Thursday, September 30, 2010

Energetics in the Hypotheses on the Origin of Life

Energy is integral to the existence of life; thermodynamic laws affirm this fundamentality. From the viewpoint of energetics, any hypothesis of life’s origins has to indicate the energy source(s) that could account for the (a) formation of reduced carbon compounds and (b) polymerization reactions. However, the field of abiogenesis (the study of life’s origins) does not always take this fundamental principle into account.

Abiogenesis hypotheses are divided into two broad ‘groups:’ “metabolism first” and “replication first.” The replication first" scenarios—including the RNA World concept—do not focus on primordial but instead focus on the chemistry of synthesis and mechanisms of information processing in replicating cycles. In contrast, the “metabolism first” concept does explicitly address the problem of energetics. Later I will address some of the hypotheses about the source of energy that drove the origin of life and what molecules are capable of utilizing energy and how.

First we must begin with the most famous experiment involving the creation of organic molecules from abiotic compounds and its limitations. This was the Miller and Urey model. In this experiment Miller and Urey mixed methane, hydrogen, ammonia and water vapor, added “sparks” which stimulated lightning and were able to form amino acids.

As amazing as this was, we now know that it has severe limitations for its historical plausibility. The reason is that this experiment was based on the assumption that the early Earth had a reducing atmosphere—with large amounts of hydrogen and almost no oxygen. 
However, many scientists no longer believe that early Earth had a reducing atmosphere, and instead believe it had a neutral atmosphere. They propose a composition of mainly carbon dioxide, with smaller amounts of nitrogen and hydrogen, similar to the modern atmospheres of Mars and Venus.

This means that the Miller-Urey experiment under the new atmospheric assumptions, does not produce amino acids.

This creates a dilemma for how life could have plausibly began, chemically or physically, because of the reality of energetics. Life needs energy. Living organisms can only exist if there is a source of energy flow like solar radiation or chemical reactions.

However, in order to reduce carbon dioxide in a carbon dioxide-rich atmosphere, there needs to be a source of electrons in order to create complex compounds.

Indeed, this is where other hypotheses of the energetics of abiogenesis come into play.

Many of these hypotheses believe that life began deep in the ocean. It has been proposed that the oxidation of FeS to FeS2 at the sea floor was used to drive the reduction of CO2 or CO. Let’s look first at the possible reduction of CO2.

It is known that the free energy of this redox transistion is sufficient to drive the reduction of CO2 (at least under some conditions), however so far all attempts to reduce CO2 at the expense of FeS oxidation have failed to yield measurable CO2 reduction under simulated conditions. The reason for this failure is that the reducing potential of the FeS/FeS2 redox pair is higher than the redox potential needed to drive Co2 reduction at a high enough rate; thus thermodynamics alone is not enough.

But what about CO?

The reduction of CO by FeS has been reported but only at unphysiologically high temperatures. Besides, CO is not a major part of the atmosphere now, nor (most likely) ever was. But even if it could rise in primordial settings though the reduction of CO2, however, this is not thermodynamically favorable and thus was very unlikely to have occurred.

Other theories involve marine hydrothermal systems which answer the question of energetics by proposing geochemical energy sources. This model depends on the formation of cellular building blocks from inorganic reactants. But the question from the energetics viewpoint is, can these anabolic processes yield energy? Amend and McCollom proposed that redox reactions occurred at “the interface between two end-member fluids—low temperature (25 °C), mildly acidic (pH 6.5), relatively oxidized (Eh -0.30 mV) seawater and moderately hot (140 °C), alkaline (pH 9), reduced (Eh -0.71 mV) hydrothermal vent fluid.”

They demonstrated that biomass synthesis is most favorable at moderate temperatures, where the energy contributions from HCO3- and H+ in seawater coupled to the reducing power in hydrothermal fluid are optimized. The models show that the net synthesis of cellular building blocks may yield small amounts of energy.

In a similar scenario, put forward by Russell and co-workers, hydrogen and hydrocarbons were produced below the sea floor in complex "serpentinization" reactions and then brought to the surface by hydrothermal fluids. The proposed energy source is the pH gradient across the inorganic membranes between alkaline hydrothermal fluids and the acidic primordial ocean. This concept is analogous to the transmembrane proton gradients on the membranes of modern bacteria cells, however, the evolution of these gradiants seems to be a relatively recent evolutionary advance.

Some also suggest the role of Radiation Chemistry. This concept relates the understanding that any energy able to create ionized and excited molecules can be responsible for the formation of carbon compounds also containing other elements with the fact that there were much higher levels of ionizing radiation on early Earth. Scientists of this field claim that radiation played a role in the formation of organic compounds because radiation abstracts electrons from single compounds, and forms free radicals which can create ew combinations and form compounds of higher molecular weight.

Finally, a new and increasingly acknowledged hypotheses explaining the energetics of the origin of life is the role of zinc sulfide.

Zinc has a unique ability to store the energy of light. Indeed, this is why it is used in sunscreen (as zinc oxide) and in glow-in-the-dark items. This unique ability is also important in possibly solving the conundrum of how to provide energy in a neutral atmosphere; because Zinc, once illuminated by UV light, can efficiently reduce carbon dioxide. This is similar to what plants do. Notably, zinc sulfide particles precipitate only at deep-sea hydrothermal vents today, however, it is proposed that life may have originated at photosynthetically-active, porous structures made of zinc sulfide, similar to today’s deep-sea hydrothermal vents. This means that life would have begun on Earth’s surfaces so that there was access to UV light. Previously, many scientists thought that UV light was a hindrance to the origin of life because of its ability to degrade compounds, however, the fact that UV light in combination with zinc sulfide, allows for the reduction of CO2 makes it a very interesting hypothesis for a primordial energy source. To back up their hypothesis, the scientists who propose this new theory of the origin of life contend that they “have found that proteins that are considered ‘evolutionarily old’ and particularly those related to handling of RNA specifically contain large amounts of zinc.”

There appear to be many ideas for the role of energetics in the origin of life. Indeed, this is a hot field at the moment and will continue to be important because of fundamentality of energy to the existence of life.





Finding Life in Unexpected Places

I wanted to start off with a few articles here and here that I found referencing a certain planet named Gliese581g in the Gliese581 system, nicknamed the "Goldilocks" planet, and I'm sure you can imagine why:

One of the articles refers to a laser signal coming from its solar system, while the other claims that there is no doubt that this planet has water on it, possibly an atmosphere, and is just the right distance away from its star to harbor a stable, reasonable temperature.

Of course, as it points out, we're on a fantastic delay when it comes to communicating with the distant 20-light-year path to its star, taking around forty years to actually get a response, and a lot can happen in forty years.

What I wanted to do in this blog post, however, is talk about the limits of life. Is water truly a necessity as these articles seem to claim? What about ammonia? I found a National Academies of Science report on The Limits of Organic Life in Planetary Systems that took this idea and asked a few important questions. Here are some I believe are more relevant to the topic at hand:

"What life forms are possible, still based on carbon, but not functioning in water?"

"Can mineral systems be identified that interact in interesting ways with organic compounds in nonaqueous systems?"

"Can asymmetric induction, and spontaneous resolution that leads to the homochirality assumed to be necessary for life, be achieved in nonaqueous solvents, especially those found on solar system bodies other than Earth?"

"Can a system capable of Darwinian evolution be demonstrated in the laboratory using nonstandard monomers and/or biopolymers in nonaqueous environments?" (preface. x)

So, there's the question at hand: is water all that necessary?

Here's what the report says about why water is just so great:

"Many specific properties of water are cited to make the case that water is an ideal biosolvent uniquely suited to support life: Frozen water floats. Water is an excellent solvent for salts. Water is liquid over a broad range of temperature. Indeed, the concept of a habitable zone, a region around a star where life is presumed to be possible, largely posits a region in which a planet’s surface or subsurface might support liquid water" (69).

So, let's take a look at ammonia, since that's the one we were talking about last class.

Ammonia stays liquid throughout a large range of temperatures, 195-240 K, and it's reasonably good at being a solvent. It's also abundant in the cosmos. However, something strikes it down when compared with our own living situation:

"The increased strength of the dominant base in ammonia,as well as the corresponding enhanced aggressivity of ammonia as a nucleophile, implies that ammonia would not support the metabolic chemistry found in terran life" (72).

So, as I look through some of the other profiles for other biosolvents (things like carbon dioxide clouds and sulfuric acid), I've noticed how different the workings of a non-water planet might be, even if it may be able to sustain "life" as we don't know it. This leads me to believe that the likelihood of finding intelligent life--according to the current definition--is much slimmer in these environments, since many of their missing aspects have contributed greatly to our evolution.

One of the more interesting topics is whether evolution is a necessity, or if a constantly changing environment may continuously create new and different types of life. While this may hinder intelligent life, it might have untold positive effects elsewhere.

"The unity of biochemistry among all Earth’s organisms emphasizes the ability of organisms to interact with other organisms to form coevolving communities, to acquire and transmit new genes, to use old genes in new ways, to exploit new habitats, and, most important, to evolve mechanisms to help to control their own evolution. Those characteristics would probably be present in extraterrestrial life even if it had a separate origin and a unified biochemistry different from that of Earth life" (8).

So, maybe not necessarily traditional evolution as we know it, but there are similarities that would make life on Earth and life on a non-water-based planet--if it is filled with life--very similar in terms of what we consider biochemical progress Although from what I've read, I can't imagine it would be the intense, laborious evolution that would breed what we would consider intelligent life.

Water is just too convenient in too many ways.

Wednesday, September 22, 2010

Search for other planets

In contrast to the imagination-provoking blog about the possible existence of life on other planets that resemble the ecology of Avatar, this entry deals with the current status of scientists' search for habitable planets. The article I am referring to was featured in the NYT on August 26th and is entitled: "Telescope Detects Possible Earth-Size Planet." .

With the trillions of stars that exist in the universe (not to mention the possibility of multiple universes), many of which have planets orbiting around them, it seems highly improbable that Earth is the only planet habitable for life. The question for me is, therefore, not so much is there life on other planets, but rather, is it possible to ever discover this life? And then the most intriguing question of all, what could this life be like?

Astronomers took the first step to answer this question 15 years ago when the first planet outside of our solar system was discovered. In March of 2009, the Kepler mission sent a spacecraft out in search of habitable planets and planetary systems. It found the first approximately Earth-sized candidate 2000 light years away in August of this year, but by then had found 700 planets overall. Around the same time, a European team found an even smaller planet only 127 light years away that is closer to the size of Earth.

But does this mean there is potential for life on these planets? It's highly unlikely. They are too close to the sun--they are likely too hot and their orbits are very short. However, it gets me much does another planet need to be habitable in the sense ours is? and to what extent can life be different from ours? What if the very building blocks of life were different? Is this possible? Or is it really that lucky that Earth just happened to get everything perfectly right? These are questions to be addressed later on.

For now, another interesting part of this article is how exactly astronomers go about looking for planets. One way is by spotting when a planet passes in front of a star, thereby dimming it slightly. From this scientists can figure out how big it is. And this is just what the Kepler mission is doing by focusing on an area of the night sky and looking for changes in the luminesence of stars. Scientists can also pick out planets based on the pull of their orbits on the star in their solar system.

However, even when the Kepler mission does find a planet, it cannot tell what the atmosphere is like. It can tell the approximate diameter, mass, and distance from the star but this is just a first step in discovering if there is the possibility of life there.

It truly is amazing to consider how far space technology has come over the past years and yet how far it has to come to ever find out if life actually does exist on another planet. Is it ever conceivable to be able to see that life? Judging just by the distance between us and other planets, it would take so long to get there or to pass a signal there, that whoever sent out a message would not be alive to get the result. Not to mention that the possible habitability of another planet as we see it today, is not the exact state of the planet itself today, since looking out into space is looking back into time.

Monday, September 20, 2010

Avatar's New Twist on Plants

Director James Cameron released Avatar in December of last year after spending four years creating what can be deemed nothing short of an epic masterpiece of a movie. Not only was it hailed as the groundbreaking 3D release of its time, it has effectively set an entirely new standard by which all blockbusters are measured. Although I can only speak for myself, after spending a little over two and a half hours with the Na’avi people on Pandorain a pure, unmitigated visual and auditory experience I was in sheer awe.
I’m under the impression other viewers felt the same, and although I didn’t quite experience the surprisingly common “post-Avatar-depression” that some did (their support blog can be found here:, I can’t help but assume that anyone who has seen this movie was at least a little intellectually provoked. For me, it was the biological and ecological design of Pandora and its inhabitants that consumed my thoughts for the following weeks after leaving the theater. I just kept thinking myself in circles, ultimately coming back to the thought: “somewhere, in some time, could this be possible?” Conveniently, for my first blog entry, I found an article that addresses this very question in regard to the terrestrial life on Pandora.From the very beginning, however, this article points out that these terrestrial beings were most certainly not "plants" by the Earth definition of the word.

On Pandora, the plants glow, shoot poison leaf tips, communicate with each other, and serve as messengers from the spirits of greater beings. Jodie Holt, a physiologist from the University California, explains that if the plants that make up the lush rainforest environment of Pandora had been too bizarre, viewers would have dismissed them as unreal. In the minds of viewers, the fact that Pandora could potentially exist as a planet adds an entirely new dimension to the movie. Hence, the extreme reactions to the film mentioned above.

One of the most fascinating plants on Pandora is the "helicoradian". It's this orange, spiraled plant that folds up when touched. According to Holt (who acted as a "botany consultant" for Mr. Cameron) plants on Earth can display this kind of touch sensitivity, however, it is greatly exaggerated in the helicoradians on Pandora. This exaggeration of Earth characteristics is an ongoing theme for the terrestrial life in Avatar.
Yet in the article, Holt admits that since there is really no one characteristic that distinguishes plants from other life kingdoms; it makes it rather ambiguous for her to consider a characteristic as being “exaggerated” within the plant kingdom.

Holt goes on to explain that she didn't invent any new vegetation for the film, but rather, described certain plant characteristics and then left it up to what was known about Pandora’s environment to simulate what kind of features would be advantageous, to mock the natural selection that may have occurred, had Pandora been a real place. There turned out to be a lot more science, creativity, and calculation that went into this than most viewers would otherwise have expected. Aspects of Pandora including the soil, and atmospheric composition, and weak gravity and high magnetic fields were all taken into consideration for each plant species. From the dynamic of life on Pandora, Holt gave certain characteristics to the plants that an Earth-like species may have adapted should it have been placed under the similar stresses of a Pandora-like environment. For example, Holt explains that gigantism (the sheer height of the majority of the trees on Pandora) would have been likely to occur due to the higher levels of atmospheric carbon dioxide and lower gravitational pull on Pandora compared to Earth. The bioluminescence (glow) that some of the plants were capable of giving off could be explained by the long periods of darkness experienced on Pandora.

However, of most importance to the terrestrial life on Pandora was the ability of the plants to communicate with each other. Unfortunately, in the article, Holt states with extreme certainness that: “there is absolutely no way this could happen.” She explains that the only trait that could ever resemble this is single transduction - seen in terrestrial plants on Earth. Signal transduction is the capability of plants to communicate within their structures to consolidate the use of water in periods when it is not abundant. Like, when a root is not getting enough water, it will "tell" the leaves that it feeds to wilt until water becomes available again. To go from signal transduction, to actual communication between plants is quite an evolutionary stretch, and was certainly not as realistic of a quality as other aspects of terrestrial life on Pandora.

In conclusion, I was really impressed to read about the technicality involved in designing the terrestrial life of Pandora. I loved the movie, so I really would’ve been in to any article that offered even a remote explanation of the potential for life like that on another planet. I know that the science points to no, but I still believe that theoretically, a planet like Pandora could exist somewhere else. Who is to say that evolution occurs the same on Earth as it would elsewhere? Maybe in a non-carbon based environment, mutations occur more readily, or the time between generations is faster, allowing more natural selection to occur compared to evolution in our "Earth years". Regardless of if these are legitimate considerations, I like to thinks its possible….