Saturday, October 30, 2010

The hunt for extremophiles in Lake Untersee

In early 2008, a team of NASA scientists left the United States for Antarctica to explore one of the strangest lakes on our planet: Lake Untersee. This body of water is fed by glaciers and permanently shielded by an ice layer, however, what makes it particularly interesting to scientists is its basicity. Lake Untersee is extremely alkaline, with a pH comparable to that of extra-strength laundry detergent. Additionally, the lake’s sediments produce more methane than any other natural body of water on Earth, and thus, if life in any form is found in these waters, the implications will be unbelievable. This should sound familiar to us: Predominantly icy areas? The presence of liquid methane? These are the exact same sort of characteristics possessed by the exotic planets that we talked about in class a couple weeks ago. The icy moons of Jupiter (Europa, Io) and Saturn (Titan, Enceladus), Mars, and Venus are for the most part, cold, methane-rich places where the potential for life has been visited over the years.

Anyway, these NASA researchers are going to Lake Untersee with the intent to search for extremophiles – tough microbes that thrive in conditions that are often considered to be too extreme for most other living things.

Richard Hoover, expedition leader of NASA’s Marshall Space Flight Center, notes that in recent years researchers have begun to realize that “Goldilocks zones” that contain what we consider to be perfect temperature and pH aren’t necessarily imperative for the existence of life. Researchers have found microbes in ice, boiling water, and even nuclear reactors – these extremophiles that were once considered to be oddities, may be the norm elsewhere in the cosmos. Of the expedition Hoover said:

With our research this year, we hope to identify some new limits for life in terms of temperature and pH levels. This will help us decide where to search for life on other planets and how to recognize alien life if we actually find it.”

What I found to be the most interesting discovery of Hoover’s expedition though, was the phenomenon of the “ice geyser” that the researchers discovered when they triggered one by drilling into a localized pocket of high pressure air in the upper layer of the ice sheet that covered Lake Untersee. This phenomenon may be pertinent to the recently discovered “ice geysers’ that erupt from the cracks in the “tiger strip” area of Enceladus. The ice bubbles that were found throughout the surface of Lake Untersee were also observed (by high-resolution dark field microscopy) to contain motile bacteria. The presence of viable bacteria frozen in the ice of this body of water suggests that maybe it isn’t completely necessary to drill through the thick icy crusts to search for life in the seas of the frozen moons of Jupiter and Saturn – viable cells may be cryptopreserved in the upper layers of the ice crust!

Thus, from this we learn that complex robots and machinery need not be capable of drilling down thousands of feet beneath the surface of these icy lakes and risk degradation by extreme conditions. They really only need to be able to drill down several hundred feet in order to encounter one of these ice bubbles in which life forms may have the potentially been preserved.

The Limits to the Habitability of Water

Water is vital for life as we know it and is one of the key factors we associate with habitability and look for in search of life elsewhere in the universe. But not all water has life living in it. Researching extreme environments has helped to distinguish the limits of what constitutes habitable water conditions on our planet, which could help us determine what types of water are more likely to contain life on other planets. This suggests that the principle of looking for water in order to find life may need to be refined because not all water is habitable.

On Earth, we know that life can survive in a wide variety of water temperatures and pressures, and yet there are watery places where no living things have been found.
Scientists have found that only 12 percent of the volume of the Earth where liquid water exists is known to host life. The remaining fraction of liquid water seems strictly uninhabitable – both here and possibly on other distant worlds. Although this is just taking into consideration the ability of our life form to live in these type of watery environments, not other alien life forms.

Although we typically think of water being liquid between zero and 100 degrees Celsius, this is only true for pure water at Earth’s sea level atmospheric pressure. If salt is present, water's freezing point drops below zero degrees and its boiling point rises above 100 degrees. At high pressure, as well, water remains liquid above 100 degrees Celsius. In fact, the authors estimate that liquid water can exist to a maximum depth of 75 kilometers below the Earth's surface, where the temperature is more than 400 degrees Celsius and the pressure is 30,000 times that at the surface.
Conditions on Earth do not allow liquid water below a depth of about 75 km, which leaves a thin outer shell where liquid water can exist. This means that out of the entire Earth volume, 3.3 percent has the right conditions for liquid water but only 0.2% has the potential for habitable water.

The highest temperature known to support life--an Archaea named "Strain 121"--is 121 degrees Celsius. Some biologists believe organisms might survive at even higher temperatures, but nothing has broken the record yet. This means that the upper bound of habitable water, in terms of temperature, is about 121 degrees. At the other end of the thermometer, liquid water can be found on Earth at 89 degrees below zero in thin films, however, the coldest water temperature known to support active life is 20 degrees below zero, which is what the researchers take as their lower habitable boundary.

In terms of pressure limits, life has been found as far down as 5.3 km below the surface, where the pressure is 1500 times that at the surface. No one has yet dug deeper in search of life so we are not sure if life can survive in higher pressures than this. As for low pressure, life has been found high up in the atmosphere where the air is thin, but these microorganisms are typically dormant and are only revived when given the necessary nutrients. The authors therefore take the low pressure limit for active life to be one third of atmospheric pressure, which corresponds to the altitude at the top of Mt. Everest.

Biosphere limits

According to the above limits, life on our planet is restricted to a thin shell that roughly extends from 10 kilometers above the surface down to 5 kilometers below (or to depths of 10 kilometers in the ocean). This leaves uninhabited 88% of the volume where water exists on Earth which suggests that life and water are not equivalent and there seems to be a lot of water present that is hostile to life.

What is even more interesting is that nearly all of Earth's liquid water is located in habitable regions, so that only a small fraction of the water conditions on Earth are friendly to life. But this is slightly misleading because the only truly constraining factor in this analysis is the observation that life apparently can't survive above 122 degrees Celsius.

What does this mean for water on Mars?

Jones and Lineweaver are currently modeling the crust, mantle and core of Mars and using heat flow estimates to construct a Martian water phase diagram, like the one they made for Earth's water. The results will show at what depths potentially habitable water (as defined by the current study) might be found on Mars.

This sort of "habitable water" analysis could also be used for the liquid oceans that are thought to lie beneath the icy crusts of Jupiter’s moon Europa and Saturn’s moon Enceladus. And it may help characterize exoplanets for which a reasonable phase diagram can be estimated.

This may halp us focus our search for life. It also adds complexity to the idea that water and habitability are equivalent.

Another interesting point is that there may be more to the inhabitability of water besides just pressure and temperature. Perhaps there are regions that are too salty? or too high in certain chemicals? or too polluted?

One related recent discovery is that of methane-eating bacteria at "Lost Hammer":
there have been microbes found that live in water that is so salty it is liquid at subzero temperatures, contains no consumable oxygen, and has high amounts of bubbling methane. This spring is located in a highly unique spring--Lost Hammer--on Axel Heiberg Island in Canada's extreme North. Despite these incredibly harsh conditions, researchers from the McGill University have found life. This life consists of methane-consuming bacteria.

They were surprised not to find methanogenic bacteria that produce methane but instead to find these very unique anaerobic organisms that survive by essentially eating methane and probably breathing sulfate instead of oxygen. "The point of the research is that it doesn't matter where the methane is coming from," Whyte explained. "If you have a situation where you have very cold salty water, it could potentially support a microbial community, even in that extreme harsh environment."

It has been very recently discovered that there is methane and frozen water on Mars. Photos taken by the Mars Orbiter show the formation of new gullies, but no one knows what is forming them. One answer is that there could be that there are springs like Lost Hammer on Mars. There are places on Mars where the temperature reaches relatively warm -10 to 0 degrees and perhaps even above 0ºC and on Axel Heiberg it gets down to -50, easy. The Lost Hammer spring is the most extreme subzero and salty environment we've found and provides a model of how a methane seep could form in a frozen world like Mars, providing a potential mechanism for the recently discovered Martian methane plumes.

How has the moon impacted life on Earth?

If we condense the time of Earth’s existence into 24 hours, the moon would form just 10 minutes after the Earth was born. The Earth formed 4.56 billion years ago, and the Moon formed about 30 million years later. An impactor about the size of Mars struck the Earth at an oblique angle, and removed some of the magmatic mantle which was put in orbit around the Earth, together with some of the debris from the impactor itself, and this material eventually formed the Moon.

The tidal effect of a body increases as a cube of the distance, so the effect of the Moon’s tidal forcing on the Earth was extremely high at this time and provided some additional energy to the heating from radioactive elements present. As Earth started to cool, the Moon still was a source of heating that may have had some geological effect, keeping the Earth’s magma hot and perhaps forcing additional convection in the Earth’s mantle. With further cooling, the first crust started to float on top of the magma. During this period the Earth was subjected to increased meteor bombardment. Many of the large basins on the Moon are evidence of this late heavy bombardment. In this way, the Moon is a history book for the inner solar system and the Earth.

The usefulness of the moon for learning about early Earth:

The Earth was hit more often than the Moon because Earth is larger and has more gravity. When some of these impactors hit the Earth, the explosion caused some rocks and dirt from Earth to shoot up and land on the Moon. There is potentially a LOT of material from early Earth buried beneath the surface of the moon--up to a few hundred kilograms of Earth material per square kilometer of the Moon’s surface. It would be very interesting to dig this material up and sample these rocks from early Earth because almost nothing from this time period has survived on the Earth tiself. This is because of tectonic recycling of the crust plates and atmospheric weathering. We would try to detect some organics within those rocks, and that could tell us about the history of organic chemistry on Earth. Some of these rocks could even have preserved fossils of life. Such rocks could help us look further back into the fossil record, which now stops at 3.5 billion years ago. This way, we could possibly learn about the emergence of life on Earth.

By exploring the Moon, we also can get clues on how the Earth has evolved. We can study processes on the Moon that have also shaped the Earth, like volcanism and tectonics. Because the Moon is smaller than the Earth, the Moon’s radiogenic heating dissipated much faster. Because the Moon offers different conditions than the Earth, we can better understand how physical processes work generally by studying a larger range of parameters than just the Earth’s.

Lunar effects other than tides:

There are people who propose that the tidal effect of the Moon may have helped trigger the convection on the Earth that led to the multi-plate tectonics. The other planets don’t have the same tectonic cycle. For most of them, the crust is like a lid that doesn’t move much horizontally, and the magma and heat are blocked by this lid on the surface. The Earth instead has rolling convective motion that drags the crust, and then the crust plunges back down into the mantle and gets recycled.

There are some very subtle effects of the Moon in the climate and the oceans. One pattern that has been found recently is related to the El Niño phenomenon. You have a cold undersea current coming from the Antarctic sea, and that creates the Humboldt stream which keeps the sea around the South American coast near Peru and Chile quite cold. Because of this, there are fewer clouds and less precipitation there. Sometimes this current drifts away from the coast, and then you have much more cloud formation and a period of very bad weather over South America which we call El Nino. People have connected some newly discovered streams with how the Moon’s tidal effect influences the mixing of the deep ocean. If you took away the Moon suddenly, it would change the global altitude of the ocean. Right now there is a distortion which is elongated around the equator, so if we didn’t have this effect, suddenly a lot of water would be redistributed toward the polar regions.

In addition, the Moon has been a stabilizing factor for the axis of rotation of the Earth and thus has contributed to the maintenance of a stable climate. Mars, in contrast to Earth, has wobbled quite dramatically on its axis over time due to the gravitational influence of all the other planets in the solar system. Because of this obliquity change, the ice that is now at the poles on Mars would sometimes drift to the equator. But the moon has helped stabilize our planet so that its axis of rotation stays in the same direction and consequently, we had much less climatic change than if we had no moon. And this has changed the way life evolved on Earth, allowing for the emergence of more complex multi-cellular organisms compared to a planet where drastic climatic change would allow only small, robust organisms to survive.

We know that the Moon has influenced biology because of tides, but it has had other influences on biology, as well. For instance, the eyesight of many mammals is sensitive to moonlight and the level of adaptation of night vision would be very different without the Moon. Thus the moon has influenced evolution in this respect.
Human vision is so sensitive that we are almost able to work by the light of the Milky Way. The full Moon has more light than we need to see at night. For most of our history, we were hunting and fishing or doing agriculture, and we organized our lives by using the Moon. It determined the time for hunting, or the time where we could harvest. That’s why most of our calendars are based on the Moon and there are many examples of human behavior that may have been based on lunar phases.

Studying the Moon helped us determine distances in the solar system and the size of celestial objects. By studying lunar phases, for example, people were able to determine how far the Moon is from the Earth, the size of the Earth, and our distance from the sun. The Moon has inspired humankind to learn how to travel to space, and to bring life beyond Earth’s cradle.

Understanding the influences of the moon on life on Earth is important for recognizing the importance of moons to life in general. If moons are deemed necessary for life, then the search for life can be further narrowed to only planets with moons. Is the moon essential for life on Earth? I am not sure. But there are many helpful influences of the moon on Earth. The one that seems particularly interesting (besides tides which i discussed in an earlier blog) is that of the moon's role in the stabilization of Earth's rotation around its axis. I had never thought about how this related to the stability of Earth's climate, but this may be an important consideration for habitability. This also depends on how many other planets are in the solar system, however, and how the other planets influence the rotation of the exoplanet of interest. Nonetheless, this is an intersting thought. Learning more about our moon both helps us learn more about Earth itself, but also about the importance of moons in general. Now the question is: And are the presence of moons any indication of increased habitability on exoplanets?

The Arecibo Message and the search for extraterrestrial life

In 1974, mankind put forth its first attempt at communication with extraterrestrial intelligence (CETI). The effort consisted of a message beamed toward the star cluster M13 by the Arecibo radio telescope. This star cluster is the most prominent globular cluster in the northern half of the sky, and happens to lie in the constellation, Hercules. It spans well over 150 light-years, although the bulk of its over one million stars are concentrated into a core region with a diameter of about 100 light-years.

The Arecibo message consists of a string of 1679 binary digits that can be arranged into 73 rows and 23 columns (prime number multiples of 1679) to represent a picture describing human life on Earth. The uppermost portion of the message establishes that the number system on Earth is binary through a display of dots in formations one through ten, reading right to left. Beneath this appears the atomic numbers for the main biological elements: carbon, hydrogen, oxygen, nitrogen, and phosphorous, beneath which is a model of the chemical structure of DNA. The remaining portion of the message addresses the appearance, size, and number of human beings, as well as our location within our solar system.

Realistically, over the course of its 25,000-year-long journey, its likely that the Arecibo Message will be degraded beyond recognition by its interaction with cosmic dust and particles in the interstellar medium. With the loss of even a few bits of information, the signal will most likely be rendered undecipherable, however, a much larger duplicate message was sent on the 2001 Encounter Mission to address this problem.

The search for extraterrestrial life (SETI) initially began with microwave observation, and has just recently been expanded to include an optical search for extraterrestrial laser pulses. The basic strategy first involves the search for an indicator – a focused radio beam, a brilliant pinpoint of light – that is identifiable as intelligently controlled rather than a purely natural phenomenon (pulsars or quasars) or a human artifact (unexpected transmission from a “lost” satellite). However, the conformation that so many SETI scientists base their career upon could occur today, tomorrow, or never. A thorough search really depends on the exact magnitude of space, the number of technologically advanced civilizations that coincide with ours, as well as the search rate.

In searching for extraterrestrial life, some researchers probe galaxies beyond ours; however, most searches are limited to subsets of the billions of stars within our own galaxy. Additionally, of the searches that are performed, researchers either use an “all sky survey” mentality, which involves an encompassing but superficial look at unselected stars or a “targeted” search which is based on a closer inspections of the five to ten percent of stars that are believed to be promising hosts for life-bearing planets. With the advent of newer, more advanced, technologies, the search for extraterrestrial life by astronomers is looking more and more promising.

What I find to be a particularly interesting aspect of SETI today are the often-overlooked cultural, intellectual, and emotional factors that shape the search as well as the mindsets of the searchers. These factors bring an anthropological, psychological, sociological, as well as historical aspect to the discovery of extraterrestrial life that could help outline interstellar communications that can be understood in cultures that are radically different from our own. Specifically, anthropology (including archaeology and linguistics) along with psychology and cognitive science could be used to decrypt and interpret any message that we may intercept. Then, social psychologists and communications specialists could be used to facilitate the orderly dissemination of news to the public. The understanding of the media and mass communications, organizational functioning, social and psychological influences on attitude formation and change, as well as rumor control can make a huge difference when presenting information to the public. The way in which the information is presented to the public plays a huge role in their response, thus an understanding of human reactions is imperative when it comes to SETI discoveries. It seems like this would be an incredibly difficult task for these specialists appeal to the interests, knowledge, and beliefs of not just one or two nations or regions, but rather the entire human race though. The way that our cultures and societies have diverged in our time on Earth has made it incredibly difficult for these specialists to make this information culturally relevant and available to everyone – as all humans deserve to know if we are not alone in our universe.

Friday, October 29, 2010

Climate Change and Habitability continued

As a branching off point from my previous blog, another interesting comment I came across in the "Hot Zone" blog (about Climate Change) on the astrobiology magazine website was the following: Peter Ward, author of The Medea Hypothesis (2009), has taken the viewpoint (among other scientists) that life is rare in the universe because it is fundamentally harmful in its destabilizing affect on a planet’s climate. This statement is hard to refute in today's world as man's impact of Earth is becoming more and more obvious. I had never heard this theory before, but it is incredibly interesting. What is it about life that is so destabilizing?

This theory seems to go against a prevailing sentiment in society that the workings of the natural world have reached a dynamic equilibrium that is incredibly elegant and durable. Indeed, the notion of biomimetics in which nature is used as a template for man's engineering is based on this sentiment, as are the environmental laws that try to minimize the damaging influence of humans on land and the atmosphere.
This sentiment shows up in Henry David Thoreau's dictum, "In wildness is the preservation of the world." How could we have been so wrong, according to Peter Ward?

Peter Ward, a paleontologist at the University of Washington who specializes in mass extinctions, attacks no prevailing theory as strongly as he does the Gaia Hypothesis: the idea introduced in the 1970s that describes every living thing on Earth as part of one gigantic self-regulating organism. Indeed, in opposition to this hypothesis, Ward named his own hypothesis the Medea Hypothesis (for the Greek sorceress who killed her own children).

First off, what are some of Ward's reasons for this new conception of nature's role on Earth? In his view, the earth's history makes clear that, left to run its course, life is poisonous. He claims that long before humans came onto the scene, primitive life forms were trashing the planet. For example, around 3.7 billion years ago, they created a planet-girdling methane smog that threatened to extinguish every living thing; a little over a billion years later they pumped the atmosphere full of poison gas. (That gas, ironically, was oxygen, which later life forms adapted to use as fuel.)

Ward explains how he sees the story of life on earth as a long series of suicide attempts. Four of the five major mass extinctions since the rise of animals were caused by bacteria, and twice, he argues, the planet was transformed into a nearly total ball of ice thanks to the voracious appetites of plants. In other words, "it's not just human beings, with our chemical spills, nuclear arsenals, and tailpipe emissions, who are a menace. The main threat to life is life itself."

A main point Ward derives from his hypothesis is that the planet would not be better off without humans, rather that life would destroy itself anyways. He believes that environmentalism needs to restructure its underlying philosophy and he believes that humans are needed to save the planet from destruction. This is the start of quite a tangent so I won't go down that path, however, this hypothesis does have significant meaning for astrobiology as well.

This is incredibly important to the search for life on other planets. If life is indeed so toxic, life may be much less likely to exist than we have previously thought. Perhaps, it was not the origin of life that was so lucky on Earth, but rather the perpetuation of that life.

To further relate the Medea Hypothesis to climate change and astrobiology, Ward claims that the evidence of past extinctions - written in fossils and in the chemical makeup of deeply buried rock sediments - as well as the workings of today's oceans, atmosphere, and myriad food chains, shows that Earth tends not toward harmony but towards extremes. Stability appears to occur simply as respites between catastrophic boom-and-bust cycles. He attributes one of the largest extinctions in history to the out-of-control proliferation of plankton feeding on upwellings of nutrients from the ocean floor. Rather than being brought back to equilibrium, the tiny organisms reproduced until they choked off much of the life in the upper ocean. Exhausting their newfound food supply, they died en masse, and decaying by the trillions used up all the oxygen in the water, killing off everything else.

As for the earth's temperature control, more often than not positive feedback loops appear to be common--with warming triggering more warming, and cooling more cooling. In a process we're seeing today, as the planetary temperature rises, warming increases the rate at which soil releases greenhouse gases - not only carbon dioxide, but methane and nitrous oxide. It leads to more forest growth in places that formerly were barren tundra, even as more carbon dioxide in the air makes plants hardier and better able to grow in areas once given over to desert. More plants in more places means a darker earth, and therefore a more heat-absorbent and warmer one. It's an escalating feedback loop that becomes even more powerful as the planet's white, ice-covered poles give way to darker open water.

What does this mean for the search for planets with stable atmopsheres and temperature gradients? Ward's theory does not suggest that we should look for life on planets without stable atmospheres; it does suggest, however, that the origin of life may be relatively common, but that the existence of life may not be. Changes in climate may be driven by life on longer time scales than we are able to observe on other planets. Rather, we still need to look for relative stability to find life, because Ward supposes that life causes instability and thus ultimately condemns itself for extinction. Thus, though climate instability may be an consequence of life, it is not a criteria associated with habitability--it is quite the opposite.

It is also very important to realize that Ward's hypothesis, though incredibly provocative, is not as straight forward as he makes it seem. Though he emphasizes the occurance of positive feedback loops, there are plenty examples of negative feedback loops like those exemplified in the Gaia hypothesis. Indeed, these may still be more common; it may just be that since they are not as prone to catastrophism they are less obvious to observe.

READ THIS: A Debate about the searching for different life forms

Read this article if you have time, it is interesting to think about and tie together some of the things we have been discussing:

"...Let's say we go to Titan, and we find life that has had a separate creation, with no communication with Earth-like life ever. That's not just a separate phylum, kingdom, domain, or dominion, it's a separate tree. As taxonomists, we have to be ready to build a bigger house. Because it's coming -- either we'll find it or we're going to build it, but there will be life as we don't know it in a diversity of form on this planet in this next century. It's being built in many places right now." (Peter Ward)

Climate change and our understanding of habitability.

I was just checking out the astrobiology magazine website, and noticed that there is an entire blog dedicated t o Climate Change and Global Warming:

I initially thought this surprising because it didn't strike me as obvious that astrobiology and climate change would be related, but upon reading more, I learned that the process of watching climate change on Earth and noticing the effects, helps us to understand how climate and habitability relate. Understanding Earth's own climate is necessary to understanding what makes a planet habitable. Climate change makes us appreciate how influential climate is on habitability which is especially vital for the field of astrobiology because of the need to determine the importance of various habitability factors.

It is true that the knowledge gleaned from the study of climate change is most applicable to 'our' life form. Discovering the tipping points that govern whether a temperature is habitable for certain species is incredibly important for determining the habitability of our own planet for our life form, but how can this be extrapolated to other life forms? For one thing, all life will be dependent on climate and it is essentially impossible to imagine life will be adaptable to highly variable climates. Thus a stable climate over time may be crucial. The effects of climate change will be interesting to assess in our life time because of the short time frame in which climate is changing.

One notable thing that climate change has taught us is an appreciation for the interconnectedness of Earth. Timothy Herbert, of Brown University (!) recently wrote a paper on this and highlighted this interconnectedness: “What surprised us is that the tropics seemed to shiver when the polar latitudes get cold, and they warm up when the ice ages pass.” He suggests that the link between the oceans has to do with CO2 levels. The polar oceans absorb a lot of it and can draw down atmospheric levels by as much as 30 percent. This impacts the tropical oceans, which have a powerful influence over global climate conditions. Warm tropical oceans produce water vapor, which drives global rainfall patterns and is a potent greenhouse gas warmer.

Climate change also enhances the importance of relatively stable climate niches for the evolution of life. Such niches like deep sea vents, glaciers, and sub-surface environments are crucially removed from the fluctuating climate. This may be crucial for the ability of life to possibily originate in these niches, and to perhaps remain most primitive because of low levels of selection. Understanding where these niches are located and what makes them stable for life to evolve relatively un-disturbed may shed light on what features to look for in exoplanets to find life.

What are some other ways that climate change can help inform astrobiologists?

Tuesday, October 26, 2010

Nanobacteria: A Different Type of Life???

Nanobacteria (singular nanobacterium) is the name of a proposed class of living organisms, specifically cell-walled microorganisms with a size much smaller than the generally accepted lower limit size for life (about 200 nanometres for bacteria). The status of nanobacteria is controversial, with some researchers suggesting they are a new class of living organisms capable of incorporating radiolabeled uridine and others attributing to them a simpler, abiotic nature.

The term 'calcifying nanoparticles' (CNPs) has also been used as a conservative name regarding their possible status as a life form. The most recent research tends to agree that these structures exist, and probably replicate in some way. Their status as living entities is still hotly debated, though some researchers now claim that the case that they are nonliving crystalline particles is conclusively proven.

They were first described in 1981 by Torella and Morita and were discovered because of their implication in the formation of both kidney stones and arterial plaque. Early in 1989, geologist Robert L. Folk found what he later identified as nannobacteria (written with double "n"), that is, nanoparticles isolated from geological specimen in travertine from hot springs of Viterbo, Italy. He proposed that nanobacteria are the principal agents of precipitation of all minerals and crystals on Earth formed in liquid water, that they also cause all oxidation of metals, and that they are abundant in many biological specimens. In 1996, NASA scientist David McKay published a study suggesting the existence of nanofossils — fossils of Martian nanobacteria — in ALH84001, a meteorite originating from Mars and found in Antarctica.

According to the Finnish researcher Olavi Kajander and Turkish researcher Neva Ciftcioglu, the particles self-replicated in microbiological culture, and the researchers further reported having identified DNA in these structures by staining.

A paper published in 2000 led by John Cisar further tested these ideas and claimed that what had previously been described as "self-replication" was a form of crystalline growth. The only DNA detected in his specimens was identified as coming from the bacteria Phyllobacterium mysinacearum, which is a common contaminant in PCR reactions. An article in PLoS in 2008 focused on the comprehensive characterization of nanobacteria. The authors say that their results rule out the existence of nanobacteria as living entities, instead revealing that they are a unique self-propagating entity and that they are self-propagating mineral-fetuin complexes. Another 2008 PNAS article reported that blood nanobacteria are not living organisms and stated that "CaCO3 precipitates prepared in vitro are remarkably similar to purported nanobacteria in terms of their uniformly sized, membrane-delineated vesicular shapes, with cellular division-like formations and aggregations in the form of colonies."

The growth of such "biomorphic" inorganic precipitates was studied in detail in a 2009 Science paper, which showed that unusual crystal growth mechanisms can produce witherite precipitates from barium chloride and silica solutions that closely resemble primitive organisms. The authors commented on the close resemblance of these crystals to putative nanobacteria, stating that their results showed that evidence for life cannot rest on morphology alone.

This once again relates back to the definition of life and how we determine if something is alive if we are dealing with an alien life form. Another example is that of viruses, in which some scientists, like the paleontologist Peter Ward, classify as living. He says that our current tree of life leaves no room for viruses which he suggests are living things, and will likely be an entirely useless concept for classfying alien life. Indeed, some evolutionary biologists today believe the current phylogenetic tree to be incapable of classifying life in an accurate way because it is a human construct that is organized not necessarily according to classifications defined by nature itself, but by ease of convenience for human understanding. Thus the search for alien life needs a restructuring of how we think about life itself.

Monday, October 25, 2010

Exoplanet Atmospheric Studies

Look at the Exoplanet timeline:

To astronomers, a "potentially habitable" planet is one that could sustain life. Habitability depends on many factors, but having liquid water and an atmosphere are among the most important. Thus determining the characteristics of the atmospheres of exoplanets and the possible implications of these characteristics on habitability are key areas of research in astrobiology.
A history of the detection of exoplanet atmospheres is brief because the technology that it takes to do this work has been recently invented and applied. Visible-light telescopes can detect exoplanets and determine certain characteristics, such as their sizes and orbits, but not much can be inferred about their atmospheres or what they look like. Therefore, exoplanet atmospheric studies was largely pioneered in 2005 by Spitzer, when it became the first telescope to directly detect photons from an exoplanet by examining their infrared light and using spectrometry to detect the molecules present in the exoplanet atmospheres by their unique ‘spectral fingerprint.’ Since then, Spitzer, along with NASA's Hubble Space Telescope, has studied the atmospheres of several hot Jupiters (very hot, giant gas planets that orbit very closely to their star), finding water, methane, carbon dioxide and carbon monoxide. The first near-infrared emission spectrum obtained for an exoplanet was that of HD 189733b.
The Hubble telescope was conceived primarily for observations of the distant universe, yet it is also important for exoplanet atmospheric studies because we can use Hubble's near infrared camera and multi-object spectrometer to study infrared light emitted from planets. Gases in the planet's atmosphere absorb certain wavelengths of light from the planet's hot glowing interior and the molecules leave a unique spectral fingerprint on the radiation from the planet that reaches Earth. This observation is best done on planets with orbits tilted edge-on to Earth because of the usefulness of eclipses. The eclipses allow an opportunity to subtract the light of the star alone, when the planet is blocked, from that of the star and planet together prior to eclipse. That isolates the emission of the planet and makes possible a chemical analysis of its atmosphere. Searching for molecules in exoplanet atmospheres is important because molecules present are expected to: (1) influence strongly the balance of atmospheric radiation, (2) trace dynamical and chemical processes and (3) indicate the presence of disequilibrium effects. Thus searching for molecules is a high priority because they have to potential to
reveal atmospheric conditions and chemistry which will help us infer the habitability of the planet.

05.09.07, “NASA Finds Extremely Hot Planet, Makes First Exoplanet Weather Map.”
On this date, researchers using NASA's Spitzer Space Telescope learned what the weather is like on two distant, exotic worlds—giant gas planets: HD 189733b and HD 149026b. They mapped the weather patterns on HD 189733b by using the Spitzer telescope to measure the infrared light coming from the planet as it circled around its star and from this, they created a map of the temperature of the entire surface of the planet based from a quarter of a million data points. They found that the planet is likely whipped by roaring winds and that temperatures are fairly even considering the planet is tidally locked: 650 degrees C (1,200 F) on the dark side to 930 degrees C (1,700 F) on the sunlit side. It is assumed that many hot Jupiters are tidally locked so it is interesting that the planet's overall temperature variation is mild and at the time, scientists believed winds must be spreading the heat from its permanently sunlit side around to its dark side. Such winds occur at up to 9600 kph (6,000 mph); in comparison, jet streams on Earth travel at 322 kph(200 mph). This is interesting because now we are beginning to see how these hot Jupiters deal with the incredible amount of energy blasted at them—20,000 times more energy per second than Jupiter. Also of interest, HD 189733b has a warm spot 30 degrees east of ‘high noon.’ Assuming the planet is tidally locked to its parent star, the researchers at the time suggested that this implies that fierce winds are blowing eastward.
The main interesting finding regarding HD 149026b was that it was the hottest planet found to date at a scorching 2,038 degrees C (3,700 F), which is even hotter than some low-mass stars. This suggests that the heat is not being spread around in contrast to HD 189733b. HD 149026b is the smallest and densest known transiting planet, with a size similar to Saturn's and a core suspected to be 70 to 90 times the mass of Earth. It also probably reflects almost no starlight, instead absorbing all of the heat which means HD 149026b might be the blackest planet known, in addition to the hottest.

The near-infrared transmission spectrum of the planet HD 189733b, described above, shows the presence of methane and water vapor. This is the first time that water was found to exist in the atmosphere of an exoplanet. The discovery of methane was interesting because, on thermochemical grounds, carbon monoxide is expected to be abundant in the upper atmosphere of hot-Jupiter planets like HD 189733b. The detection of methane rather than carbon monoxide in such a hot planet could signal the presence of a horizontal chemical gradient away from the permanent dayside, or it may imply an ill-understood photochemical mechanism that leads to an enhancement of methane. The Hubble Space Telescope also discovered carbon dioxide in the atmosphere. This marked an important step toward finding chemical biotracers of extraterrestrial life even though in this instance, HD 189733b is way too hot for life to be feasible. But because organic compounds can be a by-product of life processes, their detection on an Earth-like planet someday may provide the first evidence of life beyond our planet.
In contrast to the larger than expected amount of methane found on HD 189733b, GJ 436b has very little methane. This is peculiar because models of planetary atmospheres indicate that any world with the common mix of hydrogen, carbon and oxygen, and a temperature up to 1,000 K (1,340 degrees F)—cooler than HD 189733b—should have a large amount of methane and a small amount of carbon monoxide. However, at about 800 Kelvin (or 980 F), GJ 436b does not. This again demonstrates the lack of scientific understanding of atmospheres of exoplanets and also the diversity of exoplanets that exist.

There have been various models created to better understand the possible atmospheric characteristics of different exoplanets. One type of planet that has been modeled is that of planets occurring in the habitable zone of red dwarfs. Planets within the habitable zones of M dwarfs are likely to be synchronous rotators (tidally locked with a fixed light and dark side). Scientists have made three-dimensional simulations of the atmospheres of such planets and determine that near the ground, a thermally direct longitudinal cell exists, transporting heat from the dayside to the nightside. The circulation is three-dimensional, with low-level winds returning mass to the dayside across the polar regions and higher up, the zonally averaged winds display a pattern of strong super-rotation due to these planets' finite (albeit small) rotation rate. The main claim is that planets orbiting M stars can support atmospheres over a large range of conditions and, despite constraints such as stellar activity, are very likely to be habitable.

Simulations of atmospheres of Earth-like aquaplanets that are tidally locked to their star have also been created and described. These models illustrate how planetary rotation and insolation distribution shape climate. In these models, the winds are ‘approximately isotropic and divergent at leading order in the slowly rotating atmosphere but are predominantly zonal and rotational in the rapidly rotating atmosphere.’ Furthermore, ‘free-atmospheric horizontal temperature variations in the slowly rotating atmosphere are generally weaker than in the rapidly rotating atmosphere.’ A curious result is that the surface temperature on the night side of the planets does not fall below ∼240 K in either the rapidly or slowly rotating atmosphere which means that heat transport from the day side to the night side of the planets efficiently reduces temperature contrasts in either case. This creates a relatively mild temperature difference across even a tidally locked aquaplanet. Also described is the distribution of winds, temperature, and precipitation, with rotational waves and eddies of primary influence in the rapidly rotating atmosphere and simpler divergent circulations influential in the slowly rotating atmosphere. Both the slowly and rapidly rotating atmospheres exhibit equatorial superrotation which varies non-monotonically with rotation rate, however, the surface temperature contrast between the day side and the night side does not vary strongly with changes in rotation rate.

In the near future, astronomers look forward to using the James Webb Space Telescope (to be hopefully completed around 2014) to look spectroscopically for biomarkers on a terrestrial planet near the size of Earth. The Webb telescope should be able to make much more sensitive measurements of these primary and secondary eclipse events than the technology currently available which will hopefully bring us a much greater ability to detect and characterize exoplanet atmospheres.

The importance of tides and tidal heating for habitability.

The importance of the moon to the origin of life on Earth is a debated topic. It is also very relevent to the search for extraterrestrial life because theories that suggest that the moon was crucial for life’s origination on Earth, may imply that researchers should look to exoplanets with their own moons in their search for extraterrestrial life. The importance of the moon largely revolves around the importance of tides for the development of life. However, much more generally, not just the tidal effects of moons, but the mechanism of tidal heating in various types of exoplanets should be scrutinized in order to better understand the effect this has on the habitability of planets. Below I will discuss one theory about the importance of tides for the emergence of life on Earth, and will also discuss some important things to think about in terms of the effect of tidal heating on habitability.

The effect of our Moon’s tides

Richard Lathe, a scientist at Pieta Research in the UK, has recently discussed his theory about the cruciality of tides to the origin of life on Earth. He claims that without tides, life could not have evolved.

The story begins approximately 4.5 billion years ago when the moon is believed to have form. At about 4 billion years ago, when life is believed to have evolved, the Moon orbited much closer to us than it does now; in addition, the Earth itself rotated much faster. The combined result was that tidal cycles occurred every two to six hours, with tides extending several hundred kilometres inland. Due to the much greater tidal strength, coastal areas saw dramatic cyclical changes in salinity. Lathe believes that these frequent, cyclical changes in salinity enabled the formation and evolution of self-replicating molecules.

One theory for the origin of life suggests that DNA or RNA formed when small precursor molecules in the primordial ‘soup’ polymerized into long strands which then served as templates, creating double-stranded polymers similar to DNA. In order for this to happen, an external force was needed to dissociate the two strands. Lathe uses PCR (polymerase chain reactions)—a commonly used experiemtnal method of amplifying DNA—to explain this need for a constantly changing environment. In PCR, DNA is cycled between two temperatures in the presence of appropriate enzymes--at the lower temperature of about 50 °C, single DNA strands act as templates for synthesizing complementary strands and at the higher temperature of about 100 °C, the double strands break apart, doubling the number of molecules. When the temperature is lowered, the synthesis begins again.

In the case of tides, when they rolled in, the salt concentration was very low and this would cause DNA to dissociate because of the repulsion of the charged phosphate groups. However, when the tides rolled out, the salt concentration would dramatically increase, which would encourage the strands to associate. The tides could thus lead to the repeated association and dissociation of double-stranded molecules similar to DNA. The tidal force is absolutely important, because it provides the energy for association and dissociation of polymers.

There are many problems to this theory; one major one being that it assumes a very specific origin of life. This origin would have had to occur in the ocean which is a problem for those who believe that life may have more efficiently evolved on surfaces, around hydrothermal vents, or in cell membranes (which can not stabilize in the high salinity of oceans). It also presumes that DNA and RNA were the first replicating molecules, however, some believe that much simpler "genetic" material formed first, from the crystallisation of clay minerals.

Despite these limitations, the importance of a constantly changing environment needs to be highlighted. This is probably a crucial factor for life to evolve. This is also something that needs to be taken into consideration as we think about the necessary compontents of a habitable planet and where to most efficiently search for life.

Tidal Heating of Terrestrial Extra-Solar Planets and the Implications for Habitability

Tidal heating may affect a planet’s habitability in various ways including:
(a) It may be great enough to drive plate tectonics for a length of time that depends sensitively on the host star and planet’s masses and the planet's initial orbit,
(b) It may be so great as to make the planet uninhabitably volcanic (Io),
(c) It may drive outgassing from the planet’s interior, continually replenishing the planet’s atmosphere against loss, and
(d) It may also be sufficient to produce a habitable subsurface ocean on an icy planet, or to mitigate life- challenging “snow-ball” conditions on a terrestrial planet (Europa).

Tidal heating may be critical for the creation and maintenance of the atmospheres of terrestrial planets. As heat induces internal convection within the mantles of these planets, volatiles trapped in the mantle may be outgassed, feeding the atmosphere.
In the habitable zone of M stars, atmospheres may be depleted by vigorous stellar activity or impact erosion and in this case, tides may be crucial to drive adequate outgassing to replenish the atmosphere, enabling the planet to remain habitable.
In other cases, planets may be habitable even without an atmosphere. Tidal heating of an icy planet may generate a habitable subsurface ocean, analogous to Jupiter’s moon Europa. For these planets, an atmosphere may not be necessary for habitability, if, as proposed for Europa, life could exist below the icy surface. As a source of caution, tidal heating may be an obstacle to life when volcanic activity becomes too intense, such as the case of Io. Indeed, tidal heating of the innermost planet in the recently discovered system HD 40307 may exceed Io’s, suggesting that, if the planet is rocky, it may be volcanically active. This would clearly not be a habitable place.

For the Earth, tidal heating is negligible, and adequate heating is provided by decay of radionuclides. Plate tectonics help stabilize a planet’s atmosphere and surface temperature many millions of years. Because a stable surface temperature is probably a prerequisite for life, plate tectonics may be required for a planet to be habitable. However, if in situ formation of terrestrial planets is common, many terrestrial planets we find may have too little radiogenic heating to drive long-lived plate tectonics. The implication of the existence of tidal heating is that even without radiogenic heating, tides may provide adequate internal heating and hence may be critical in determining planetary habitability.

Friday, October 22, 2010

Going to the Beach at Sunset?

Astronomers have observed a distant planet (upsilon Andromedae b), with a hot spot in an unexpected place. This gas-giant planet, in the hot Jupiter category, orbits its star with one face perpetually facing it. One would expect that this face would be the hottest part of the planet, but to the observers surprise, the hot spot was actually offset by a whopping 80 degrees, so that it was located on the side of the planet instead of directly under the star's glare.

The planet was observed from NASA's Spitzer Space Telescope, which was the first telescope to directly detect photons from an exoplanet (2005). Upsilon Andromedae b does not cross in front of its host star, so it was detected by measuring the total combined light from the star and the planet, as the planet orbited the star (with a period of 4.6 days). Spitzer could not see the planet directly, so it detected variations in the total infrared light from the system that occur when the hot side of a planet comes into Earth's field of view. The hottest part of the planet gives off the most infrared light, and this occurred when the planet was not directly towards or away from us, but rather when the hot Jupiter had its side facing the Earth. This would be equivalent to the Earth being warmest during sunset, as opposed to when we are directly under the sun!

Previous observations have shown slight variations in the hot spots of these so-called hot Jupiters, which were thought to be due to fierce winds pushing around hot material, but this observation may throw this theory into question. The findings show that astronomers understand less about the atmospheric energetics than they previously thought, and this is opening the floor for some new theories. One speculation involves star-planet magnetic interactions, but the several emerging theories will be tested against a growing pool of examined hot Jupiters.

Studying how these distant solar systems form and evolve can provide us with crucial information that will help astrobiologists determine where to search for habitable worlds.

More on Titan

So, we've been getting a ton of information on Titan--for good reason--since it gives strong evidence of Earth's burgeoning atmosphere in the throes of planetary formation several billion years ago, in the Hadean eon, named for how ruthlessly chaotic it was.

Titan: not so much.

A few facts we know right off the bat about Titan we've learned, tying it closer to our own planet:

Largest moon of Saturn.
It is the only moon we know of with a fully developed atmosphere.
When it comes to atmospheric pressure, Titan is the Earth's closest relative, just one and a half times thicker (1).
It was the site of the first ever, up close picture of extra-terrestrial liquid (whaat?)
It's still really cold (-178 celsius?!) (2)

So let's get to the heart of astronomy: what could it be?

Already, many astronomers are itching to find out how similar the atmosphere is to Earth and what it can tell us about our early Earth's atmosphere.

We've figured out that its atmosphere is "controlled by five major processes: CH4 photolysis and photosensitized dissociation, H-to-H2 conversion and hydrogen escape, higher hydrocarbon synthesis, nitrogen and hydrocarbon coupling, and oxygen and hydrocarbon coupling" (3). We've learned about photolysis/photosensitized dissociation--the process by which compounds are broken up by photons, as well as the basics of escape due to thin atmospheric conditions and low-gravity--and the combinations here contribute to its familiar atmospheric composition.

However, there's also something to look for in Titan's haze. Many point to it as the lifeblood of the planet--a haze that could have very easily influenced our own planet's life-origin. In fact, scientists have begun working on trying to imitate the haze of Titan through analogous lab-produced aerosol (4). They explain that when sunlight hits a methane/nitrogen atmosphere, this type of aerosol is produced--so this could be the start of an experiment much like the aforementioned Miller-Urey experiment.

With all of the similarities seen, including Galia's recent post mentioning the possible similarities between a methane weather cycle and our own Earth's water cycle as well as last week's discussions of Mars, it seems that we could afford to spend more money looking at Mars and Titan to understand our own origins.

Monday, October 18, 2010

Sailing on seas of methane?

As of November of last year, NASA researchers have started planning a 2015 mission to go sailing on a lake… composed entirely of methane and ethane… over 1300 million kilometers from our planet. This ambitious adventure involves the use of a raindrop-flecked camera placed on a nuclear-powered capsule directed to land on Ligeia Mare – one of the largest lakes on Titan, Saturn’s largest moon.

Scientists have particular interest in Titan as it is the only natural satellite to contain a dense atmosphere, as well as the only celestial object other than Earth for which clear evidence of stable bodies of surface liquid have been found. Titan itself is primarily composed of water ice and rocky material. Prior to 2005, however, the physical characteristics of Titan were largely unknown due to its dense, opaque atmosphere that prevented man-made spacecrafts from gaining visual access to its surface. However, with the arrival of the Cassini-Huygens mission to Titan, scientists discovered the abundant liquid, hydrocarbon lakes in the satellite’s polar regions. Additionally, the spacecraft revealed a mountainous terrain, including several possible cryovolcanoes on the planet’s surface.

Since, the Cassini-Huygens mission arrived in Saturn’s ring system, a much greater understanding of Titan has been gained in the past five years. We now know that the atmosphere of Titan is largely made up of nitrogen and minor components of methane and ethane gas. It’s these hydrocarbon gases that lead to the formation of the orangey clouding and smog that prevented visual access to Titan in years past. Titan’s climate includes wind and occasional rain which contribute to the shockingly similar surface features to Earth, such as: sand dunes and rivers, lakes, and seas of liquid methane ethane, as well as shorelines dominated by seasonal weather patterns. With the existence of liquids and robust nitrogen atmosphere, Titan is considered to be a model of early Earth but at a much lower temperature. It has been cited as one of four bodies in our galaxy that could potentially host microbial extraterrestrial life, or at least, as a prebiotic environment rich in complex organic chemistry.

Thus, for all of these reasons, NASA scientists want to know more. This nuclear-powered “boat” that they are proposing to send to Titan would float about on Ligeia Mare while radioing photos and other data to Earth for a period of about six months. The scientists picked Ligeia Mare in particular as it is over 300 miles wide, which they believe is a big enough target for them to accurately direct their probe straight into the methane sea. The mission is called TIME for Titan Mare Explorer. The probe itself is to be built by the same scientists that created the Beagle 2, the British craft that crashed on Mars on Christmas Day of 2003, as well as the US company, Proxemy Research of Maryland. This British group is being led by Professor John Zarnecki, head of the Centre for Earth, Planetary Space and Astronomical Research at the Open University in Milton Keynes. In regard to the TIME mission he says:

We want to discover more about Titan's methane weather cycle - like the water cycle on Earth… We want to determine the depth of the lake and if it is murky or clear and what is floating in it, plus look at the shorelines. We'd also want to look for organic materials. Understanding Titan better might also tell us more about whether it is possible for life to develop there."

As I learned from the research I did for my presentation last week, Titan is absolutely swimming with organic chemicals necessary for life, so if the TIME mission could just find some sort of energy source in these methane lakes, the idea of extraterrestrial life could suddenly be much more feasible.

Sunday, October 17, 2010

The role of carbohydrate polymers in chemical evolution

This blog entry is on the same topic as the presentation that I gave in class a couple weeks ago concerning some of the possible chemistry that was involved in the beginning of life on Earth. As emphasized by the other presentations that week, it is fairly well established that life is sustained and perpetuated through the DNA/protein world that we know to exist today. Additionally, we now understand some theories regarding the RNA world that pre-dated this DNA/protein world as well.

I presented a literature review that contended that a carbohydrate polymer world most likely existed before modulating into the RNA world, which eventually then gave way to the DNA world we know today. Personally, I really enjoyed reading about the chemistry of the origin of life. Although I don’t know nearly enough about chemistry to have fully understood all that this article was saying, just considering how the complex array of chemical life seen today came to existence from simple building blocks amazes me. We had all heard of the Miller-Urey experiment which attempted to recreated those early Earth conditions; Methane, ammonia, and hydrogen were circulated over boiling water, electrodes were introduced to mimic lightning, and then after a certain period of time, the composition of the mixture was analyzed and a number of amino acids were detected. But this article questions: did that really recreate the conditions of early Earth?

This paper includes some interesting conditions that hadn’t really occurred to me before. It’s pretty widely accepted that the reducing conditions of early Earth didn’t include significant amounts of oxygen. No oxygen means no ozone. No ozone means no protection from high energy UV light. And UV light perhaps provided a significant amount of energy that was needed to drive these early reactions.

Also, the paper presents the idea that as more and more complex molecules were created, the concentration still remained considerably small, even if they were all dissolved in the early oceans. Thus, for these molecules to randomly collide to form polymers would be highly unlikely. The authors of this paper thus contended that maybe these early molecules would adhere to mineral-rich clay particles in water. The clay would enable the reactants to congregate on a common surface and the minerals (aluminum, iron, magnesium, calcium, sodium, and potassium to name a few) would serve as catalysts for these early reactions. Eventually more and more complex molecules would be synthesized, and the authors hypothesized that saccharides would have been among the first complex molecules to be formed. Furthermore, the authors presented the claim that since only the simplest molecules were present on early Earth, it was likely that formaldehyde was one of them present in non-trivial amounts. They speculated that maybe formaldehyde self-polymerizes on these clay surfaces to form small saccharides, which eventually undergo aldol condensation to form more advanced hexoses and pentoses.

With this theory about the origin of chemical life, it isn’t at all difficult to then see how these carbohydrate polymers gave way to an RNA-based world. The authors suspect that carbohydrates polymerized along with abundant phosphates to form longer chain polymers. Several polymers are capable of forming with this method, one of them resembling RNA without the base pairs. So essentially, just a series of ribofuranose units linked by phosphate groups (structure sown below). The highly oxidized purine and pyrimidine bases probably only came about a little later, and when they did arrive, only a simple substitution was need to create the first strands of RNA (also shown below).

With the theories presented in this review, the RNA world hypothesis gains some much-needed support after past failures to experimentally recreate the formation of RNA. Certain bonds are simply unable to bond to sugars to form a complete RNA molecule under early Earth conditions. Now, all that is left to do is to show how these nucleotides produced life in a primitive RNA world…

Can Silicon serve as a replacement for Carbon based life?

So, unfortunately there is really no way I can relate this blog entry to Avatar. From what I remember from the movie, there was no mention of the chemical foundations of Pandora. The trees and plants did form these complex electrochemical connections that effectively acted as neurons, creating some sort of a planet-wide brain that had achieved sentience… which was incredibly awesome, but not really elaborated upon on a chemical basis.

Anyway, this topic of Silicon, as opposed to carbon-based life has major astrobiological implications. All known life on earth is built upon the sixth element, carbon, and carbon-based compounds. Most life forms contain a large majority of the elements hydrogen and oxygen (from water) as well. But the chemical processes that give something the status of “living” require carbon based molecular structures. The human body in particular uses some of carbon’s most unique chemical properties to function, mainly involving the storage of energy and creation of highly complex molecules and structures.

However, as illustrated with the creation of the creature called “Horta” in episode 26 of the original Star Trek series, its been speculated that another element (such as Silicon) could potentially replace carbon to form a very different biological basis of life. In fact, the first count of this speculation came from the German astrophysicist, Julius Scheiner, in 1891 when he suggested the suitability of silicon as a basis for life. Several years later the British chemist, James Reynolds, actually based his opening address to the British Association for the Advancement of Science on the fact that silicon has heat-stabilizing properties that could allow life to exist at extremely high temperatures (as we see with thermophiles on Earth).

Okay, so yeah people are and have been talking about silicon-based life for years, but when it comes down to the biochemistry it’s hard to justify as a potential reality. At first glance it is promising though. Silicon is the second-most common element in the Earth’s crust (far more abundant than carbon), though like carbon, is a “p-block” element of group IV of the periodic table suggesting significant similarities in their basic chemical qualities. For example, just as carbon commonly combines with four hydrogen atoms to form methane (CH4), silicon yields silane (SiH4), and in addition to these tendencies, both elements form long chains (polymers) in which they alternate with oxygen.

However, a significant difference in size and orbital energy between carbon and silicon may be the determining factor in the existence of silicon-based life. A silicon atom has eight more electrons than a carbon atom does, and its’ homogenous bond length is considerably greater than carbon’s: 235 pm in comparison to carbon’s 77 pm. Silicon’s larger electron cloud subjects its’ bonds to a greater magnitude of shielding, thus a silicon bond is generally weaker than a carbon bond. This difference alone is enough to explain why carbon makes life and silicon makes rocks, at least, in standard terrestrial conditions. Additionally, for these reasons, silicon is known to be largely incapable of forming as diverse a range of molecules as carbon under natural conditions, in addition to silicon’s strong affinity for oxygen molecules.

Silicon’s affinity for oxygen would be problematic for life formation, because when carbon is oxidized during the respiratory process of a terrestrial organism, it becomes gaseous carbon dioxide - a waste material that is easy for a creature to remove from its body. The oxidation of silicon, however, yields a solid because immediately upon formation, silicon dioxide organizes itself into a lattice in which each silicon atom is surrounded by four oxygens. Disposing of a substance such as this would pose a major respiratory challenge.

Additionally, in carbon-based biota, the basic energy storage compounds are carbohydrates in which the carbon atoms are linked by single bonds into a chain. A carbohydrate is oxidized to release energy (and the waste products water and carbon dioxide) in a series of controlled steps using enzymes. These enzymes are large, complex molecules (usually proteins), which catalyze specific reactions because of their shape and "handedness." A feature of carbon chemistry is that many of its compounds can take right and left forms, and it is this handedness (also called chirality) that gives enzymes their ability to recognize and regulate a huge variety of processes in the body. Silicon's failure to give rise to many compounds that display handedness makes it hard to see how it could serve as the basis for the many interconnected chains of reactions needed to support life.

So, ultimately it seems as though it’s pretty unlikely that silicon-based life could exist in a terrestrial setting in an Earth-defined biological sense. However, that hasn’t held back the imaginations of science fiction writers. As mentioned above, the Horta, a silicon-based life formed appearing in Star Trek existed on the planet, Janus IV. Apparently every 50,000 years, all the Horta die except for one individual who survives to look after the eggs of the next generation. Personally, the Horta seems to be the most unlikely form of a functional biological organism in terms of what we define “life” as on Earth. But see for yourself:

Friday, October 8, 2010

Star Clusters are Rough Neighborhoods

John Debes and Brian Jackson of NASA's Goddard Space Flight Center have some news for planet hunters: stay away from clusters. In their recent publication in Astrophysical Journal, they claim that most of the easily detectable "hot Jupiters" that astronomers search for in star clusters were likely destroyed by their stars.

When the search for planets in star-packed globular clusters began, expectations were high. One cluster, 47 Tucanae, was expected to yield at least a dozen planets from around its 34,000 candidate stars, but the search was unsuccessful. More than 450 exoplanets have been found, but most of them have been detected around single stars.

Why are planets not being found in these neighborhoods? Jackson explains that "there are lots of stars to beat up on them and not much for them to eat." The high density of stars increases the chances that a nearby star will affect a planets orbit and potentially kick it out of its solar system. Additionally, surveys of globular clusters have shown that they are rather poor in metals, which are essential for making planets (this is known as low metallicity). In essence, planets in these neighborhoods get their lunch money stolen and get kicked out of town, which is why the search for planets in these areas have come up short.

The research also suggests that "hot Jupiters" are more likely to be found in younger star clusters than older ones. This is because in addition to the problems listed above, the large planets that are very close to the sun could be destroyed by their cramped orbits. Since the planets are at least 3 times closer to their host stars than Mercury is to our sun, the gravitational pull of the planet on the star can create a tide on the star. This bulge on the star is always just a little behind the planet, and its gravity essentially tugs back on the planet, reducing the energy of its orbit. As this energy drops, the planet becomes closer to the star, and this bulge gets even bigger. Eventually, the planet will crash into the star or it will be torn apart by the star's gravity, according to the researcher's model of tidal decay.

Debes and Jackson modeled this effect on a hypothetical 47 Tucanae, and it predicted that most of the planets would have been destroyed, regardless of metallicity. This would explain the unsuccessful search for exoplanets, especially since the model predicts that more than 96% of the hot Jupiters would be destroyed by the time a cluster was as old as 47 Tucanae (11 billion years). The researchers look forward to the results of the Kepler mission, which is searching for hot Jupiters as well as smaller planets, to test their model. If their model is right, finding planets could be getting harder since the large and obvious ones may be long gone.

Taking this all in, star clusters are tough places for planets to hang out. Perhaps the search for exoplanets should focus on younger, higher metallicity, and less dense clusters that haven't bullied their planets just yet.

Monday, October 4, 2010

Why did life originate?

This entry is based on an article on by Lisa Zurg in 2008 called “Why Life Originated (and why it continues).” Link:

There are numerous researchers who devote their lives to determining how life evolved in the attempt to discover both the origin of life on Earth but also how life could evolve elsewhere. Much of the public has heard about the primordial soup theory and may have heard of the famous Miller and Urey experiment whereby amino acids where spontaneously created from elemental materials and energy. However, how often do we stop to think not about how life was created but why? Why did life originate and why has it continued to evolve?

We know that based on the theory of Darwinian evolution, we evolve in relation to our ecosystems; that organisms are naturally selected on through the process of reproduction and that over time, those traits that are most advantageous in a population will be increasingly passed down to future generations. We know that evolution is random and chaotic in the sense that there is no defining direction that evolution is heading in. Even if we evolve to become better equipped to live in our habitat, that habitat itself not a static entity.

But, according to Arto Annila of the University of Helsinki and Erkki Annila of the Finnish Forest Research Institute, this is not the most basic understanding of evolution and of life. The guiding principle of the universe, and thus of life as well, is the tendency to reduce energy differences. The process of natural selection is at its most fundamental level, nothing more than the drive to increase entropy and decrease energy differences. It is understood that chemicals will spontaneously mix and that elements can spontaneously organize into molecules. All this is done within the context of thermodynamics. All life is merely an assembly of molecules via chemical reactions. The molecules involved in the origin of life likely “underwent a series of more and more complex reactions to minimize mutual energy differences between matter on Earth and with respect to high-energy radiation from Sun. The process eventually advanced so far that it cumulated into such sophisticated functional structures that could be called living.”

Could be called living…That is an interesting concept in and of itself. Because if the principles that operate within living creatures are the same that operate everywhere else in the universe, what exactly distinguishes living from non-living. Indeed, the Annilas stress that there is no distinction between animate and inanimate; that “processes of life are, in their principles, no different from any other natural processes.” Biologists would argue that the most fundamental component of life, indeed the definition of the beginning of life, was the creation of a self-replicating molecule capable of storing information. But is this only a concept that we have since imposed on this molecule. What in reality separates it from its most basic physical and chemical elements?

What this means for us is a substantial de-significance of what it means to be not just an individual, or a human, or an animal, but to be alive itself. What is life really but the product of the tendency to increase entropy? “Our “purpose,” so to speak, is to redistribute energy on the Earth, which is in between a huge potential energy difference caused by the hot Sun and cold space.” Cells, genetic code, cellular metabolism all originated as ways to increase entropy and decrease energy differences. Thus, “the order and complexity that characterize modern biological systems have no value in and of themselves, but structure and hierarchical organization emerged and developed because they provided paths for increasing energy flows.” Though this makes sense at some fundamental level, what does this mean for things like the human brain. Is the ability to think, to write, to cry merely a way to increase entropy, or is there a distinction between the fundamentality of thermodynamics to the origin or life and to the continued evolution of life now? Or is this something we want to believe only because it gives us comfort to think of ourselves as special, as being in some fundamental way different from a pot of boiling water?

This is getting us closer to the philosophical conundrum of the definition of life, however, this also relates to the search for the origin of life. And thus relates to the biological foundations of life, and indeed the meaning of “biological” foundations in the first place. Because, “’according to thermodynamics, there was no striking moment or no single specific locus for life to originate, but the natural process has been advancing by a long sequence of steps via numerous mechanisms so far reaching a specific meaning – life.’” So how are we supposed to determine a particular moment, compound or reaction that distinguishes animate from inanimate? We can look at the structures and processes that we know occur in life and try to figure out how they came to evolve, but we may never be able to define the point at which life originated. At least, not if life itself is indefinable. There is no definite beginning.

This makes the title of the article I’m describing inconsistent. While the article argues that there can be no single point of origin of life, the title implies that there was. Despite this inconsistency, the article does take an interesting but also disconcerting look at the “origin” of life from a different perspective. Whether this perspective is irrelevant to the study of astrobiology is unanswered.
It is a fundamental principle of science to conceptualize nature and to define things in an arbitrary but significant way, indeed that is a tendency of humanity itself, and thus to conceptualize ‘life’ may not only be inevitable but also essential. I would argue that this tendency is pivotal to the ability to do science and learn about the world. So perhaps it is not so important to get stuck on the fact that life is indefinable, but it is important, I would argue, to understand the point of this article and the fundamentals of the argument that life is just a human concept. Indeed, this way of thinking about life may be important for astrobiology as we begin to get closer to discovering the origin of life, only to discover that there is no concrete origin. It also may help us to think outside the box in terms of what we consider to be possibilities of life on other planets; taking a step back to look at life as the product of thermodynamics (another concept and label we impress on nature though obviously based on true phenomena) may help us search for life elsewhere.

It is also important to note that this is not a new perspective on life; Buddhists, Taoists and many philosophers in history have conveyed the understanding that everything is made out of atoms and that at the most basic level, everything is of the same and life is only a human construction.

As the Anillas say, “To ask how life started would be the same as to ask when and where did the first wind blow that quivered the surface of a warm pond.”