Scientists have thought for a decade that iron-bearing structures in the homing pigeon’s beak help the bird find its location by “reading” Earth’s magnetic field. Now, it turns out that this iron occupies cells that battle infection, rather than nerve cells.

Oops!

The new results leave a chasm in our understanding of bird navigation, says Charles Walcott, an expert on the subject at Cornell University, who was not involved in the study. “It’s astonishing that we have what seems like a terribly simple-minded problem. Take a homing pigeon any direction, and after circling a couple of times, it heads for home … and we don’t understand how these animals do this?”

Study leader David Keays, of the Institute for Molecular Pathology in Vienna, did not set out to debunk a beautiful theory, but rather to explore the nerve cells in the beak that supposedly register magnetism. “My background is in molecular biology and genetics, and I thought there must be some incredible biology involved. I wanted to get a handle on the molecules and create an artificial receptor.”

Because the “magnetic neurons” in the beak contained iron, Keays applied a blue stain that gloms onto iron. Christoph Treiber and Marion Salzer generated one-quarter million slices for microscope slides, each one-hundredth of a millimeter thick.

(Makes us dizzy … Didn’t they outlaw slavery?)

A fly in the ointment!

Although the magnetic neurons were said to number just six, iron-rich cells showed up all over the beak. One beak had about 108,000 blue-stained cells while another had just 200, Keays says. “This did not make sense. If these were magnetoreceptors, we would expect a similar number in birds of the same age and sex.”

When the scientists treated the samples with stains that attach to neurons, there was almost no overlap with the iron-bearing areas.

As questions accumulated, the researchers got a lucky break. One bird’s infected beak attracted blue cells that resembled macrophages, immune cells that fight infection (and also process iron). “You could see the cells’ tentacles engulfing other cells,” Keays says.

Stains that attach to immune cells overlapped heavily with the iron stain, Keays says; further evidence that the iron was inside macrophages, not neurons.

The study is “quite interesting and convincing,” says Walcott, and it explains why scientists have found no connection between the iron crystals and the nervous system. “If this is going to be seen as a sense organ, I think the two ought to be connected.”

Paradigm paranoia

Although the new study overthrows the accepted explanation for the pigeon’s magnetic mastery, Walcott says magnetism isn’t the whole story in navigation; birds also use vision, memory and smell.

Looking at the sun can help the bird figure out direction, but magnetic methods are needed to find a location on the globe.

Confusingly, birds seem to have a mechanism in the eye that detects Earth’s magnetic field. But because this works only when the sun is shining, it’s unlikely to explain nighttime navigation.

Keays says attitudes have changed since he “released a cat among the pigeons” at a conference a year ago. “Half of the audience wanted to hug me, they had been very skeptical, but the other half wanted to kill me.”

Since then, however, “We were able to persuade some big players in the field that the original reports were wrong. I think the great thing about science is that it is a self-correcting enterprise. If we get it wrong, somebody is going to come along and work out what the truth is.”

At this point, though, mystery rules. “It’s absolutely clear that birds, pigeons, can detect magnetic fields,” Keays says, “but the way they do that is the mystery.”

As honeybee colonies in the United States and Europe continue to suffer from a mysterious syndrome called colony collapse disorder (CCD), scientists are scrambling for answers. Another answer arrived this week, with a publication¹ that implicates a widely used insecticide.

CCD endangers many crops, but none more than almonds, which are pollinated by bees in more than a million hives trucked to California during the flowering season. Trucking stresses the bees, and stress is one of several likely contributors to the collapse syndrome.

Indeed, CCD could be several conditions lumped under one name, but here’s the trademark: The bees die away from the hive, obscuring the cause or causes of the collapse.

In the new study, scientists in France glued radio frequency identification tags to bees. Half were fed non-lethal doses of thiamethoxam, a common insecticide, then all the bees were released 1 kilometer from the hive. At the hive, the scientists used a radio-frequency gizmo to count how many flew home.

The tags did not affect the results, says Mickaël Henry, a researcher at the French National Institute for Agricultural Research, in Avignon. “Previous studies have shown that they do not impair movement or behavior of bees, or their time budgets for foraging activity.”

In any case, the control bees also sported tags.

What’s wrong?

How did the insecticide reduce the return rate so significantly? Most likely by causing difficulties with orientation, or locomotor activity, or both, Henry says.

When the experiment was repeated over a distance of just 70 meters, 92 percent of exposed and 98 percent of control bees returned, so both sets of bees were able to fly. The major impairment of exposed bees on the unfamiliar, longer route suggests that the insecticide was most damaging to the ability to learn a new route.

The neonicotinoid insecticides, the category that includes thiamethoxam, trigger nicotinic acetylcholine receptors, which are normally excited by a signal from a neurotransmitter. According to the new study, “Effects of sublethal neonicotinoid exposures in honey bees may include abnormal foraging activity, reduced olfactory memory and learning performance, and possibly impaired orientation.”

These insecticides make bees stupid, in other words.

The experiment was designed to count how many bees failed to return rather than pinpoint the reasons for that failure, Henry stresses. “The next step is to go into deeper detail about the behavior, with time-activity budgets, and looking at their foraging.”

Not the whole story

“This is a nice study, and it does clarify something that a lot of people have pointed to in the disappearance of bees,” says Phil Pellitteri, a faculty associate in entomology at the University of Wisconsin-Madison. “Insecticides have been known to cause bees to get lost, that’s one symptom of collapse. But colony collapse is a complex thing, and you can’t hang it all on one factor.”

Honeybees have long been attacked by viruses, protozoans and mites, Pellitteri says, and pesticides may decrease immunity, thus increasing susceptibility to pathogens. These, combined with the stress of long-distance travel and the scarcity of natural foraging grounds “are the general direction a lot of CCD research is pointing to. It’s a number of things, and their interactions.”

Henry and colleagues fed their data on return rates into a mathematical model, which predicted a perilous slide in colony populations. “The disappearances we observed may cause the colony to reach a population size low enough to be sensitive to other stressors,” he says. “Most bees are exposed to pesticides, and this confirms that exposure can put the colony at risk of collapse; this is the take-home message.”

Should an artificial waterway in Chicago be closed to block two highly destructive fish from entering Lake Michigan and then the other four Great Lakes?

On Feb. 27, the Supreme Court said ‘no’ when it declined to revisit an appeal by the State of Michigan, which wanted to compel closure of the Chicago Ship and Sanitary Canal. The canal, created to drain stormwater and wastewater from Chicago, could allow silver and bighead carp from the nearby Des Plaines River to enter Lake Michigan.

Since the two carp, native to Asia, escaped from fish ponds in the South in the 1970s, they have occupied much of the Mississippi River system, and have become extremely abundant in rivers near the Canal. Biologists, state agencies and the Great Lakes Commission warn that once the fish reach Lake Michigan, they will likely spread through the five lakes, then into the St. Lawrence River.

The Great Lakes hold almost 20 percent of the world’s fresh water and border eight states and two Canadian Provinces. Given the silver carp’s fearful jumping habits, and the potential for both species to steal food from the mouths of sport fish, the invasion could threaten recreational boating and commercial, sport and tribal fishing that gross $16.4 billion per year.¹

Although the Great Lakes already house at least 180 invasive species, ecologists warn about irreparable harm from Asian carp. They say prevention is cheaper and easier than eradication — which may be a practical impossibility.

Originally, the watersheds of the Great Lakes and Mississippi River were separate. The two were united by the Chicago Sanitary and Ship Canal, which drains stormwater and treated wastewater into the Mississippi River system.

Don’t fence me out!

Although three electric “fences” across the canal have apparently managed to block the fish from entering Lake Michigan, many scientists view the barriers as stopgaps at best, and Asian carp DNA has been found several times beyond the fences.

While that DNA suggests that the carp are already in Lake Michigan, the fish have not been found there. Still, ecologists, accustomed to studying the disastrous aftermath of invasives on land and in water, would love to protect the Great Lakes from the carp by closing the canal. That would also protect the Mississippi River from invasion from the Lakes.

“The Asian carp situation is analogous to medicine, where an ounce of prevention is worth a pound of cure,” says Jake Vander Zanden, a professor of zoology at University of Wisconsin-Madison, and an expert on freshwater invasive species. “It makes so much more sense to keep them out, rather that let them in and deal with the consequences forever.”

The shipping industry, reliant on these waterways, wants to keep the Chicago waterways open, said Mark Biel, chairman of UnLock Our Jobs by email. “Nobody wants to see the Asian carp get into the Great Lakes… This is, however, a manageable issue that requires a long-term, comprehensive plan, and separation is simply not a solution. Given the size, scope and complexity of separating the two bodies of water, it’s clear that the costs would be enormous and the timeline — if it’s possible at all — would do nothing to address the immediate threat of Asian carp.”

Invasions can be expensive. The Environmental Protection Agency figured that just the invasives delivered in ballast water cut commercial fish landings by 13 percent to 33 percent in the U.S. Great Lakes, at an annual cost of $200 million. The estimate did not cover Canada’s part of the lakes, or species that arrived by other means.

What’s the problem with carp? What can be done to prevent their entry into the Great Lakes and beyond? Are invasive species always so damaging to ecosystems?

What’s the beef about carp?

Asian carp are heavy-bodied fish native to Asia that have occupied large parts of the Mississippi River watershed, where their rapid reproduction, voracious feeding (up to two or three times their body weight in plant and animal plankton per day), and made-for-home-video jumps are making life miserable for native fish and fishing people alike. The two carp considered most threatening to the Great Lakes — silver and bighead — originated in Southern fish ponds, where they were placed as natural vacuum cleaners to suck plankton from dirty ponds.

Since at least 1980, when the escape of the silver and bighead was detected, that voracious appetite was transformed from selling point to sticking point.

You might observe — correctly — that species have been moving since life began. It’s true that invasions are an old story, but it’s only half the story: the process has been force-fed by commerce and technology. “This is a natural process; it was once a trickle, but the rate at which it happens now is so devastating,” says Vander Zanden. “With globalization, trade, travel, things are moving so fast, it’s a fundamentally different process, and the implications are huge.”

It’s impossible to predict exactly how well Asian carp would fare in the Great Lakes; their abundance will depend on temperature, food supply, the emergence of diseases and predators, and factors that we can’t predict. But the lakes have a wide variety of habitats, and inevitably some would be conducive to the invaders.

The fundamental reason why invasive species reach nuisance levels resides in the predators, diseases or competitors they leave behind in their homeland. In the new habitat, the traveling species often gets an unfair advantage, enabling it to grow to astonishing abundance and crowd out native species.

Asian carp provide a perfect example of the process. They were deliberately imported to work on Southern fish ponds, and their ability to outcompete native fish for food and habitat “has led to the widespread establishment of Asian carp in the Mississippi River, impacting the natural balance of the aquatic ecosystem,”².

Can we keep carp from the greatest lakes?

On January 31, 2012, the Great Lakes Commission, an international body charged with maintaining the environmental and economic vitality of Earth’s largest lakes, issued a report describing three options for physically separating the two giant drainages to block invasions in both directions. The report was greeted by a number of officials from the region, including Michigan Senator Debbie Stabenow and Chicago mayor Rahm Emanuel.

The Obama Administration opposes closure of the Chicago canal, and in February it proposed to spend $51.5 million on Asian carp research. The money will buy more trapping and netting, to assess whether the fish have reached Lake Michigan, research on fish trapping with chemical attractants, and noisemakers to scare carp from entrances to the lake.

The focus on Chicago is misleading, according to Biel, who notes that the Great Lakes and Mississippi River Interbasin Study, from the Army Corps of Engineers, found “18 aquatic pathways throughout the region (not just Chicago alone) by which the Asian carp could get into the Great Lakes. The existence of these other pathways, which cannot simply be closed, demonstrates the importance of a regional solution to control Asian carp populations. That’s why we have to expand our sights beyond Chicago to determine a comprehensive control plan that implements measures in all of the pathways… .”

Philip Moy is a senior scientist at the Aquatic Sciences Center at UW-Madison who previously worked on the issue for the Corps of Engineers. “Electric barriers buy us time, and we need to do two things,” Moy says. “We should look into additional barrier technologies that can be added to augment the electrical approach… . We need to look pretty hard at the Great Lake Commission report suggesting that the lake and river can be re-separated. It would cost a lot of money, a century of infrastructure has built up there, but what’s the logic of waiting another 10 years to get started on a project that can take a generation to complete?”

The “mid-system separation alternative” proposed by the Great Lakes Commission was estimated to cost $3.26 to $4.27 billion. The latest federal appropriation for monitoring and research related to Asian carp will bring the three-year cost for controlling Asian carp in the area to $156.5 million.

Separation, Biel wrote, “would effectively end waterborne commerce through the Chicago Area Waterway System. The Great Lakes Commission report mischaracterizes how vessels could move containers around the Chicago rail gridlock, giving the impression that there would be a way to facilitate both separation and continued cargo movement.”

Muscling in on the mussels

There are good reasons why zebra and quagga mussels are often mentioned in discussions about invasives in the Great Lakes. Since the zebra entered the lakes in ballast water used to stabilize ships a couple of decades ago, it has clogged water intakes at power plants and water utilities.

Along with a later arrival, the quagga mussel, the zebra has eaten enough plankton to change the ecology of the lakes, and the zebra is now spreading to smaller lakes and rivers.

To prevent further hitchhikers in ballast water, ships now must replace their ballast water in the ocean with salt water, which carries organisms that are unlikely to survive in the freshwater lakes. “Every ship coming in is inspected by the Coast Guard before it reaches the Great Lakes,” Moy says, “and we haven’t discovered another ballast-related species since 2006. In the lakes, there is a growing spirit of cooperation between the companies that operate ships and the states.”

p. 74, “Aquatic invasive species in the Rio Bravo/Laguna Madre Ecological Region”

Salt-water invaders are carried in ballast water and through the pet and fishery trades.

Species invasions also plague smaller lakes, which explains the growing push to prevent the movement of invasive fish, mollusks and plants, by requiring boaters to clean and dry their boats and trailers as they leave a lake.

In Wisconsin, at least, that effort seems to be succeeding, even though not every boater complies, Moy says. “Some people say, ‘If this guy didn’t do it, it’s not the end of the world if I don’t also,’ but it usually takes multiple introductions over time to establish a population. If we reduce the number of introductions per year, we reduce the potential for establishment. Every person makes a difference.”

Buying time, but could time be on our side?

As ecologists pursue the science of invasives, what to do about the carp now knocking on the door of the Great Lakes? Biel, of the shipping industry, says, “Despite the uptick in hysteria on this issue, Asian carp populations in Illinois haven’t actually moved up river in six years. That said, we fully support funding the existing electric control barriers because their effectiveness has been demonstrated over and over again.”

Despite “substantial strides” in controlling Asian carp in Illinois and Indiana, including a third electric barrier and physical barriers along the Des Plaines River and the Illinois and Michigan Canal, “there’s simply not enough being done by other Great Lakes states,” Biel says. “Continued calls for lock closure remain a higher priority for our neighbors and other like-minded groups than actually implementing tactics for prevention.”

During the years it would take to seal the Chicago waterways, control technology may improve, says Moy, who points to fresh ideas from the U.S. Geological Survey. Instead of using the pesticide rotenone as a “big hammer” to kill all fish, he says, the Survey is testing a coating for rotenone that would make a deadly fish feed. Once sprinkled in the water, carp and other filter feeders would eat the feed, but only Asian carp have the enzyme that can dissolve the coating to release the rotenone. “It’s much more specific; an elegant application that takes advantage of the fish’s feeding behavior and internal physiology, using an existing, certified” chemical agent, Moy says.

There are benefits to working several angles at once, Moy adds. “These invasions are not inevitable. We can reduce the rate of invasions and the number of introductions per year, and that reduces the likelihood of establishment, and each year we delay introduction to a lake gives research time to come up with a solution.”

It’s a basic question about the evolution of life: When was the first forest, and what lived there? For almost a century, the Riverside quarry in Gilboa, near Albany, New York, has been considered the grand-daddy of fossil forests, with hundreds of tree stumps dating from about 390 million years ago.

These strange Eospermatopteris trees contained no wood, but some stood more than 10 meters tall, says William Stein, an associate professor of biology at the nearby University of Binghamton.

Although Eospermatopteris did not have leaves, it was topped by a crown of branches.

The development of trees is a milestone in the development of life on land — as trees offer habitat for animals, alter the soil and landscape, and affect the atmosphere by using up carbon dioxide.

The Riverside quarry was excavated to supply stone for a dam in the 1920s, and it was at that site that paleontologist Winifred Goldring studied fossils of big, ancient trees. Ever since, her work has been considered essential evidence for arboreal evolution.

In 2010, Stein and Frank Mannolini of the New York State Museum obtained access to the same site for 10 days after contractors exposed the old rock in a search for stone to rebuild the dam. Although many of the Eospermatopteris stumps had been removed in the 1920s, the researchers found fossils of their roots “beautifully preserved in the ancient soil,” says Stein.

Palming it

The tree is comparable to a modern palm, Stein says, with “branches that act like fronds; they are very large structures that allow photosynthesis and reproduction.”

Those branches are studded with branchlets — but no leaves — that pick up energy from the sun, Stein says. “All photosynthesis takes place on the branchlets that surround the frond; there is a hand-like structure with four fingers and hundreds of little branchlets surrounding it.”

Leaves are not the only tree feature that’s missing, Stein says. “They are without the standard woody tissue you would expect in a tree of this size, and we don’t really understand how it works. Our best guess is that they are hollow, like an overgrown bamboo, with a very extensive outer structure that is thicker in the larger trees.”

Heard it through the grapevine?

Eospermatopteris was known from the 1920s, but the real surprise was fossils of a large, woody rhizome plant about as big around as an anaconda. (Botanical blip: A rhizome is a vine-like plant that runs along the ground.)

This was no average rhizome — but rather a monster up to 15 centimeters in diameter. At the site — a coastal location that repeatedly flooded — the rhizome apparently cohabited with Eospermatopteris, Stein says. “We can see it growing around the root mounds, which indicates that they were well aware of the tree’s presence.”

Based on microscopic samples of mineralized plant material, “to my surprise, we found that this was an Aneurphytalian, a very early group of woody plants.”

“It’s amazing to walk around these trees, to see where they were placed, the Aneurophytales looking like snakes, to see three major tree types when we thought there was only one,” says Stein. Based on evidence from nearby sites, the site probably also featured insects and fish, although it was too early for land-dwelling animals.

Radical rhizome

The Aneurophytalean rhizome may have grown like a vine on the Eospermatopteris trees, Stein says. “There is a pretty good indication that it climbed. That makes a lot of ecological sense, but the evidence is circumstantial.”

Rhizomes are typically thought of as “prostrate or semi-prostrate, producing leaves that go upward,” says Stein. “This is in our heads, based on botanical terminology, as opposed to the actual plants, which will do whatever they want” based on the abilities evolved by their ancestors.

Whether it was a rhizome or a vine, Stein says the Aneurophytalean is also a very early ancestor of all woody, seed-bearing plants. “Ultimately, wood was good invention,” says Stein. “Once it had the capability to grow, there is nothing beside orientation and some structural adaptations standing in the way of these rhizomes becoming a tree. They inherited the earth.”

The seas’ most sought-after fish are swimming between a rock and a hard place: the fisherman’s net and an encroaching mass of suffocating water.

A recent study has uncovered a new dose of bad news for ocean fish and the fishing industry. Areas of the deep ocean with little dissolved oxygen, called dead zones, are expanding and, thus, shrinking many fishes’ watery homes.

One driving force behind the predicament is none other than that pesky climate problem.

“Climate change is actually working in tandem with overexploitation of the animals to push these populations into a real dangerous place in terms of population collapse,” said Eric Prince, a fisheries biologist with the National Oceanic and Atmospheric Administration’s Southeast Fisheries Science Center and co-author of the study.

For example, Prince and his colleagues calculated that the Atlantic blue marlin, an economically valuable fish that was a focus of their study, has lost about 15 percent of its habitat from expanding dead zones since 1960. Dwindling habitat threatens not only the lives of fishes, but also the sustainability of the already ailing fishing industry.

Breathing room

Like their above-water brethren, fish need oxygen, which is dissolved in the water. Big, predatory fish, such as the blue marlin, need more dissolved oxygen than most, because they require lots of energy to grow and survive. Without sufficient oxygen, they’ll suffocate.

The level of oxygen in the water thus partly delineates fish habitat boundaries. Dead zones often draw these borders.

As climate change causes open ocean dead zones to balloon, fish habitat deflates.

Diagram modified from one originally published in Deep Sea Research Part I: Oceanographic Research Papers, Vol 57, Issue 4, Lothar Stramma, Sunke Schmidtko, Lisa A. Levin, & Gregory C. Johnson. Ocean oxygen minima expansions and their biological impacts, 587-595, Copyright Elsevier (2010).

Technically known as oxygen minimum zones, dead zones are actually a natural occurrence. Found at depths of between 200 and 1000 meters, they are caused partly by seawater circulation and partly by the decomposition of organic matter, namely deceased sea critters that sink from surface waters.

As aerobic bacteria nosh on the organic matter, they use up the oxygen in the water. Eventually, hypoxia happens—the water becomes so depleted of oxygen that many creatures can’t survive.

Since deep-sea dead zones are insulated from the ocean’s surface, where the water borrows oxygen from the atmosphere, they can only reload with oxygen if currents make a long-distance delivery, according to Sunke Schmidtko, an oceanographer at the University of East Anglia, the other co-author of the study.

Deep-sea dead zones are different from their coastal cousins like the one in the Gulf of Mexico. Coastal dead zones form due to a buildup of agricultural fertilizer that rivers, such as the Mississippi, collect and then flush out to sea, causing abnormal blooms of plant life.

De-fizzing the ocean

But climate change is turning what Mother Nature does normally into a big problem. As the air is getting hotter, so is the water, and warmer water can hold less oxygen than colder water.

This is similar to what happens to a soft drink on a hot day. After sitting in the heat and sun, the fizz fizzles, and you are left with a flat, carbon dioxide-depleted beverage.

Also, warmer surface waters are less likely to sink to the ocean’s lower layers, because warm water is lighter than the colder water below, Schmidtko explained. In other words, as the oxygen-rich surface layers heat up, they could have a harder time delivering oxygen to the deeper ocean.

Schmidtko clarified that oceanographers are still trying to determine how exactly climate change is affecting the ocean, but with their knowledge of how water works, these represent their current speculations.

The rock below

With less oxygen to go around, oxygen minimum zones are swelling and intruding on many fishes’ living zones.

For example, marlins often dive deep to feed, sometimes as far down as 800 meters. However, in the eastern Atlantic’s growing dead zone, which is already one of the largest in the world, Prince found that marlins can’t dive as deep as their west-side counterparts.

“They need to go where the food is and where they can breathe,” he said.

With less breathing room below, the floor of their habitat rises, and they are pinned to the surface layers. With nowhere to go but up, marlins become squished into tighter, testier quarters with other predatory fish and their prey. They also find it harder to dodge a waiting fishing hook or net.

“Concentrating them makes it much easier for overexploitation by [humans],” said Prince.

The increasing concentration of animals at the top could also lead to a boost in the amount of sinking organic matter, which would further worsen the oxygen shortage below.

Softening the hard place above

As a prized catch, Atlantic blue marlins are already victims of overharvesting. In fact, their populations have dropped 60-64 percent over the past three fish generations (14-18 years).

But the growing dead zones can actually fool scientists and fishermen into thinking fish populations are doing just fine, since more fish are squeezed into a smaller area. Thus, to ensure the dead zone-fishing vise does not become their demise, Prince said scientists must more carefully monitor fish populations, as well as the expansion of the dead zones.

While fish stock assessments are starting to incorporate this information, Prince warned the pace needs to quicken.

And if the Earth is to continue warming, as most scientists predict, Schmidtko added that humans should chill out on fishing.

After all, we will never be capable of “ventilating the ocean,” he said.

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’ve hung around a big-city park, you may think that pigeons are countless — or uncountable. But according to scientists from New Zealand, pigeons now join the short list of animals that can count — or at least, can places images containing two countable items in numerical order.

It’s blue news for those who think only humans deserve human capacities. From empathy and altruism to murder and war, animals seem to have caught on to some of our best — and worst — tricks.

Now Damian Scarf, a post-doctoral researcher at the University of Otago, with his colleagues, has taught three pigeons to order pairs of numbers in the range from one through nine.

This is not exactly counting, but it certainly is a sign of numerical awareness in birds.

More important, the researchers have taught these retired racing pigeons the concept of smaller-to-larger, Scarf says. “Previously, this number abstraction was only known in primates, and now we have shown that it is not unique to primates.”

Serious screen-time serves science

The experiment began with a year-long training period, during which the birds were shown pairs of images, each containing one, two or three countable items. If the birds pecked at both images, smaller number first, they were rewarded with some wheat. (Although the images never contained a numeral, we refer to the “number” they contain for brevity.)

To prevent the birds from focusing on color, shape or other non-numerical details, the images showed a range of items, so that the only correct answer would reflect their number rather than other distinctions.

“The training time reflects how difficult it is for them to abstract,” Scarf says. “It’s such a foreign situation, number is not the first port of call when presented with a stimulus to discriminate. That’s why we had so many shapes, colors, surface areas.”

Even if the birds originally made their judgments based on color, “we pushed them to use a different strategy, to break away from that. Number is not the default discrimination mechanism” for pigeons, says Scarf, who worked under advisor Michael Colombo of Otago.

A genius for abstraction?

This does not mean that the birds are counting, says Scarf. “It’s more a fuzzy representation in the brain of what ‘three’ is. We can apply this verbal label to three, but they cannot. Pigeons, and animals in general, don’t have a definite idea of a number, that’s why they don’t perform perfectly, and why we see the distance effect.”

When the numbers on the test pair are further apart, Scarf found, “the fuzziness overlaps a little less.”

A greater distance between the numbers produced a quicker response and greater accuracy. For adjacent numbers, like four and five, the birds scored about 66 percent accuracy, compared to more than 95 percent for numbers separated by at least six. Once the difference rose to at least three, the pigeons did as well as monkeys in a path-breaking 1998 study that opened the field of numerical “thinking” in animals.

Scarf stresses that the birds were not just regurgitating what they had learned, but were learning numerical rules. “The goal was to find out whether they could acquire an abstract rule. We were just training for one through three, but they learned some flexibility, an abstract, ascending rule for ordering numbers” that would apply to other numbers on the screen.

Rooted in evolution, but where?

Being able to recognize that one thing is more numerous than another could help an animal survive, Scarf says. “When food is available in multiple places, an animal has to develop an optimal strategy for figuring out where the most food is, and I think we have subverted that capacity for this task.”

Where this capacity arose is anybody’s guess at this point. The evolutionary lineage of mammals and birds divided about 300 million year ago, Scarf says. “If this derived from a common ancestor, it’s very old. It’s also possible that primates and birds have evolved this independently.”

“I do think it’s important, just as our study of mirror self-recognition in monkeys, from the fundamental standpoint of how these abilities come about,” says Luis Populin, a professor of anatomy at the University of Wisconsin-Madison, who has found that, under certain conditions, monkeys can recognize themselves in a mirror. “It’s very nice and is yet another step toward understanding how our cognitive functions develop.”

You have to hand it to these birds, which have set a new standard for avian aptitude. “The new part is the idea that this abstraction of numbers is not tied to training,” says Scarf. “Most numerical tests with animals involve training and testing with the same numbers, but we were training with a limited set of numbers and testing them with numbers outside the range. They learned an abstract rule, and that’s what makes this study unique.”

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

Among all animals, amphibians are in the worst shape; fully 30 percent are classified as threatened or endangered. Amphibians – including frogs, toads and salamanders — are under attack by a deadly fungus. They are losing habitat to farms and cities, and collected as food or pets. Amphibians are suffering from chemical pollution and the warming climate.

The present is harsh enough, but the future seems worse.

This week, Nature publishes the first global attempt to forecast the impact of three big threats to amphibians by 2080 – a year chosen to be one century after the study’s baseline data.

By comparing areas with plenty of amphibian species with projections of climate change, land use change and the chytridiomycosis fungus, the researchers forecast a grim future for these cold-blooded, four-legged vertebrates. “The bad news is that more than two-thirds of all high-richness regions will probably be affected, to a high intensity, by one of these three threats,” said lead author Christian Hof, who did the work as a Ph.D. student and post-doctoral fellow at the University of Copenhagen.

The geographic study of data on 5,527 amphibian species found little overlap between the cool, moist areas afflicted by fungal serial killer chytridiomycosis, and the places likely to suffer the worst effects of changes in climate and land use.

And the losers win!

In forecasting the future of amphibians, the study coined two technical terms: “losers” — species that are expected to suffer due to disease or changes in climate or land use, and the less numerous “winners,” which are expected to prosper by 2080.

The projection hinged on whether an expected change would make a habitat more or less suitable to the species, says Hof, who’s now at the Biodiversity and Climate Research Center in Frankfurt, Germany. “We ran a number of climate-change models and based on them, calculated a change in climate suitability for each region across the globe.”

Based on these changes in suitability due to climate, land use and disease, Hof adds, “We calculated the number of species that would probably decline due to a decline in habitat suitability. We classify the species as a loser in a particular region, but that does not mean it will decline across its whole range.”

Overall, the researchers found an increasingly dire future for amphibians. For example, 54 percent of frogs are likely to be “climate losers” in the average grid cell of their model. And heavy impacts are projected for about two-thirds of the regions with the highest species richness in frogs and salamanders.

In fact, the future could be even worse, since the study ignored a number of potentially damaging factors, including chemical pollution from cities, factories and agriculture.

Photo: Robert Fletcher, Ohlone Preserve Conservation Bank

Tougher times might await this prowling California tiger salamander, an endangered California native.

Going down!

It’s frustrating but understandable that the study could not predict rates of decline among amphibians. “For many species, we are not sure about the actual distribution, many have tiny ranges and we don’t know where they occur, so we can’t relate historic changes to, say, climate change. We were very careful not to predict extinctions, based on these uncertainties.”

Data are scarce in the study of amphibians, agrees Anna Pidgeon, an assistant professor of forest and wildlife ecology at University of Wisconsin-Madison. “It’s frustrating, amphibians are out at night, often in remote areas, they are small and many are cryptic, so it’s a huge challenge” to understand their populations and ecologies. “We work with the best data we have all the time … and try to make inferences from what we know about close relatives.”

Pidgeon, an expert on habitat needs of vertebrates, says predicting 70 years into the future is always dicey, but that the study’s analysis of multiple threats and global scope are major accomplishments. “They did a lot of things to make sure they were using consensus data, and that makes it a pretty solid approach.”

Although the study looked at overlapping threats, it did not actually look at interactions between those threats, Hof says. “What needs to be done, and we could not do that with our model, is to look at, for example, how climate change would affect susceptibility to the fungus. How would habitat fragmentation affect susceptibility to climate change?”

Although the study does not suggest practical changes that could sustain amphibians in the short run, “The general conclusion is that it’s very important, when thinking about the future for amphibians, to consider different threats together,” says Hof. “Just looking at one threat will not give us the whole picture.”

– David J. Tenenbaum

She asks if she’s overweight, and you wait half-a-second before responding, “Of course not, dear! I’ve just been noticing how slim you look these days.”

Any well-schooled husband knows the pitfalls of faltering in this “marital duet.”

And now, we find a similar phenomenon among a singing duet by plain-tailed wrens, natives of the cloud forest in Ecuador.

Pairs of these wrens engage in a high-speed duet that relies on perfect timing: She utters a call, and if he chimes in on cue, she sings her part, and the duet continues.

If he’s late or silent, she is slow to resume the song.

This is cooperative behavior, but close examination also reveals a new mental phenomenon, says Eric Fortune, an associate professor of psychological and brain sciences at Johns Hopkins University. Fortune, first author of a study of the wrens that appears today, says his research “indicates that the full mental representation of the song exists in both birds, even though each one contributes only half of the song.”

The study looked at the interaction between the hearing and motor circuits in the brain via a concept called “mirror neurons.” Discovered in 1983 by Dan Margoliash of the University of Chicago, mirror neurons were “a key discovery that has profoundly shaped our thinking,” Fortune says. “He showed that an area of the brain used to control song responded only when the bird heard a playback of its own song, but not of any other bird’s song.”

Zina Deretsky,
National Science Foundation

Takes two to tango: The song of the plain-tailed
wren is a his-and-hers production.

These nerve cells, since seen in people, other primates and birds, are now called mirror neurons. In simple terms, mirror neurons allow a bird that hears its own song to “imagine” singing that song.

Brainiest birds?

In the new study, however, the mirror response occurs when an individual in a pair hears both birds singing — a sound that each bird cannot produce by itself.

In 2006, scientists identified the plain-tailed wren’s song as a two-part composition that required cues from both partners. “When we heard about these wrens, where one-half of the song is produced by the female, and the other half by the male, we thought, ‘This is amazing. Here’s a song this bird has learned completely in the sensory part of the brain, but it has only half of the motor program.’”

How could this work?

To unravel the sensory-motor linkage, Fortune, with Gregory Ball of Johns Hopkins and Melissa Coleman of Claremont McKenna College, recorded pairs of plain-tailed wrens, manipulated the songs in various ways, and then played them back.

They found that the birds not only sang in pairs, but sometimes also sang solo, making the same calls it would otherwise contribute to the duet, but with altered timing. They found that when a male flubbed his lines, the female might continue to sing, but with a measurable delay. “She’s waiting for him, then gives up and sings anyway,” Fortune says.

The birds were basing their behavior on what they heard — not very surprising. But the fascinating part emerged from the fact that they were engaged in a truly cooperative, back-and-forth behavior that was deeply embedded in the mirror neurons.

Both images courtesy Eric Fortune and Melissa Coleman

Like many field worker, Fortune had to make do with local material, as
shown in this laboratory. Rollover for a look at their solar and
hydro-powered neurophysiological rig, featuring a home-made version
of a $7,000 vibration damper.

Such cooperation, also evinced by dancers and musical ensembles, requires each party to know its own part, but the brain studies showed that they knew much more than that, says Fortune, who is also a visiting professor at Catholic University in Quito, Ecuador. “Both birds had very similar patterns of activity. The neurons responded most strongly to the combined song, not to their own part. The brain knows that they were trying to do this together.”

Got my eye (and ear) on you, mister!

Although Fortune says the songs are probably used to defend territory, he suspects she is also checking him out, gauging his evolutionary fitness, much as female birds rate a fellow’s feathers. “The female is testing the male’s ability to cooperate,” Fortune says. “She produces a long song, and the male has to work hard to insert his syllables at exactly the right time.”

Louis Vest

People also learn cooperatively. Do these
tango dancers hold a representation of the
complete dance in their heads, or is this just
another example of sexual selection at work?

These wrens, he says, “are wired to cooperate. There is a set of rules and the male’s job is to respond rapidly and accurately to the female’s challenge.”

It’s not just feathery guys that fail to respond on cue, and the evolutionary significance could extend far beyond birds. “This happens a lot in people,” Fortune speculates. “Why do women get annoyed when you forget their birthday? They are challenging your neural circuitry. It’s not like flexing your muscles; they are probing your brain. That’s a stronger cue for sexual selection.”

Bringing it back to birds, Fortune says, “It’s most surprising that these animals have a memory of their cooperative behavior in the brain, which includes the performance of another animal; this had not been shown before on a neurological basis. You can take their own half of the song, and play it back, and the motor neurons fire,” but the response is much more powerful when the bird hears the full, two-part song.

— David J. Tenenbaum