Living in the Universe

The Aerial Biome

First Week of March 2008

Here’s a scary thought. What if the air we breathe was alive? Well it turns out that it is. There’s a story making the rounds in the news services that I came across on CNN about snowflakes that contain bacteria. Most snow and rain forms in chilly conditions high in the sky, and atmospheric scientists have long known that under most conditions the moisture needs something to cling to in order to condense.

A new study published in the journal Science finds a surprisingly large share of those so-called nucleators turn out to be bacteria that can affect plants. Brent Christner, an Assistant Professor of Biology at Louisiana State University who led the study said, “Bacteria are by far the most active ice nuclei in nature.” He and his colleagues sampled snow from Antarctica, France, Montana, and the Yukon, and they reported their findings last week. In some samples, 85% of the nuclei were bacteria. The bacteria were most common in France, which makes sense given all their live cheese and yogurt, followed by Montana and the Yukon and were even present to a lesser degree in Antarctica. The most common bacteria found was something called Pseudomonas syringae, which can cause disease in several types of plants including tomatoes and beans. The study used twenty samples of snow from around the world, and subsequent research also found bacteria in summer rainfall in Louisiana.

The focus on Pseudomonas in the past has been to try and eliminate it, but it now turns out to be a major factor in encouraging snow and rain. So the lead author of this study wonders if that’s a good idea. Would elimination of this type of bacteria result in less rain or snow, or would it be replaced with other nuclei such as soot or dust? “The question is,” said Christner, “are they a good guy or a bad guy? And I don’t have the answer to that.” What is clear is that Pseudomonas is effective at getting moisture in a cloud to condense. Killed bacteria are sometimes even used as an additive in snow making at ski resorts, which raises the question of whether planting crops known to be infected by Pseudomonas in areas with drought might help increase precipitation there by adding more nuclei to the atmosphere.

Let’s consider the larger issues raised by this study. It’s been known for a long time that microbes, insects, and algae blow around in the atmosphere. Back in 1832, Charles Darwin was at sea on the H.M.S. Beagle, and he noticed that dust had landed on the ship, and from the position of the wind on the ship concluded that it must have come at least three hundred miles from the coast of Africa. He collected it and sent it off for analysis, and it turned out to contain numerous species of African freshwater algae. Clouds have been trapping microbes and sending them traveling around the planet in a sort of bus system for millennia.

More information on this subject comes from Olivia Judson, a columnist for the New York Times and a biologist at my alma mater Imperial College in London. She referred in a recent column to a paper from 2001 called “Bacterial Growth in Supercooled Cloud Droplets.” This paper takes the idea of airborne microbes one step further. It claims not only that microbes travel via cloud but some of them are actually living there: growing, metabolizing, and reproducing, until they plummet back to Earth in the form of rain.

This is intriguing because clouds are not thought to be very hospitable conditions for life and its evolution. Water is supercooled. It’s often very acidic and contains toxins such as formaldehyde, and because of the proximity to the Sun and the high level in the atmosphere, there’s a lot of ultraviolet light that can damage the DNA. Also, clouds represent physical conditions with extreme fluctuations, and generally it’s thought that life does not like extreme fluctuations. But apparently this isn’t a problem because the microbes that live in clouds have adapted themselves to the extremes they find there. As to their metabolism, and the question of what these microbes eat, clouds are apparently much more nutritious than they look and much more substantial, more nutritious even than freshwater lakes. Cloud water contains organic acids and alcohols and useful elements such as nitrogen and sulfur. Lab experiments have shown that for growing bacteria or fungi, cloud water contains plenty of potential food.

All of this conjures up the idea of an aerial biome, and the possibility that life can exist not only in addition to life on the surface of a planet but perhaps independent of it. The 1970’s saw an extreme speculation by famous astronomer Carl Sagan and his Cornell colleague Ed Salpeter. They imagined buoyant jellyfish living in circulation patterns in the cloudscapes of Jupiter. Even if that’s unlikely to be correct, it makes for a very appealing image and the general point they raised is important for astrobiologists to consider. What if life on planets in the far-flung galaxy exists on nothing more than air?

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Life in the Lost City

Third Week of February 2008

The topic today is Life in the Lost City. I’m not referring to Atlantis but to another subterranean world. In the 1970s, deep under the ocean, just when we thought we knew everywhere life was on Earth, entire ecosystems were found living in total darkness where magma superheated water and emerged into frigid water at the bottom of the ocean. There were microbes, blind krill and translucent fish, and all sorts of living organisms this far from the Sun’s energy.

Two papers recently have brought to light a place called the Lost City, a contender for one of the places where life may have started four billion years ago deep under the ocean. Hydrocarbons, the molecules critical for life, are being generated in this region by the interaction of seawater with the rocks at the Lost City hydrothermal vent. This place is located in the middle of the Atlantic Ocean.

The lead authors on the paper, Giora Proskurowski and Deborah Kelley, say that they’ve ruled out carbon from the biosphere as a component of the hydrocarbons in Lost City vent fluids. Hydrocarbons, molecules with different combinations of hydrogen and carbon, are key to cellular life. For example, cell walls can be built from simple hydrocarbon chains, and amino acids are short hydrocarbon chains hooked up with nitrogen, oxygen, or sulfur. According to Proskurowski, “The generation of hydrocarbons was the very first step. Otherwise, Earth would have remained lifeless.”

There are two hypotheses for how life on Earth started. Some researchers still believe that the building blocks of life made their way from outer space. Others hypothesize that the right ingredients were generated by geological processes on Earth, perhaps at hydrothermal vent systems where seawater seeps into the seabed, picks up heat and minerals, until the water is so hot it vents back into the ocean. The hydrothermal vents in the Lost City were discovered by Deborah Kelley and her colleagues during an expedition in 2000 and they are very different from the black smoker vents that scientists have known about since the 70s. Black smokers are called this because it looks like smoke is billowing from them. The smoke is in fact dark iron and sulfur rich minerals precipitating when the super hot vent waters, they can be as hot as 800° F, meet the icy cold depths. The spires and mounds that form from the superheated water are modeled mixtures of sulfide minerals.

By contrast, the Lost City structures are nearly pure carbonate, the same material as limestone in caves, and they range in color from white to cream to grey. The structures and the cliffs in the Lost City range from the size of little mushrooms to an eighteen-story column called Poseidon that dwarfs most of the black smoker vents by hundreds of feet. The field was named Lost City in part because it’s on top of a submerged mountain named Atlantis, and it was discovered by chance during an expedition on board the research vessel Atlantis. The water venting at Lost City is 200° F. The fluids don’t get as hot as the black smokers because the water isn’t heated by magma but rather by heat released by chemical processes.

Natural occurring carbon dioxide is locked in mantle rocks, and at Lost City the reaction between rock and seawater produces ten to a hundred times more hydrogen and the hydrocarbon methane than a typical black smoker system. That’s why it makes excellent raw materials for life. Analysis of the rocks from Lost City shows that the hydrocarbons are not coming from the living biosphere. Rock in contact with seawater has a very consistent ratio of carbon dioxide to helium, but the rock at Lost City had a strikingly different ratio. It turns out that the depleted amount of carbon dioxide in the rocks roughly equals the amount of hydrocarbons being produced in the fluids. “Lost City is exceptional,” as Deborah Kelley says, “Because chemical reactions in the sea floor produce acetate, formate, hydrogen, and alkaline fluids. All of these substances may have been key to the emergence of life on Earth.”

In addition, acetate and formate found in the Lost City fluids may have been an important energy source for the ancestors of methanogens, the microorganisms that live off the methane at places like Lost City. It’s one more bit of evidence about where life may have originated. Where is this bizarre place? It’s about 2300 miles east of Florida on the Mid-Atlantic Ridge at a depth of 2600 feet. Microorganisms there thrive in alkaline vent fluids, some of which are nearly as caustic as liquid drain cleaner. The Lost City microbes live off methane and hydrogen instead of the carbon dioxide that’s a key energy source for life at the black smoker vents. In the early Earth there were probably plenty of places where mantle rock may have met the bottom seawater and produced complex and interesting chemical reactions, so Kelley is sure that there are other Lost Cities waiting to be found.

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Space Germs Get Mean

Fourth Week of October 2007

Today I’d like to catch up with a story from a couple of weeks ago based on a paper published in the Proceedings of the National Academy of Sciences. That’s normally a fairly serious and stodgy journal, but this story has the plot of a scary B movie. Germs go into orbit on a spaceship and come back stronger and deadlier than ever. Yes, it really happened. The germ was salmonella, best known as a culprit in food poisoning.

The trip? Space Shuttle mission STS-115 back in September, 2006. The reason salmonella were sent into orbit? Scientists wanted to see how space travel affects germs so they took some along, carefully wrapped for the ride. The result? Mice that were fed the space germs were three times likelier to get sick and died more quickly than mice fed identical germs that remained behind on Earth. Cheryl Nickerson, a team member for the experiment and an associate professor at the Center for Infectious Diseases and Vaccinology at Arizona State University, said, “Whenever humans go, microbes go. You can’t sterilize humans. Wherever we go, under the oceans or orbiting the Earth, the microbes go with us, and it’s important that we understand how they’re going to change.”

Learning about how germs change also has the positive potential to novel new countermeasures for infectious diseases. So the researchers placed identical strains of salmonella in containers and sent one into space on the shuttle while the second was kept on Earth under similar temperature conditions. Mice were given varying oral doses of the salmonella and then watched. After three weeks, forty percent of the mice given Earth-bound salmonella were still alive, compared with only ten percent of those dosed with the germs in space, and the researchers found that the amount of bacteria it took to kill half the mice was three times larger for normal salmonella than the space germs. When looked at in detail, the researchers found that a hundred and sixty-seven genes had changed in the salmonella that went into space.

Why? Members of the research team simply don’t know, but they think it’s a force called fluid sheer. According to Nickerson, “Being cultured in microgravity means the force of the liquid passing over the cells is low. Those cells are responding not to microgravity but indirectly to microgravity in the low fluid sheer effects. There are areas in the body which are low sheer such as the gastrointestinal tract where obviously salmonella finds itself. So it’s clear this is an environment not just relevant to spaceflight but to conditions here on Earth, including in the infected host.” She said it’s an example of a response to a changed environment. These bugs can sense where they are by changes in their environment. The minute they sense a different environment, they change their genetic machinery so they can survive.

Obviously this result has enormous implications for astrobiology. If microbes can indulge in this kind of genetic adaptation to what’s considered an extremely hostile environment in space, then potentially their survival ability in very harsh situations is greater. So this degree of adaptation to space environment is another positive indication that microbes could travel through space, seeding life between planets. This idea is called panspermia, and the main objection to it has been the long time taken for space rocks with microbes to travel between solar system and the hazard of the space environment. In biology, it seems that duress can spur survival. Maybe we would never want to run into the kind of germs that are mean enough to thrive in outer space.

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Immortal Bacteria

Third Week of September 2007

This week I want to talk about a story from a few weeks ago about the decay rate of bacterial DNA, indicating that the information coding molecule of biology has a half life for degrading due to radiation in the environment of about a million years. A team of researchers has talked about cells that are essentially immortal, in their words. If confirmed, immortal cells could prove the potential for life on Mars and Europa, one of Jupiter’s moons.

The cells come from Antarctica, home to the largest body of ice on Earth. Prior to about ten years ago, nobody thought that life could exist beneath the Antarctic life sheets, which can be more than two miles thick in places, because the conditions were believed to be too extreme. However, Brent Christner, assistant professor of biological sciences at LSU, spent a great deal of time in the world’s most hostile environment conducting research that proves otherwise. Christner’s discoveries of viable microbes in ancient ice cores in sub-glacial environments, coupled with the realization that large quantities of liquid water exist beneath the Antarctic ice sheet, have changed the way biologists view life in Antarctica. “More than a hundred and fifty lakes have been discovered underneath nearly two and a half miles of ice in Antarctica,” said Christner, “and most of these bodies of water have likely been covered by ice for at least fifteen million years.” The environmental conditions in the deep cold biosphere are unlike anything on the Earth’s surface, and this biome represents one of the most extreme habitats for life on the planet.

A time frame of up to one million years is required for microbes in the atmosphere to be transported through the sheet of ice and enter an Antarctic sub-glacial lake. Even though cells are preserved in the ice, the question of how the DNA in these organisms remains unscathed over such long periods of time remains. According to Christner there are two possible explanations for how these microbes could survive frozen for many millennia.

First, they may be dormant in the ice and possess very effective repair mechanisms that are initiated when the cells are introduced into a growth situation. He said that given enough time, dormant cells without active DNA repair mechanisms would eventually incur lethal levels of radiation induced damage from natural background sources in the ice. Alternatively, Christner suggests that the microbes might stay metabolically active while entrapped in the ice giving them the ability to repair damage as it occurs. If this is the case, these microbes may be essentially immortal when frozen, assuming a continuous energy supply is available. That’s an exciting prospect because we imagine there will be many cold environments out there in space on moons and planets.

Christner’s current laboratory research has shown that glacier microbes are capable of metabolic activity when frozen down to minus twenty degrees Celsius. Again, in his words “Our experiments have revealed the potential for microbes to metabolize under frozen conditions, but we lack the smoking gun which proves this occurs in nature. We’re taking what we learned in the lab at LSU and designing experiments which address this question in real Antarctic ice samples.” He and some students are heading down to the Antarctic in October, next month, and staying through January 2008 to continue the research.

Christner says, “The implication of our research is that large sheets of Antarctic which make up seventy percent of the planet’s fresh water resource may represent actual biomes, substantially expanding the known boundaries for life on Earth. Terrestrial glacier environments provide analogues to address questions relevant to the search for past or present microbial life in extraterrestrial ice on planets and moons in our Solar System. Based on everything we know about the tenacity of life in Earth’s deep cold biosphere, microbial life surviving and persisting in the ice on Mars or Europa is not that much of a stretch.” That’s exciting research; it lends extra motivation for a future return to Europa.

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Microbes in the Deep Freeze

Fourth Week of August 2007

Last week I talked about creating life from scratch in the lab. This week I want to talk about bringing life back into being after it’s been long dead, reanimating life. A recent paper in the Proceedings of the National Academy of Science talks about the DNA of ancient microorganisms which, long frozen in glaciers, may return to life as the glaciers melt.

“This finding is really significant,” according to Kay Bidle, the author of the study and an assistant professor of marine and coastal sciences at Rutgers University, “because scientists didn’t know until now whether such ancient frozen organisms and their DNA could be revived at all or for how long cells are viable after they’ve been frozen.” Bidle and his coauthors melted five samples of ice ranging in age from a hundred thousand to eight million years old to find the microorganisms trapped inside. The researchers wanted to find out how long cells could remain viable and how intact their ice was in the youngest and oldest ice.

First they asked if they could detect organisms at all, and they did detect more in the young ice than the old. The group tried to grow them in media and the young stuff grew very effectively. They recovered the microorganisms easily, and they could plate them and isolate colonies which doubled every couple of days. By contrast, the microorganisms from the oldest ice samples grew very slowly, only doubling only every sixty or seventy days. Not only were the microorganisms in the oldest ice slowest to grow, the researchers were unable to identify them as they grow because their DNA deteriorates.

In fact DNA in the five samples examined showed an exponential decline after one million years and according to Bidle this constrains the geological preservation of microbes in icy environments and the possible exchange of genetic material to the oceans. He said, “There’s still DNA left after a million years, but a million years is the half life. That is, every one million years the amount of DNA gets chopped in half.” Bidle said the average size of DNA in the old ice was two hundred and ten base pairs. That is two hundred and ten units of genetic code strung together. By contrast, the average genome size of the simplest bacteria is three million base pairs. Two hundred and ten base pairs is not a viable organism, although actually the smallest possible replicating piece of genetic code is about that size.

These researchers chose the Antarctic glaciers for their research because the polar regions are subject to more cosmic radiation than the rest of the planet, and they contain the oldest ice on the planet. It’s this cosmic radiation that’s blasting the DNA into pieces over geological time, and most of the organisms simply can’t repair that damage. Because the DNA had deteriorated so much in the old ice, the researchers concluded that life on Earth, however it arose, did not ride in on a comet or other debris from outside the solar system. According to Bidle again, “The preservation of microbes and their genes in icy comets may have allowed the transfer of genetic material among planets. However, given the extremely high cosmic radiation flux in space, our result suggests it’s highly unlikely that life on Earth could have been seeded by genetic material external to this solar system.”

So a small, localized study on the Antarctic glaciers has produced a result that has serious and important implications for how life arose on Earth and, by implication, how life may transmit and arise in other solar systems. Since interstellar travel times of rocks ejected by meteoric impact are likely to be millions of years, it’s very unlikely that life primitive life could hitchhike between the stars.

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An Extreme Microbiologist

Second Week of July 2007

I’d like to note the passing and celebrate the career of Imre Friedmann, an extreme microbiologist who died at the age of eighty-five. Conventional wisdom says that life stands no chance at all on the surface of Mars. Fields of reddish oxidized rock stretch to the horizon. Carbon dioxide fills the atmosphere, and UV radiation burns through it. Deep cold and dryness are everywhere. There may have been water, for the poles have icecaps and the ground shows channels, gullies, and shifting shorelines, but water alone is no proof of life. That’s what science says, but human curiosity and hope say otherwise.

For Imre Friedmann hope lay in a squarish grey lump of rock known as ALH84001, the meteorite picked up in 1984 in the Allan Hills of Antarctica. Traces of gas inside it seemed to prove that it came from Mars, and there were also microscopic strings of pearls, as Friedmann described it, flexible chains of crystals that seemed to have been formed by an organic process. They were like fossilized internal compasses of magnetotactic bacteria of which kind examples still exist on Earth, and since such bacteria need oxygen their presence suggested that photosynthesizing organisms must have lived on Mars too.

Well, the promise of the life in the Mars rock faded away and Friedmann was disappointed too, but his long search for life in the most daunting places on Earth mirrored the bleakness of the Martian terrain. The organisms he studied were nothing much to see. They lay under the stony floor of deserts like the Negev, the Gobi, and the Atacama, or in the bone-dry valleys of the Antarctic. He called them cryptoendoliths or hiders in rocks. Most of them were cyanobacteria, familiarly known as blue-green algae, organisms that cling precariously to life in the most extreme conditions of heat, cold, dryness, or salinity.

For many years the scientific world was indifferent to Doctor Friedmann’s studies of these organisms. Fame engulfed him in 1978 not long after the first Viking lander when Mars had disappointingly concluded that the planet’s soil was sterile. So NASA scientists recalled that two years before Friedmann with his wife, also a microbiologist, had published a paper on bacteria surviving in terrain almost as hostile as Mars, and suddenly the dead rocks began to suggest a different story. Friedmann always felt a certain tenderness for his cryptoendoliths. “Always hungry, always too cold, in this grey zone,” he said. In human terms, you could compare them to the most miserably living generations of pariahs in India. They are born. They live, and they die in the gutter like pariahs, or like him when as a Jew growing up in Budapest he was debarred from university, then forced into a labor camp, driven into a life of hiding from both Germans and Russians bent on killing him as though he was the most contemptible form of life.

His enthusiasm for science had started in boyhood in his mother’s kitchen, but his taste for extreme microbiology began in the 1950s at the Hebrew University of Jerusalem. He’d gone there as a refugee to restart his academic career. As a student of seaweed he had the outlandish idea that he might find a single-celled version of seaweed in the desert, and he did indeed find under the limestone surface of the Negev a greenish layer like a copper compound that turned out to be algae alive. When he moved to Florida State University, and with NASA’s interest, money began to come in. He traveled frequently in search of more. Well into old age he could be spotted in bright red parka and frozen beard lying full length on the Antarctic sandstone to snap pictures of some tiny life containing fissure in the rocks, or he could be seen in the Atacama desert gently attaching sensors to rocks as if they were living bodies so his data boxes could record for seven years the least intimation of something interesting happening inside them.

Any such movement on Mars had long since ceased. About three billion years ago, by the best estimates, life has died out there. But Friedmann was fascinated by the thought that Mars might well have been warm, wet, and biologically pulsing before the Earth was. This provided another data point from which to explore the origins of life. It was possible too that life had originally come from Mars, since it was much easier to make that journey that way than in reverse, and that it’d come in the form of bacteria locked in meteorites like Allan Hills 84001. Almost as a dare, Friedmann suggested that future voyagers might try to terraform Mars by reintroducing pioneer organisms, the cyanobacteria he had discovered. Like the Martian dreams of most earthlings, it seemed beyond all bounds of probability, but Friedmann’s plucky little organisms, life at its most resilient, most resistant, could never be counted out for anything.

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Life as We Don’t Know It

First Week of July 2007

This week a panel of senior scientists convened by the country’s leading science advisory group says the hunt for extraterrestrial life should be greatly expanded to include what they call weird life, organisms that lack DNA or other molecules found in life as we know it. The scientists conclude in their report that their investigation makes it likely that life is possible in forms different from those on Earth.

Experts have hailed this report as an important rethinking on the search for life. NASA’s lead scientist for the Mars Exploration Program, Mike Meyer, says, “It’s going to help us a lot to make sure we’re going exploring with our eyes wide open.” Starfish, sequoia, salamanders, and the rest of the Earth’s residents may seem diverse, but they’re surprisingly similar at the molecular scale. All species that scientists have studied need liquid water to survive, for example, and they all rely on DNA to carry genetic information. And they all use that information to build proteins from the same set of building blocks, twenty different amino acids.

NASA has long looked to life on Earth to guide its search for life on other worlds. Planets and moons that have hints of liquid water have always ranked high on the list of potential sites for life detection missions. In fact NASA’s summary of its strategy is: follow the water. But there’s now good reason to suspect that other kinds of chemistry could support life as well, the authors of this new report argue.

Weird life could differ from life as we know it in big or small ways. For example, while DNA uses phosphorous in its backbone, it might be possible to build a backbone out of arsenic instead, and life might exist in liquids other than water, perhaps ammonia or methane. The report even explores the possibility of life based on silicon, not carbon, although Mike Meyer who was not part of this study thinks that astrobiologists should limit their search to carbon-based life forms. “When we look in the universe,” he said, “the only compounds we see with more than six atoms are all based on carbon chemistry. That’s a strong hint that looking for carbon chemistry may be the best bet. There we have some idea what to look for.” The report calls both NASA and the NSF to fund research into weird life.

“Chemists need to investigate chemical possibilities for what life forms might take,” said one member of the committee, Steve Benner, who’s a Distinguished Fellow at the Foundation for Applied Molecular Evolution in Gainesville. Scientists should also continue to search the Earth for weird life. “There’s so much about Earth life we don’t understand,” says the panel’s chairman, John Baross, who’s a professor of oceanography at the University of Washington. Benner also said, “There’s good evidence that the life we know on Earth was preceded by a weird form of life.” It may have been based on RNA, a single stranded form of DNA. Although DNA based life out-competed earlier forms, RNA life may still exist in particular refuges.

One potential hiding place is deep below the ocean floor. “It’s an incredibly primordial world down there,” said John Baross. If you’re going to look for remnants of an RNA world, those are the environments you want to look in. To find weird life, however, scientists will have to build completely new types of detectors. There’s no question that the surveys of life on the planet we’ve done so far would have missed it.

The scientists also said that the possibility of weird life should prompt NASA to reorder its future missions. They’ve singled out Saturn’s moon Titan as particularly promising. The Huygens probe that visited Titan in 2005 found evidence for liquid methane raining down on its surface as well as a mix of water and ammonia seeping out from the interior. Since then we’ve seen large liquid lakes as big as the Great Lakes made of ethane, methane, and ammonia. These large bodies of liquid could conceivably support life, although not necessarily life as we know it. Nothing, the report concludes, would be more tragic in the American exploration of space than to encounter alien life and fail to recognize it.

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Can Life Survive in Space?

Third Week of June

Can life travel from planet to planet? When a rocky world is hit by a comet or a meteorite, the impact can send pieces of the planetary surface off into space, and some of these ejected rocks may land elsewhere. Here on Earth, we’ve collected a number of meteorites originating from the Moon and Mars, and there are likely to be rocks from Earth sitting on the surfaces of our planetary neighbors. On Earth we know that tiny organisms like bacteria and lichen can live in the crevasses and holes that permeate rocks. These types of life are already adapted to the uncomfortable environment of living inside a rock, and they seem to be resilient when subjected to the harsh conditions of space, surviving radiation and frigid temperatures for short periods of time.

Could life be carried from its rocky home to another world, and once it landed start life on an alien planet? This theory of traveling life is called panspermia. Some scientists have just suggested that life on Earth could be alien-born or have originated on Mars or even further afield, and then have been brought to Earth by a meteorite. Today’s story is experiments of the European Space Agency, where scientists send microbes inside rocks into outer space to see if they could survive the journey.

The first so-called STONE experiments were conducted in 1999 with a goal of confirming that sedimentary rocks could cross the Earth’s atmosphere without being destroyed. On the first STONE flight three different rock samples were fixed into the heat shield of a Photon rocket re-entry capsule: igneous basalt, sedimentary dolomite, and a simulated Martian regolith. The sedimentary dolomite was not totally destroyed by atmospheric re-entry, which indicated it’s possible for similar rocks from Mars to enter the Earth’s atmosphere intact. The dolomite did not acquire a fusion crust. Instead, the surface was exposed to heat and it burned off. This could be one reason why we’ve not yet found a sedimentary Martian meteorite. It lacks that telltale black fusion crust that meteorite hunters are usually looking for. The entry speed of the satellite was seven and a half kilometers per second.

The basalt sample was included in the test because it would develop a fusion crust at the appropriate speed. Unfortunately, that sample was lost, but the simulated Martian regolith provided the proof that the team was looking for. According to one of the team members, “The artificial Martian meteorite was made of small pieces of basalts cemented by carbonated sulfate, and this small bit of basalt had developed a fusion crust.” After launch the rocket orbited the Earth for sixteen days. It then re-entered the Earth’s atmosphere and landed in the Kazakh desert. The dolomite sample dropped out of its casing and landed in the surrounding soil, but it was recovered and the scientists collected the surrounding soil so they could subtract any added contamination. The rocket’s landing was softened by a parachute, which is not a comfort to a meteorite in real life.

Would organisms traveling within a meteorite survive the hard impact of landing in the Earth’s surface? To test this theory people are looking at the stresses bacterial spores receive when they’re ejected from a planetary body. Bacterial spores survive when they are subjected to as much as a million G’s in a centrifuge. Other people looking at impact shocks have put bacterial spores into bullets and then shot them into sand. The spores survive this impact shock, so it seems good evidence that even if there’s no parachute for a meteorite, the shock will not kill the spores. The team confirmed that some microorganisms survive very high impact pressures. Some microorganisms were put between two plates, and a small explosion was used to shock the plates together. The microbes did survive, but scientists also found that photosynthetic organisms with large vegetative cells can’t survive this type of pressure.

While organisms might survive the launch into space and even the impact of the landing, they still might not survive the journey to another world. In the 2004 STONE experiment, all the organisms that were launched into space were killed. There was no evidence for their DNA, and no organisms could be cultured from the recovered rocks. The scientists say this suggests that all of the organisms had completely burned up from the heat of re-entry.

Team member Cockell from Britain’s Open University says, “You might think this is uninteresting because there’s no survival, but in fact it’s very interesting. Because cyanobacteria are photosynthetic, they have to live near the surface of a rock to get enough light energy for their growth. During entry the rock heated up to below the minimum depth at which life would be able to photosynthesize. In other words, because photosynthetic organisms need to be near the surface of a rock to get light, they end up getting extinguished during entry. What this demonstrates is a very specific dispersal filter against photosynthetic microbes being transferred from one planet to another.” Cockell says that organisms might be able to get around this problem by living deeper inside a rock, but still this experiment shows that atmospheric re-entry is a very strong barrier against most photosynthetic organisms, and even bacterial and fungal spores, from being spread between planets.

The story doesn’t end here. Cockell added new microbes to the metamorphic gneiss to see if anything would grow inside. He discovered that organisms grew very quickly. The glassy fusion crust that formed during atmospheric re-entry acted as a tiny greenhouse improving the temperature inside the rock and trapping moistures. He said, “This demonstrates that something biologically damaging such as atmospheric entry improved the habitat for the organisms that survive and later colonized the rock.” Meteorites, while they can be destructive to life when they hit the Earth and may not act as an effective spaceship for life traveling between the worlds, can also create new opportunities for life in the aftermath of an impact.

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Parsing the Microbial World

First Week of April 2007

One of the strong implications of life on Earth is its fantastic bacterial diversity and what that implies for the diversity of microbial life beyond the Earth. The range of organisms on Earth at the level of single-celled organisms is fantastic, and this is just one environment. There are many cosmic environments out there. Two reports released in the last week shed light on the microbial diversity of this planet which we believe is only just beginning to be explored.

One is based on a National Academy of Sciences study, and it’s about a field called metagenomics which is the field where the DNA of entire communities of microbes is studied simultaneously. According to this report this field presents, perhaps since the invention of the microscope, the greatest chance to revolutionize understanding of the microbial world. Microorganisms are essential to the Earth transforming key elements into energy, maintaining the energy and chemical balance in the atmosphere, providing plants and animals with nutrients, and performing other functions necessary for survival. There are billions of benign microbes in the human body for example that help digest food, break down toxins, and fight of disease-causing microbes. Microbes are used commercially for many purposes including antibiotics, getting rid of oil spills, enhancing crop production, and producing biofuels. Microbes are the most likely candidate for life on other planets, in the solar system and beyond, because they are the heartiest organisms on Earth and can survive our planet’s harshest and most unique environments.

Historically, microbiology focused on individual species of organisms that could be grown in the laboratory and examined under a microscope, but it turns out that most of the microbial diversity of the Earth is not studied because the organisms cannot be cultured in the lab. Most of the life supporting activities of the microbes are carried out by complex communities of microorganisms. Metagenomics will transform modern microbiology by giving scientists the tools to study communities of microbes, the vast majority of which are likely to be unknown species, and how they interact to perform such functions as balancing the atmosphere’s composition, fighting disease, supporting plant growth.

Metagenomic studies begin by extracting DNA from all of the microbes in a particular environment sample. There could be thousands or even millions of organisms in one sample. The extracted genetic material consists of millions of random fragments of DNA that can be cloned into a form capable of being maintained in laboratory bacteria. These bacteria are then used to create a library that includes the genomes of all the microbes found in a habitat. Although the genomes are fragmented, new DNA sequencing technology and powerful super- computers are now allowing scientists to make sense of this jigsaw puzzle. They can examine gene sequences with thousands of previously unknown organisms or induce bacteria to express proteins that can then be screened for capabilities that might help us with medicine and health. This is very exciting. The goal of these projects should be to characterize in great detail carefully chosen microbial communities and habitats worldwide according to the report.

These studies will unite scientists from different disciplines in their studies of a particular habitat. The large projects would be virtual centers collecting data from scientists working in many locations and probably will take a decade or more to work out. Craig Venter, one of the founders of the human genome project, has started on this work. In a ship he explores the oceans and trolls for new bacterial strains. Through a recent series of expeditions he found many strains previously unknown on Earth.

The second study comes from a report by the American Society of Microbiology. Until a decade ago scientists characterized microbes almost exclusively by their physical characteristics, how they looked, what they ate, and their byproducts, but with the advent of genomic sequencing techniques our understanding of the relationship between microorganisms has changed. In the light of this new knowledge, what exactly is the definition of a microbial species, and how should microbiologists be categorizing microorganisms? According to the report it’s clear that the current system of designating microbial species is functional but highly inadequate in many ways. It’s unclear whether this system should be replaced or renovated.

In the late 1800s, to make sense of the diversity of microbes, taxonomists developed a system of placing microorganisms into categories in which each organism was granted a genus and a species category. At the time the physical properties were the only means of describing microbes, so the system was based on measurable and observable characteristics. In the late twentieth century molecular biology discovered the genetic relationships between microbes, and some of the secrets of microbes that had yet to be cultured in the lab were revealed. Quoting from the report, “Much of this new knowledge was incorporated into species descriptions, but difficulties in classification persist and novel issues have arisen. Conflicts exist between phenotypic and phylogenic information. The means for classifying non-cultured microbes are limited under the current paradigm, and microbial species do not always demonstrate the phenotypic or genetic cohesiveness expected of them. For these reasons and others it has become clear that the species classification framework is not capable of fully portraying and organizing microbial diversity.”

The shorthand of this report is the genetic sequencing techniques are going to be the way we understand the microbial diversity of Earth, and if we could only get our hands on microbes from space the excitement of wondering about their genetic diversity would keep us busy for years.

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Fire, Ice, and Earth’s Oceans

Second Week of February 2007

This week saw an interesting story about conditions on the early Earth and the way in which the Earth managed to be hospitable for life in its first billion years. Earth is subject to something called the Faint Earth Paradox. It’s been habitable for four billion years, but the early Sun was twenty-five to thirty percent dimmer than it is today. And with the distance the Earth is from the Sun, that should have been enough to freeze it over, and yet life existed in this early part of the Earth’s history.

Geologists and paleontologists are trying to understand how that might have happened. This recent study finds that carbon dioxide, the greenhouse gas that’s now become a bane of life for modern society because of global warming, may have saved the Earth from freezing over early in its history. Scientists have theorized for years that high concentrations of greenhouse gases could have helped the Earth avoid global freezing in its youth, by allowing the atmosphere to retain more heat than it’s lost. But now a team from the Universities of Chicago and Colorado have analyzed ancient rocks from the shores of Hudson Bay in northern Quebec and found the first direct field evidence to support this idea.

The study shows that carbon dioxide in the Earth’s atmosphere could have sustained surface temperatures above freezing before 3.8 billion years ago. Previous studies had shown liquid water existed at the Earth’s surface, even though the weak Sun should have been unable to warm the planet above freezing condition. These ancient rocks from Quebec contain carbon and iron carbonates believed to have precipitated from the ancient oceans. Since iron carbonate could only have formed in an atmosphere containing much more carbon dioxide than found in Earth’s atmosphere today, the researchers concluded that the early Earth’s environment was rich in carbon dioxide. Lead scientist Steve Mojzsis of the University of Colorado said, “We now have direct evidence the Earth’s atmosphere was loaded with carbon dioxide early in its history which kept the planet from freezing and going the way of Mars.” The carbon dioxide could even have acted as a planetary thermostat, since cold, icy conditions on Earth would have decreased normal chemical weathering of rocks and increased the amount of carbon dioxide moving into the atmosphere, ratcheting up Earth’s temperature.

A companion paper shows talks about the technique they used, based on what’s called uranium-lead dating, the decay rate of radioactive elements contained in tiny zircon crystals. The CU Boulder team analyzed the rocks by crushing them into powder and dating zircon crystals present in the rock. This technique allowed them to calculate the geological age of the crystals based on the radioactive decay rate of the uranium and lead isotopes in relation to each other. This technique is accurate to one percent. As Mojzsis says, “Zircon is nature’s best time keeper.” The tests showed that the rocks in Quebec are roughly 3.8 billion years old, about the same age as the other oldest outcropping known in west Greenland.

This important work has given us a reason to understand how the life on Earth could have been hospitable over four billion continuous years of its history. You may also recall that a few years ago a zircon crystal provided the evidence for the oldest rock yet found on Earth, although not evidence for life necessarily. The same team from the University of Colorado, this time working in Western Australia, were able to find zircon crystals 4.4 billion years old. That’s a short hundred and fifty million years from the formation of the Earth itself, so those are the oldest rocks yet known.

A second study this week from the University of Washington gives us a sense of the strangeness of life in the deep-sea ocean. It’s a story about noises of the deep. Right now there are some enormously varied and wide ecosystems that exist on volcanic ridges one or two miles below the surface of the Earth where the Sun never shines. It’s pitch black, but what’s that rumbling? It must be one of those pesky black smokers. Those babies can fry your face off, as superheated water charges out of a volcanic vent. The long-held assumption that black smokers were silent is apparently wrong.

It’s prompting scientists to wonder, could the sound and vibrations of black smokers be the reason that fish living in total darkness avoid being poached by water as hot as seven hundred and fifty degrees Fahrenheit, and might similar signs guide them to the smorgasbord of tubeworms, muscles, shrimp, snail, and other fauna at vents with more temperate waters?

Hydrothermal vents were discovered in the 1970s along volcanically active ridges where seawater seeps into the seafloor, picks up heat and minerals, and vents back into the ocean depths. The hottest and most violent of these vents are called black smokers because when the fluids they emit hit the icy cold seawater, minerals in the fluid precipitate out, and it looks like dark, billowing, smoke underwater. It had been suspected that the vents were silent, but a number of scientists suspected the vents could be generating sounds so new recording devices were used to test this assumption. Funding from the Keck Foundation was used to build a deep-sea digital acoustic recording system and drop it close to a vent in the Juan de Fuca ridge about an hour off the coast of Seattle. The researchers recorded dozens of hours of sound at a vent that scientists had called Sully and another hundred hours at a vent called Puffer. They likened the sound of these vents to the rumbling of an avalanche or forest fire. If you were sitting a foot away it would sound like a very loud conversation. You would unfortunately be dead because the pressure is so high you would implode.

Four mechanisms might be causing the noise. The flow could be pulsating its volume as the waters cool. Dissimilar fluids in the flow could mix and generate noise, or fluids rushing through the nooks and crannies of the smoker vent itself could be creating noise. Buried within the rich sounds that produce the rumbling, the analysis also found some surprising resonant tones which could be caused by a number of things. Flows along the bumps and cavities inside vent structures could cause tones, in the same way jug band members produce sound by blowing across the mouths of their jugs causing the air inside the jug to resonate and produce a deep tone. Both the Sully and Puffer vents produce resonant tones at several different frequencies that we can’t discern with all the other noise, but perhaps some of the creatures that live in these environments can discern them. If fish are actually using the sounds to navigate, distinctive tones may be how fish find their way back to cooler vents where the eating is particularly good.

It’s fascinating work, and it leads to the supposition that life adapted to a deep sea environment that have sensory apparatus quite different from our own. Hydrothermal vents are also the best model we have for what might be found deep under the icepack of Europa, the giant moon of Jupiter, where we hope to go one day and find evidence of extrasolar life within our own solar system.

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