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The following are quotes added to my Unclassified Quotes database in February 2007 (2). The date format is dd/mm/yy. See copyright conditions at end.
[Jan, Feb (1); Mar, Apr, May, Jun, Jul, Aug, Sep, Oct, Nov, Dec]
15/02/2007 "The neo-Darwinian theory of evolution is not only suffering from an identity crisis but may also be radically transformed to account for the growing number of scientific anomalies that continue to plague it. These were the underlying themes that could be inferred from presentations made by prominent scientists in the recently completed symposium entitled `What happened to Darwinism between the Two Darwin Centennials, 1958-1982?' The symposium was convened under the auspices of the 148th Annual Meeting of the prestigious American Association for Advancement of Science held from January 3, 1982, to January 8, 1982, at Washington, D.C. ... The symposium was a disappointment to the true believers of neo-Darwinism. Implicit in their counteroffensive to stamp out creationism was the recognition that they had to contain and mend the fissures that were increasingly undermining the scientific foundation of their own neo-Darwinist position. To their dismay, the Provine symposium aggravated and deepened the fissures." (Perlas, N., "Neo- Darwinism Challenged at AAAS Annual Meeting," Towards, Vol. 2, Spring 1982, pp.29-30. In Morris, H.M., "Evolution in Turmoil: An Updated Sequel to The Troubled Waters of Evolution," Creation-Life Publishers: San Diego CA, 1982, pp.45-46) 15/02/2007 "Mutation consists of abrupt heritable changes in the composition or arrangement of genes, which are composed of deoxyribonucleic acid (DNA). Most mutations producing effects large enough to be observed are deleterious, although other mutations may produce effects of little or no consequence, and certain rare mutations may even be advantageous. The magnitudes of spontaneous mutation rates, the way selection acts on various gene combinations, and the size and structure of human populations are sufficient to maintain a rich source of genetic variability. An artificially increased mutation rate, however, is potentially capable of producing a general decline in genetic health unless balanced by increased selection against deleterious mutant genes; while such selection occurs extensively in most natural populations, the efficacy of modern medicine may increasingly tend to reduce selection against deleterious traits in many human populations. ... Being an error process, mutation consists of all possible changes in the genetic material (excluding recombination and segregation). Furthermore, the severity of any given mutation depends both upon the importance of the affected gene or genes and upon the nature of the mutational lesion itself. ... Since the vast majority of detectable mutations are deleterious, an artificially increased human mutation rate would be expected to be harmful in proportion to the increase." (Environmental Mutagenic Society, "Environmental Mutagenic Hazards," Science, Vol. 187, 14 February 1975, pp.503-514, pp.503-504, 512) 15/02/2007 "Another controversy that has been aroused by the finding of large amounts of variation in populations is the problem of genetic load. If large numbers of less fit alleles are maintained in populations by heterozygote superiority, there will be a very high probability that at each generation a zygote will be homozygous at one or more loci for a disadvantageous allele. As a result a large number of less fit zygotes might be expected, which could be a burden of mortality and infertility too great for the population to bear. Yet it must be remembered that each locus is not subject to selection separate from the others, so that thousands of selective processes would be summed as if they were individual events. The entire individual organism, not the chromosomal locus, is the unit of selection, and the alleles at different loci interact in complex ways to yield the final product. Since alleles are more likely to be tested as members of groups than as isolated units, the cost of maintaining variation in a population is actually far lower than was originally believed." (Ayala, F.J., "The Mechanisms of Evolution," Scientific American, Vol. 239, No. 3, September 1978, p.56) 15/02/2007 "In any case there can be no doubt that the staggering amount of genetic variation in natural populations provides ample opportunities for evolution to occur. Hence it is not surprising that whenever a new environmental challenge materalizes-a change of climate, the introduction of a new predator or competitor, man-made pollution populations are usually able to adapt to it. A dramatic recent example of such adaptation is the evolution by insect species of resistance to pesticides The story is always the same: when a new insecticide is introduced, a relatively small amount is enough to achieve satisfactory control of the insect pest. Over a period of time however, the concentration of the insecticide must be increased until it becomes totally inefficient or economically impractical. Insect resistance to a pesticide was first reported in 1947 for the housefly (Musca domestica) with respect to DDT. Since then resistance to one or more pesticides has been reported in at least 225 species of insects and other, arthropods. The genetic variants required for resistance to the most diverse kinds of pesticides were apparently present in every one of the populations exposed to these man-made compounds." (Ayala, F.J., "The Mechanisms of Evolution," Scientific American, Vol. 239, No. 3, September 1978, pp.56-57) 15/02/2007 "Natural selection is more intense in open environments, because it must offer more efficient resistance to the variations of the populations which live in them, and for this reason it favors a single genotype only. It plays a conservative rather than an innovating role. The mutations which diverge from the wild type or from the privileged genotype are swept away when the environment changes; hence the stability of the species." (Grassé, P.-P., "Evolution of Living Organisms: Evidence for a New Theory of Transformation," [1973], Academic Press: New York NY, 1977, p.87) 15/02/2007 "Panchronic species, which like other species are subject to the assaults of mutations, remain unchanged. Their variants are eliminated except possibly for neutral mutants. In any event, their stability is an observed fact and not a theoretical concept." (Grassé, P.-P., "Evolution of Living Organisms: Evidence for a New Theory of Transformation," [1973], Academic Press: New York NY, 1977, p.87) 15/02/2007 "Bacteria, the study of which has formed a great part of the foundation of genetics and molecular biology, are the organisms which, because of their huge numbers, produce the most mutants. This is why they gave rise to an infinite variety of species, called strains, which can be revealed by breeding or tests. Like Erophila verna, bacteria, despite their great production of intraspecific varieties, exhibit a great fidelity to their species. The bacillus Escherichia coli, whose mutants have been studied very carefully, is the best example. The reader will agree that it is surprising, to say the least, to want to prove evolution and to discover its mechanisms and then to choose as a material for this study a being which practically stabilized a billion years ago!" (Grassé, P.-P., "Evolution of Living Organisms: Evidence for a New Theory of Transformation," [1973], Academic Press: New York NY, 1977, p.87) 15/02/2007 "What is the use of their unceasing mutations, if they do not change? In sum, the mutations of bacteria and viruses are merely hereditary fluctuations around a median position; a swing to the right, a swing to the left, but no final evolutionary effect. Cockroaches, which are one of the most venerable living relict groups, have remained more or less unchanged since the Permian, yet they have undergone as many mutations as Drosophilia, a Tertiary insect. It is important to note that relict species mutate as much as others do, but do not evolve, not even when they live in conditions favorable to change (diversity of environments, cosmopolitianism, large populations)." (Grassé, P.-P., "Evolution of Living Organisms: Evidence for a New Theory of Transformation," [1973], Academic Press: New York NY, 1977, p.87) 15/02/2007 "How does the Darwinian mutational interpretation of evolution account for the fact that the species that have been the most stable-some of them for the last hundreds of millions of years have mutated as much as the others do? Once one has noticed microvariations (on the one hand) and specific stability (on the other), it seems very difficult to conclude that the former (microvariation) comes into play in the evolutionary process." (Grassé, P.-P., "Evolution of Living Organisms: Evidence for a New Theory of Transformation," [1973], Academic Press: New York NY, 1977, pp.87-88) 15/02/2007 "The God of the Old Testament is arguably the most unpleasant character in all fiction: jealous and proud of it; a petty, unjust, unforgiving control-freak; a vindictive, bloodthirsty ethnic cleanser; a misogynistic, homophobic, racist, infanticidal, genocidal, filicidal, pestilential, megalomaniacal, sadomasochistic, capriciously malevolent bully." (Dawkins, R., "The God Delusion," Bantam Press: London, 2006, p.31) 15/02/2007 "I am not attacking the particular qualities of Yahweh, or Jesus, or Allah, or any other specific god such as Baal, Zeus or Wotan. Instead I shall define the God Hypothesis more defensibly: there exists a superhuman, supernatural intelligence who deliberately designed and created the universe and everything in it, including us. This book will advocate an alternative view: any creative intelligence, of sufficient complexity to design anything, comes into existence only as the end product of an extended process of gradual evolution. Creative intelligences, being evolved, necessarily arrive late in the universe, and therefore cannot be responsible for designing it. God, in the sense defined, is a delusion; and, as later chapters will show, a pernicious delusion." (Dawkins, R., "The God Delusion," Bantam Press: London, 2006, p.31. Emphasis original) 16/02/2007 "The all-pervading message of the Cambridge meeting was that genomic DNA is in a surprisingly dynamic state. ... The most obvious comment to make about the genomes of higher organisms is that biologists understand the function of only a tiny proportion of the DNA in them: namely, the genes that code for proteins. In the human genome, for instance, these protein-coding genes constitute marginally more than 1 percent of all the DNA. The rest of the genome is the target of much speculation, but few secure answers." (Lewin, R., "Do Jumping Genes Make Evolutionary Leaps?," Science, Vol. 213, 7 August 1981, p.634) 16/02/2007 "Allan C. Wilson and his associates at the University of California at Berkeley compared blood proteins- specifically hemoglobin, albumin, and transferrin-of various vertebrates to see whether changes in structural genes are related to anatomical evolution. They reasoned that, if structural genes change as organisms evolve, then the most similar species, defined as those that can mate and produce offspring (hybridize), should have the most similar structural genes. If blood proteins are a representative sample of proteins coded by structural genes, the most similar species should have the most similar blood proteins. Wilson and his colleagues found, however, that structural genes for blood proteins accumulate mutations at rates that appear independent of anatomical evolution. Species that diverged most recently, rather than species that are most closely related, have the most similar blood proteins. ... Additional evidence that changes in structural genes may not be correlated with anatomical evolution was recently reported by Mary-Claire King of the University of California at San Francisco and Wilson. They compared a group of 44 proteins of human beings and chimpanzees- two species so dissimilar that they are placed by taxonomists in different families. However, King and Wilson found that the human proteins are, on the average, 99 percent identical to those of the chimpanzees. This means that the structural genes coding for these 44 proteins are as similar as the structural genes of species classified as sibling species. Sibling species, unlike human beings and chimpanzees, are virtually identical morphologically. King and Wilson suggest that changes in gene regulation rather than changes in structural genes are the key to anatomical evolution." (Kolata, G.B., "Evolution of DNA: Changes in Gene Regulation," Science, Vol. 189, 8 August 1975, pp.446-447, p.446) 16/02/2007 "The question of how changes in gene regulation can lead to anatomical changes is open to speculation. Gould, though, has resurrected the `fetalization theory,' proposed in the 1920's by the Dutch anatomist Louis Bolk to explain what sort of regulatory changes could have allowed human beings and chimpanzees to evolve from a common ancestor while retaining nearly identical structural genes. Bolk wrote that `man, in his bodily development, is a primate fetus that has become sexually mature,' and listed more than 20 traits that human beings share with fetal apes and monkeys to support his hypothesis. For example, people and embryonic apes and monkeys have rounded, bulbous craniums, small jaws, and an unrotated nonopposable big toe. Although Bolk's fetalization theory never gained widespread acceptance, Gould suggests that it is essentially correct. Changes in gene regulation, he claims, retarded developmental changes by retarding the sequence of gene expression in humans more than in apes and enabled human beings and apes to evolve from a common ancestor without substantial changes in structural genes. Both Gould and Wilson point out that there are large differences in chromosome structure between human beings and other primates that conceivably could be tied to this developmental slowdown. According to Gould, the adaptive significance of retarded development may be to permit more advanced animals a longer period to mature and thus a longer period in which to learn. Primates mature more slowly than other mammals and, among the nonhuman primates, more advanced species, such as apes, mature more slowly than less advanced species, such -as monkeys. The answer to the question of how species evolve, then, apparently involves changes in gene regulation and so awaits further studies of chromosome organization and control of gene expression in higher organisms. It thus seems evident that the old method of comparing proteins of different species may no longer be the primary tool for investigating the mechanisms underlying the-evolution of organisms." (Kolata, G.B., "Evolution of DNA: Changes in Gene Regulation," Science, Vol. 189, 8 August 1975, pp.446- 447, p.447) 16/02/2007 "Research, not on the archeogenes themselves but on the proteins encoded and determined by them, has not yielded the phylogenetic information expected. Such has been the case of the `paleoproteins,' the cytochromes. The cytochrome c of man differs by 14 amino acids from that of the horse, and by only 8 from that of the kangaroo (Macropus). Similar facts are found in the case of hemoglobin; the ß chain of this protein in man differs from that of the lemurs by 20 amino acids, by only 14 from that of the pig, and by only 1 from that of the gorilla. The situation is practically the same for other proteins." (Grassé, P.-P., "Evolution of Living Organisms: Evidence for a New Theory of Transformation," [1973], Academic Press: New York NY, 1977, p.194) 17/02/2007 "The last quote is from Gillespie again and it concerns Hooker. If you think about it, Hooker was the only professional systematist amongst the Darwin coterie. He was also Darwin's oldest confidant in reading all of Darwin's manuscripts and talking to him solidly since 1840 and yet he remained unconverted to evolution until 1859. Here is Gillespie on the reason Hooker was not converted. `Hooker adopted a view that species were immutable and each descended from a single parent. It was not necessarily his belief but a methodological postulate to make classification possible...Hooker believed that a taxonomist, who was an evolutionist, must ignore his theory and proceed as if species were immutable.' [Gillespie, N.C., "Charles Darwin and the Problem of Creation," University of Chicago Press: Chicago IL, 1979, p.49] In other words, evolution may very well be true but basing one's systematics on that belief will give bad systematics." (Patterson, C., "Evolutionism and Creationism," Transcript of Address at the American Museum of Natural History, New York NY, November 5, 1981, p.14) 17/02/2007 "Not all instances of biblicism, however, involved a direct theological influence. In his New Zealand flora, Hooker adopted the view that species were immutable (save for local variation) and each descended from a single pair. This was not necessarily his belief, but a methodological postulate to make classification possible. This, one of the most common instances of biblicism in natural history, disturbed Asa Gray, who suggested substituting for `single pair' the phrase `common stock,' which could better accord with the facts and requirements of nature. Hooker, however, continued the usage. In the flora of Tasmania (1860) he considered that the geographical distribution of species from a common center was `all but conclusive evidence in favour of the hypothesis of similar forms having had but one parent, or pair of parents.' Hooker, it should be noted, had by this time been a Darwinian for two years. The doctrine of centers of creation, that each species was thought to have originated as a single pair in a given locality, was, with its aura of Eden, historically an instance of biblicism, if not logically so, as Hooker's usage, and Wollaston's also, show. It could, and did, promote work in understanding the nature of natural barriers and was easily incorporated into Darwin's theory." (Gillespie, N.C., "Charles Darwin and the Problem of Creation," University of Chicago Press: Chicago IL, 1979, p.49) 17/02/2007 "The fundamental tenet of the molecular clock hypothesis is, that evolutionary rate. of homologous proteins are regular, so that the interval separating having species from common ancestors is reflected in the degree of protein dissimilarity between them. In general, the difference between species in numbers of individuals is accorded a relatively insubstantial role as a determinant of protein divergence measures, a neglect implicit in the concept itself. The postulation of clock-like divergence presupposes protein divergence rates to be uniform despite this (or other) outstanding differences. Indeed, the appeal of one explanation of such stochastic regularity, the neutral mutation-random drift theory (Kimura, 1968, 1960; King, and Jukes, 1969), lies in its assignment of the rate of amino acid replacement to the nucleotide mutation rate alone, assuming the latter to be constant. In order that an equilibrium between mutation and eventual replacement by drift be completely realized, however, the theory requires that species number remain unchanged over indefinitely extended intervals. The difficulty in evaluating empirically the theory's central thesis, that the majority of such replacements are indifferent (or nearly so) to natural selection. is therefore greatly compounded by ordinary recurrent circumstances in the natural history of species-stochastic variation in species number (see, e.g.. Haigh and Maynard Smith, 1972; Nei et al., 1975; Chakraborty, 1977). Perhaps in partial consequence, the validity of the neutrality hypothesis (or more properly, the extent of its applicability) is problematic after a decade of debate." (Korey, K.A., "Species Number, Generation Length, and the Molecular Clock," Evolution, Vol. 35, No. 1, 1981, pp.139-147, p.139) 18/02/2007 "The field of genetics has shed little light on the nature of importance of quantum speciation, in part because the role of regulatory genes in large-scale adaptive transitions has only recently become apparent. Simple estimates of overall genetic distance between species reveal little about degrees and rates of morphologic divergence." (Stanley, S.M., "Macroevolution: Pattern and Process," [1979], The Johns Hopkins University Press: Baltimore MD, Revised, 1998, pp.61-62) 18/02/2007 "When we consider the net degree of morphologic change between some ancestral mammal species and their living descendants, the mean number of selective deaths per generation is extraordinarily small. Maintenance of continuous selection pressures as feeble as the measured means is virtually impossible. Excluding genetic drift from consideration because of the adaptive nature of the transitions, we must invoke either stepwise evolution within lineages or quantum speciation." (Stanley, S.M., "Macroevolution: Pattern and Process," [1979], The Johns Hopkins University Press: Baltimore MD, Revised, 1998, p.62. Emphasis original) 18/02/2007 "The fossil record has failed to yield unequivocal examples of rapid phyletic evolution that produced marked transformations in morphology. Whether this condition militates against the gradualistic model depends upon the quality of the record." (Stanley, S.M., "Macroevolution: Pattern and Process," [1979], The Johns Hopkins University Press: Baltimore MD, Revised, 1998, p.62. Emphasis original) 18/02/2007 "The fossil record demonstrates that phyletic evolution (evolution within established species) proceeds very slowly. Especially in episodes of adaptive radiation, origins of higher taxa have generally been too rapid to be attributed to phyletic transformation. Particularly convincing evidence of this relationship is offered by Plio-Pleistocene mammals, for which it is possible to construct histograms representing chronospecies longevities and rates of phyletic evolution. The measured rates are much too slow to account for the origins of genera that appeared during the Pleistocene. Most of these, and in fact most genera of animals in general, must have formed rapidly, by divergent speciation. If typical for genera, this mode of origin must characterize the origins of families and other still higher taxa. Phyletic evolution in the Hominidae (human family) has apparently been even slower than that for other groups of the Mammalia, implying a punctuational pattern in the ancestry of Homo sapiens. The fossil record of marine invertebrates is also complete enough on an appropriate scale to document generally slow rates of phyletic transition. For both vertebrates and invertebrates, increase in body size may be the most conspicuous form of structural change accomplished by phyletic evolution." (Stanley, S.M., "Macroevolution: Pattern and Process," [1979], The Johns Hopkins University Press: Baltimore MD, Revised, 1998, p.63) 18/02/2007 "The sudden appearance of a large self-copying molecule such as RNA was exceedingly improbable. Energy-driven networks of small molecules afford better odds as the initiators of life." (Shapiro, R., "A Simpler Origin for Life," Scientific American, February 12, 2007) 18/02/2007 "The Watson-Crick structure triggered an avalanche of discoveries about the way in which living cells function today. These insights also stimulated speculations about life's origins. Nobel Laureate H. J. Muller wrote that the gene material was `living material, the present-day representative of the first life,' which Carl Sagan visualized as `a primitive free-living naked gene situated in a dilute solution of organic matter.' In this context, `organic' specifies material containing bound carbon atoms. Organic chemistry, a subject sometimes feared by pre-medical students, is the chemistry of carbon compounds, both those present in life and those playing no part in life. Many different definitions of life have been proposed. Muller's remark would be in accord with what has been called the NASA definition of life: Life is a self-sustained chemical system capable of undergoing Darwinian evolution." (Shapiro, R., "A Simpler Origin for Life," Scientific American, February 12, 2007) 18/02/2007 "Richard Dawkins elaborated on this image of the earliest living entity in his book The Selfish Gene: `At some point a particularly remarkable molecule was formed by accident. We will call it the Replicator. It may not have been the biggest or the most complex molecule around, but it had the extraordinary property of being able to create copies of itself.' When Dawkins wrote these words 30 years ago, DNA was the most likely candidate for this role. As we shall see, several other replicators have now been suggested. ... Unfortunately, complications soon set in. DNA replication cannot proceed without the assistance of a number of proteins--members of a family of large molecules that are chemically very different from DNA. Proteins, like DNA, are constructed by linking subunits, amino acids in this case, together to form a long chain. Cells employ twenty of these building blocks in the proteins that they make, affording a variety of products capable of performing many different tasks--proteins are the handymen of the living cell. Their most famous subclass, the enzymes, act as expeditors, speeding up chemical processes that would otherwise take place too slowly to be of use to life. The above account brings to mind the old riddle: Which came first, the chicken or the egg? DNA holds the recipe for protein construction. Yet that information cannot be retrieved or copied without the assistance of proteins. Which large molecule, then, appeared first in getting life started--proteins (the chicken) or DNA (the egg)?" (Shapiro, R., "A Simpler Origin for Life," Scientific American, February 12, 2007) 18/02/2007 "A possible solution appeared when attention shifted to a new champion--RNA. This versatile class of molecule is, like DNA, assembled of nucleotide building blocks, but plays many roles in our cells. Certain RNAs ferry information from DNA to structures (which themselves are largely built of other kinds of RNA) that construct proteins. In carrying out its various duties, RNA can take on the form of a double helix that resembles DNA, or of a folded single strand, much like a protein. In 2006 the Nobel prizes in both chemistry and medicine were awarded for discoveries concerning the role of RNA in editing and censoring DNA instructions. Warren E. Leary could write in the New York Times that RNA `is swiftly emerging from the shadows of its better-known cousin DNA.' For many scientists in the origin-of-life field, those shadows had lifted two decades earlier with the discovery of ribozymes, enzyme-like substances made of RNA. A simple solution to the chicken-and-egg riddle now appeared to fall into place: Life began with the appearance of the first RNA molecule. In a germinal 1986 article, Nobel Laureate Walter Gilbert of Harvard University wrote in the journal Nature: `One can contemplate an RNA world, containing only RNA molecules that serve to catalyze the synthesis of themselves. & The first step of evolution proceeds then by RNA molecules performing the catalytic activities necessary to assemble themselves from a nucleotide soup.' In this vision, the first self-replicating RNA that emerged from non-living matter carried out the functions now executed by RNA, DNA and proteins." (Shapiro, R., "A Simpler Origin for Life," Scientific American, February 12, 2007) 18/02/2007 "A number of additional clues seemed to support the idea that RNA appeared before proteins and DNA in the evolution of life. Many small molecules, called cofactors, play a necessary role in enzyme-catalyzed reactions. These cofactors often carry an attached RNA nucleotide with no obvious function. These structures have been considered `molecular fossils,' relics descended from the time when RNA alone, without DNA or proteins, ruled the biochemical world. In addition, chemists have been able to synthesize new ribozymes that display a variety of enzyme-like activities. Many scientists found the idea of an organism that relied on ribozymes, rather than protein enzymes, very attractive. The hypothesis that life began with RNA was presented as a likely reality, rather than a speculation, in journals, textbooks and the media. Yet the clues I have cited only support the weaker conclusion that RNA preceded DNA and proteins; they provide no information about the origin of life, which may have involved stages prior to the RNA world in which other living entities ruled supreme. Just the same, and despite the difficulties that I will discuss in the next section, perhaps two-thirds of scientists publishing in the origin-of life field (as judged by a count of papers published in 2006 in the journal Origins of Life and Evolution of the Biosphere) still support the idea that life began with the spontaneous formation of RNA or a related self-copying molecule. Confusingly, researchers use the term `RNA World' to refer to both the strong and the weak claims about RNA's role prior to DNA and proteins. Here, I will use the term `RNA first' for the strong claim that RNA was involved in the origin of life. ... The attractive features of RNA World prompted Gerald Joyce of the Scripps Research Institute and Leslie Orgel of the Salk Institute to picture it as `the molecular biologist's dream' within a volume devoted to that topic. They also used the term `the prebiotic chemist's nightmare' to describe another part of the picture: How did that first self-replicating RNA arise? Enormous obstacles block Gilbert's picture of the origin of life, sufficient to provoke another Nobelist, Christian De Duve of Rockefeller University, to ask rhetorically, `Did God make RNA?'" (Shapiro, R., "A Simpler Origin for Life," Scientific American, February 12, 2007) 18/02/2007 "RNA's building blocks, nucleotides, are complex substances as organic molecules go. They each contain a sugar, a phosphate and one of four nitrogen-containing bases as sub-subunits. Thus, each RNA nucleotide contains 9 or 10 carbon atoms, numerous nitrogen and oxygen atoms and the phosphate group, all connected in a precise three-dimensional pattern. Many alternative ways exist for making those connections, yielding thousands of plausible nucleotides that could readily join in place of the standard ones but that are not represented in RNA. That number is itself dwarfed by the hundreds of thousands to millions of stable organic molecules of similar size that are not nucleotides. The RNA nucleotides are familiar to chemists because of their abundance in life and their resulting commercial availability. In a form of molecular vitalism, some scientists have presumed that nature has an innate tendency to produce life's building blocks preferentially, rather than the hordes of other molecules that can also be derived from the rules of organic chemistry. This idea drew inspiration from a well known experiment published in 1953 by Stanley Miller. He applied a spark discharge to a mixture of simple gases that were then thought to represent the atmosphere of the early Earth. Two amino acids of the set of 20 used to construct proteins were formed in significant quantities, with others from that set present in small amounts. (A description of the Miller experiment and the chemical structures of an amino acid and a nucleotide can be found in "The Origin of Life on the Earth," by L. E. Orgel; Scientific American, October 1994.) In addition, more than 80 different amino acids, some present and others absent from living systems, have been identified as components of the Murchison meteorite, which fell in Australia in 1969. Nature has apparently been generous in providing a supply of these particular building blocks.By extrapolation of these results, some writers have presumed that all of life's building could be formed with ease in Miller-type experiments and were present in meteorites and other extraterrestrial bodies. This is not the case. A careful examination of the results of the analysis of several meteorites led the scientists who conducted the work to a different conclusion: inanimate nature has a bias toward the formation of molecules made of fewer rather than greater numbers of carbon atoms, and thus shows no partiality in favor of creating the building blocks of our kind of life. (When larger carbon- containing molecules are produced, they tend to be insoluble, hydrogen-poor substances that organic chemists call tars.) I have observed a similar pattern in the results of many spark discharge experiments." (Shapiro, R., "A Simpler Origin for Life," Scientific American, February 12, 2007) 18/02/2007 "Amino acids, such as those produced or found in these experiments, are far less complex than nucleotides. Their defining features are an amino group (a nitrogen and two hydrogens) and a carboxylic acid group (a carbon, two oxygens and a hydrogen) both attached to the same carbon. The simplest of the 20 used to build natural proteins contains only two carbon atoms. Seventeen of the set contain six or fewer carbons. The amino acids and other substances that were prominent in the Miller experiment contained two and three carbon atoms. By contrast, no nucleotides of any kind have been reported as products of spark discharge experiments or in studies of meteorites, nor have the smaller units (nucleosides) that contain a sugar and base but lack the phosphate. To rescue the RNA-first concept from this otherwise lethal defect, its advocates have created a discipline called prebiotic synthesis. They have attempted to show that RNA and its components can be prepared in their laboratories in a sequence of carefully controlled reactions, normally carried out in water at temperatures observed on Earth. Such a sequence would start usually with compounds of carbon that had been produced in spark discharge experiments or found in meteorites. The observation of a specific organic chemical in any quantity (even as part of a complex mixture) in one of the above sources would justify its classification as `prebiotic,' a substance that supposedly had been proved to be present on the early Earth. Once awarded this distinction, the chemical could then be used in pure form, in any quantity, in another prebiotic reaction. The products of such a reaction would also be considered `prebiotic' and employed in the next step in the sequence. The use of reaction sequences of this type (without any reference to the origin of life) has long been an honored practice in the traditional field of synthetic organic chemistry. My own PhD thesis advisor, Robert B. Woodward, was awarded the Nobel Prize for his brilliant syntheses of quinine, cholesterol, chlorophyll and many other substances. It mattered little if kilograms of starting material were required to produce milligrams of product. The point was the demonstration that humans could produce, however inefficiently, substances found in nature. Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA." (Shapiro, R., "A Simpler Origin for Life," Scientific American, February 12, 2007) 18/02/2007 "I will cite one example of prebiotic synthesis, published in 1995 by Nature and featured in the New York Times. The RNA base cytosine was prepared in high yield by heating two purified chemicals in a sealed glass tube at 100 degrees Celsius for about a day. One of the reagents, cyanoacetaldehyde, is a reactive substance capable of combining with a number of common chemicals that may have been present on the early Earth. These competitors were excluded. An extremely high concentration was needed to coax the other participant, urea, to react at a sufficient rate for the reaction to succeed. The product, cytosine, can self-destruct by simple reaction with water. When the urea concentration was lowered, or the reaction allowed to continue too long, any cytosine that was produced was subsequently destroyed. This destructive reaction had been discovered in my laboratory, as part of my continuing research on environmental damage to DNA. Our own cells deal with it by maintaining a suite of enzymes that specialize in DNA repair. The exceptionally high urea concentration was rationalized in the Nature paper by invoking a vision of drying lagoons on the early Earth. In a published rebuttal, I calculated that a large lagoon would have to be evaporated to the size of a puddle, without loss of its contents, to achieve that concentration. No such feature exists on Earth today. The drying lagoon claim is not unique. In a similar spirit, other prebiotic chemists have invoked freezing glacial lakes, mountainside freshwater ponds, flowing streams, beaches, dry deserts, volcanic aquifers and the entire global ocean (frozen or warm as needed) to support their requirement that the `nucleotide soup' necessary for RNA synthesis would somehow have come into existence on the early Earth. The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non- living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck." (Shapiro, R., "A Simpler Origin for Life," Scientific American, February 12, 2007) 18/02/2007 "Many chemists, confronted with these difficulties, have fled the RNA-first hypothesis as if it were a building on fire. One group, however, still captured by the vision of the self-copying molecule, has opted for an exit that leads to similar hazards. In these revised theories, a simpler replicator arose first and governed life in a `pre-RNA world.' Variations have been proposed in which the bases, the sugar or the entire backbone of RNA have been replaced by simpler substances, more accessible to prebiotic syntheses. Presumably, this first replicator would also have the catalytic capabilities of RNA. Because no trace of this hypothetical primal replicator and catalyst has been recognized so far in modern biology, RNA must have completely taken over all of its functions at some point following its emergence. Further, the spontaneous appearance of any such replicator without the assistance of a chemist faces implausibilities that dwarf those involved in the preparation of a mere nucleotide soup. Let us presume that a soup enriched in the building blocks of all of these proposed replicators has somehow been assembled, under conditions that favor their connection into chains. They would be accompanied by hordes of defective building blocks, the inclusion of which would ruin the ability of the chain to act as a replicator. The simplest flawed unit would be a terminator, a component that had only one `arm' available for connection, rather than the two needed to support further growth of the chain. There is no reason to presume than an indifferent nature would not combine units at random, producing an immense variety of hybrid short, terminated chains, rather than the much longer one of uniform backbone geometry needed to support replicator and catalytic functions. Probability calculations could be made, but I prefer a variation on a much-used analogy. Picture a gorilla (very long arms are needed) at an immense keyboard connected to a word processor. The keyboard contains not only the symbols used in English and European languages but also a huge excess drawn from every other known language and all of the symbol sets stored in a typical computer. The chances for the spontaneous assembly of a replicator in the pool I described above can be compared to those of the gorilla composing, in English, a coherent recipe for the preparation of chili con carne. With similar considerations in mind Gerald F. Joyce of the Scripps Research Institute and Leslie Orgel of the Salk Institute concluded that the spontaneous appearance of RNA chains on the lifeless Earth `would have been a near miracle.' I would extend this conclusion to all of the proposed RNA substitutes that I mentioned above. " (Shapiro, R., "A Simpler Origin for Life," Scientific American, February 12, 2007) 18/02/2007 "Life With Small Molecules Nobel Laureate Christian de Duve has called for `a rejection of improbabilities so incommensurably high that they can only be called miracles, phenomena that fall outside the scope of scientific inquiry.' DNA, RNA, proteins and other elaborate large molecules must then be set aside as participants in the origin of life. Inanimate nature provides us with a variety of mixtures of small molecules, whose behavior is governed by scientific laws, rather than by human intervention. Fortunately, an alternative group of theories that can employ these materials has existed for decades. The theories employ a thermodynamic rather than a genetic definition of life, under a scheme put forth by Carl Sagan in the Encyclopedia Britannica: A localized region which increases in order (decreases in entropy) through cycles driven by an energy flow would be considered alive. This small-molecule approach is rooted in the ideas of the Soviet biologist Alexander Oparin, and current notable spokesmen include de Duve, Freeman Dyson of the Institute for Advanced Study, Stuart Kauffman of the Santa Fe Institute, Doron Lancet of the Weizmann Institute, Harold Morowitz of George Mason University and the independent researcher Günter Wächtershäuser. I estimate that about a third of the chemists involved in the study of the origin of life subscribe to theories based on this idea." (Shapiro, R., "A Simpler Origin for Life," Scientific American, February 12, 2007. Emphasis original) 18/02/2007 "Origin-of-life proposals of this type differ in specific details; here I will try to list five common requirements (and add some ideas of my own). (1) A boundary is needed to separate life from non-life. Life is distinguished by its great degree of organization, yet the second law of thermodynamics requires that the universe move in a direction in which disorder, or entropy, increases. A loophole, however, allows entropy to decrease in a limited area, provided that a greater increase occurs outside the area. When living cells grow and multiply, they convert chemical energy or radiation to heat at the same time. The released heat increases the entropy of the environment, compensating for the decrease in living systems. The boundary maintains this division of the world into pockets of life and the nonliving environment in which they must sustain themselves. Today, sophisticated double-layered cell membranes, made of chemicals classified as lipids, separate living cells from their environment. When life began, some natural feature probably served the same purpose. David W. Deamer of the University of California, Santa Cruz, has observed membrane-like structures in meteorites. Other proposals have suggested natural boundaries not used by life today, such as iron sulfide membranes, mineral surfaces (in which electrostatic interactions segregate selected molecules from their environment), small ponds and aerosols." (Shapiro, R., "A Simpler Origin for Life," Scientific American, February 12, 2007. Emphasis original) 18/02/2007 "(2) An energy source is needed to drive the organization process. We consume carbohydrates and fats, and combine them with oxygen that we inhale, to keep ourselves alive. Microorganisms are more versatile, and can use minerals in place of the food or the oxygen. In either case, the transformations that are involved are called redox reactions. They involve the transfer of electrons from an electron rich (or reduced) substance to an electron poor (or oxidized) one. Plants can capture solar energy directly, and adapt it for the functions of life. Other forms of energy are used by cells in specialized circumstances--for example, differences in acidity on opposite sides of a membrane. Yet others, such as radioactivity and abrupt temperature differences, might be used by life elsewhere in the universe. Here I will consider redox reactions as the energy source." (Shapiro, R., "A Simpler Origin for Life," Scientific American, February 12, 2007. Emphasis original) 18/02/2007 "(3) A coupling mechanism must link the release of energy to the organization process that produces and sustains life. The release of energy does not necessarily produce a useful result. Chemical energy is released when gasoline is burned within the cylinders of my automobile, but the vehicle will not move unless that energy is used to turn the wheels. A mechanical connection, or coupling, is required. Each day, in our own cells, each of us degrades pounds of a nucleotide called ATP. The energy released by this favorable reaction serves to drive processes that are less favorable but necessary for our biochemistry. Linkage is achieved when the reactions share a common intermediate, and the process is speeded up by the intervention of an enzyme. One assumption of the small-molecule approach is that coupled reactions and primitive catalysts sufficient to get life started exist in nature." (Shapiro, R., "A Simpler Origin for Life," Scientific American, February 12, 2007. Emphasis original) 18/02/2007 "(4) A chemical network must be formed, to permit adaptation and evolution. We come now to the heart of the matter. Imagine for example that an energetically favorable redox reaction of a naturally-occurring mineral is linked to the conversion of an organic chemical A to another one B within a compartment. The favorable, energy releasing, entropy-increasing reaction of the mineral drives the A-to-B transformation. I call this key transformation a driver reaction, for it serves as the engine that mobilizes the organization process. If B simply reconverts back to A or escapes from the compartment, we would not be on a path that leads to increased organization. By contrast, if a multi-step chemical pathway--say, B to C to D to A--reconverts B to A, then the steps in that circular process (or cycle) would be favored because they replenish the supply of A, allowing the continuing discharge of energy by the mineral reaction. If we visualize the cycle as a circular railway line, the energy source keeps the trains traveling around it one way. Each station may also be the hub for a number of branch lines, such as one connecting station D to another station, E. Trains could travel in either direction along that branch, depleting or augmenting the cycle's traffic. Thanks to the continual depletion of A, however, material is drawn from D to A. The resulting depletion of D in turn tends to draw material from E to D. In this way, material is `pulled' along the branch lines into the central cycle, maximizing the energy release that accompanies the driver reaction. The cycle could also adapt to changing circumstances. As a child, I was fascinated by the way in which water, released from a leaky hydrant, would find a path downhill to the nearest sewer. If falling leaves or dropped refuse blocked that path, the water would back up until another route was found around the obstacle. In the same way, if a change in the acidity or in some other environmental circumstance should hinder a step in the pathway from B to A, material would back up until another route was found. Additional changes of this type would convert the original cycle into a network. This trial-and-error exploration of the chemical `landscape' might also turn up compounds that could catalyze important steps in the cycle, increasing the efficiency with which the network utilized the energy source." (Shapiro, R., "A Simpler Origin for Life," Scientific American, February 12, 2007. Emphasis original) 18/02/2007 "(5) The network must grow and reproduce. To survive and grow, the network must gain material at a rate that compensates for the paths that remove it. Diffusion of network materials out of the compartment into the external world is favored by entropy and will occur to some extent, especially at the start of life when the boundary is a crude one established by the environment rather than one of the highly effective cell membranes available today after billions of years of evolution. Some side reactions may produce gases, which escape, or form tars, which will drop out of solution. If these processes together should exceed the rate at which the network gains material, then it would be extinguished. Exhaustion of the external fuel would have the same effect. We can imagine, on the early Earth, a situation where many startups of this type occur, involving many alternative driver reactions and external energy sources. Finally, a particularly hardy one would take root and sustain itself." (Shapiro, R., "A Simpler Origin for Life," Scientific American, February 12, 2007. Emphasis origina) 18/02/2007 "A system of reproduction must eventually develop. If our network is housed in a lipid membrane, then physical forces may split it, after it has grown enough. (Freeman Dyson has described such a system as a "garbage-bag world" in contrast to the "neat and beautiful scene" of the RNA world.) A system that functions in a compartment within a mineral may overflow into adjacent compartments. Whatever the mechanism may be, this dispersal into separated units protects the system from total extinction by a localized destructive event. Once independent units were established, they could evolve in different ways and compete with one another for raw materials; we would have made the transition from life that emerges from nonliving matter through the action of an available energy source to life that adapts to its environment by Darwinian evolution." (Shapiro, R., "A Simpler Origin for Life," Scientific American, February 12, 2007. Emphasis original) 18/02/2007 "Changing the Paradigm Systems of the type I have described usually have been classified under the heading `metabolism first,' which implies that they do not contain a mechanism for heredity. In other words, they contain no obvious molecule or structure that allows the information stored in them (their heredity) to be duplicated and passed on to their descendants. However a collection of small items holds the same information as a list that describes the items. For example, my wife gives me a shopping list for the supermarket; the collection of grocery items that I return with contains the same information as the list. Doron Lancet has given the name `compositional genome' to heredity stored in small molecules, rather than a list such as DNA or RNA. The small molecule approach to the origin of life makes several demands upon nature (a compartment, an external energy supply, a driver reaction coupled to that supply, and the existence of a chemical network that contains that reaction). These requirements are general in nature, however, and are immensely more probable than the elaborate multi-step pathways needed to form a molecule that can function as a replicator. Over the years, many theoretical papers have advanced particular metabolism first schemes, but relatively little experimental work has been presented in support of them. In those cases where experiments have been published, they have usually served to demonstrate the plausibility of individual steps in a proposed cycle. The greatest amount of new data has perhaps come from Günter Wächtershäuser and his colleagues at the Technische Universität München. They have demonstrated portions of a cycle involving the combination and separation of amino acids, in the presence of metal sulfide catalysts. The energetic driving force for the transformations is supplied by the oxidation of carbon monoxide to carbon dioxide. They have not yet demonstrated the operation of a complete cycle or its ability to sustain itself and undergo further evolution. A `smoking gun' experiment displaying those three features is needed to establish the validity of the small molecule approach." (Shapiro, R., "A Simpler Origin for Life," Scientific American, February 12, 2007. Emphasis original) 18/02/2007 "The principal initial task is the identification of candidate driver reactions--small molecule transformations (A to B in the example before) that are coupled to an abundant external energy source (such as the oxidation of carbon monoxide or a mineral). Once a plausible driver reaction has been identified, there should be no need to specify the rest of the system in advance. The selected components (including the energy source) plus a mixture of other small molecules normally produced by natural processes (and likely to have been abundant on the early Earth) could be combined in a suitable reaction vessel. If an evolving network were established, we would expect the concentration of the participants in the network to increase and alter with time. New catalysts that increased the rate of key reactions might appear, while irrelevant materials would decrease in quantity. The reactor would need an input device to allow replenishment of the energy supply and raw materials, and an outlet to permit the removal of waste products and chemicals that were not part of the network. In such experiments, failures would be easily identified. The energy might be dissipated without producing any significant changes in the concentrations of the other chemicals or the chemicals might simply be converted to a tar, which would clog the apparatus. A success might demonstrate the initial steps on the road to life. These steps need not duplicate those that took place on the early Earth. It is more important that the general principle be demonstrated and made available for further investigation. Many potential paths to life may exist, with the choice dictated by the local environment." (Shapiro, R."A Simpler Origin for Life," Scientific American, February 12, 2007. Emphasis original) 18/02/2007 "An understanding of the initial steps leading to life would not reveal the specific events that led to the familiar DNA-RNA-protein-based organisms of today. However, because we know that evolution does not anticipate future events, we can presume that nucleotides first appeared in metabolism to serve some other purpose, perhaps as catalysts or as containers for the storage of chemical energy (the nucleotide ATP still serves this function today). Some chance event or circumstance may have led to the connection of nucleotides to form RNA. The most obvious function of RNA today is to serve as a structural element that assists in the formation of bonds between amino acids in the synthesis of proteins. The first RNAs may have served the same purpose, but without any preference for specific amino acids. Many further steps in evolution would be needed to `invent' the elaborate mechanisms for replication and specific protein synthesis that we observe in life today." (Shapiro, R., "A Simpler Origin for Life," Scientific American, February 12, 2007. Emphasis original) 18/02/2007 "If the general small-molecule paradigm were confirmed, then our expectations of the place of life in the universe would change. A highly implausible start for life, as in the RNA-first scenario, implies a universe in which we are alone. In the words of the late Jacques Monod, `The universe was not pregnant with life nor the biosphere with man. Our number came up in the Monte Carlo game.' The small-molecule alternative, however, is in harmony with the views of biologist Stuart Kauffman: `If this is all true, life is vastly more probable than we have supposed. Not only are we at home in the universe, but we are far more likely to share it with unknown companions.'" (Shapiro, R., "A Simpler Origin for Life," Scientific American, February 12, 2007. Emphasis original) 18/02/2007 Where did life come from? Natural selection explains how organisms that already exist evolve in response to changes in their environment. But Darwin's theory is silent on how organisms came into being in the first place, which he considered a deep mystery. What creates life out of the inanimate compounds that make up living things? No one knows. How were the first organisms assembled? Nature hasn't given us the slightest hint. If anything, the mystery has deepened over time. After all, if life began unaided under primordial conditions in a natural system containing zero knowledge, then it should be possible - it should be easy - to create life in a laboratory today. But determined attempts have failed. International fame, a likely Nobel Prize, and $1 million from the Gene Emergence Project await the researcher who makes life on a lab bench. Still, no one has come close. Experiments have created some basic materials of life. Famously, in 1952 Harold Urey and Stanley Miller mixed the elements thought to exist in Earth's primordial atmosphere, exposed them to electricity to simulate lightning, and found that amino acids self-assembled in the researchers' test tubes. Amino acids are essential to life. But the ones in the 1952 experiment did not come to life. Building-block compounds have been shown to result from many natural processes; they even float in huge clouds in space. But no test has given any indication of how they begin to live - or how, in early tentative forms, they could have resisted being frozen or fried by Earth's harsh prehistoric conditions. Some researchers have backed the hypothesis that an unknown primordial `soup' of naturally occurring chemicals was able to self- organize and become animate through a natural mechanism that no longer exists. Some advance the `RNA first' idea, which holds that RNA formed and lived on its own before DNA - but that doesn't explain where the RNA came from. Others suppose life began around hot deep-sea vents, where very high temperatures and pressures cause a chemical maelstrom. Still others have proposed that some as-yet-unknown natural law causes complexity - and that when this natural law is discovered, the origin of life will become imaginable. Did God or some other higher being create life? Did it begin on another world, to be transported later to ours? Until such time as a wholly natural origin of life is found, these questions have power. We're improbable, we're here, and we have no idea why. Or how." (Easterbrook, G., "topWhat We Don't Know: How did life begin?," WIRED magazine, Issue 15.02, February 2007) 19/02/2007 "The absence of fossil evidence for intermediary stages between major transitions in organic design, indeed our inability, even in our imagination, to construct functional intermediates in many cases, has been a persistent and nagging problem for gradualistic accounts of evolution." (Gould, S.J., "Is a new and general theory of evolution emerging?," Paleobiology, Vol. 6, No. 1, January 1980, pp.119-130, p.127) 19/02/2007 "St. George Mivart (1871), Darwin's most cogent critic, referred to it as the dilemma of "the incipient stages of useful structures"-of what possible benefit to a reptile is two percent of a wing?" (Gould, S.J., "Is a new and general theory of evolution emerging?," Paleobiology, Vol. 6, No. 1, January 1980, pp.119-130, p.127) 19/02/2007 "The dilemma has two potential solutions. The first, preferred by Darwinians because it preserves both gradualism and adaptation, is the principle of preadaptation: the intermediary stages functioned in another way but were, by good fortune in retrospect, preadapted to a new role they could play only after greater elaboration. Thus, if feathers first functioned "for" insulation and later "for" the trapping of insect prey (Ostrom 1979), a proto-wing might be built witho