Probability's Nature and Nature's Probability
A Call to Scientific Integrity
Donald E. Johnson
Don Johnson is a Ph D Chemist with also a PhD in Computer and Information Sciences. He writes in compact fashion, the kind of style you might expect from a scientist. My second impression was that the book is a goldmine of quotes - he has really read a lot of stuff, and has compact collections of relevent quotes, sort of like "data bursts" of quotes.
p5 "It was science, and not his religion, that caused his disbelief in the explanatory powers of nature in a number of key areas including the origin and fine-tuning of mass and energy, the origin of life with its complex information content, and the increase in complexity in living organisms. "
1. Introduction to Probability
p8 "chance has no causative effect" This is an interesting line that I ought to make use of. He rolls it out as a phrase like it is an old friend, and it is a compact way of communicating the idea that no matter how many times you roll the die, the probability of throwing a 5 on the next throw is still 1/6. Pure chance does not value experience or history; nothing about its history affects the probability for the next roll. This chapter is a compact summary of basic probability and maybe I ought to use it to review my probability treatment.
2. Chance: Possible, Probable, and Feasible
p 11 Expression for the number of tries for an outcome to be probable, i.e., have a probability higher than 0.5.
3. Mass and Energy: Source and Fine-Tuning
p 20 A databurst of good quotes about string theory, multiverse and speculating beyond our horizon.
An overview of amino acids, enzymes, DNA, helicases, the smallest genome, a characterization of a single cell.
p 26 Interesting comments about the effects of enzyme catalysts. Wolfenden of the UNC School of Medicine found evidence of a biochemical reaction that would take a trillion years without a catalyst, but in biological environment takes place in 10 seconds. I printed the two-page news article from UNC and filed it under enzymes. Wolfenden's quote "Without catylysts, there would be no life at all, from microbes to humans. It makes you wonder how natural selection operated in such a way as to produce a protein that got off the ground as a primitive catylyst for such an extraordinarily slow reaction."
p 31 Data on brain, as on p30 in Prog Life. More thorough in Prog Life.
p 31 Data on number of cells in body, 300 trillion, and number of hemoglobin molecules, and rate of operation to produce the hemoglobin.
5. The Origin of Life
p 32 Small genome of Mycoplasma to set stage for minimum complexity. More on Mycoplasma on p43 of Prog Life
p 32 Dawkins just happened quote.
p32 "more than 30 years of experimentation on the origin of life in the fields of chemical and molecular evolution have led to a better perception of the immensity of the problem of the origin of life on Earth rather than to its solution" Klaus Dose, "The Origin of Life: More Questions Than Answers," Interdisciplinary Science Reviews: 13 (4), 1988, p348. Though now over 20 years ago, the assessment is still about the same.
p 33 "What creates life out of the inanimate compounds that make up living things? No one knows. How were the first organisms assembled? Nature hasn't given us the slightest hint. If anything, the mystery has deepened over time." Greg Easterbrook, "Where did life come from?'" Wired Magazine, 2/07, p108.
p 33-35 Several of the contradictory statements about the nature of the prebiotic era and its chances of generating life. This is a good collection of the statements you see often.
p 35 Summarizes with "The intractable DNA/RNA/protein origin problem has led most scientists to abandon the DNA as the first life, even though that is the only life that is known."
p 35 Panspermia discussion. Remarkable quote of Wickramasinghe about the improbability of forming the necessary chemicals of life.
p 37 RNA World discussion. Also discusses this topic on p21 of Prog Life, but this discussion is a little more thorough and contains more quotes, particularly of Orgel. A databurst of quotes that are doubtful of Orgel's scenario, including a number from Orgel himself.
p 39 Discussion of mineral surfaces as possible templates for the formation of origin-of-life molecules. Robert M. Hazen in his "Genesis: Rocks, Minerals and the Geochemical Origin of Life" in Elements: 1, 6/05, p135-137 takes an optimistic view of this scenario. But he gets pounced upon by Orgel and Constanzo, et al from the chemical point of view. But there are other challenges based on Shannon information - regular crystal structures as templates for organic molecules are too regular to contain much information. You would have to depend upon imperfections in the crystals to insert information.
p 40-41 A databurst of quotes expressing skepticism about the undirected origin of life culminating in the Prigogine quote.
p41 Statement that is a good summary of Johnson's viewpoint: "Since there is no known scientific procedure to generate life in the laboratory, let alone by some unknown prebiotic mechanism, one could assume the probability of life from undirected natural causes is zero. What often is assumed is that since life obviously exists and the only allowable mechanism is undirected and natural, it must have occurred that way, despite the improbability. This is an obvious tautology since the propositions "life exists" and "life can only be the result of undirected natural sources" uses the second proposition to prove itself (the first proposition is obviously true)."
6. The Information Contained in Life
p43 One of a number of quotes from Werner Gitt, "In the Beginning Was Information", 1997. Also quotes from Davis, Sagan and Voie with the general theme that if you haven't explained the origin of the information, you haven't explained life.p 43 Remarkable quote by Wilder-Smith using for the cell an analogy of a house plan that could build the house if you but threw it into the garden.
p 45 Discusses the distinction between Shannon information and "traditional/functional' information. These are discussed in more detail in Chs 2 and 5 of Programming of Life.
p 50-51 In discussing the complexity of the information storage in cells, quotes Meyer, Yockey and Ridley on overlapping genes and the nature of the genetic information storage. Same Trevors quote that he uses in Programming of Life.
p52-53 Overview of the things that add complexity to the genetic information system.
p53 Set of impossibilities from the "Universal Laws of Information". It is impossible:
p54 Yockey quotes on rules for information transfer.
p54 Talks about the Origin of Life prize
p55-61 Discussion of some of the technical details and uses of functional information and Shannon information.
7. Increasing Complexity of Life
p62 Databurst of Dawkins quotes.
p62 Quote of Dembski on the intractable problems for naturalistic creation.
p 64 More Dawkins quotes.
p 64-67 Discussion of junk DNA
p 70 The fossil record
p 72 The trilobite eye
p 74 Cambrian explosion, long Meyer quote
p 75 Computer simulations, including Dawkins
p 77 Avida
p 79 Irreducible complexity and the bacterial flagellum.
p 83 Recombinant DNA
p 84 Evolutionists that support ID
8. Going Where Data Lead
p86 Starts with quotes from Del Ratzsch, Science and its Limits, 2000 p123-124 and from Jonathan Wells, Icons of Evolution to make the case that "Follow the evidence where it leads" should apply to those who philosophically refuse to consider any non-materialistic cause.
p 88 Quotes Thomas Woodward's "Doubts About Darwin: A History of Intelligent Design. Another quote from Fred Hoyle.
p 89 Long quote from Discovery Institute defining ID.
p 91 Interesting quotes from Michael Denton, whose "Nature's Destiny" has statements like "the cosmos is a seamless unity" and "the cosmos is a unique whole with life and mankind as its end and purpose..." Interesting that Denton takes an evolutionary view, yet embues it with purpose and takes an anthropic view of humanity.
p 92 He quotes an agnostic, Bill Schultz, to make the point that advocates of intelligent design do not necessarily presume a supernatural creator.
p 94 Points out that the implications of fully naturalistic evolution for human ethics are so stark that even Dawkins backs away from the implications, describing his "un-Darwinian" behaviors that are counter to his own statements in The Blind Watchmaker.
p 95 Quotes from Meyer's paper that got published in the Biological Society of Washington, leading to the sacking of the Editor, Richard Sternberg, whom he also quotes.
p 97 Interesting quote from Pagels who waxes eloquent about a "universal building code" and hints at intelligence but stays pretty well mainstream.
p 98 Continues to quote Dawkins form Blind Watchmaker and The Necessity of Darwinism as Dawkins hammers on his point that evolution is the only cause that could in principle explain the existence of order in life.
p 98-100 After the Dawkins broadside, Johnson replies with what he calls "revolutionary views" including Davies, Skell, and Stravropoulos. More fascinating quotes from Hoyle, who thought and wrote about this subject over a long period. Then more focused criticisms of the evolutionary paradigm from Gilder, Meyer, Grasse', and Eldridge. Ends this particular databurst with a delightful quote from Hoyle which lifts up Paley. He throws in Phillip Johnson with his story of the Chinese paleontologist who quips "Americans can criticize the government but not Darwin."
p 101 His final quote in this intense chapter is of J. T. Trevors and D. L. Abel, whom he obviously values and whom I should investigate further.
p101 "Evolution has been a knowledge-stopper instead of an enlightener." Discusses vestigial organs and junk DNA, which were not valued because of evolutionary bias that treated them as useless evolutionary history.
9. Why Intelligent Design?
p103 Definitions of intelligent design, irreducible complexity
p103-104 Quotes from Dembski
p105 About the designer's identity: "It is important to stress that the refusal of ID proponents to draw scientific conclusions about the nature or identity of the designer is principled rather than merely rhetorical." Some quotes Conway Morris, Einstein
p106 Detectability of design
p107 The limits of science
p108 The benefits of an ID model
p109 Occam's razor
p110 Recap of ID arguments.