Living in the Universe

Hanging by a Thread

 First Week of May 2008

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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An Astrobiology Cornucopia

Fourth Week of April 2008

Ladies and Gentleman, boys and girls, earthlings and aliens, I just came back from AbSciCon, the astrobiology science conference in Santa Clara, and my head is so full of astrobiology that I think it might explode. Three days, six hundred and fifty papers, two thousand authors total, twenty-eight countries represented. I gave an education talk on my Second Life work, but the breadth of research results made it an incredible meeting. I can barely give you a sense of what was involved, but I’ll select three papers to talk about in particular.

The keynote address at the beginning of the first day was a wonderful overview of the cosmic context of life given by Lord Martin Rees. Yes, if you weren’t aware of it, over in Britain there’s a scientist who’s so famous he not only was knighted and became Sir Martin Rees but he is now in the House of Lords. Even Isaac Newton didn’t go beyond a knighthood. Martin Rees is also the Astronomer Royal, and he made a joke about the fact that his primary duty there involves casting the queen’s horoscope. He’s the president of the Royal Society, and he holds Newton’s Chair of Astronomy hundreds of years later. He also happens to be a really nice guy.

Rees a brilliant and preeminent cosmologist, and he talked about the setting for life in the universe on the largest scales. He reminded the audience that we expect the universe to be fecund and have material that can form life and biology because of the way carbon has been created and flung out from stars through cosmic time. He also—unusually for most scientists—was strongly supportive of SETI, pointing out that it’s an important philosophical experiment to actively look for extraterrestrial intelligence, though he noted that we’re only likely to detect a small fraction of all the possible brains out there. He made several references to science fiction and in one aside said that he preferred first-rate science fiction to second-rate science any day, but mostly he was talking about cosmology.

He homed in on the six numbers that describe the universe on the largest scales and the fact that some of those numbers are poised at values that permit the existence of life. These cosmic coincidences have begged an explanation by cosmologists, and the most popular one involves the fact that we live in a multiverse, a “small” pocket of space-time that could be part of a much larger construct. Most of these universes in the multiverse are sterile because their physical properties would not permit stable atoms or long-lived stars or biology of any kind, but ours of course is not. He also gave a sense of how vast the totality of the universe could be, so vast that it’s kaleidoscopic in proportion and so vast that all the possible probability outcomes may occur somewhere in space and time. It was a head spinning talk, and it really set the scene for all the work that would follow.

The second talk I want to highlight was given by Richard Muller at the University of California, Berkeley. He gave a wonderful overview of a new signal seen in the extinction of marine creatures on Earth in the past half billion years, that shows a strong periodicity. We know there have been mass extinctions in the history of life on Earth, but it’s mostly been thought that they were random, probably caused by cosmic impacts from space or some sort of climate catastrophe. But Muller has used an enormous compendium by the late Jack Sepkoski of fossil marine data to do a new analysis, and he’s found a very strong evidence for a sixty-two million year cycle in the death of species.

His new analysis involves a lot of new data that he was willing to share with anyone in the audience, making available his Excel spreadsheet. It involves tens of thousands of marine species. The sixty-two million year cycle only leaps out when a new age calibration is used. It turns out that the ages for fossil dating over the past half billion years had errors of up to ten or twenty million years, and that was enough to smear out this signal. But with the new age calibration it was obvious in all his graphs. It’s seen separately in trilobites, bivalves, porifera, and brachiopods, less strongly in gastropods, cephlopods, and fish. He also sees weaker evidence for a hundred and forty million year cycle. The existence of two periodicities in the extinction of marine creatures over half a billion years begs for an astronomical explanation because something that’s periodic is probably coupled to orbits or gravity in some way.

The potential explanation of these two cycles was provided by a pair of talks that followed by Mikhail Medvedev and Adrian Melott. The hundred and forty million year cycle, for which the evidence is still fairly weak, is probably caused by the periodic passage of the Sun and the Solar System through the spiral arms of the Milky Way galaxy. The sixty-two million year cycle exactly matches the period of the Sun’s motion up and down in the plane of the Milky Way galaxy.

Imagine the Milky Way and its disk as an old style phonograph record, a 33 record, warped by heat so it is corrugated and the Sun travels up and down and in and out of the plane of the galaxy as it goes round, with a two hundred and fifty million year orbit and a sixty-two million year cycle for the up and down motion. At its maximum excursion from the plane of the Milky Way, the Earth and the Solar System sees an increased flux of cosmic rays, and this increased flux of cosmic rays causes mutation of DNA, climate change, and the combination is a one-two punch that kills species. So we have a very neat explanation for the periodicity of extinctions. It’s caused by our large-scale astrophysical environment, and we might wonder if other life bearing planets in the Milky Way galaxy are subject to similar periodicities.

The last talk I want to mention was by Denise Herzing from the Wild Dolphin Project in Florida. The Wild Dolphin Project is just what you might imagine. This woman has an incredible job. For nearly twenty-five years she’s spent five months of the year out in the Bahamas tracking, playing, and working with Atlantic spotted dolphins. She’s a behaviorist, and they try to be as least intrusive as possible in the dolphin culture. For that span of time they’ve studied two hundred individuals over three generations, and they know many of these individuals by sight and behavior after that length of time.

Remember, these are wild dolphins. This is not a controlled situation, and yet they’ve managed to record sounds to correlate behavior and vocalization and learned an enormous amount about dolphins that wasn’t known before. As Carl Sagan noted some years ago, we’ve managed to train dolphins to speak about two hundred words of English by tapping out symbols on a keyboard but we still speak exactly zero words of dolphin. So who’s smarter? Denise’s presentation made it clear that these incredible creatures display fantastically complex behavior and socializations.

She and her colleagues were able to train the dolphins to use a portable underwater keyboard to tap out symbols and essentially communicate with the humans. The dolphins that participated were mostly the young females. It seems that the young males were off fighting, as in other species, and what she summarized was a rich tapestry of subtle behavior, plus evidence of substantial intelligence and problem-solving abilities and of distinct personalities amongst the dolphins. That’s perhaps a good way to leave the idea of astrobiology from this major recent gathering of astrobiologists—while we look for intelligent, interesting creatures out in space, we should remember that we share a planet with extraordinary creatures that we don’t yet fully understand.

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Your Next Vacation?

 Third Week of April 2008

The way Will Whitehorn tells it, the story began in 2003 in Mojave California on a visit to Scaled Composites, a company with a reputation for designing futuristic aircraft. Whitehorn is one of the top executives in Richard Branson’s Virgin Group, and Virgin Atlantic, Sir Richard’s airline, was sponsoring Global Flyer, a Scaled Composites creation, on a non-stop voyage around the world. On his way out of the factory, Whitehorn saw something unusual and asked what it was. Burt Rutan, head of Scaled Composites, told him it was a spaceship. He was building it for another customer, but he couldn’t say any more.

Rutan’s customer turned out to be Paul Allen, one of the Microsoft founders.  When Spaceship One, as the aircraft was called, reached space for the second time on October 4, 2004, it won the ten million dollar Ansari X Prize. The craft was taken to high altitude by White Knight, a more-or-less conventional aircraft, and then dropped whereupon its engines ignited to shoot it a hundred kilometers above the planet and thus officially into space. It reentered the atmosphere and glided onto a conventional runway.

This was an epochal moment in the history of space because it was the first time space travel began to move from the realm of governments to the realm of private enterprise. But Mr. Allen is a billionaire only interested in proving that spaceship technology would work, not in exploiting it commercially himself, and this left Rutan a problem: he had a very cool spaceship on his hands but no way of making money from it. That’s where Sir Richard Branson came in. Virgin Galactic, the company in the Virgin stable headed by Mr. Whitehorn, decided to license the technology for Spaceship One and White Knight. Virgin Galactic wants to offer sub-orbital flights to paying passengers by the end of the decade.

Virgin Galactic has accumulated a number of commercial rivals in the space tourism market so free enterprise is working. One of them is led by billionaire Jeff Bezos, the founder of Amazon, who is building a competing sub-orbital spaceship at a ranch in Texas. His space company Blue Origin is so secretive that it won’t even answer questions about its logo. But Virgin Galactic has passed an important milestone. At an event held at the American Museum of Natural History in New York in January, the company unveiled the design of its new generation of space vehicles and said the first examples have almost been finished out at Mr. Rutan’s factory. White Knight II, as it’s called, is due to roll out of the hanger soon. Test flights of Spaceship Two will start towards the end of 2009.

How does this space technology work? The combination of a carrier aircraft and a spaceship to get into space is sort of like building a two-stage rocket. Air launch rockets have a long history. Spaceship One and White Knight are essentially vastly improved and cheaper versions of the X-15 rocket plane that set speed and altitude records in the 1960s, and the B-52 Bomber that carried the Rocket Plane under its wings. However, pure rockets such as the ones that lifted the Space Shuttle won out because the space race between America and Russia emphasized speed over cost. Rockets were a cheap and proven technology, having already been developed as intercontinental ballistic missiles.

Rockets were a dead-end for the space program because they consume a huge amount of power as they claw their way up through the Earth’s thick atmosphere, and they spend most of that power lifting the fuel itself. By contrast, a rocket lifted by an airplane with wings before being launched can be made much smaller and lighter. The plane itself is light because engines breathe air. It thus needs to carry less fuel than a rocket and no chemical oxidant to burn that fuel as a rocket would. That also makes it safer, since chemical rockets are essentially giant firecrackers.  Each craft, the plane and the rocket, can therefore be optimized to do its own job. It’s also easier than designing a single vehicle with a lot of compromises to be able to do both jobs.

Virgin Galactic’s second generation of craft are based on Spaceship One and White Knight, but there are plenty of differences. White Knight II has been redesigned wholesale to lift a much larger spaceship with eight people on board instead of three. It has a wingspan similar to a Boeing 757. It’s three times larger than its predecessor and is the largest aircraft ever made from purely composite materials like carbon fiber. It has engines by Pratt & Whitney—tested and mature technologies, and with its twin boom and long wing it looks more like Global Flyer than its predecessor.

The new spaceship has been engineered to give the thrill of passengers having zero gravity swoops on the way down after they’ve watched the spaceship be released for its trip into space. There will be two pilots up front and six passengers who will have enough room to bounce around in the zero gravity. The spaceship is fueled by a hybrid rocket; called that because it contains both liquid and solid propellants. These rockets are cheaper to develop and operate, and the fuel is safer to store than purely liquid fuel ones. Spaceship One used as materials rubber and laughing gas, or nitrous oxide. Scaled Composites is studying alternatives to rubber that may improve performance. All of this pioneering technology leaves NASA and its European equivalent, ESA, in the dust.

Work is now beginning on another factory to start turning out these spacecraft in significant numbers. Virgin Galactic has ordered five spacecraft and two carrier aircraft. The spaceships will take longer to refuel for their next flight than the carrier aircraft do so thinking just as an airline would the firm has concluded it needs more spaceships than carriers. Each spaceship would eventually be capable of making two trips into space every day and the launch aircraft three or four flights. Rutan says they could operate from a number of airports and spaceports around the world. Virgin Galactic believes the fleet it has ordered should be large enough to furnish its space tourism business in the early years. Trips are expected to cost some two hundred thousand dollars each to start with, and hundreds of people have put down a total of thirty million dollars in deposits. Space travel is becoming real. As the price comes down, could this be your next vacation?

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Living in the Outer Solar System

 Second Week of April 2008

What would it be like to live in the outer solar system? It turns out to be not too bad and so life out there might not be as unlikely as we once thought. Past the orbits of Jupiter and Saturn, the Sun is a feeble dot in the sky. Temperatures are extremely cold, and yet under the surface of Titan, Saturn’s large moon, a vast ocean of water and ammonia may be lurking.

Astronomers have not directly observed this ocean, but recent observations with NASA’s Cassini spacecraft of Titan’s rotation and shifts in the location of surface features suggest a liquid ocean perhaps sixty miles under the surface. Titan is Saturn’s largest moon and the second biggest in the solar system, only slightly smaller than Jupiter’s moon Ganymede. It’s larger than Mercury and the recently demoted dwarf planet Pluto. Cassini has been looking at Saturn and its moons for several years and it has collected measurements using radar that penetrate Titan’s thick atmosphere, doing nineteen passes over the moon between 2005 and 2007.

Data from these early observations allowed researchers to locate fifty landmarks, including lakes, canyons and mountains on Titan’s surface. They looked at later radar data and found that prominent surface features had shifted by up to nineteen miles. That’s a lot. The spin of Titan’s crust is linked to winds that blow through its atmosphere, but this large a displacement of surface features would be hard to explain unless the crust were separated from its core by an internal ocean allowing the crust to essentially float. According to Ralph Lorenz of the Johns Hopkins University, who led the study, “It’s because Titan’s crust seemed so mobile that we infer this internal ocean.” He says the ocean is probably water, with a few percent ammonia, while the atmosphere is made up of nitrogen with other hydrocarbons that give Titan its orange color. Titan’s atmosphere consists of compounds that may have existed in the Earth’s primordial atmosphere, but Titan has more of the chemicals ethane and methane.

Titan is perhaps the most Earth-like landscape in the solar system and it probably has the most Earth-like weather. It’s much colder than the Earth, but the same processes that go on in our weather, particularly the formation of clouds and rain, happen on Titan, but in this case with liquid methane and not with water. Titan is thought to have hundreds of times more liquid hydrocarbons than all the known oil and gas reserves on the Earth. On Titan, these hydrocarbons rain from the sky and collect in vast deposits that form lakes and dunes.

Now the evidence of an underground ocean raises anew the possibility that life might exist deep under Titan’s surface. Similar underground oceans have been found on Europa, Calisto, Ganymede, and tiny Enceladus. Saturn’s tiny moon Enceladus is the subject of a second recent story. It has all the ingredients needed for life erupting in geysers beneath its surface and spewing into the atmosphere.  Instruments on the Cassini mission a few weeks ago revealed a concentration of water vapor, carbon dioxide, carbon monoxide, and organic material twenty times denser than expected, and the temperatures were higher than previously measured. Dennis Matson, the project scientist for Cassini, said, “Enceladus has got warmth, water, and organic chemicals, some of the essential building blocks needed for life.  We have quite a recipe for life on our hands.”

Saturn’s moons have long been of interest to scientists, particularly Titan with its enormous and significant atmosphere, but Enceladus’ chemical components are surprising because previously they’d only been found in comets. Cassini also measured surprisingly warm temperatures near the north pole. It doesn’t seem warm to us, but minus ninety-three degrees Celsius or minus a hundred and thirty-five Fahrenheit is tens of degrees warmer than scientists had expected. But it’s the liquid water that’s surprising, and those high temperatures near the surface make it likely that there’s liquid water not far below the surface.

There you have it. In the frigid depths of the outer Solar System, ranging from a large moon Titan to a tiny moon Enceladus, we have liquid water. We also have organic material, and we have energy: all the ingredients necessary for microbial life. Now, we just need a few billion dollars in NASA’s budget to send spacecraft out there with instruments that can make the careful measurements needed to be sure, and that’s at least a decade or more away. Astrobiology is not a subject for those in need of instant gratification.

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RNA World

 First Week of April 2008

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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Methane on a Distant World

Fourth Week of March 2008

Last week saw the exciting detection of the molecule methane for the first time in the atmosphere of a planet outside the solar system. The finding comes from the extrasolar system called HD 189733. It’s a system that’s been in the news before because the star has a gaseous hot Jupiter locked in a tight orbit around it.  They are both 63 light years away. According to the team, who are from NASA’s Jet Propulsion Lab and the University College of London, the observations decisively show that methane is present, in addition to water. The same team reported last year that they’d identified water vapor in the atmosphere of this planet using a similar technique.

This story conjures up thoughts of cow farts on Alpha Centauri, but although we earthlings associate methane with gassy cows and ruminants, it is a common and perfectly non-biological constituent of other atmospheres in the solar system, including Mars and Titan, as well as the gas giants Jupiter, Saturn, Uranus, and Neptune. There’s been a debate in the past few years over the presence of methane in the thin Martian atmosphere and whether that methane could point to microbial life under the surface. But the methane on Mars is at such a low concentration—a few parts per billion—that it doesn’t decisively indicate biological metabolism at work. It could easily come from geological processes. Researchers believe that methane and water will be common constituents of planetary atmospheres outside the solar system; nonetheless, it’s an important ingredient.

Methane as a tracer is part of a larger debate over biomarkers. Which atmospheric tracers are most likely to indicate biology? Measuring the relative abundance of elements in an atmosphere allows researchers to infer details about how the planet has formed and its weather patterns. The planet and star HD 189733 present an exciting opportunity because it’s one of the few extrasolar planets suited to such measurements.  It’s a transiting exoplanet, which means it crosses in front of its parent star, and because it’s on such a tight orbit it does so every 2.2 days. And because it’s a big planet, Jupiter-sized, it blocks two percent of the parent star’s light each time it does so.

The eclipse technique relies on the fact that the planetary atmosphere is backlit by the star. Every molecule absorbs light most strongly at particular wavelengths so by measuring the amount of light blocked at different wavelengths in the planetary atmosphere, researchers can infer its composition.  There’s extra absorption at the particular wavelengths corresponding to methane when the planet is in transit.  Researchers reported their results in the journal Nature. They saw the telltale patterns of both methane and water. The instrument used was NICMOS, the Near Infrared Camera and Multi-Object Spectrometer on the Hubble Space Telescope, which was the same instrument they’d used to detect water the years before.

We might wonder if this technique can find interesting gases in planets more like Earth, but the technique is difficult. Jupiter, remember, is ten times larger than the Earth so if an Earth-like planet passes in front of its star it blocks ten squared, or a hundred times, less light.  In other words the technique would have to be a hundred times more sensitive to find methane in an Earth-like planet, assuming we can find Earth-like planets.

In an accompanying commentary by planetary scientist Adam Showman, who works across the street at the Lunar and Planetary Lab, the implication is that a third constituent carbon monoxide is waiting to be found in the atmosphere of this planet. Planets are presumed to form from the same material as stars but Showman notes that the intensity of the methane absorption implies that the planet has a low methane-to-hydrogen ratio, no more than five parts per hundred thousand, which is only ten percent of its parent star. The scorching temperature of this planet, around a thousand Kelvin or thirteen hundred degrees Fahrenheit, may cause the carbon in its atmosphere to prefer joining oxygen as carbon monoxide instead of forming methane. “Finding the carbon monoxide and mapping its distribution with that of methane will illuminate the planet’s exotic weather patterns,” according to Showman. He says, “These are exciting times for studies of extrasolar planets.  Researchers are finally moving beyond simply discovering them to truly characterizing them as worlds.”

This is slow and painstaking research, but over the next decade we can anticipate that dozens of extrasolar planets will have spectral diagnostics and we’ll begin to truly understand the nature of their atmospheres. And that is an important step along the road to using biomarkers to detect microbial life on those planets.

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The Passing of a Space Giant

 Third Week of March 2008

This week saw the passing of a visionary of space and a giant of science fiction.  Arthur C. Clarke died at the age of ninety. The author of almost a hundred books, he was an ardent promoter of humans’ destiny beyond the confines of Earth, most famously in the book and following movie 2001: A Space Odyssey. His work was also foretelling of the future. His forecast of telecommunications satellites in 1945 came more than a decade before the first orbital rocket flight.

Clarke set his sights high. He did a lot of his best writing during the cold war, and he suggested that exploring space could serve as the moral equivalent of war, giving humans an outlet to their energies that might otherwise lead to nuclear holocaust. He influenced a huge number of American scientists and inspired a number of people to become astronauts. Carl Sagan was influenced by him, and producer Gene Roddenberry said that Clarke’s writings gave him the courage to pursue Star Trek in the face of ridicule from TV executives.

His ideas were often ahead of his time. The article he wrote on telecommunications satellites was almost rejected by the magazine Wireless World as too farfetched and ridiculous. Decades later he wrote a wry article called “A Short Pre-History of Comsats, Or: How I lost a Billion Dollars in My Spare Time” in which he claimed that a lawyer had dissuaded him from applying for a patent for the idea because the lawyer said the idea of relaying signals from space was too outrageous to be taken seriously.

Arthur Charles Clarke was born in 1917 in southern England. His father was a farmer and his mother a post office telegrapher. He had four siblings and was educated in the regular schools of his town. His childhood imagination was awakened by rambling along the Somerset shoreline, by pictures of dinosaurs he found in cigarette packets, and by the gift of a Meccano set, which is the British equivalent of Erector. He also spent time, like young Galileo before him, mapping the Moon with a telescope he constructed himself from a cardboard tube and a couple of lenses.

The year his father died, when he was just thirteen, he found his first copy of Astounding Stories of Super Science, then the leading American science fiction magazine, and so his path was set. While still a schoolboy he joined the British Interplanetary Society, a small band of enthusiasts who held the view that space travel was not only possible but could and should be achieved in the not too distant future. He wrote his first story, Against the Fall of Night, when he was twenty, but it wasn’t published until sixteen years later.

He’s most famous of course for the movie and book 2001. Its genesis was a short story called The Sentinel published in a science fiction magazine in 1951. It tells the story of an alien artifact found on the moon, a small crystalline pyramid, that explorers from Earth destroy while trying to open it. One explorer realizes that the artifact is a kind of failsafe beacon, and by silencing it, humans have signaled their existence to their far-off creators. The power of “2001: The Movie” came from the brilliance of Stanley Kubrick who was fresh from his triumph in Dr. Strangelove.  When these two met they formed an immediate bond and a great team. Arthur C. Clarke wrote the novel. Stanley Kubrick produced and directed the film, and they are jointly credited with the screenplay. Even though it has the usual elements of hard science fiction, many reviewers and audience members were puzzled by the final scenes which seem almost ethereal, when the alien returns to orbit as a star child. The most memorable character in the movie is not a person, but HAL, the mutinous computer, a kind of smug machine that believed too strongly in its own infallibility.

Clarke’s reputation as a prophet of the space age rests on more than a few accurate predictions. Many people were influenced by him. Listen to Charles Kohlhase who planned NASA’s Cassini mission. He said of Mr. Clarke, “When you dream what is possible and add a knowledge of physics, you make it happen.” Another scientist Torrence Johnson said Clarke’s work was a major influence on many people in the field. He recalled a meeting of planetary scientists and rocket engineers where talk turned to the author. “All of us around the table said we read Arthur C. Clarke,” he said. “That was the thing that got us there.”

Clarke was a British citizen who lived most of his life in Sri Lanka. He was knighted by Queen Elizabeth II in 1998. Along with Jules Verne and H.G. Wells, Clarke said his greatest influence as a writer was Olaf Stapledon, the quirky British philosopher who wrote speculative narratives of extraordinary imagination. Clarke was also influenced by Herman Melville’s Moby Dick. A statement from Clarke’s office says he had recently reviewed the final manuscript of his last novel called The Last Theorem, co-written with Frederik Pohl, which will be published later this year as his memorial. Some of his best-known books are Childhood’s End from 1953, The City and the Stars from 1956, The Nine Billion Names of God in 1967, Rendezvous with Rama in 1973, and The Songs of Distant Earth in 1986.

Clarke also wrote non-fiction books about nature and diving. He got interested in diving in the early 1950s when he realized that he could find underwater something close to the weightlessness of outer space, and he settled in Sri Lanka in the 1950s.  He suffered polio early in his life, and later in his life it returned and debilitated him, limiting him to a wheelchair. But of course his mind was never bounded by anything. He liberated himself and millions of people who, like him, would never leave the Earth, allowing them to vault into space on their imaginations.

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Building life, Brick by Brick

Second Week March 2008

I want to catch up with a couple of stories that are a couple of months old; they got lost in the crush of the holidays. The stories are from the frontiers of artificial life. You might have heard of a man called Craig Venter. He got exasperated with the slow pace of the federally funded effort to sequence the human genome, so he founded his own institute and private company to do it, using his own DNA, and he forced the government pace. In the end the race was declared an honorable but the competition greatly accelerated the process of genetic engineering.

Back in 1995, Venter led an effort to make the first genetic sequence of a living organism, and since then he’s been trying to make the first world’s artificial organism from scratch. In the journal Science he reports the replication of the genome of Mycoplasma genitalium, the species that was the subject of their original sequencing effort. It’s not actually life, but it’s getting very close. Venter is an interesting man. He has a fancy yacht called The Sorcerer II, and he goes on trips each year across the oceans, not just to enjoy himself, but also to sample the microbial diversity of the oceans and use it to fuel his research.

Sequencing an organism is one thing. Building it from scratch is entirely different. It’s a formidable task. Perhaps most noteworthy about what he’s done is that the starting point was not the raw nucleotides, or the chemical layers that DNA is made of, but a set of preassembled cassettes of DNA that the team had ordered from commercial suppliers. This means that almost anyone with a reasonably well-equipped genetics lab could do what they did. Mycoplasma genitalium’s genome is a single circular chromosome that’s 580,076 base pair letters long and contains 485 protein-coating genes. The team divided it on paper into a hundred and one units. Those are the cassettes, each containing four or five genes.

They also took the precaution of editing one gene in particular so that it would not work. The gene in question is crucial to the organism’s ability to stick to mammal cells and thus become infectious. Disrupting it forestalled the risk of anything too nasty happening. You can think of this as the kill gene. All that remains to create what most researchers in the field would be willing to recognize as an artificial organism is to insert such a chromosome into a bacterial cell that has had its own chromosome removed. At the moment no one is clever enough to make all the cellular machinery that translates genes into the stuff of life, so they use this shortcut. But if the newly constituted cell were able to grow and reproduce, the nature of its progeny would be dictated by the implanted chromosome, and they would have made artificial life.

Craig Venter wants to understand how life works. One way to do this is to discover what he calls the minimal genome. This is a platonic idea of life that would contain only the genes necessary for survival and reproduction, and it would shed light on the nature of what’s called LUCA, the last universal common ancestor of life on Earth. In practice that ideal is very difficult to reach since many genes cover for each other. Venter knows that about one hundred of Mycoplasma genitalium’s five hundred genes could be eliminated individually without killing it. But eliminate all of them and it dies. Assembling “mix and match” genomes with a lot of different combinations of cassettes that each contain a handful of genes might be the way to figure out what’s going on.

Venter also has practical goals. He hopes to use modified bacteria to make fuels. Natural bugs can turn out both hydrogen and methane. There’s talk of modifying them to produce high value liquid fuel for jets for example, and there are other companies seeking to do the same thing. Either way the field of artificial life is going to be fueled by commercial objectives and not just simple curiosity.

The second part of this story is an event that took place at Berkeley at the end of last year. Fifty-six teams from twenty countries convened in an event called the Genetically Engineered Machine competition, popularly known as iGEM. The underlying goal of the competition is to figure out whether biological organisms and devices can be built from a collection of standard “off the shelf” parts just as someone might build a plane or a car from a kit. The people taking part were students, undergraduates. For them it’s an amazing opportunity to construct whatever they can imagine: living organisms that crank out biofuel, detect and remove pollutants, or even gauge the purity of olive oil.

These students are helping to build a new field called synthetic biology. To solve the problems of synthetic biology, iGEM has an annual competition, and they hope to develop a library of DNA snippets, each with a specific function, that have been engineered to snap together with other library parts like genetic legos. These are called biobricks, and they’re created according to strict guidelines so that each one is compatible with the others in the collection, which officially is the Register of Standard Biological Parts. The registry contains about 2000 different biobricks. With the biobricks, the competition’s founders want to eliminate much of the drudgery and unpredictability of genetic engineering and give students the freedom to do invent new biological functions.

Here’s an example. Austin Day, who’s a senior at UC Berkeley, holds up an IV bag filled up with a brown-red liquid resembling Bloody Mary mix. The unsavory concoction is Berkeley’s entry into the genetic engineering competition, a blood substitute called bactoblood made from modified bacteria. Spurred by a worldwide shortage of human blood for transfusions, the Berkeley team developed a synthetic version by tinkering with the DNA of the common bacterium E. coli. The young biologist and his team added a collection of genes to produce hemoglobin, the molecule in red blood cells that carries oxygen around our bodies. Then they inserted more genes to create BactoBlood suitable for freeze-drying. For safety, like Craig Venter, they installed a genetic kill switch to destroy the E. coli DNA, leaving essentially just a bag of hemoglobin. It’s a disease-free, self-replicating, and universally compatible substance. Not too bad for ten weeks of work by a group of undergraduates.

This is the future of biology, and Craig Venter says this: “The way biology is normally taught, it comes across as pretty dismal. You memorize a lot of facts, and then you regurgitate them to people.” He thinks that the approach of biobricks and involving undergraduates is the best way forward. The grand prize winner at the Berkeley competition was a first-time team from Beijing University. Yifan Yang, a fourth year biology major, built a bacterial assembly line in which a task is divided amongst genetically identical cells that have specialized but are able to cooperate. This division of labor mimics the human body, where genetically identical cells differentiate into heart, liver, and muscle cells for example. This is the divide-and-conquer strategy used by all multicellular organisms. Representing his team, Yang proudly hoisted iGEM’s trophy over his head: a gigantic silver Lego brick.

The greatest legacy of all from the students in this competition will be the new biobricks they build. The newly formed Biobricks Foundation is drafting a public license that will ensure that the DNA bricks are freely available to all researchers and that they remain open source. Eventually the library of biobricks will reach a critical mass that will enable people to build sophisticated organisms that can carry out useful functions. This is a very exciting prospect; it’s the maturation of the new field of synthetic biology. The biology that results might not look anything like terrestrial biology, and it could have capabilities undreamt of presently. Perhaps some of those capabilities already exist somewhere in the universe.

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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 at the Red Edge

Last Week of February 2008

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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