Discussion and news about the modern effort to understand the nature of life on Earth, finding planets around other stars, and the search for life elsewhere in the universe

Thursday, October 28, 2010

1 in 4

Having sweated over my previous post I'm hesitant to knock it off the top slot, but this is too good to pass up. Appearing in the 29th October issue of Science is a wonderful paper by Howard et al. The bottom line is that they have made as careful a statistical study of Doppler detected planets as seems practical at this time. The results of monitoring 166 relatively nearby normal stars for five years indicates that an astonishing 1 in 4 such stars may harbor small Earth-mass planets on close orbits.

It's important to be very clear, the planets actually detected in this survey are rocky objects a few times the mass of the Earth, and they are emphatically not in the classically defined habitable zone of these stars - orbiting within 0.25 AU (a quarter of the distance of the Earth from the Sun). However, the extrapolation to true Earth-mass objects is pretty likely to be robust. It'd better be, this claim is effectively saying that there are tens of billions of such planets in our galaxy and that they outnumber giant worlds in close orbits.

This presents a big challenge to certain aspects of how we think planets form. Most current models suggest that there should in fact be a deficit in small rocky worlds in these close-in orbits, since the processes of orbital migration or runaway planet growth tend to thin this population drastically. Something is afoot - and it may also indicate that those holy grail worlds - the Earths in the habitable zone - are far more numerous than we had dared to hope. Indeed, the authors of this paper suggest that Earth-mass planets orbiting at 1AU could be more numerous than their close-orbit cousins.

Howard et al. end their paper by evaluating the implications for Kepler results. It's awfully promising - as many as 260 Earth sized (1 to 2 times Earth radius) planets with 50 day or less orbital periods should be coming our way, and who knows what in the habitable zone of Kepler stars...

Megavirus vs Bicosoecid

It would make an excellent B-movie (if that's not an oxymoron). Giant virus attacks! Come see the battle for supremacy in technicolor 3D-surround sound!

Viruses lurk at the hairy edge of what we generally consider to be 'living' things. Small infectious structures, they replicate only by digging into a host's intracellular environment and hitching a ride. The smallest are barely 10 nanometers across - the size of a wavelength of ultraviolet light - and coded for by only a few thousand nucleotide base-pairs (compared to the more than 3 billion that code a human). Vast numbers of viruses exist in nature. In marine environments there can be 250 million individuals per milliliter of water, most of them so-called bacteriophages - targeting microbial hosts. Viruses play fast and loose with genetic material, clipping, swapping, dropping and incorporating at a mind-boggling rate. There is no doubt that they have played a critical role in the molecular evolution of life on Earth over the past 4 billion or so years. Our human genome contains millions of fragments of viral DNA - accumulated by our distant, distant ancestors and ourselves. Viruses bring into question even the very notion of 'species', we are all molecular ragdolls, a button sewn on here, a piece of thread incorporated there.

A newly discovered virus steps up the ante (and adds to the zoo of such things). Infecting a single-celled marine organism known as Cafeteria roenbergensis (good name, apparently it's a voracious eater) this virus is a monster. Its genetic makeup is 730,000 base-pairs, with 500 regions that look like bona-fide genes, many likely involved in making protein structures - something most viruses don't bother with. Like all viruses it's not a cellular organism, but here it is doing much of what regular living things do. It not only seems to have genes that could help make cell membranes, it even seems to have stolen genes directly from bacteria.

The line between this remarkable structure and 'life' is thin indeed and I think makes it very clear that there is more of a continuum than any dramatic 'jump' between complex molecules and what we clearly recognize as organisms. We have barely scratched the surface in our understanding of the relentless activity of the microscopic world. Intriguingly this Megavirus infects one of the major predators of the marine microbial environment. In that context it's hitching a ride with an organism that hoovers up both bacteria and viruses as food. What an excellent smorgasbord of genetic material it must see, one cannot help but wonder if that opportunity has helped it build its own massive library.

In the quest for life in the cosmos, and particularly as we continue to poke around in our own solar system, we need to think carefully about what we are looking for. Fragments of DNA from a formerly aqueous environment on Mars - should they ever be found - would likely offer a window into this borderworld  between molecules and self-contained organisms. It's going to be messy.

Monday, October 25, 2010

Scale-free mobility

Some ideas feel like an itch that you can't quite scratch because it's hard to pin down, but you really want to. A recent paper by Young et al. in Nature Physics (and available here), along with a commentary by Brockmann feels a little bit like that - at least when seen through the soupy goggles of astrobiology. On the surface this paper appears pretty innocent. It studies the nature of human mobility. With the rise of data-logging; from global positioning, cell-phone records, and the colossal airline databases of 3 billion annual travelers there is unprecedented material for studying exactly how we move around the planet. Not surprisingly we exhibit particular statistical patterns. For both distances traveled and 'rest times' (how long we linger over a cup of coffee or beneath the umbrella of some tropical beach) the distributions are inverse power laws. In plain language this means that we are more likely to travel short distances and to spend little time in any one place during travel.

There's nothing that sounds particularly revolutionary about that. But it gets more interesting. As Young et al. discuss, the particular shape of the statistics appears to be modeled rather well with a form of 'preferential return'. In other words although we may explore - making new journeys - we are more likely to travel to locations that we already know.  Not only that but the more locations that we already know the less likely we are to explore new ones at all. This naturally produces a so-called scale-free distribution - if you go out to any particular pub then there will be another pub that you are twice as likely to visit, and another one that is half as likely to have your patronage. The Young et al. model boils down to assigning a probability for any given 'step' in an individual's travels that results in exploration (a new location). They give this as the number of prior travel steps to the inverse-power of....0.2.

Why 0.2 ? Nobody knows, but this describes the way human populations explore the world - individuals will deviate from this pattern, but en-masse this is what we do. It's a deceptively simple, but extremely provocative result. Does this same kind of probabilistic scaling apply to other species? Do other species have a different power law value than 0.2? What are the implications for the occupation of niches by organisms on a planetary scale and throughout the history of life? This implicit tendency for exploration to slow down in favor of re-visiting known locations makes me wonder about a recent discovery on the global East-West divide in marine microbial genetics. While environmental differences are the most obvious root bio-physical cause (particularly the differing soluble phosphorus amounts in the Atlantic vs. Pacific oceans), does this give rise to a similar 'preferential return' scaling?

Then, to return to a popular theme - is there something to be learnt from this model for the questions of life exploring the cosmos beyond a planetary homeworld? On the face of it the more you explore the more likely you are to slow down and just keep circulating amongst the places you know. Clearly the present data represents humans who are not, we presume, exploring for survival or vital resources - lattes don't count. Nonetheless it is reasonable to hypothesize that humans behave this way because there is some circumstantial evolutionary advantage to it. The hard-to-pin-down-itch is that one suspects there is something deeper - perhaps universal -  in all this, waiting to be ferreted out.

Friday, October 22, 2010

Blowing hot and cold

Understanding the structure, dynamics, and chemistry of planetary atmospheres is key to exoplanetary science. It's sobering then that as of now it is still an enormous challenge to even model the atmospheres of planets in our own solar system. Despite great advances a variety of trickery has to be employed to simulate something like the Jovian atmosphere, such as pretending that it has a very different soupiness and energy transport in order to overcome computational demands. Modeling the atmospheres of gas giant exoplanets is even more in its infancy. An intriguing result in the past week has come from Crossfield et al. and their study of how we see the infrared light varying in the planetary system of Upsilon Andromedae. Their Spitzer space telescope phase photometry on Ups And reveals the glow emitted by the innermost, roughly Jupiter sized, planet around this F dwarf star (about 1.3 times the mass of the Sun).

The planet orbits very tightly, every 4.6 days, and is expected to have been evolved by tidal interaction with the star to a state of spin-orbit-synchronicity - in other words, in the simplest case, its day will equal its year and there will be permanent day/night sides. This sets the planet up for an extreme case of thermal disparity. We'd expect hot atmosphere from the dayside to flow to the cold night half of the planet - in doing so there might be great jet-stream like structures, and the hottest point of the planet might get shifted along in the direction of these winds. Something like this seems to be happening on Ups And b, but to an extent that is truly puzzling. As it zips around in its orbit the glow of its hot atmosphere betrays the temperature distribution and is seen in the varying number of infrared photons collected by Spitzer. It's not in synch with the planet orbit - or more specifically it is systematically offset or phase shifted by almost 90 degrees. In other words the hottest side of the planet is almost at right angles to the direction of the star. On the Earth this would be a bit like saying the hottest time of day is at sunset instead of noon.

It's a puzzle. Some amount of offset might be expected, driven by the strong hot to cold winds, but this is extreme. There are various possibilities - maybe the stellar heating is reaching to greater depths in the planetary atmosphere than expected and altering the fundamental dynamics. Perhaps the winds are so strong that they are going supersonic, forming great shock waves that pile energy up on this side of the planet. It's a tough call - even models of these hot Jupiter-like planets disagree on such things, and none of them predict exactly what we see on Ups And b. The good thing about this result is that it challenges the modelers to really sort out what works and what doesn't - advances will be made.

Crossfield et al. also end their paper with an interesting fact. This system of Ups And is actually too bright for the upcoming James Webb Space Telescope (JWST) to observe at shorter wavelengths - its sensitive instruments would simply be saturated with photons. They further point out that a small space telescope dedicated to studying the phase curves of nearby hot-Jupiter systems might just provide the data needed to crack the problems of these extraordinary regimes of planetary atmospherics. This is a sentiment that could also apply to the hunt for terrestrial-type exoplanets - especially those that transit stars much closer than the distant Kepler objects - we need a dedicated all-sky survey to find the targets for powerhouse instruments like JWST.

Tuesday, October 19, 2010

Cosmic minds

In recent months there has been more discussion around about the idea that 'advanced' life in the universe might employ artificial intelligences to do the dirty work of exploring. Indeed, AI might just push off on its own accord and could, it is presumed, be made effectively immortal. These patient devices could then withstand the enormous times and extreme environments involved in crossing interstellar, or even intergalactic, space. In part these ideas are an attempt to narrow the search parameters for our efforts to spot signs of intelligent life in the universe - as nicely discussed by Paul Gilster. There is something intriguing about these notions, but they also raise some other questions. I thought I'd try to stir things up a bit.

Without getting too deeply into the meaning of AI (Turing tests and the like), it's interesting to consider the history of attempts to build such things here on Earth. In the late 1950's there was a huge push to construct an AI, everyone felt it was only a decade or so away, governments dumped money into research - to little obvious avail except for general advances in computing. In the early 1980's there was another bout of enthusiasm and billions of dollars got funneled into AI work. Most of the focus was on the idea of expert systems - the idea that much of intelligence stems from the ability to assimilate and utilize large amounts of data; knowledge was the fuel for AI. Another bubble has happened more recently with the notion that true AI cannot be some disembodied piece of code, it needs a robotic avatar in the real world. Incredible things have been done in the name of AI. The fundamentals of modern programming have to some extent been reshaped by this thinking, and we indeed now experience the rudiments of AI every time Amazon or Netflix gleefully present us with 'suggestions' for what we might want to spend our money on. However, the true AI that we all imagine is nowhere yet to be seen.

Indeed, there are even deeper questions and doubts about the whole idea of a physical machine that can mimic a living mind. Roger Penrose in his dense but fascinating 480 page argument - The Emperor's New Mind - made a pretty sobering case that quantum mechanical processes are central to our type of intelligence. Of course this was written prior to gains in quantum computation, but its thesis has not yet been disproved.

So where am I going with all this? I think there are two important, although speculative, points that come from our baby-steps in AI. The first is the idea that if we keep working at it then one day an AI will 'appear', like a new iPad or model of car. What if that conceit is just wrong? It certainly appears incorrect so far.  It may be that AI is something that emerges very, very gradually. So gradually in fact that we barely realize it's happening, just like the processes of natural selection and evolution. As we upload more and more of ourselves - our knowledge - onto Google or Facebook we may actually be pushing the process along, but we could have a thousand years or more to go. The second point is related. What if Penrose is correct, and only quantum processes have access to the right amount and type of computing power for intelligence? True AI may well be indistinguishable from biology.

What this could mean is that there will never be AIs in the universe that can be distinguished from their biological parents (I know, shades of Battlestar Galactica, but fiction is often prescient). There could be 'dumb' AI explorers - complex machines of limited flexibility - but there will never be true AI exploration, because those AI would likely be subject to the same problems that we have with interstellar distances and timescales. Thus,  if we want to try to define a more targeted set of search criteria for 'intelligent' life in the universe (which is certainly not a bad idea), there are probably two options. One set of life is going to be just like us - whether it's AI or not. The other is going to be extremely machine-like, not super-Turing-test-smart, but well programmed and equipped with a big knowledge base. So the question is, what would exo-Google be doing out there in the universe?....

Monday, October 18, 2010

Through the halo

The technology for detecting planets continues to advance. A new paper by Sascha and colleagues contains the first direct imaging data of a planet obtained with an emerging optical technology called an apodized phase plate. Interestingly this builds on a set of ideas that have also been kicking around for a while in microscopy - the techniques for peering into the infinitesimal can also help us peer into the infinite.

The classic difficulty in looking directly at exoplanets is that they always appear extraordinarily close to their parent stars on the sky. Stars are millions to billions of times brighter than planets (depending on the precise wavelength of observation), and the wave nature of light always results in the blurring, or diffraction, of light as it passes through any kind of optical instrument. So the starlight ends up swamping out the feeble emission or reflection from any orbiting planets. Getting rid of the starlight is an entire field of research unto itself. Methods such as coronagraphy, and the rather ominous sounding nulling interferometry all seek to remove or suppress the light of the star, leaving behind the glimmer of any planets. It's been likened to trying to spot fireflies in the glare of a searchlight when you're thousands of miles away - that's not a bad analogy.

The apodized phase plate is a nifty bit of trickery. An earlier paper in 2007 by Kenworthy et al. describes the application to astronomy. In a nutshell the plate (combined with a coronagraph - a disk directly blocking some of the light of the star in the image) is a transparent chunk of material - in this case zinc selenide which is highly transparent in infrared wavelengths - that is modified to introduce a complex spatial pattern of phase changes to incoming light. Ok, so that's not so much a nutshell as a mouthful of walnut. Imagine a watery surface with light reflecting from it. You've undoubtedly seen this happen - wonderfully varied patterns of light and dark occur in the reflected light, the stuff of a summers day, shimmering on the hulls of boats, or off the dirty dishes in a kitchen sink. What you're observing are the phase shifts in the light - tiny time delays because a watery surface is not perfectly flat. If the phase shifts are out of sync light cancels out, if they're in sync it adds together - and we see dark and light regions in the reflected images.

The phase plate exploits the same physics, but in a careful, mathematically controlled way. Its 'rippled' surface adds time delays in pre-determined locations across the beam of light from a distant stellar system. These are cleverly designed so that on one side of the final image the light of the star gets blanked out (nulled), but the light of any planets remains. It's a tough challenge to get this to work. You also have to remove as much of the other sources of blurriness - like that induced by Earth's own atmosphere - as possible. Sascha et al. seem to have accomplished this, re-detecting a giant planet around the young star beta Pictoris, on an orbit of a mere 7 astronomical units (that's between Jupiter and Saturn if it were our solar system).

It's a terrific step. There are certainly many side effects of such trickery - a narrow waveband, imagery of only one side of the star, calibration challenges - but together with many other emerging techniques it does seem that we're well on our way to doing even richer exoplanetary science.

Wednesday, October 13, 2010

We salute you...

Bacteria. Asexual lords and masters of the planet. An extraordinary and fascinating piece of work has popped up that indicates a form of bacterial networking that inches this sentiment even further along from the figurative to the literal. In a study of the bacterium S. oneidensis (an organism capable of actually reducing, or 'breathing', heavy metals) El-Naggar and colleagues find that when stressed these microscopic lifeforms can grow so-called bacterial nano-wires. These incredibly thin protrusions - really stalks of protein - exhibit electrical conductivity. This work builds on earlier studies that also hinted as this property.
They're no piece of copper when it comes to transporting electrons, but they seem to be on a par with semi-conductor materials.

The experimental work is quite wonderful, and shows that colonies of S. oneidensis may actually link themselves together in a remarkable type of electrical grid. Why do they do this, are they just engaged in some form of microbial Facebook? The answer may be one of survival. The respiration of S. oneidensis is acutely dependent on the ability to off-load unwanted electrons - performing chemical reduction on anything able to accept the electrons. If a single individual can't dump its electrons it dies. So, if you can send out nano-wires and make an electrical connection with someone else you can pass off your particles - and if that individual can't accept them it can simply re-route the current further along the network, until eventually it gets slurped up. It's an incredible ability, the colony comes to the rescue of the few, and nobody has to get out of their armchair.

As the researchers point out, beyond enabling the group to respire and survive, bacterial nano-wires open up a whole new avenue of fast communication - much speedier than chemical signaling. One cannot help but see a parallel between this situation and the web of neurons and electrical synapses lurking between our own ears. The more we learn about life on Earth, the more blurred the line becomes between 'simple' and 'complex' life, and the more archaic that classification appears.

Monday, October 11, 2010

Shaken, stirred, shaken, stirred

Water never ceases to amaze. Two protons, one oxygen nucleus, 10 electrons. A simple molecular configuration, two sides of a triangle, an obtuse angle of 104.45 degrees and a tendency for the electrons to huddle close to the oxygen by about a factor of ten - leading to an electrical dipole. As basic as this structure is it lends itself to an incredible array of situations. From a physical building block of planets to an extraordinarily solvent to an integral piece of terrestrial biochemistry, there is excellent reason why many astrobiologists extoll the virtues of 'following the water' in the search for life in the universe. Despite this, our deeper understanding of exactly what it is that makes water so very, very special is still surprisingly limited.

An intriguing new study by Rao, Garrett-Roe & Hamm in the Journal of Physical Chemistry (B), appears to offer a clue or two. By applying modeling techniques usually reserved for the study of complex and dynamic systems, they investigated what might be going on in liquid water on a moment-by-moment basis. The dipolar nature of water molecules means that weak electrostatic bonds (hydrogen bonds) are readily made and broken between structures. So in a crowd of water molecules all manner of temporary arrangements can be made as they jostle around. This new study indicates that there may be two main flavors of these arrangements - one a rather 'blobby' mass of several molecules, and the other a more regular, crystalline arrangement. These structures are exceedingly fleeting - breaking up and re-assembling many times a second at room temperature. The result is, and this is a very crude phrasing, a bit like a 3D piece of velcro that is constantly morphing into different shapes.

So, all jolly nice, but why do we care? Imagine throwing some other molecules into this sticky nest. Perhaps some carbonates, some amino acids, even some proteins. The shape-shifting water structures can provide the perfect chemical incubator - from catalyzing reactions to determining structural forms of complex organic molecules.  This cuts to the heart of one of the long running discussions that crops up in the search for life. Why couldn't you have biology that uses something other than water? Why not methane, or hydrogen peroxide, or ammonia?

The answer may now be clearer - as far as anyone knows these other solvent-like molecules do not exhibit this same type of behavior - so it may be that they offer far fewer, if any, pathways for complex chemistry. Water may be far more intertwined in the processes of life than we had suspected.

Wednesday, October 6, 2010


Overcoming preconceptions and received wisdom is central to making progress in science, and to be quite honest in pretty much anything else as well. I was reminded of this after a somewhat doleful conversation following last week's burst of exoplanetary adrenaline. It went along the lines of 'even if GL 581g was full of intelligent and occasionally amusing aliens, we're just not a spacefaring race and we'll never get to meet them'. Most of this statement is certainly true, but I was struck by the glum expression of certitude about our Earth-bound nature.

A while ago National Geographic published one of their terrific graphic illustrations that summarized 50 years of human space exploration. I can't do it justice here, so go take a look. The incredible thing is just how much space exploration we've actually tried (and often succeeded at). One target is particularly evocative, and that is Mars. I think it's fair to say that going to Mars has always been far less about politics than some other destinations. Mars looms big in our imaginations, the red planet, awfully familiar, yet awfully different. There is incredible poignancy in the list of missions to Mars. A majority have been failures, years of effort and extraordinary technological know-how thrown to the sacrificial plinth of the void. Yet those that succeeded have genuinely transformed both our understanding of this other world, and transformed our relationship to space exploration.

Here's the list, starting in 1960: Marsnik 1 (failed), Marsnik 2 (failed), Sputnik 22 (failed), Mars 1 (failed), Sputnik 24 (failed), Mariner  3 (failed), Mariner 4 (flyby), Zond 2 (failed), Mariner 6 (flyby), Mariner 7 (flyby), Mars 1969A (failed), Mars 1969B (failed), Mariner 8 (failed), Cosmos 419 (failed), Mariner 9 (orbit), Mars 2 (orbit), Mars 3 (lander), Mars 4 (failed), Mars 5 (orbit), Mars 6 (failed), Mars 7 (failed), Viking 1 (orbit/lander), Viking 2 (orbit/lander), Phobos 1 (failed), Phobos 2 (failed), Mars Observer (failed), Mars Global Surveyor (orbit), Mars 96 (failed), Mars Pathfinder (rover), Nozomi (failed), Mars Climate Orbiter (failed), Mars Polar Lander (failed), 2001 Mars Odyssey (orbit), Mars Express (orbit), Beagle 2 (failed), Spirit (rover), Opportunity (rover), Mars Reconnaissance Orbiter (orbit), Phoenix (lander).

Each of these launches, each chunk of alloy and package of electronics, was made to reach across interplanetary space. There was nothing glum about this. Bottles cast into the currents full of tentative human optimism and love and care. All the hallmarks of a space faring species negotiating its first steps. All for a minuscule fraction of resources across the years compared to wars, financial crises, pharmaceuticals, and political shenanigans. To my mind we are already a space faring species, we just haven't quite realized it yet.

This has a direct bearing on our search for life in the universe . Even as the next generations of giant telescopes and advanced optics are being built on terra firma,  the ultimate goal has to be placing instruments in space - away from atmosphere, unstable environments, and with room to stretch out. Whether it's an occulting optic on a 200,000 mile virtual optical bench, or an array of interferometric mirrors, the high mountaintop of space remains where we need to go if we ever want to truly study, even map, another Earth-type planet or a related species. 

Friday, October 1, 2010

A distant cousin

It seems worth following up on the previous post with a little more on the planet GL 581g. With media attention temporarily swirling around this announcement and numerous opinions being offered it can be a little difficult to locate the core truths. Now that Vogt et al.'s actual scientific report is live we can see the basis for their public commentary. It's a very nice piece of work. It's also a remarkably, and refreshingly, chatty report - not something that scientific papers are particularly known for. The incredibly tricky and slippery nature of extracting planet detections from radial velocity (or Doppler 'wobble') data on the star is nicely laid out. Boy did they have to work hard on this. 11 years of data, including some from a 2nd instrument. Although there were over 200 discrete measurements of the star's motion these were, of course, spaced across a decade in time. This kind of sparse sampling - a necessary evil given the nature of telescope time allocation, weather, and competition - presents many challenges when you're looking for numerous overlaid time-varying signals.

Nonetheless, they pulled out the best solutions they could, checking against gravitational simulations of the system to make sure these answers resulted in a real, stable, system of planets and observing the star for signs of luminosity variation - sunspots and the like - that could dupe us into seeing things. All seems good. It is interesting too that they present an age for the system of 4.3 billion years, based on spectral analysis of the star - rather younger than the 7-12 billion years previous measurements had given, and the basis of some of my previous comments. Dating stars is tricky, so I'll pause on any extrapolations from that.

All of which brings us back to asking whether this really is Earth 2.0 as so many headlines have been suggesting. It's not, is the simple answer. Two big tick boxes get filled in - close to Earth mass and in the 'habitable' zone of a normal star. This alone does not make for tropical islands, lush forests, or highway systems.  The real reason for being excited about this planet is that despite being extraordinarily alien, it nonetheless exhibits characteristics that place it firmly as a distant cousin. Imagine you were a hugely pampered but not overly prejudiced western explorer in the 1500's, and that no one from your neck of the woods had ever set foot beyond Lisbon. Setting off across the oceans you arrive at Papua New Guinea. You would immediately recognize other humans, however they would be engaged in complex and utterly alien work and social customs, like nothing you'd seen or experienced before. Their completely different lifestyle would confound you - but it would be obvious that you shared essential biology and characteristics. I think that's a fair analogy here. GL 581g and Earth are distant relatives, products of a universal set of mechanisms that build planets. The key is that GL 581g is the least distant relative we've come across so far.