Living in the Universe

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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