Astronomers have just discovered two Earth-size, rocky planets around a nearby star. Though the planets are way too broilsome for life, they suggest that steady improvements in telescope technology has made the discovery of habitable planets just a matter of time.

But as astrobiologists continue to search for life in space, geo-biologists (ok, we coined that) continue to find bizarre life in strange places on Earth: in the dark ocean depths, between grains of sand, and at roasty-toasty temperatures once considered deadly.

Hot, humid, and totally alive!

Fifty years ago, nobody believed organisms could survive near the boiling point of water. When Thomas Brock started probing the hot springs in Yellowstone in the 1960s, he was not looking to overthrow a ground rule of biology. Instead, the University of Wisconsin-Madison professor, then at Indiana University, sought to study bacteria in a simplified, real-world environment.

At the time, and even today, precious little was known about how bacteria live their lives — unless they cause disease.

As Brock sampled his way up a hot stream, he approached its source in a hot spring, and the water temperature rose steadily.

At the time, biologists thought life would not tolerate temperatures near 80° C. But Brock kept finding bacteria, so he kept looking. Eventually, he found some that could live and reproduce near the temperature of boiling water — 100° C.

The prize of his collection was a bacterium he named Thermus aquaticus (for its hot-water habitat) and placed in a public repository for study by other scientists.

Over the years, T. aquaticus proved interesting indeed. For one thing, it was the first of more than 50 species of thermophilic bacteria known to tolerate or require temperatures near water’s boiling point.

For another, it was the first of the Archaea (ancient ones), primitive microorganisms that scientists now regard as a separate and highly primitive kingdom of life.

Deep roots indeed

Because thermophiles are Archaeans, and prefer the steamy conditions typical of early Earth, many scientists think they may tell us about the origin of life itself.

To any basic scientist, those contributions would be enough. But because their enzymes work in high temperatures, where chemical reactions are faster, the thermophiles have proven to be extraordinarily useful.

Today, enzymes derived from thermophiles are used to convert millions of pounds of corn (maize) into sugar to sweeten soft drinks.

But more important, at least to scientists who don’t guzzle fizzy pop at the lab bench, T. aquaticus supplied TAQ polymerase, the essential enzyme for polymerase chain reaction, AKA PCR.

PCR is an artificial technique that does what living critters do every day — replicate DNA. But PCR is the rocket ship of replication, since it allows you to multiply a piece of DNA a billion times in a few hours. That produces enough DNA to analyze to your heart’s content — for genetic engineering, biotechnology and forensic purposes.

PCR depends on TAQ polymerase.

Aware that PCR and soda pop are both billion-dollar industries, corporations and scientists around the world have frantically searched for other thermophiles that may have equally useful enzymes. They’re looking in odd places — not just hot springs and volcanoes, but also deep-sea vents, hot petroleum-bearing rock, the outflow of geothermal power plants, and smoldering piles of garbage.

Prowling for glow-in-the-dark squid

Call me Bob.

Short for bobtail squid. (Did I mention that I’m a 3-4 centimeter cephalopod, formally Euprymna Scolopes?)

Anyway, I hang out in shallow waters around Hawaii. Save your crocodile tears — somebody’s got to live in the sunny, tropical ocean. Anyway, here’s my problem: Even though I have 10 tentacles, I don’t have spines, poisons, or any other decent defense.

So I spend my days burrowed in sand at the ocean bottom, trying to keep out of mischief. Still, a fellow’s got to eat, don’tcha know, so I cruise at night, looking to grab a bite.

Here’s the snag: All sorts of nocturnal predators seem to have this thing about calamari sushi.

Light before flashlights

A long time ago, my ancestors evolved a nifty defense against their big teeth: stealth. Even their tiny squid brains figured out that predators could see them from below, as tasty dark blobs against the bright ocean surface.

Since this was before flashlights, my relatives had to improvise. So they press-ganged billions of luminescent bacteria into making light for them. The idea was to make us just as bright as the ocean surface — and hence invisible.

At least, this is how my great-aunt Tentacla tells it. To tell the truth, I think it had more to do with the evolutionary advantage of being hard to see.

Anyway, my ancestors fed the bacteria, and gave them a home in two specialized light-emitting organs. These “photophores” have a reflective membrane to shine all their light down, toward the hungry predators. They use a diaphragm to control brightness, and even have a lens to spread the light.

The photophore reminds me of a backwards eye — one that makes light rather than detects it.

My folks even figured out how to switch the bacteria “on” when needed.

In return, the bacteria got room and board, in the biological deal they call “symbiosis” or “mutualism.” Sometimes I think people could learn from this cooperative spirit….

But that’s enough thinking for today. My squid brain is squashed.

As I burrow into the sand for another daytime nap, permit me to introduce somebody who considers me almost as fascinating as I do.

Seriously speaking…

Margaret McFall-Ngai, a biologist at University of Wisconsin-Madison, says the bobtail squid may pretend it’s cooperating in a symbiosis with those light-making bacteria, but the reality is more ominous.

She says there’s evidence that this may be slavery, not symbiosis, since the squid, “inhibits the growth of the bacteria to enhance their luminescence.” The bacteria, Vibrio fischeri, could make a better living drifting in the ocean, or in the gut of another marine animal, McFall-Ngai observes.

The concept of bacterial enslavement broadens our perspective on the many possible relationships in the living world.

Most people, if they think about bacteria at all, conjure up disease and decay, but people would be dead without bacteria, since the little critters play essential roles in producing vitamins and preventing disease.

Since the bacteria in our guts vastly outnumber the cells in our bodies, it helps that they’re helpful!

Nevertheless, and for understandable reasons, bacteriologists have traditionally focused on disease-causing organisms, and, for simplicity, on one species at a time. But that skews our view of how bacteria actually live, says McFall-Ngai.

Three cheers for complexity!

Complexity and subtlety may be the hallmarks of these interactions, and the complexity begins by recognizing that V. fischeri is closely related to V. cholerae, which causes the human intestinal disease, cholera.

Cholera is caused by a V. cholera toxin similar to a toxin produced by the light-emitting bacterium. But far from harming the poor little bobtail, that toxin signals it to secrete food for V. fischeri, so the toxin is really a chemical “dinner bell.”

And this raises the intriguing notion that a cholera bug secretes toxins not to kill its host but to discuss its menu. If so, our whole notion of pathogenesis may need rewriting, McFall-Ngai suggests. “Maybe when we’ve been studying cholera pathogenesis we’ve been studying an aspect of a normal conversation that’s gone wrong.”

Indeed, the traditional bacteriological view of bacteria as pathogens to be studied in pure culture may be “like trying to understand the complexity of all the cultures that lived in Paris by studying the activity of the Nazi occupiers,” McFall-Ngai suggests. “You are studying groups that don’t belong there, and have disrupted the normal activities.”

Want more on how the flashlight squid bullies its bacterial brethren?

Between the grains

(1996 story, only photos have been updated)

To zoologist Robert Higgins, small is beautiful. His infatuation with small creatures — “meiofauna” — dates to a student job in a biology lab that paid 35 cents an hour. Instead of quitting for more lucrative work, Higgins was intrigued.

He’d heard about tiny, amazingly diverse creatures, and put grains of sand and muck through a fine mesh, and used a microscope to find hundreds of organisms.

Forty-four years later, Higgins has retired from the Smithsonian Institution, but he’s still goggling at meiofauna — a complex group of animals found in most Earthly environments.

Indeed, a handful of wet sand could contain more biological diversity than a whole rain forest, Higgins says.

In the course of peering through countless microscopes, Higgins has discovered hundreds of species. With Danish biologist Reinhardt Kristensen, he found an entire phylum, called Loricifera.

Phyla are the broadest categories of organisms, based on structure, and according to the International Association of Meiobenthologists, “The majority of recognized phyla have meiofaunal representatives. Currently, 20 phyla considered to be meiofaunal from the 34 recognized phyla of the Kingdom Animalia. Out of these 20 phyla, five are exclusively meiofaunal in size.”

Photo: Giulio Melone, department of biology, Milan University.

A bdelloid (a type of meiofauna) shrinks when it undergoes anhydrobiosis. The dormant, dehydrated bdelloid has greater resistance to environmental stress but is ready to spring back to the active form in conducive conditions.

Meiofauna living between grains of sand have made some fancy adaptations to their harsh environment. Some have hooks on their feet, used to grab the sand. Others have hooked mouthparts, also useful for locomotion.

Beyond freeze-dried

To survive a difficult environment, meiofauna called tartigrades have evolved an amazing adaptation called “anhydrobiosis.” In this form of suspended animation, the animals replace water in their cell membranes with sugar, protecting the membrane from destruction through radiation and freezing. Microorganisms die when their cell membrane ruptures.

During anhydrobiosis, organisms are rather like plant seeds or bacterial spores, Higgins explains. “They can dry up for 100 years, and be rewetted, and come right back to active metabolism.”

Fun is fun. But what is the practical importance of studying stuff that can hardly be seen, doesn’t seem to cause disease, and is — at least to some — utterly ugly?

In other word, who cares about microscopic beach crud?

Meet the beach-cleaning crew

Anybody who likes to hang on the sand should be interested, Higgins says. “This is the system that helps keep our beaches clean.” Plankton, bacteria, all sorts of dead material is continually washing ashore, and a lot of people love to sit on beaches.

There’s a public-health angle here. Hookworms occur on beaches where dogs defecate, but meiofauna may consume hookworms, along with other nematodes. “So if we upset that, we could upset beach cleanliness,” Higgins says.

Higgins notes that meiofauna comprise a basic part of the food web, and disturbing them could have unforeseen consequences for the entire system.

Still, it’s hard to escape the notion that most of the motivation here is the pure scientific urge to discover, to classify, to understand. Meiofauna, Higgins notes, were seen under the microscope Anton van Leeuwenhoek invented in 1683.

The key to finding these things, Higgins indicates, in patience, technology, curiosity — and institutional support. “If you stare through a microscope for hour after hour, you have a chance of finding these things, but if you need to get out a certain number of papers each year, you have to take shortcuts and you won’t find as much.”

Fantastic freak show

If you drop a worker ant from an Amazonian treetop, what happens? In the species Cephalotes atratus, 87 percent of the time, that ant will wind up back where it started — a few meters lower down the same tree. Drop things that drift down at random, and only 5 percent of them will hit the tree.

In other words, these ants are controlling their flight — even though they don’t have wings.

That finding, which Stephen Yanoviak, Robert Dudley and Michael Kaspari¹ reported in 2005, provides a great starting point for untangling one of the mysteries of biology:

When and how did so animals take to the air?

Fly high

Flight is pretty common — among critters with wings, or something that resembles them, like a stretched membrane of skin. Birds, bats, moths and butterflies can fly. Even some lizards, snakes, fish and squirrels can glide under control toward the ground, which is not the same thing as falling.

Studies of ants in South America provide good data on “controlled aerial descent,” says Dudley, a professor of integrative biology at the University of California at Berkeley. In the course of some rather entertaining research, he and his colleagues have found that Cephalotes atratus ants:

During the controlled descent, at speeds above 4 meters per second, the ants perform “rapid postural adjustments,” Dudley says. “The limbs are moving, it’s not like a paper airplane.”

Dudley, an expert in the biomechanics of flight, says hundreds of species of tree-living ants in tropical Amazonian forests have evolved controlled gliding. Dropping to the forest floor can make them a meal for a mean and hungry ground-dwelling ant.

Looking at evolution

Perhaps the coolest part of the story is its evolutionary angle. Previously, scientists intrigued by the origin of flight have looked for evidence of wings and feathers, which appear more than 100 million years back in the fossil record.

But if flight really originated in arthropods that could not survive a fall from a tree or a cliff, that could wind the evolutionary clock back a good deal further. (Arthropods are animals with external skeletons and jointed legs, including spiders, insects and crustaceans like the horseshoe crab.)

Gliding under control is neither rare nor constrained to ants, Dudley says. “There are wingless aphids and flat spiders that live under the bark that can glide at a 45° angle. Controlled aerial descent has hundreds or thousands of independent origins in terrestrial arthropods.”

As old as the hills?

Over all, Dudley says, directed descent probably originated about 280 million years. If jumping like a flea or grasshopper is also deemed a form of flight, the origin could date back more than 400 million years.

The gliding hypothesis would not only help explain the origin of a common and cool behavior, but could take wind out of the sails for a favorite anti-evolutionary argument. Creationists, Dudley notes, have long demanded to know how wings evolved by asking, “What good is half a wing?” But according to the gliding hypothesis, wings unable to hold an animal airborne could still have evolved to help control a descending behavior that had long been in existence.

Flight of the control freaks?

Controlled gliding, Dudley says, “preceded the origin of wings, and so the evolution of flight is more about control than about the formation of wings.”

The new analysis “addresses qualms about the [supposed] lack of intermediate forms in the fossil record,” Dudley says. “Here is a viable intermediate form. There are lots of behavioral and ecological contexts where stubby, partial airfoils are useful.”

– David J. Tenenbaum

Since they were discovered 200 years ago, the plesiosaurs have posed a riddle. Long, brawny, toothy, their skeletal architecture was unsuited to laying eggs and sitting on a nest — and yet, there was no evidence that these reptiles gave birth to live young.

Until now.

In the journal Science tomorrow, a pair of paleontologists will describe a stunning fossil that shows a maturing plesiosaur inside its mother’s abdomen.

The fossil, dating to 78 million years ago, had lain in a museum basement for many years, says first author F. Robin O’Keefe, professor of biological science at Marshall University in Huntington, West Virginia. “Finding a pregnant animal fossil is always really rare, for any group of aquatic reptiles, and finding an undisturbed specimen is very unusual.”

O’Keefe collaborated with Luis Chiappe, director of the Dinosaur Institute at the Natural History Museum of Los Angeles, in studying the fossil, which is part of a new dinosaur-era exhibit at the museum.

Common, but curious

The plesiosaurs were monsters of the deep, says O’Keefe, having lived from roughly 200 million years ago until they went extinct along with the dinosaurs 65 million years ago. “These were apex predators, killer-whale size, and there is a very long, diverse fossil record.”

The specimen in question was complete, except for the head and some neck vertebrae, and was about 4.65 meters long.

Although the fetus was no midget – at 1.5 meters long — it was not ready to be born, O’Keefe says. “It’s really a guesstimate, but we think it is maybe two-thirds developed, definitely not ready for prime time. We have a bit of the back of its skull, and it’s poorly ossified [hardened]. If it was born like that, it would be like having your head made of Play Doh. It had no teeth, tiny flippers, and could not move around.”

The Cretaceous ocean, with its range of giant predators, was “not a place to be that helpless.”

Pride of the plains?

The pregnant plesiosaur was excavated in 1987 by Kansas landowner Charles Bonner. “He knew at the time that this was something interesting, but when it comes out of the ground, it’s inside a plaster jacket,” O’Keefe says. Removing a 15-foot specimen embedded in rock “is a time-intensive and expensive operation.”

But when the natural history museum decided to mount a new paleontology exhibit, the plesiosaur seemed a logical display, and director Luis Chiappe contacted O’Keefe. “He knew it was something interesting, thought it’s maybe a baby,” says O’Keefe. “Would I be interested in working on the specimen?”

A question answers itself

Would any paleontologist not be? And so O’Keefe found himself handling ancient evidence of reptilian motherhood. “My first thought was not some great scientific thought: ‘It’s really cool, you don’t often see fossils that neat.’”

When the rocks spoke, they revealed that this well-known reptile was, finally, in a maternal mood. “So here we have a pregnant plesiosaur, after 200 years of mystery, we have the smoking gun, we now know they gave live birth.”

To prove that, however, the scientists had to discount alternative explanations for finding an embryo inside an adult of the same species:

Does momma care?

We tend to think of reptiles as egg layers, but various flavors of birthing live young have evolved at least 80 times among marine reptiles. “The mother could retain the egg and have it develop inside her, or it could go all the way to a full-blown mammalian pattern, using a placenta to connect to the uterine wall,” O’Keefe says. “Given how big this fetus was, there probably had to be some pretty significant communication between mother and young.”

Paleontology shows structure, not behavior. O’Keefe says the new find suggests that mother plesiosaurs probably cared for their young, a rarity among modern reptiles. If one offspring “has absorbed all your reproductive energy, it makes a lot of sense to take care of it,” he points out.
In raising this possibility, he says, “We climbed out as far out on a limb as we thought we could get.”

And although there is no suggestion that the plesiosaurs nursed their young, live birth would distinguish them from many reptilian relatives and move them closer to modern, maternal marine mammals like whales and dolphins.

– David J. Tenenbaum

Wondrous weevils sport super screw!

In animal appendages, some joints resemble hinges. Others, like your hip, are unmistakably akin to the ball-and-socket joint, another mechanical mainstay.

Now, scientists have found a biological screw in a type of beetle called a weevil. Obliquely described as having “rotational movement combined with a single-axis translation,” the new screw-and-nut assembly was first seen in a weevil from New Guinea, says entomologist Alexander Riedel.

The discovery of the first biological screw-and-nut assembly emerged from an exploration of the weevil’s characteristic defense mechanism, says Riedel, an entomologist and curator who specializes in weevil classification at the State Museum of Natural History in Karlsruhe, Germany.

Two things weevils have in common are small size – the Trigonopterus oblongus under study was about 4 millimeters long – and legs that fold under the body. “We wanted to look at their particular defense mechanism,” says Riedel, “to know how it works.”

Using a microscopic counterpart to CT scanning, German researchers snapped electron micrographs of the weevil’s trochanter (“screw”) and (ROLLOVER) coxa (“nut”).”

Image © Science/AAAS

It’s all in the scan, man!

Given the small size, the scientists relied on a kind of micro CT scan driven by X-rays from a synchrotron, “We realized there is a very nice screw joint,” Riedel says, “We’ve had this information for some time, but while talking with a herpetologist colleague, we realized there is no other case in the whole animal kingdom, in all of biology, with a similar screw joint.”

The nut-and-screw are located at one of three major joints in the beetle’s leg; when the leg is retracted, the screw tightens in the nut, which remains stationary, Riedel says. Overall, the screw and nut would be able to turn 345 ° although the leg itself does not move that much.

A (good) turn of the screw!

“The weevils, or snout beetles, have been known from ancient times,” says Riedel. “There are grain weevils and lots of other species, including the boll weevil [a cotton pest]. Many other species are not pests … and so are of no particular interest to humans, which is why nobody knows much about them.”

Why does every weevil species that that Riedel examined have such a mechanism? Weevils, which spend a lot of time climbing on vegetation, apparently evolved from beetles that usually walk on a flat surface or underneath bark, Riedel says. “If a weevil is sitting on the edge of a leaf and wants to walk on a small twig, it’s essential that it can grip under its body, and this motion goes very nicely with this screw joint. A ground [walking] beetle would have great difficulty walking in similar conditions.”

The screw joint now joins the hinge, ball-and-socket and saddle joint as fundamental technologies invented by evolution, Riedel says. Historians of technology have long wondered about the origin of the incredibly useful screw, and it turns out that screws and nuts were in their flour bins all along – but only visible to those who happened to have a handy synchrotron!

– David J. Tenenbaum

Trust Charles Darwin to be his own severest critic. Having expounded a revolutionary evolutionary theory of natural selection, he realized that the past gives birth to the present. Darwin knew about fossils, including the famous, three-section trilobites, that dated to the Cambrian period, now known to have begun about 540 million years ago.

Never one to duck logic, Darwin wrote:

Indeed, according to J. William Schopf, professor and director of the Center for the Study of Evolution and the Origin of Life at UCLA, what came before was totally mysterious when Darwin wrote “Origin of Species” in the 1850s. “Darwin knew about the Cambrian era, and the big extinctions after that were known, but he knew nothing about the earlier fossil record. This was the case for about 100 years.”

And then, starting in 1953, University of Wisconsin-Madison geologist Stanley Tyler noticed ring-like structures in rocks in Minnesota and Ontario’s Gunflint formation.

The rock — a fine-grained quartz relative called chert — was 1.9 billion years old – almost four times as old as the earliest Cambrian fossils.

Tyler, collaborating with Elso Barghorn at Harvard, recognized the circular structures as stromatolites, mushroom-shaped rocks formed by layers of microorganisms called cyanobacteria. In 1965, the two reported that stromatolites were the oldest fossils ever seen.¹

I can see you now!

Why did it take so long for Precambrian life to be recognized? “They had assumed that it would be like younger life, there would be coral, snails and trilobites,” said Schopf, an expert on the oldest life. “The basic problem was that a wrong assumption had been made. Life in the Precambrian turned out to be substantively different in organization and size.”

By exploring the interior of rocks using an increasing array of scientific techniques, Schopf and a growing group of colleagues have found life as early as 3.5 billion years ago.

Not bad for a planet with an estimated age of 4.7 billion years.

Double-not-bad, considering the exceeding scarcity of truly ancient rocks, hidden through the constant tectonic churning of the crust. The oldest rocks yet located are 3.8 billion years old, but any fossils they contain have been distorted by severe heat and pressure.

Still, Schopf said, four lines of evidence show the ancient roots of life on our planet: microfossils, molecular biomarkers, proportions of carbon isotopes and stromatolites. Stromatolites are layered rock formed by layers of microorganisms called cyanobacteria (formerly blue-green algae), which produce oxygen in sunlight.

While some of the fossilized microorganisms found in ancient rock apparently have gone extinct, the cyanobacteria closely resemble living organisms, Schopf told an audience at the University of Wisconsin-Madison on April 26. “Cyanobacteria do the same sort of photosynthesis as a blade of grass today. These are the guys that invented this process, probably 3-plus billion years ago.”

As testimony to nature’s predilection for retaining stuff that works, other fossil microorganisms resemble modern counterparts that require oxygen, cannot tolerate oxygen, or use it when convenient. “We’ve found 12 to 15 major families of cyanobacteria, the same ones that are important today, the same ones that are seen throughout the geological record,” Schopf says.

Tyler did not live to see the publication of his 1965 article, but it revolutionized paleontology, and has been cited by scientists at least six times since 2010.

“Stanley Tyler was a hero for this world,” says Schopf. “As [microbiologist Louis] Pasteur said, chance favors a prepared mind. Here was an economic geologist [concerned with finding minerals and mines] … and yet he saw these scrubbly things, and thought, ‘I bet they are fossils,’ even though they were almost two billion years old. This is the guy who made the discovery.”

– David J. Tenenbaum

Using the tools of ultra-fast DNA sequencing, scientists have recently reported four ant genomes.

Before you doze off, take a moment to appreciate ants. These social insects are some of the most successful critters on the planet: Ants are invaders. Armies. Pests. Even farmers.

Ants live in colonies with dozens to millions of members, and whether judged by weight or impact, they can dominate ecosystems.

Explanations for the ants’ extraordinary success lie in their genomes – their entire catalog of genes. In the last month, scientists have published four ant genomes, adding to two published last year.

One of the new genomes covered the highly invasive Argentine ant, which has spread from its native South America to Europe, California and Japan. The ant “is a species of special concern because of its enormous ecological impact,” said Neil Tsutsui, associate professor at the Department of Environmental Science, Policy and Management at the University of California at Berkeley. “When the Argentine ants invade, they devastate the native insect communities while promoting the population growth of agricultural pests.”

ENLARGE

 

Photo: Thmazing

The Argentine ant is an ocean-crossing invader that harasses homeowners and native insects alike.

Like all social insects, Argentine ants communicate via chemical signals, and in 2009 Tsutsui ignited an ant war among friendly ants by doping them with chemicals that trigger aggressive behavior. Similar endeavors could be aided by the new genome map, which detected 367 genes for odor and 116 for taste.

Although the human genome project has yet to deliver its promised cargo of health benefits, Tsutsui said the new genome for the pesky ant “will provide a huge resource for people interested in finding effective, targeted ways of controlling the Argentine ant” by manipulating genes to interfere with mating, sparking inter-colony wars, developing repellants or luring ants into traps.

Ants practice agro-forestry

Another new ant genome covers the industrious leaf-cutter ant, which lives in giant colonies and farms fungus for a living. (Seen the ant-cam?)

Leaf-cutters nibble tree leaves into pieces, then haul them, porter style, to underground “gardens” where the leaves are devoured by a fungus.

This is not ornamental gardening. The fungus is the only thing these ants eat.

After million of years, the ants and fungi have evolved together, developing a serious case of co-dependency. “The ants need the fungus, and if they lose it, they die,” says Garret Suen, an assistant professor of bacteriology at the University of Wisconsin-Madison.

Suen, a key author of a recent genome of the leaf-cutter, adds that the reverse may also be true, since fungus has never been found outside ant gardens, and “it has co-evolved in tight association with the ants.”

ENLARGE

 

Photo: Hans Hillewaert

Give us this day our daily leaf: Leaf-cutter ant delivers leaf fragments to the garden.

This is some crazy co-evolution! The subterranean garden of one ant colony can reach a volume of 600 cubic meters. To feed the fungus, leaf-cutters ants can harvest as much as 17 percent of the leaves in a forest –- making this tiny critter the biggest herbivore in many new-world tropical forests. (Leaf-cutters don’t live in Asia, Africa or Europe.)

Other insects, like termites, house symbiotic microbes that “eat” biomass for them, but with the leaf-cutters, the symbiotic microbes live externally.

The new genome emphasizes the fundamental nature of the symbiosis, says Suen, because it showed that the ants lack a gene for synthesizing the amino acid arginine. Amino acids are building blocks of proteins, and all ants require arginine, but the pathway to make arginine in the leaf-cutter is broken, Suen says. “Presumably it used to be complete, and it’s complete in all other ants and many other social insects, except for our ant.”

When Suen and his colleagues finish analyzing the genetic sequence of the fungus, he suspects it may well show an enhanced ability to make arginine.

Photo: Wolfgang Hoffmann, University of Wisconsin-Madison.

Giant colonies of leaf-cutter ants are major but indirect plant-eaters in New-World tropical forests, where they harvest up to 17 percent of all leaves. The leaves support the huge underground fungus gardens that feed the ants.

 

Photo: Adrian Smith

The red harvester ant, native to the Southwest United States, has many detoxification genes, perhaps a response to past environmental changes. Red harvester ants have at least 344 genes related to smell, more than any other known insect.

Losing a gene

Evolution selects for genes that are needed for survival and reproduction, but since it’s wasteful to make things that have no purpose, genes that are no longer needed tend to break down or disappear over time.

Because leaf-cutter ants descended from ants that grew fungus with less sophistication, in much smaller gardens, the gene may have disappeared even before the leaf-cutters evolved between 8 and 12 million years ago, says Cameron Currie, associate professor of bacteriology at UW-Madison and study co-author. “They could have lost the genes 30 million years ago. Other symbiotic systems that are dependent on each other for nutrition have evidenced a similar loss of genes.”

The leaf-cutter also has a deficit in genes for making trypsin, an enzyme that breaks down proteins in food to make amino acids. “They are feeding on the fungus and it provides them with free amino acids, so it does not need these enzymes,” Suen says.

Another gene that evolution has shortchanged – but not totally eliminated – makes the protein hexamerin, which stores amino acids until they are needed during development. ”We think the developing brood has a constant source of amino acids from the fungus,” Suen says, “so it does not have to store them.”

Photo: Jürgen Liebig

Royalty reigns! When a jumping-ant queen dies, the workers battle to replace her. These new queens outlive their worker siblings. A recent jumping-ant genome showed that these replacement queens make many proteins linked to longevity.

Family obligations

Beyond confirming predictions of evolutionary theory, these genetic deletions could explain the long-lasting mutualism between ant and fungus, says Currie. If the ants would die without their fungus crop, they have a survivalist interest in blocking the entry of other fungi.

Although such a symbiosis looks like a great deal for both parties, cheaters can sabotage symbioses. “Evolution predicts that there should be instability, or cheating, in these cooperative relationships,” Currie says. “If I am giving a benefit to you at a cost to me, you can just take your benefit and not provide anything in return, which means you would be more successful compared to someone who cooperates and pays the cost.”

If you take your ailing auto to the car-fix, you could save money – once — by writing a rubber check. But repeated interaction is conducive to cooperation, Currie says. “If you write a bad check, next time you will not get your car fixed, and this applies to mutualism as well.”

In the ant-fungus relationship, Currie says, “The partners just can’t go and find new partners; they are locked together.”

In other words, the deletion of the ant’s arginine gene could explain why the co-dependency has lasted upwards of 8 million years.

Leave the leaves alone!

As ants don’t do a lot of reading and talking, chemical communication will likely be a focus for further genomic analysis. Plants dislike being eaten by any herbivore, so they produce toxic compounds to deter would-be browsers. Although the ant-fed fungus can eat more than 10 percent of the species of tree in the forest, some leaves are toxic to the fungus.

How do the ants know which type of leaves will kill it’s sole food, and how do they “talk about it”? It’s clear that the ants keep an eye on their crops, Suen says. When, as an experiment, scientists treated leaves with fungicide, the ants quit collecting that species, Suen says. “The ants remember and won’t touch those trees for two weeks because they are killing the fungus. How they do this, we have no idea, but now we can do an experiment to see what genes are being turned on or off” under those circumstances, and therefore must be involved in recognizing the death, and warning the colony about it. “We are pretty sure there is some communication between the fungus and the ant,” Suen says.

Social structure

More broadly, information about the genes of a highly successful organism with millions of cooperating individuals ought to be intriguing to another highly successful, but sometimes less cooperative, organism that has more brains, fewer legs, and equally large cities.

Leaf-cutter ants live a complicated life, and the identical set of genes allows them to become queens, soldiers, or several types of worker. “They do this with a brain that is incredibly small, but it’s collective, hard-wired behavior,” Currie says. “It’s amazing; there are 5 to 10 million ants with many different tasks that are done by different workers of different sizes,” and it all starts from the same genes.

The genome has yet to reveal a “farmer gene,” Currie says. He expects that candidate farmer genes will emerge when the leaf-cutter’s genome is compared to close relatives that do not farm. These may explain the leaf-cutter’s curious capacity for growing its food with the help of fungi, “But we are a long way from that.”

Even people who can’t distinguish the periodic table from a dining table know arsenic is poisonous, although few realize why. Arsenic is chemically akin to phosphorus, one of life’s essential elements. But it’s not identical, and when arsenic substitutes for phosphorus, it produce a toxic compound instead of a protein or chunk of DNA.

So we weren’t the only ones to be surprised by a study in today’s Science that identifies a bacterium that thrives on arsenic, at least in the lab, and incorporates this normally-poisonous element into proteins, fats and DNA.

Image: Wikipedia

A more typical reaction to arsenic comes from the elderly poisoning victims in the macabre comedy “Arsenic and Old Lace.” In that play and movie, two dotty spinsters spiked elderberry wine with arsenic, strychnine and cyanide for a freelance euthanasia project.

The new study is the first to show that it is possible to substitute for one of the elite elements (carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur) that were thought to be found in all life, says Ariel Anbar, a professor of earth and space exploration at Arizona State University. “No one has previously shown that arsenic can be substituted, and I am not aware that anyone has found a substitution for any of the six essential elements. And that’s why this is a big deal.”

Arsenic: It’s what’s for dinner

Felisa Wolfe-Simon, a former post-doctoral fellow with Anbar, gathered sediment and water from salty, alkaline, arsenic-rich Mono Lake in California and placed them in cultures intended to replicate Mono Lake water.

Images courtesy of Science/AAAS

These bacteria, viewed under an electron microscope, metabolized arsenic as if it were phosphorus. Mouseover to see the same strain of bacteria growing with phosphorus but without arsenic.

“Over time we made serial dilutions, one in 10, one in 10,” always including a strain of lake microbes, says Wolfe-Simon.

Wolfe-Simon, who is now at the NASA Astrobiology Institute and U.S. Geological Survey, says the dilutions removed “essentially all” of the phosphorus. In some samples, she jacked up the arsenic roughly 2,000 times above the concentration in Mono Lake, which gets its arsenic from rocks and is already about 20,000 times above the Environmental Protection Agency standard for arsenic in drinking water.

“This is a huge amount of arsenic,” Wolfe-Simon says. “It’s surprising that they could grow, even with phosphorus, in that condition.”

Although the bacteria died in the absence of phosphorus and arsenic, they survived if only arsenic was available. “The arsenic seems to be substituting for phosphorus,” says Wolfe-Simon. “We have identified arsenic in cellular structures that are consistent with where we would expect to see phosphorus.”

Photo: ©2010 Henry Bortman

Mono Lake, California, is salty, alkaline conditions, and toxic to many organisms. The lake is ideal for the study of extremophiles, microbes that live under bizarre temperature or chemistry.

Stepping out of line

This elemental swaperoo could operate more broadly, since the elements in each column of the periodic table have chemical similarities. If one neighbor of phosphorus can sustain life without phosphorus, could the elements below carbon, nitrogen or oxygen do the same?

Photo: ©2010 Henry Bortman

“This is not just about arsenic or Mono Lake,” says Wolfe-Simon. Life on Earth and the rest of the universe will be limited if it always requires six elements, but “If microbes can use arsenic as they can use phosphorus, that opens the door. What else can life do that is not yet known?”

In searching for life in the universe, NASA has focused on liquid water, another prerequisite for known life, but Anbar asserts that a search for the chemistry of life should stay broad. “Felisa’s results say we should think harder about which elements we should follow. We don’t want to be too influenced by the particular example of life on Earth. We want to push the boundaries.”

Call it “Arsenic in a new place.” Roll cameras!

Cells are the basic unit of biology: the site where energy is transformed. It is the locale where DNA, RNA and proteins perform the timeless dance of cellular reproduction.

But cells are small (a mammalian cell is about 10,000 nanometers in diameter, which sounds large until you remember that one million nanometers equals one millimeter).

Photo: © Science/AAAS

That angled piece of ultra-slender wire at the end carries a transistor, and is about to slip inside one of the cells just above it. The two legs allow current to flow through the transistor.

Tracking events inside individual cells may get a lot easier, courtesy of a new transistor that is engineered to slip easily inside a cell and is just 50 nanometers wide.

This transistor, mounted on a much-thinner-than-a-hair wire, can detect and amplify faint electrical signals inside cells.

Several innovations from chemistry and material science were needed to construct ultra-mini transistors on a hairpin-shaped piece of wire, says Charles Lieber, a professor of chemical biology at Harvard University.

The nanowire itself is silicon, the basic material of solid-state electronics. To give the wire its hairpin shape, the researchers created two 120-degree bends, which had never been done before with nanowire, says Lieber.

To form a tiny transistor at the bend, Lieber, Bozhi Tian, who’s now a post-doctoral fellow at MIT, and colleagues “doped” the silicon wire with precise dollops of elements.

Small is indeed beautiful

The invention has advantages over the “patch clamp,” which was developed more than 25 years ago to measure voltage at ion channels on the cell surface, says Lieber.

Photo: The Athlete’s Heart Blog

Because the transistor “is an active device that amplifies the signal,” it can be much smaller than the patch clamp, Lieber says. The new probe is so small, he adds, that “you could envision putting several of these into the same cell to measure things on a scale that’s never been measured.”

The fabrication techniques impressed Xudong Wang, an expert in nanowire at the University of Wisconsin-Madison. “In making nanowires, it’s most difficult to grow a certain shape, and to put a specific function at a specific location.”

Although most early nanoelectronics are planar, Wang adds, “They made this part that is three-dimensional, so you can study something in 3D space.”

A matter of the heart

Because heart muscle cells exhibit an electrical rhythm that causes spontaneous contractions, Lieber’s research group used the probe to examine chicken heart cells in the lab. Inserting the nanowire did not seem to affect the cells, Lieber says. “The cell is beating, and as the device goes in, there is no change in the beat frequency or in the electrical potential.”

In contrast, harpooning a cell with a pipette — the slender glass tube used in the patch clamp — often disturbs it, Lieber says. And because that pipette also contains a liquid, “You will always have an exchange of medium from the measurement tool and the cell.” The new probe uses no fluids.

Photo: © Science/AAAS

Inside a single cell, this nanowire probe can measure electricity and may eventually be able to detect proteins and RNA.

King of nano-camo?

Photo: © Science/AAAS

To help the ultra-small probe enter cells, the researchers coated it with a layer that resembles a cell membrane, which causes the probe to be pulled into the cell. Cells use a similar process to devour viruses and bacteria.

Beyond measuring voltage inside a cell, Lieber suggests that the transistor could carry receptors for proteins or RNA, enabling it to measure chemistry in real time inside cells. That, in turn, would open a window on many basic biological mechanisms.

“It’s almost like a dream to be able to wire up a transistor, which is the fundamental unit in digital electronics, with a cell, which is the basic unit of information processing in biology,” says Lieber. “It does not take a lot of imagination to think there will be a lot of wild things that one can do with this technology.”

– David J. Tenenbaum

Photo: Fiorenzo Omenetto

But you sure can copy her. That’s an engineering approach called biomimetics – the quest to exploit the three billion-year evolutionary process that has perfected structures and materials as strong, spare and sophisticated as the hawk’s eye and mother-of-pearl.

Now we read about progress in the effort to make artificial silk – the light, ultra-tough fiber produced by spiders and silkworms. Like plastic, silk is a polymer – a series of repeated structures that can be altered to produce different results.

But unlike plastic, the sub-units in silk are proteins. And silk can’t be made in the lab – yet.

In fact, it’s not yet clear how silk is made inside silkworms and spiders. As silk is forming, its proteins are so dense that they should glom together before the animal can spin the silk fiber.

Because a glance at a spider’s web proves that silk is possible, biologists and engineers are exploring the chemistry and physics of silk production.

By controlling the acidity and flow of the liquid pre-silk, and using mechanisms that are presently mysterious, spiders and silkworms create a fiber that shames even Kevlar, the fiber that is blended with polymer for lightweight canoes and bullet-proof vests.

Strong, ‘n silky?

In terms of tensile (pulling) strength, silk approaches high-tensile steel, and is one-quarter as strong as Kevlar. But if you bend Kevlar, it “will fail immediately,” says David Kaplan, a professor of biomedical engineering at Tufts University.

In contrast, silk excels in a quality called toughness – the Rambo factor, which combines tensile strength and flexibility. “Silk is really good at tensile strength and toughness, and you can’t emulate that with a synthetic material,” Kaplan says.

Silk has many other desirable properties, adds Kaplan, co-author of a review on silk technology being published in tomorrow’s Science. The silkworm’s silk cocoon must protect the developing moth against rain and other environmental perils, yet the moth must digest the cocoon as it emerges.

Silk can also be highly elastic. “To catch prey, the spider can throw the silk like a lasso, and it sticks so the spider can reel the prey back in.”

Courtesy of what Kaplan calls “a glue-like feature that holds the fibers together through a protein-protein interaction,” spider-web silk can also adhere to itself, and to vegetation.

Because spiders and silkworms are only distantly related, the genes for silk must have evolved several times, Kaplan says. “That’s a vote for the simplicity and utility of the system, which clearly provides an important survival function.”

Finally, these remarkable materials are made with the ultimate green chemistry, with neither heat nor toxic byproducts, and using only water as the solvent.

Medical miracle?

Silk has been used for surgical suturing since Egyptian times. But Kaplan and others envision using this ultra-tough, biodegradable material as a

* scaffold to hold stem cells to regenerate diseased tissues, such as bone, kidney and cartilage;

* container to introduce cells, drugs or growth factors; and

Photos: University of Akron

For sheer toughness, spider silk trumps such synthetic fibers as carbon fiber and Kevlar.

* an injectable goop of silk precursors and the appropriate drugs or cells which would transform into a gel state and deliver its cargo before slowly degrading.

In 2009, Serica Technologies, Inc., got Food and Drug Administration approval for a silk-based material to be used as a supportive mesh in soft-tissue repairs. (Serica has since been acquired by Allergan, Inc.)

If silk is so slick, can it be made in larger quantities with traditional, in-glass chemistry? Perhaps, but Kaplan is more excited about moving the silk genes into plants or animals, so biology can make the precursors, or possibly a finished silk fiber.

As mentioned, the study of silk illustrates how engineers can be inspired by biology. Seventy-five percent of silk is composed of just two amino acids, Kaplan says, yet “this material is unique. It can make incredibly strong, tough, interesting materials, and do it through a green process. I can’t imagine where you can get more interesting properties from a simpler system.”

David J. Tenenbaum

Photo: Vince Panzano

A hungry fruit fly (Drosophila melanogaster) extends its proboscis to feed on a droplet of sugar water. The proboscis contains sensors that detect irritating chemicals such as the ones in wasabi. Quite similar sensors occur inside the human mouth.

Whether you are a cobra or a cocker spaniel, a raccoon or a raconteur, lots of natural, reactive chemicals will cause pain and possibly damage your cells. Even fruitflies quickly learn to shy away from sugar water that contains caffeine or chemicals found in cinnamon, cigarette smoke, onion and horseradish.

These chemicals trigger activity at receptors on cell surfaces which eventually results in an “ouch” signal being sent brain-ward.

In a study published in Nature this week, a group lead by Paul Garrity, an associate professor of biology at Brandeis University, showed that a major class of pain receptors have ancient roots. We are talking older than yesterday: the report shows that TRPA1 (transient receptor potential A1) receptor was found in the critter that spawned both vertebrates (green tree snakes, bullfrogs, dinosaurs and talk-show guests) and invertebrates (horse flies, crabs, quahog clams and talk-show hosts) at least 500 million years ago.

The investigation, spearheaded by Kyeongjin Kang in Garrity’s lab, showed that the TRPA1 receptor is so similar across the entire vert-invert realm that it must have evolved once, and then descended through countless generations without significant changes. “The fly and human proteins in this receptor appear, to a very, very high degree of significance, to be from a common ancestor,” Garrity told us.

The pain in Spain

Unlike TRPA1, many other chemical receptors, like those involved in most smell and taste, vary greatly between animals, Garrity added. “There are big families of these receptors that look quite different in different species, so there is a lot of flexibility and change, but this TRPA1 is pretty much fixed.”

When structures have remained constant over long periods, scientists conclude that the evolutionary pressures that favored them were also static. Fish retain fins because they still live in water. We retain eyes because seeing is so handy.

And the stasis of the TRPA1 receptor “suggests there has been some sort of strong evolutionary pressure in these toxic chemicals that was maintained since the receptor was invented,” says Garrity. The chemicals in question are made by plants or other organisms as self-protection, and they can damage or destroy proteins and nucleic acids, at least in high doses, and therefore are to be avoided.

Fans of horseradish and wasabi know that a nibble can be tasty but a gobble can cause an eruption of coughing.

Image: NIH

A human taste bud, shown here, contains some types of chemical receptor, but the TRPA1 receptors that first formed 500 million years ago are found elsewhere in our mouths, in structures called chemical nociceptors.

Work by study co-author Doug Theobold, also at Brandeis, suggested the original TRPA1 receptor arose after the jellyfish branched away from our lineage about 700 million years ago. The first TRPA1 receptor was apparently present in the last common ancestor of vertebrates and invertebrates, which lived between 500 million and 550 million years ago.

And that means we may have the same tastes in food as fruitflies, but not jellyfish. “It’s bad enough to think about shooing the flies away from the sushi bar, but jellyfish, well, they may be on the menu, but I don’t want to see one on the stool,” growls the resident Why Files cynic.

How they did it

To explore the responses to these reactive chemicals, Garrity and his colleagues offered sugar water to fruit flies. Some of the water was tainted with pungent chemicals derived from cinnamon or wasabi. Some of the fruit flies had genetic mutations affecting the TRPA1 receptor. In some trials, the flies touched the toxic chemical with their legs; in others, they drank it.

Flies extend their proboscis (snout) toward something they want to eat, and the scientists measured this behavior as they offered a droplet of food five times. All flies extended the proboscis at the first offering.

Curiously, when the fruitflies drank sweetened caffeine-bearing water, they turned jittery and stayed up all night, devouring junk food and cramming for a biochemistry exam. Just java jiving…

So what?

Finding such a long-term similarity in a major class of pain receptors could have broad implications, Garrity says. TRPA1 receptors exist on the aphids that spread disease to many crops and the mosquitoes that carry malaria. If compounds that trigger these receptors while sparing those of benign species can be found, they could be developed into pesticides that inflict pain and cause the nasty bugs to stay away from where they are not wanted.

A second application, which may be closer to fruition, depends on the similarity of receptors between fruit flies and mammals, Garrity says.

Compounds derived from capsaicin, the active agent in hot peppers, are already used to treat pain. Although TRPA1 receptors respond to a totally separate group of pungent compounds, drug companies are already searching for TRPA1 antagonists that might treat chronic pain, asthma, arthritis or migraine headache, Garrity says.

The TRPA1 receptor responds to oxidative stress caused by nasty compounds called free radicals. “It is a key to many aspects of pain and inflammation,” Garrity says.

- David J. Tenenbaum