 state-of-art Zeiss microscopes and create some pretty amazing images.

What you see in the slideshow are the results of only a couple of days of working on our stained and incubated specimens with Zeiss Axio Observer regular and inverted microscope systems(as well as other microscopes). We managed to produce some 'virtual 3D' contrast views and brilliant fluorescent-tagged images (and movies) of fragile live cells, embryos and other critters.

It starts at the spines. Sea urchins are spiny creatures. These spines are, in fact, probably their most distinguishing characteristic, from the human perspective. Sea urchins do have two separate sexes, but it's not easy to tell which is which. Luckily for the urchins, they don't really need to spend much time worrying about it. In nature, sea urchins breed by releasing eggs and sperm into the ocean and letting the sex cells find each other. In the lab, an injection of potassium chloride prompts the urchins to release eggs and sperm. Ashley and the other fellows had to "milk" the urchins to collect these cells.

Get the sperm and egg together, and you're on the road to cell division.

In this image you can see multiple fertilized sea urchin eggs at different stages of mitosis. Mitosis is an important part of cell division. During this process, the chromosomes (in blue) are separated out into two identical sets and those sets shift into position so that the cell can split, creating two cells that carry all the information necessary for life. Microtubules, protein bands that help maintain cell structure, (shown in green) make sure the chromosomes get sorted accurately and line up where they need to be.

Seven cell divisions later, when you have a 128 cells, what you've got is a blastula. Blastula are little hollow balls of cells. See how one side of the wall of the ball is thicker, though? That's important. That thick part will eventually become the sea urchin's digestive tract.

A week after fertilization, you get to the pluteus—a larval stage that now includes a basic skeletal structure. These little arrow shaped creatures move through the water, eating whatever they can. But they don't move in the direction that their arrow points. That's because the mouth of the pluteus in between its arms, and larval sea urchins deal with the world mouth-first. In fact, those arms probably help direct food towards the mouth.

A month later, this little larva will go through a stage of metamorphosis and become, officially, a baby sea urchin. Ashley and the other fellows weren't around long enough to see that happen, but if you want to know more about sea urchin development (and see more photos) I recommend checking out these links:

• The Early Development of Sea Urchins — from the book Developmental Biology, by SF Gilbert
• Echinoderms, an introduction — from Dr. Jeff Hardin at the University of Wisconsin-Madison
• The sea urchin: A stinging, but amazing, animal — by Jean-Marie Cavanihac in the July 2000 issue of Micscape Magazine

Scientists measure trees for a wide variety of reasons. When I visited the Harvard Forest last week, I measured them as part of studying carbon sequestration by plants. But you can't just go out into the woods with any old tape measure and expect to collect some significant data.

That's because where you measure the tree matters. If you want to compare the diameters of two trees, you have to make sure you're measuring them in the same place. If you measured one tree at the wide base and the other further up the trunk, where trees usually get narrower, the comparison wouldn't mean much.

That's where diameter breast height (DBH) comes in. It's a way of standardizing the measuring process.

As the name implies, DBH is meant to be a diameter measurement of a tree trunk taken at, roughly, breast height on an adult. Of course, where exactly "adult breast height" is varies greatly from person to person. So DBH has been set to a standard height—1.4 meters in the United States.

In a research forest, you'll often see some kind of marker on the trees showing where this official "breast hight" is, so people can quickly move through the woods, taking diameter measurements, without having to measure vertically on each tree. In some cases, DBH is marked with yellow spray paint. In others, metal bands. These metal bands actually help measure diameter, too. Set with springs, the bands expand as the tree does, so all researchers have to is measure the distance between two dots on the band and see how far apart the dots have moved since last time.

Read all the Dispatches from Harvard Forest

Earlier this week, I showed you how scientists can use a simple, hand-operated tool to collect stratified core samples of mud at the bottom of a swamp. The deeper the samples go down, the older the mud is—until, eventually, you're looking at 6000-year-old muck, the remains of a lake bed that filled in with sediment and became swamp.

The core samples are narrow logs, each 50 cm long. (In all honesty, they looked like less-colorful versions of the 3 pound gummi worm I ordered for my 30th birthday party last year.) For the most part, they're some variation on the shade of brown, with occasional streaks of red and burnt umber, until you get to the very bottom. There, the samples turn grey. Put a bit in your mouth, as I was encouraged to do by Harvard Forest director David Foster, and you'll taste clay and feel grit between your teeth.

That's all well and good. But what do you do with core samples once you have them? For this installment of Dispatches From Harvard Forest I'm going to leave the woods and head into the lab, to see what happens to the parts of the Forest that scientists take home.

Step one: Make dirt cupcakes

We cut samples out of the samples. (Insert your "yo dawg, I heard you like samples" joke here.) Every 25 cm, so twice for each core, we cut off a little hunk from the side. We put the pieces into ceramic cups that had been weighed and labeled, so we'd know later where in the chain each sample had come from and what the samples weighed.

Then we baked them.

Seriously. The Marine Biological Laboratory (or MBL as it prefers to be known these days) has a great big industrial oven. The cups went in a roasting pan. The roasting pan went into the oven. Several hours later, all the liquid had been cooked off and we were left with dry samples.

Out of all the little samples, there were really just three main types. Near the top, we had a lot of crumbly black earth, studded with roots and sticks and fibers.

Further down, that petered out, and you ended up with solid lumps. The lumps had some stuff in them, but not nearly as much. By the time mud is this old, a lot of the biological material in it has decomposed. These samples looked brown when we first cut them off the mud cylinders. After baking, they turned greyish-green, mottled with brown spots.

Finally, at the very bottom, was the grey clay. After baking, I could see that the grid I'd tasted was actually mica. It made the whole sample sparkle.

We weighed the baked samples and we wrote down a short description of what they looked like. This being science, "I think this lump of dirt looks kind of bluish-green" was not considered to be an accurate description.

How do you take something subjective, like color, and bring it into the world of the objective? This looks like a job for official color charts.

The Munsell Soil Color Chart book is like Pantone for dirt. You just take your sample and match it up to one of the color chips. The number of the chip is what gets recorded. That way, other people can go back and verify (or challenge) your interpretation.

Step 3: Burn off all the carbon

Next, the samples go back in the oven and the heat gets turned way up—hot enough to burn away all the organic material. What your left with is stuff like minerals, metals, and rock. If you weigh the samples and then compare that to what they weighed after first baking, you know how much of the sample was organic material and how much wasn't.

Naturally, the results changed as you moved from the surface down. Barely any weight remained in the uppermost samples. The lowest ones had barely changed. That's the difference between soil filled with plant material, and lumps of mica-filled clay.

This is, to say the least, probably not a huge revelation. But it leads to something really cool. After the carbon was burned off, the samples looked amazing. Some were chalky moonscapes, others had turned into piles of dark red fibers.

The fibers, pictured above, are what you should be paying attention to. Because they don't really make sense. We just burned off all the carbon-based material...which should include plant fibers. So, then, what in the sam hill are those things?

According to Rich McHorney, one of my advisors in the MBL Science Journalism Fellowship, the red color is from iron oxide—rust. What you're seeing here isn't plant fibers, but a shell of rust that had formed around plant fibers that were on their way to fossilizing. We burned away the plants. But the iron oxide remained. In a way, it's a bit like the casts of bodies from Pompeii. How cool is that?

Read the rest of my Dispatches from Harvard Forest

Seventy-one feet above the Harvard Forest, you can stand on a plywood platform attached to a slightly swaying tower of metal scaffolding, and look out over miles of hemlock groves. On the ground, the trees are massive—trunks reaching up and up and up. From the top of the tower, though, the view feels a bit like hanging out in a Christmas Tree farm. All you see are the friendly, conical tops.

The Hemlock Eddy Flux Tower is one of four research towers in the Harvard Forest. Since 2001, data collection systems on the top of this tower have measured carbon dioxide, water vapor, and wind currents. These measurements are made five times every second.

Thanks to this system, we now know that even a relatively old forest like this can still capture and store a decent amount of carbon dioxide. The hemlocks around the tower are pushing 230. That's not terribly old by tree standards, but it's old for this part of North America—most of which was once clear cut. It's also old enough to challenge some previously held conventional wisdom about what kinds of forests are best for carbon sequestration. Previously, scientists thought only young forests, where the trees were still growing rapidly, did that job very well. Sites like the Hemlock Tower have shown a different story.

Also: It's rather terrifying to climb. The tower lives, it is not stationary. A network of steel cables keep it from toppling over, but you can still feel it tilting one way and then the other underneath you. And, at every landing on the stairs, there's a precarious little gap you have to step over. I took my camera with me in one hand as I made the ascent. About partway up, the filming quality takes a notable turn for the worse as I found myself clinging a bit more tightly to the hand rails. How's that for an awesome tool of science?

Video Link

I spent last weekend in the Harvard Forest, participating in hands-on science experiments as part of the Marine Biological Laboratory's science journalism fellowship. The goal was to give us an inside look at what, exactly, scientists actually do. When you're reading a peer-reviewed scientific research paper, where did all that data come from?

Sometimes, it comes from a swamp.

On Saturday, we walked into the Forest's Blackgum Swamp to take core samples out of the muck. There was no standing water in this swamp, at least not when we visited. But I wouldn't call the ground "solid", either. Instead, it was more like a moss-covered sponge. With every step, the ground beneath me would sink and smoosh. In some of the lower patches, that meant a shoe-full of water. In other spots, it was just a disconcerting sensation.

Taking core samples involves a little machine that's like a cross between a shovel and a straw. Made of heavy, solid metal, it has an extendable handle on one end. At the other, there's a hollow, cylindrical chamber that can be opened and closed by turning the handle counterclockwise. You drive the chamber into the ground, turn the handle, and then pull it back out. Once everything is back on the surface, you can open the chamber and see a perfect cylinder of earth, pulled up from below. That cylinder is removed from the chamber, wrapped in plastic wrap, labeled, and put in a long wooden box. Then you do all of that again, in 50 centimeter increments, until you hit stone. We got to about 475 centimeters—15 feet deep. By that point, you'll have collected 1000s of years of layered sediment.

This is not as easy as it sounds.

Second, as you get deeper, it becomes harder and harder to pull the coring tool back out of the hole. First off, there's the handle. Each extension adds weight and unwieldiness. Then, there's the swamp itself—water-saturated mud that forms a suction around the coring tool. By the end, it took three people to remove the tool from the ground—two to pull it out, and one to catch the comically tall handle as it emerged from the Earth. When the tool came out of the ground, it came with a gush of water, like we'd just struck oil, and indescribably hilarious squirpple-plushhh-blurp sound.

In this series of photos, you can see journalist Eric Niiler, one of my co-fellows in the program, push the coring tool into the ground and begin to take it back out. Bear in mind, this is early in the process. The handle was MUCH longer than this by the end.

In these final two shots, Harvard Forest director David Foster and scientist Rich McHorney open the cylindrical chamber and move a fresh core from the tool to a plastic wrap sheath.

Video Link

Read the rest of my series of dispatches from the Harvard Forest

I'm currently attending the Marine Biological Laboratory's 10-day science journalism fellowship. As part of that, I get to do some hands-on science experiments and get a better perspective on how the work of science is done and how data is collected. Along with five other fellows, I spent last weekend collecting A LOT of data in Massachusetts' Harvard Forest—3,500 acres of extremely well-documented wilderness.

All this week, I'll be posting some of the highlights from my trip—videos and photos that will introduce you to the Harvard Forest, how science is done in the field, and to some of the key ideas that I'm learning during my time here.

This will be the central access point for all those posts. Check back every day to see what's new.

In This Series:
Scientific Research in a Forest
How Past Land Use Affects the Current Landscape
How To: Collect 6000-year-old swamp mud
Climbing a rickety stair to the top of the forest
What's your diameter breast height?
The secret world of swamp mud

Do you see how the ground level is higher on the left-hand side of this photo? To the right of the stone wall, the ground distinctly drops by a foot or more.

That wall is more than 200 years old. It marks the border between what was once a plowed field (on the left) and grazing pasture (on the right). Today, this site is woodland—part of the Harvard Forest, the most-studied forest in the world. But for generations, this land was farmed by Jonathan Sanderson and his descendants. And, even two centuries later, you can still see the way different uses of the land changed the land.

For instance, the ground level is higher on the left because plowed fields erode more easily. This site is on a slight slope. Water runs downhill, toward the right hand corner of the photo. As it did that, it carried bits of plowed field along with it—sediment that washed up against the stone wall and stayed there. Over many years, the effect changed the level of the land.

This isn't necessarily a catastrophic thing. But it is change. I spent last weekend in the Harvard Forest, participating in science in a hands-on way as part of the Marine Biological Laboratory's science journalism fellowship. One of the things I learned during my stint in the forest: The past ain't past. History is recorded in geology and ecology as surely as it's recorded in books. Very cool stuff!

I spent Friday, Saturday, and Sunday in the Harvard Forest—the most-studied forest in the world. It's an interesting place, with a complicated history. Originally forest, it was clear-cut in the decades following European settlement. By 1830, less than 90% of this part of Massachusetts had any forest left. But that trend had already begun to reverse itself by 1850, spurred by urbanization and cheaper, more-efficient farming in the "West" (i.e., Ohio).

What is now the Harvard Forest was farmland for many years. Then it was used for tree plantations. Then it became forest again, studied first by Harvard University's forestry program in the early 20th century, and then by ecologists and other environmental scientists beginning in the 1980s. Today, these 3,500 acres are home to dozens of individual studies and long-term, interdisciplinary projects led by scientists from more than 15 universities and institutions.

This particular study, led by Dr. Jerry Melillo of the Marine Biological Laboratory, is studying the nitrogen and carbon cycles of forests, and how those cycles are affected by rising soil temperatures. They're trying to understand how climate change will affect the growth of wild plants, and how it will affect those plants' ability to absorb and store carbon dioxide. I'll get more in-depth on this study later. Right now, I thought that this site offered a really great view of what a research forest looks like—it's a chance to see detail-oriented science and wild nature interacting and overlapping.

Here's a couple more photos that will give you an idea of the kind of things you might find in a research forest.

They include electronics in odd places. This junction box delivers power that runs several sensors driven into the forest floor. Another key feature are various home-built collection systems meant to capture leaves and debris that fall off of trees. These baskets, and what's inside them, can help scientists back-calculate the volume of leaves the trees in this area grow in a given year.

Also common in a research forest: Lots and lots of signage and color-coded tags. In order for science to happen, you have to know exactly what you're looking at. When you make comparisons at the same spot over time, you have to know you're dealing with the same plants, or the same section of the woods. Signs help. You can't see it here, but the trees, themselves, are also labeled. In this particular study, every tree has a number that it wears tacked to its trunk like a little dog tag.

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