Darwin's Gift To Science and Religion
This book is like a breath of fresh air and lets your spirit calm down from the intensity of the battle between religion and evolution. Raised and educated in Spain and becoming aware of the evolution struggle as a seminary student in Spain, he first encounters a spirit that welcomed evolution. Certainly there was no thought that evolution was anti-God, and it helped the theologians deal with the theodicy issue - the fact that some freedom of development was established with life helped to deal with birth defects and genetic errors so that they could be accepted along with other unfortunate contingencies that we encounter in life.
Ayala's approach is calm and clear, obviouly coming from someone who has immersed himself in the subject for a long time and who has a passion for it, but he tends to stay fairly clear of the confrontational passion of so many others, and just presents his view of things in clear and readable prose. It is a delightful book.
Ayala began his doctoral study at Columbia in 1961 in genetics and evolution. He was never exposed to religious opposition in his education or church through his bachelors degree. Only in coming to the US for graduate school did he encounter it.
Ch 1 Introduction
p1 Hume quote "Is God willing to prevent evil, but not able? Then he is impotent. Is he able, but not willing? Then he is malevolent. Is he both able and willing? Whence then evil?" Dialogues Concerning Natural Religion, p. 244
p2 Thomas Aquinas 1224-1274 , William Paley 1743-1805
p3 "Evolution ... had provided theologians with the 'missing link' in the explanation of evil in the world or, in theological parlance, evolution had solved the 'theodicy' problem. A dictionary definition of theodicy is 'defense of God's goodness and omnipotence in view of the existence of evil.' "
p3 "Traditional theology distinguishes three kinds of evil: (1) moral evil or sin, the evil originated by human beings; (2) pain and suffering as experienced by human beings; (3)physical evil, such as floods, tornados, earthquakes, and the imperfections of all creatures."
p4 "..the 1950 encyclical Humani generis by Pope Pius XII had put the matter to rest. Biological evolution, the Pope wrote, is compatible with the Christian faith."
p4-5 "Later, when I was studying theology in Salamanca, Darwin was a much-welcomed friend. The theory of evolution provided the solution to the remaining component of the problem of evil. As floods and drought were a necessary consequence of the fabric of the physical world, predators and parasites, dysfunctions and diseases were a consequence of the evolution of life. They were not a result of deficient or malevolent design: the features of organisms were not designed by the Creator."
"Evolution by natural selection is Darwin's answer to Paley. It is also the solution of the last prong of the problem of evil. Theology professors in Salamanca saw in the theory of evolution a significant, even definitive, contribution to theodicy. I was, therefore, much surprised when I became aware of the creationist movement in the United States and the pervasive reservations against the theory of evolution."
p5 about his lectures and writings about the subject "The message has always been twofold: (1) evolution is good science and (2) there need not be contradiction between evolution and religious beliefs."
p6 "My conviction is that the theory of evolution is theology's disguised friend, not its enemy."
p6 Tribute to Paley and to Charles Bell
p7 emphasizes that "natural selection" was Darwin's main emphasis.
p7-10 Outlines the coming chapters.
p10 Similarities of life. Human and chimpanzee genomes each consist of some 3 billion letters and differ by little more than 1 percent. "The chemical components of life and their proportions, DNA, the genetic code that conveys the genetic information from the nucleus to the cell, the twenty amino acid components of proteins and enzymes - they are the same in all organisms from bacteria and protozoa to plants and animals.
Ch 2 Intelligent Design, the Original Version
p15 William Paley "I know no better method of introducing so large a subject, than that of comparing a single thing with a single thing: an eye, for example, with a telescope. As far as the examination of the instrument goes, there is precisely the same proof that the eye was made for vision, as there is that the telescope was made for assisting it." Natural Theology, Chap III, p 20.
p15 Paley was an anti-slavery crusader and a widely sought after speaker on that subject. But in 1800 the gave up the public speaking for health reasons and spent two years studying biology and wrote Natural Theology.
p16 "Paley's keystone claim is that 'There cannot be design without a designer; contrivance, without a contriver; order, without choice; ...means suitable to an end, and executing their office in accomplishing that end, wthout the end evey having been contemplated.' "
p16 Praises Paley's biological understanding -- quite notable coming from one of the top biologists in this country.
p17 Paley's telescope
p19 the classic Paley quote, the watch
p20 "I am filled with amazement and respect for Paley's extensive and profound biological knowledge." goes on with multiple examples
p21 Nature's Imperfections
p21 criticizes Paley's chapter "Of the Personality of the Deity" "well-meaning, if naive, arrogance, as Paley seems convinced that he can determine that God is a person, God's 'personality', and what his attributes are."
p23 Augustine (354-430) Augustines intelligent design statement, Acquinas variation.
p24 John Ray (1627-1705), The Wisdom of God Manifested in the Works of Creation (1691). Ray was an English clergyman and naturalist. "the most convincing argument of the Existence of a Deity is the admirable Art and Wisdom that discovers itself in the Make of the Constitution, the Order and Disposition, the Ends and uses of all the parts and members of this stately fabric of Heaven and Earth."
p25 Recap of other ID references, including the Bridgewater Treatises and Charles Bell's "The Hand, Its Mechanisms and kVital Endowments as Evincing Design", one of the Bridgewater Treatises.
Ch 3 Darwin's Revolution: Design Without Designer
p27 "There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that ... from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved." Charles Darwin, The Origin of Species, p. 490
p27 "The main subject of this chapter is the claim that Darwin's The Origin of Species is, first and foremost, a sustained effort to solve Paley's problem of how to account scientifically for the design of organisms."
p27-30 A good overview of the content of The Origin of Species
p32-35 Tracing other evolutionary theories
p35 Description of the Voyage of the Beagle
p38-42 Copernicus and Darwin. Comparing the Copernican revolution to the Darwinian revolution - saying that up until Darwin, there was a split-personality state of affairs. "Scientific explanations, derived from natural laws, dominated the world of nonliving matter, on the Earth as well as in the heavens. Supernatural explanations, such as Paley's explanation of design, which depended upon the unfathomable deeds of the Creator, accounted for the origin and configuration of living creatures - the most diversified, complex, and interesting realities of the world."
p40 photo Darwin's finches.
p43 Emphasis on natural selection as Darwin's theory rather than evolution.
p46 The Darwinian Aftermath. Talks about T.H. Huxley, "Darwin's bulldog" who generated much of the controversy. Also Herbert Spencer who extrapolated Darwin's ideas and coined the phrase "survival of the fittest". Darwin was disapproving of Spencers extrapolations into what has come to be called Social Darwinism.
Ch 4. Natural Selection
p49 "I can see no limit to this power [natural selection], in slowly and beautifully adapting each form to the most complex relations of life." Charles Darwin, The Origin of Species, p. 469.
p49 "Can it, then, be thought improbable, seeing that variations useful to man have undoubtedly occurred, that other variations useful in some way to each being in the great and complex battle of life, should sometimes occur in the cours of thousands of generations? If such do occur, can we doubt (remembering that more individuals are born than can possibly survive) that individuals having any advantage, however slight, over others, would have the best chance of surviving and procreating their kind? On the other hand, we may feel sure that any variation in the least degree injurious would be rigidly destroyed. This preservation of favorable variations and the rejection of injurious variations, I call Natural Selection."
p53 Darwin's Monk. birth of genetics with Gregor Mendel's meticulous study of pea variations.
p54 Mutations and DNA
p60 A powerful example with E Coli. Few bacteria in culture that require histidine. With histidine, in two days produce 20 to 30 billion. Hit with drop of streptomycin, most will die but after a day or two back to 20 to 30 billion, all resistant to streptomycin. Then remove histidine and nearly all die, but in a day or two back to 20 to 30 billion, all of which can reproduce without histidine. So two steps in a few days whereas the straight probability of such a dual change would be infinitesimal. On pg 154 he refers back to this example in his response to Dembski's numerical calculations.
p61 A Monkey's Tale. His version of the monkeys and the typewriters.
p63 Light and dark colored mice adapted to their different colored environments with a change in only one gene.
p66 Only prokaryotes first 2 billion years. 1.5 billion ago the first multicellular eukaryotes.
p67 Baldwin Effect and sex determination.
p71 An inventory of 2 million species with estimate that there are at least 10 million living species. 99% of those that have lived are extinct. Number of species that have lived on Earth likely > 1 billion.
p72 Hawaii story of variaties.
p76 Chance and necessity
Chap 5 Arguing for Evolution
p79 Why should the species which are supposed to have been created in the Galapagos Archipelago, and nowhere else, bear so plain a stamp of affinity to those created in America? Charles Darwin, The Origin of Species, p. 398
p79 "The following assertion may bewilder some readers: Gaps of knowledge in the evolutionary history of living organisms no longer exist. This statement will come as a surprise to those who have heard again and again about "missing links", about the absence of fossil intermediates between reptiles and birds or between fish and tetrapods, and about the "Cambrian Explosion".
p79 "The evolutionary explosion that has occurred in recent years concerns knowledge, not the Cambrian: molecular biology has made it possible to reconstruct the "universal tree of life", the continuity of succession from the original forms of life, ancestral to all living organisms, to every species now living on Earth."
p81 Fossil record
p84 Archaeopteryx (animal intermediate between reptiles and birds) and Tiktaalik (intermediate between fishes and tetrapods, animals with four limbs.).
Ch 6 Human Evolution
p95 "The missing link is no longer missing. Not one, but hundreds of fossil remains belonging to hundreds of individual hominids have been discovered since Darwin's time."
p111 Brain to Mind puzzle
Ch 7 Molecular Biology
p118 The Unity of Life "The molecular components of organisms are remarkably uniform - in the nature of the components as well as in the ways in which they are assembled and used."
p119 "The unity of life reveals the genetic continuity and common ancestry of all organisms. There is no other rational way to account for their molecular uniformity, given that numerous alternative structures and fundamental processes are in principle equally likely. The genetic code may serve as an example. Each particular sequence of three nucleotides (called a 'triplet' or 'codon') in the nuclear DNA acts as a code for exactly the same particular amino acid in all organisms. " "The universal correspondence between the DNA language (codons) and the protein language (amino acids) is no more necessary than it is for any two spoken languages to use the same combination of letters for representing the same particular concept of object."
p119 Genetic information
p120 "molecular biology offers two kinds of arguments for evolution. Using the alphabet analogy, the first argument says that languages that use the same alphabet (the same hereditary molecule, the DNA made up of the same four nucleotides, and the same 20 amino acids in their proteins) as well as the same dictionary (the same genetic code) cannot be of independent origin. The second argument concerns the degree of similarity in the sequences of nucleotides in the DNA (and thus the sequence of amino acids in the proteins); it says that books with very similar texts cannot be of independent origin."
p121 Mendel to Dolly
p122 E Coli and lactate story.
p123 Egg to Adult
p123 "A human being consists of 1 trillion cells of some 300 different kinds, all derived by sequential division, each cell dividing into two, from the fertilized egg."
p124 "The information that controls cell and organ differentiation is ultimately contained in the DNA sequence, but mostly in very short segments of it. In mammals, insects, and other complex organisms, there are control circuits that operate at higher levels than the control mechanisms that activate and deactivate individual genes. These higher-level circuits (such as the so-called homeobox, or hox, genes) act on sets of genes rather than individual ones."
p125 Cytochrome-c has 104 amino acids. In humans and chimpanzees the cytochrome-c consists of the same 104 amino acids in exactly the same order. Rhesus monkeys differ in 1 amino acid. Horses differ in twelve. Tuna differ in 33.
p126 argument for DNA sequence data. "The degree of similarity reflects the recency of common ancestry. Thus, the inferences from paleontology, comparative anatomy, and other disciplines that study evolutionary history can be tested in molecular studies of DNA and proteins by examining the sequences fo nucleotides and amino acids. The authority of this kind of test is overwhelming: each of the thousands of genes and thousands of proteins contained in an organism provides an independent test of that organism's evolutionary history."
p127 Ribosomal RNA are very slowly evolving and can test back billions of years.
p128 more details about using cytochrome-c and implications about how long ago the lineages diverged. Useful for constructing a tree of ancestry.
p131 Diagram of evolutionary history of 20 species based on cytochrome-c.
p134 number of nucleotide substitutions as a clock. Diagram.
Ch 8 Follies and Fatal Flaws
p137 Recaps Paley, Aquinas and Ray's intelligent design positions.
p138 Judge's response to arguments by Behe, Johnson, Dembski in school case.
p139 Evolution is Only a Theory
p141 the three issues of evolution common descent, history of lineages, mechanisms or processes.
p143 The Two-Explanations Fallacy Judge Jones in Dover: "ID is at bottom premised upon a false dichotomy, namely that to the extent evolutionary theory is discredited, ID is confirmed. "
p144 quote to draw parallels to defense of creation science.
p144 The Eye of the Octopus. Discussion of the evolutionary development of the eye.
p144 The Bacterial Flagellum, Blood Clotting, and Other Improbabilities
p150-151 Refers off to Miller's Finding Darwin's God for dealing with Behe's arguments.
p153 "Theodosius Dobzhansky, one of the greatest evolutionists of the twentieth century and a religious person, has written: 'There are people, however, to whom the gaps in our understanding of nature are pleasing for a different reason. These people hope that the gaps will be permanent, and that what is unexplained will also remain inexplicable. By a curious twist of reasoning, what is unexplained is then assumed to be the realm of divine activity. The historical odds are all against the "God of the gaps" being able to retain these shelters in perpetuity. There is nothing, however, that can satisfy the type of mind which refuses to accept this testimony of historical experience.' "
p153 case against Dembski's "complex specified information"
p154 "What are we to make of this calculation? The answer is simple, namely, that this calculation, as well as Dembski's other numerology exercises, is totally irrelevant because Dembski's assumptions are wrong. Natural selection proceeding stepwise can accomplish outcomes with prior probabilities immensely smaller than Dembski's calculations. " refers back to his E Coli example on pg 60.
p154 In Praise of Imperfection
p154 Takes on Behe's (and Rana's, I'm afraid) arguments about optimization of design under constraints leads to things that appear to be imperfections.
p154-158 points to some imperfections and non-optimizations
p158 David Hull quote ending in "not the sort of God to whom anyone would be inclined to pray."
p159 Argues that evolution explains the problems and flaws. Aubrey Moore "Darwinism appeared, and, under the guise of a foe, did the work of a friend." "the theory of evolution, which at first had seemed to remove the need for God in the world, now has convincingly removed the need to explain the world's imperfections as failed outcomes of God's design."
p160 "this is how matters appear to a biologist concerned that God not be slandered with the imputation of incompetent design."
Ch 9 Beyond Biology
p161 quotes the Judge in the Dover case
p162 "If they are assessed correctly, they cannot be in contradiction, because science and religion concern non-overlapping realms of knowledge." This represents the most disturbing line in Ayala's writing to me. He touches on this, which seems to buy Gould's NOMA hook line and sinker, in several places and I'm surprises by this, given his otherwise open approach to faith.
p162-163 But despite my reservations about NOMA, I laud Ayala's tipping of the importance in the opposite direction that Gould tipped it. The flavor of that is captured by "once science has had its say, there remains much about reality that is of interest: questions of value, meaning and purpose that are forever beyond science's scope." He says this at the end of the story of Picasso's Guernica in which Picasso expressed his anguished outrage at the bombing of the Basque village of that name and the killing of many civilians.
p163 Scathing attack on Darwinism by a contemporary theologian, Charles Hodge who equated it to the denial of God. Contrasted is A. H. Strong's view of evolution as "the method of divine intelligence"
p164 More positive evaluations of evolution starting from the 1950 papal encyclical to Pope John Paul II's 1996 statement, and statements by Presbyterians, Lutherans, Jewish organizations.
p167 more review of Augustine's statements
p168ff Fundamentalism, Creationism and the Public Schools
p170 Evolution or Religious Beliefs? The Arrogance of Exclusivity
p172 good summary paragraph
p173 Quotes Futuyma, Dawkins and Provine as examples of making philosophical and metaphysical projections from science.
p174 blasts the above referenced statements. Quotes Academy of Sciences statements about science and faith.
p176 Science as a Way of Knowing
p177 Beyond science "Astonishing to me is the assertion made by some scientists and others that there is no valid knowledge outside science."
p178 more examples of value outside science
p179 Freeman Dyson quote " As human beings, we are groping for knowledge and understanding of the strange universe into which we are born. We have many ways of understanding, of which science is only one ... Science is a particular bunch of tools that have been conspicuously successful for understanding and manipulating the material universe. Religion is another bunch of tools, giving us hints of a mental or spiritual universe that transcends the material universe." "Religion from the Outside", The New York Review (June 22, 2006), 4-8.