Tuesday, January 01, 2008

PoE: Bibliography "A"

This is the Bibliography "A" page for authors' surnames beginning with "A" which I may

[Left: "The Mirror of Creation" (1990), by Edmund J. Ambrose, Emeritus Professor of Cell Biology at the University of London. Ambrose is a Christian and a critic of fully materialistic- naturalistic evolution in general and Darwinism in particular. See PS below.]

refer to in my book outline, "Problems of Evolution."


PROBLEMS OF EVOLUTION
© Stephen E. Jones, BSc. (Biology)


CONTENTS

BIBLIOGRAPHY "A"

Abbott, E.A., 1884, "Flatland: A Romance of Many Dimensions," Dover: New York NY, Reprint, 1992.
Aczel, AD., 1998, Probability 1: Why There Must Be Intelligent Life in the Universe," Abacus: London, Reprinted, 2000.
Adair, R.K., 1987, "The Great Design: Particles, Fields, and Creation," Oxford University Press: New York NY.
Adams, F.C. & Laughlin, G., 1999, "The Five Ages of the Universe: Inside the Physics of Eternity," The Free Press: New York NY.
Adams, P., 1985, "Adams vs God," Nelson: Melbourne.
Ager, D.V., 1993, "The New Catastrophism: The Importance of the Rare Event in Geological History," Cambridge University Press: Cambridge UK.
Agosta, W.C., 1996, "Bombardier Beetles and Fever Trees: A Close-up look at Chemical Warfare and Signals in Animals and Plants," Addison-Wesley: Reading MA.
Alcock, J., 1993, "Animal Behavior: An Evolutionary Approach," [1975], Sinauer Associates: Sunderland MA, Fifth Edition.
Aldridge, S., 1996, "The Thread of Life: The Story of Genes and Genetic Engineering," Cambridge University Press: Cambridge UK.
Alexander, R.M., 1975, "The Chordates," Cambridge University Press: Cambridge UK, Reprinted, 1977.
Allaby, A. & Allaby, M., eds, 1999, "Oxford Dictionary of Earth Sciences," [1990], Oxford University Press: Oxford UK, Second edition.
Allaby, M., 1989, "Guide to Gaia," Optima: London.
Allaby, M., ed., 1994, "The Concise Oxford Dictionary of Ecology," Oxford University Press: Oxford UK.
Allaby, M., ed., 1999, "Oxford Dictionary of Zoology," [1991], Oxford University Press: Oxford UK, Second edition.
Alberts, B., et al., 1994, "Molecular Biology of the Cell," [1983], Garland: New York NY, Third edition.
Allbrook, D.B., 1971, "The Evolution of Man: Part I-Origins of Man," Jacaranda Press: Queensland, Australia, Reprinted, 1975.
Allbrook, D.B., 1971, "The Evolution of Man: Part II-People of Our World," Jacaranda Press: Queensland, Australia, Reprinted, 1975.
Alters, B.J. & Alters, S.M., 2001, "Defending Evolution in the Classroom: A Guide to the Creation/Evolution Controversy," Jones & Bartlett Publishers: Sudbury MA.
Alvarez, W., 1997, "T. Rex and the Crater of Doom," Princeton University Press: Princeton NJ.
Ambrose, E.J., 1990, "The Mirror of Creation," Theology and Science at the Frontiers of Knowledge, Number 11, Scottish Academic Press: Edinburgh.
Andrews, E.H., 1979, "From Nothing to Nature: A Young People's Guide to Evolution and Creation," Eurobooks: Welwyn UK.
Andrews, E.H., 1980, "God, Science & Evolution," Evangelical Press: Welwyn UK, 1985, Fourth impression.
Andrews, E.H., 1986, "Christ and the Cosmos," Evangelical Press: Welwyn UK.
Andrews, P. & Stringer, C., 1989, "Human Evolution: An Illustrated Guide," British Museum of Natural History: London.
Angela, P. & Angela, A., 1996, "The Extraordinary Story of Life on Earth," Prometheus Books: Amherst NY.
Ankerberg, J. & Weldon, J., 1993, "The Facts on Creation vs. Evolution," Harvest House: Eugene OR.
Ankerberg, J. & Weldon, J., 1998, "Darwin's Leap of Faith," Harvest House Publishers: Eugene OR.
Angier, N., 1995, "The Beauty of the Beastly: New Views on the Nature of Life," Houghton Mifflin: Boston MA.
Appleman, P., ed., 1979, "Darwin: A Norton Critical edition," [1970], W.W. Norton & Co: New York NY, Second edition.
Appleyard, B., 1992, "Understanding the Present: Science and the Soul of Modern Man," Picador: London.
Appleyard, B., 1999, "Brave New Worlds: Staying Human in the Genetic Future," HarperCollins: London.
Ardrey, R., 1961, "African Genesis: A Personal Investigation into the Animal Origins and Nature of Man," Fontana: London, 1971, Seventh impression.
Ardrey, R., 1967, "The Territorial Imperative: A Personal Inquiry into the Animal Origins of Property and Nations," Fontana: London, Reprinted, 1969.
Ardrey, R., 1970, "The Social Contract: A Personal Inquiry into the Evolutionary Sources of Order and Disorder," Fontana: London, Reprinted, 1972.
Ardrey, R., 1976, "The Hunting Hypothesis: A Personal Conclusion Concerning the Evolutionary Nature of Man," Fontana: London, Reprinted, 1977.
Armstrong, K., 1993, "A History of God: From Abraham to the Present: The 4000-Year Quest for God," Vintage: London, Reprinted, 1999.
Armstrong, P., 1985, "Charles Darwin in Western Australia: A Young Scientist's Perception of an Environment," University of Western Australia Press: Nedlands WA, Australia.
Arnold, A., 1992, "The Corrupted Sciences: Challenging the Myths of Modern Science," Paladin: London.
Arthur, W., 1987, "Theories of Life: Darwin, Mendel, and Beyond," Penguin: Harmondsworth UK.
Ashpole, E., 1989, "Where is Everybody?: The Search for Extraterrestrial intelligence," Sigma Press: Wilmslow UK, Reprinted, 1997.
Ashton, J.F., ed., 1999, "In Six Days: Why 50 Scientists Choose to Believe in Creation," New Holland: Sydney, Australia.
Asimov, I., 1963, "The Human Body: Its Structure and Operation," Mentor: New York NY.
Asimov, I., 1964, "A Short History of Biology," Scientific Book Club: London, Reprinted, 1965.
Asimov, I., 1966, "Science, Numbers, and I," Ace Books: New York NY, Reprinted, 1976.
Asimov, I., 1966, "The Universe: From Flat Earth to Quasar," Penguin: Harmondsworth UK, Reprinted, 1980.
Asimov, I., 1970, "Photosynthesis," George Allen & Unwin: London.
Asimov, I., 1972, "Asimov's Guide to Science: Volume 1: The Physical Sciences," Penguin: Harmondsworth UK, Reprinted, 1978.
Asimov, I., 1972, "Asimov's Guide to Science: Volume 2: The Biological Sciences," Penguin: Harmondsworth UK, Reprinted, 1975.
Asimov, I., 1973, "Please Explain: The Myriad Mysteries of the Universe Revealed," Coronet: Sevenoaks UK, Reprinted, 1978.
Asimov, I., 1974, "The Stars in Their Courses," Panther: St. Albans UK, Reprinted, 1975.
Asimov, I., 1979, "Extraterrestrial Civilizations," Crown: New York NY.
Asimov, I., 1981, "In The Beginning...: Science Faces God in the Book of Genesis," Crown Publishers: New York NY.
Asimov, I., 1983, "The Roving Mind," Oxford University Press: Oxford, 1987.
Asimov, I., 1987, "Beginnings: The Story of Origins of Mankind, Life, the Earth, the Universe," Walker & Co: New York NY.
Asimov, I., 1988, "The Relativity of Wrong," Oxford University Press: Oxford UK, 1989.
Asimov, I., Zebrowski, G. & Greenberg, M.H., eds, 1983, "Creations: The Quest for Origins in Story and Science," Harrap: London, Reprinted, 1984.
Atkins, P.W., 1992, "Creation Revisited," Penguin Books: London, Reprinted, 1994.
Atkins, P.W., 1995, "The Periodic Kingdom: A Journey into the Land of the Chemical Elements," Basic Books: New York NY.
Attenborough, D., 1979, "Life on Earth: A Natural History," Fontana/Collins: London, Second impression, 1984.
Attiwill, P. & Wilson, B., eds, 2003, "Ecology: An Australian Perspective," Oxford University Press: South Melbourne Vic, Australia.
Audi, R., ed., 1995, "The Cambridge Dictionary of Philosophy," Cambridge University Press: Cambridge UK, Reprinted, 1996.
Augee, M.L. & Fox, M.D., 2000, "Biology of Australia and New Zealand," Pearson Education Australia/Benjamin Cummings, Sydney, Australia.
Augros, R.M. & Stanciu, G.N., 1987, "The New Biology: Discovering the Wisdom in Nature," New Science Library, Shambhala: Boston, MA.
Avise, J.C., 1998, "The Genetic Gods: Evolution and Belief in Human Affairs," Harvard University Press: Cambridge MA, Second printing, 2001.
Aw, S.E., 1982, "Chemical Evolution: An Examination of Current Ideas," Master Book Publishers: San Diego CA.
Awbrey, F. & Thwaites, W., eds, 1984, "Evolutionists Confront Creationists," Proceedings of the 63rd Annual Meeting of the Pacific Division, American Association for the Advancement of Science, Vol. 1, Part 3, April 30.
Austin, C.R., 1989, "Human Embryos: The Debate on Assisted Reproduction," Oxford University Press: Oxford UK.
Axelrod, R.M., 1984, "The Evolution of Cooperation," Basic Books: New York NY.
Ayala, F.J. & Kiger, J.A., 1984, Jr., "Modern Genetics," [1980], Benjamin/Cummings: Menlo Park CA, Second edition.

PS: The `tagline' quotes below are all from Ambrose's book. I could have added more such quotes, but this post was already too long. To save repeating "emphasis original" many times, emphases in italics are original and emphases in bold are mine).

Stephen E. Jones, BSc. (Biology).
My other blogs: Jesus is Jehovah! & TheShroudofTurin


"The British Association for the Advancement of Science, with which I have worked, is one of the few organisations, perhaps the only organisation which, over the years, which has provided coordinated presentations of major developments in science. What I have learned at the B.A. and from my own research in the field of molecular, cell and developmental biology, is that modern science objectively interpreted, provides an inspiring and wonderful picture of the Divine Creation, on a scale both in magnitude and complexity far exceeding anything visualised by earlier generations." (Ambrose, E.J., 1990, "The Mirror of Creation," Theology and Science at the Frontiers of Knowledge, Number 11, Scottish Academic Press: Edinburgh UK, p.xi).

"Modern astronomy has provided striking evidence that our entire Universe was generated from a minute speck of gigantic energy. But this minute object had vast potential: as it expanded and unfolded, it was capable of generating the various building units which later formed atoms and molecules, also the forces which hold the building units together. The sizes of the units and the forces between them provided the unique conditions which have made possible the existence of our Universe. Had they been otherwise, stars, galaxies and planets could not have come into existence. But it was not only the properties of the elementary particles which led to the development of our Cosmos. As the original speck of energy expanded, Cosmologists have identified a series of critical stages where additional `fine tuning' was required to make it possible for our water planet to come into existence." (Ambrose, 1990, p.xiii).

"If such conditions have controlled the emergence of the Cosmos, we should surely expect to find evidence for a similar progressive building up of order in the biological world. The purpose of this book is to provide this bridge between the physical and the biological worlds, a subject at present almost totally neglected by many biologists. The first chapters provide a general summary of cosmology. Subsequent chapters give an account of the unique features of our planet which have made it a cradle for life, also the origin of life, of higher organisms and the origin of the species. In the concluding chapters, the present evidence for design and order both in the cosmos and the living world as found on our planet is shown to give us a glimpse into the wonder of the Divine Work of Creation." (Ambrose, 1990, p.xiii).

"Examples of Fine Tuning The tuning of the radio detector circuit can be likened to tuning of a violin string by tension or an organ pipe where length determines the wave length of the sound wave which will fit the pipe. Something rather similar to the fine tuning described above has been recognised in recent years to exist within the Cosmos. One way of studying this aspect of the Cosmos is to consider what would be the effect of a minute alteration in the magnitude of the various sizes of building units, the strength of the glues which hold them together, the rate of expansion, etc. The extraordinary conclusion is that the minutest deviation from the fine tuning as it exists would have meant either that no Universe could have existed for more than a brief time or that the Universe would have had a constitution which would have made it impossible for planets and certainly for life to exist." (Ambrose, 1990, p.27).

"Initial density and rate of expansion of the Universe At 10-43 seconds after the initial event which created it, the Universe is believed to have had the prodigious density of 5x10-9 kg per cubic centimetre. If the density had been appreciably less than this the Universe would have expanded as a gas, becoming ever more and more attenuated; no region could subsequently have achieved sufficient density to draw other matter to itself by the snowball effect due to the force of gravity. On the contrary, if the initial density had been slightly greater, expansion could only have continued for a relatively short period; the force of gravity would have overcome the expanding pressure and within a comparatively short time the Universe would have been sucked back again almost like a backfire so returning into a singularity (a point) or a fluctuation." (Ambrose, 1990, p.28).

"The exactness of the fine tuning of the expansion of the Universe was in the first moments of Creation regulated to within 1 part in 1060. To give some conception of the precision of this control, it can be likened to firing a bullet across the greatest distance in the Universe in the range of 20,000 million light years; 1 light year being 6x1012 miles the distance could be at least 6x1012 x 2 x 1010 = 12 x 1022 miles. Travelling this distance the bullet would be aimed at a target 1 inch in diameter and hit it! Paul Davies has used this example to illustrate the level of fine tuning. He recognises that this level of tuning is one of the great mysteries of the Cosmos." (Ambrose, 1990, p.28).

"The Uniformity of the Universe There was need for control of the initial expansion also in various directions. ... The precision with which this was controlled can actually be measured. The background radiation, originally studied by Penzias and Wilson [Penzias, A.A. & Wilson, R.W., Astrophysics. J., 142, 1965, p.419], has now been plotted extremely accurately throughout the heavens. It does not vary beyond 1 part in 10,000 anywhere. To have achieved this regularity the original expansion in various directions must have been `fine tuned' to 1 part in 1040. One simple model for the expanding Universe, would be to think in 2 dimensions instead of 3. If it was a sheet, one side expanding faster than the other, it could assume peculiar curved forms. Only in special cases could it be flat or nearly flat. As mentioned ... our Universe is an almost flat Universe. Only in a Universe in which this level of uniformity is expressed in three dimensions is it possible for us to exist." (Ambrose, 1990, pp.28-29).

"The preponderance of matter over antimatter The way in which it came about that for every 1,000,000,000 particles of antimatter there are 1,000,000,001 particles of matter is possibly due to the unsymmetrical decay of the corresponding heavy particles called baryons already mentioned. This represents a fantastic level of fine tuning, leading to quite unexpected asymmetry of the Universe. There is something extremely special about this process of matter predominance, without which the Universe could not have existed at all." (Ambrose, 1990, p.30).

"Hydrogen the nuclear fuel of the Universe Without the nuclear fuel, hydrogen, which causes the stars to shine, the Universe would be `dead' with everything near to absolute zero. The processes which, in the early stages of the expansion, produced 74% of hydrogen out of a total of all matter in the early gas clouds involved extremely precise `tuning'. There was a continuous conversion of protons into neutrons and vice versa in the early stages of expansion of the Universe until the temperature had fallen to 1010°K; after that the proportion of protons to neutrons and hence the amount of hydrogen formed from protons was `frozen'. Two factors which were precisely tuned to provide the necessary amount of hydrogen were the strength of the weak nuclear force and the temperature at which the necessary reaction occurred. A neutron plus a neutrino can produce a proton plus an electron because the difference in mass between the neutron and proton is only slightly greater than the mass of an electron; this relationship between the masses of these particles provides the necessary fine tuning; the reverse reaction involves antimatter which is eventually annihilated. Even so, a few per cent increase in the strength of the nuclear force would later cause protons to stick together in pairs, leading to all the hydrogen being converted into helium. On the delicate balance between all the above factors has depended the existence of the nuclear fuel to feed the stars." (Ambrose, 1990, p.31).

"The nuclear furnace in the stars In the stars it is the nuclei, the protons of the hydrogen atoms, which provide energy. In this reaction two protons react together to generate a nucleus of deuterium consisting of 1 proton + 1 neutron. If the strong nuclear force were 5% weaker deuterium could not exist while if the force were 2% stronger two protons would form a diproton; this would lead to an explosive reaction and no stable stars could exist. Deuterium acts as a brake on the nuclear reaction so leading to a steady conversion of protons into helium nuclei. Matter is steadily converted into energy during this conversion so that the process can last for thousands of millions of years and enables the stars to continue to shine." (Ambrose, 1990, pp.31-32).

"The formation of Carbon, the key element for life During the burning of the nuclear furnaces, hydrogen protons are converted into the nuclei of the gas helium. In older stars, where the temperature has fallen, two helium nuclei He + He are able to fuse together; they then collect a third He nucleus to produce a carbon nucleus. Hoyle has pointed out that a simultaneous collision between three helium nuclei would be an extremely rare event and it would be expected that carbon would be an extremely rare element in the Universe, but in fact it is one of the most common heavier elements. Imagine two golf balls falling on the green from the approach shots of two players. A collision between two balls is a rare event. But suppose that a third player's ball also arrives at the same moment and collides with the other two: we should never expect to see such an event. Yet in the star this type of event takes place. When the two helium nuclei collide they form a nucleus which is an isotope of the chemical element beryllium Be8. Each of the orbits of atoms has a frequency like a violin string or an organ pipe. It is called the resonance frequency. It was found by Hoyle that the frequency of the dihelium or beryllium nucleus was similar to the frequency of a single helium nucleus. This was like tuning the radio set to the frequency of the carrier wave ... . This harmony of `tuning in' makes it possible for carbon to be formed readily within the stars. But even so, the carbon nucleus need not be long lived; it could in turn be `burnt up' as nuclear fuel in another reaction. It could collide with another helium nucleus to form oxygen. But in this case the tuning or resonance frequency of oxygen is safely below that of carbon. Oxygen is therefore produced in the nuclear reactions only slowly from carbon. About equal amounts of carbon and oxygen, key elements for life, are produced in the stellar synthesis. Hoyle [Hoyle, F., "The Universe, Some Past and Present Reflections," Cardiff University Press: Cardiff UK, 1982, p.16] has stated in characteristic style, `A common sense interpretation of the facts suggest that a superintellect has monkeyed with the laws of physics as well as chemistry and biology, and that there are no blind forces worth speaking about in nature'. Hoyle was a pioneer in elucidating the origin of the chemical elements within the stars." (Ambrose, 1990, pp.32-33).

"Given an infinite time, it was concluded that anything could happen. We are all familiar with the monkey which continues to tap on the keys of a typewriter until all the plays of Shakespeare are produced by chance; so in spite of its extreme improbability it was believed by the materialists that given an infinite time the Universe, as we find it, together with the planets our earth and life could have arisen by chance. ... the general conclusions of late 20th Century cosmology are that the Universe had a beginning. This presents immense problems for the materialistic interpretation as most have fully recognised." (Ambrose, 1990, p.34).

"One way in which the materialists have approached their difficulty has been to assume that the Universe which arose from a `point' expanded to an enormous volume; the mass was sufficient for the force of gravity to draw it back again; it was steadily drawn towards a point or singularity. This would be drawing the matter back to a gigantic `black hole' through the power of gravity. Once again it could expand. This cycling process would once again provide a possibility for infinite permanence of the Universe in terms of cycles. John D. Barrow and Joseph Silk [Barrow, J.D. & Silk, J., "The Left Hand of Creation," Heineman: London, 1984, p.256] have pointed out that the point, singularity or `black hole' as it may be called; is a region of no return ... the generation of disorder is not reversible. This is a basic law of physics; the second law of thermodynamics .... The background radiation would simply build up in each cycle. ... The fact that there is so little disorder in our Universe, the background reaching only 3° above absolute zero, shows that we must be in a first expansion from the beginning of the Universe." (Ambrose, 1990, pp.34-35).

"Prior to the time of Copernicus, it was believed that the earth was the centre of the Universe. Since the time of Copernicus there has been a succession of astronomical discoveries revealing not only that our earth is a planet circulating round the sun, but that our sun is one of thousands of million of stars in our galaxy, that our galaxy is itself one amongst hundreds of millions at least. The immensity of the Universe disclosed by 20th Century science has led some materialists to question whether there can really be any significance to the lives of inhabitants of a minute assembly of cosmic dust. To anyone who thinks deeply it is obvious that the key to understanding what the Universe is about is complexity, not size. The Universe itself was generated from a speck of energy far smaller than the smallest atom. It had to be its present size in order that it could be an almost flat Universe of the sort in which planets could be generated. Above all it had to continue to expand for 15,000 million years or more to reach its present size in order to allow the various chemical elements which form planets to be generated and for them to be suitably disposed in cosmic dust clouds." (Ambrose, 1990, p.35).

"Once the fine tuning of the Universe was recognised, cosmologists began a return to the concept of an earth-centred Universe once more. This was expressed by Brandon Carter, a leading cosmologist in ... the Anthropic Principle. The weak Anthropic Principle states that we have to observe a Universe finely tuned, because no Universe which was not finely tuned could contain any observers. The Strong Anthropic Principle goes further. It states that there is a compulsion in the Universe to generate intelligent beings, this being the reason for fine tuning. There are two ways of accounting for this Strong Principle: (a) That the Universe is the work of a Creator; clearly the most straight forward explanation. (b) We the observers influence the observed world; this is the case in a limited sense, according to quantum theory; time also is now known to have unexpected properties. But the Universe originated 15,000 million years before we came into existence as intelligent beings. ... the tine tuning of the Universe, which forms the basis of the Anthropic Principle, took place in the main within a matter of minutes after the initial event which generated the cosmos. To believe that intelligent observers can have influenced events so far in the distant past is philosophically unacceptable. We note that even the weak Anthropic Principle represents a departure from the older materialistic interpretation of origins based on chance." (Ambrose, 1990, p.36).

"An obvious conclusion from the Strong Anthropic Principle would be that the Creator has made the Universe the way it is in order that the earth could be formed as suitable for the emergence of life and for our existence also. It is sad that reference to the Creator has become unfashionable amongst most modern scientific popularisers, particularly when the evidence is now so strong that there is much design and fine tuning in the Universe. Most modern scientists accept this; in the past the greatest physicists had no hesitation, Isaac Newton, Michael Faraday and many others." (Ambrose, 1990, pp.36-37).

"So we move from the gigantic perspective provided by the Cosmos to the living world on our planet. If we accept the Anthropic Principle of the Astronomers, it would indeed be surprising if the same principle could not be extended to the formation of our earth and the establishment of the living world. But we now encounter a change of emphasis; we think less in terms of fine tuning and more in terms of the generation of order ... and the need to account for the vast input of new information involved to account for both the origin of life and the building up progressively of high and higher levels of complexity in the living world. At the molecular level, we encounter the great discovery that life has an alphabet and a language. Written in that language is the nature of each species of organism on the face of the earth. We find that a beautiful harmony exists, a symphony written in the language of life is expressed in the perfectly controlled development of an organism from a single cell, first as an embryo, then an adult and functioning plant or animal. A striking feature of the living world is its diversity; hundreds of thousands of species of both plants and animals are found in various regions of the planet. Nevertheless, the basic building plan, based on information, as expressed in language, governs the development of every one of these species of plant and animal." (Ambrose, 1990, p.49).

"Water has an extremely high specific heat. We all know how long it takes to boil a kettle even when strongly heated. The large heat content of water helps to stabilise the temperature of the earth, which is basically a water planet, as is clearly seen in photographs of the earth from space. The temperature range at which life can exist is covered by the temperature range at which liquid water can exist. If other molecules existed in the Universe with the properties of water molecules and were present in large numbers, it would have been conceivable that they also might have formed the basis for life. This is not the case. In addition water molecules contain within themselves the capacity to form stable gossamer like bonds. These bonds are responsible for the decrease in density of water on freezing, a property not shown by other liquids of common occurrence. For this reason ice floats on water. If this did not happen lakes and rivers would remain frozen solid in winter and all life in the waters would be destroyed." (Ambrose, 1990, p.52).

"Water is a unique solvent; it can dissolve more substances than any other known solvent. Not only does it dissolve many carbon compounds, it also dissolves salts which can carry electrical charge. The electrical phenomena that are the key to life processes are dependent on this power of water to dissolve salts. Above all, water has the capacity to dissolve gases in limited amounts, oxygen without which respiration could not occur, and carbon dioxide the source of the carbon molecules which play a key role in all living structures. So water and carbon are essential for life. ." (Ambrose, 1990, p.52).

"The unique feature of the carbon molecule is connected with the `tuning' of the orbits in which the outer four electrons lie. This enables carbon to form long chains and rings all essential for life; also to combine with oxygen, and nitrogen, within the temperature range of liquid water. The orbits of the four planetary electrons of carbon are so arranged that they can form bonds lying at the four corners of a tetrahedron. Not only does this enable many compounds to be formed with the other light elements, but many carbon atoms can be joined together in strings, forming the long chains of fat molecules, also essential for life." (Ambrose, 1990, pp.52-53).

"However suitable the four elements hydrogen, carbon, oxygen and nitrogen may be for generating the molecules that form living organisms, it is evident that these alone could not provide the environment for life. No gaseous star however much it cooled could do so. There was a need for a solid surface upon which water molecules could condense. This has come from the magic dust generated by supernova explosions. ... the giant stars, which exploded to release the heavier chemical elements, had a layered structure ... The supernova explosion, which is now believed to have generated most of the elements described ... is thought to have occurred about 200 million years before the solar system was formed. .... a second supernova explosion occurred shortly before the solar system was formed. During this explosion the important element aluminium which forms a large part of the earth's crust was generated. In fact this second supernova explosion may have provided the shock wave which initiated the formation of the solar system." (Ambrose, 1990, pp.53-55).

"From the foregoing evidence it is clear that the steps which gave rise to our solar system, the planets and our earth were complex. Although there is now some evidence from infrared studies that a cosmic dust cloud surrounds the star Vega, it is by no means certain that this cloud could generate a planet like our earth. We cannot exclude the possibility that our planet is unique." (Ambrose, , 1990, p.55).

"Before considering this subject it is as well to point out that in trying to explain the origin of life, purely in materialistic terms, we are in much the same situation as those who put forward hypotheses concerning the first moments after the creation of the Universe. There is no possible way in which this event can be studied in a strictly scientific manner. Whatever the prelife and first life may have been like, it was certainly minute and without any hard structures. No trace has ever been, or is likely to be detected, in the most ancient rocks. Models can be built up in the laboratory but their interpretation in terms of the actual origin of life will always remain as hypotheses; they can be reasonable guesses and no more." (Ambrose, 1990, p.61).

"So the first requirement for life is that it should receive a continuous supply of energy: it must have a steady supply of matter also. Simple molecules called metabolites enter the cell, are built up into the proteins and other structures of the cell and are continuously broken down again. So a living organism can be likened to a river. As we stand beside the river, the banks appear to us to be unchanging, certainly during any period for which we can continue to observe them. And the river appears unchanging. But in the river water molecules are continuously flowing along because they are driven by energy due to the force of gravity drawing them to sea level. What is stable about the river is its pattern, the form of currents and flow of the water. Likewise a living cell imposes, with the help of its energy supply, a pattern upon the molecules which enter it and flow through it. It is this form, this `ephemeral design' which we call a species. Immediately, we recognise that we have to do with something totally new, outside anything to be seen in the natural nonliving world. Therefore we find that we have to use a new language to describe living organisms, a language that has no meaning in chemistry. ... The living cell can be more appropriately described in the language used by engineers. In fact a modern mass production factory operating by computers and robotics, is of considerable help in trying to find a model to represent the way in which the simplest known living cell is able to operate." (Ambrose, 1990, pp.74-75).

"The power house (The Solar panel) ? because a living organism is in a dynamic (moving) state it must have a continuous supply of energy. But this energy must be provided in a highly regulated, coordinated manner. ... In the cell's robotics factory, the energy originates through the green substance of plants, chlorophyll in almost all cases. Even our fossil fuels, oil, gas or coal come from ancient green plants. The chlorophyll molecule can absorb a packet or quantum of light energy in the red region of the light spectrum. This enables an electron within the molecule to jump to a new orbit of a higher energy. This electron then behaves rather like the baton in a relay race, being shifted from one runner (molecule) to another. But it is a downhill race. At each transfer, some energy from the electron is passed on. Finally the electron returns, in the case of blue green algae (cyanophytes), to its original low level home in the chlorophyll. This is like an electric circuit, except that the circuit is made by various carbon compounds instead of the copper in the wire of an electric circuit. The wires in the electric circuit are coated with polyvinyl; the electron circuit in the living cell must also be protected. In this case the insulation is provided by lipid membranes. The end product of these various complicated flow processes is to produce molecules which contain a store or reserve of energy; they are like electric batteries which have been charged by the light of the sun. In the mass production factory, energy is distributed to various parts of the plant by electrical wires; in the cell this is much more simply achieved by these energy carrying molecules. Their name is adenosine triphosphate, or ATP for short. They contain three key atoms of phosphorus. On the basis of present evidence from the rocks, the earliest known living organisms derived their energy from the sun by the process described above which is known as photosynthesis." (Ambrose, 1990, pp.75-76).

"The machine tools Each step along the factory production line involves a machine tool fitted to the particular step in drilling, milling, etc., to produce the end product. In the living cell this is achieved by beautifully designed molecules called proteins. These molecules consist of a string of beads in which the individual beads are the amino acids. ... In three dimensions this has the shape of a tetrahedron, in which the groups can be arranged in either left or right handed screw. In the living organisms, the amino acids are left handed or L-amino acids. ... The key to the effectiveness of these giant molecules is the gossamer threads which can be formed and broken easily at room temperature ... hydrogen bonds ...The protein chains have a complicated structure so the folded molecule is not totally compact; it can be likened in some ways to a Rubik cube, with a gap at one corner. This gap is shaped like a lock. It can act as a catalyst. ... Chemical reactions have ... been likened to hurdles in which so called activation energy must be provided to overcome a barrier ... The catalyst acts to reduce the height of the hurdle by absorbing the molecules which are going to react at its surface. In the protein molecule the substances that are going to react become absorbed inside the lock and fit the lock beautifully like a key. So the protein molecules, which are called enzymes, literally direct chemical reactions in a manner favourable to the life of the organism; a truly wonderful phenomenon, already seen at the level of molecules. These are the machine tools of life." (Ambrose, 1990, pp.76-77).

"The earliest known organisms on earth, the cyanophytes, and some bacteria were able to fix nitrogen in the atmosphere by attaching hydrogen to it. This generates a molecule soluble in water which cells can utilise. This these microorganisms were able to do with the greatest of ease, which is the case with the corresponding modern species also. The fascinating process by which these minute organisms, only fractions of a millimetre in diameter, are able to fix the comparatively unreactive nitrogen molecules of the atmosphere, has only recently come to light after many years of intensive research. The work of Hughes, Pickett and Talarmin of Sussex University and Pombeiro of Lisbon [Emsley, J., "Molybdenum lies at the heart of Nitrogen Fixation," New Scientist, 10th April 1986, p.30) has shown that there is a key enzyme, a nitrogenase, which contains an atom of molybdenum. Molybdenum can, in association with the special protein, attract a nitrogen molecule N2. The nitrogen is then swamped with hydrogen ions H+ from water while the molybdenum supplies electrons. Ammonia NH3 is formed. So simple yet so wonderful and beautifully refined. Attempts are now being made to imitate the behaviour of the enzyme and the molybdenum combination in the laboratory and so do away with complicated fertilizer plants which at present operate only at high temperatures and great expense. The living cells do all their work at room temperature utilising the 'solar panel' energy of chlorophyll." (Ambrose, 1990, p.80).

"High Technology The above brief summary of some of the key features of a living cell may have given an inkling of the level of complexity and coordination that exists in the smallest known independent organisms. The degree of sophistication seen already at the level of individual molecules within the cell can be truly astonishing. The earliest known organisms on earth were able to obtain energy, produce protein membranes, etc., grow and multiply, utilising only simple constituents from the inorganic world, the cradle of life. This is already seen at the first stage of energy uptake, in the 'fine tuning' of the chlorophyll molecule which absorbs quanta of light derived from the sun. The electron so liberated from chlorophyll must have just sufficient energy to enable a carrier molecule FAD to pick up hydrogen atoms. This carrier molecule passes on its energy to the complicated chemical reactions which finally produce the molecules that carry the essential chemical energy to all parts of the cell, and enable carbon dioxide from the atmosphere to be 'fixed' and used to build up the proteins, etc., based on the key element carbon. If chlorophyll had been so constituted that it absorbed light of slightly longer wavelength, this would not have provided enough energy to enable all the complex reactions needed for life to start within the cell. Alternatively, absorption of shorter wavelength light can damage the delicate chlorophyll molecule itself. So the beautiful `fine tuning' of the chlorophyll molecule recalls to us the Anthropic Principle, already seen in the `fine tuning' of the emerging cosmos ..." (Ambrose, 1990, pp.80-81).

"But the level of sophistication within the 'simplest' living cell goes far beyond this. We need to think in terms of what modern engineers call high technology. A spade is an example of low technology. To function for digging a garden all that a spade requires is a 'willing' and hard working gardener, to take it up and use it; the spade's function to turn over the earth is so fulfilled. But after finishing the digging, the gardener decides to relax by going for a drive in the car. All that is required is to sit at the wheel, operate the starter and move forwards. The car represents high technology; it contains many components which function together, for example a steering wheel, road wheels, internal combustion engine, fuel system, ignition system, etc. Each of these components is interesting and requires skill to make, but each has no meaning in terms of function by itself unlike the spade whose function is complete in itself. This interdependency of parts is what is meant by high technology. Let us think of a group of such components A, B, C, D, E,...etc. We then say that A relates to B, C, D, E, etc...B also relates to A, C, D, E, etc. C relates to A, B, D, E, etc. In the case of the car A, B, C, D and E will be the components described above. In the simplest known living cell these are, the outer membrane, the energy supply system, the molecule-making plant and so on. Biologists now call these interrelationships supermolecular organisation. There is at present no explanation for it, in known physical terms." (Ambrose, 1990, p.81).

"As we encounter high technology, in the articles we use everyday, we immediately think in terms of engineering design. This aspect of a living cell involves vast interrelated phenomena rather like a complicated telephone exchange. It can be illustrated in systems which have been worked out most beautifully by biochemists in recent years. These are the so-called enzyme pathways involving a group of enzymes cooperating. In an enzyme pathway a simple starting molecule is passed step by step along a production line to produce an end product. In a car factory a body member will start as a steel ingot, be rolled in a rolling mill, to a sheet cut to a shape, drilled and pressed into a girder. Each of these steps must be closely integrated with the previous step to provide a useful final product. In an enzyme pathway similarly there are enzymes E1, E2, E3, E4, etc. For example in making the long hydrocarbon chains of lipids CH2.CH2CH2...that form the lipid barrier of the cell membranes, the process starts with pyruvic acid (CH3.CO.COOH); E1 is the enzyme pyruvate oxidase; it catalyses a reaction between pyruvate and coenzyme A: coenzymes are molecules that assist in enzyme pathways. The product acetylcoenzyme A can react with carbon dioxide with the help of enzyme E2- so successive carbon atoms are added to the lipid chain CH2CH2CH2.... In all, 6 enzymes are involved in this production line. Cell biochemistry in toto is vastly complex; products of one pathway are utilised by another pathway, as in the case of factory production lines. There can be a hundred or more different enzymes within the compass of one minute bacterium only a few ten-thousandths of a millimetre in diameter! This is because each enzyme consists of a sequence of amino acids arranged in a different order along the protein chains. This ensures that each enzyme has a pocket or lock of special form. All the pockets are interrelated. The product originating from the lock of E1 fits the lock in E2, the product coming from E2 fits the lock in E3 and so on. So here we have a beautiful example of supermolecular organization directly operating within the domain of protein molecules. How could it have arisen? Supermolecular organisation extends also beyond the molecular level, to coordinate all the diverse components of the cell." (Ambrose, 1990, pp.82-83. Ellipses original).

"The Central Computer A factory in which the various production lines worked independently could never produce a car. It is evident that some centre must also exist within a living cell to account for its closely integrated function. In a factory the coordination depending upon changing needs is, to a large extent, now dependent on computers; the stored information is in the form of binary language ... The cell also has a language, a wonderful language. ... The language of the cell contains four letters not the two (1 or 0) of the computer. It is written on long chain molecules called nucleic acids. They were given the name because they were first isolated from the nucleus or central region of cells. In place of the amino acids of proteins which easily form long chains, the units of nucleic acid chains are disc-like molecules which can pack on top of each other like a pile of coins. The discs are formed from rings of carbon atoms with nitrogen also. Thymidine (T) and cytosine (C) contain one ring. Adenine (A) and guanine (G) consist of two rings joined together. In each case they are joined to a sugar ring and a phosphate group. The phosphate and sugars are linked together to produce a long chain molecule with the disc-like regions sticking out at right angles to the chain. The language of life is written in the order in which A, C, G and T are strung together along the chain. It was mentioned that computer memories carry vast information due to the number of bits. Similarly the nucleic acid chain with its four letter alphabet is able to carry a vast amount of information within the minute volume of a living cell." (Ambrose, 1990, p.83).

"The first function of this memory store is to control the synthesis of the various other molecules inside the cell. ... Proteins contain 21 amino acids. How can a language written in 21 letters, like our alphabet, be generated by the 4 letter alphabet of nucleic acids? It is fascinating to find that molecular biologists, in describing the way nucleic acids function, have been forced to adapt the language of writing, editing, printing and so on. There may be only one master copy of the message of nucleic acid the so-called DNA. ... But in the working part of the cell, `the shop floor' many copies of the `blueprints', the messages, are required. So equipment rather like a photocopier exists; these copies are made on slightly different nucleic acid molecules called RNAs. This is the process of transcription of the message like converting a written message into print. The messenger RNAs carry the information to the actual production line where protein chains are formed. The bases in the DNA and so also in the RNA are arranged in groups of three. Each set of three bases can code for one particular amino acid out of the 21 possible. ... This master code is all very well but how can it control the order in which amino acids are added to protein chains? Clearly there must be a decoder, a translator. The translators are also RNA molecules but of a different sort called transfer RNAs. Parts of these molecules fit the appropriate code in the messenger molecule, as a key fits a lock. There are 21 translator molecules. They can each pick up their own amino acid from a pool of amino acids inside the cell. ... The successive transfer RNAs come along as the protein chain grows in length; the protein chain is formed, carrying the message translated from the message stored in the DNA molecules. Protein chains reel off the production line one by one being formed within a few minutes. ... I never cease to contemplate this phenomenon of protein synthesis under nuclear control without awe and wonder. It surely represents the ultimate in dynamic engineering at the molecular level." (Ambrose, 1990, pp.83-84).

"There is no such thing as a self replicating molecule, only a self replicating system, involving flow of energy and molecules through it; involving a structural relationship between molecules also. This is ignored by many biologists, but is essential in terms of the laws of physics and chemistry. Natural selection could only operate on a complex system of interacting molecules. In so far as our planet is concerned the time interval between the arrival on earth of conditions in which life would be possible and the known existence, as revealed in the fossil records, of organisms 'engineered' in the manner described in this chapter, has become shorter and shorter as fossils in progressively more ancient rocks have been found. When it is realised that the total number of hydrogen atoms in the Universe is only 1078, the magnitude of the improbability of the code in the DNA message which controls that 'engineering' i.e. 1 in 102,000,000 having arisen by chance can be appreciated." (Ambrose, 1990, p.95).

"The fact that a living cell represents high technology in which the components have no meaning, except in relation to the function of the whole, has proved to be a great stumbling block in the attempts to bridge the gap between nonliving and living. For example all life processes are dependent upon energy being supplied by a chemical carrier like ATP. To make the carrier from a primary source of energy requires enzymes. The protein chains of enzymes are themselves built up both with the help of the DNA, messenger RNA and transfer RNA molecules, all steps being dependent on an energy supply, ATP. The necessary concentration of material inside the cell to enable it to function depends on a lipid barrier, the very synthesis of DNA to transmit the key message to daughter cells depends both on ATP and on a protein enzyme. Hutchison [Hutchinson, R., "The Search for our Beginning," Oxford University Press: New York NY, 1983] points out that the complexity of the process is staggering for to make a living cell a host of compounds must be available yet individually, each must have been useless!" (Ambrose, 1990, pp.95-96).

"These difficulties have led Cairns-Smith to propose that self replication really started with clay particles, as low technology, on which organic structures were progressively built up. Electron microscopy reveals highly complex layers, films, etc., generated within clay particles. But life with its self replication depends on an extremely delicate balance between the forces holding molecules together, as with the hydrogen bonds in nucleic acids and proteins leading to the stepwise formation of strong chemical bonds. Whereas the bonds in clay particles are of enormous strength, silicates being formed at high temperatures are hardly suitable for self-replication at lake temperatures. In any case Bernal pointed out that the element silicon is found only rarely in living organisms, never in their functional parts, similarly with aluminium the other main component of clays. If life had developed out of clay replication processes, these elements would still be found in more abundance in living organisms." (Ambrose, , 1990, p.96).

"If this is the case, a single gene mutation cannot generate a structure of new complexity. But according to neo-Darwinism, genes are distributed within the population. To produce a significantly new structure 3 or 10, or more generally 30-40 genes closely cooperating would have to be brought together in the same individual. To design a new style of dress for women, the designer would have to bring together the suppliers of fabrics with their various colours, suppliers of lace, suppliers of ribbons, etc. Working as a team, the final design would emerge. So it would be with the group of newly modified genes, which together, working in harmony would generate the new complexity. The rate of mutation is 1 in million, out of these non harmful mutations are 1 in 1000. For 2 such to occur would be 1 in 103 x 103. For 5 to occur 1 in 1000 million million (1 in 1015)." (Ambrose, 1990, p.167).

Wednesday, December 12, 2007

PoE: Bibliography "C"

This is the Bibliography "C" page for authors' surnames beginning

[Left: Organic chemist and origin-of-life theorist, Graham Cairns-Smith's, "Seven Clues to the Origin of Life" (1985). Though a devout materialist, Cairns-Smith demolishes all other origin-of-life theories except his own clay theory, which however, as Wikipedia notes, "the 'clay theory' of abiogenesis has not been widely accepted"! See `tagline' quotes below (my emphasis bold), all from Cairns-Smith's books.]

with "C", of books and journals which I may refer to in my book outline, "Problems of Evolution."


PROBLEMS OF EVOLUTION
© Stephen E. Jones, BSc. (Biology)

CONTENTS

BIBLIOGRAPHY "C"

Cairns-Smith, A.G., 1971, "The Life Puzzle: On Crystals and Organisms and on the Possibility of a Crystal as an Ancestor," University of Toronto Press: Toronto ON, Canada.
Cairns-Smith, A.G., 1982, "Genetic Takeover and the Mineral Origins of Life," Cambridge University Press: Cambridge UK, Reprinted, 1987.
Cairns-Smith, A.G., 1985, "Seven Clues to the Origin of Life: A Scientific Detective Story," Cambridge University Press: Cambridge UK, Reprinted, 1993.
Calder, N., 1984, "Timescale: An Atlas of the Fourth Dimension," Chatto & Windus: London.
Calvin, M., 1969, "Chemical Evolution : Molecular Evolution Towards the Origin of Living Systems on the Earth and Elsewhere," Clarendon Press: Oxford UK.
Calvin, M. & Jorgenson, M.J., 1968, "Bio-Organic Chemistry: Readings from Scientific American," W.H. Freeman & Co: San Francisco CA.
Calvin, W.H., 1986, "The River That Flows Uphill: A Journey from the Big Bang to the Big Brain," Macmillan: New York NY.
Calvin, W.H., 1991, "The Ascent of Mind: Ice Age Climates and the Evolution of Intelligence," Bantam Books: New York NY.
Calvin, W.H., 1997, "How Brains Think: Evolving Intelligence, Then and Now," Phoenix: London, Reprinted, 1998.
Camp, A.L., 1994, "The Myth of Natural Origins: How Science Points to Divine Creation," Ktisis Publishing: Tempe, AZ.
Campbell, B.G. & Loy, J.D., 1995, "Humankind Emerging," Harper Collins: New York NY, Seventh edition.
Campbell, J., 1982, "Grammatical Man: Information, Entropy, Language and Life," Penguin: Harmondsworth UK, Reprinted, 1984.
Campbell, J., 1989, "The Improbable Machine: What the New Discoveries in Artificial Intelligence Reveal about How The Mind Really Works," Touchstone Books: New York NY, Reprinted, 1990.
Campbell, J.H. & Schopf, J.W., eds, 1994, "Creative Evolution?!: Proceedings of a Symposium Sponsored by the Center for the Study of Evolution and the Origin of Life at the University of California, Los Angeles, in March, 1993," Jones & Bartlett: London.
Campbell, N.A., Reece, J.B. & Mitchell, L.G., 1999, "Biology," [1987], Benjamin/Cummings: Menlo Park CA, Fifth edition.
Campolo, A., 1983, "A Reasonable Faith: The Case for Christianity in a Secular World," Word Publishing: Dallas TX .
Carey, J., ed., 1995, "The Faber Book of Science," Faber & Faber: London.
Carlson, R.F., ed., 2000, "Science & Christianity: Four Views," Intervarsity Press: Downers Grove IL.
Carnell, E.J., 1952, "An Introduction to Christian Apologetics," [1948], Eerdmans: Grand Rapids MI, Fourth edition.
Carr, A., 1963, "The Reptiles," Time/Life Books: Netherlands, Reprinted, 1964.
Carrington, R., 1956, "A Guide to Earth History," Penguin: Harmondsworth UK, Reprinted, 1958.
Carrington, R., 1963a "The Mammals," Time/Life Books: Netherlands, Reprinted, 1965.
Carrington, R., 1963b "A Million Years of Man: The Story of Human Development as a Part of Nature," Mentor, New York NY, Reprinted, 1964.
Carroll, J., 1993, "Humanism: The Wreck of Western Culture," Fontana: London.
Carroll, R.L., 1988, "Vertebrate Paleontology and Evolution," W.H. Freeman & Co: New York NY.
Carroll, R.L., 1997, "Patterns and Processes of Vertebrate Evolution," Cambridge University Press: Cambridge UK.
Carroll, S.B., 2005, "Endless Forms Most Beautiful: The New Science of Evo Devo," W.W. Norton & Co: New York NY.
Carroll, V. & Shiflett, D., 2002, "Christianity on Trial: Arguments Against Anti-Religious Bigotry," Encounter Books: San Francisco CA.
Carter, R., 2002, "Consciousness," Weidenfeld & Nicolson: London.
Casti, J.L., 1989, "Paradigms Lost: Images of Man in the Mirror of Science," Cardinal: London.
Casti, J.L., 2000, "Paradigms Regained: A Further Exploration of the Mysteries of Modern Science," Abacus: London, Reprinted, 2001.
Caudill, E., 1997, "Darwinian Myths: The Legends and Misuses of a Theory," The University of Tennessee Press: Knoxville TN.
Cavalli-Sforza, L.L. & Bodmer, W.F., 1971, "The Genetics of Human Populations," Dover: Mineola NY, Reprinted, 1999.
Cazeau, C.J., 1986, "Science Trivia: From Anteaters to Zeppelins," Plenum Press: New York NY.
Chalmers, A.F., 1976, "What is this thing called Science?: An Assessment of the Nature and Status of Science and its Method," University of Queensland Press: St Lucia Qld, Australia, Second edition, Reprinted, 1994.
Chalmers, A.F., 1990, "Science and its Fabrication," Open University Press: Milton Keynes UK.
Chambers, P., 1999, "Life on Mars: The Complete Story," Blandford: London.
Chancellor, J., 1973, "Charles Darwin," Taplinger: New York NY, Reprinted, 1976.
Chapman, C., 1972, "Christianity on Trial," Lion: Tring UK, Reprinted, 1981.
Cherfas, J., ed., 1983, "Darwin Up to Date: A New Scientist Guide," IPC Magazines: London.
Chesterton, G.K., 1908, "Orthodoxy: A Personal Philosophy," Fontana: London, Reprinted, 1961.
Chiari, J., 1973, "The Necessity of Being," Gordian Press: New York NY.
Chittick, D.E., 1984, "The Controversy Roots of the Creation-Evolution Conflict," Multnomah Press: Portland OR, Reprinted, 1993.
Chomsky, N., 1988, "Language and Problems of Knowledge: The Managua Lectures," MIT Press: Cambridge MA, Tenth printing, 1999.
Chown, M., 1993, "Afterglow of Creation: From the Fireball to the Discovery of Cosmic Ripples," Arrow: London.
Churton, T., 1987, "The Gnostics," Weidenfeld & Nicholson: London.
Cicero, 1972, "The Nature of the Gods," McGregor, H.C.P., transl., Penguin: Harmondsworth UK, Reprinted, 1986.
Ciochon, R.L., Olsen, J. & James, J., 1991, "Other Origins: The Search for the Giant Ape in Human Prehistory," Gollancz: London.
Clack, J.A., 2002, "Gaining Ground: The Origin and Evolution of Tetrapods," Indiana University Press: Bloomington IN.
Clark, G.H., 1952, "A Christian View of Men and Things," The Trinity Foundation: Jefferson MD, Second edition, 1991.
Clark, G.H., 1993, "An Introduction to Christian Philosophy," [1968], The Trinity Foundation: Jefferson MD, Second edition.
Clark, K.J., ed., 1993, "Philosophers Who Believe: The Spiritual Journeys of Eleven Leading Thinkers," Intervarsity Press: Downers Grove IL.
Clark, R.E.D., 1946, "Creation," Tyndale Press: London, Reprinted, 1953.
Clark, R.E.D., 1948, "Darwin: Before and After: The History of Evolutionary Theory," Paternoster: London, Reprinted, 1972.
Clark, R.E.D., 1949, "The Universe: Plan or Accident?: The Religious Implications of Modern Science," Paternoster: London, Third edition, 1961.
Clark, R.E.D., 1967, "The Christian Stake in Science," Paternoster: Exeter UK.
Clark, R.T. & Bales, J., 1966, "Why Scientists Accept Evolution," Baker: Grand Rapids MI, Second printing, 1967.
Clark, R.W., 1985a, "The Life of Ernst Chain: Penicillin and Beyond," Weidenfeld & Nicolson: London.
Clark, R.W., 1985b, "The Survival of Charles Darwin: A Biography of a Man and an Idea," Random House: New York NY.
Clark, R.L., 1998, "God, Religion and Reality," SPCK: London.
Clark, W.E.L.G., 1962, "The Antecedents of Man: An Introduction to the Evolution of the Primates," [1959], Quadrangle: New York, Revised, Reprinted, 1978.
Cloud, P., 1978, "Cosmos, Earth, and Man: A Short History of the Universe," Yale University Press: New Haven CT.
Coder, S.M. & Howe, G.F., 1966, "The Bible, Science and Creation," [1965], Moody Press: Chicago IL, Revised.
Cloud, P., 1988, "Oasis in Space: Earth History from the Beginning," W.W. Norton: New York NY.
Coffin, H.G. & Brown, R.H., 1983, "Origin by Design," Review and Herald Publishing Association: Washington DC.
Cohen, J. & Massey, B., 1982, "Living Embryos," [1963], Pergamon Press: Oxford UK, Third edition.
Cohen, J. & Stewart, I., 1994, "The Collapse of Chaos: Discovering Simplicity in a Complex World," Penguin: London, Reprinted, 1995.
Cohen, J. & Stewart, I., 2002, "What Does a Martian Look Like?: The Science of Extraterrestrial Life," Ebury Press: London, Reprinted, 2004.
Cohn-Sherbok, D. & Lewis, C., eds, 1995, "Beyond Death: Theological and Philosophical Reflections on Life After Death," Macmillan: Basingstoke UK.
Colbert, E.H., 1997, "The Age of Reptiles," [1965], Dover: Mineola NY, Revised.
Colbert, E.H., 1989, "Digging Into the Past: An Autobiography," Dembner: New York NY.
Colbert, E.H. & Morales, M., 1990, "Evolution of the Vertebrates: A History of the Backboned Animals Through Time," [1955], John Wiley & Sons: New York NY, Fourth edition, Second printing, 1992.
Collins, F.S., 2007, "The Language of God: A Scientist Presents Evidence for Belief," Free Press: New York NY.
Collins, H.M. & Pinch, T., 1993, "The Golem: What Everyone Should Know About Science," Cambridge University Press: Cambridge UK, Reprinted, 1996.
Collinson, D., 1987, "Fifty Major Philosophers: A Reference Guide," Routledge: London.
Colp, R., 1977, "To Be an Invalid: The Illness of Charles Darwin," University of Chicago Press: Chicago IL.
Colson, C.W. & Morse, A., 1997, "Burden of Truth: Defending Truth in an Age of Unbelief," Tyndale: Wheaton IL.
Colson, C.W. & Pearcey, N.R., 1999, "How Now Shall We Live?," Tyndale: Wheaton IL.
Comins, N.F., 1993, "What If the Moon Didn't Exist?: Voyages to Earths That Might Have Been," HarperCollins: New York NY.
Conklin, E.G., 1943, "Man Real and Ideal: Observations and Reflections on Man's Nature, Development, and Destiny," Charles Scribner's Sons: New York NY.
Conway Morris, S., 1998,"The Crucible of Creation: The Burgess Shale and the Rise of Animals," Oxford University Press: Oxford UK, Reprinted, 1999.
Conway Morris, S., 2000, "Evolution: Bringing Molecules into the Fold," Cell, Vol. 100, January 7.
Conway Morris, S., 2003, "Life's Solution: Inevitable Humans in a Lonely Universe," Cambridge University Press: New York NY.
Cook, P., 2006, "Evolution versus Intelligent Design: Why all the Fuss?: The arguments for both sides," New Holland Publishers: Sydney NSW, Australia.
Cookson, W., 1994, "The Gene Hunters: Adventures in the Genome Jungle," Aurum Press: London.
Copan, P., 1998, "True for You, but Not for Me: Deflating the Slogans That Leave Christians Speechless," Bethany House Publishers: Minneapolis MN.
Copi, I.M., 1986, "Introduction to Logic," [1953], Macmillan Publishing Co: New York, Seventh edition.
Coppedge, J.F., 1973, "Evolution: Possible or Impossible?," Zondervan, Grand Rapids MI, Seventh printing, 1980.
Corey, M.A., 1993, "God and the New Cosmology: The Anthropic Design Argument," Rowman & Littlefield: Lanham MD.
Corey, M.A., 1994, "Back to Darwin: The Scientific Case for Deistic Evolution," University Press of America: Lanham MD.
Corey, M.A., 1995, "The Natural History of Creation: Biblical Evolutionism and the Return of Natural Theology," University of America Press: Lanham MD.
Corey, M.A., 2001, "The God Hypothesis: Discovering Design in Our `Just Right' Goldilocks Universe," Rowman & Littlefield: Lanham MD.
Cornell, J., ed., 1989, "Bubbles, Voids and Bumps in Time: The New Cosmology," Cambridge University Press: Cambridge UK, Reprinted, 1991.
Corner, M., 1991, "Does God exist? Bristol Classical Press: Bristol UK.
Corrick, J.A., 1987, "Recent Revolutions in Biology," Franklin Watts: New York NY.
Coulson, C.A., 1955, "Science and Christian Belief," Fontana: London, Reprinted, 1958.
Coveney, P. & Highfield, R., "The Arrow of time: A Voyage Through Science to Solve Time's Greatest Mystery," W.H. Allen: London, 1990.
Cox, C.B. & Moore, P.D., 1993, "Biogeography: An Ecological and Evolutionary Approach," [1973], Blackwell Science: London, Fifth edition, Reprinted, 1995.
Craig, W.L., 1994, "Reasonable Faith: Christian Truth and Apologetics," [1984],Crossway Books: Wheaton IL, Revised edition.
Crawford, M. & Marsh, D., 1989, "The Driving Force: Food, Evolution and the Future," Heinemann: London.
Cremo, M.A. & Thompson, R.L., 1994, "The Hidden History of the Human Race: Major Scientific Coverup Exposed," Govardhan Hill: Badger CA.
Crick, F.H.C., 1966, "Of molecules and Men," University of Washington Press: Seattle WA.
Crick, F.H.C., 1981, "Life Itself: Its Origin and Nature," Simon & Schuster: New York NY.
Crick, F.H.C., 1988, "What Mad Pursuit: A Personal View of Scientific Discovery," Penguin: London, Reprinted, 1990.
Crick, F.H.C., 1994, "The Astonishing Hypothesis: The Scientific Search for the Soul," Touchstone: New York NY, Reprinted, 1995.
Croft, L.R., 1988, "How Life Began," Evangelical Press: Durham UK.
Cromer, A., 1993, "Uncommon Sense: The Heretical Nature of Science," Oxford University Press: New York NY.
Croswell, K., 1995, "The Alchemy of the Heavens: Searching for Meaning in the Milky Way," Anchor: New York NY.
Cronin, H., 1991, "The Ant and the Peacock: Altruism and Sexual Selection From Darwin to Today," Cambridge University Press: Cambridge UK, Reprinted, 1993.
Croswell, K., 1997, "Planet Quest: The Epic Discovery of Alien Solar Systems, "Free Press: New York NY.
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Currey, J.D., 2002, "Bones: Structure and Mechanics," Princeton University Press: Princeton NJ.
Cutler, A., 2003, "The Seashell on the Mountaintop: A Story of Science, Sainthood and the Humble Genius Who Discovered a New History of the Earth," Heinemann: London, Reprinted, 2004.
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Stephen E. Jones, BSc. (Biology).
My other blog: TheShroudofTurin


"There is no difficulty in principle in accounting for the existence of many different kinds of proteins. A chain of 150 amino acid units represents quite a small protein; but with 20 alternative possibilities for each link the total number of different chain sequences that are possible is 20150, i.e. 10195-far more than `the number of electrons in the universe'-and most proteins are far longer than 150 units. But the central problem remains: how can diversity of sequence give rise to such a rich diversity of function? Why is it, for example, that the sequence ... corresponds to a molecule that can store oxygen, while ... , although quite incompetent as a one-molecule oxygen cylinder, is very good at breaking up RNA molecules by splitting just one kind of bond in the main chain in just one way? Then again, how is it that ... lacks any appetite for RNA but has a neat way of destroying bacteria by unstitching their overcoats? How can specific complex functions be carried out by such molecular cryptograms? The broad answer seems to be this: the 'cryptogram'- the primary structure-determines in detail the way in which the chain will collapse on itself, its tertiary structure. The `cryptogram' may thus determine accurately the form of a piece of machinery about a millionth of a centimetre across." (Cairns-Smith, A.G., "The Life Puzzle: On Crystals and Organisms and on the Possibility of a Crystal as an Ancestor," University of Toronto Press: Toronto ON, Canada, 1971, pp.34-35).

"Now, how would you go about making a machine which could reproduce itself? ... The mathematician, von Neumann, demonstrated in the 1940s that a self-reproducing machine was in principle quite possible-and he outlined a general design (Taub, 1963; Moore, 1964). Von Neumann imagined some kind of stockroom containing fairly simple mechanical parts-such as screws, metal plates, wire, and so on. The problem was to invent a machine that could move about such a stockroom selecting the pieces required to make another machine like itself, and then proceed to do so. The centre of von Neumann's design was a set of instructions written, say, on magnetic tape or punched cards, giving an account of how to make the rest of the machine-where to find the parts and how to put them together. The machine would include a manufacturing unit which could follow the instructions and act on them. There is a special point about the instructions themselves, however; they could not be remade by following instructions that were different from themselves. ... At some point it must be the cards themselves that instruct their own formation, i.e. the cards must be replicated. Only in this way can an infinite regression be avoided. So in addition to a manufacturing unit that can make all kinds of things by following instructions, there must be another unit with the more limited task of copying them. ... Von Neumann's machine solves the problem of 'self-reproduction' in much the same way as it is solved in organisms: by separating the system formally into two parts. One part is completely coded in the form of replicable plans for its construction held in the other part. The machine has a phenotype and a genetic material (which may be cardboard) holding a genotype." (Cairns-Smith, 1971, pp.52-53).

"But these processes do not occur in vacuo. DNA, RNA, and protein are made out of units which must either be provided by the environment or synthesised by the cell from molecules which are provided. In the latter case whole teams of enzymes may be required. But even if the units are already available in the general environment, the replication of DNA still needs at least one protein, the synthesis of RNA another, and the synthesis of protein needs yet another polymerising enzyme, together with at least a couple of dozen more proteins in the enzymes which prime the transfer RNAs. To make one protein the cell already has to have dozens of proteins. There is nothing immediately illogical in this situation: a factory for making nuts and bolts can be made with the help of nuts and bolts, but it does mean that a cell must inherit more than a book of instructions from its parent. It must inherit also enough pre-formed equipment to read the book. It must inherit a `minimum phenotype'. A reproducing cell, then, must consist of at least a minimum phenotype together with the instructions required to reproduce it-a minimum genotype. Morowitz (1966) has estimated that for a minimum cell consistent with the current viewpoint of molecular biology one would need at least 45 proteins. ... It is still a gross oversimplification since, among other things, it ignores reactions required to provide energy for the various processes, as well as essential mechanical structures such as cell membranes. The problem of the origin of life is simply that any conceivable such minimum unit would seem to be necessarily far too complex to have arisen by chance-to have `nucleated' spontaneously-under any reasonable circumstances. `Life can only come from life' is no longer a dogma as it was in the immediate post-Pasteur era: but it nevertheless seems that life in fact always does arise this way, and that in nature it must-for any form built on the modern DNA -> protein design." (Cairns-Smith, 1971, pp.60-61).

"Surely there was a radically simpler plan to begin with. What was it like? Von Neumann's 'self-reproducing' machines seem to indicate that quite a complex phenotype, together with a corresponding genotype is essential for any reproducing system. Is there a way out? There must be if life really did originate spontaneously as a reasonably probable physico-chemical event during the history of the Earth." (Cairns-Smith, 1971, pp.61-62. Emphasis original).

"It seems to me that the idea of coupling agents putting together polypeptides on a lifeless Earth adds another dimension of unreality to an already unreal line of thought. Remember that primordial simulations generally give only low yields of amino acids. Remember that the products are tars and that suggestions for prevital work-up procedures are usually absent. Remember the difficulties anyway in building up concentrations of solutions of amino acids or of the cyanide or phosphate to make a coupling agent. Remember that even from laboratory bottles the agents in question do not work very well. Remembering all that, now add the thought that coupling agents are rather unspecific. If a well chosen coupling agent under well chosen laboratory conditions can effectively join the acyl group A to the nucleophile B that is because among the choices exercised by the experimenter was the crucial one of only putting A and B into a flask for the coupling agent to couple. Compared with such carefully arranged marriages the affairs of a primordial soup would have been grossly promiscuous." (Cairns-Smith, A.G., 1982, "Genetic Takeover and the Mineral Origins of Life," Cambridge University Press: Cambridge UK, Reprinted, 1987, pp.52-53).

"One can get an impression of what is needed in practice for the synthesis of peptides by considering the machinery that is used in automated procedures. One such piece of equipment is shown in figure 1.11. Merrifield, Stewart & Jernberg (1966) describe its construction and operation in nine close pages of diagrams and descriptions. I quote (more or less at random) from the middle of their paper: `... the rear disk contains a center port and one circumferential port which are joined by a 1.5 mm hole within the disk. As this disk is turned it connects one at a time the 12 inlet ports to the central outlet port. A leak-free seal between the two teflon disks of the valve ...' And that is one of the less terse passages. Not shown in figure 1.11 is a programmer, like a musical box drum, that puts appropriate operations (mixings, rinsings, shakings, etc.) in sequence. There have to be many pegs on the drum because one cycle of the automatic synthetic procedure that extends the peptide chain by one unit requires nearly 90 steps. Now I am not saying that for peptide synthesis without human intervention there has to be something physically like Merrifield's machine. There does not have to be that particular piece of engineering. But I think there has to be engineering. Another example of automatic peptide synthesis is the synthesis by the ribosome in the modern cell. ... There are no tubes or valves or metering pumps here: but in the design of the ribosome, the adaptor RNA molecules and their activating enzymes; in the whole system, with its message tapes and its code, there is surely at least as much engineering as in Merrifield's machine. ... Perhaps there is some other way of making peptides with more or less specified amino acid sequences; and perhaps this way does not need detailed control. Perhaps it could then have operated before there was life on Earth, before that engineer, natural selection, appeared on the scene. But it is difficult to see how this could have been so. I think we would know by now if there was some much easier way." (Cairns-Smith, 1982, pp.53,55).

"The implausibility of prevital nucleic acid If it is hard to imagine polypeptides or polysaccharides in primordial waters it is harder still to imagine polynucleotides. But so powerful has been the effect of Miller's experiment on the scientific imagination that to read some of the literature on the origin of life (including many elementary texts) you might think that it had been well demonstrated that nucleotides were probable constituents of a primordial soup and hence that prevital nucleic acid replication was a plausible speculation based on the results of experiments. There have indeed been many interesting and detailed experiments in this area. But the importance of this work lies, to my mind, not in demonstrating how nucleotides could have formed on the primitive Earth, but in precisely the opposite: these experiments allow us to see, in much greater detail than would otherwise have been possible, just why prevital nucleic acids are highly implausible. Let us consider some of the difficulties. First, as we have seen, it is not even clear that the primitive Earth would have generated and maintained organic molecules. All that we can say is that there might have been prevital organic chemistry going on, at least in special locations. Second, high-energy precursors of purines and pyrimidines had to be produced in a sufficiently concentrated form (for example at least 0.01 M HCN). Third, the conditions must now have been right for reactions to give perceptible yields of at least two bases that could pair with each other. Fourth, these bases must then have been separated from the confusing jumble of similar molecules that would also have been made, and the solutions must have been sufficiently concentrated. Fifth, in some other location a formaldehyde concentration of above 0.01 M must have built up. Sixth, this accumulated formaldehyde had to oligomerise to sugars. Seventh, somehow the sugars must have been separated and resolved, so as to give a moderately good concentration of, for example, D-ribose. Eighth, bases and sugars must now have come together. Ninth, they must have been induced to react to make nucleosides. (There are no known ways of bringing about this thermodynamically uphill reaction in aqueous solution: purine nucleosides have been made by dry-phase synthesis, but not even this method has been successful for condensing pyrimidine bases and ribose to give nucleosides (Orgel & Lohrmann, 1974).) Tenth, whatever the mode of joining base and sugar it had to be between the correct nitrogen atom of the base and the correct carbon atom of the sugar. This junction will fix the pentose sugar as either the α- or ß-anomer of either the furanose or pyranose forms ... For nucleic acids it has to be the ß-furanose. (In the dry-phase purine nucleoside syntheses referred to above, all four of these isomers were present with never more than 8 % of the correct structure.) Eleventh, phosphate must have been, or must now come to have been, present at reasonable concentrations. (The concentrations in the oceans would have been very low, so we must think about special situations - evaporating lagoons and such things (Ponnamperuma, 1978).) Twelfth, the phosphate must be activated in some way - for example as a linear or cyclic polyphosphate - so that (energetically uphill) phosphorylation of the nucleoside is possible. Thirteenth, to make standard nucleotides only the 5'-hydroxyl of the ribose should be phosphorylated. (In solid-state reactions with urea and inorganic phosphates as a phosphorylating agent, this was the dominant species to begin with (Lohrmann & Orgel, 1971). Longer heating gave the nucleoside cyclic 2',3'-phosphate as the major product although various dinucleotide derivatives and nucleoside polyphosphates are also formed (Osterberg, Orgel & Lohrmann, 1973).) Fourteenth, if not already activated - for example as the cyclic 2',3'- phosphate - the nucleotides must now be activated (for example with polyphosphate; Lohrmann, 1976) and a reasonably pure solution of these species created of reasonable concentration. Alternatively, a suitable coupling agent must now have been fed into the system. Fifteenth, the activated nucleotides (or the nucleotides with coupling agent) must now have polymerised. Initially this must have happened without a pre-existing polynucleotide template (this has proved very difficult to simulate (Orgel & Lohrmann, 1974)); but more important, it must have come to take place on pre-existing polynucleotides if the key function of transmitting information to daughter molecules was to be achieved by abiotic means. This has proved difficult too. ...Sixteenth, the physical and chemical environment must at all times have been suitable - for example the pH, the temperature, the M2+ concentrations. Seventeenth, all reactions must have taken place well out of the ultraviolet sunlight; that is, not only away from its direct, highly destructive effects on nucleic acid-like molecules, but away too from the radicals produced by the sunlight, and from the various longer lived reactive species produced by these radicals. Eighteenth, unlike polypeptides, where you can easily imagine functions for imprecisely made products (for capsules, ion-exchange materials, etc.), a genetic material must work rather well to be any use at all - otherwise it will quickly let slip any information that it has managed to accumulate. Nineteenth, what is required here is not some wild one-off freak of an event: it is not true to say `it only had to happen once'. A whole set-up had to be maintained for perhaps millions of years: a reliable means of production of activated nucleotides at the least. Now you may say that there are alternative ways of building up nucleotides, and perhaps there was some geochemical way on the early Earth. But what we know of the experimental difficulties in nucleotide synthesis speaks strongly against any such supposition. However it is to be put together, a nucleotide is too complex and metastable a molecule for there to be any reason to expect an easy synthesis. You might want to argue about the nineteen problems that I chose: and I agree that there is a certain arbitrariness in the sequence of operations chosen. But if in the compounding of improbabilities nineteen is wrong as a number that would be mainly because it is much too small a number. If you were to consider in more detail a process such as the purification of an intermediate you would find many subsidiary operations - washings, pH changes and so on. (Remember Merrifield's machine: for one overall reaction, making one peptide bond, there were about 90 distinct operations required.)." (Cairns-Smith, 1982, p.56-59. Emphasis original).

"Problems for primitive heterotrophs Let us suppose that all the difficulties that we have been discussing were somehow overcome, and let us now consider how the very first organisms might have fared. According to the doctrine of chemical evolution these organisms were heterotrophs, that is to say they depended on organic foods. The diet of primordial soup was so adequate, it is said, that these organisms had no need for metabolic pathways to begin with. Such pathways could evolve gradually as the foods ran out (by the mechanism proposed by Horowitz in 1945; see figure 1.12). A -> B -> C -> D .... According to Horowitz (1945 [Horowitz, N.H., "On the Evolution of Biochemical Syntheses," Proc. Natl Acad. Sci. USA, Vol. 31, No. 6, June 1945, pp.153-157]), a metabolic pathway would have evolved backwards. D was at first a vital molecule available in the environment. D gradually ran out, giving organisms time to evolve an internal source - by converting C, some simpler precursor, that was still in the environment. As C ran out there would then be selection pressures to find some other environmental molecule, B, and the means to convert it to C. Hence complex molecules that were originally provided by a primordial soup came to be made instead from simple commonly available molecules such as CO2 and N2. To have one's food provided sounds like an easy sort of life, but in reality there would be great difficulties with such an idea. There are problems of assimilation. To be a heterotroph implies an ability to recognise molecules, or at the very least to distinguish between classes of them. For the eventual evolution of metabolic pathways, specific recognition devices would be required. Thinking along the lines of current means of biomolecular control, some kind of structure would seem to be needed that could form specific sockets corresponding to the molecules in the environment. But until you have the ability to recognise at least some molecular units, how do you reach the point of being able to manufacture such specific devices? ... The trouble is that a socket (such as that in an enzyme or a transport protein) that can recognise another molecule is much more difficult to engineer than the molecule itself. ... So what were the control techniques? How was tarry chaos avoided? If the enzymes in today's cells can cope so well this is partly because the molecules that they come across belong to a quite limited set. An enzyme may distinguish between D- glucose and D-fructose, because these are among the relatively few kinds of molecules that it encounters: but it can easily be confused by molecules from a larger range. ... A primitive organism, lacking such customs control and living in a tarry `broth' that contained for every `correct' molecule a myriad of similar `incorrect' ones would have to have far more accurate enzymes to bring about any particular sequence of reactions. So that is the problem: how to evolve accurate recognising structures from a molecular technology that probably could not tell glycine from alanine, let alone D from L. Until you know one molecule from another how do you start to do the kind of sophisticated chemistry needed to make the membranes, the active centres and so on, on which molecular discrimination depends?" (Cairns-Smith, 1982, pp.59-60).

"Was 'chemical evolution' the connection? I do not think so. The building up of a primordial soup, if such a thing ever happened, would have been part of environmental evolution. The oceans would have accumulated organic molecules in much the same way as any other geochemical process would have taken place. Unless you take a religious or mystical view there was no guiding hand to contrive an outcome suitable for the origin of life. Mountains were made and worn down, the wind blew, the sun shone - and a soup did or did not form: all such processes were on an equal footing; it would only have been with an eye to the future that some of these processes might have been given a special label and called 'chemical evolution'. Biological evolution, on the other hand, is special, as discussed in the opening pages of this book. Above all what makes it special is heredity. This is the great divide: either there is a long-term hereditary mechanism working or there is not. If there is not then there is no accumulation of 'know-how' as Kuhn (1976) put it: the survival or non-survival of some putative half-organism will not be 'remembered' in the distant future to have any effect. Things would change, systems such as coacervates would come and go, but you could not expect them to become more efficient: you would not expect them to become more efficient at organic chemical operations, for example. Only evolving organisms can progress in that sort of way. Suppose that by chance some particular coacervate droplet in a primordial ocean happened to have a set of catalysts, etc. that could convert carbon dioxide into D- glucose. Would this have been a major step forward towards life? Probably not. Sooner or later the droplet would have sunk to the bottom of the ocean and never have been heard of again. It would not have mattered how ingenious or life-like some early system was; if it lacked the ability to pass on to offspring the secret of its success then it might as well never have existed." (Cairns-Smith, 1982, pp.69-70).

"There are two counter-intuitive aspects here. Using higher animals as models we would be much more inclined to see the organism as dynamic and the environment as static. But the only bit of an organism that is unambiguously not part of the environment is the bit that is static - the genotype. The other counter-intuitive idea is that, in computer jargon, it is software in organisms that lasts, while hardware is being perpetually replaced. Consider, for example, the instructions about how to make cytochrome c molecules: that software has remained little altered in essentials while mountain ranges have risen and been worn away many times. Yet the hardware, the actual individual protein molecules, individual DNA molecules, and so on, have been quite evanescent, flickering in and out of existence on a geological time scale. And this is very close to the heart of the problem ... we might say that life can begin to appear when mechanisms exist for retaining and propagating a kind of software - genetic information - indefinitely." (Cairns-Smith, 1982, p.80).

"Perhaps the simplest kinds of organisms would be hardly more than pieces of unencumbered information-printing machinery - `naked genes' as they have been called (Muller, 1929). To have the potential for indefinite evolution into the future, the potential information capacity of these naked genes would have to be very high. ... the idea of a 'naked gene', as the simplest and first kind of organism, has a long history. It is somewhat out of favour now mainly on account of two kinds of argument that are put up against it. First, there is a practical argument. Even if it could evolve in principle, it is said, such a structure would be too improbable in practice: it would be exceedingly unlikely to form, and the Earth would be exceedingly unlikely to continue to provide the highly specialised components needed to keep it replicating. If we think about a naked nucleic acid molecule such an attitude seems justified. Second, there is a formal argument. To evolve, a system must have both a genotype and a phenotype. Pure information is no use: it is the phenotype on which selection operates to give genetic information a meaning. Formally this argument is impeccable, but it is largely irrelevant. A `naked gene' would not be - could not be - pure genotype. Clearly what is meant by a gene, in this context at least, is some sort of structure that is holding information - something analogous to a DNA molecule or a punched card. Such a thing is not pure software as it includes the structure that is holding the information, and that is hardware. And at least some aspects of hardware could very well be phenotype." (Cairns-Smith, 1982, p.81).

"All such speculations that I have come across are evolutionary - they talk of the gradual perfection of this and that subsystem. But there is only one engine for the evolution of ingenious competence that I know of and that is natural selection. To evolve, the subsystems have to be part of an organism of some sort. Now there might be no need to postulate an earlier kind of life if some minimum nucleic acid-protein system could be conceived of as having formed spontaneously on the primitive Earth. But I do not see such a system as conceivable. You say yourself that naked nucleic acid genes are no good, and anything else would be more complicated - nucleic acid plus something else. I see no alternative to postulating some other kind of starter life to provide the milieu within which our kind of life system began its evolution." (Cairns-Smith, 1982, p.130).

"Biology has become, quite simply, the study of the causes and effects of evolution, and the question of the origin of life is, first, the question of the origin of evolution." (Cairns-Smith A.G., 1985, "Seven Clues to the Origin of Life: A Scientific Detective Story," Cambridge University Press: Cambridge UK, 1993, Reprinted, p.1).

"The optimism persists in many elementary textbooks. There is even, sometimes, a certain boredom with the question; as if it was now merely difficult because of an obscurity of view, a difficulty of knowing now the details of distant historical events. What a pity if the problem had really become like that! Fortunately it hasn't. It remains a singular case (Sherlock Holmes' favourite kind): far from there being a million ways in detail in which evolution could have got under way, there seems now to have been no obvious way at all. The singular feature is in the gap between the simplest conceivable version of organisms as we know them, and components that the Earth might reasonably have been able to generate. This gap can be seen more clearly now. It is enormous." (Cairns-Smith, 1985, p.4).

"Now I cannot deny all these possibilities: life on the Earth may be a miracle, or a freak, or an alien infection. And I agree that the confidence was misplaced that supposed in the fifties that the answer to the origin of life would appear in some footnote to the answer to the question of how organisms work. Something much more will be needed. Something odd." (Cairns-Smith, 1985, p.8).

"So please respect the humble bacterium that is playing this game. It can reproduce, it can evolve. E. coli must have some sort of long-term memory about how to make itself that can outlast its substance. That means that an E. coli must be an automatic factory containing something analogous to control tapes and automatic manufacturing equipment. And that is only part of it. All the equipment must be contained, organised, fed. Pieces for it to work on, energy to drive it, must be provided by the E. coli cell. Apart from the manufacturing machinery that can follow instructions, there has also to be another kind of machinery that instead reprints them - something analogous to a Xerox machine or a tape copier. All these things have to be contrived through the manufacturing machinery duly instructed by appropriate bits of the Library tape. It may seem hardly surprising that no one has ever actually made a self-reproducing machine, even though Von Neumann laid down the design principles more than 40 years ago. You can imagine a clanking robot moving around a stock-room of raw components (wire, metal plates, blank tapes and so on) choosing the pieces to make another robot like itself. You can show that there is nothing logically impossible about such an idea: that tomorrow morning there could be two clanking robots in the stock-room...(I leave it as a reader' home project to make the detailed engineering drawings.) There is nothing clanking about E. coli; yet it is such a robot, and it can operate in a stock-room that is furnished with only the simples raw components. Is it any wonder that E. coli's message tape is long? (... about 10 kilometres long.) Is it any wonder that no free-living organisms have been discovered with message tapes below '2 kilometres'? Is it any wonder that Von Neumann himself, and many others, have found the origin of life to be utterly perplexing?'" (Cairns-Smith, 1985, pp.14-15. Emphasis original).

"There are many thoughtful and knowledgeable people, nowadays, who don't understand the origin of life. This is in spite of a 'big picture' provided by a theory known as 'chemical evolution'. Like the phlogiston theory, 'chemical evolution' looks good from a distance, and there is a common-sense about it. But, to my mind, like the phlogiston theory, it fails to carry through an initial promise: it fails at the more detailed explanations." (Cairns-Smith, 1985, p.34).

"I will grant that the path of chemical evolution seems sensible and in the right direction. There are a few obvious puddles to be avoided and some of the flagstones are a bit uneven, perhaps. but there is the promise of an easy walk up to the foothills of the mountain that we can see straight ahead of us. It is a promise that is unfulfilled. The trouble with this path is that it leads us toward, but it does not lead us to expect, a sudden near-vertical cliff-face. Suddenly in our thinking we are faced with the seemingly unequivocal need for a fully working machine of incredible complexity: a machine that has to be complex, it seems, not just to work well but to work at all." (Cairns-Smith, 1985, p.37).

"It is true that some of the simpler amino acids have been found in complex mixtures generated under conditions simulating those that might have been present on the primitive Earth. Even nucleotide letters have been found in mixtures that are said to be plausible simulations of probiotic products. But all such 'molecules of life' are always minority products and usually no more than trace products. Their detection often owes more to the skill of the experimenter than to any powerful tendency for the 'molecules of life' to form." (Cairns-Smith, 1985, pp.44-45).

"Sugars are particularly trying. While it is true that they form from formaldehyde solutions, these solutions have to be far more concentrated than would have been likely in primordial oceans. And the reaction is quite spoilt in practice by just about every possible sugar being made at the same time - and much else besides. Furthermore the conditions that form sugars also go on to destroy them. Sugars quickly make their own special kind of tar - caramel - and they make still more complicated mixtures if amino acids are around." (Cairns-Smith, 1985, p.44).

"In sum the ease of synthesis of 'the molecules of life' has been greatly exaggerated. It only applies to a few of the simplest and in no case is it at all easy to see how the molecules would have been sufficiently unencumbered by other irrelevant or interfering molecules to have allowed further organisation to higher-order structures of the kinds that would be needed: message tapes, selective control structures, etc. Finally, even if ... primitive geochemistry had shown a precision in organic reaction control quite unlike modern geochemistry; even if it had produced all 'the molecules of life' and nothing but 'the molecules of life' in ample amounts; even then it would still only have reached the edges of the real problem ... Still, somehow, an evolving machine had to be made." (Cairns-Smith, 1985, p.44).

"Nucleotides and lipids have yet to be made under conditions that are realistic simulations of primitive Earth conditions. Nucleotides and lipids are much too complicated and particular for this to be surprising. They have all the appearance of molecules specially contrived for particular purposes. ... Perhaps you still feel that `time, and more time, and the resource of oceans' could have overcome the problems of how the more complex 'molecules of life' were originally made. I will now try to dispel such optimism by considering in more detail the most critical of all 'the molecules of life'. ... The Sigma Company is one of several that compete to supply biochemicals for research purposes. Looking through their catalogue I find that I can buy a gram of ATP - a primed ('wound-up') RNA nucleotide - for about £5. ATP is only as cheap as this because it is relatively easy to extract from bulk biological materials - horse meat to be more specific.The other three primed RNA nucleotides are about ten times the price, and the primed DNA nucleotides cost about £300 per gram. But even these are only as cheap as they are because they are derived from natural biological materials. As with postage stamps the price of nucleotides rises steeply with more abnormal types. The version of ATP with the sugar arabinose in the connector piece in place of ribose comes in at about £6000 a gram. But even such abnormal nucleotides, if they are synthetic (man-made) at all, are never wholly synthetic. Their manufacture will have started with components such as ribose obtained from biological sources. ... So £6000 a gram (or if you prefer £6M a kilogram) is a low estimate for the cost of a primed nucleotide 'in the open Universe' as it were. What would these materials cost if it were not for the horses (and others) that do most of the hard work? What would it actually cost to manufacture primed nucleotides from methane, ammonia and phosphate rock? I hate to think. Contrast glycine and alanine, the two simplest amino acids. These really can be said to be easily made-they have been detected frequently in complex mixtures from sparking experiments, in meteorites, etc. Glycine comes in at about 1p a gram, and alanine (as a mixture of 'left-handed' and 'right-handed' forms) about 8p. (I may say that at these prices you get 99% pure material; thunderstorm simulations give you 99% impure material.) Not only are they difficult to make, but primed nucleotides are rather unstable. Sigma recommend that the DNA primed nucleotides should be shipped in dry ice to avoid decomposition in transit, and nucleotides generally should be stored at below freezing point. Expensive and fragile, primed nucleotides (or unprimed ones for that matter) are, I think, implausible as significant geochemical products - as minerals - at any time." (Cairns-Smith, 1985, pp.45-46. Emphasis original).

"In Genetic Takeover I listed 14 major hurdles that would have to be overcome for primed nucleotides to have been made on the primitive Earth - from the build-up of sufficient and separate concentrations of formaldehyde and cyanide to the final 'winding-up' of the nucleotides. In practice each of these processes would be subdivided into separate unit operations that would have to be suitably sequenced. In carrying out an organic synthesis in the laboratory there are tens or hundreds of little events: lifting, pouring, mixing, stirring, topping-up, decanting, adjusting etc., etc. There may not be much to these unit operations in themselves, but their sequencing has to be right. There is a manufacturing procedure that has to be followed, and when such a procedure is at all prolonged it becomes absurd to imagine it being carried out by chance. That is why simple amino acids are plausible probiotic products, primed nucleotides are not. It is not that one cannot imagine plausible unit processes on the primitive Earth that, taken together, might have yielded primed nucleotides - as one can imagine a coin falling heads a thousand times in a row. Yes, you can imagine the primitive Earth doing the kinds of things that the practical organic chemist does. You can see a pool evaporating in the sun to concentrate a solution, or two solutions happening to mix because a stream overflows, or a catalytic mineral dust being blown in by the wind. you can imagine filtrations, decantations, beatings, acidifications: you can imagine many such operations taking place through little geological and meteorological accidents. But to show that each step in a sequence is plausible is not to show that the sequence itself is plausible. But, you may say, with all the time in the world, and so much world, the right combinations of circumstances would happen some time? Is that not plausible? The answer is no: there was not enough time, and there was not enough world. Let me try to justify this. It would be a safe oversimplification, I think, to say that on average the 14 hurdles that I referred to in the making of primed nucleotides would each take 10 unit operations - that at least 140 little events would have to be appropriately sequenced. (If you doubt this, go and watch an organic chemist at work; look at all the things he actually does in bringing about what he would describe as 'one step' in an organic synthesis.) And it is surely on the optimistic side to suppose that, unguided, the appropriate thing happened at each point on one occasion in six. But if we take this as the kind of chance that we are talking about, then we can say that the odds against a successful unguided synthesis of a batch of primed nucleotide on the primitive Earth are similar to the odds against a six coming up every time with 140 throws of a dice. Is that sort of thing too much of a coincidence or not? There are 6 possible outcomes from throwing a dice once; 6 x 6 from a double throw; 6 x 6 x 6 from a triple throw; and 6 multiplied by itself 140 times from 140 throws. This is a huge number, represented approximately by a 1 followed by 109 zeros (i.e. ~ 10109). This is the sort of number of trials that you would have to make to have a reasonable chance of hitting on the one outcome that represents success. Throwing one dice once a second for the period of the Earth's history would only let you get through about 1015 trials: so you would need about 1094 dice. That is far more than the number of electrons in the observed Universe (estimated at around 1080). Of course you might argue that in practice a synthesis might be carried through in different ways, and that is true, but remember what generous allowances we made in cutting down the actual amount of sheer skill that organic synthesis requires. And remember too that a manufacturing procedure is not usually very forgiving about arbitrary modifications: it all too easily goes off the rails never to recover. This is especially true of chemical processes, where it is usually not good enough to add the acid at the wrong time or throw away the wrong solution, or even use an ultraviolet lamp of the wrong sort. Careless organic synthesis only works when the product that is wanted belongs to that inevitably small set of molecules that are especially stable - molecules like carbon dioxide and water, even perhaps glycine and adenine in a much more limited way. But nucleotides are not like that to judge from the price. One's intuition can lead one astray when thinking of the role of vast times and spaces in generating improbable structures. The moral is that vast times and spaces do not make all that much difference to the level of competence that pure chance can simulate. Even to get 14 sixes in a row (with one dice following the rules of our game) you should put aside some tens of thousands of years. But for 7 sixes a few weeks should do, and for 3 sixes a few minutes. This is all an indication of the steepness of that cliff-face that we were thinking about: a three-step process may be easily attributable to chance while a similar thirty-step process is quite absurd." (Cairns-Smith, 1985, pp.46-48).

"In one way the eye is eminently understandable. It is so like a camera that you wonder why there is not a law suit going on somewhere for breach of patent. The dark box, the lens, the iris diaphragm, the light-sensitive surface - each of these components is there in each case. At deeper levels there are certainly patentable differences in design. The light-sensitive area at the back of the eye is not actually much like a film. It, and many other things about the eye, are not by any means fully understood. But what is eminently understandable about the eye is that it should consist of rather definite components working in collaboration: as remarked ... this is what really efficient pieces of machinery are usually like. The bit that is not so clear about the eye -and a favourite challenge to Darwin - is how its components evolved when the whole machine will only work when all the components are there in place and working. Not that this problem is peculiar to the eye. Organisms are full of such machinery, and it is a widely held view that this appearance of having been designed is the key feature of living things." (Cairns-Smith, 1985, p.58).

"Evolution started with 'low-tech' organisms that did not have to be, and probably were not made from 'the molecules of life'. The first part of this statement might seem rather obvious were it not for the baleful conclusion ... that the design of any conceivable organism is inevitably very very complicated - with robot machines that can make other machines (including ones like themselves) under instructions held in an information store that can be replicated by means of yet more machinery whose construction is also specified in the information store and can be executed by the robot machines... But that was another Big Red Herring. It arose from the unstated assumption that you actually need any machinery at all in an organism. Once you think you will need any, then you will think that you need a lot. If, for example, the organism has to have some kind's of printing machinery in it, so that it can replicate its genetic information, then it will need manufacturing machinery also to make this printing machinery. And then this manufacturing machinery, some sort of robot, must also be able to make other machines exactly like itself. The circle closes eventually, but not until after a long journey - too long to be a practicable piece of engineering even for us, and much too long for Nature before its engineer, natural selection, had come on the scene." (Cairns-Smith, 1985, pp.65-66. Emphasis original).

"So why start on such a journey? Only the messages are in principle essential for evolution, although in practice there has to be a material to hold the messages and physical means for their replication. But the components for making the genetic material can be provided by the environment and so can any machinery that is needed to work with these components to bring about the replication of the messages. An organism need be no more than a naked gene if the environment is kind enough. ... But does this not simply shift the difficulty from the organism to the environment? Certainly it shifts the difficulty, but it does not simply shift the difficulty. The difficulty changes, and it becomes much less severe. There do not have to be robots anywhere. The environment might possibly have to provide some sort of printing or replicating machinery, but it would not have to provide another instructable machine to make such machinery. Indeed it is a matter to be decided whether the environment would even have to provide anything that could be called replicating machinery, or machinery of any sort. There would be but three things that an environment would have to provide for 'naked genes': (i) material units out of which new genes could be made (by template replication); (ii) conditions that would allow this to happen (whether or not these conditions included any sort of replication machinery); and (iii) reasons why some genes should do better than others (what are called selection pressures). It is true that now for RNA, the material units are probably too complex as primitive Earth products; and it looks as if a big enzyme has indeed to be included under (ii). But these are incidental features, not vital. They are specific objections to RNA. They depend on particular attributes of RNA molecules - and, anyway, we had decided in the last chapter that neither RNA nor DNA was the original genetic material." (Cairns-Smith, 1985, pp.66-67. Emphasis original).

"A particular trouble with organic molecules is that they only self-assemble properly when they are fairly large. Only then will there be a sufficient overall cohesion between the molecules, or between the parts of a foldable molecule. (A soap molecule needs to have a long tail; a protein chain has to have some twenty units in it before it will start to fold up coherently.) But large molecules are difficult to come by, especially at the kinds of concentration and purity needed for precise self-assembly processes. The massive objections that there are to the idea that good supplies of nucleotides could have been pre-arranged by the primitive Earth ... apply with a similar force to almost any organic molecule of that sort of size - the sort of minimum size needed for organic molecules to be able to self-assemble in water into higher-order structures." (Cairns-Smith, 1985, pp.72-73).