When astrobiologists think about life on Earth or life in the universe, they tend to assume life will persist. It’s lasted for four billion years on the Earth. They also think that intelligence or the advancement of life through evolution is a more or less steady process. But recent studies show that human beings—the pinnacle of intelligent life on Earth—had a brush with total extinction just seventy thousand years ago.

The human population at that time was apparently reduced to small, isolated groups in Africa because of drought. A large new analysis and a separate study by researchers at Stanford shows that a number of early humans may have shrunk as low as two thousand, before the numbers began to expand again in the early Stone Age. Let’s hear from Spencer Wells who works at the National Geographic Society and has the magnificent title “Explorer in Residence,” which makes you wonder why is he in residence when he should be out and about exploring:  “This study illustrates the extraordinary power of genetics to reveal insights into some of the key events in our species’ history. Tiny bands of early humans, forced apart by harsh environmental conditions, coming back from the brink to reunite and populate the world. Truly an epic drama written in our DNA.” Wells is Director of the Genographic Project, which was launched in 2005 to study anthropology using genetics.

The report I’m talking about was published in the American Journal of Human Genetics, and it uses mitochondrial DNA, which is passed down through mothers. DNA is a wonderful tool for tracing life’s history on Earth. Mitochondrial DNA is remarkable, a remnant of a strange evolutionary event: the merger of an ancient bacterium with the cell ancestral to all plant and animal life. It also carries the imprint of more recent evolution. In many species, humans included, it passes only from mother to child. No paternal genes get mixed in to it. That makes it easy to see when particular genetic mutations happen and thus to construct a family human tree. Various branches of that tree are now well studied.

Humans began in Africa, spread to Asia around sixty thousand years ago, then to Australia fifty thousand years ago, Europe thirty-five thousand years ago, and the Americas fifteen thousand years ago. What hasn’t been so well examined, though, are the tree’s African roots. The genetic diversity of Africans probably exceeds that of the rest of the world put together, but the way that diversity evolved is unclear.

This new study has shed light on this issue using the mitochondrial DNA of more than six hundred living Africans to show how genetic diversity developed in Africa, and in doing so, they’ve shed light on how modern man spread around his home continent long before he took his first tentative steps into the bigger, wider world. The team paid particular attention to samples from the Khoi and San people of southern Africa. These people, known colloquially as Bushmen, make their living hunting and gathering. Indeed, their way of life is thought by anthropologists to resemble quite closely that of the pre-agricultural people throughout the world.  Comparing Khoi and San DNA with other Africans shows that the first big split in Homo sapiens happened shortly after the species emerged two hundred thousand years ago. Most people now alive are on one side of the split. Most Bushmen are on the other.

The consortium’s analysis of which DNA “matrilines” are found where suggest that for much of its history the species was divided into two isolated populations, one in Eastern Africa and one in the south of the continent. The two groups were defined by this split. However, few other matrilineal lines from the first hundred thousand years of the species history have survived to the present day. This suggests that the early human population was tiny and reinforces the idea that Homo sapiens may indeed become close to extinction. Indeed, there may have been one point as few as two thousand people left to carry humanity forward. This shrinkage coincides with a period of prolonged drought in Eastern Africa and was probably caused by it. The end of the drought was followed by the appearance of many new matrilines that survive to the present day.

The researchers estimate that by sixty to seventy thousand years ago, the period when the exodus that populated the rest of the world began, as many as forty such groups were flourishing in Africa, though the migration only involved two of those groups. The African matrilines seem to have remained isolated from each other for tens of thousands of years after the exodus. It wasn’t until forty thousand years ago that they began to reestablish conjugal relations, quite possibly as a result of the technological revolution of the late Stone Age, which yielded new, finely crafted tools. Only the Bushmen seem to have missed out on this party. They were left alone until a few hundred years ago, when their homelands were invaded from the north by other Africans and from the south by Europeans—not a particularly happy event for the Bushmen.

So we have this extraordinary story of humanity in early Africa, shrinking at one point through environmental diversity almost to the point of extinction. Look at us now, 6.6 billion people strong. We dominate the world (and also mess it up). Our technology, space travel, computers, and genetic engineering are marvels. But back then we were simple hunter-gatherers, no more successful and far less abundant than the apes of our earlier lineage, reduced to two thousand strong, the size of a village. We were maybe bad winter away from total extinction. The success in this world, and in this universe, of intelligent life is not guaranteed. For all our power and intelligence, there was a time when humanity was hanging by a thread.

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This story for the first week of April 2008 is not a prank. Recent lab results have shed light on an era in the Earth’s history that’s been shrouded in darkness: the time, perhaps four billion years ago, when the motor of life first turned over. There’s essentially no physical evidence that comes down to us unaltered from four billion years ago, so we have to speculate on how life started.

The origin of life is the ultimate chicken and egg problem. On the one hand there’s DNA, the information storing molecule or the genetic code, and on the other hand there are the many proteins that facilitate life’s chemical reactions. The origin of life contains this enigma: How did the complex phenomenon of a working cell get started? Historically the explanation has revolved around DNA because that’s the molecule that serves as the pattern for building proteins. Proteins in turn can form enzymes, which catalyze or facilitate biochemical reactions including the crucial construction of DNA, and thereby is the paradox. Genes require enzymes, but enzymes require genes. Which came first?

Most scientists have focused on DNA, but other life scientists have focused on a concept called “RNA World” which postulates that life began with RNA. RNA, like DNA, is built of chains of molecules called nucleotides. Our understanding of RNA has come a long way since the 1960s when what is called the central dogma of molecular biology held that RNA was just a messenger boy that carried DNA’s information to ribosomes, the cellular factories where proteins get built. In the 1980s biologists realized that not only could RNA transfer information but like proteins it could also process chemicals; it could catalyze reactions. The ability to do both jobs suggested that RNA, and not DNA, could be the primary molecule of life. Much of this work was done by Thomas Cech of the University of Colorado, who won the Nobel Prize in chemistry in 1989 for these insights.

According to the lead scientist of the study under consideration, done by NASA and funded under the Exobiology and Evolutionary Biology program, DNA stores information like a computer hard drive. Niles Lehman, professor of chemistry at Portland State, says, “Beyond that, DNA doesn’t do anything. RNA on the other hand can fold into a 3-D structure that allows it to catalyze a chemical reaction.” Even if RNA can catalyze chemical reactions, in modern cells it gets information from DNA, so how could RNA have been assembled before DNA even existed?
The recent experiments by Lehman and others may have revealed the answer. Individual units or nucleotides of RNA can spontaneously self-assemble. Lehman and his colleagues started their experiments by removing from a bacterium an RNA molecule that works as a self-replicating enzyme. They cut it into chunks, each about fifty nucleotides long, and watched the chunks reassemble themselves into a working enzyme. He said, “We mix the fragments together in salt water at forty-eight degrees, have lunch, come back, and we have self-replicating RNAs in the test tube.” Obviously reassembling an enzyme you’ve stolen from bacteria and then sliced into pieces doesn’t prove that a working enzyme could have formed in the prebiotic world, but there was a method to the apparent madness of Lehman’s experiment. Fifty bases may be a magic number. Lehman quotes chemist James Ferris of Renssalaer Polytechnic Institute who’s been able to string together forty or fifty RNA nucleotides using clay as the catalyst. It’s conceivable that that could have happened in the prebiotic world too.

Summarizing the results these experiments, RNA World begins with three steps: prebiotic synthesis of the individual RNA nucleotides, assembly of intermediate chains, and then final assembly into longer chains. Ferris and Lehman between them have demonstrated steps two and three, but Ferris notes that nobody has yet demonstrated a prebiotic synthesis for individual nucleotide basis from which he constructs the RNA strands. Still, the new results are interesting enough to suggest that RNA can achieve enough complexity to transition from the chemical to the biological realms. The idea that RNA can begin to replicate itself from fragments is very exciting because it identifies the leap in complexity required to kick-start biology.

The astrobiological implications of this work are obvious. The raw materials, the chemical ingredients for life, are known to exist everywhere in the universe, and they will be present on the surface of planets, in many cases with the liquid medium of water available to dissolve them. Once you’ve gone up the first few steps to form fifty base nucleotides, nature and natural processes take over. Life will self-assembly and a replicating molecule will emerge from the chemical mix. If it happened on Earth four billion years ago, it probably could have happened on any similar location. Removing the mystery of the formation of life of Earth will give us a much clearer sense of how often the event can occur elsewhere in the universe.

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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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My topic this week is a story based on a press release from up the I-10 freeway at Arizona State University. They’re our deadly rivals in sports, but in science we all get along. Researchers from ASU and Washington University are reporting in an online edition of the Proceedings of the National Academy of Sciences that they have sequenced the genome of a cyanobacterium called Acaryochloris marina. Through its production of chlorophyll d, this microbe can absorb “red edge” or near-infrared long-wavelength light, light with such a long wavelength that it’s invisible to the naked eye.

Acaryochloris marina has a massive genome of over 8.3 million base pairs, and it’s among the largest of fifty-five known strains of cyanobacteria in the world. It’s the first organism containing chlorophyll d to be sequenced, and the data will help scientists understand how it and its unique genes have evolved over time. For a recap on photosynthesis: in this process, plants convert energy from the Sun into chemical energy in the form of glucose or sugar. The chlorophyll in plants, mostly of the a and b varieties, absorbs more blue and red light from sunlight and less green light. It reflects the green light, and so plants appear green. That’s normal chlorophyll. Chlorophyll d harvests light from a region of the spectrum that few other organisms can, and this enables the organism to carve out its own special evolutionary niche.

There are major implications of this work for agriculture. One could imagine the transfer of this biochemical mechanism to other plants where they can then use a wider range of the light spectrum and thus become plant powerhouses, deriving increased energy by employing a new photosynthetic pigment. There’s also a bioenergy link. Chlorophyll d could be used for crops that are turned into fuels or to generate biomass. It may also have interesting implications for space science, helping develop productive crops for use in space stations or settlements where energy efficiency is very important.

The leader of the study is Robert Blankenship from Washington University. He says that with every gene of Acaryochloris marina now sequenced and annotated the immediate goal is to find the enzyme that causes a chemical change that makes chlorophyll d different not only from the more common a and b forms but also from the nine other forms of chlorophyll. “The synthesis of chlorophyll by an organism is complex, involving seventeen different steps,” said Blankenship. “Somewhere near the end of this process, an enzyme transforms a vinyl group to a formyl group to make chlorophyll d. This transformation of chemical forms is not known in any other chlorophyll molecules.”

The researchers said that harvesting solar power through plants or other organisms that could be genetically altered with the chlorophyll d gene could make them solar power factories that could generate and store solar energy. Imagine a seven-foot tall corn plant genetically engineered with the chlorophyll d gene to be expressed at the base of the stock. While the rest of the plant is synthesizing chlorophyll a, and absorbing short wavelength light, the base is absorbing red edge light at seven hundred nanometers. Energy could be stored at the base without competing with any other part of the plant for photosynthesis. The altered corn using that synthetic chlorophyll d gene would be a super plant because of its extra ability to harness energy from the Sun.

This model actually may be similar to how Acaryochloris marina operates in the South Pacific, specifically Australia’s Great Barrier Reef. Discovered just eleven years ago, the cyanobacterium lives in a symbiotic relationship with a sponge-like marine animal popularly called a sea squirt. Acaryochloris marina lives underneath the sea squirt, which is a marine animal that lives attached to rocks just below the surface of the water. The cyanobacterium absorbs red edge light through the tissues of the nearly transparent sea squirt. “The genome,” says Blankenship, “is fat and happy. Acaryochloris marina lies down there using far red light that no one else can use. The organism has never been under strong selection pressure to maintain a modest genome size. It’s in a sweet spot. Living in this environment allowed it to have such a dynamic genome expansion.”

The general conclusion for this work for astrobiology is important. If energy from the invisible infrared can be harnessed by normal biological mechanisms familiar on Earth, that means life doesn’t need a Sun-like star, one that puts out most of its energy as visible light. Biology could be happy on a planet around a very dim red star, and most stars in the universe are just like that. The real estate that we should consider habitable just got a whole lot larger.

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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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If you want to find life elsewhere in the universe, follow the water according to NASA and many astrobiologists. The Earth is a water world, and in addition to the Earth it’s likely that Mars may liquid water kept under pressure on its surface, and also perhaps half a dozen moons in the outer solar system. As far from the Sun as they are, moons of gas giant planets may have liquid water under a crusty surface.

Water is one of the most abundant molecules in the universe so it’s sensible to follow the water as a strategy for looking for life, but as we were reminded late last year in a report for the National Academies of Science, we should also to loosen the envelope of what we consider life. That report, titled The Limits of Organic Life in Planetary Systems, said that there are so many ways that life might evolve and so many chemical and biochemical bases for life that we should be generous in considering what is a minimum requirement. Following on from that, a paper in Astrobiology Magazine recently says we should follow the energy in looking for life. The opening paragraph of the paper which summarizes the rationale and the approach:

“A key challenge in astrobiology is to comprehend life and its interaction with the environment at a level sufficiently fundamental to embrace alternative biochemistries that may be encountered in a search for life elsewhere. Life on Earth presents us with a single, albeit highly diversified, biochemical model around which to build this comprehension. This model is extremely valuable in providing an empirical starting point for understanding metabolic potential and environmental tolerance and as a continuing reality check on whatever generalized concepts of life may be developed. Reference to this single example, however, also carries the risk of narrowing our sense of possibility of leading us to define biochemistry, habitability, and biosignatures in terms so specific that they may exclude different forms of life.”

Sixty years ago Nobel Prize winner Erwin Schrödinger brought life’s definition down to its fundamental elements. Life consumes and transforms energy, and so energy is perhaps more fundamental to the definition of life than water, which is simply an ingredient. Water is a very useful solvent and clearly essential to life on Earth but maybe not elsewhere.

The study of terrestrial life in terms of its energy usage reveals several common principles. First, the core metabolic processes function across all organisms from human beings to the tiniest microbes. Second, energy usage encompasses two fundamental ideas: power, or how energy is used over time, and something that’s called voltage, which is the amount of energy in a metabolic event. There seem to be minimum values of power and voltage in the way that life uses energy; below these values life is simply not possible on Earth. Finally, there is a direct and obvious link from environment to biology by a small number of biochemical schemes in molecules, and every form of life on Earth uses one of these small number of biochemical schemes.

So while water is important in general, and essential on Earth and maybe other locations, there is energy everywhere including places where there’s no water. If we think of energy as fundamental, life could get it in many ways. It could get it from gravity. It could get it from starlight or geothermal energy deep within a planet. Most importantly, life on Earth and probably elsewhere gains energy by rearranging molecules. There is abundant free chemical energy simply waiting to be tapped in many environments. Some terrestrial microbes get their energy from metals that we would consider toxic, for example, and since molecules will exist elsewhere in the universe in different concentrations and in very different physical forms than the Earth, there’s an abundance of ways life could gain its energy. The most general way to look for life is to follow the energy in the universe, and that may be the bottom line for astrobiology.

To close, here’s a tag on a story from a few weeks ago about the best message to send ET. Perhaps sending the classics is the best idea. No I don’t mean classical music; I mean the Beatles. On Monday, NASA broadcast the Beatles song Across the Universe a little ways across the galaxy to Polaris, the North Star. The first ever beaming of a radio song by the space agency directly into deep space is driven by nostalgia for the most part, not science. It celebrates the fortieth anniversary of the song, the forty-fifth anniversary of NASA’s deep space network, and the fiftieth anniversary of NASA. Paul McCartney told NASA through a Beatles historian, “Send my love to the aliens. All the best, Paul.” The song, written by McCartney and Lennon, may have a ticket to ride and will be flying at the speed of light, but it will still take 431 years to reach its destination because Polaris is 2.5 quadrillion miles away.

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The theme this week is water, which is considered to be one of the fundamental and essential ingredients for life in the universe. In a story based on an Ohio State University news release, scientists for the first time have directly observed how water lubricates the motions of protein molecules to enable their different functions to occur. Scientists are one step closer to understanding how proteins move when they perform essential life functions. This finding was based on using ultra-fast light pulses to reveal how the water molecules link up with proteins and enable them to move around.

The research has practical benefits. Researchers hope to find new treatment for diseases such as Alzheimer’s, Parkinson’s, cataracts, cystic fibrosis, and diabetes. In addition, understanding the role of proteins in living cells can help scientists decipher how the first cells on our planet began to function. The work also sheds light on the role liquid water plays in living organisms. Scientists were able to map the motions of water molecules at different locations on a very much larger protein molecule. The team took laser snapshots of a single myoglobin molecule, which is the protein that carries oxygen inside muscle tissue, while it was immersed in water in the laboratory. They were able to observe how fast the water molecules were moving around the protein and see how those rapid motions related to the characteristics of the protein at that moment, the electrical charge at a particular site for example, or changes in the protein shape.

Proteins can execute motions in as little as a few billionths of a second. Water normally moves a thousand times faster on a scale of a trillionth of a second. In previous work, researchers showed that water molecules slow down substantially as they get close to a protein. This new study shows that water molecules slow even more once they reach the protein. The water forms a very thin layer only three molecules thick around the protein, and this layer is the key to maintaining the protein structure and flexibility and lubricating its movements. These findings challenge the conventional wisdom of theorists trying to envisage what occurs on these tiny scales. They usually use computer simulations to fill the gap, but now the observations are direct.

We move from this story of how water works within the context of life to a more distant location: Europa. Europa is perhaps Jupiter’s most exciting moon, the water moon. Its icy shell is scarred with a crazy quilt pattern of cracks and grooves, and beneath that outer layer of ice hides a global ocean. Astronomers would love to know if there is life swimming in that ocean. The answer partly depends on the flavor of the water. Earth’s oceans are full of minerals that have shed into the water from the erosion of rocks or from volcanic eruptions. Chlorine and sodium are the primary elements in the solution, and they give our ocean its distinctive salty taste. Europa’s ocean too is believed to be salty, but is it just like the Earth’s ocean? Or does it have its own unique recipe based on different ingredients, and how would those different ingredients affect the likelihood of life in the Europan ocean?

Kevin Hand, who’s a planetary scientist with NASA’s JPL says, “The conventional wisdom is that Europa’s ocean is dominated by magnesium sulfate. The reason for that,” he says, “if you take a bunch of chondrite, space rocks, and crunch them all together to form a planet or a moon as we think occurred around the Jovian system, the dominant cation and anion that come out of that leached material is magnesium and sulfate.” He says that while scientists have seen evidence for the sulfate, the anion or the negatively charged ion, in spectroscopic measurements of Europa’s icy surface, they’ve not been able to discern what the dominant positively charged cation is. There’s active debate over whether that cation is really magnesium or if it could instead be sodium as it is on Earth. A third possibility is that it might even be hydrogen. There is a lot of hydrogen in the Jovian system because the planet that it belongs to is ninety percent hydrogen, and hydrogen is available on the surface of Europa. If that’s the case, then Europa’s ocean could be a searing cauldron rather than a placid sea because hydrogen combined with sulfate creates sulfuric acid.

Europa’s ice chemistry is further complicated by its neighboring moon, Io. This volcanic moon is constantly spewing particles out into space, and those particles become trapped in Jupiter’s rapidly rotating magnetosphere. Europa is continually bathed in this charged ionic stew. Another researcher in the team chips in, “Io contributes sodium, sulfur, chlorine, and other ions to Europa’s surface. These charged particles, along with electrons and protons from the hydrogen ions, stimulate chemistry in the surface material and have probably altered its chemical makeup.” Another complication is that Europa’s oceans still could be adding its own salts to the surface ice because scientists have shown that the ice has more salt than can be explained by simple radiolytic processing from Io’s contribution. To determine the ocean’s chemistry from remote spectral data, scientists would need to tease out that native source of salt from the other salts present in the surface.

However, yet another complication is that over long timescales the ocean and the surface may exchange material thanks to the cracking and shifting of the ice shelf. By now you’ve probably got the sense that this is a difficult problem to solve. To summarize, Hand says, “Right now, many people think that the spectra on Europa may be best matched by a one-third mixture of magnesium, sodium, and hydrogen as cations.” It’s going to be awhile before we know exactly what Europa’s ocean water is like. In fact, to really know we’ll have to send a mission there designed to pierce through the ice. Scientists don’t even agree on how thick that ice shell is, but it likely varies a great deal from one place to another. The best Galileo data suggest an average thickness of four kilometers or two and a half miles. Hand says, “That’s comparable to the Antarctic ice sheet, and we’re boring down through that now on our way to Lake Vostok. It may be comparable to what we need to do on Europa.” Around the year 2015, hopefully NASA will launch the Europa explorer mission, which could include a lander that will melt through the ice pack, allowing us to answer these questions directly for the first time.

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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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Two related discoveries in the last few weeks talk about the possibility of Earth-like planets and in particular the fact that Earths can survive the death of their Sun, at least physically. It’s not clear if life or a biosphere would survive such an event. Chemical elements have been observed around a burned out star known as a white dwarf that give evidence that an Earth-like planet or several Earth-like planets once orbited it, indicating that worlds like our own may not be rare in the cosmos since most stars end their lives as white dwarfs.

The astronomers were at UCLA and the University of Kiel in Germany, and they studied a white dwarf called GD362 which is about a hundred and fifty light years away. They figured out that the composition of a huge asteroid must have been ripped apart by gravitational forces as it approached this star and found that the composition was similar to the Earth’s crust. It’s rich in iron and calcium and low in carbon just like a strong rock on the Earth is. The white dwarf is surrounded by dusty rings which were probably made of objects shredded as they ventured too close. It’s like a version of Saturn’s rings.

GD362 was once a star similar to the Sun, but after billions of years it exhausted its nuclear fuel and ballooned into a red giant; part of its death process expelled most of its outer material and then degenerated into a burned out remnant called a white dwarf. The fact that the asteroid that surrounded it and was ripped apart is similar to the makeup of the Earth as well as the Moon indicates that rocky planets like our own may have orbited the star eons ago. “The rocky asteroid that’s inferred by these observations had a diameter of about a hundred and twenty-five miles and may have been smashed by the white dwarf between a hundred thousand and a million years ago,” said the astronomers who did this research. While the white dwarf has a mass close to that of our Sun, it has collapsed now to the point where its diameter is about the size of the Earth.

Well, this evidence is a little indirect, but another discovery just in the last week is a better indication that the Earth might survive the Sun’s demise, which is going to happen in five billion years. Astronomers have found another planet, in this case a gas giant three times as massive as Jupiter. It orbits a hundred and fifty million miles from a faint star in Pegasus known as V391 Pegasi. It’s about forty-five hundred light years away, not very close at all. Before that star blew up as a red giant and lost half its mass, the planet must have been about as far from its star as the Earth is from the Sun, almost ninety million miles according to calculations by an international team of astronomers led by Roberto Silvotti of the Observatorio Astronomico de Capodimonte in Naples. Dr. Silvotti said the results show that the planet at the Earth’s distance can survive a red giant, and he said he hoped the discovery would prompt more searches. To quote him, “With some statistics and new detailed models we will be able to say something even more to the destiny of our Earth, which as we all know has more urgent problems by the way.” This from an email he wrote in the Nature magazine, showing that astronomers do sometimes care about things closer to home.

The star V391 Pegasi is about half as massive as the Sun, and it burns helium into carbon. It will eventually shrug off another shell of gas and settle into eternal death as a white dwarf. Meanwhile, the star’s pulsations cause it to brighten and dim every six minutes. After studying the star for seven years, Dr. Silvotti and his colleagues were able to find subtle modulations in the six-minute cycle, suggesting the star was being tugged to and fro over a three-year period by a massive planet. Essentially the observers were using the star as a clock as if it were a GPS satellite moving around the planet. This is a very clever technique for finding giant planets, but it’s not actually the first time it’s been used. The first time a pulsing star was found to have planets was the pulsar PSR1257+12 back in 1992 actually making those the first planets ever discovered beyond the solar system, but the Pegasus planet had to survive less lethal conditions, although it must have had a bumpy ride over its ten billion years of existence.

Alan Boss of the Carnegie Institute of Washington has said, “Stellar evolution can be a wild ride for a planet that’s trying to survive, especially inner planets like the Earth.” When our own Sun begins to graduate from a hydrogen-burning main sequence star to a red giant, two effects will compete. First, the Sun will blow off mass to conserve angular momentum, and the Earth will retreat to a more distant safer orbit, this not by any intention but happening just by the forces of gravity. At the same time, tidal forces between the Earth and the expanding star will drag the planet inward, or try to, where it could be engulfed. The latter is very difficult to compute. As a result, Earth’s fate is most uncertain because it’s at the borderline between being engulfed and surviving.

“A particularly dangerous time for the Earth,” said Dr. Silvotti, “would be the end of the red giant phase when the Sun’s helium ignites in an explosive flash.” In the case of V391 Pegasi, that explosion sent a large fraction of the mass of the star flying outward. So planets like the Earth could physically survive the death of their stars, but of course conditions in the lead up to that time would be intolerable and very difficult for life. However, as Dr. Silvotti pointed out, we do actually have slightly more proximate worries on the Earth.

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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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