Monday, November 05, 2007

PoE: Bibliography "K"

Here is the Bibliography "K" page of my book outline, "Problems of Evolution," for authors' surnames beginning with "K."

[Left: Dr. Stuart A. Kauffman, University of Calgary. See PS below.]

As I will do for other such pages, to save time in the future, I am populating it with books that I will probably later refer to.

© Stephen E. Jones, BSc. (Biology)



Kauffman, S.A., 1993, "The Origins of Order: Self-Organization and Selection in Evolution," Oxford University Press: New York NY.
Kauffman, S.A., 1995, "At Home in the Universe: The Search for Laws of Self-Organization and Complexity," Penguin: London, Reprinted, 1996.
Keith, A., 1946, "Essays on Human Evolution," Watts & Co: London, Third impression, 1947.
Kelly, K., 1994, "Out of Control: The New Biology of Machines," Fourth Estate: London, Reprinted, 1995.
Kerkut, G.A., 1960, "Implications of Evolution," in Kerkut, G.A., ed. "International Series of Monographs on Pure and Applied Biology, Division: Zoology," Volume 4, Pergamon Press: New York NY.
Koestler, A., 1967, "The Ghost in the Machine," Pan: London, Reprinted, 1970.
Koster, J.P., 1989, "The Atheist Syndrome," Wolgemuth & Hyatt: Brentwood TN.
Kuhn, T.S., 1996, "The Structure of Scientific Revolutions," [1962], University of Chicago Press: Chicago IL, Third edition.
Kuppers, B-O., 1990, "Information and the Origin of Life," [1986], MIT Press: Cambridge MA.
Kurtén, B., 1972, "Not From The Apes," Pantheon Books: New York NY.

PS: In order to `kill two birds with one stone' on what would otherwise be a boring series of Bibliography posts, I will add interesting `tagline' quotes at the end of them, by author(s) listed.

However, the quotes below are all by Stuart Kauffman, who is perhaps the world's leading theoretical biologist. Dr. Kauffman is a standing embarrassment to Darwinists because he should not exist! That is, due to his outstanding intellectual gifts, Kauffman was once regarded as an up-an-coming future Darwinist leader, who studied under the late leading British Darwinist biologist John Maynard Smith. But, having had an unparalleled opportunity to learn the evidence for Darwinism at the feet of one of its greatest ever teachers, Kauffman saw through Darwinism and rejected it, as these quotes, arranged in chronological order, reveal (bolded emphases mine). As can be seen, many of these quotes are devastating to Darwinism! However, Kauffman's fully naturalistic alternative to Darwinism's natural selection of random mutations, namely self-organisation, has proven to be inadequate also.

Stephen E. Jones, BSc. (Biology).
My other blog: TheShroudofTurin

"FOR as long as he can remember Stuart Kauffman has held a deep conviction about nature: that natural selection cannot be the sole or even the most important source of order in the biological world. Almost three decades ago, Kauffman, then a young medical student at the University of California, San Francisco, set out to prove he was right and that the rest of the biological community was wrong. `What I found was profound,' says Kauffman. `I knew that then and I'm still convinced of it.' ... The mechanism of controls by feedback that Jacob and Monod found in these systems struck a chord in Kauffman's still unformulated thinking about order in biological systems, and led to the computer simulation experiments. `The results were so powerful, and seemed to confirm what I felt instinctively must be true, that I dismissed natural selection as being totally unimportant,' says Kauffman." (Lewin, R., 1993, "Order For Free," New Scientist, 13 February, Supplement, pp.10-11).

"Darwin and evolutionism stand astride us, whatever the mutterings of creation scientists. But is the view right? Better, is it adequate? I believe it is not. It is not that Darwin is wrong, but that he got hold of only part of the truth. For Darwin's answer to the sources of the order we see all around us is overwhelmingly an appeal to a single singular force: natural selection. It is this single-force view which I believe to be inadequate, for it fails to notice, fails to stress, fails to incorporate the possibility that simple and complex systems exhibit order spontaneously." (Kauffman, S.A., 1993, "The Origins of Order: Self-Organization and Selection in Evolution," Oxford University Press: New York NY, p.xii).

"Is the Concept of Natural Selection Circular? First among the criticisms is the concern that the theory is circular, a mere tautology: the survival of the survivors. In its neo-Darwinian reformulation, in which the microevolutionary event is a change in gene frequencies, the worry is restated as the circularity of defining natural selection as the differential reproductive success of genotypes and then defining the fitness of a gene as its average probability, over all genetic backgrounds, of being propagated to the next generation. This restatement again leads to the possibility of circularity, survival of the survivor." (Kauffman, 1993, p.16. Italics original).

"The more restricted interpretation of Darwinism has been that some but not all features of organisms are present as a result of positive selection. But this sensible application of Darwinism has always faced the difficulty of discriminating which features were present even if they were not favored by selection, and has always faced the danger of facile constructions of `just-so' stories plausibly positing a use for a feature in the face of no possible tests at all. This has truly been one of the major problems in evolutionary biology, for most biologists, myself included, would deny a panselectivist view but hold to the claim that many aspects of organisms are present due to past or continuing selection. The overall problem here is great." (Kauffman, 1993, p.17).

"I believe this to be a genuinely fundamental restraint facing adaptive evolution. As systems with many parts increase both the number of those parts and the richness of interactions among the parts, it is typical that the number of conflicting design constraints among the parts increases rapidly. Those conflicting constraints imply that optimization can attain only ever poorer compromises. No matter how strong selection may be, adaptive processes cannot climb higher peaks than afforded by the fitness landscape. That is, this limitation cannot be overcome by stronger selection. ... it is clear that conflicting constraints are a very general limit in adaptive evolution. Each part of a complex system costs something. For example, additional genes and proteins require metabolic energy. .... This argument shows that there is again a limit on the complexity which can be attained. The marginal increase in fitness for the next part must be positive. The complexity-catastrophe due to conflicting constraints ... is therefore a general property of complex systems." (Kauffman, 1993, pp.53-54).

"... we turn our attention to the wonderful problem of the origin of life. ... To many recent scholars - Wald (1954), Hoyle and Wickramasinghe (1981), and others - improbable features of current organisms imply improbable origins. If the probability that a protein catalyzes a given reaction is 10-20 and if a minimal contemporary organism such as a pleuromona-like organism has on the order of 1000 or 2000 enzymes, then the probability of their joint occurrence by chance is, say, 10-40 000. More likely that, as Hoyle says, the whirlwind assemble a 747 from scraps in a junkyard. Yet here we are, in quite clear contravention to Hoyle's unhappy conclusion. We the lucky, or we the expected?" (Kauffman, 1993, p.287).

"The creationists so animating one another, the lay public, and our contemporary court system today rest uneasy with Darwin's heritage. Natural selection, operating on variations which are random with respect to usefulness, appears a slim force for order in a chaotic world. Yet the creationists' impulse is not merely misplaced religion. Science consists in discovering that point of view under which what did occur is what we have good grounds to expect might have occurred. Our legacy from Darwin, powerful as it is, has fractures as its foundations. We do not understand the sources of order on which natural selection was privileged to work. As long as our deepest theory of living entities is the geneology [sic] of contraptions and as long as biology is the laying bare of the ad hoc, the intellectually honorable motivation to understand partially lying behind the creationist impulse will persist." (Kauffman, 1993, p.643).

"We live in a world of stunning biological complexity. Molecules of all varieties join in a metabolic dance to make cells. Cells interact with cells to form organisms; organisms interact with organisms to form ecosystems, economies, societies. Where did this grand architecture come from? For more than a century, the only theory that science has offered to explain how this order arose is natural selection. As Darwin taught us, the order of the biological world evolves as natural selection sifts among random mutations for the rare, useful forms. In this view of the history of life, organisms are cobbled-together contraptions wrought by selection, the silent and opportunistic tinkerer. Science has left us as unaccountably improbable accidents against the cold, immense backdrop of space and time. Thirty years of research have convinced me that this dominant view of biology is incomplete. As I will argue in this book, natural selection is important, but it has not labored alone to craft the fine architectures of the biosphere, from cell to organism to ecosystem. Another source self-organization-is the root source of order." (Kauffman, S.A., 1995, "At Home in the Universe: The Search for Laws of Self-Organization and Complexity," Penguin: London, 1996, Reprinted, p.vii).

"How Darwin and his theory of evolution by natural selection devastated all this! We, who are heritors of Darwin, who see the living world through the categories he taught us more than a century ago, even we have trouble with the implications: man as the result of a chain of accidental mutations, sifted by a law no more noble than survival of the fittest. Creation science is no accident in late-twentieth-century America. Its proponents adhere to it in an ardent effort to forestall the feared moral implications of humans as descendants of a haphazard lineage branching from some last common ancestor more remote in time than the Cambrian explosion some 500 million years ago. The science in creation science is no science at all, but is the moral anguish so foolish? Or should creationism be viewed rather more sympathetically-misguided, to be sure, but part of a broader quest to reinvent the sacred in our secular world?" (Kauffman, 1995, p.6).

"Further, it was supposed, simple organic molecules in the atmosphere, along with other more complex ones, would be expected to dissolve slowly in the newly formed oceans, creating a prebiotic soup. From this soup, it was hoped, life would somehow form spontaneously. This hypothesis continues to have many adherents, though it suffers from considerable difficulties. Chief among them is the fact that the soup would be extremely dilute. The rate of chemical reactions depends on how rapidly the reacting molecular species encounter one another-and that depends on how high their concentrations are. If the concentration of each is low, the chance that they will collide is very much lower. In a dilute prebiotic soup, reactions would be very slow indeed. A wonderful cartoon I recently saw captures this. It was entitled `The Origin of Life.' Dateline 3.874 billion years ago. Two amino acids drift close together at the base of a bleak rocky cliff; three seconds later, the two amino acids drift apart. About 4.12 million years later, two amino acids drift close to each other at the base of a primeval cliff. ... Well Rome wasn't built in a day." (Kauffman, 1995, pp.34-35. Ellipses original).

"Miller had performed the first prebiotic chemistry experiment He had discovered plausible means whereby the building blocks of proteins might have been formed on the early earth. .... Similar experiments have shown that it is possible (though with much greater difficulty) to form the nucleotide building blocks of DNA RNA, and fatty molecules and hence, through them, the structural material for cellular membranes. Many other small molecular components of organisms have been synthesized abiogenically. But substantial puzzles remain. Robert Shapiro notes in his book Origins: A Skeptic's Guide to the Creation of Life on Earth that even though scientists can show that it is possible to synthesize the various ingredients of life, it is not easy to get them to cohere into a single story One group of scientists discovers that molecule A can be formed from molecules B and C in a very low yield under a certain set of conditions Then, having shown that it is possible to make A, another group starts with a high concentration of the molecule and shows that by adding D one can form E-again in a very low yield and under quite different conditions. Then another group shows that E, in high concentration can form F under still different conditions. But how, without supervision, did all the building blocks come together at high enough concentrations in one place and at one time to get a metabolism going? Too many scene changes in this theater, argues Shapiro, with no stage manager." (Kauffman, 1995, p.36).

"The Limits to Selection If selection could, in principle, accomplish `anything,' then all the order in organisms might reflect selection alone. But, in fact, there are limits to selection. Such limits begin to demand a shift in our thinking in the biological sciences and beyond. We have already encountered a first powerful limitation on selection. Darwin's view of the gradual accumulation of useful variations, we saw, required gradualism. Mutations must cause slight alterations in phenotypes. But we have now seen two alternative model `worlds' in which such gradualism fails. The first concerns maximally compressed programs. Because these are random, almost certainly any change randomizes the performance of the program. Finding one of the few useful minimal programs requires searching the entire space-requiring unthinkably long times compared with the history of the universe even for modestly large programs. Selection cannot achieve such maximally compressed programs. Our second examples are NK landscapes. If the richness of epistatic couplings, K, is very high and approaches the maximum limit, K = N - 1, landscapes approach and become completely random. Again, locating the highest peak or one of the few highest peaks requires searching the entire space of possibilities. For modestly large genomes, this is simply impossible. But the matter is even worse on such random landscapes. If an adapting population evolves by mutation and selection alone, it will remain frozen in an infinitesimal region of the total space, trapped forever in whatever region it started in. It will be unable to search long distances across space for the high peaks. Yet if the population dares try recombination, it will be harmed, on average, not helped." (Kauffman, 1995, p.183).

"There is a second limitation to selection. It is not only on random landscapes that selection fails. Even on smooth landscapes, in the heartland of gradualism, just where Darwin's assumptions hold, selection can again fail and fail utterly. Selection runs headlong into an `error catastrophe' where all accumulated useful traits melt away. Let us return to our image of a population of bacteria evolving on a rugged fitness landscape. The behavior of the population depends on the size of the population, the mutation rate, and the structure of the landscape. Suppose we consider holding population size constant-say, by using a chemostat-and landscape structure constant, and tuning the mutation rate from low to high by some experimental technique. What will happen? Suppose the population is initially genetically identical; hence all bacteria are located at the same point in genotype space. If the mutation rate is very low, then at long intervals a fitter variant arises and rapidly sweeps through the population. Thus the population as a whole `hops' to the fitter neighboring genotype. Over time, the population performs just the kind of adaptive walk we have considered, climbing steadily uphill to some local optimum and remaining there." (Kauffman, 1995, pp.183-184).

"But what happens if the mutation rate is so high that many fitter and less fit variants are found over very short intervals? Then the population will spread out from the initial point in genotype space and climb in many directions. The more surprising property is this: even if the population is released on a local peak, it may not stay there! Simply put, the rate of mutation is so high that it causes the population to `diffuse' away from the peak faster than the selective differences between less fit and more fit mutants can return the population to the peak. An error catastrophe, first discovered by Nobel laureate Manfred Eigen and theoretical chemist Peter Schuster, has occurred, for the useful genetic information built up in the population is lost as the population diffuses away from the peak." (Kauffman, 1995, p.184).

"To summarize: as the mutation rate increases, at first the population climbs a local hill and hovers in its vicinity. As the mutation rate becomes higher, the population drifts down from the peak and begins to spread along ridges of nearly equal fitness on the fitness landscape. But if the mutation rate increases still further, the population drifts ever lower off the ridges into the lowlands of poor fitness. Eigen and Schuster were the first to emphasize the importance of this error catastrophe, for it implies a limit to the power of natural selection. At a high enough mutation rate, an adapting population cannot assemble useful genetic variants into a working whole; instead, the mutation-induced `diffusion' over the space overcomes selection, pulling the population toward adaptive peaks." (Kauffman, 1995, p.184).

"This limitation is even more marked when seen from another vantage point. Eigen and Schuster also emphasized that for a constant mutation rate per gene, the error catastrophe will arise when the number of genes in the genotype increases beyond a critical number. Thus there appears to be a limit on the complexity of a genome that can be assembled by mutation and selection!" (Kauffman, 1995, p.184. Italics original).

"Selection, then, confronts twin limitations: it is trapped or frozen into local regions of very rugged landscape, and, on smooth landscapes, it suffers the error catastrophe and melts off peaks, so the genotype becomes less fit." (Kauffman, 1995, pp.184-185).

"Finally, Kauffman. like Gould and Margulis, has struggled to define his relationship to Darwin. In his interview with me he said he viewed antichaos as a complement to Darwinian natural selection. At other times, he has proclaimed that antichaos is the primary factor in evolution and that natural selection's role has been minor or nonexistent. Kauffman's continued ambivalence over this issue was starkly revealed in a typeset draft of At Home in the Universe, which he gave me in the spring of 1995. On the book's first page, Kauffman proclaimed that Darwinism was `wrong,' but he had crossed out `wrong' and replaced it with `incomplete.' Kauffman went back to `wrong' in the galleys of his book, released several months later. What did the final, published version say? `Incomplete.'" (Horgan, J., 1996, "The End of Science: Facing the Limits of Knowledge in the Twilight of the Scientific Age," Little, Brown & Co: London, Reprinted, 1997, p.135).

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