My main purpose in writing this little book, was to place in a permanent form a description of my wonderful preservation from death in a chance encounter with a Royal Bengal Tiger. My life had been adventurous up to that time. I had shot big game of various kinds. But this episode, so marvellous in itself, so important in its influence upon my after life and character, marks the close of my career as a hunter of big game.

Illustrative plates from How I Killed the Tiger (1902) ]]> http://boingboing.net/2013/05/17/howto-kill-a-tiger-1902.html/feed 14 http://boingboing.net/2013/05/17/what-tigers-and-kiwi-birds-hav.html http://boingboing.net/2013/05/17/what-tigers-and-kiwi-birds-hav.html#comments Fri, 17 May 2013 19:51:24 +0000 Maggie Koerth-Baker http://boingboing.net/?p=230935 Beyond the risk of inbreeding, genetic diversity supplies the tools that help a species adapt to change. If there's not enough of it, then the species is more likely to die out when subjected to stressful conditions ... like, say, climate change. ]]> http://boingboing.net/2013/05/17/what-tigers-and-kiwi-birds-hav.html/feed 6 http://boingboing.net/2013/05/16/mammal-school.html http://boingboing.net/2013/05/16/mammal-school.html#comments Thu, 16 May 2013 12:26:35 +0000 Rob Beschizza http://boingboing.net/?p=230649 http://boingboing.net/2013/05/16/mammal-school.html/feed 11 http://boingboing.net/2013/05/15/the-technology-that-links-taxo.html http://boingboing.net/2013/05/15/the-technology-that-links-taxo.html#comments Wed, 15 May 2013 15:28:23 +0000 Maggie Koerth-Baker http://boingboing.net/?p=230283

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

Via Graham Linehan, "a #unicornchaser from yesternet." Previously: Do not mess with baby deer.]]> http://boingboing.net/2013/05/09/deer-steals-wife.html/feed 25 http://boingboing.net/2013/05/08/whats-climate-change-ruining-4.html http://boingboing.net/2013/05/08/whats-climate-change-ruining-4.html#comments Wed, 08 May 2013 20:51:53 +0000 Maggie Koerth-Baker http://boingboing.net/?p=229077 The warmer it gets in the American Midwest, the more painted turtle society turns into whatever the opposite of a sausage fest is. Now, depending on your personal inclinations, you could argue that this might actually improve turtle sex — but it definitely puts a damper on creating new generations of baby turtles. ]]> http://boingboing.net/2013/05/08/whats-climate-change-ruining-4.html/feed 17 http://boingboing.net/2013/05/06/bee-deaths-and-historical-cont.html http://boingboing.net/2013/05/06/bee-deaths-and-historical-cont.html#comments Mon, 06 May 2013 19:09:28 +0000 Maggie Koerth-Baker http://boingboing.net/?p=228616 "Colony Collapse Disorder" is probably more than one thing, with more than one cause. Another important detail to keep in mind as you read media reports on bee deaths — the collection of symptoms that we call Colony Collapse Disorder is also probably a lot older than you think. In a guest post at Bug Girl's blog, bee expert Doug Yanega explains that CCD didn't start in 2006. In fact, periods of mass bee die-offs with the same collection of symptoms have been recorded at least 18 times, dating back to 1869. ]]> http://boingboing.net/2013/05/06/bee-deaths-and-historical-cont.html/feed 0 http://boingboing.net/2013/05/06/a-beautiful-bacterium.html http://boingboing.net/2013/05/06/a-beautiful-bacterium.html#comments Mon, 06 May 2013 16:41:55 +0000 Maggie Koerth-Baker http://boingboing.net/?p=228577

David Goodsell of the Scripps Research Institute made this lovely watercolor illustration of a cell of Mycoplasma mycoides. This bacterium is the cause of a deadly respiratory disease that affects cattle and other cud-chewing animals.

If you've ever read much about zoonoses — diseases that pass from animals to humans — then you know that the domestication of livestock played a huge role in introducing many diseases to people. Living in close proximity to the animals we ate provided ample opportunities for those animals' diseases to jump over to us. What's interesting about Mycoplasma mycoides is that it represents a disease of animals that seems to have its origins in domestication, as well.

In 2012, scientists found evidence that suggests domesticating livestock — a process that resulted in closer living conditions for the animals and in animals from one herd being moved to other herds they likely wouldn't have otherwise had contact with — helped Mycoplasma mycoides evolve and spread. Today, different species of Mycoplasma mycoides cause a range of diseases that can kill between 10 and 70 percent of the cows they infect.

Goodsell's illustration is an attempt to show all the different parts of the bacterial cell, in the shapes, sizes, locations, and concentrations that those parts take in the real world. If you go to his site, you can see a legend explaining what everything is.

Writer Darren Naish, who blogs at Tretrapod Zoology, took this photo of a Larus gull attempting to chow down on an awkwardly shaped starfish. (And, really, are there any other kind of starfish? Especially when you're trying to fit them in your mouth whole?)

You might remember Larus gulls from a recent piece I wrote on speciation and evolution. According to Naish, they might have another place in the story of evolution, as well. Regardless of how Sisyphean this gull's dinner plans may appear, Larus gulls actually (successfully) eat a lot of starfish. So many, in fact, that, as Naish explains in a recent post, they might be prompting one species of starfish to slowly turn a different color — an adaptation that makes the species less visible to gulls.

David Mizejewski writes:

The video below shows some fascinatingly odd animal behavior that I've never heard of before: baboons stealing stray puppies from their mothers and raising them as part of their troop. This kind of interspecies interaction where one species raises another species specifically for companionship and protection--in other words, keeping pets--is behavior that is typically attributed only to humans. To see it happening with baboons and dogs is nothing short of amazing.

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.

Please enjoy this very serious, scientific Tumblr that posts exactly what it promises — pictures of the strange and fantastic creatures that live deep in the ocean ... with googly eyes photoshopped onto their bodies.

The specimen above is an animal known as the pigbutt worm. Yes, seriously. With the googly eyes in place, you can't quite get a full understanding of how weird looking this animal is, so please be sure to check out the "before" photo, as well.

The site is maintained by a deep sea ecologist (he's anonymous, but I've verified that this is true). So you can trust the information provided here. For instance, when readers ask how the heck a pigbutt worm counts as a worm:

The pigbutt worm, Chaetopterus pugaporcinus, is a very weird looking worm, for sure. All Annelid worms are segmented, and the pigbutt is no exception. If you look at an ordinary earthworm, you can see those segments, but in Chaetopterus pugaporcinus, the middle segments are super inflated compared to the rest of its body. The rear segments are visible in the area that looks like the anus on a mammal’s buttocks (although others have noted that this section of the pigbutt worm looks more like a disembodied vulva than a floating buttock).

Black leopard compared to black house cat. "Duality," directed by Rich Kuras.]]> http://boingboing.net/2013/04/05/black-leopard-compared-to-blac.html/feed 20 http://boingboing.net/2013/04/04/a-cat-video-about-the-science.html http://boingboing.net/2013/04/04/a-cat-video-about-the-science.html#comments Thu, 04 Apr 2013 19:26:40 +0000 Maggie Koerth-Baker http://boingboing.net/?p=222987

Two things I learned from this video:
1: I am my cat's Facebook page. That rubbing-up-against-you-and-leaving-scent thing? It's not just to mark you as "theirs". It's also a way of communicating information about themselves to other cats that you might encounter.
2: My cats poop in a box and bury it as a gesture of submissiveness to me. Good cats.

"That's the stuff: Ralph The Cat," a photo by Darren Sethe of Portland, Oregon, shared in the Boing Boing Flickr pool.]]> http://boingboing.net/2013/03/30/caturday-8.html/feed 4 http://boingboing.net/2013/03/21/the-fish-of-nightmares.html http://boingboing.net/2013/03/21/the-fish-of-nightmares.html#comments Thu, 21 Mar 2013 20:43:47 +0000 Maggie Koerth-Baker http://boingboing.net/?p=220185

This is not a Photoshop job. This is the very real toothy smile of sheepshead fish. It lives in North America, writes Becky Crew at the Running Ponies blog. And, like humans, it has both incisors and molars — perfect for masticating an omnivorous diet. Apparently, they also taste good, which should be some consolation. Worse comes to worse, we can always eat them.