Silicon/Silicone based life

Mine and Rei's speculations aren't the same: all empirical evidence to date supports my "speculation", but no empirical evidence to date supports Rei's. So it is a bit misleading trying to equate the two.[This message has been edited by DNAunion, 11-16-2003]

Too bad you couldn't make it through an entire reply without whining about how the style of my posts rather than the substance.Ah, I see you've edited your post to withdraw your sarcasm. Nonetheless I'll leave it in my post so people know what I'm talking about. To what evidence are you referring? Preciesly how much of the universe do you think we've examined for silicon-based life?[This message has been edited by crashfrog, 11-16-2003]

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Mine and Rei's speculations aren't the same: all empirical evidence to date supports my "speculation", but no empirical evidence to date supports Rei's. So it is a bit misleading trying to equate the two.

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All empirical evidence to date supports that there is no God, but no empirical evidence to date supports the presence of a God. So, there's no God.Right?Want me to take your argument style further?-----------
So, you invoke this mystery deity to explain the presence of life. Using some sort of "magical", "god-processes" which noone has observed, your deity is supposed to have whisked chemicals together into a single early lifeform. What sort of enantioselective factor did your God use to do this? How did your God deal with enantioisomeric cross-inhibition? Where did this God come from, thin air? You've supplied no mechanism or experimental evidence to explain why this God would exist in this environment.
-----------Do you know what's wrong with this kind of argument (apart from its belittling and insulting nature)? You're arguing from a miniscule sample size. Just like we don't have any sample data to look at how silicon-based life would develop (or even carbon-based life), you use that lack of data to claim that it didn't happen. That's faulty logic, just like it would be for me to claim that because we have no evidence of your God, that your God doesn't exist.And it's just plain insulting.------------------
"Illuminant light,
illuminate me."

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Mine and Rei's speculations aren't the same: all empirical evidence to date supports my "speculation", but no empirical evidence to date supports Rei's. So it is a bit misleading trying to equate the two.

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All empirical evidence to date supports that there is no God, but no empirical evidence to date supports the presence of a God. So, there's no God. Right?

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Uhm, why did you drag God into this? I was comparing my speculation that only "life as we know it" is possible with your speculation that silicon-based life is possible. Neither one deals with God.

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So, you invoke this mystery deity to explain the presence of life.

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That's news to me!! Where did I say that?

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Using some sort of "magical", "god-processes" which noone has observed, your deity is supposed to have whisked chemicals together into a single early lifeform. What sort of enantioselective factor did your God use to do this? How did your God deal with enantioisomeric cross-inhibition? Where did this God come from, thin air? You've supplied no mechanism or experimental evidence to explain why this God would exist in this environment.

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Geez, I guess I am forced once again to point out how someone has stuffed words into my mouth!

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Do you know what's wrong with this kind of argument (apart from its belittling and insulting nature)?

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Uhm, the real problem with that argument is that it's not mine.

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That's faulty logic, just like it would be for me to claim that because we have no evidence of your God, that your God doesn't exist.

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My God? Please tell me which God I believe in and why.

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And it's just plain insulting.

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If you find it so insluting, why'd you make it all up??*******************************Rei, all I know about you is what has been said in our exchanges here at the EvC forums. I have a hunch I'd like to check out...are you a theistic evolutionist?[This message has been edited by DNAunion, 11-16-2003]

I kinda think he's right, Rei. If you bring up God, you are putting words into his mouth. Just because he's taking a generally anti-abiogenesis position doesn't mean he's Kent Hovind. After all, nobody asked DNA what his alternative explanation is, and he's hardly offered one. I think it's premature to take the offensive against a position he hasn't said he holds, don't you think?Myself, I don't bring up God until the other person does. Since I don't believe in any gods, after all.If you don't mind my asking, DNA, what is your alternate hypothesis?

Thanks for jumping in here Crash,I agree that DNA hasn't brought up god and to make assumptions on his beliefs when he hasn't stated them is premature.I think that the participants in all these interconnected threads, (peptides, absence of evidence, silicon) need to step back before posting and think about what their posts sound like. Even the posts that aren't resorting to ad hominems still have that sound to them.Lets read the posts carefully and reply to what is actually in the post instead of making assumptions concerning the direction the poster seems to be going in.------------------
AdminAsgara
Queen of the Universe

Sure. But I think it is valid to make assumptions based on directions the poster has already gone in, in particular the context that led to the absence of evidence thread. In that situation I hardly think it inappropriate in a discussion of what's evidence to bring up how that evidence has already been used.

I agree Crash, I was mainly refering to the assumption of god when god hasn't actually been brought into the equation yet. Whether this is because god isn't a part of the equation or is being kept in the wings for when a "point" seems to have been made, is as yet, moot.------------------
AdminAsgara
Queen of the Universe

I don't see where my having or not having religious beliefs matters in this discussion of hypothetical silicon-based life.I also don't see where my pointing out actual problems with OOL theories in another thread means I have to offer and alternative to those theories in this thread.So I'm done with these topics: we should get back to discussing pros and cons of silicon-based life.

So, your answer as to what you feel created life is?(insert answer here)And then, how close my post was to being an inversion of your line of argument?(insert answer here)If I was correct, I have nothing to take back, although I apologize for having to resort to it to get you to address how when you've only looked at a miniscule percentage of the total sample size, you can't effectively argue from absense. For you see, in this case, I have a much larger percentage of the sample size (beliefs of people as to where life came from) to observe from than you have been arguing from on each of these three topics, and can consequently make more reasonable, statistically backed estimates as to what your views are on this subject.In short, I was demonstrating how, given that you wouldn't accept this sort of argument against your viewpoints (now would you?), why should I be forced to accept it against mine.Of course, if I was incorrect about your views, I offer my sincerest apologies I seriously doubt that I am, however. Please, prove me wrong.I too would like to get back to the topic of silicon-based life - under the understand that what we're doing here is theorizing, based on *knowns* - what is possible and what is impossible with silicon based chemistry. Not this sort of "Mine and Rei's speculations aren't the same: all empirical evidence to date supports my "speculation", but no empirical evidence to date supports Rei's."------------------
"Illuminant light,
illuminate me."[This message has been edited by Rei, 11-17-2003]

A number of people have considered whether silicon-based life is possible, and the answer seems to be perhaps, but not without overcoming some pretty big problems. While the bonding of silicon makes it appear that it could make some interesting molecules, the problem arises in capturing, storing, and metabolizing energy from silicon based molecules. Carbon dioxide is gas, diffusable and soluble in water; silicon dioxide, well, is sand. So how would this life work? I know of no scenario for silicon-based life.The chemotrophic life forms from deep-sea vents have as you mentioned
contributed tremedously to our understanding of diversity, although I would stop short of saying these discoveries have revolutionized evolutionary biology. They haven't, but they have contributed to our understanding of how and where life arose. Put very simply, the temperature and chemistry of these deep ocean vents makes certain synthetic reactions energetically easy, syntheses of certain molecules will take place here readily that would require enzymes, thus implying preexisting life, elsewhere.If you are interested in this subject, a book by B. D. Dyer and R. A. Obar, Tracing the History of Eukaryotic cells: The Enigmatic Smile, provides a very good introduction for a knowledgeable reader.

Finally, back on track - thanks, JIM

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While the bonding of silicon makes it appear that it could make some interesting molecules, the problem arises in capturing, storing, and metabolizing energy from silicon based molecules.

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What do you see as being particularly difficult about having different energy states in silicon-based polymers?

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Carbon dioxide is gas, diffusable and soluble in water; silicon dioxide, well, is sand. So how would this life work? I know of no scenario for silicon-based life.

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Actually, we're comparing a carbon backbone with a silicone (alternating Si/O chains) backbone, so if we want to compare simple natural forms of each, the comparison would be between "sand" and "graphite/diamond". Naturally, both silicone and carbon can take far more forms than the basic forms do. There are large amounts of inert carbon-based material on earth, just like there are large amounts of inert silicon-based material. The question is, like carbon, must silicon be intert? Many forms of silicon that occur even on earth, such as your silanols, are water soluable and stable, and have quite interesting chemistry.Some people have expressed concerns about how silicon doesn't double bond as readily as carbon; I personally don't think that's much of a problem, because I would expect the R groups to help determine folding patterns pretty well. I think some of the half-life concerns of long silicon chains might be relevant, though - I'd have to do more research.

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If you are interested in this subject, a book by B. D. Dyer and R. A. Obar, Tracing the History of Eukaryotic cells: The Enigmatic Smile, provides a very good introduction for a knowledgeable reader.

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I'll have to check it out. ------------------
"Illuminant light,
illuminate me."

First, let’s look at the competition. Carbon, the MVP in all known biological molecules from sugar to DNA and even squid ink, is unique in that its bonding versatility allows it take on many forms: long side chains that make up fatty acids and cell membranes, ring structures that compose hormones and sugars, and even simple gaseous molecules like methane (CH4) or carbon dioxide (CO2). Can silicon compete?The short answer is probably not, at least to me, Rei. Silicon simply doesn’t have the moves. While carbon is perfectly comfortable in a variety of different structures (rings, long chains, multi-ring chains, and double-bonded carbon catenations), silicon’s analogous structures are comparatively unstable and sometimes highly reactive. Additionally, such analogous silicon compounds may never occur in nature; the largest silicon molecule ever observed had only six silicon atoms. In contrast, some carbon-based molecules can have tens of thousands!Silicon also has the formidable disadvantage of being less abundant in the universe. The birthplace of all heavier elementsolder starstend to produce far more carbon than silicon. Thus the likelihood of a living system to evolve based on silicon is lower based on the sheer rarity of naturally produced silicon compared to carbon. In fact, astronomical observations of the spectra of various stars and nebulae reveal that organic carbon ring structures (also known as polycylic aromatic hydrocarbons, or PAH’s) exist even in the far reaches of space. The absence of silicon-based biology, or even silicon-based prebiotic chemicals, is also suggested by astronomical evidence. Wherever astronomers have looked - in meteorites, in comets, in the atmospheres of the giant planets, in the interstellar medium, and in the outer layers of cool stars-they have found molecules of oxidized silicon (silicon dioxide and silicates) but no substances such as silanes or silicones which might be the precursors of a silicon biochemistry. I understand that but another chemical property unique to carbon chemistry that silicon lacks is chirality, or handedness. All organic carbon molecules may be found naturally in left or right-handed conformations. However, life as we know it utilizes only the right-hand form of sugars, integral components in DNA structure, and the left-hand form of amino acids, the building blocks of proteins. Very few silicon compounds have handedness at all. The biochemical reactions of life are incredibly specific, and in fact, many larger biomolecules are so precise that a single conformational change (right to left) around one carbon atom would block the reaction. Without chirality, the ability of biomolecules to recognize specific substrates would be crippled, ultimately limiting the number of different reactions available and achievable by a silicon-based system.Unless you can enlighten me in other way I would be very interested.So, while the chances for silicon-based life may be slim, silicon may have played a role in emergence of life on Earth. I would like to see this theory of yours flourish and encourage me to a different understanding of my gloomy prognosis.I do understand that both left- and right-handed molecules could have interacted with the chiral surface, and were aligned according to silica (SO2) handedness, as well. And in this manner chiral molecules were separated and sorted in preparation for pre-biological selection or "primordial soup" theory.So even if silicon is an unlikely participant in the biological reactions of life, it could have certainly lent a helping hand to the origin of life.I like this idea by the way.

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First, lets look at the competition. Carbon, the MVP in all known biological molecules from sugar to DNA and even squid ink, is unique in that its bonding versatility allows it take on many forms: long side chains that make up fatty acids and cell membranes, ring structures that compose hormones and sugars, and even simple gaseous molecules like methane (CH4) or carbon dioxide (CO2). Can silicon compete?

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In everything but the last category, and that condition that I attach is only applicable in an oxygenated atmosphere. A silicone chain has two R groups per central monomer and three per end monomer; consequently, it has no problem at all with side branches and attaching functional groups to give it a diversity of properties; it also readily forms cyclic structures as per carbon (although no benzene-style arrangements). SiH4 is a colorless gas with a repulsive odor, and is more readily combustable than CH4. There are probably others, but this is just one that I could think of off hand.

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The short answer is probably not, at least to me, Rei. Silicon simply doesnt have the moves. While carbon is perfectly comfortable in a variety of different structures (rings, long chains, multi-ring chains, and double-bonded carbon catenations),

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As is silicon (except the last one, in most cases). For rings and multi-ring chains, check out cyclic oligosilicanes; for long chains, look at your nearest silicon-based gel (your silicon-based sealants are going to be short silanes, designed to denature on exposure to air, so those don't count) (most artificially manufactured silicon gels are rather "uncreative" structures, usually with the same, simple R group, such as Cl, CH3, etc, similar to how most manmade carbon polymers are rather repetitive - so don't expect too much from them, except long chains). Silicon can be made to double bond, but it doesn't like to; as I mentioned, though, the R groups should determine folding fine on their own if they're asymmetrical.

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silicons analogous structures are comparatively unstable and sometimes highly reactive.

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Silicon polymers don't like raw atmospheric oxygen, especially silanes Without oxygen, though, they generally do pretty well.

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Additionally, such analogous silicon compounds may never occur in nature; the largest silicon molecule ever observed had only six silicon atoms

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Largest pure silicon (...-Si-Si-Si-...) molecule. Not silicone (..-Si-O-Si-O-...). Although, I'd be surprised if even that were true - most pure silicon is amorphous, but there's been much research into crystaline silicon in the semiconductor industry, especially in recent times.

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Silicon also has the formidable disadvantage of being less abundant in the universe. The birthplace of all heavier elementsolder starstend to produce far more carbon than silicon. Thus the likelihood of a living system to evolve based on silicon is lower based on the sheer rarity of naturally produced silicon compared to carbon. In fact, astronomical observations of the spectra of various stars and nebulae reveal that organic carbon ring structures (also known as polycylic aromatic hydrocarbons, or PAHs) exist even in the far reaches of space.

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However, on the crust of a planet, that's not true at all. For example, the crust of Earth, it is the second most abundant element by mass (second to oxygen) at 28%. Carbon and hydrogen together account for only 0.2%. It gets even more dramatically different in other observed bodies in our solar system, which have mostly silicate crusts. Quantity is anything but a problem. Oxygen is actually the problem - we have too much oxygen here in the crust, and far too much free in the atmosphere. You'll get your most interesting polymerization where it's having to compete over oxygen.

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The absence of silicon-based biology, or even silicon-based prebiotic chemicals, is also suggested by astronomical evidence. Wherever astronomers have looked - in meteorites, in comets, in the atmospheres of the giant planets, in the interstellar medium, and in the outer layers of cool stars-they have found molecules of oxidized silicon (silicon dioxide and silicates) but no substances such as silanes or silicones which might be the precursors of a silicon biochemistry.

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We see occasional silanes, and especially silanols even here on Earth in great quantity, despite our heavily oxygenated atmosphere. Depending on which one you're looking at, silanols can form sheets, catylize reactions, polymerize, and a number of other things.

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I understand that but another chemical property unique to carbon chemistry that silicon lacks is chirality, or handedness. All organic carbon molecules may be found naturally in left or right-handed conformations. However, life as we know it utilizes only the right-hand form of sugars, integral components in DNA structure, and the left-hand form of amino acids, the building blocks of proteins. Very few silicon compounds have handedness at all.

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The very first compound that came to my mind - quartz - has chirality. It either extends in left or right handed spirals.

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The biochemical reactions of life are incredibly specific, and in fact, many larger biomolecules are so precise that a single conformational change (right to left) around one carbon atom would block the reaction. Without chirality, the ability of biomolecules to recognize specific substrates would be crippled, ultimately limiting the number of different reactions available and achievable by a silicon-based system.

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Not at all. What R groups you have is far more important at where you're going to get bonding to different substrates. Besides, most people seem to think chirality is more of a problem than a benefit (I personally don't, I see it as relatively neutral of an issue)

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So, while the chances for silicon-based life may be slim, silicon may have played a role in emergence of life on Earth.

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On the note of that early emergence, here's one possible role that silicon could have indeed played (although its mostly speculative.. an interesting concept, though). Another possible role is as a 2d substrate to align molecules of specific chiralities (as you mentioned in your post).Basically, here's my view on the subject: silicon seems, from my viewpoint, not to have any "showstoppers", and even has some interesting catalytic possibilities that carbon doesn't (zeolites (silicon-metal crystaline forms), for example, can form superacids, and readily form molecular sieves). However, we only have one datapoint for life so far, and it's carbon. So, if I had to place a bet on what the next form of life we find will be based on, I'd bet carbon. However, with such an awful degree of confidence on our dataset (the worst you can get, apart from zero samples), I certainly wouldn't bet *against* silicon-based life. ------------------
"Illuminant light,
illuminate me."

I was searching PNAS.org for any recent articles on OOL and ran across this, which says a few things related to carbon-based vs. silicon-based life.

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What Is Life?
An early question that needs to be confronted, indeed a question that in the last analysis requires definition, is: What is life? Most biologists would agree that self-replication, genetic continuity, is a fundamental trait of the life process. Systems that generally would be deemed nonbiological can exhibit a sort of self-replication, however (2). Examples would be the growth of a crystal lattice or a propagating clay structure. Crystals and clays propagate, unquestionably, but life they are not. There is no locus of genetic continuity, no organism. Such systems do not evolve, do not change in genetic ways to meet new challenges. Consequently, the definition of life should include the capacity for evolution as well as self-replication. Indeed, the mechanism of evolutionnatural selectionis a consequence of the necessarily competing drives for self-replication that are manifest in all organisms. The definition based on those processes, then, would be that life is any self-replicating, evolving system.

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The processes of self-replication and evolution are not reliably detectable, even in the terrestrial setting. Consequently, in the practical search for life elsewhere we need to incorporate information on the nature of the chemistries that can provide the basis for self-replication and evolution. Considering the properties of molecules likely to be needed to replicate and evolve, it is predictable that life that we encounter anywhere in the universe will be composed of organic chemicals that follow the same general principles as our own organic-based terrestrial life. The operational definition of life then becomes: Life is a self-replicating, evolving system expected to be based on organic chemistry.

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Why Organic Chemistry?
The basic drive of life is to make more of itself. The chemical reactions required for the faithful propagation of a free-living organism necessarily require high degrees of specificity in the interactions of the molecules that carry out the propagation. Such specificity requires information, in the form of complex molecular structurelarge molecules. The molecules that serve terrestrial organisms typically are very large, proteins and RNAs with molecular weights of thousands to millions of daltons, or even larger as in the case of genetic DNA. It is predictable that life, wherever we encounter it, will be composed of macromolecules.

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Only two of the natural atoms, carbon and silicon, are known to serve as the backbones of molecules sufficiently large to carry biological information. Thought on the chemistry of life generally has focused on carbon as unique (3). As the structural basis for life, one of carbon's important features is that unlike silicon it can readily engage in the formation of chemical bonds with many other atoms, thereby allowing for the chemical versatility required to conduct the reactions of biological metabolism and propagation. The various organic functional groups, composed of hydrogen, oxygen, nitrogen, phosphorus, sulfur, and a host of metals, such as iron, magnesium, and zinc, provide the enormous diversity of chemical reactions necessarily catalyzed by a living organism. Silicon, in contrast, interacts with only a few other atoms, and the large silicon molecules are monotonous compared with the combinatorial universe of organic macromolecules.

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Life also must capture energy and transform that energy into the chemistry of replication. The electronic properties of carbon, unlike silicon, readily allow the formation of double or even triple bonds with other atoms. These chemical bonds allow the capture and delocalization of electronic energy. Some carbon-containing compounds, therefore, can be highly polarized and thereby capture "resonance energy" and transform this chemical energy to do work or to produce new chemicals in a catalytic manner. The potential polarizability of organic compounds also contributes to the specificity of intermolecular interactions, because ionic and van der Waals complementarities can shift to mesh with or to repulse one another. Finally, it is critical that organic reactions, in contrast to silicon-based reactions, are broadly amenable to aqueous conditions. Several of its properties indicate that water is likely to be the milieu for life anywhere in the universe (2).

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The likelihood that life throughout the universe is probably carbon-based is encouraged by the fact that carbon is one of the most abundant of the higher elements. Astronomical studies find complex organic compounds strewn throughout interstellar space. Moreover, the common occurrence of carbonaceous meteorites testifies to an organic-rich origin for our own solar system. If life indeed depends on the properties of carbon, then life is expected to occur only in association with second- or later-generation stars. This is because carbon is formed only in the hearts of former stars, so far as we know.

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The Universal Nature of Biochemistry
Life as we know it builds simple organic molecules that are used as building blocks for large molecules. Amino acids are used to construct the long chains of proteins; simple sugars combine with the purine and pyrimidine bases and phosphate to construct the nucleic acids. It seems logical that the evolution of any organic-based life form would similarly result in the construction of complex molecules as repeating structures of simple subunits. Indeed, it seems likely that the basic building blocks of life anywhere will be similar to our own, in the generality if not in the detail. Thus, the 20 common amino acids are the simplest carbon structures imaginable that can deliver the functional groups used in life, with properties such as repeating structure (the peptide unit), reactivity with water, and intrinsic chirality. Moreover, amino acids are formed readily from simple organic compounds and occur in extraterrestrial bodies such as meteorites, so are likely to form in any setting that results in the development of chemical complexity necessary for life.

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Similarly, the five-carbon sugars used in nucleic acids are likely to be repeated themes, perhaps in part because they are the smallest sugars that can cyclize and thereby confer spatial orientation on other molecules, for instance the purines and pyrimidines that comprise the genetic information of terrestrial organisms. Further, because of the unique abilities of purines and pyrimidines to interact with one another with particular specificity, these subunits, too, or something very similar to them, are likely to be common to life wherever it occurs. Differences in evolutionary systems likely will lie at the higher-order levels: the structures of the large molecules assembled from the simple units, and the mechanisms by which they are assembled and in which they participate.

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Themes that are probably common to life everywhere extend beyond the building blocks. Energy transformation is a critical issue. The processes of life require the capture of adequate energy, from physical or chemical processes, to conduct the chemical transformations requisite for life. Based on thermodynamics there are only two such energy-capturing processes that can support "primary productivity," the synthesis of biological materials from inorganic carbon dioxide. One process, termed lithotrophy, involves the oxidation and concomitant reduction of geochemical compounds. For instance, methanogenic organisms gain energy for growth by the use of hydrogen (H2) as a source of high-energy electrons, which are transferred to carbon dioxide (CO2), forming methane (CH4). Other microbes might use hydrogen sulfide (H2S) as an energy source, respiring with oxygen (O2), to produce sulfuric acid (H2SO4). It is thought that the earliest life on Earth relied on lithotrophic metabolism.

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The second general process for obtaining energy, photosynthesis, captures light energy and converts it into energetic electrons that can be used to accomplish biochemical tasks. Photosynthesis arose early in the history of terrestrial life and probably drives most primary productivity on Earth today. The contribution of lithotrophy to terrestrial primary productivity remains unknown, however, because there currently is little information on such organisms that may be distributed throughout the Earth's crust, wherever the physical conditions permit. (Normal R Pace, The Universal Nature of Biochemistry, PNAS, January 30, 2001, vol. 98, no. 3, p805-808)

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