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Website: Descent of Man Revisited
The most confusing aspect of the study of evolution is the nature of the first step, natural selection. The debate over evolution tends to degenerate into a conflict of science and religion, deflecting our attention from the basic problem with Darwin’s theory: the limits of selectionist explanation with ‘Just So Stories’, or adaptationist scenarios. It is very convenient for Darwinists to confront Creationist critics who tend to reject the fact of evolution. This deflects attention from the real problem. In the final analysis the proposition of natural selection would seem implausible. The original criticisms of the first generation of Darwin critics in many ways still stand. T. H. Huxley himself, ironically, warned Darwin on the eve of publication of the problem with natural selection. The intractable character of the debate is no mystery and arises from the violation of the limits of observation, Karl Popper famous ‘metaphysical research program’.[i]
In general some process of self-organization is at work beyond the limits of selectionist oversimplifications. In the words of S. Kauffman in his At Home in the Universe ,
The existence of spontaneous order is a stunning challenge to our settled ideas in biology since Darwin . Most biologists have believed for over a century that selection is the sole source of order in biology, that selection is the tinkerer that crafts the forms. But if the forms selection chooses among were generated by laws of complexity, then selection has always had a handmaiden. It is not, after all, the sole source of order, and organisms are not just tinkered-together contraptions, but expressions of deeper laws. If all this is true, what a revision of the Darwinian worldview will lie before us! Not we the accidental, but we the expected![ii]
In general, severe, almost certainly fatal, mathematical challenges have always stood in the way of selectionist assumptions. In a now classic text, Evolution From Space, Hoyle and Wickramasinghe give one version of this objection.
Darwinian evolution is most unlikely to get even one polypeptide right, let alone the thousands on which living cells depend for their survival. This situation is well known to geneticists and yet nobody seems prepared to blow the whistle on the theory.[iii]
This viewpoint has been ‘refuted’ so many times that we forget genetic research has essentially confirmed it with the discovery of new developmental structures and processes. The full random run is in fact ‘compressed’ by the existence of some other process of development. In general, we must be wary of statistical reasoning applied to evolution. Even the suspicion of a directional process will throw any calculations here out of kilter. The amount of sophistry attempting to counter Hoyle, strewn over the Internet, is remarkable. Current thinking has quietly shifted to claims for the emergence of some ‘evolutionary toolkit’. Now it is claimed this arises by chance alone.
The literature critiquing natural selection is considerable, and we will assume some familiarity with such. A number of classic studies beggar the idea that all critics are religiously motivated. Beside Soren Lovtrup’s Darwinism: Refutation of a Myth, we have Robert Reid’s Evolutionary Theory, The Unfinished Synthesis, where the author notes, “I thought my failure to understand selection theory fully was the result of the specialization of the subject beyond my simple comprehension. Confident that every aspect of natural selection was for the best, I little knew that it had long been criticized for just that Panglossian felicity”. In Beyond Natural Selection, Robert Wesson gives a naturalist’s second opinion of the gritty details that mount up and cast a shadow on the Neo-Darwinian Synthesis, noting, “Natural selection is credited with seemingly miraculous feats because we want an answer and have no other. There probably cannot be another general answer. Biologists, it seems, must do without a comprehensive theory of evolution.” Wesson summons up an impressive list of oddities that current theories simply disregard. Simple things, like the absence of selective advantage in dreaming, the failure of sexual selection in practice to feedforward intelligence, the six-leggedness of insects, a host of discrepancies. “Many very simple facts, such as that all the millions of species of insects, and no species of non-insects have six legs, might well might well be considered to disprove natural selection as a generalization.”[iv]
Again, as S. Kauffman notes in At Home in the Universe,
“Since Darwin, we turn to a single, singular force, Natural Selection, which we might well capitalize as though it were the new deity. Random variation, selection-sifting. Without it, we reason, there would be nothing but incoherent disorder. I shall argue in this book that this idea is wrong. For, as we shall see, the emerging sciences of complexity begin to suggest that the order is not all accidental, that vast veins of spontaneous order lie at hand. Laws of complexity spontaneously generate much of the order of the natural world. It is only then that selection comes into play, further molding and refining.” [v]
We are still without a theory of evolution, in part because we have never observed its mechanics in action, confused by the superficial surface of evolution, selection-sifting.
Historical Counter-evidence Debates over natural selection are mostly repetitive propaganda exchanges. The debate revolves around a set of abstractions. But a picture is worth a thousand words. It can help to examine a rich data set such as that of the eonic effect in order to see how misleading the claims for natural selection can be. We soon discover that natural selection is often counter-evolutionary, and can lead to degradation of evolutionary forms. A close look at world history shows that the fittest survivors are a problem historical evolution is required to solve.
The Axial Age/Eonic Effect World history seen at close range suggests something entirely different at work than natural selection. The competition of cultures and empires rarely leads to advance, which comes from a different source. The competition in history that we see too often degrades the outcome. Compare Axial Age Greece and Imperial Rome. The latter is a clear winner of competition. The former shows a state of higher realization that declines very quickly as it enters a stage of empire.
[i] Sherrie Lyons, Thomas Henry Huxley (New York: Prometheus, 1999), p. 231. Soren Lovtrup, Darwinism: Refutation of a Myth (New York: Croom Helm, 1987), Robert Reid, Evolutionary Theory, The Unfinished Synthesis (New York: Cornell, 1985), Robert Wesson, Beyond Natural Selection (Cambridge: MIT, 1991), Michael Denton, Evolution: A Theory in Crisis (New York: Adler & Adler, 1985), Kevin Kelly, Out of Control (New York: Addison-Wesley, 1994), Stephen J. Gould, The Structure of Evolutionary Theory, (Cambridge: Harvard University Press, 2002), Mark Kirschner & John Gerhart, The Plausibility of Life (New Haven: Yale University Press, 2005). Popper’s essay, “Darwinism as a Metaphysical Research Program”, can be found in his intellectual biography, Unended Quest, (New York: Open Court, 1976). A new wave of critics is emerging, Suzan Mazur, The Altenberg 16: An Exposé of the Evolution Industry (Wellington, New Zealand: Scoop Media, 2009). Jerry Fodor & Massimo Piatelli-Palmarini, What Darwin Got Wrong (New York: Farrar, Strauss and Giroux, 2010).
[ii] Stuart Kauffman, At Home in the Universe (New York: Oxford University Press, 1995), p. 9.
[iii] Cf. F. Hoyle & N. Wickrmasinghe , Evolution From Space (London: Dent, 1981), p. 148.
[iv] Robert Wesson, Beyond Natural Selection (Cambridge: MIT, 1994), p. xii.
[v] Stuart Kauffman, At Home in the Universe (New York: Oxford: Oxford University Press, 1995), p. 8.
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Neo-Darwinism: time to reconsider
By Richard Milton
For the full story of how this article was commissioned, in 1995, and then censored visit the website for Conversation for Exploration.
Richard Milton is a science writer and journalist. He is the author of "The Facts of Life" (Transworld/Corgi, London, 1993) a critical review of neo-Darwinism and "Forbidden Science" (Fourth Estate, London, 1994) a critical analysis of censorship and intolerance in science.
It was the dazzling gains made by science and technology in the nineteenth century through the application of rational analysis that led people to think of applying reason to other fields.
Following the brilliant success of reason and method in physics and chemistry -- especially in medicine -- it was natural for science to seek to apply the same analytical tool to the most intractable and complex problems: human society and economic affairs; human psychology; and even the origin and development of life itself. The result was the great mechanistic philosophies of the last century: Marxism, Freudianism and Darwinism.
The simplicities and certainties of these systems mirrored the intellectually well-ordered life of Victorian society with its authoritarian values and institutionalised prejudices. Now, a century later, all three systems have run their course, have been measured by history, and have been ultimately found to be inadequate tools of explanation.
Unlike Marx and Freud, Darwin himself remains esteemed both as a highly original thinker and as a careful researcher (his study of fossil barnacles remains a text book example for palaeontologists). But the theory that bears his name was transformed in the early years of this century into the mechanistic, reductionist theory of neo-Darwinism: the theory that living creatures are machines whose only goal is genetic replication -- a matter of chemistry and statistics; or, in the words of professor Jacques Monod, director of the Pasteur Institute, a matter only of "chance and necessity". 
And while the evidence for evolution itself remains persuasive -- especially the homologies that are found in comparative anatomy and molecular biology of many different species -- much of the empirical evidence that was formerly believed to support the neo-Darwinian mechanism of chance mutation coupled with natural selection has melted away like snow on a spring morning, through better observation and more careful analysis.
Marxist, Freudian and neo-Darwinist systems of thought ultimately failed for the same reason; that they sought to use mechanistic reductionism to explain and predict systems that we now know are complexity-related, and cannot be explained as the sum of the parts.
In the case of neo-Darwinism, it was not the mysteries of the mind or of the economy that were explained. It was the origin of the first single-celled organism in the primeval oceans, and its development into the plant and animal kingdoms of today by a strictly blind process of chance genetic mutation working with natural selection.
In the first five decades of this century -- the heyday of the theory -- zoologists, palaeontologists and comparative anatomists assembled the impressive exhibits that generations of school children have seen in Natural History Museums the world over: the evolution of the horse family; the fossils that illustrate the transition from fish to amphibian to reptile to mammal; and the discovery of astonishing extinct species such as "Archaeopteryx", apparently half-reptile, half-bird.
Over successive decades, these exhibits have been first disputed, then downgraded, and finally shunted off to obscure museum basements, as further research has shown them to be flawed or misconceived.
Anyone educated in a western country in the last forty years will recall being shown a chart of the evolution of the horse from "Eohippus", a small dog-like creature in the Eocene period 50 million years ago, to "Mesohippus", a sheep-sized animal of 30 million years ago, eventually to "Dinohippus", the size of a Shetland pony. This chart was drawn in 1950 by Harvard's professor of palaeontology George Simpson, to accompany his standard text book, "Horses", which encapsulated all the research done by the American Museum of Natural History in the previous half century.
Simpson plainly believed that his evidence was incontrovertible because he wrote, 'The history of the horse family is still one of the clearest and most convincing for showing that organisms really have evolved. . . There really is no point nowadays in continuing to collect and to study fossils simply to determine whether or not evolution is a fact. The question has been decisively answered in the affirmative.' 
Yet shortly after this affirmation, Simpson admits in passing that the chart he has drawn contains major gaps that he has not included: a gap before "Eohippus" and its unknown ancestors, for example, and another gap after "Eohippus" and before its supposed descendant "Mesohippus".  What is it, scientifically, that connects these isolated species on the famous chart if it is not fossil remains? And how could such unconnected examples demonstrate either genetic mutation or natural selection? Even though, today, the bones themselves have been relegated to the basement, the famous chart with its unproven continuity still appears in museum displays and handbooks, text books, encyclopaedias and lectures.
The remarkable "Archaeopteryx" also seems at first glance to bear out the neo-Darwinian concept of birds having evolved from small reptiles (the candidate most favoured by neo-Darwinists is a small agile dinosaur called a Coelosaur, and this is the explanation offered by most text books and museums.) Actually, such a descent is impossible because coelosaurs, in common with most other dinosaurs, did not posses collar bones while "Archaeopteryx", like all birds, has a modified collar bone to support its pectoral muscles.  Again, how can an isolated fossil, however remarkable, provide evidence of beneficial mutation or natural selection?
Neo-Darwinists were quick to claim that modern discoveries of molecular biology supported their theory. They said, for example, that if you analyse the DNA, the genetic blueprint, of plants and animals you find how closely or distantly they are related. That studying DNA sequences enables you to draw up the precise family tree of all living things and show how they are related by common ancestry.
This is a very important claim and central to the theory. If true, it would mean that animals neo-Darwinists say are closely related, such as two reptiles, would have greater similarity in their DNA than animals that are not so closely related, such as a reptile and a bird.
In 1981, molecular biologists working under Dr Morris Goodman at Ann Arbor University decided to test this hypothesis. They took the alpha haemoglobin DNA of two reptiles -- a snake and a crocodile -- which are said by Darwinists to be closely related, and the haemoglobin DNA of a bird, in this case a farmyard chicken.
They found that the two animals who had _least_ DNA sequences in common were the two reptiles, the snake and the crocodile. They had only around 5% of DNA sequences in common -- only one twentieth of their haemoglobin DNA. The two creatures whose DNA was closest were the crocodile and the chicken, where there were 17.5% of sequences in common -- nearly one fifth. The actual DNA similarities were the _reverse_ of that predicted by neo- Darwinism. 
Even more baffling is the fact that radically different genetic coding can give rise to animals that look outwardly very similar and exhibit similar behavior, while creatures that look and behave completely differently can have much in common genetically. There are, for instance, more than 3,000 species of frogs, all of which look superficially the same. But there is a greater variation of DNA between them than there is between the bat and the blue whale.
Further, if neo-Darwinist evolutionary ideas of gradual genetic change were true, then one would expect to find that simple organisms have simple DNA and complex organisms have complex DNA. In some cases, this is true. The simple nematode worm is a favorite subject of laboratory study because its DNA contains a mere 1,000 nucleotide bases. At the other end of the complexity scale, humans have 23 chromosomes which in total contain 3,000 million nucleotide bases.
Unfortunately, this promisingly Darwinian progression is contradicted by many counter examples. While human DNA is contained in 23 pairs of chromosomes, the humble goldfish has more than twice as many, at 47. The even humbler garden snail -- not much more than a glob of slime in a shell -- has 27 chromosomes. Some species of rose bush have 56 chromosomes. So the simple fact is that DNA analysis does _not_ confirm neo- Darwinist theory. In the laboratory, DNA analysis falsifies neo- Darwinist theory.
An even more damaging blow to the theory was the discovery that the very centerpiece of neo-Darwinism, Darwin's original conception of natural selection, or the survival of the fittest, is fatally flawed. The problem is: how can biologists (or anyone else) tell what characteristics constitute the animal or plant's 'fitness' to survive? How can you tell which are the fit animals and plants? The answer is that the only way to define the fit is by means of a post-hoc rationalization -- the fit must be "those who survived". While the only way to characterize uniquely those who survive is as "the fit". The central proposition of the Darwinian argument turns out to be an empty tautology. C.H. Waddington, professor of biology at Edinburgh University wrote; "Natural selection, which was at first considered as though it were a hypothesis that was in need of experimental or observational confirmation, turns out on closer inspection to be a tautology, a statement of an inevitable although previously unrecognized relation. It states that the fittest individuals in a population (defined as those who leave the most offspring) will leave most offspring. Once the statement is made, its truth is apparent." 
George Simpson, professor of paleontology at Harvard, sought to restore content to the idea of natural selection by saying; "If genetically red-haired parents have, on average, a large proportion of children than blondes or brunettes, then evolution will be in the direction of red hair. If genetically left-handed people have more children, evolution will be towards left- handedness. The characteristics themselves do not directly matter at all. All that matters is who leaves more descendants over the generations. Natural selection favours fitness only if you define fitness as leaving more descendants. In fact geneticists do define it that way, which maybe confusing to others. To a geneticist, fitness has nothing to do with health, strength, good looks, or anything but effectiveness in breeding."
Notice the words; "The characteristics themselves do not directly matter at all." This innocent phrase fatally undermines Darwin's original key conception: that each animal's special physical characteristics are what makes it fit to survive: the giraffe's long neck, the eagle's keen eye, or the cheetah's 60 mile-an-hour sprint.
Simpson's reformulation means all this must be dropped: it is not the characteristics that directly matter -- it is the animals' capacity to reproduce themselves. The race is not to the swift, after all, but merely to the prolific. So how can neo-Darwinism explain the enormous diversity of characteristics? Not only are neo-Darwinist ideas falsified by empirical research, but other puzzling and extraordinary findings have come to light in recent decades, suggesting that evolution is not blind but rather is in some unknown way _directed_. The experiments of Cairns at Harvard and Hall at Rochester University suggest that microorganisms can mutate in a way that is beneficial. 
Experiments with tobacco plants and flax demonstrate genetic change through the effects of fertilizers alone.  Experiments with sea squirts and salamanders as long ago as the 1920s appeared to demonstrate the inheritance of acquired characteristics.  Moreover, as Sir Fred Hoyle has pointed out, Fossil micro-organisms have been found in meteorites, indicating that life is universal -- not a lucky break in the primeval soup. This view is shared by Sir Francis Crick, co- discoverer of the function of DNA 
In the light of discoveries of this kind, the received wisdom of neo-Darwinism is no longer received so uncritically. A new generation of biologists is subjecting the theory to the cold light of empirical investigation and finding it inadequate; scientists like Dr Rupert Sheldrake, Dr Brian Goodwin, professor of biology at the Open University and Dr Peter Saunders, professor of mathematics at King's College London.
Not surprisingly, the work of this new generation is heresy to the old. When Rupert Sheldrake's book "A New Science of Life" with its revolutionary theory of morphic resonance was published in 1981, the editor of "Nature" magazine, John Maddox, ran an editorial calling for the book to be burned -- a sure sign that Sheldrake is onto something important, many will think. [12, 13] The current mood in biology was summed up recently by Sheldrake as, 'Rather like working in Russia under Brehznev. Many biologists have one set of beliefs at work, their official beliefs, and another set, their real beliefs, which they can speak openly about only among friends. They may treat living things as mechanical in the laboratory but when they go home they don't treat their families as inanimate machines.' It is a strange aspect of science in the twentieth century that while physics has had to submit to the indignity of a principle of uncertainty and physicists have become accustomed to such strange entities as matter-waves and virtual particles, many of their colleagues down the corridor in biology seem not to have noticed the revolution of quantum electrodynamics. As far as many biologists are concerned, matter is made of billiard balls which collide with Newtonian certainty, and they carry on building molecular models out of coloured table-tennis balls. One of the twentieth century's most distinguished scientists and Nobel laureates, physicist Max Planck, observed that; 'A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.'
It may be another decade or more before such a new generation grows up and restores intellectual rigour to the study of evolutionary biology.
 Monod, Jacques, 1972 edn. Chance and Necessity. William Collins. Glasgow.
 Simpson, George G. 1951. Horses. Oxford University Press.
 Simpson, George G. 1951. Horses. Oxford University Press.
 Norman, David. 1985. Encyclopaedia of Dinosaurs. Salamander Books. London.
 Patterson, Colin, presentation to the American Natural History Museum, 5 November 1981.
 Waddington, C.H., 1960, Evolutionary Adaptation in Tax Vol. 1, pp 381-402.
 Simpson, George G. 1964, This View of Life, Harcourt Brace and World. New York.
 Cairns, J., J. Overbaugh, S. Miller. 1988. The origin of mutants. In Nature 335: 142-145. Hall, Barry G. Sept. 1990. Spontaneous point mutations that occur more often when advantageous than when neutral. In Genetics Vol. 126, pp. 5-16.
 Durrant, Alan. 1958. Environmental conditioning of flax. in Nature, Vol. 81, p. 928-929. Hill, J. 1965. Environmental induction of heritable changes in Nicotiana rustica. in Nature, Vol. 207, pp. 732-734. Cullis, C.A. 1977. Molecular aspects of the environmental induction of heritable changes in Flax. in Heredity. Vol. 38, p. 129-154.
 See Koestler, Arthur. 1978. The Case of the Midwife Toad. Hutchinson. London, for an account of the experiments of Paul Kammerer at the Vienna Institute for Experimental Biology 1903-1926.
 Hoyle, F. 1983. The Intelligent Universe. Michael Joseph. London.
See also, Crick, Francis, 1981. Life Itself. Macdonald. London.
 Sheldrake, Rupert, 1988 edn. A New Science of Life, Paladin London.
 Nature 1981, Vol. 293, pp 245-246.
 Milton, Richard, 1993 edn., The Facts of Life: Shattering the myths of Darwinism, Transworld/Corgi, London.
 Milton, Richard, 1995 edn., Forbidden Science: Exposing the Secrets of Suppressed Research, Fourth Estate, London.
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These books offer a third way instead of Intelligent Design or Darwinism.
Jerry Fodor and Massimo Piattelli-Palmarini. (2011) What Darwin Got Wrong. Picador; Reprint edition ISBN 031268066X
Numbers, Ronald L. (2006). The Creationists: from scientific creationism to intelligent design. Cambridge, Mass.: Harvard University Press. ISBN 0674023390. OCLC 69734583.
Lebo, Lauri (May 13, 2008). The Devil in Dover: An Insider's Story of Dogma v. Darwin in Small-town America. New Press. p. 256 pages. ISBN 1595582088.
Stanley Salthe (2003). Development and Evolution: Complexity and Change in Biology. The MIT Press. ISBN 0262513838
James A. Shapiro (2011). Evolution: A View from the 21st Century. ISBN 0132780933
Robert Shapiro (1986). Origins; A Skeptic's Guide to the Creation of Life on Earth. New York, N.Y.: Summit
David Stove (2006). Darwinian Fairytales: Selfish Genes, Errors of Heredity and Other Fables of Evolution. ISBN 1594031401
Norman Macbeth (1971). Darwin Retried. Boston: Harvard Common Press
Hubert Yockey (2011). Information Theory, Evolution, and The Origin of Life. Cambridge University Press; Reissue edition. ISBN 0521169585
Amit Goswami (2008). Creative Evolution: A Physicist's Resolution Between
Darwinism and Intelligent Design. Quest Books; 1st Quest Ed edition. ISBN 0835608581
Bernard Haisch (2010). The Purpose-Guided Universe: Believing In Einstein, Darwin, and God. New Page Books; 1 edition. ISBN 1601631227
Robert Lanza (2010). Biocentrism: How Life and Consciousness are the Keys to Understanding the True Nature of the Universe. BenBella Books; 1 edition. ISBN 1935251740
Robert G. B. Reid (1985). Evolutionary Theory: The Unfinished Synthesis. Cornell Univ Pr. ISBN 0801418313
Ervin Laszlo (1987). Evolution: The Grand Synthesis. Shambhala. ISBN 0877733899
Paul Davies (2007). Cosmic Jackpot The Goldilocks Enigma: Why is the Universe Just Right for Life?. ISBN 9780618592265
James Le Fanu (2009). Why Us?: How Science Rediscovered the Mystery of Ourselves. Pantheon. ISBN 037542198X
Richard Milton (2000). Shattering the Myths of Darwinism. Park Street Press. ISBN 0892818840
Francis Hitching (1983). The Neck of the Giraffe or Where Darwin Went Wrong. Signet. ISBN 0451622324
Brian Goodwin (2001). How the Leopard Changed its Spots: The Evolution of Complexity. Princeton University Press. ISBN 0691088098
Lee Spetner (1998). Not by Chance!: Shattering the Modern Theory of Evolution. Judaica Press. ISBN 1880582244
Albert Low (2008). The Origin of Human Nature: A Zen Buddhist Looks at Evolution. Sussex Academic Pr. ISBN 1845192605
Carl Johan Calleman (2009). The Purposeful Universe: How Quantum Theory and Mayan Cosmology Explain the Origin and Evolution of Life. Bear & Company. ISBN 1591431042
Michael Corey (2007). The God Hypothesis: Discovering Design in Our Just Right Goldilocks Universe. Rowman & Littlefield Publishers. ISBN 0742558894
George Greenstein (1988). The Symbiotic Universe: Life and mind in the Cosmos. Morrow. ISBN 0688076041
James N. Gardner (2003). Biocosm: The New Scientific Theory of Evolution: Intelligent Life Is the Architect of the Universe. Inner Ocean Publishing. ISBN 1930722265
Mae-Wan Ho (1984). Beyond Neo-Darwinism: An Introduction to the New Evolutionary Paradigm. Academic Pr. ISBN 012350080X
Johnjoe McFadden (2002). Quantum Evolution: How Physics' Weirdest Theory Explains Life's Biggest Mystery. W. W. Norton and Company. ISBN 0393323102
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A good website which cites some of the obscure non-Darwinian evolutionists from 1880 - 1950s and a few others, see for example the theory of idealistic morphology. There are also some debates going on about the role of natural selection in evolution.