IRRESPECTIVE OF BOX COLLECTN
////////////////..........If you smart at the term "imperialism", one can conclude that you are
smarting all the time, and doing so at numerous other terms circling
each heated sphere of discourse: those terms that are synonymous with,
and bear the same innocuous proof of base, unlawful power. I mean
words like globalization, piracy, terrorism, totalitarianism, fascism,
despotism, etc. These words evoke a rampage of emotion, yes. But they
reveal real movements, predilections, tendencies in current world
politics.
/////////////////
Old age is an excellent time for outrage. My goal is to say or do at least one outrageous thing every week.
~Maggie Kuhn~
/////////////////Gin, Television, and Cognitive Surplus", Clay Shirky noted that after WWII we were faced with something new: "free time. Lots and lots of free time. The amount of unstructured time among the educated population ballooned, accounting for billions of hours a year. And what did we do with that time? Mostly, we watched TV."
//////////////////An evaluation study of 350 Cornell students found that those who were asked "deep questions" (that elicit higher-order thinking) with frequent peer discussion scored noticeably higher on their math exams than students who were not asked deep questions or who had little to no chance for peer discussion. Dr. Terrell explains: "It's when the students talk about what they think is going on and why, that's where the biggest learning occurs for them…. You can hear people sort of saying, 'Oh I see, I get it.' … And then they're explaining to somebody else … and there's an authentic understanding of what's going on. So much better than what would happen if I, as the teacher person, explain it. There's something that happens with this peer instruction."
/////////////////A Human Language Gene Changes the Sound of Mouse Squeaks
NICHOLAS WADE
People have a deep desire to communicate with animals, as is evident from the way they converse with their dogs, enjoy myths about talking animals or devote lifetimes to teaching chimpanzees how to speak. A delicate, if tiny, step has now been taken toward the real thing: the creation of a mouse with a human gene for language.
The gene, FOXP2, was identified in 1998 as the cause of a subtle speech defect in a large London family, half of whose members have difficulties with articulation and grammar. All those affected inherited a disrupted version of the gene from one parent. FOXP2 quickly attracted the attention of evolutionary biologists because other animals also possess the gene, and the human version differs significantly in its DNA sequence from those of mice and chimpanzees, just as might be expected for a gene sculpted by natural selection to play an important role in language.
Researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have now genetically engineered a strain of mice whose FOXP2 gene has been swapped out for the human version. Svante Paabo, in whose laboratory the mouse was engineered, promised several years ago that when the project was completed, "We will speak to the mouse." He did not promise that the mouse would say anything in reply, doubtless because a great many genes must have undergone evolutionary change to endow people with the faculty of language, and the new mouse was gaining only one of them. So it is perhaps surprising that possession of the human version of FOXP2 does in fact change the sounds that mice use to
////////////////evoln of DISGUST
.Some evolutionary psychologists believe that disgust emerged as a protective mechanism against health risks, like feces, spoiled food or corpses. Later, many societies came to apply the same emotion to social "threats." Humans appear to be the only species that registers disgust, which is why a dog will wag its tail in puzzlement when its horrified owner yanks it back from eating excrement.
/////////////PANMIND-NOOSPHERE-THINKING ENVELOPE ON EARTH
//////////////// Gould wrote that "Humans are here by the luck of the draw
///////////////"A species with humanlike intelligence was no more "in the cards" than a species with an elephantlike trunk--both are just handy biological gadgets
//////////////Apes began to morph into humans, and the species Homo erectus emerged some two million years ago, Mr. Wrangham argues, for one fundamental reason: We learned to tame fire and heat our food.
“Cooked food does many familiar things,” he observes. “It makes our food safer, creates rich and delicious tastes and reduces spoilage. Heating can allow us to open, cut or mash tough foods. But none of these advantages is as important as a little-appreciated aspect: cooking increases the amount of energy our bodies obtain from food.”
He continues: “The extra energy gave the first cooks biological advantages. They survived and reproduced better than before. Their genes spread. Their bodies responded by biologically adapting to cooked food, shaped by natural selection to take maximum advantage of the new diet. There were changes in anatomy, physiology, ecology, life history, psychology and society.” Put simply, Mr. Wrangham writes that eating cooked food — whether meat or plants or both —made digestion easier, and thus our guts could grow smaller. The energy that we formerly spent on digestion (and digestion requires far more energy than you might imagine) was freed up, enabling our brains, which also consume enormous amounts of energy, to grow larger. The warmth provided by fire enabled us to shed our body hair, so we could run farther and hunt more without overheating. Because we stopped eating on the spot as we foraged and instead gathered around a fire, we had to learn to socialize, and our temperaments grew calmer.
There were other benefits for humanity’s ancestors. He writes: “The protection fire provided at night enabled them to sleep on the ground and lose their climbing ability, and females likely began cooking for males, whose time was increasingly free to search for more meat and honey. While other habilines” — tool-using prehumans — “elsewhere in Africa continued for several hundred thousand years to eat their food raw, one lucky group became Homo erectus — and humanity began.”
//////////////////.....He then delivers a thorough, delightfully brutal takedown of the raw-food movement and its pieties. He cites studies showing that a strict raw-foods diet cannot guarantee an adequate energy supply, and notes that, in one survey, 50 percent of the women on such a diet stopped menstruating. There is no way our human ancestors survived, much less reproduced, on it. He seems pleased to be able to report that raw diets make you urinate too often, and cause back and hip problems.
///////////////.........Even castaways, he writes, have needed to cook their food to survive: “I have not been able to find any reports of people living long term on raw wild food.” Thor Heyerdahl, traveling by primitive raft across the Pacific, took along a small stove and a cook. Alexander Selkirk, the model for Robinson Crusoe, built fires and cooked on them.
Mr. Wrangham also dismisses, for complicated social and economic reasons, the popular Man-the-Hunter hypothesis about evolution, which posits that meat-eating alone was responsible. Meat eating “has had less impact on our bodies than cooked food,” he writes. “Even vegetarians thrive on cooked diets. We are cooks more than carnivores.”
///////////////..........Among the most provocative passages in “Catching Fire” are those that probe the evolution of gender roles. Cooking made women more vulnerable, Mr. Wrangham ruefully observes, to male authority.
“Relying on cooked food creates opportunities for cooperation, but just as important, it exposes cooks to being exploited,” he writes. “Cooking takes time, so lone cooks cannot easily guard their wares from determined thieves such as hungry males without their own food.” Women needed male protection.
////////////////........Marriage, or what Mr. Wrangham calls “a primitive protection racket,” was a solution. Mr. Wrangham’s nuanced ideas cannot be given their full due here, but he is not happy to note that cooking “trapped women into a newly subservient role enforced by male-dominated culture.”
“Cooking,” he writes, “created and perpetuated a novel system of male cultural superiority. It is not a pretty picture.” As a student, Mr. Wrangham studied with the primatologist Jane Goodall in Gombe, Tanzania, and he is the author, with Dale Peterson, of a previous book called “Demonic Males: Apes and the Origins of Human Violence.” In “Catching Fire” he has delivered a rare thing: a slim book — the text itself is a mere 207 pages — that contains serious science yet is related in direct, no-nonsense prose. It is toothsome, skillfully prepared brain food.
“Zoologists often try to capture the essence of our species with such phrases as the naked, bipedal or big-brained ape,” Mr. Wrangham writes. He adds, in a sentence that posits Mick Jagger as an anomaly and boils down much of his impressive erudition: “They could equally well call us the small-mouthed ape.”
/////////////A Juicy Fact to Digest
Q: True or false — fruit juice is a good substitute for whole fruit.
A: False. Nutritionally speaking, the primary difference between the two is in the fiber content. Whole fruit has it, and fruit juice doesn't (unless it's been added).
When it comes to weight, my issues with fruit juice are threefold. First, it takes longer to eat a piece of fruit than to drink the equivalent calories as juice (one orange contains 60 calories and one 8-ounce cup of orange juice contains 120 calories). Second, people tend to drink juice while also eating something else, whereas when you eat a piece of fruit, you're typically not eating or drinking anything else. Third, even though both whole fruit and fruit juice are high in sugar, the fiber in whole fruit keeps a lid on the effect dietary sugar has on your blood-sugar level. This is important because increased blood sugar causes your body to pump out insulin, a hormone that can make you hungrier in the long run.
//////////////////............
//////////////////.........A Juicy Fact to Digest
Q: True or false — fruit juice is a good substitute for whole fruit.
A: False. Nutritionally speaking, the primary difference between the two is in the fiber content. Whole fruit has it, and fruit juice doesn't (unless it's been added).
When it comes to weight, my issues with fruit juice are threefold. First, it takes longer to eat a piece of fruit than to drink the equivalent calories as juice (one orange contains 60 calories and one 8-ounce cup of orange juice contains 120 calories). Second, people tend to drink juice while also eating something else, whereas when you eat a piece of fruit, you're typically not eating or drinking anything else. Third, even though both whole fruit and fruit juice are high in sugar, the fiber in whole fruit keeps a lid on the effect dietary sugar has on your blood-sugar level. This is important because increased blood sugar causes your body to pump out insulin, a hormone that can make you hungrier in the long run.
////////////////////..............CA PREVN
But, she said, the institute has identified three steps people could take to dramatically affect the chances of developing cancer:
Eat a mostly plant-based diet.
Maintain a healthy weight.
Exercise regularly.
"The data is pretty clear that we can make a significant drop in the cancer rate with these three changes," Collins said. "We can prevent about one-third of cancers with these changes. And if you add tobacco prevention, which reduces about 30 percent of cancers, over half of today's cancers could be prevented."
///////////////////am sc..........The Origin of Life
A case is made for the descent of electrons
James Trefil, Harold Morowitz, Eric Smith
As the frontiers of knowledge have advanced, scientists have resolved one creation question after another. We now have a pretty good understanding of the origin of the Sun and the Earth, and cosmologists can take us to within a fraction of a second of the beginning of the universe itself. We know how life, once it began, was able to proliferate and diversify until it filled (and in many cases created) every niche on the planet. Yet one of the most obvious big questions—how did life arise from inorganic matter?—remains a great unknown.
Our progress on this question has been impeded by a formidable cognitive barrier. Because we perceive a deep gap when we think about the difference between inorganic matter and life, we feel that nature must have made a big leap to cross that gap. This point of view has led to searches for ways large and complex molecules could have formed early in Earth’s history, a daunting task. The essential problem is that in modern living systems, chemical reactions in cells are mediated by protein catalysts called enzymes. The information encoded in the nucleic acids DNA and RNA is required to make the proteins; yet the proteins are required to make the nucleic acids. Furthermore, both proteins and nucleic acids are large molecules consisting of strings of small component molecules whose synthesis is supervised by proteins and nucleic acids. We have two chickens, two eggs, and no answer to the old problem of which came first.
In this article we present a view gaining attention in the origin-of-life community that takes the question out of the hatchery and places it squarely in the realm of accessible, plausible chemistry. As we see it, the early steps on the way to life are an inevitable, incremental result of the operation of the laws of chemistry and physics operating under the conditions that existed on the early Earth, a result that can be understood in terms of known (or at least knowable) laws of nature. As such, the early stages in the emergence of life are no more surprising, no more accidental, than water flowing downhill.
The new approach requires that we adopt new ways of looking at two important fields of science. As we will see below, we will have to adjust our view of both cellular biochemistry and thermodynamics. Before we talk about these new ideas, however, it will be useful to place them in context by outlining a little of the history of research on the origin of life.
The Origin of Origins
Most historians would say that the modern era of experimental research in origin-of-life studies began in a basement laboratory in the chemistry department of the University of Chicago in 1953. Harold Urey, a Nobel laureate in chemistry, and Stanley Miller, then a graduate student, put together a tabletop apparatus designed to look at the kinds of chemical processes that might have occurred on the planet soon after its birth. They showed that organic molecules (in this case amino acids) could be created from inorganic materials by natural environmental conditions such as acidic solution, heat and electrical discharge (lightning), without the mediation of enzymes. This finding triggered a wave of new thinking about both the origin and nature of life. (Today, the consensus is that Miller and Urey had the wrong atmospheric components in their apparatus, so the process they discovered was probably not representative of the emergence of life on Earth. It nevertheless pointed to the potential fecundity and diversity of nonenzymatic primordial chemistry.)
Since 1953, we have found many of the same simple organic molecules in meteorites, comets and even interstellar gas clouds. Far from being special, then, the simplest of the molecules we find in living systems—life’s building blocks—seem to be quite common in nature. To many, the real question was how these basic building blocks got put together into living systems, and, equally important, how the molecules that led to modern life were selected out of the messy molecular milieu in which they arose.
The ubiquity of simple molecules suggested an appealing scenario that had a profound effect on the way investigators approached the origin of life throughout the last half of the 20th century. The scenario went like this: After the Earth cooled enough to allow oceans to form, the Miller-Urey process or something like it produced a rain of organic matter. In a relatively short time, the ocean became a broth of these molecules, and given enough time, the right combination of molecules came together by pure chance to form a replicating entity of some kind that evolved into modern life.
Scientists called this scenario the Oparin-Haldane conjecture, but it was given a provocative nickname that endures in the popular consciousness—Primordial Soup.
The essential legacy of the Primordial Soup was twofold: It simplified the notion of the origin of life to a single pivotal event, and then it proposed that that event—the step that occurred after the molecules were made—was a result of chance. In the standard language, life is to be seen, in the end, as a “frozen accident.” In this view, many fundamental details about the structure of life are not amenable to explanation. The architecture of life is just one of those things. Although many modern theories are less extreme than this, frozen-accident thinking still influences what some of us ask about the origin of life and how we prioritize our experiments.
RNA World
The next major advance came in the early 1980s, when Thomas Cech and Sidney Altman showed that some RNA molecules can act as enzyme-like catalysts. The frozen-accident argument was then replaced by a suggestive scenario in which something like RNA was assembled by chance, and was then able to fill twin roles as both enzyme and hereditary molecule in the runup to life. The RNA systems were then acted upon by natural selection, leading to greater molecular complexity and, eventually, something like modern life. Whereas most scientists believe, on the basis of Cech and Altman’s work, that life went through an early RNA-dominated phase (dubbed “RNA World”), the “RNA First” scenario has again a quality of frozen accident. Between prebiological chemistry and RNA World, a large leap occurs, requiring that molecules appear having at least a familial resemblance to the complex molecules in the vials of Cech and Altman, for that is the assumption upon which the relevance of their findings to the origin of life depends.
Inserting RNA molecules into an RNA First scenario without explaining how they got there seems to us an inadequate foundation for an origin theory. The RNA molecule is too complex, requiring assembly first of the monomeric constituents of RNA, then assembly of strings of monomers into polymers. As a random event without a highly structured chemical context, this sequence has a forbiddingly low probability and the process lacks a plausible chemical explanation, despite considerable effort to supply one. We find it more natural to infer that by the time complex RNA was possible, life was already well on the road to complexity. We believe further that we can see the primordial chemical architecture preserved in the universal metabolic chemistry we observe today.
The compelling feature of RNA World is that a primordial molecule provided both catalytic power and the ability to propagate its chemical identity over generations. As the catalytic versatility of these primordial RNA molecules increased due to random variation and selection, metabolic complexity began to emerge. From that stage, RNA had roles in both control of metabolism and continuity across generations, as it does today. Depending on which function one prefers to emphasize, these overall models have been called “Control First” or “Genetics First.” In either case, the proliferation of metabolism depended on RNA being there first.
Adherents have come to call the other possibility “Metabolism First” (though by this they have meant many slightly different things). In our version of Metabolism First, the earliest steps toward life required neither DNA nor RNA, and may not even have involved spatial compartments like cells; the earliest reactions could have occurred in the voids of porous rock, perhaps filled with organic gels deposited as suggested in the Oparin-Haldane model. We believe this early version of metabolism consisted of a series of simple chemical reactions running without the aid of complex enzymes, via the catalytic action of networks of small molecules, perhaps aided by naturally occurring minerals. If the network generated its own constituents—if it was recursive—it could serve as the core of a self-amplifying chemical system subject to selection. We propose that such a system arose and that much of that early core remains as the universal part of modern biochemistry, the reaction sequences shared by all living beings. Further elaborations would have been added to it as cells formed and came under RNA control, and as organisms specialized as participants in more complex ecosystems.
Networks of synthetic pathways that are recursive and self-catalyzing are widely known in organic chemistry, but they are notorious for generating a mass of side products, which may disrupt the reaction system or simply dilute the reactants, preventing them from accumulating within a pathway. The important feature necessary for chemical selection in such a network, which remains to be demonstrated, is feedback-driven self-pruning of side reactions, resulting in a limited suite of pathways capable of concentrating reagents as metabolism does. The search for such self-pruning is one of the most actively pursued research fronts in Metabolism First research.
A Pair of Analogies
Sidebar: Metabolism 101
Here’s an analogy that will provide an outline for the argument we make: Consider the requirements of the U.S. Interstate highway system. The system includes an enormously complex network of roads; major infrastructure devoted to extracting oil from the Earth, refining oil into gasoline and distributing gasoline along the highways, a major industry devoted to producing automobiles; and so on. If we wanted to explain this system in all of its complexity, we would not ask whether cars led to roads or roads led to cars, nor would we suspect that the entire system had been created from scratch as a giant public works project. It would be more productive to consider the state of transport in preindustrial America and ask how the primitive foot trails that must certainly have existed had developed into wagon roads, then paved roads and so on. By following this evolutionary line of argument, we would eventually account for the present system in all its complexity without needing recourse to highly improbable chance events.
In the same way, we argue, the current complexity of life should be understood as the result of a multistep process, beginning with the catalytic chemistry of small molecules acting in simple networks—networks still preserved in the depths of metabolism—elaborating these reaction sequences through processes of simple chemical selection, and only later taking on the aspects of cellularization and organismal individuality that make possible the Darwinian selection that biologists see today. Our task as origin-of-life researchers is to look at the modern highways and see what they reveal about the original foot trails.
The very robustness of modern life makes such questions difficult, because the metabolism that we see today seems to be one on which life has converged, and around which it reorganizes after historical shocks such as the oxygenation of the atmosphere at the beginning of the paleoproterozoic era, the emergence of multicellularity, dramatic climate changes that have reshaped environments and so on. To avoid confusing this convergent form with one toward which evolution was “directed,” we focus instead on the nonliving world that preceded life and ask “what was wrong” with such a world, which created the first steps toward life as a departure. In other words, what was the “problem” that a lifeless earth “solved” by the emergence of life?
Another analogy will illustrate how this question should be understood. Imagine a large pond of water sitting on top of a hill. We know that there are any number of other states—any in which the water is lower than it is at the top—which have lower energy and are therefore states toward which the system will tend to evolve over time. In terms of our question, the ”problem” faced by the system is how to get water from its initial state to any state of lower energy—how to get the water down the hill. We need not think of the laws of physics as being endpoint directed; rather, they simply adjudicate between states of higher or lower energy, with a preference for lower. Can we apply the same reasoning to the chemistry of life?
For real hills, we understand not only that the water will flow downward but also many things about how it will do so. Molecules of water will not each flow down a random path. Instead the flowing water will cut a channel in the hillside. In fact, the flow of water is at once constructing a channel and contributing to the collapse of the energy imbalance that drives the entire process. In addition, if we look at this process in detail, we see that what really matters is the configuration of the earth near the top of the hill, for it is there that the channeling process starts. This part of the analogy turns out to be particularly appropriate when we consider early chemical reactions.
In the analogy, the “problem” is the fact that the water begins in a state of high energy; the creation of the channel ”solves” this problem by allowing the water to move to a lower energy state. Furthermore, the dynamics of the system are such that once the channel is established, subsequent flow will reinforce and strengthen it. There are many such systems of channels in nature—the lightning bolt is an example, although in that case the forces at work are electrical, not gravitational. (When lightning occurs, positive and negative charges become separated between clouds and the ground. The charge separation ionizes atoms in the air, creating a conducting channel through which the charges flow—the lightning bolt—much as water flows down a hill).
We argue that the appearance of life on our planet followed the creation of just such a channel, except that it was a channel in a chemical rather than a geological landscape. In the abiotic world of the early Earth, likely in a chemically excited environment, reservoirs of energy accumulated. In effect, electrons (along with certain key ions) were pumped up chemical hills. Like the water in our analogy, those electrons possessed stored energy. The “problem” was how to release it. In the words of Albert Szent-Gyorgi: “Life is nothing but an electron looking for a place to rest.”
For example, carbon dioxide and hydrogen molecules are produced copiously in ordinary geochemical environments such as deep sea vents, creating a situation analogous to the water on the hill. The energy of this system can be lowered if the electrons in the hydrogen ”roll down the hill” by combining with the atoms of carbon dioxide in a chemical reaction that produces water and acetate (a molecule with two carbon atoms). In the abiotic world, however, this particular reaction takes place so slowly that the electrons in the hydrogen molecles find themselves effectively stranded at the top of the energy hill.
In this example, the problem that is solved by the presence of life is getting energized electrons back down the chemical hill. This is accomplished by the establishment of a sequence of biochemical channels, each contributing to the whole. (Think of the water cutting multiple channels in the hill). The reactions that create those channels would involve simple chemical transactions between small organic molecules.
How can we translate these sorts of general arguments into a reasonable scenario for the appearance of the first living thing? One way would be to look closely at the metabolic chart shown earlier, the diagram that maps the basic chemical reactions in all living systems.
At the very core of metabolism—the starting point for the synthetic pathways of all biomolecules—is a relatively simple set of reactions known as the citric acid cycle (also called the tricarboxylic acid cycle or the Krebs cycle). The cycle involves eight molecules, each a carboxylic acid (a molecule containing —COO groups). In most present-day life forms on Earth, the citric acid cycle operates to break organic molecules down into carbon dioxide and water, using oxygen to produce energy for the cell—in effect, ”burning” those molecules as fuel. (Technically, a molecule like glucose is first broken down into smaller molecules like pyruvate, which is then fed into the citric acid cycle. Full decomposition of pyruvate to CO2 and water is facilitated by transfer of high-energy electrons to certain coreactants that, in the modern cell, ferry the electrons to other reactions). When the cycle operates in this way, we say that it is in its oxidative mode.
The cycle can also operate in the opposite direction, taking in energy (in the form of high-energy electrons) and building up larger molecules from smaller ones. This is called the reductive mode of the cycle. If an organism has access to high-energy electrons like those produced by geochemical processes, in fact, it can thrive with the cycle exclusively in the reductive mode, having no use for the oxidative mode at all. One way to think about the two modes of the cycle is this: In the oxidative mode, the input is an organic molecule, and the output is chemical energy, carbon dioxide and water. In the reductive mode, the input is chemical energy, carbon dioxide and water, and the output is a more complex molecule.
This must have been the way the cycle operated on the early Earth, because molecular oxygen was not available primordially to support the oxidative mode, and because we see it operating this way today in some anaerobic organisms that seem to have preserved this aspect of the biochemistry of their ancestors. In the reductive mode, the cycle provides a way for high-energy electrons to flow down the chemical hill. It is similar to the acetate reaction shown earlier, which is thermodynamically feasible but very slow, but with the addition of a network of small molecules—the reductive citric acid cycle—acting to mediate and speed up the reaction. On biochemical and thermodynamic grounds, then, the reductive citric acid cycle (or some simpler precursor) would be a good candidate for the threshold of early life—the point where the pond of high-potential water is breached and the downhill pathway is etched out. The slow uncatalyzed conversion of carbon dioxide and hydrogen into acetate and water, shown earlier, occurs efficiently as the energy and reactants enter a primordial network of reactions like the modern-day reductive citric acid cycle.
In the metabolic maps of all modern organisms, the small molecules and reactions of the citric acid cycle are the starting point of every biosynthetic pathway—all roads lead from the citric acid cycle. However, in some organisms the reactions do not form a closed—cyclic—reaction sequence. For that reason, even among researchers convinced that these reactions are vestiges of the first metabolism, debate remains over whether the very first metabolic footpath was a cycle. However, because only cycles can act as self-amplifying channels, and because in organisms not running the closed cycle, sophisticated compensating adaptations are required, we consider a primordial reductive citric acid cycle the most likely route from geochemistry to life—the rivulet that formed at the top of the energy hill, through which the pond of energy began its thermodynamic escape. We then ask how, from this simple beginning, could the complexity we see in the modern cell arise. The first thing to notice is that, taken by itself, the cycle captures only part of the energy in the carbon dioxide and hydrogen that constitute its input. In transforming the carbon dioxide to acetate, for example, the cycle harvests only about a third of the energy available in the electrons. Even in the deep core of metabolism, however, we do not see the cycle in isolation. Its lowest-energy molecule, acetate, is the starting point for other pathways that make the essential oils used in cell membranes, harvesting another third of the electron energy. Further reactions, such as those that generate methane, can capture the remaining available energy, though methane is a gas and therefore a waste product, unlike the earlier molecules in the pathway, which are constituents of biomass.
Selection Begins
We note that there is a fundamental difference between the way chemical reaction systems could have operated before the appearance of the first self-replicating molecules and the way they operate now that self-replicating systems have developed. In the beginning, the only potential source of order would have been networks of chemical reactions operating according to the laws of chemistry and physics. After molecules appeared that could replicate more or less independently, such as RNA, however, evolution could have proceeded according to the rules of natural selection, with the success of subsequent generations dependent on adaptive properties. Exactly when and how this transition occurred remains an open question debated by researchers, but the fact that it did occur is plain. Another way of saying this is that before the appearance of the first self-replicating molecules or assemblages of molecules (and, again, we have to emphasize that these may or may not have been inside cells), what mattered was the persistence of the chemical network; after such a system appeared, natural selection took on its more familiar form of selection among rival reproducing “individuals.”
Once natural selection began, systems with slightly different chemistry would appear on the scene through random accident. For example, acetate can be used in two ways to make oily molecules, and the major domains of life divide, in part, according to which class they make and how they use them. Methane production purely for energetic purposes may have been primordial, or it may have been coupled to metabolism in a later, more complicated age (another topic of serious debate among researchers investigating the deepest branches of the tree of life).
The important pattern to appreciate is that the primordial cycle provides the stability and starting materials that make an age of selection possible. We think it was at the transition to this stage that geochemistry began to take on the features of replication and selection recognized by Darwin as distinctive of life. After such an age has begun, it can maintain the complexity and diversity needed to explore for refinements—in efficiency, in adaptation to the geological environment or in specialized division of labor within communal systems. The same pattern repeated itself when the environment was changed by the accumulation of a destructive toxin—oxygen—that was produced by primordial organisms as a waste product. As they adapted, organisms did not abandon the reductive citric acid cycle, which we believe was the unique foundation for biosynthesis. Instead they acquired the ability to run the cycle in reverse, extracting energy from the breakdown of molecules similar to those the cycle formerly produced.
The role of the citric acid cycle as a foundation for complexity applies not only to subsequent adaptation by organisms under selection; it can be seen even within the chemical structure of the metabolic core itself. A particularly powerful way to make this point is to rework the schematic chart of current metabolism first developed by Nicholson. The original Nicholson chart was developed to elaborate human metabolism and was gradually expanded to incorporate the complex webs of chemistry on which humans depend. Recently, one of us (Morowitz) and Vijay Srinivasan used evidence from microbiology to distill the Nicholson chart, with its complex modules and domains of metabolism, down to a minimal common core, the necessary and sufficient network of reactions to make a living system. Within this core chart, which will be published soon, we arrayed pathways as layers built around citric acid cycle precursors. A fragment of that detailed chart is shown in Figure 4. The innermost layer consists of molecules that can be built from cycle intermediates with one chemical reaction, the next layer consists of those that can be built with two reactions, and so on. (Once you get past the first few layers, the counting becomes ambiguous, as the reactions often involve molecules that were themselves the products of layers farther in).
From this layered structure we believe we can see the chemical cascade that comprised the earliest steps in the evolution of life.
The primordial core chart is simpler than the elaborate chart made by combining organisms today, but it is not much simpler biosynthetically. It contains the major modules for sugars, oils and amino and nucleic acids, and we have proposed that it was—at least in broad outline—the agency of chemical selection in an era that preceded natural selection on distinguishable organisms.
If this notion turns out to be true, it will have important implications for a deep philosophical question: whether we should understand the history of life in terms of the working out of predictable physical principles or of the agency of chance. We are, in fact, arguing that life will appear on any planet that reproduces the environmental and geological conditions that appeared on the early Earth, and that it will appear in order to solve precisely the sort of ”stranded electron” problem discussed above. The currently popular view that complex life was something of a frozen accident was set forth in Jacques Monod’s classic book Chance and Necessity (1970). We, of course, are arguing the opposite, if only for a significant part of basic chemical architecture. (It is important to appreciate that Monod studied regulatory systems, and in the domain of his expertise, we recognize the importance of accident, though we believe he advocated it too broadly.) It has not escaped our notice that the mechanism we are postulating immediately suggests that life is widespread in the universe, and can be expected to develop on any planet whose chemistry resembles that of the early Earth.
The view of life originating as a network of simple chemical reactions will require a lot of testing before it is adopted by the scientific community. We identify two areas where research is being pursued: the development of the theory of nonequilibrium statistical mechanics and the experimental pursuit of those first nonenzymatic chemical reactions that led to modern life.
On the theoretical side, we have to start with the realization that if we apply standard equilibrium thermodynamics to living systems, we arrive at something of a paradox. Living systems possess low entropy, which makes them very improbable from the equilibrium thermodynamic viewpoint. From the point of view of theoretical physics, the basic problem is that classical thermodynamics has only been well developed for systems in equilibrium—systems that do not change over time—or that change only by moving through successive, infinitesimally different equilibrium states. What is needed, therefore, is an extension of ordinary thermodynamics so that it can apply to systems maintained far from equilibrium by the flow of energy.
One promising approach was first suggested by E. T. Jaynes in the mid-20th century. He recognized that information (and hence entropy) is associated not just with states but with whole histories of change, which can include channel flows of the sort we have been discussing. Technically, one cannot talk about the entropy “of a state” if the state depends for its context on a process of change; only the entropy of the whole process is expected to be maximized. To return to our pond on the hill, there is not a separate entropy of the pond, except as an approximation. Rather, there is an entropy of paths of change that include pond, channel, construction and relaxation. When such a formulation is analyzed for a simple system, the establishment of a channel can be seen as a phase transition, similar to the freezing of an ice cube or, to use a more precise mathematical analogy, the formation of a magnet from molten iron. (In the latter case, the phase transition occurs as the metal cools when the atomic dipole magnets line up in the same direction—paradoxically, a more ordered state). The full entropy of the process will be maximized in the system, even though the approximate entropy associated with the “state” of the channel may not be, thereby eliminating the paradox.
Current research into this foundational question now centers on the fact that the chemical substrate of living systems is much more complex than that of simple physical systems that have been examined so far. One important new direction of research involves the development of small-molecule catalysts in increasingly complex cooperative networks. The hope is that when a full theory is available, we will see the formation of life as an inevitable outcome of basic thermodynamics, like the freezing of ice cubes or the formation of magnets.
On the experimental side, some researchers, such as George Cody at the Carnegie Institution of Washington, D.C., are trying to work out the basic rules of organic chemistry for exotic environments that might have been relevant to the origin of life. Cody, for example, has worked on unraveling organic interactions at the kinds of temperatures and pressures that obtain at deep ocean vents. Mike Russell at the Jet Propulsion Laboratory in Pasadena, California, (author of “First Life,” January–February 2006) is building a large chamber to model the geochemistry of those environments. Shelley Copley at the University of Colorado at Boulder has been sorting out the intermediate chemistry leading to the current nucleic acid–protein system of genetic coding, with an eye toward resolving the chicken-and-egg problem. These experiments represent a major paradigm shift from the top-down control envisioned in RNA World scenarios. Rather than supposing that a few large RNA molecules control the adaptation of a passive small-molecule reaction network, Copley supposes that whole networks of intermediate molecules support each other on the path toward complexity. In this experimental setting, networks of small and randomly synthesized amino acids and single RNA units aid each others’ formation, assembly into strings and evolution of catalytic capacity. Both types of molecules grow long together. Complexity, adaptation and control are distributed in such networks, rather than concentrated in one molecular species or reaction type. Distributed control is likely to be a central paradigm in the development of Metabolism First as a viable theory. We eagerly anticipate more experimental efforts like these to explore the many facets of small-molecule system organization.
In a larger sense, however, the future of the experimental program associated with the Metabolism First philosophy is tied to the development of the appropriate theory, guided by experimental results. The hope is that the interplay of theory and experiment, so familiar to historians of science, will produce a theory that illuminates the physical principles that led to the development of life and, hence, give us the ability to re-create life in our laboratories.
Assuming the experimental and theoretical programs outlined above work out well, our picture of life as a robust, inevitable outcome of certain geochemical processes will be on firm footing. Who knows? Maybe then someone will write a book titled Necessity, Not Chance.
Bibliography
Morowitz, H. J. 1999. A theory of biochemical organization, metabolic pathways, and evolution. Complexity 4:39–53
Smith, E., and H. J. Morowitz. 2004. Universality in intermediary metabolism. Proceedings of the National Academy of Sciences of the U.S.A. 101:13168–13173.
Morowitz, H. J., and E. Smith. 2007. Energy flow and the organization of life. Complexity 13:51–59.
Srinivasan, V., and H. J. Morowitz. 2009. The canonical network of autotrophic intermediary metabolism. Biological Bulletin. In Press.
///////////////////////METABOLISM FIRST THEORY-Wächtershäuser's hypothesis
Main article: iron-sulfur world theory
Deep-sea black smoker
Another possible answer to this polymerization conundrum was provided in 1980s by Günter Wächtershäuser, in his iron-sulfur world theory. In this theory, he postulated the evolution of (bio)chemical pathways as fundamentals of the evolution of life. Moreover, he presented a consistent system of tracing today's biochemistry back to ancestral reactions that provide alternative pathways to the synthesis of organic building blocks from simple gaseous compounds.
In contrast to the classical Miller experiments, which depend on external sources of energy (such as simulated lightning or UV irradiation), "Wächtershäuser systems" come with a built-in source of energy, sulfides of iron and other minerals (e.g. pyrite). The energy released from redox reactions of these metal sulfides is not only available for the synthesis of organic molecules, but also for the formation of oligomers and polymers. It is therefore hypothesized that such systems may be able to evolve into autocatalytic sets of self-replicating, metabolically active entities that would predate the life forms known today.
The experiment produced a relatively small yield of dipeptides (0.4% to 12.4%) and a smaller yield of tripeptides (0.10%) but the authors also noted that: "under these same conditions dipeptides hydrolysed rapidly."[37]
////////////////////CHILLI-Bolivia is believed to be the chili's motherland, home to dozens of wild species that may be the ancestors of all the world's chili varieties—from the mild bell pepper to the medium jalapeño to the rough-skinned naga jolokia, the hottest pepper ever tested. The heat-generating compound in chilies, capsaicin, has long been known to affect taste buds, nerve cells and nasal membranes (it puts the sting in pepper spray). But its function in wild chili plants has been mysterious.
///////////////People have been spicing up their food with chilies for at least 8,000 years. At first they used wild chilies, likely adding them to potatoes, grain and corn, says Linda Perry, an archaeobotanist at Smithsonian's National Museum of Natural History. She has found traces of chilies on ancient milling stones and cooking pots from the Bahamas to southern Peru. Based on her studies of potsherds from different archaeological sites, she concludes that people in the Americas began cultivating chilies more than 6,000 years ago. Just why they did is a matter of scholarly debate. Perry believes it was a question of taste. "Chilies were domesticated early and spread very quickly just because people like them," she says. "Do you want a big pot of yams or a pot of yams with chilies thrown in?" Other researchers, such as Jennifer Billing and Paul Sherman at Cornell University, argue that people learned early on that chilies could reduce food spoilage. And some scholars point to medical uses. Ancient Mayans incorporated chilies into medicinal preparations for treating infected wounds, gastrointestinal problems and earaches. Laboratory studies have shown that chili pepper extracts inhibit a number of microbial pathogens, and capsaicin has been used in a local anesthetic.
Whatever the benefits, chilies spread around the world with astonishing speed, thanks in part to Christopher Columbus. In 1492, the explorer encountered some plants cultivated by the Arawak Indians in Hispaniola. Convinced he had landed in India, he referred to them as "pepper," an unrelated spice native to the subcontinent. "The land was found to produce much ajÃ, which is the pepper of the inhabitants, and more valuable than the common sort [black pepper]," he later wrote. "They deem it very wholesome and eat nothing without it." Columbus took chilies back to Spain, but they initially were unappreciated in Europe. The Portuguese got acquainted with chilies at their trading post in Pernambuco, Brazil, and carried them, with tobacco and cotton, to Africa. Within 50 years of Columbus' voyages, Pernambuco chilies were being cultivated in India, Japan and China. Chilies made it to the American Colonies with the English in 1621.
///////////////////Obama's climate guru: Paint your roof white!
By Steve Connor, Science Editor
Wednesday, 27 May 2009SHARE PRINTEMAILTEXT SIZE NORMALLARGEEXTRA LARGE
ALAMY
Houses with white roofs, like these in Greece, would be able to reflect light back through the atmosphere, according to Steven Chu, the US Secretary of Energy
ENLARGE
Some people believe that nuclear power is the answer to climate change, others have proposed green technologies such as wind or solar power, but Barack Obama's top man on global warming has suggested something far simpler – painting your roof white.
Steven Chu, the US Secretary of Energy and a Nobel prize-winning scientist, said yesterday that making roofs and pavements white or light-coloured would help to reduce global warming by both conserving energy and reflecting sunlight back into space. It would, he said, be the equivalent of taking all the cars in the world off the road for 11 years.
Speaking in London prior to a meeting of some of the world's best minds on how to combat climate change, Dr Chu said the simple act of painting roofs white could have a dramatic impact on the amount of energy used to keep buildings comfortable, as well as directly offsetting global warming by increasing the reflectivity of the Earth.
/////////////////The white revolution: How it would work
* The idea of painting surfaces white to conserve energy is being actively pursued by the US. Earlier this month, Barack Obama's chief scientific adviser, John Holdren, received a scientific memorandum on the subject.
* Scientists estimate that making roofs and pavements white or more light-coloured would counter global warming with "negative radiative forcing" – reflecting sunlight back into space. They said that retrofitting urban roofs and pavements in tropical and temperate regions with solar-reflective materials would offset about 44 billion tonnes of carbon dioxide.
* The scientists said it would lower the cost of air conditioning, making buildings more comfortable and mitigate the "urban heat island" effect caused by the concentration of concrete surfaces in cities.
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Teflon was invented by Roy J. Plunkett in 1938 while he was experimenting with refrigerants at DuPont Labs. His patent was granted in 1941.
Velcro was invented by Swiss electrical engineer Georges de Mestral, who said he got the idea from burrs he picked up on a hike. He obtained a patent on his hook-and-loop fabric fastener in 1955.
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Dear Cecil:
OK, no bullshit now. I got a simple question, I want a simple answer: how come you can see through glass?— Daniel C., Washington, D.C.
Dear Daniel:
Not to beat around the bush or anything, Dan, but the reason you can see through glass basically is that there is no reason for you not to be able to see through it. Despite its appearance, glass is really a highly viscous liquid rather than a solid, and you can see through it for the same reasons that you can see through water.
Having supplied that admirably simple answer, permit me to elaborate. Conventional liquids, when cooled, have a freezing point at which they suddenly become solid. Liquid glass, by contrast, simply gets gradually stiffer as it cools. At room temperature its rate of flow is so slow that it would take billions of years to ooze out of shape, and for most practical purposes it may be treated as a solid.
Its internal structure, though, is not the regular crystalline latticework of your standard solid, but rather
///////////////////Anger is a wind which blows out the lamp of the mind.
~ Robert G Ingersoll
////////////////// AN EFFING AWFUL
//////////////////UTI in Preterm Infants
May 6, 2009 | F. Bruder Stapleton, MD | Pediatrics and Adolescent Medicine
Breast-feeding was associated with lower risk for UTI.
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