Living in the Universe

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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Is Mathematics Universal?

Third Week of December and Last Blog Entry of 2007

This week I want to ask a very big question and catch up with a story from a few weeks ago. In earlier posts I’ve asked and answered the question of whether or not carbon is universal in the context of life. The answer is an emphatic yes. Carbon is everywhere, produced by stars, and spat out into interstellar space where it can be incorporated into planets and people or other life forms. The same question applies to water. Is water universal? It’s clearly an important part of our form of life. The answer once again is yes. Water is one of the most abundant molecules anywhere in the universe and will be found most places we can look. We expect there to be watery planets scattered throughout our galaxy and beyond.

Astrobiology of course is based on framing the question, is life universal? Again, we don’t know the answer yet, but astronomers are optimistic that many biological experiments will have taken place. We really have no idea whether technology and intelligence are universal, but with a smaller probability they’re likely to be found out in space as well.

Physicists and mathematicians are prone to ask another question. Is mathematics universal? Over the past few hundred years we have discovered laws of nature that are exquisitely described by elegant and sometimes very difficult mathematics. We naturally wonder: is this a universal phenomenon? Should we expect intelligent entities elsewhere in the universe to have stumbled upon the same mathematical rigor and beauty that we have? It’s a pretty profound question for science.

A recent op-ed piece in the New York Times by my colleague Paul Davies up the road at the Arizona State University caused a real storm. Paul Davies is a prolific cosmologist who’s written almost thirty books. He asserted in his op-ed piece that science, not unlike religion, rested on faith, not in God but in the idea of an orderly universe. “Without that presumption,” he said, “a scientist couldn’t function.” His argument of provoked a lot of mostly adverse reactions from other scientists, who objected to the claim that science depends on faith at all. Scientists generally reject that idea and consider science to be a logical, rigorous process that’s immune from any belief system.

But Davies did make an important point, which is the fact that the universe and its orderliness has been a predicate or a premise of science for two thousand years of observation and theorizing. That’s interesting, and it leads to a chicken-and-egg problem about the universe and the laws that describe it. Which came first: the laws or the universe? If the laws of physics are to have real explanatory power, they have to be good anywhere and everywhere including the big bang and every other galaxy in the universe. If the mathematics that describes them is potent then it will also prescribe everything in the universe.

Many thinkers going back to the Ancient Greeks have suspected that mathematics is at the heart of rational logic. Pythagoras famously said that the universe is based on number, that is was number. That must have been a very strange concept to an Ancient Greek for whom a rock was a rock and a tree was a tree and a fish was a fish. What on Earth did Pythagoras mean by saying that number was everything? But this rational idea of logic was built into science from the start. In addition to Pythagoras and his followers, Plato envisaged a higher realm of ideal geometric forms—perfect circles, chairs, perfect galaxies—in which the phenomena of the sensible world, the world we experience, were just flawed reflections of perfect mathematical forms. This transcendental idea of the essence of nature has been popular with scientists ever since.

Modern physicists are particularly attracted to this idea. Perhaps the most extreme example is Max Tegmark, who’s a cosmologist at MIT. In talks and recent papers he speculated that not only that mathematics describes the universe, but also that it is the universe. He maintains that we’re part of a mathematical structure, albeit one much more complicated than a circle, a multiplication table, or the symmetries of modern particle physics. Other mathematical structures, he predicts, exist as their own universes in some cosmic Pythagorean democracy, although not all of them will prove as rich as ours. In the New Scientist he said “Everything in our world is purely mathematical.”

That would explain why math works so well in describing the cosmos and also would answer a question posed by Stephen Hawking, noted English cosmologist, in his famous book A Brief History of Time. Hawking had asked “What is it that breathes fire into the equations and makes a universe for them to describe?” It’s mathematics that’s on fire, according to this idea, which has a long history. In the seventeenth century, Galileo said that the universe is a grand book written in the language of mathematics, and the famous physicist Eugene Wigner in the 1960’s said that the unreasonable effectiveness of mathematics demands an explanation.

If we know anything from modern physical theory it’s that mathematics underlies the heart of our explanations for the physical world, and if that realization means anything, then we must imagine that it applies elsewhere in the universe, and that mathematics will be universal, and that other intelligent creatures, should they exist, will have discovered and relished and used mathematics in similar ways to us. That’s an intriguing thought to bind everyone in this universe together as we close Living in the Universe for the year 2007. Join me again next year to explore what’s new in astrobiology.

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The Earliest Life in the Universe

Second Week of December 2007

A research report this week suggests that the first heavy elements in the universe could have been created half a billion years earlier than previously thought. New astrophysical simulations of conditions in the early universe suggest the earliest galaxies could have created heavy elements by the formation and then destruction of very massive stars, perhaps a hundred times more massive than the Sun. This moves forward in the timeline of the Universe by half a billion years the time at which carbon, nitrogen, oxygen, and other life giving elements could have been created.

This may seem to be of esoteric interest, but it shed light on an important issue in astrobiology, which is how long ago could life have possibly formed. The universe is known to be 13.7 billion years old. This recent research pushes back the time at which the first planets and carbon-based life forms could have been created to within a couple of hundred million years after the big bang. Let’s think about that for a minute. That means that the first planets and life could have formed thirteen billion years ago. Remember, the Earth is four and a half billion years old. That means that life elsewhere could have had a head start of eight or nine billion years on life on Earth.

Imagine an Earth clone that’s existing in space thirteen billion years ago, forming its microbial life, and that life becomes more advanced, eventually develops large animals, perhaps brains and technology as happened on the Earth. Where would that life have got to in those extra billions of years? It’s an extraordinary thought. Perhaps the best way to bring it into focus is to consider what I call futurology, the difficulty of predicting the future by mapping it backwards into the past. Think of our current situation: fifty years into the space race, thirty or twenty years into the age of computers, barely a decade into the age of the Internet. If we imagine our world just over ten years ago, there was no Internet. A hundred years ago, no mass transportation. A thousand years ago, no medicine. Ten thousand years ago, no civilizations or cities; Humans were hunter-gatherers. A hundred thousand years ago, no agriculture. We were very primitive at that point. And a million years ago we were barely becoming human.

If we project this timeline forward into the future, it’s very difficult to predict past the first two orders of magnitude of powers of ten. Ten years from now, we might safely predict technology, but a hundred years or a thousand or ten thousand? Not a chance. Our predictions almost always go badly wrong. Yet we are now faced with imagining what a civilization like ours might amount to, given billions of years of extra evolution because we’re saying that carbon-based life could have existed for billions of years before the Earth even formed. This possibility and this type of extrapolation is almost impossible for us to bend our minds around. However in astrobiology, where biological experiments could have been spawned billions of years before the Earth was even formed, we must consider the potential and the capabilities of extremely advanced life forms. They’d be as advanced to us as we are to bacteria on our planet. That provocation, spurred by this recent research, is the food for thought this week.

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Teleportation

Second Week of November 2007

Space travel is so easy in science fiction and in TV and movies; but the reality is less inspiring. Our best rocket technology is only capable of accelerating a payload to a small fraction of the speed of light. At such a speed, the distance to even close stars would take more than a human lifetime to travel, and any significant voyage would require us to go into hibernation. Multigenerational space arks are required for the voyage. How much better if we could do it the way they do on TV? What episode of Star Trek would be complete without Captain Kirk and his colleagues beaming off the enterprise onto the surface of some distant planet?

Well, teleportation, long a staple of science fiction, is finally being talked about as a serious scientific possibility. More than just talked about. Over the past couple of years, physicists working independently in Australia, Austria, and Denmark have all achieved a rudimentary form of teleportation, albeit at the quantum level of atoms and photons rather than the macroscopic level of objects and actual people. Chuck Bennett at the IBM Research Center says, “Exact teleportation was thought to be impossible. However, it is now shown to be possible.”

The term teleportation was first coined by the writer and paranormal investigator Charles Fort in his 1931 book Lo!, It’s defined by the Oxford English Dictionary as the instantaneous transportation of persons or objects across space by advanced technological means. The idea of transporting an object or person in the blink of an eye has been in science fiction of course for ages, and it even crops up in Islamic mystical tradition in the concept of Tay-al-Ard, or the folding up of the Earth. In this concept a person is, without actually moving, miraculously transported to a far off destination by the world spinning very rapidly beneath their feet.

Sadly for the science fiction enthusiasts, the work being carried out is not quite producing the type of teleportation that we love from science fiction. Instead, physicists have been focusing on what is known as quantum teleportation. The whole idea is surrounded by a mystique and a mathematical complexity that makes it difficult to understand, but basically it’s the idea that the information of atoms can be teleported but not the atoms themselves. Chuck Bennett says, “In effect you’re disembodying the complete quantum state of an atom and reincarnating it in another atom of the same sort at a distant location.” Teleportation like this is not as we tend think of it, an object appearing in one place having disappeared in another. Rather it is the transfer of information and, in particular, the quantum property of spin from one location to another at the speed of light.

One way of imagining this is to think of a snooker table with balls on it. In the traditional view of teleportation, a spinning ball would dematerialize at one end of the table, and exactly the same ball will rematerialize at the other end. In quantum teleportation the spinning ball stays where it is, but its spin is transferred to another ball elsewhere on the table, creating what the Germans call a doppelganger. It is this aspect or property of the original ball that’s transmitted rather than the ball itself. Although, to complicate matters, the process of transmission would destroy the original ball.

How is this quantum teleportation actually achieved? It involves two separate particles acting as if they were one and the same even though they are separated by a great distance. Changes to one particle are mirrored in the other. This isn’t quite as dramatic, involving as it does, subatomic particles, as the teleportation of an actual person, but it’s a proof of concept that shows that the laws of physics do not prohibit information, and in principle extremely complex information, from being transmitted instantaneously over large distances. Another professor involved in this work, Neil Johnson at the University of Miami’s Physics Department, says, “Although we are still way off from building a quantum computer, which is the main application of this technology, the possibilities are extraordinary. In theory it could contain an infinite amount of information and move that information around at almost the speed of light.”

Chuck Bennett believes in principle at least that it’s feasible to teleport humans without violating any of the laws of physics. However, it could only be done to a certain degree, not literally. “Teleporting a person,” he said, “would not require reproducing the quantum state of everything exactly. Everything we know about biology and how molecules fit together to produce a living being, including the brain, indicates that creating some level of approximation would give you a real person who is a serviceable replica of the original in terms of looking the same and thinking the same thoughts without necessarily being a perfect quantum replica. The teleported person would end up slightly different, but not in a biologically important way.” The implication of this is you could scan a person using some advanced form of the technology used to perform MRI scans and transmit that scanned information somewhere else using electrical or sound signals where it would then be reassembled into an approximation of the original.

Chuck Bennett says, “It’s the same principle as a fax machine. When you fax something, what comes out the other end obviously looks like the original and contains the same information, but it’s not the same paper, however, or the same type of ink. It’s the same but not the same. We already have three dimensional fax machines,” he points out, so the basic theory is in place. “What happens to the original person when their bio-molecular details are faxed somewhere else, and whether the average person on the street would be happy to be assembled as a similar but not the same or identical person,” thinks Bennett, “are moot points.”

With each person being made of trillions and trillions of atoms, ten to the power twenty-eight to be precise, the technology will never exist to make an absolutely accurate scan and reproduce every quantum property of a human over a large distance. So this approximation teleportation will probably be what we develop maybe tens, maybe hundreds of years in the future. However, the story is exciting because it means that teleportation may be a part of our future.

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Lonely Stars and Planets

Fourth Week of September 2007

We imagine the skies that we see would be similar to the skies that other intelligent creatures around the galaxy might see, but that may not be the case. There may be very lonely skies and very lonely creatures out there in the galaxy. This past week, astronomers have found evidence that stars have formed in a long tail of gas that extends well outside its parent galaxy. The discovery suggests that orphan stars may be much more prevalent than previously thought.

The comet-like tail was discovered in the X-ray light with the NASA Chandra Observatory and in the optical light with the Southern Astrophysical Research Telescope in Chile. The feature extends for more than two hundred thousand light years and was created as gas was stripped from a galaxy called ESO137001 that is plunging towards the center of a giant cluster of galaxies. This is one of the longest tails that anyone has ever seen, and it’s a wake of creation, not destruction, because observations indicate that the gas in the tail has formed millions of stars. Because the large amounts of gas and dust needed to form stars are typically only found within galaxies, astronomers previously thought it was unlikely that stars could form outside a galaxy.

Team member Megan Donahue says, “This isn’t the first time stars have been seen to form between galaxies, but the number of stars forming here is unprecedented.” The evidence includes twenty-nine regions of ionized hydrogen glowing in optical light thought to be found nearby new stars. These regions are all downstream of the galaxy located in or near the tail. Two Chandra X-ray sources are seen near these regions, another indication of star formation activity. The researchers believe the orphan stars formed within the last ten million years which makes them very young stars. Mark Voit, another member of the team, says, “By our galactic standards, these stars are extremely lonely. If life were to form out there on a planet a few billion years from now, they would have incredibly dark skies.”

The gas that formed the stars was stripped out of its parent galaxy by pressure induced by the motion of the galaxy through the multi-million degree gas that pervades the intergalactic space. Eventually most of the gas will be scoured from the galaxy, depleting raw material for new stars and stopping star formation in the galaxy. This process may represent an important but short-lived stage in the transformation of a galaxy. Although apparently rare in the present-day universe, tails of gas and orphan stars may have been much more common billions of years ago when galaxies were younger.

This discovery leads to a speculation: what type of life might form, and what skies and vision of their galaxy might life have in other neighborhoods. Our Sun is an undistinguished star living in an unremarkable suburb of the Milky Way, but what if we were transported to a different part of the Milky Way and a different star? If we examine our expectations for life beyond Earth, we’re bounded not only by the history of our planet but also by our particular cosmic environment. So let’s do the visualization.

Our first stop isn’t far from home as the crow flies, eighteen hundred light years. We’re in Orion, a bustling region of star formation that traces a spiral arm of the Milky Way. Our journey through a wormhole dumps us near a hot, young star a hundred times brighter than the Sun. Cobwebs of gas drape the sky, and most stars look slightly red due to the gauze of dust. Four trapezium stars blaze brightly, and other massive stars litter the sky. There’s evidence of past supernovae and heavy elements have been ejected liberally. With so much material for planets, most stars have a dozen or more. On the other hand, many stars live less than a hundred million years, and those that live longer must contend with the violent death of their massive neighbors. Among the habitable planets there are many truncated biological experiments. The cosmic environment favors life with a fast evolutionary clock and life that develops below water and lives in rock.

Our next hop through the wormhole drops us near the urban center of the galaxy where the density of stars is a thousand times higher than near the Sun. The entire scene is lit brighter than a full moon sky on Earth, an unfamiliar sight. Where stars are crowded the tightest, the sky crackles with the high-energy radiation from the heart of darkness in the Milky Way galaxy, a supermassive black hole. A cool dwarf hangs like a blood orange over our heads. It has six planets on tight orbits, two of which are in the habitable zone. This seems like a promising environment for life. There’s a lot of iron and silicon for building planets and lots of carbon for life. Planets are drifting among the stars, ripped from their gravity moorings from stellar encounters. A few are shrouded in thick atmospheres and massive enough not to need external life support from a star. With a high density and many planets per star, the spread of life is guaranteed. Life-bearing rocks are routinely ejected from planet surfaces by impacts resulting in an inefficient but extensive shuttle system for life. The high degree of stellar concentration means the signaling time between intelligent civilizations, if they exist, is short. If there is an interstellar Internet anywhere in the galaxy, this is the place.

Our last jump takes us thirty thousand light years into the halo, and this is similar to the environment we started the story with. There’s dark matter here of course, like there is everywhere, but no gas or dust and very few stars. The two-armed spiral of our disk is laid out below like a Persian rug, blue light knots of star formation set into a sparkling yellow star field. The white dwarf nearby is hot, titanium white. Formed a long time ago with not much grist for planets, it has three the size of Mercury, and they’re all long dead. The nearest star is a hundred light years away. Biology is sprinkled lightly in the attic of the galaxy. It’s lonely here and a shame that such a gorgeous view is wasted.

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