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Molecular Fossils

Tue, 05 Aug 2008 13:12:25 +0200

Molecular fossils are ambiguous. They tell us practically nothing about the size and shape of what producedthem. They can, however, clearly indicate the biochemical capabilities and functions of what produced them. There are, as we know, a variety of organic molecules synthesized by living systems, but they are stable to very different degrees. Proteins and their constituent amino acids would be fascinating fossils, but proteins are essentially non-existent as fossil molecules and extensive searches for amino acids have led to the following conclusions. Amino acids are present in ancient rocks and the majority are in the L-form, which is characteristic of life. However, in rocks over 60 million years old, the L- and D-forms occur in about equal amounts. Hence, it appears that L-amino acids, when associated with ancient rocks (Precambrian, over 600 million years old), are probably of relatively recent origin.

The most useful, it now seems, of the fossil molecules are the straight-chain hydrocarbons. These are very stable compounds and are easily recovered from ancient rocks by washing in benzene and methane. The occurrence of pristane and phytane, products of the chlorophyl molecule, can be used to infer the presence of organisms capable of photosynthesis.

However, there is still lively debate regarding the interpretation of molecular fossils. The work on the generation of organic compounds in the absence of life has shown, as we discussed earlier, a quite extraordinary array of spontaneously formed substances. Amino acids were among them. Someorganic geochemists suggest that the long-chain hydrocarbons should be added to this list. And so the search is still underway for unambiguous fossil molecules. The field is, nonetheless, considered to be a promising one by many researchers.

Finally, under problems of direct observation of fossils, we must consider the species problem. Unavoidably, fossil specimens are named and classified and this places them beside extant or neontological forms. The problem now is this: Are the criteria for species identification the same for paleontological and for neontological material? We raise this question because both are used in the study of evolution. And when evolutionary sequences are constructed from extinct forms leading to modern extant forms, we might wonder if we are using comparable terms for both forms. In brief, the answer is that we are not. The problem is not a serious one if we keep in mind certain precautions.

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Fossil Forms

Tue, 05 Aug 2008 13:12:23 +0200

To describe apparently related fossil forms as members of different species we apply the kinds of differences apparent between comparable extant species. Some workers prefer to work only with differences that justify generic names. This degree of caution is not always necessary, but it is more desirable than the reverse case in which every little difference between two fossils is used as an excuse for describing new species. The necessary precautions come down to an awareness of the natural variation that occurs in any species, a sense of the genetic basis for such variation, and then a cautious usage of species designations. In this way we can quite confidently combine our data on extinct and extant forms and expand the data base used for evolutionary studies.

The relative positions of fossils: Chronology. The most informative aspect of the fossil record is that it allows us to perceive evolutionary history directly. This can happen, however, only when we have determined the relative ages of fossils correctly. The basic rule is that the oldest fossils are toward the bottom of the pile. The pile we refer to is the bedded sequence of fossils. The oldest fossil beds are laid down first, the next oldest on top of them, and so on up to the surface where today's forms are living. Ideally, then, the evolutionary sequence is simply read from bottom to top. But things are rarely ideal. Two phenomena, at least, can confuse the ideal state of affairs. One of these is that fossil beds can be moved. Geological folding and uplift, which can obscure an otherwise quite readable story, occur. Folding often reorients layers or strata of fossil beds relative to each other and uplift in one areacan raise a bed that was at the bottom, and quite old, in another area. Another troublesome phenomenon is the loss of strata or beds. Erosion can remove millions of years of sedimented history and thus produce gaps in the fossil record. Such gaps, depending on the amount of discontinuity they cause, can pose genuine problems in our understanding of how one form evolves into another.

The answer to the foregoing largely depends on common sense as well as the competence of the geologist and the paleontologist. Common sense tells us to go slow in interpreting sequences from fossil beds until the geologist can determine the degree of folding, uplift, and erosion. The paleontologist can then compare the results from one stratum with those from a comparable stratum elsewhere and thus carefully reconstruct historical sequences. Ultimately, when we deal with history, we look for absolute measures of time, not just relative ones. We want to know precisely how long ago a certain event occurred and not just that it occurred earlier or later than other events. The most informative method in this regard is an analysis that depends on the amount of specific radioisotopes present in a fossil bed or a fossil.

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Interpreting Fossils

Tue, 05 Aug 2008 13:12:05 +0200

There are two aspects to learning what fossils can teach us. The first comes from the direct observation of fossil evidence. The second is less direct because it is concerned with the relative position of fossils in the rocks where they are found.

Direct observation of fossils. Except for rare cases in which organisms are immediately preserved, e.g., the frozen mammoth or, another case, insects trapped in amber, fossil remains present us only with a part of some organism. So, obviously, one problem in interpretation is the reconstruction of the whole organism. Perhaps the most famous practitioner in this area was Cuvier, the father of paleontology. A fossil tooth was a fascinating clue to Cuvier. From it he could make educated guesses as to the size of the original organism and its age and its food. The latter then allowed cautious speculation as to the nature of such internal organs as the digestive system. This led to more information on body size and shape. And so on. Comparable work is being done today and the reconstruction of whole humans from parts of their skull is a case in point. Such reconstructions can be extremely useful in casting light on the creatures of bygone times. In some cases specially preserved fossils, such as the impression of dinosaur skins, allow us to reconstruct details that we would otherwise have had no knowledge of.

More difficult to interpret are the traces left by organisms, such as worm tracks left in the mud of ancient seas or the molecular fossils, mentioned earlier. In these instances we may never know the exact nature of the organism that left such evidence of its existence. Nonetheless the information we do have is useful. It helps complete the picture of what type of organism was alive at a certain time in the past history of this earth. Worm tracks, for example, document, at the least, that worms were present. Even though we may not be able to say which species or class or maybe even which phylum, we do know that crawling things of a certain approximate size were part of the ecosystem under study. That enhances, though admittedly in a limited way, our understanding of past life.

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Finding Fossils

Tue, 05 Aug 2008 13:11:50 +0200

Fossils appear when erosion or digging uncovers them. Erosion goes on all the time, in total disregard of the presence or absence of fossils. Hence many fossils are uncovered and may be casually destroyed. The ideal fossil is one whose position in its surroundings is still identifiable; and it represents as complete a record as possible of the original organism. Isolated bones and teeth are important--they have told us much about human evolution--but complete skeletons are, of course, much more informative, though much less likely to be found.

Sedimentary formations are naturally the richest source of fossils for the paleontologists who seek them. Here fossils were formed and preserved through deposition of muds and silt. When such a bed of fossils is found great care is taken in the removal of specimens. Often, chunks of the sedimentary material are removed and worked on with special tools in a laboratory so as to assure intact specimens. Depending on the size and nature of the fossil, the paleontologist's tools are appropriately varied. In looking at microscopic fossils, the techniques of a gem cutter and polisher are utilized. This assures thin, transparent preparations for the microscope. Larger fossils may require accurate splitting of sedimentary layers followed by the addition of preservatives, e.g., plastics, to protect the fossil remains. And large dinosaur bones are often covered with plaster at the site of their excavation to protect them from rain and other wear and tear. Most fossils are destroyed before they catch the eyes of fossil-hunters. Sedimentary rocks are changed through movements of the earth's crust or through heating, and this damages or destroys fossils. When we put this fact together with the realization that relatively few organisms are successfully fossilized, we can conclude that the fossils we have recovered are a very limited sample of the fife of the past. But that conclusion protects against the extremes of wild speculation orpessimistic conservatism in interpreting the fossil record. Neither the extreme of assuming we have a complete record of the past nor the extreme of assuming we can say nothing of the past is justified.

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Fossil Formation

Tue, 05 Aug 2008 13:11:21 +0200

Any trace of life from the past can be called a fossil. This includes the molecular products of life as well as worm tracks in the mud of some bygone time. It also includes various kinds of hard parts, such as shells, bones, or teeth. It can include the impressions left by soft parts, which may be flattened and distorted by the pressures of the overlying mud that turned to rock or replaced by chemicals, which have no direct connec-tion to living systems, but nonetheless are a record of fife in the past. Perhaps the most extraordinary fossils are the living things that were frozen during an Ice Age. A mammoth, which is an extinct relative of the elephant, has been found which was trapped in the frozen Alaskan tundra some milllions of years ago and preserved there. Discovered and recovered some years ago, it provides us with an extraordinary fossil.

Fossils are obviously formed in a variety of ways, and therefore, there is no one answer to our first question, How are fossils formed? Fossil formation is a chance event. It depends on living things, or any of their many products, being in a place where they are relatively undisturbed. Or, if they are disturbed, where the resulting changes still retain the record of the past. The examples of petrified wood show this dramatically. Here the original wood has been completely replaced by various chemicals from the environment. These latter were selectively deposited in various parts, even down to cellular details of the wood. Thus, despite replacement of the original living parts, a marvelously detailed record of that life is retained.

More typically, the fossilization of an animal, such as one of the ancestors of present-day horses, occurs along the following lines. The organism in question, say, for example, the grazing form called Merychippus that lived about 20 million years ago, died on the grassland where it lived. In a relatively short time the scavengers of that time--giant hyenas and vultures, and a whole array of other forms including beetles and flies and their larvae--would have consumed and dismembered the carcass of Merychippus. Such a fate would have precluded any fossil formation and was by all odds the most common situation. Another, less likely possibility was that a Merychippus was drowned while crossing a river. If the body sank and was covered by silt, the possibility of a fossil resulting is more likely. However, if the river dried up--perhaps our grazer was simply caught in a flash-flood--before the drowned animal was well buried, scavengers could have destroyed the carcass.

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Oxygen

Tue, 05 Aug 2008 13:11:04 +0200

Oxygen penetrates surface waters and enters the soil to some extent. These areas have also evolved oxygen-dependent life forms, but also important are the accumulated organiccompounds that have dissolved in water and that continually enrich the soil. Such compounds transform a barren dust or sand to the rich topsoil that supports plant life and forms the basis for all food chains on land. Similarly, organic compounds are important to oceanic plankton and zooplankton. Plankton form the basis for life in the surface waters of the ocean. That life supplies not only organic compounds at the surface, but also contributes to the quiet rain of detritus that reaches the ocean floor and sustains life even at the greatest ocean depth. Such fife lives in permanent darkness, with minimal oxygen and almost always low temperatures. But the fact that it exists has changed the ocean from an originally lifeless dilute soup of
1. The methanogens have at least two enzymes, related to methane metabolism, and not known to occur in other organisms.
2. The methanogens contain no cytochromes, the proteins widely used by other organisms for electron transport.
3. Most prokaryotes have peptidoglycan in their cell walls; Wthanogens have none.
4. The transfer RNA (tRNA) of other organisms carries a distinctive squence TψCG in one part of each tRNA molecule. In its place, the methanogens have either ψψCG or UψCG. (ψ is a modified uridine.)
5. Changes occur in rRNA after it has been transcribed. (The change of uridine to "pseudo-uridine" or ψ, in 4 above, is an example.) Such changes in the methanogen 16S rRNA are very different from those found in other prokaryotes.

Altogether, then, significant differences are seen between the methanogens and typical prokaryotes. Whether this will justify a new kingdom of organisms, as hinted at by Carl Woese and his colleagues, remains to be seen. For the present it is convenient to refer to the methanogens as a very special group of prokaryotes. spontaneously formed compounds to a collection of complex ecosystems with interdependent inhabitants. This awareness of co-evolution, the concept that life evolves along with the changes it produces in its environment, is emerging as a key concept in our search for life on other planets. This search is called exobiology--life beyond the limits of this earth, or outer life--and one of its leading practitioners in the United States, Cyril Ponnamperuma, of the University of Maryland, uses it as a criterion for predicting the probabilities of extraterrestrial life. In his laboratory Ponnamperuma mimics extraterrestrial conditions on the moon or on Mars, for example, so that he can study the spontaneous formation of molecules needed for life. When the first satellite descriptions were received on earth from Mars, Ponnamperuma set up his Mars atmosphere on earth and correctly showed that life on Mars was highly unlikely, a result confirmed by subsequent tests performed by the spacecraft that landed on the surface of Mars.

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The Methanogens

Tue, 05 Aug 2008 13:10:53 +0200

One of the most interesting evolutionary finds in recent years is the prokaryotic form, the methanogen. Their special evolutionary significance has been described by the American biophysicist and microbiologist Carl Woese and his colleagues. The methanogens are best classified as chemoautotrophs. They live in a hot, reducing environment. Their cell walls, their enzymes, and certain of their nucleic acids differ markedly from those of other prokaryotes, although their overall cellular organization is clearly prokarvotic. But especially because the nucleic acids of their ribosomes (essential in protein synthesis) are so different from any others known, Carl Woese and his colleagues have suggested that the methanogens might merit a kingdom of their own. That suggestion has not been acted upon, but it is worth mentioning to highlight the special significance of the methanogens. For our purposes, they represent a group of extraordinary chemoautotrophs that depend on a reducing atmosphere. They could wellbe living representatives of early chemoautotrophs--of those forms that first emerged when the ecosystems were evolving and that retain a need for a reducing atmosphere.

The Gaia hypothesis. This brings us to consider somewhat more carefully the changes that occurred in the atmosphere, hydrosphere, and the surface soils of the earth as life originated and evolved. The idea that life and its environment have co-evolved has been called the Gaia hypothesis by the British scientist James E. Lovelock. As the by-products of liv-ing systems accumulated on the surface waters and in the air and the soil of the earth, living things had to adapt to ever new surroundings. We have already said that the appearance of oxygen as a by-product of photosynthesis changed the atmosphere from a reducing one to an oxidizing one. This made possible chemical respiration as we know it today. Most living things are aerobic and animals, in particular, depend on oxygen for fife. Hence the change to an oxidizing atmosphere was an essential precursor to animal life and evolution.

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The Evolution of Biosyntheses

Tue, 05 Aug 2008 13:10:26 +0200

Horowitz's proposal goes as follows. Suppose an early organism needs organic substance A as a precursor for a vital substance. Substance A eventually comes into short supply because many similar organisms are competing for it. Suppose, further, that A is being produced spontaneously from the following reaction, occurring outside the cell, B + C → A. Any cell that can take up B and C from the environment and produce A now has a selective advantage over all the other cells that depend on an outside source of A.

The uptake of B and C may require, first, a changed membrane protein. This can occur through mutation. Proteins already in the cell might catalyze the reaction B + C → A. Further, mutations could yield a more efficient catalyst. The cell with such new capabilities would now predominate in those parts of the early seas in which survival was possible. And then, in time, B or C or both would come into short supply. What then? A situation like that regarding the formation of A would occur. The cell or cells able to form B from its precursors and C from its precursors would be at a selective advantage. And this situation could repeat itself many times throughout the early history of the earth, which is now reliably estimated as being 4.6 × 109 years old.

The overall result of this early evolution would be the emergence of biosynthetic pathways. Such pathways would be like those known today, in which reactions are catalyzed by highly specific enzymes formed under the control of genes. Also, of necessity, there would be a general direction in this evolution. The biosynthetic pathways would belengthening in the direction of simpler and simpler precursors. Eventually, organisms would probably become so biosynthetically sophisticated as to require only such inorganic precursors as carbon dioxide, water, ammonia, sulfur, and phosphorus or their compounds or both. They might, also, by this time have evolved means for capturing energy from sunlight for biosynthesis. In short, nutritionally, they would have evolved from being chemoheterotrophs to being photoautotrophs.

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The Interlocking of Nutritional Cycles

Tue, 05 Aug 2008 13:10:25 +0200

Microbiologists often say that if there is an energy-yielding reaction in nature, then there will be an organism that can make use of it. The relevance of that comment to the origin of life is that chemoheterotrophs evolved to various kinds of autotrophs. Some used sunlight, as various photosynthetic prokaryotes do today, bit others used such energy-yielding reactions as theoxidation of sulfur or iron. However, these latter reactions would imply the presence of a significant amount of gaseous oxygen in the environment. We have mentioned, in connection with Miller's work, that the early atmosphere was a reducing one. The change to an atmosphere such as today's probably is the result of the release, by photosynthetic organisms, of large amounts of oxygen as a metabolic by-product. But nevertheless, in this early nutritional evolution we need not think of evolution as following a single path from chemoheterotrophy to photoautotrophy. Along the way there were opportunities for chemoautotrophs, as well as photoheterotrophs, to emerge.

Biogenic macromolecules. Up to this point we have only discussed spontaneously occurring molecules (organic and inorganic) as nutritional building blocks and sources of energy
II. Nomenclature based upon ability to synthesize essential metabolites
A. AUTOTROPHY All essential metabolites are synthesized
1. Autotrophy sensu stricto
2. Ability to reduce oxidized inorganic nutrients
3. Mestrophy Inability to reduce one or more oxidized inorganic nutrients, i.e., need for one or more reduced inorganic nutrients

B. HETEROTROPHY Not all essential metabolites are synthesized i.e., need for exogenous supply of one or more essential metabolites (growth factors or vitamins)
C. HYPOTROPHY The self-reproducing units (bacteriophages, viruses, genes, and so on) multiply by reorganization of complex structures of the hostalong with sunlight or even heat. This means we have been ignoring another and by then extremely important source of molecules. These are the molecular products of organismic metabolism or biogenically produced compounds. If these compounds had not been utilized, the resources of the earth would have been eventually exhausted by living organisms. When, through natural selection, organisms began to utilize the products of other organisms, then recycling emerged on earth.

From this emergence of recycling, there appeared ecosystems, and new interrelationships of life on earth. In fact, organisms became interlocked in mutual dependence. Sometime at this point in evolutionary history, there were again many chemoheterotrophs. Organic compounds were again in an abundance, but now they were not formed spontaneously but as a result of biosynthesis, or they were formed biogenically. These secondary chemoheterotrophs were likely quite similar, nutritionally, to the prokaryotic or bacterial chemoheterotrophs of today. We shall call them chemoheterotrophs II to distinguish them from the earlier chemoheterotrophs I, which extend back (speculatively) to the origin of life. In between these two types of chemoheterotrophs, distinguished by the source of the organic compounds they use, there were the photoautotrophs and various combinations of chemotrophs, phototrophs, heterotrophs, and autotrophs.

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The Importance of the Proteins

Tue, 05 Aug 2008 13:10:13 +0200

Increasing the survival interval and decreasing the formative interval make improving the proteins even more important. Their increased efficiency and stability as components of membranes and enzymes will have a very significant selective advantage as will their regular distribution to daughter protocells. At this point the advantage of informed proteins--proteins from information-containing templates--becomes obvious. Such templates can ensure selective formation of the needed proteins; this does not happen in reflexive catalysis. The latter process probably generates many useless proteins (in terms of cell survival) for each useful protein generated. Also, distribution of a few templates could be an efficient way of assuring that protocells can form needed proteins.

How could such a template system arise? We are still speculating here, but we can be guided by the known dependence of protein formation today on nucleic acid templates. Perhaps ribonucleic acid was the first template that absorbed the amino acids needed to form a selectively advantageous enzyme, for instance. If so, that nucleic acid would also be selected for. And if a DNA molecule assured formation of the needed RNA, it too would be selected for. Today these speculations are taking the form of research into the transfer RNA molecules as being the first informed nucleic acids.

We know that nucleic acids are maintained in cells. We also know that their precursors are concentrated and preserved in cells. The interior of protocells may, therefore, be the most likely place in which nucleic acids formed spontaneously, and in which if a nucleic acid that could act as a template were formed, it would be selected for. This point of view might get us around our present impasse of postulating the spontaneous formation of nucleic acids in a nonliving environment. Evolution of the template might have followed a path that is the reverse of today's protein synthesis. But that path would form the basis for understanding protein biosynthesis.

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Notion of an Organism

Tue, 05 Aug 2008 13:09:44 +0200

Many biologists today recoil at the notion of an organism without genetically functional nucleic acids. True, such an organism would be more efficient if it had genes. And genes would have to emerge before such a living microsphere could transform into cells as we know them today. However, it might just be that such a system would provide the possibility for the spontaneous formation of uninformed nucleic acids and their transition to informed ones. Let us speculate further on how that might occur.

Because these early organisms or protocells could be termed living, they would also be evolvable. That means natural selection would act on their variations and preserve the more advantageous ones. What would be the nature of such selection pressures? This can be made clearer by looking at a basic reality faced by all organisms. If a species is going to persist, the individual organism must survive long enough to form more of itself. Some rocks and other tough substances persist simply because they are durable. Organisms, by comparison, are not durable. In fact, they are comparatively delicate, but organisms that persist do so because they reproduce faster than they are destroyed. If we indicate the average period of duration of an individual as the survival interval, and the average period needed to form more of itself as the formative interval, then, for persistence, the survival interval must be greater than the formative interval. Therefore, selection will favor anything that increases the survival interval or decreases the formative interval. These selection pressures are unavoidably present; they arose with the first living thing and have been the basic reality of survival down to the present, and will continue to be.

What increases the survival period of the protocell? There are at least three conditions that increase survival: (1) an improved selective uptake of substances from the environment, (2) an increased concentration of reactants needed for the life of the protocell, and (3) stabilized functional (enzymatic) and structural (membranes, in particular) proteins. All three are, of course, interrelated. What decreases the formative period? Two points deserve emphasis: (1) speeded up reactions needed for the life of the cell, which can be the result of increasing the concentration of reactants and improving the efficiency of enzymes, and (2) proper distribution of functional and structural components.

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The Emergence of Cellular Life

Tue, 05 Aug 2008 13:09:38 +0200

As problematical as the approach admittedly is, we must go back to the proteinaceous microspheres as possible protocells. We will approach them from the point of view of Oparin's coacervates, but adding that they contain uninformed proteins capable of some reflexive enzymatic activity. Enough has been said to show that such an approach is full of problems. But it is also clear why this seems to be the most promising approach. Frankly, at this point, we are speculating, but speculating within the rules of scientific inquiry; we are searching for testable explanations regarding the origin of life.

A coacervate containing reflexive enzymes can fulfill our definition of a living system. It could even be called an organism, since it could exploit its environment for the matter and energy to maintain itself. These would include spontaneously generated amino acids, nucleotides, sugar, and other organic compounds, including uninformed proteins, and as an energy source, heat or even possibly ATP. In the latter case one of the proteins might enzymatically split off the phosphate radicals and the released energy kept to help form more protein. This might or might not be part of the reflexive catalysis, but in any case, it contributes to formation of proteins making up the coacervate. Growth of the coacervate would come from the formation within it of various organic compounds, especially proteins. Large coacervates have been seen by Oparin and others to pinch in two when they reach a certain size. Apparently they are unstable above a certain size. This is growth and reproduction aided and abetted by the selective uptake of compounds and their enzymatically controlled reactions within the coacervate. Extensive study of coacervates as proteinoid microspheres as come from the laboratory of Sidney Fox and his colleagues at the Institute for Molecular and Cellular Evolution at the University of Miami. They have confirmed and greatly extended Oparin's initial ideas. Variations in these microspheres might come about through variations in the folding of the proteins.

Another source of variations has been suggested by the distinguished Japanese protein chemist Akabori. He proposed that proteins absorbed on clays could undergo reactions to amino acid side chains. This would change the sequence of the amino acids and change the conformations of the proteins, as well. This is a very important suggestion in three respects. First, it points to how an uninformed protein could take on the functions of an informed one, if side-chain substitutions led to enzymatic activity. Second, it could help explain how amino acids not arising spontaneously could become part of a protein with informed activities. And, third, instead of absorbing on clays, perhaps these early proteins absorbed on structures within the microspheres and there underwent side-chain substitutions. And their new properties could be immediately advantageous within microspheres.

If, and we repeat, if such microspheres arose they could be regarded as living. And because life would be associated with a discrete, three-dimensional structure--not a set of reactions in an organic soup--such a system would also be recognized as an organism.

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The Origin of Nucleic Acids

Tue, 05 Aug 2008 13:09:22 +0200

Now let us turn to the nucleic acids. Nucleotides are formed spontaneously in a Miller-type experiment. These nucleotides contain among them the allimportant one adenine triphosphate or ATP. Its importance ties in the role it plays in living cells as a source of energy as well as a precursor for DNA. The other nucleotides needed for DNA, which contain cytosine, guanine, and thymine, as well as uridine for RNA, are also formed spontaneously. Also simple sugars have been found in these experiments.

The next question is whether or not uninformed DNA and RNA are formed. The answer really is no. Short lengths of nucleotide polymers, called oligomers, do appear. But so far no RNA with molecular weights similar to those of transfer or ribosomal or messenger RNA has been found. (These are, of course, the three main categories of informed RNA.) And nothing approaching a high molecular weight double helix of DNA has appeared spontaneously. The researchers in this areaconclude, so far, there is no reason to suppose that nucleic acid molecules comparable in size to informed nucleic acids are formed spontaneously. It is always possible that tomorrow some researcher will find a way to effect the spontaneous formation of uninformed nucleic acids. And that may then provide the clue for the transition to informed molecules. But this is at present nowhere in sight. It forces us to think that perhaps informed nucleic acids did not arise spontaneously. That is, when they arose it was within living systems. Such living systems would have to be based on proteins. This, though somewhat implausible for the reasons given above, brings us back to a consideration of the origin of the first living system on the basis of proteins and, from that, the emergence of cellular life.

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Amino Acids

Tue, 05 Aug 2008 13:08:49 +0200

Amino acids and many other organic compounds tend to form microspheres in solution. The process is a kind of selective mutual adsorption in response to the surrounding charged molecules of water. In fact, the water molecules form a polarized film around the microsphere. This behavior is found in the hydrophilic and hydrophobic behavior of the protein and lipid components, respectively, of cell membranes. In other words, such orientation of molecules and formation of microspheres is common and may parallel the behavior of cells and their membranes. This observation is strengthened by onelast one. The microspheres can accumulate certain substances from their watery environment by selective absorption. This, too, parallels the uptake of substances from their environments by cells through their semipermeable membranes.

Now what can be said regarding the emergence of informed proteins? Very little, and this is a major problem in the study of the spontaneous origin of life on earth. In addressing the problem this way, we have narrowed down the central issue. Instead of asking, How do we get living cells from a nonliving environment? we are asking, How do we get informed proteins from noninformed ones? This restatement of the problem helps us see the problem more clearly. Here the problem has two parts. First, we need to find how an uninformed protein can act like an informed one and, second, we need to find, then, a way it could be formed. The second part of the problem says that it must be formed from some kind of information-containing template. We will return to the problem of templates after first discussing the origin of nucleic acids and the emergence of cellular life. Returning to the first aspect of the problem, we can say that if a spontaneously formed, or uninformed, protein acts enzymatically, then it is acting like an informed protein. Very briefly, that brings us back to something like reflexive catalysis as a possible way both to generate such a protein and to advance a theory on the emergence of living systems as we know them today. But, as we have seen, there are serious problems with the experimental analysis of the proposal, so far.

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The Origin of Proteins

Tue, 05 Aug 2008 13:08:45 +0200

Protein precursors became an area of vigorous research when Stanley Miller, working with Harold Urey at the University of Chicago, published his experimental results in 1953. Miller placed CO 2, H 2 O, NH 3, and CH 4 (methane) in a system of glass tubes such that by boding the water the mixture of gases was forced past an electrical spark and returned to the water again. When this system was allowed to operate for some days there appeared a dark precipitate in the water. Upon analysis this precipitate turned out to contain various amino acids.

Miller's basic experiment, including various modifications, has been repeated many times to reveal that not only can many essential amino acids be formed by this technique, but nonessential amino acids, significant amounts of proteins, and various other organic molecules. The answers to our first two questions regarding proteins are clearly in hand. Amino acids are the precursors of proteins, and they are readily formed spontaneously. And from them certain uninformed proteins are made. Now what can we conclude from this? Regarding the formation of amino acids there are two important points. First, it has become clear that an atmosphere in which amino acids will appear must be a reducing one (one in which H2 is present). That was true of Miller's experimental set-up. In an oxidizing atmosphere (one in which 02 is present) no amino acids were obtained.

Second, not all the essential amino acids are formed in this type of experiment and some amino acids were formed that are not found in organisms today. All of this is not so much a lesson as a puzzle. Why were only the 20 essential amino acids incorporated into living systems when some of them are not readily formed spontaneously, and why were others readily formed that are not incorporated? We cannot answer that question today.

And, then, the uninformed proteins require study. These proteins can be formed in large amounts from certain amino acids. That is, certain proteins are favored as are the aminoacids that constitute them. None of them has been shown to have enzymatic activity. These proteins tend to aggregate and form small spheres and, most interesting, these spheres differentiate in a way that suggests cellular structure. In the electron microscope they show a dense outer layer; internally, there is a mass of material of differing densities. Biochemist Sidney Fox and his collaborators have been especially active in studying these proteinaceous spherules. They suggest that these entities represent a structure that could anticipate cells at a later stage in the origin of life. Such microspheres are optimistically called protocells. A better term, coacervate, was first used by the Russian biologist Oparin, in 1924, in his pioneering examination of the origin of life. We will return to Oparin's coacervate after we have considered, in more detail, the transition from precellular living systems to cellular ones.

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Asian Terrorism

Wed, 11 Jun 2008 13:39:27 +0200

The potential for conflict will arise from rivalries in Asia, ranging from India-Pakistan to China-Taiwan, as well as among the antagonists in the Middle East. Their potential lethality will grow, driven by the availability of WMD, longer-range missile delivery systems, and other technologies.

Internal conflicts stemming from religious, ethnic, economic, or political disputes will remain at current levels or even increase in number. The United Nations and regional organizations will be called on to manage such conflicts because major states—stressed by domestic concerns, perceived risk of failure, lack of political will, or tight resources—will minimize their direct involvement.

Export control regimes and sanctions will be less effective because of the diffusion of technology, porous borders, defense industry consolidations, and reliance on foreign markets to maintain profitability. Arms and weapons technology transfers will be more difficult to control.

Prospects will grow that more sophisticated weaponry, including weapons of mass destruction—indigenously produced or externally acquired—will get into the hands of state and non-state belligerents, some hostile to the United States. The likelihood will increase over this period that WMD will be used either against the United States or its forces, facilities, and interests overseas. … Rapid advances and diffusion of biotechnology, nanotechnology, and the materials sciences, moreover, will add to the capabilities of our adversaries to engage in biological warfare or bio-terrorism.

Most adversaries will recognize the information advantage and military superiority of the United States in 2015. Rather than acquiesce to any potential U.S. military domination, they will try to circumvent or minimize U.S. strengths and exploit perceived weaknesses. IT-driven globalization will significantly increase interaction among terrorists, narco-traffickers, weapons proliferators, and organized criminals, who in a networked world will have greater access to information, to technology, to finance, to sophisticated deception-and-denial techniques and to each other. Such asymmetric approaches—whether undertaken by state or non-state actors—will become the dominant characteristic of most threats to the U.S. homeland.

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