More complicated than you think

Biodiversity

A new, giant virus is confounding old certainties

BIODIVERSITY is not just a matter of tigers and whales, or butterflies and trees, or even coral reefs and tuna. It is also about myriad creatures too small to see that live in numbers too large to count in ways too numerous to imagine. It is easy to forget, especially at meetings like the one to discuss the Convention on Biological Diversity that has been taking place in Nagoya under the auspices of the United Nations, that most of biology is in fact microscopic. Indeed, the more microscopic biology gets, the more diverse it becomes.

In that context, the discovery by Curtis Suttle of the University of British Columbia and his colleagues of a critter they propose to call Cafeteria roenbergensis virus, or CroV, should not be surprising. But for those brought up on a textbook definition of what a virus is, it is still a bit of a shock. For CroV is not a very viruslike virus. It has 544 genes, compared with the dozen or so that most viruses sport. And it may be able to make its own proteins—a task that viruses usually delegate to the molecular machinery of the cells they infect.

CroV, as its full name suggests, is a parasite of Cafeteria roenbergensis, a single-celled planktonic organism that was itself discovered only in 1988. Despite the recentness of its discovery, C. roenbergensis is one of the commonest creatures on the planet. It is also reckoned by some, given that it hunts down and eats bacteria, to be the most abundant predator on Earth. It is found in every ocean. The samples of C. roenbergensis from which Dr Suttle and his team extracted their quarry were collected off the coast of Texas.

To see a world in a grain of sand

That quarry’s nature, reported this week in the Proceedings of the National Academy of Sciences, is not a complete surprise. A larger virus, called Mimivirus, which lives in freshwater amoebas, turned up in 2003 and a few other, similar, viruses have been found since then. But CroV is by far the biggest to come out of the sea.

Those who like their categories cut and dried may wonder whether viruses are alive or not. Wise biologists do not struggle too much with such questions. Viruses have genes, can reproduce and are subject to the evolutionary pressures imposed by natural selection. That is enough for biology to claim them. As for CroV, those 544 genes (composed of 730,000 base pairs, the DNA letters in which the language of the genes is written) mean its genome is bigger than those of several bacteria—creatures which everyone agrees are alive.

The problem with categorical thinking in biology is that evolution does not work like that. It actually works by whatever works working. If an organism can successfully subcontract part of the business of metabolism to another while retaining the rest itself, rather than offloading the whole lot as most viruses do, then there are no rules to stop it happening.

CroV seems to do just that. Besides the genes that relate to protein synthesis it has others which encode DNA repair mechanisms and still others which are involved with protein recycling and signalling within cells. This is not mere hijacking. It is tantamount to a complete personality transplant for the infected cell.

About a third of CroV’s genes are similar to Mimivirus genes, suggesting they share a distant ancestor. On the other hand, two-thirds are not. A significant chunk of them seem to have been copied from bacteria. But the majority are unique, and previously unknown to science. A whole new chapter of life, in other words, has been opened.

This discovery, then—and the earlier one of C. roenbergensis itself—speak volumes, albeit in a microscopic language, about biodiversity. Two centuries after Carl Linnaeus invented the system now used to describe it, and a century after Charles Darwin worked out what causes it, the ability of that diversity to surprise is still staggering.

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Full article and photo: http://www.economist.com/node/17358573

Five Best Books on Animal Survival

To Know a Fly

By Vincent G. Dethier (1962)

Vincent Dethier spent a lifetime researching the senses, in particular those of insects. His “To Know a Fly” (not an easy task—there are more than 50,000 species) is an exuberant investigation of such matters as taste, hunger and satiation and their role in the survival of the humble housefly. He observes that a pregnant female fly will stop consuming sugar—an “adequate food for her, but useless for her eggs,” preferring instead protein that is good for the eggs but won’t nourish her. “In some quarters it would be hailed as maternal instinct,” he writes, “and by so naming it we would be no nearer an understanding of what it is.” Dethier’s learning from countless fly experiments is vast, but he is bracing in his acknowledgment of what remains unknown. “To espouse ultimate understanding of even so simple a brain,” he says, “reflects an optimism outside the natural order.” But he is entirely convincing when he says that a properly conducted experiment is “an adventure, an expedition, a conquest” and that to know a fly “is to share a bit in the sublimity of Knowledge.”

Nerve Cells and Insect Behavior

By Kenneth D. Roeder (1963)

This book presents Kenneth Roeder’s most famous discovery—that some moths are able to detect the calls of echo-locating bats and employ defensive measures to evade the predators. The revelation was made all the more remarkable by its timing: only a few years after Donald Griffin astonished the scientific community in 1958 with his revelation that bats “see” the world with their ears. Roeder examines the senses and behavior of insects at the level of neural mechanisms, and along the way we learn about not only the tactics of escape-artist moths but also about the evasive maneuvers of cockroaches and other insects. The study is the product of neuron monitoring via electrical eavesdropping, which means that there is a lot of technical writing in “Nerve Cells and Insect Behavior”—a fascinating work if you stay with it.

Desert Animals

By Knut Schmidt-Nielsen (1964)

Despite extremes of heat and lack of water, the desert is home to “a richer animal life than we can imagine,” Knut Schmidt-Nielsen says in this pioneering study. The animals that survive in such extreme conditions are aided by a variety of adaptations. For instance, the camel’s body temperature fluctuates wildly—camels start out “cold” in the morning so that they overheat less easily later in the day. The kangaroo rat’s kidney produces only small amounts of highly concentrated urine, enabling the animal to forgo water for long periods and live on air-dried food. After reading Schmidt-Nielsen’s evocation of a world where countless hardy animals thrive, you’ll never again look at a desert expanse and think it barren.

Honeybee Democracy

By Thomas D. Seeley (2010)

In ‘HONEYBEE DEMOCRACY,’ Thomas Seeley explains how a honeybee colony divides and reproduces: A contingent of 10,000 bees or more communicate among themselves and arrive unanimously at a decision about the best available new home. Building on a lifetime of observation and experimentation, Seeley relates the story with admirable clarity as we see his beloved honeybees—which have been in the consensus-building business for perhaps 200 million years—embark on the establishment of a new outpost. The process begins with a few scout bees and involves a vigorous debate before an agreement is reached. Then, on a signal, the group leaves en masse for the chosen place, likely a hollow tree some kilometers distant that the majority of the bees have never seen before. This spirit of cooperation, Seeley says, has much to tell us about solving complex human problems.

The Beak of the Finch

By Jonathan Weiner (1994)

Darwin made the Galápagos finches famous, but biologists Peter and Rosemary Grant and their graduate students deepened our understanding of how these small birds have survived and adapted across the centuries. Darwin supposed that the various kinds of finches, with their varying beaks and body sizes, came from diverse genetic backgrounds. But he later concluded that the finches were closely related and had thus likely evolved from a common stock. The Grants—working for three decades on the islands—bolstered Darwin’s insight that species are not immutable, as had been thought. One potential problem with Darwin’s theory had been that species appeared to be largely static, but the Grants succeeded in showing that evolution can be very rapid—beak shapes could change from year to year in response to, say, heightened mortality rates caused by food scarcity. Evidence of speedy adaptation has added meaning today as we witness insects becoming resistant to insecticides and bacteria surviving despite the most potent antibiotics.

Mr. Heinrich is the author of “The Nesting Season: Cuckoos, Cuckolds, and the Invention of Monogamy.”

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Full article and photo: http://online.wsj.com/article/SB10001424052702304510704575562250721139246.html

Cracking the Mystery of How Sloths Got Long Necks

NO RIBS? An anatomical quirk may tell why sloths have up to 10 vertebrae.

It is not quite how the elephant’s child got his long nose, but still it is research worthy of Rudyard Kipling: scientists said Monday that they have figured out how sloths got their long necks.

Throughout the animal kingdom, most mammalian creatures, from mice to giraffe, have a seven-vertebrae neck.

Sloths, however, are a puzzling exception. They can have as many as 10 vertebrae, posing one of the enduring enigmas for scientists, who have long wondered what explains the anatomical quirk.

Scientists at the University of Cambridge in England said they now think they have the answer.

After analyzing the development of the vertebral column in sloths they made a startling discovery: the part of the skeleton which they had long believed to be part of the sloth rib cage is, in fact, analogous to the bottom of the mammal’s “neck.”

In other words, the bottom neck vertebrae of sloths show a similar sequence of development as the top rib cage vertebrae of other mammals, both of which start at eight vertebrae down from the head.

The research, published Monday in the journal The Proceedings of the National Academy of Sciences, showed that the bottom “neck” vertebrae of sloths are developmentally the same as rib cage vertebrae of other mammals — just without ribs.

“Even though they’ve got eight to 10 ribless vertebrae above the shoulders, unlike the seven of giraffes, humans, and nearly every other species of mammal, those extra few are actually rib cage vertebrae masquerading as neck vertebrae,” said Robert Asher, of the zoology department at Cambridge.

By observing the position of bone formation within the vertebral column, they determined that all mammals, including sloths, are similar in when they develop the eighth vertebra down from the head — whether or not it is actually part of the neck.

The unusual anatomy has to do with how the sloth evolved millions of years ago, in contrast to other mammals.

The Cambridge researchers said the new results support the interpretation that the limb girdles and at least part of the rib cage derive from different embryonic tissues than the vertebrae, and that during the course of evolution, they have moved in concert with each other relative to the vertebral column.

In sloths, the position of the shoulders, pelvis, and rib cage are linked with one another, and compared to their common ancestor shared with other mammals, have shifted down the vertebral column to make the neck longer, the researchers said.

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Full article and photo: http://www.nytimes.com/2010/10/19/science/19sloth.html?_r=1&ref=science

Scientists Square Off on Evolutionary Value of Helping Relatives

NO ANT EGGS OF THEIR OWN Dr. William Hamilton believed that helping your relatives could spread your genes faster

Why are worker ants sterile? Why do birds sometimes help their parents raise more chicks, instead of having chicks of their own? Why do bacteria explode with toxins to kill rival colonies? In 1964, the British biologist William Hamilton published a landmark paper to answer these kinds of questions. Sometimes, he argued, helping your relatives can spread your genes faster than having children of your own.

For the past 46 years, biologists have used Dr. Hamilton’s theory to make sense of how animal societies evolve. They’ve even applied it to the evolution of our own species. But in the latest issue of the journal Nature, a team of prominent evolutionary biologists at Harvard try to demolish the theory.

The scientists argue that studies on animals since Dr. Hamilton’s day have failed to support it. The scientists write that a close look at the underlying math reveals that Dr. Hamilton’s theory is superfluous. “It’s precisely like an ancient epicycle in the solar system,” said Martin Nowak, a co-author of the paper with Edward O. Wilson and Corina Tarnita. “The world is much simpler without it.”

Other biologists are sharply divided about the paper. Some praise it for challenging a concept that has outlived its usefulness. But others dismiss it as fundamentally wrong.

“Things are just bouncing around right now like a box full of Ping-Pong balls,” said James Hunt, a biologist at North Carolina State University.

Dr. Hamilton, who died in 2000, saw his theory as following logically from what biologists already knew about natural selection. Some individuals have more offspring than others, thanks to the particular versions of genes they carry. But Dr. Hamilton argued that in order to judge the reproductive success of an individual, scientists had to look at the genes it shared with its relatives.

We inherit half of our genetic material from each parent, which means that siblings have, on average, 50 percent of the same versions of genes. We share a lower percentage with first cousins, second cousins and so on. If we give enough help to relatives so they can survive and have children, then they can pass on more copies of our own genes. Dr. Hamilton called this new way of tallying reproductive success inclusive fitness.

Each organism faces a trade-off between putting effort into raising its own offspring or helping its relatives. If the benefits of helping a relative outweigh the costs, Dr. Hamilton argued, altruism can evolve.

Dr. Hamilton believed that one of the things his theory could explain was the presence of sterile females among ants, wasps, and some other social insects. These species have peculiar genetics that cause females to be more closely related to their sisters than to their brothers, or even to their own offspring. In these situations, a female ant may be able to spread more genes by helping to raise her queen mother’s eggs than trying to lay eggs of her own.

But as the years passed, Dr. Wilson’s enthusiasm for the theory waned. “It was getting tattered,” he said. Many species with sterile females, for example, do not have the strange genetics of ants and wasps. And many species with the right genetics have not produced sterile females.

After reading a 2008 article in which Dr. Wilson aired his misgivings, Dr. Nowak got in touch with him. Dr. Nowak and Dr. Tarnita were studying the mathematical underpinnings of evolution. They wanted to carry out a mathematical analysis of natural selection in general and inclusive fitness in particular. Dr. Wilson joined them.

The scientists developed equations that described two different behaviors in a population. One strategy might be selfish and the other altruistic — leaving their nest after they hatch versus staying to help rear young, for example. The scientists then calculated the conditions in which one strategy or the other takes over the whole population.

The researchers found that inclusive fitness theory worked only under special conditions. All the effects that the animals had on each other had to take place on a one-to-one basis. In the real world, individuals may benefit from many other individuals as a group.

Standard natural selection, the scientists argue, explains everything inclusive fitness theory was supposed to, without these special conditions.

Dr. Nowak and his colleagues argue that their analysis should free scientists to think of other ways that altruism and other kinds of social behavior might evolve.

Thinking about why a worker would sacrifice her own offspring turns out be the wrong perspective on the question, they argue. Instead, they say, we should put ourselves in the queen’s perspective. They offer a mathematical model suggesting how natural selection could produce offspring that stay at a queen’s nest. If she produces daughters that stay in the nest, she can spend more time laying eggs, rather than hunting for food to feed her young.

“I think they’ve done a very thorough job,” said Michael Doebeli of the University of British Columbia. He has also grown skeptical about the importance many colleagues have put on inclusive fitness in recent years. “The people who swear by this method somehow think there’s something magic about it that explains everything,” he said.

Dr. Hunt, who studies social wasps, does not find Dr. Hamilton’s ideas useful because it is nearly impossible to calculate the costs and benefits of helping relatives.

“I have never felt that inclusive fitness has contributed to an understanding of what’s going on,” he said. The Harvard team, Dr. Hunt said, is “basically on target.”

A number of scientists strongly disagree, though. “This paper, far from showing shortcomings in inclusive fitness theory, shows the shortcomings of the authors,” said Frances Ratnieks of the University of Sussex.

Dr. Ratnieks argues that the Harvard researchers cannot rule out kinship as a driving force in social evolution because their model is flawed. It does not include how closely related animals are.

It would be as if a team of researchers carried out a study on the effects of diet and exercise on health. Their subjects get different amounts of exercise but stay on the same diet. In the end, the experiment might show that exercise makes people more healthy. But it would not make any sense to also conclude that diet plays no role.

“If you don’t vary something you cannot say how important it is,” said Dr. Ratnieks.

Andy Gardner, an evolutionary biologist at Oxford, said bluntly, “This is a really terrible article.” One problem Dr. Gardner points to is the Harvard team’s claim that the past 40 years of research on inclusive fitness has yielded nothing but “hypothetical explanations.”

“This claim is just patently wrong,” Dr. Gardner said. He points to the question of how many sons and daughters mothers produce among the many insights inclusive fitness has brought.

In most species, the balance is 50-50. But there are exceptions. In some ant species, for example, the ratio is around three daughters for every son. That is because the sterile female workers invest more into female larvae than males. Inclusive fitness theory predicts just this situation, since the workers are more closely related to their sisters than to their brothers.

Dr. Gardner and a number of other biologists have co-authored a reply that they will be sending to Nature to challenge the new paper.

Dr. Hunt hopes to move the debate toward a resolution with a meeting he is to run in October at the National Evolutionary Synthesis Center in Durham, N.C. He will be bringing together scientists who build models of all the potential factors that drive the evolution of societies, from their kinship to their ecology. Ultimately, the scientists hope to build a model that can take into account all of these factors at once. “They’re all stoked, and I am too,” Dr. Hunt said.

Carl Zimmer, New York Times

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Full article and photo: http://www.nytimes.com/2010/08/31/science/31social.html

They Crawl, They Bite, They Baffle Scientists

THE ICK FACTOR The lab of Stephen A. Kells, a University of Minnesota entomologist. Bedbugs are not known to transmit disease.

Don’t be too quick to dismiss the common bedbug as merely a pestiferous six-legged blood-sucker.

Think of it, rather, as Cimex lectularius, international arthropod of mystery.

In comparison to other insects that bite man, or even only walk across man’s food, nibble man’s crops or bite man’s farm animals, very little is known about the creature whose Latin name means — go figure — “bug of the bed.” Only a handful of entomologists specialize in it, and until recently it has been low on the government’s research agenda because it does not transmit disease. Most study grants come from the pesticide industry and ask only one question: What kills it?

But now that it’s The Bug That Ate New York, Not to Mention Other Shocked American Cities, that may change.

This month, the Environmental Protection Agency and the Centers for Disease Control and Prevention issued a joint statement on bedbug control. It was not, however, a declaration of war nor a plan of action. It was an acknowledgment that the problem is big, a reminder that federal agencies mostly give advice, plus some advice: try a mix of vacuuming, crevice-sealing, heat and chemicals to kill the things.

It also noted, twice, that bedbug research “has been very limited over the past several decades.”

Ask any expert why the bugs disappeared for 40 years, why they came roaring back in the late 1990s, even why they do not spread disease, and you hear one answer: “Good question.”

“The first time I saw one that wasn’t dated 1957 and mounted on a microscope slide was in 2001,” said Dini M. Miller, a Virginia Tech cockroach expert who has added bedbugs to her repertoire.

The bugs have probably been biting our ancestors since they moved from trees to caves. The bugs are “nest parasites” that fed on bats and cave birds like swallows before man moved in.

That makes their disease-free status even more baffling.

(The bites itch, and can cause anaphylactic shock in rare cases, and dust containing feces and molted shells has triggered asthma attacks, but these are all allergic reactions, not disease.)

Bats are sources of rabies, Ebola, SARS and Nipah virus. And other biting bugs are disease carriers — mosquitoes for malaria and West Nile, ticks for Lyme and babesiosis, lice for typhus, fleas for plague, tsetse flies for sleeping sickness, kissing bugs for Chagas. Even nonbiting bugs like houseflies and cockroaches transmit disease by carrying bacteria on their feet or in their feces or vomit.

But bedbugs, despite the ick factor, are clean.

Actually it is safer to say that no one has proved they aren’t, said Jerome Goddard, a Mississippi State entomologist.

But not for lack of trying. South African researchers have fed them blood with the AIDS virus, but the virus died. They have shown that bugs can retain hepatitis B virus for weeks, but when they bite chimpanzees, the infection does not take. Brazilian researchers have come closest, getting bedbugs to transfer the Chagas parasite from a wild mouse to lab mice.

“Someday, somebody may come along with a better experiment,” Dr. Goddard said.

That lingering uncertainty has led to one change in lab practice. The classic bedbug strain that all newly caught bugs are compared against is a colony originally from Fort Dix, N.J., that a researcher kept alive for 30 years by letting it feed on him.

But Stephen A. Kells, a University of Minnesota entomologist, said he “prefers not to play with that risk.”

He feeds his bugs expired blood-bank blood through parafilm, which he describes as “waxy Saran Wrap.”

Coby Schal of North Carolina State said he formerly used condoms filled with rabbit blood, but switched to parafilm because his condom budget raised eyebrows with university auditors.

Why the bugs disappeared for so long and exploded so fast after they reappeared is another question. The conventional answer — that DDT was banned — is inadequate. After all, mosquitoes, roaches and other insects rebounded long ago.

Much has to do with the bugs’ habits. Before central heating arrived in the early 1900s, they died back in winter. People who frequently restuffed their mattresses or dismantled their beds to pour on boiling water — easier for those with servants — suffered less, said the bedbug historian Michael F. Potter of the University of Kentucky.

Early remedies were risky: igniting gunpowder on mattresses or soaking them with gasoline, fumigating buildings with burning sulfur or cyanide gas. (The best-known brand was Zyklon B, which later became infamous at Auschwitz.)

Success finally arrived in the 1950s as the bugs were hit first with DDT and then with malathion, diazinon, lindane, chlordane and dichlorovos, as resistance to each developed. In those days, mattresses were sprayed, DDT dust was sprinkled into the sheets, nurseries were lined with DDT-impregnated wallpaper.

In North America and Western Europe, “the slate was virtually wiped clean,” said Dr. Potter, who has surveyed pest-control experts in 43 countries. In South America, the Middle East and Africa, populations fell but never vanished.

The bugs also persisted on domestic poultry farms and in a few human habitations.

One theory is that domestic bedbugs surged after pest control companies stopped spraying for cockroaches in the 1980s and switched to poisoned baits, which bedbugs do not eat.

But the prevailing theory is that new bugs were introduced from overseas, because the ones found in cities now are resistant to different insecticides from those used on poultry or cockroaches.

Exactly where they came from is a mystery. Dr. Schal is now building a “world bedbug collection” and hopes to produce a global map of variations in their genes, which might answer the question.

Experts say they’ve heard blame pinned on many foreign ethnic groups and on historic events from the fall of the Berlin Wall to the Persian Gulf war to the spread of mosquito nets in Africa. Every theory has holes, and many are simply racist.

(For example, Dr. Potter said, he has heard Mexicans blamed, but Mexican pest control companies he contacted said they rarely see the bugs except in the homes of people returning from the United States, often with scavenged furniture.)

Pest-control companies say hotels, especially airport business hotels and resorts attracting foreign tourists, had the first outbreaks, said both Dr. Potter and Richard Cooper, a pest-control specialist.

Whatever the source, the future is grim, experts agreed.

Many pesticides don’t work, and some that do are banned — though whether people should fear the bug or the bug-killer more is open to debate.

“I’d like to take some of these groups and lock them in an apartment building full of bugs and see what they say then,” Dr. Potter said of environmentalists.

Treatment, including dismantling furniture and ripping up rugs, is expensive. Rather than actively hunting for bugs, hotels and landlords often deny having them.

Many people are not alert enough. (Both Mr. Cooper and Dr. Goddard said they routinely pull apart beds and even headboards when they check into hotels. Dr. Goddard keeps his luggage in the bathroom. Mr. Cooper heat-treats his when he gets home.)

Some people overreact, even developing delusional parasitosis, the illusion that bugs are crawling on them.

“People call me all the time, losing their minds, like it’s a curse from God,” Dr. Miller said.

The reasonable course, Dr. Goddard said, is to recognize that we are, in effect, back in the 1920s “Sleep tight, don’t let the bedbugs bite” era. People should be aware, but not panicky.

However, he added, “I don’t even know what to say about them being in theaters. That’s kind of spooky.”

Well, he was asked — can you feel them bite?

“No,” he said. “If I put them on my arm and close my eyes, I never feel them. But I once got my children to put them on my face, and I did. Maybe there are more nerve endings.”

Why in the world, he was asked, would he ask kids to do that?

“Oh, you know,” he said. “Bug people are crazy.”

Donald G. McNeil Jr., New York Times

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Full article and photo: http://www.nytimes.com/2010/08/31/science/31bedbug.html

Life in the Third Realm

Archaea were first found in areas like Bumpass Hell in Lassen Volcanic National Park, where fissures and volcanic heat created hot springs.

It’s that time of the month again. Yes: it’s time for Life-form of the Month. In case you’ve forgotten, this coming Saturday is International Day for Biological Diversity, a day of celebrations and parties to appreciate the other occupants of the planet. So if you do nothing else this weekend, drink a toast to “Other Life-forms!” In honor of this event, my nomination for Life-form of the Month: May is a group of abundant and fascinating beings that are undeservedly obscure: the archaea.

Say who?

Archaea are single-celled microbes with a reputation for living in tough environments like salt lakes, deep sea vents or boiling acid. One strain can grow at temperatures as high as 121 degrees Celsius (249.8 degrees Fahrenheit), a heat that kills most organisms; others thrive at the seriously acidic pH of zero.

They are not restricted to life at the fringes, however. As we have learned how to detect them, archaea have turned up all over the place. One survey estimated that they account for as much as 20 percent of all microbial cells in the ocean, and they’ve been discovered living in soil, swamps, streams and lakes, sediments at the bottom of the ocean, and so on. They are also routinely found in the bowels of the Earth — and the bowels of animals, including humans, cows and termites, where they produce methane. Indeed, the archaeon known as Methanobrevibacter smithii may account for as much as 10 percent of all the microbial cells living in your gut.

But here’s the thing. The tree of life falls into three big lineages, or realms of life. (Confession: the technical term is “domains,” not “realms,” but I’m taking poetic license.) The most familiar realm comprises the eukaryotes — which is the blanket term for most of the organisms we are familiar with, be they mushrooms, water lilies, tsetse flies, humans or the single-celled beasties that cause malaria. Eukaryotes have many distinguishing features, including the fact that they keep their genes in a special compartment known as the cell nucleus.

The second member of the trinity is made up of bacteria. We tend to associate bacteria with disease — for they can cause a range of nasty infections, including pneumonia, syphilis, leprosy, tuberculosis and the like. But in fact, most bacteria lead blameless lives (some of which I have written about in previous columns). There are many differences between eukaryotes and bacteria; but one of the most obvious is that bacteria do not sequester their DNA in a cell nucleus.

Archaea

Methanogens, a type of archaea

The third great lineage of living beings is the archaea. At first glance, they look like bacteria — and were initially presumed to be so. In fact, some scientists still classify them as bacteria; but most now consider that there are enough differences between archaea and bacteria for the archaea to count as a separate realm.

The most prominent of these differences lies in the structure of the ribosome — the piece of cellular machinery that is responsible for turning the information contained in DNA into proteins. Indeed, it was the discovery of the archaeal ribosome by the biologist Carl Woese in the 1970s that led to their being recognized as the third branch of the tree of life.

What else sets them apart? They sometimes come in peculiar shapes: Haloquadratum walsbyi is rectangular, for example. Some archaea are ultra-tiny, with cell volumes around 0.009 cubic microns. (For comparison, human red blood cells have a volume of around 90 cubic microns. A micron is a millionth of a meter — which is extremely small.)

More diagnostic: archaeal cell membranes have a different structure and composition from those of bacteria or eukaryotes. And although archaea organize their DNA much as bacteria do (they also have no cell nucleus, for example), many aspects of the way the DNA gets processed are distinctly different. Instead, the processing is more similar to what goes in within eukaryotic cells. Archaea also have large numbers of genes that are not found in the other groups.

But to me their most telling feature is that they have their own set of extremely weird viruses. Not only do archaeal viruses also come in odd shapes — some of them look like little bottles — but the set of genes they have is unlike that of viruses that parasitize bacteria or eukaryotes. In other words, viruses can also be divided into three big groups: those that attack bacteria, those that attack eukaryotes and those that attack archaea.

The archaea still hold many mysteries. Few of them can be grown in the laboratory, so they are hard to study in detail; many of them are known from their DNA alone. Moreover, their exact position on the tree of life — when they evolved relative to the other two groups — remains disputed. Yet it may be that archaea feature in our ancestry: according to one view, eukaryotes themselves evolved from an ancient fusion between a bacterium and an archaeon.

But whether this is the case, or whether they are merely co-occupants of the planet, let’s hear it for these Other Life-forms!

Notes:

For a delightful introduction to the archaea, see Howland, J. L. 2000. “The Surprising Archaea: Discovering Another Domain of Life.” Oxford University Press. For a more technical overview, see Cavicchioli, R. (editor). 2007. “Archaea: Molecular and Cellular Biology.” ASM Press. See page 21 for a photograph of the square archaeon, Haloquadratum walsbyi; this book also contains detailed descriptions of how archaea differ from eukaryotes and bacteria.

For archaea thriving at temperatures of 121 degrees C, see Kashefi, K. and Lovley, D. R. 2003. “Extending the upper temperature limit for life.” Science 301: 934. For archaea growing at zero pH, see Fütterer, O. et al. 2004. “Genome sequence of Picrophilus torridus and its implications for life around pH 0.” Proceedings of the National Academy of Sciences USA 101: 9091-9096.

For an overview of places where archaea have been found, see Chaban, B., Ng, S. Y. M., and Jarrell, K. F. 2006. “Archaeal habitats—from the extreme to the ordinary.” Canadian Journal of Microbiology 52: 73-116. For archaeal residents of animal guts, see Lange, M., Westermann, P., and Ahring, B. K. 2005. “Archaea in protozoa and metazoa.” Applied Microbiology and Biotechnology 66: 465-474. For archaea comprising 20 percent of ocean microbes, see DeLong, E. and Pace, N. R. 2001. “Environmental diversity of bacteria and archaea.” Systematic Biology 50: 470-478. For Methanobrevibacter smithii comprising 10 percent of the human gut microbial population, see Samuel, B. S. et al. 2007. “Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut.” Proceedings of the National Academy of Sciences USA 104: 10643-10648.

Descriptions of eukaryotes and bacteria can be found in any general biology textbook. For the view that archaea are merely a type of exotic bacteria, see page 123 of Cavalier-Smith, T. 2010. “Deep phylogeny, ancestral groups and the four ages of life.” Philosophical Transactions of the Royal Society B 365: 111-132. For a robust account of the three branches view of the tree of life, see for example, Pace, N. R. 2009. “Mapping the tree of life: progress and prospects.” Microbiology and Molecular Biology Reviews 73: 565-576.

For ultra-tiny archaea (and for the volume of 0.009 cubic microns), see Baker, B. J. et al. 2010. “Enigmatic, ultrasmall, uncultivated Archaea.” Proceedings of the National Academy of Sciences USA 107: 8806-8811. I took the volume of the human red blood cell from table 1 of Gregory, T. R. 2000. “Nucleotypic effects without nuclei: genome size and erythrocyte size in mammals.” Genome 43: 895-901.

For the bizarre features of archaeal viruses, see Prangishvili, D., Forterre, P. and Garrett, R. A. 2006. “Viruses of the Archaea: a unifying view.” Nature Reviews Microbiology 4: 837-848. The origin of eukaryotes, and whether it involved the fusion between a bacterium and an archaeon, is much disputed. See, for example, Yutin, N. et al. 2008. “The deep archaeal roots of eukaryotes.” Molecular Biology and Evolution 25: 1619-1630; Kurland, C. G., Collins, L. J., and Penny, D. 2006. “Genomics and the irreducible nature of eukaryotic cells.” Science 312: 1011-1014; and Hartman, H. and Fedorov, A. 2002. “The origin of the eukaryotic cell: a genomic investigation.” Proceedings of the National Academy of Sciences USA 99: 1420-1425.

Many thanks to Jonathan Swire for insights, comments and suggestions.

Olivia Judson, New York Times

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Full article and photos: http://opinionator.blogs.nytimes.com/2010/05/18/life-in-the-third-realm/

To Help Jaguars Survive, Ease Their Commute

A jaguar in the Pantanal, Brazil, the world’s largest wetland.

Héctor Porras-Valverdo tried to adopt a Zen attitude when he discovered recently that jaguars had turned two of his cows into carcasses.

The jaguars’ numbers may have dwindled, but they still roam the forests here in eastern Costa Rica, making their presence known by devouring the occasional chicken, pig or cow.

“I understand cats do this because they need to survive,” said Mr. Porras-Valverdo, 41, a burly dairy farmer.

A few years ago, he acknowledged, his first reaction might have been to reach for a gun. But his farm now sits in the middle of land that Costa Rica has designated a “jaguar corridor” — a protected pathway that allows the stealthy, nocturnal animals to safely traverse areas of human civilization.

In the past few years, such corridors have been created in Africa, Asia and the Americas to help animals cope with 21st-century threats, from encroaching highways and malls to climate change.

These pathways represent an important shift in conservation strategy. Like many other nations, Costa Rica has traditionally tried to protect large mammal species like jaguars by creating sanctuaries — buying up land and giving threatened animals a home where they can safely eat, fight and breed to eternity.

But in the past decade or so, scientists have realized that connecting corridors are needed because many species rely for survival on the migration of a few animals from one region to another, to intermix gene pools and to repopulate areas devastated by natural disasters or disease. Placing animals in isolated preserves, studies have found, decreases diversity and risks dulling down a species — like preventing New Yorkers and Californians from getting together to procreate.

“It was kind of an epiphany,” said Alan Rabinowitz, a zoologist who is president of Panthera, an organization that studies and promotes conservation of large cats. “We were giving them nice land to live on when what they were doing — and what they needed — was an underground railway.”

He said critical migration routes were especially vulnerable in rapidly developing countries, where new roads, shopping malls, dams, playgrounds and subdivisions could spring up overnight, blocking the animals’ passage. To correct this oversight, Costa Rica and other countries have begun identifying and protecting corridors for jaguars and other large mammals, like tigers, snow leopards and pandas.

Most of the corridors are not obviously demarcated pathways, but virtual trails, “protected” in the sense that builders and planners are not permitted to introduce obstacles to the animals’ movements through the area.

The idea is not to stop building entirely, but to adjust development so that animals can move through landscapes that humans also occupy. A tall fence surrounding a shopping mall may be forbidden, for example, or a two-lane road may have to be substituted for a proposed four-lane highway.

Local residents must also be persuaded not to shoot wild intruders or otherwise drive them away when they are in transit, a shift in thinking that is already taking root here.

“Of course jaguars sometimes have conflicts with communities, but now people have been educated to change their thinking — not to see them as so dangerous,” said Víctor Fallas Ramírez, an agronomist who grows ornamental plants here.

The threat of global warming has added to the urgency of creating corridors because animals will need to shift habitats as temperatures rise from climate change.

“This is an idea that people are finding very compelling, and especially compelling now because with changing climate, species will need the capacity to move,” said Norman Christensen, a professor of ecology at Duke University, whose team is working to define corridors in Central America, India and Africa.

While Dr. Christensen called Costa Rica “the poster child” for its efforts, he said corridors for large mammals were also being created in places like Uganda and China. The World Bank is financing corridor projects in Brazil and Peru; more important, the bank’s transportation planners are working with conservationists to ensure that building highways and laying train tracks so humans can move freely does not destroy that movement for animals, Dr. Christensen said.

Part of the reason that conservationists had in the past focused exclusively on preserves was that there was a lack of good data on the travel and breeding patterns of large animals like jaguars; these big predators favor dense jungles and are nocturnal and extraordinarily shy.

So when new techniques allowed scientists to take a first look at the jaguar genome a decade ago, they were shocked to discover that jaguars from the northern reaches of Mexico had exactly the same genetic makeup as those from the southern tip of South America.

That meant that over time, some jaguars were moving up and down the Americas to breed; otherwise, the isolation of jaguar populations in different regions would have caused their genetic makeups to diverge. At least some males from Colombia were traveling to Panama to mate, and others were moving from Mexico to Belize.

“It was surprising, but it seemed to say they had one continuous habitat,” said Dr. Rabinowitz, the zoologist.

Scientists were convinced that jaguars would never cross a water barrier as wide as the Panama Canal, smack in the middle of their extended habitat. But when they set up cameras to spot jaguars near the canal, they discovered that, every so often, a brave animal took the plunge, ensuring the continuity of genes in the north and south.

Costa Rica now requires developers to consider whether a new construction project would interrupt an essential corridor, or else to make other arrangements for jaguars to travel safely through the area.

The fact that jaguars and other large cat species travel at night and do not hunt when they are on the move makes it easier for them to co-exist with humans.

“The bottom line is big cats can live with people,” Dr. Rabinowitz said. “That’s not true of all animals.”

He continued, “The problem with the paradigm of conservation is it’s been seen as a confrontation between nature and development, that won’t let progress happen.”

In Costa Rica, Panthera is conducting research to better define the routes taken by jaguars and lobbying politicians and developers to respect them. The organization also sponsors community outreach programs to resolve what the researchers term “jaguar conflict issues.”

“Many places don’t want the corridors,” said Roberto Salom, Panthera’s regional coordinator here. “We’ve made alliances with lots of leaders and educators, but it’s a very slow process.”

Here in the jungles of Central America, jaguars are regarded as mystical and dangerous. According to local legend, indigenous people turn into jaguars when they enter the jungle, and then shake off their spots when they return to the village.

“I’ve seen the tracks, but never an animal,” said Enoc Bajo Chiripó, an indigenous leader who is working with the group. “But you can smell when they’re around.”

Families in the region tell jaguar stories the way New Yorkers talk about their families’ arrivals at Ellis Island.

“My grandmother saw it at the place where agouti and peccaries come to eat,” said Jordi Ortiz-Camacho, 12, speaking of a jaguar. “My grandfather killed it with a stick because his gun didn’t work.”

While local farmers are now willing to forgive a dead cow or two to allow jaguars to survive as a species, they are often reluctant to make larger sacrifices. Just outside Las Lomas, a proposed hydroelectric project would involve building a huge dam across a valley, creating a body of water a third of a mile wide and more than three miles long. As planned, it would block a jaguar corridor.

The new project will mean jobs, an increase in property values and improved basic services for the area, including roads and piped water, said Mr. Fallas Ramírez, the agronomist. And the community, he said, cannot just forsake all that.

“For us, and the jaguars, it’s just an obstacle,” said Mr. Salom, the biologist, who is looking into alternative solutions, like an animal bridge or a smaller dam. “So we’re thinking, ‘How can we mitigate this?’ ”

Elisabeth Rosenthal, New York Times

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Full article and photo: http://www.nytimes.com/2010/05/12/science/earth/12jaguar.html