All this month, we've been telling you about a fantastic challenge from the Encyclopedia of Life. Called Armchair Taxonomist, it's an opportunity to research and write about different plants, animals, fungi, and microscopic organisms — and, in the process, help move scientific information from places where it's hard for most people to see, to an open-access sandbox on the Internet.

If you've taken the time to write up an entry, fantastic. We're looking forward to reading them. You've also got a shot at the great stuff up for grabs — including a private, behind the scenes tour of the Smithsonian's National Museum of Natural History. If you've not entered yet, though, this is the last weekend you can. The deadline is Monday, May 20th at 6:00 pm Eastern.

Read all about the Armchair Taxonomist challenge.

And be sure to check out the stories in BoingBoing's taxonomy series:
• Learn what leeches and ligers can teach us about evolution
• Meet the model animals against whom entire species are judged
• Find out what taxonomists and Mr. Spock have in common

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

This is the second story in a four-part, weekly 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!

On the sixth floor of New York's American Museum of Natural History — far away from the throngs of tourists and packs of schoolkids — there is a cold, white room, filled with white, metal cabinets.

The cabinets are full of dead things; leeches, sea anemones, lobsters ... any kind of invertebrate you can imagine. Even a giant squid. All of them have been carefully preserved. Each soaks in its own, luxuriant ethanol bath. Here they sit, some for a hundred years or more, waiting for scientists to pull them out into the light.

It's a bit like the final scene of Raiders of the Lost Ark, but for slimy, crawly, spineless things. There are collections like this all over the world, containing every species of animal, plant, and microscopic organism. Together, they serve as a record of Earth's biodiversity, a library of life. In them, you'll find more than just random specimens. Some of the individuals are special. Called "type specimens", they serve as ambassadors for their species, real-world models that define what each species is. For instance, the leech species Myxobdella maculata is both a group of leeches and exactly one leech — A leech that I got to meet on a behind-the-scenes tour with invertebrate curators Estefania Rodriguez and Mark Siddall.

Estafania Rodriguez stands in the invertebrate collections room at the American Museum of Natural History. Behind her, you can see a row of expanding cabinets used to store many different invertebrate species. These are like the library stacks, where average specimens are organized by phylum, class, order, family, genus, and species.

The specimens stored in these cabinets are meant to demonstrate diversity, the broad range of what different animals within a single species can look like. "We've got a huge collection of lobsters," Mark Siddall said. "I had a guy come in and wanted to measure all the different antenna lengths of lobsters from a huge variation across space and time to see if that's something that changes."

Across a narrow aisle are the rows of immobile cabinets that house type specimens — individual animals that serve as the definition of what an entire species ought to be like. These are the "sacred" specimens. For each species, there is only one official model animal — the holotype — in the entire world.

When scientists find a new animal, they use holotypes to figure out which species it belongs to — or whether it might represent something entirely new that we haven't seen before. It's a simple game of deciding whether a new specimen is more like one holotype or another.

"They look horrible when they are dead," said Estafania Rodriguez, holding a small jar containing a type specimen of a sea anemone from the Arctic. In another jar, she had a type specimen of an Antarctic anemone. One of her current projects involves figuring out how closely related these two species are. There's a possibility that they might be a single, bi-polar anemone.

Color doesn't preserve well in alcohol, so even the most rainbow-hued small invertebrate can end up looking like a brown lump. Because of that, some of the information about each specimen is lost — preserved in words and drawings, rather than flesh. But this is still the best way to do it. "They loose much more information if they dry out," Siddall said. Preserving the body, even in a less-attractive state, allows scientists to come back and study both internal and external anatomy.

The museum has had collections like this since it was founded in 1869. But, over the years, the methods for storing the specimens have changed. Rodriguez pointed out these jars, sealed with white gaskets. Until recently, the jars used a red rubber gasket. Unfortunately, it turned out that the red gasket dissolved into the alcohol, damaging the specimens. It also turned brittle, allowing alcohol to evaporate. And, if that wasn't enough, the dissolved red gasket was also toxic. "You live, you learn," Siddall said.

In fact, the collections room, itself, was an innovation in specimen storage, Siddall said. It's only about a decade old and is designed to reduce the risk of fiery destruction — a big deal when you're talking about a room full of ethanol. The ceiling was covered in fire-resistant foam and dotted with sprinklers. It's also engineered to support the weight of hundreds of alcohol-filled jars.

Of course, that brings up an important question. Fire, floods, theft — these are all things that can happen. What do you do if you lose a holotype?

In this photo, Mark Siddall shows me a brown blob of preserved leech at the bottom of a vial. The drawer next to him is full of not only holotypes, but also backup specimens, called paratypes. Collected in the same place, at the same time, as the holotype, paratypes help scientists understand diversity within a species. And, in the event of the holotype's demise, they can step in and take its place. When that happens, the paratype becomes known as a neotype.

A holotype and its paratypes are usually stored in different places. That's a safety precaution, but there are other reasons for doing it, as well, including making sure that the natural heritage of other countries doesn't all end up in boxes in New York and London. Here, Siddall holds a leech paratype that he collected in Madagascar in 2002. "The holotype went to Madagascar where it belongs," he said.

This is the holotype of the species Myxobdella maculata. It was found in 1914, in what was then the Belgian Congo. Scientists Herbert Lang and James Chapin went into the Congo basin in 1909. They meant to stay a year. There were there for six years. When they finally returned, they brought with them hundreds of thousands of specimens, including 100,000 invertebrates alone. Neither of them were invertebrate specialists, however. So this leech and many others like it sat in the collections, unnamed and unnoticed until 1939 when zoologist John Percy Moore pulled it out, identified it as a species, and gave it a name.

And there's nothing particularly weird about that story. Even today, the invertebrate collections contain unidentified material. People like Siddall, who specialize in one animal, will come back from expeditions with animals they aren't familiar with. Those sit in the collection, waiting for specialists to come along and examine them more closely.

It's also worth noting that all the type specimens — whether holotype or paratype — come with more than just a name. Every label tells a history; who found the specimen, when did they find it, where was it found, and who described it and gave it a name. Some even have latitude and longitudinal coordinates. That information helps scientists match the right research papers to the right type specimen. It also helps them make comparisons across time and space. If somebody finds a Myxobdella maculata in the Democratic Republic of the Congo today, they can set it side-by-side with the holotype and see whether evolution has been at work on the species.

"With mollusks, especially, we get people who want to donate us their shell collections," Siddall said. "And that's very nice and very generous. But if I don't know where it's from, when it's from and all of that information, then the specimen is of almost no scientific value."

At the very end of my tour, Estefania Rodriguez pointed out a large container, about the size and shape of a trash dumpster, sitting ominously at the end of the aisle. "There's a giant squid in that tank," she said.

Unfortunately, I didn't get a chance to see inside. Like all the other specimens, the squid is floating in ethanol. But because it's a giant squid, it's really an awful lot of ethanol. "Because of the vapor pressure inside, opening it requires four people and a fire department," Siddall said. "And when you lift the lid, it's like a big calamari martini."

PREVIOUSLY:
• What leeches and ligers can teach you about evolution
• Become an Armchair Taxonomist! A challenge from The Encyclopedia of Life

This is the first story in a four-part, weekly 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!

If you aren't totally clear on what constitutes a species, or how scientists draw the line between one species and another, don't feel bad.

Quite frankly, the scientists are a little shaky on this stuff, as well.

That's because species aren't easily defined, and there's a lot of debate over whether an individual animal, plant, fungus, or bacterium belongs in one species group or another. In fact, if you want to know what a species is, it's best to not bother trying to grope for a strict definition, taxonomists told me. Instead, every species is really a hypothesis. "It's a testable conjecture," said Mark Siddall, curator of the phylums Annelida and Protozoa at the American Museum of Natural History. "It's a hypothesis about common ancestry, and the recency of that common ancestry."

But that hasn't always been the case.

A lot of the language we use to talk about taxonomy today was handed down from the work of 18th-century European scientists. These men, including Carl Linneaus (who is called the father of taxonomy), were working off of a very different understanding of the world. To them, taxonomy was mostly about organizing the natural world that had been given to humanity, in its current form, by God.

From their perspective, the deity created things separately, and those things had remained separate. So all you had to do was look around and spot the obvious difference between one group of things and another. Leeches were very clearly different from lions. Plants with three leaves and yellow flowers could be separated from plants with four leaves and red flowers. It was a human responsibility, as God's bookkeepers, to assign names to those distinct groups.

The trouble is, that view has some pretty obvious flaws, right off the bat. Yes, there are clear delineations between a leech and a lion. But what about between leeches?

This is a leech.

And so is this.

Leeches come in a rainbow of different colors, shapes, and sizes. They live in different places. They eat different things. (In fact, there are a surprising number of leeches that do not want to suck your blood.) And how do you draw the line between a leech and a worm? It's not always an open-and-shut case.

Yup. Still totally a leech.

Today, scientists recognize roughly 700 different species of leeches, Siddall said. We also know that leeches, as a whole, are themselves a sub-class. Those 700 leech species are all types of segmented worm.

All of this flows out of our understanding of evolution. When we say those 700 species are all types of leech, we're saying that we think they share a common ancestor. When we say that leeches are a type of worm, what we're really saying is that leeches and worms share a common ancestor — and that that ancestor is not as recent as the one shared by all the different leeches.

Those are hypotheses, and they could be wrong. Because evolution is an ongoing process, the relationships those hypotheses describe could also change.

"In some ways we're still at a very early stage in taxonomy, despite doing this for 250 years," Ellinor Michel said. She's a researcher with London's Natural History Museum and an expert on mollusks. Everybody agrees that nature is clustered in units, she said, but that's about where the agreement ends. "Some people think that if you knuckle down, we'll find the right clusters to put everything in. Others say that 'what is a species' is driven by the perspectives of individual scientists and the changing needs and desires of society.".

"But wait!" you may be thinking. "Isn't this also about sex?"

Pictured: A liger.

Back in junior high and high school, sex was probably a big part of what you learned about species. In order for two living things to be part of the same species they have to be able to get it on, and make a baby — and that baby has to be capable of becoming a parent.

That's not a bad rule of thumb to start off with, Michel and Siddall say. In fact, some of the earliest work Ellinor Michel did as a taxonomist involved taking many different snails from the bottom of Tanzania's Lake Tanganyika and trying to see which ones would mate together.

"I tried to set up these little breeding experiments. I had a bench covered with little dishes of snails at the University of Burundi," she said. "But we didn't know what to do to make the snails happy enough to mate. It was a complete exercise in futility."

Today, she says, scientists agree that ability to interbreed doesn't count if you have to force it. There are examples of captive lions and tigers having baby ligers (or tigons, depending on which species is the mother and which is the father). Ligers can even produce offspring of their own. But we don't say that lions and tigers are the same species, partly because there aren't any well-documented cases of the two animals reproducing together in the wild, without urging from humans.

The process of evolution also helps to make the sexual definition of species problematic. Living things adapt to their habitats. When the habitat changes, you start to see behavioral and biological changes that can end up leading to the creation of a whole new species, somewhere down the road.

Larus gulls are one of the big examples of this. Larus is a genus, comprised of several different species, some of which live in a circle around the North Pole. One species of Larus gull lives in Norway. Another lives in Russia. Others live in Siberia, Alaska, Northern Canada, and England. The Larus gulls that live in England can interbreed with the Larus gulls that live in Canada. But they can't interbreed with the ones from Norway. As the Larus gulls' common ancestor circumnavigated the pole, its descendants ended up more and more different from the original population that had been left behind. By the time Larus gulls met Larus gulls again, they were so different as to be unable (or unwilling) to produce chicks together. But scientists consider every step in that process to be a different species — not just the gulls at either end of the broken ring.

All of this is really about species as groups — hypotheses that mark the temporary boundaries between one group and another and help us understand how different groups are related.

But species are also individuals. Very specific individuals, in fact. Next week, I'll take you behind-the-scenes at the American Museum of Natural History in New York to meet a type specimen — an individual animal by which all other animals in the species are judged.