This is the third story in a multi-part series on taxonomy and speciation. It's meant to help you as you participate in Armchair Taxonomist — a challenge from the Encyclopedia of Life to bring scientific descriptions of animals, plants, and other living things out from behind paywalls and onto the Internet. Participants can earn cool prizes, so be sure to check it out! The deadline is May 20th

As depicted on Star Trek: The Original Series, the tricorder is a device that looks like the bastard love child of a Polaroid camera and a 1970s-era portable cassette deck. It was worn around the neck on a strap. It was black and clunky and definitely not what we would, today, call a sexy piece of electronics.

What made the tricorder a great piece of fictional technology wasn't its looks, but what it did. "Mr. Spock could use it to identify any organism, plant or animal, anywhere in the galaxy," said Carlos Garcia-Robledo, postdoctoral fellow in the department of botany at the Smithsonian's National Museum of Natural History. A portable tool that could quickly identify any species anywhere would be a game changer for science. Eventually, according to Garcia-Robledo and others, we'll have just that — put a piece of leaf or fur or insect leg into a machine and out pops its taxonomic information.

But what makes this really awesome is that — aside from the portable part — this is something we can actually do already. Garcia-Robledo does it regularly in his lab. The real-world tricorder isn't just something that's going to transform science someday. It's already doing that, right now.

The non-fictional tricorder is based on an idea called DNA barcoding, which originated in 2003 with Canadian biologist Paul Hebert. He thought there might be an easy way to quickly identify species using short DNA sequences that are unique to one species or another. If you had a database of these sequences, then all you'd have to do would be to match a sample to a sequence and you'd know what species you were looking at. It's similar to the way we store fingerprints, and then use those to match prints from a crime scene with an individual person.

Of course, like fingerprinting, DNA barcoding turns out to be more complicated than it sounds. The sequence most commonly used to barcode animals is a gene called CO1. It's a piece of mtDNA. This DNA is found inside the mitochondria — organelles within a cell that produce energy. It's there because, once upon a time, those mitochondria were independent bacteria, doing their own thing as single celled organisms. MtDNA doesn't create you, it creates parts of your cells.

The mitochondria, and their DNA, get passed down from generation to generation in egg cells — sperm don't usually have them. So you carry your mother's mtDNA. And she carries her mother's. But that mtDNA doesn't travel through the generations intact. Over time, it picks up little errors and changes to the sequence. This is where DNA barcoding — and its complications — come in.

Image: A room full of DNA sequencers, a Creative Commons Attribution (2.0) image from jurvetson's photostream

The idea is that the changes that happen to CO1 should be able to serve as a marker between species. In order for that to work, though, the mutation rate has to hit a sweet spot, said Karen James, a staff scientist at Mount Desert Island Biological Laboratory. She does a lot of work with DNA barcoding and described the ideal amount of variation in the DNA sequence as being a Goldilocks sort of problem. If you have too little variation (i.e., if the mtDNA doesn't change fast enough) then you'll have too many different species that share the same barcode. But if the mutations happen too quickly and you have too much variation, then you could get a bunch different barcodes within the same species. Either way, the barcode would be useless — just as if lots of people shared the same set of fingerprints.

The good news is that, for many animal species, CO1 hits that sweet spot. The bad news is that it doesn't work for everything. In fact, it doesn't work for plants at all. Their mtDNA changes too slowly. In 2009, James was part of a team that identified alternative DNA sequences that can be used to barcode plants.

CO1 also varies in how well it works for different kinds of animals. Like plants, mtDNA changes slowly in cnidarians — a phylum made up of more than 10,000 species, including many kinds of jellyfish. The plant sequences won't work for them, either, so cnidarians are notoriously difficult to barcode.

All of this explains part of why DNA barcoding can't really be used to identify new species. If you don't know the organism well enough to know how quickly its mtDNA are mutating, than you have no idea whether the changes you see represent a new species, or just variation within an old one. But that's okay, say researchers like Garcia and James. It doesn't mean DNA barcoding is useless. Think back to the tricorder, and what Mr. Spock actually did with it. He wasn't identifying new species. Instead, he was figuring out which previously-identified species lived on which planet.

Rolled leaf beetles. Carlos Garcia-Robledo pulled half-digested plant bits out of their stomachs and used the DNA from those samples to find out what the beetles were eating. Photo by Charles Staines.

DNA barcoding can be used, along with traditional taxonomy, to help identify new species. Paul Hebert demonstrated this in 2004, when he figured out that a single species of tropical butterfly was actually 10 species of tropical butterfly, cleverly masquerading as one. But naming new species and pinning them to a board really isn't what the tool is best at — and it's not the most interesting way to use it, either. Even though the tricorder of today currently takes up a space the size of a room, it's already being used to study the world far outside the lab.

For example, Carlos Garcia-Robledo uses DNA barcoding to study the relationships between beetles and the plants they eat. His team figured out how to extract plant DNA from a beetle's stomach. Compare that DNA to a barcode library, and you start to get a good idea of what different beetles in different places are chowing down on. That matters, because the beetle's diets are changing along with the climate. As habitats get hotter, some plants can't survive. So what happens to the beetles that eat them? Garcia-Robledo uses DNA barcoding to track those patterns of adaptation and extinction.

Turns out, DNA barcoding is very good at helping us answer questions of sustainability and environmental change. It's especially important in places where it would be really hard to understand biodiversity and species interaction simply by collecting and counting — like the oceans, for instance.

We know that things people do can affect ocean ecosystems. And we know that some parts of the ocean bear more of the brunt of this than others. In order to understand what those differences really mean for wildlife, Smithsonian invertebrate zoologist Allen Collins has started collecting samples of all the biodiversity in a plot of ocean — from bacteria to charismatic megafauna. DNA barcodes tell him exactly what species live there. He can go back and sample the same spot over time to see how the mix of species has changed. And he can compare those changes in places relatively untouched by humans to what's happening in areas that have a lot of human impact. What, exactly, does "human impact" mean for ocean animals? That's what he's going to find out.

There are even consumer applications. Earlier this year, the ocean advocacy group Oceana released a report showing that restaurants and grocery stores have a habit of selling customers one fish, but labeling it as another. In fact, 33% of the 1200 samples they took over two years were mislabeled. When you think you're buying red snapper, you're often actually buying much cheaper tilapia. The secret swaps can affect your health and they can also affect fish populations. All Oceana's data came from DNA barcoding, Karen James said.

So far, all of this relies on bringing the world back to the laboratory for testing. But the real, portable tricorder is inching closer. We often talk about the $1000 genome, in terms of being able to sequence the entire thing cheaply. But the same technology that's making that dream a reality also applies to the much easier and faster task of sequencing a small strand of genome — you just have to adapt the tools to the purpose of barcoding.

Last year, a company called Oxford Nanopore announced that it had developed a miniature genome sequencer that could plug into a laptop's USB port. The device, called the MinION, isn't the real-world portable tricorder. It's designed to sequence entire genomes, for one thing, which isn't really what DNA barcoders want. It's also a one-time-use tool that's expected to cost $900 a pop — if it ever makes it to the marketplace. But the MinION is a step in the right direction. Someday (and probably someday soon), scientists will be able to study changing ecosystems instantly, while they're standing in that ecosystem — just like Mr. Spock.

Samples of organisms that Allen Collins brought back to the laboratory from a research trip to Bali. Someday, he'll be able to skip this step.

PREVIOUSLY:
• What leeches and ligers can teach us about evolution
• In the leech library: Behind the scenes at the American Museum of Natural History
• Be an Armchair Taxonomist!: A challenge from The Encyclopedia of Life

Sierra magazine selected "7 of the World's Strangest Flowers." Above is video of the Touch-Me-Not, native to Central and South America but now growing many other places:

You might easily overlook this herb, with its dainty pink flowers and delicate, fern-like leaves. The mimosa pudica doesn’t just look demure, though. Barely touching its leaves causes them to fold inward and droop downward—hence the flower’s species name, pudica, Latin for “shy, bashful, or shrinking,” as well as its nicknames, “touch-me-not” and “shy plant.” The leaves usually reopen in a few minutes. Other stimuli, including warming and shaking the plant, produce the same phenomenon. The leaves fold and wilt in the evening, too, but they stay that way until sunrise…

Plants and animals have to adapt to live in high latitudes and chilly mountain environments. With animals, we kind of instinctively know what makes a creature cold-weather ready — thick, shaggy fur; big, wide snowshoe paws. But what are the features of cold-weather plants? It's one of those really interesting questions that's easy to forget to ask.

At The Olive Tree blog, Tracey Switek has at least one answer. In cold places, you see more plants that grow in little mounded clumps. Of course, plants can't really rely on huddling together to create warmth. So you still have to ask, "Why is it better to grow in a mound when it's cold out?"

The dome-like shape which the cushions tend to take (made possible by an adaptation that makes all the plants in the clump grow upward at the same rate, so no one plant is high above all the others), and the closeness with which those plants grow, makes these clumps perfect heat traps. The temperature on or inside a cushion can be up to 15 °C more than the air temperature above it. The cushions are able to retain heat radiating up from the soil, as well as absorbing heat from the sun (a very dense, large, clump of green can get surprisingly warm on a sunny day at high altitude). Add to that the fact that the wind speed in and around a cushion can be cut by up to 98% from open areas, you have a perfect recipe to prevent heat loss. Many alpine cushion plants also have very hairy leaves, which trap even more heat within. This allows the plants to maintain a relatively stable, warmer than average microclimate that is resistant to sudden changes in weather and temperature outside (such as freezing temperatures at night or sudden storms). Interestingly enough, this stabilizing effect can also be a benefit when it gets too hot out, maintaining lower temperatures against baking sunshine.

Very cool!

Read the rest of the story

Image: Michael Haferkamp, via CC

Frycook posted this fascinating video from the Apollo era on the BoingBoing Submitterator. The basic gist: Back in the day, NASA scientists tried exposing various crops—corn, lettuce, tobacco ... you know, the essentials—to moon dust. The plants weren't grown in the dust, exactly. Instead, it was scattered in their pots or rubbed on some of their leaves. In this study, the plants that were exposed seemed to grow faster than unexposed plants.

That's pretty interesting, so I dug around a little to find out more about these studies. Turns out, growing plants in lunar soil isn't quite as promising as the video makes it sound, but it's not a ridonculous idea, either. In 2010, scientists at the University of Florida published a review of all the Apollo-era research on this subject, which amounted to exactly three published studies. From that data, we can say that the plants weren't obviously affected in any seriously negative ways by their exposure to lunar soils—which is good—but we can't really say the plants grew better their terrestrial-only cousins, either.

In the end, and as recorded in the peer-reviewed scientific literature, there were only three published primary studies of seeds, seedlings, and plants grown in contact with lunar materials. In those three cases, small amounts of lunar material were used, and the plants were relatively large. In general, the dusting of plants or the mixing of lunar fines with other support media makes plant interaction with the lunar material a small part of the plant experience. At no point were plants actually grown in lunar samples in the way that one might imagine, with the entire root structure growing through and in constant association with a lunar soil. It is no accident that the wording of most of the titles of the studies, as well as the careful discussion within the papers, refers to growth “in contact with” lunar samples—not “in” lunar samples. With only a small portion of the roots, for example, interacting with the lunar materials, it is likely that plant responses to the lunar materials were, therefore, quite attenuated due to the lack of an extensive plant/lunar soil interface. Biophysical issues, such as root penetration of dry and variously hydrated lunar sample types, were completely unaddressed. Thus, the effects of actual growth within lunar soils were simply not a part of the plant studies of the Apollo era.

On the other hand, in 2008 scientists with the European Space Agency tried growing marigolds in a medium of crushed rock—basically the much-cheaper equivalent of growing plants in moon "soil". There's no indication that the marigolds did better than those grown in real dirt, but they did grow and they did survive (even without any added fertilizer), which could be indirect evidence in support of the Moon gardeners of the future.

Watch the video on YouTube

Read a 1969 newspaper clipping about the NASA experiments

Read the 2010 review paper—available for free, in its entirety

Read a BBC story about the 2008 marigold experiment

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

This is the town of Kivalina, Alaska. Last fall, when the ocean water that almost surrounds the town started turning a gooey orange, people (understandably) got a bit freaked out.

After ruling out the scarier options—i.e.,chemical pollution and toxic algae—scientists eventually pinned the orange tide on the presence of a plant fungus. And they turned up some good news: The fungus wasn't dangerous to people or ocean life.

Now, months later, researchers have identified what, exactly, the fungus is and where it was coming from. There's a fascinating detective story here, because, as Jennifer Frazer points out on Scientific American's Artful Amoeba blog, it's rather surprising that there was a fungal epidemic big enough to turn a whole port orange and nobody noticed it on the plants.

[But] Perhaps someone did.

Last October, David Wartinbee, a professor of aquatic biology at Kenai Peninsula College in Alaska’s south-central Kenai Peninsula, emailed me to say he’d seen something strange, and wondered if it might be the same thing that hit Kivalina. Though his neck of the woods is over 600 miles southeast from Kivalina as the snow goose flies, it’s not inconceivable they could be one in the same in a place so far north.

In early September, Wartinbee traveled 70 miles west to a place called the Twin Lakes by float plane (reputedly the SUV of Alaska). He saw an orange film on the water, and the spruce needles on nearby trees were clearly poxed with something.

You can read the rest of this story (and see Wartinbee's photos!) at The Artful Amoeba.

The oldest living thing on Earth is a massive "meadow" of sea grass growing in the Mediterranean between Spain and Cyprus. It's somewhere between 100,000 and 200,000 years old and reproduces by cloning itself. Also, it's being killed by climate change.

This is not the best photo, but it is pretty damn mind-blowing. What you see here is Jerry Glover, National Geographic Emerging Explorer, holding the root system of a single perennial wheat plant. The photo was taken by Scientific American editor Mariette DiChristina at the Compass Summit in Palos Verdes, California.

There's more to this than just a freaky looking plant dreadlock. That root system represents something far bigger than itself: Soil health. Perennial plants build soil and protect against erosion in ways annual plants and their skimpy root structures simply cannot. It's why, since large-scale corn farming replaced perennial prairie, Iowa has lost some 8 vertical inches of precious topsoil. Glover's argument: To protect our farming resources for future generations we need to pay more attention to the potential benefits of perennial crops.

Beachgoers in Qingdao, Shandong province, China, were met with a fuzzy, green blanket of ocean last week, as the water there exploded with algae.

You've heard before about dead zones. These are patches of coastal ocean where river runoff full of fertilizer chemicals have produced massive algae blooms. As the algae die, their decomposition reduces the oxygen level of the water to the point that many fish and other aquatic life can no longer live there.

This is what a dead zone looks like, just before the death.

It's worth noting, when I pulled this photo out of the Reuters files, I could see similar shots, taken on the same beach, in 2010, 2009, and 2008. This isn't a fluke. It's an endemic problem.