Signature in the Cell

Stephen C. Meyer

The prologue tells the story of his personal involvement in the intelligent design movement and of his publication in the Smithsonian review that drew so much attention.

1. DNA, Darwin, and the Appearance of Design

p 11 Newton's quote in The Opticks "How came the Bodies of Animals to be contrived with so much Art, and for what ends were their several parts? Was the Eye contrived without Skill in Opticks, and the Ear without Knowledge of Sounds?... And these things being rightly dispatch'd, does it not appear from Phaenomena that there is a Being incorporeal, living, intelligent ...?"

p 5 Discusses impact of Behe and Dembski

p 12 Crick's quote "Biologists must constantly keep in mind that what they see was not designed, but rather evolved."

p 12 "But due in large measure to Watson and Crick's own discovery of the information-bearing properties of DNA, scientists have become increasingly and, in some quarters, acutely aware that there is at least one appearance of design in biology that may not yet have been adequately explained by natural selection or any other purely natural mechanism. Indeed, when Watson and Crick discovered the structure of DNA, they also discovered that DNA stores information using a four-character chemical alphabet. Strings of precisely sequenced chemicals called nucleotide bases store and transmit the assembly instructions - the information - for building the crucial protein molecules and machines the cell needs to survive."

p 12 "Just as letters in an English sentence or digital characters in a computer program may convey information depending on their arrangement, so too do certain sequences of chemical bases along the spine of the DNA molecule convey precise instructions for building proteins."

p 13 Bernd-Olaf Kuppers "The problem of the origin of life is clearly basically equivalent to the problem of the origin of biological information."

p 14 100M$ research at Harvard on origin of life - about Watson & Crick's discovery "But they discovered another mystery that remains with us to this day. This is the DNA enigma - the mystery of the origin of the information needed to build the first living organism."

p 15 Uses fax machine as picture of transmitting information - the "thing" that is transmitted is information, because the paper that comes out of the machine was already resident in it. The information carries the implication of intelligence, but the definition of information is illusory.

p 16 "Our experience of the world shows that what we recognize as information invariably reflects the prior activity of conscious and intelligent persons."

p 16 "We now know that we do not just create information in our own technology; we also find it in our biology - and, indeed, in the cells of every living organism on Earth. But how did this information arise? And what does the presence of information in even the simplest living cell imply about life and its origin? Who or what "wrote" the book of life?

p 17 "precisely sequenced bases attached to the helical backbone of DNA store the information for building proteins ..."

p 17 "the DNA molecule is the medium, it's not the message." George Williams

p 18 "Biology is the study of complex things that appear to have been designed for a purpose." Dawkins

p 17 living organisms "appear to have been carefully and artfully designed." Richard Lewontin

p 19 Francisco Ayala " The functional design of organisms and their features would .. seem to argue for the existence of a designer. It was Darwin's greatest accomplishment [however] to show that the directive organization of living beings can be explained as the result of a natural process, natural selection, without any need to resort to a Creator or other external agent." from "Darwin's Greatest Discovery"

p 20 After conceding that things are often not what they seem in science, he yet muses "Even so, there is something curious about the scientific denial of our ordinary intuition about living things." He then goes on to reflect on the fact that evolutionary biologists still use the language of purpose in describing living systems, while formally denying that there is any purpose.

p 20 "For almost a hundred and fifty years, since its putative explanation by Darwinian theory, this impression of design persists as incorrigibly as ever. Public opinion polls suggest that nearly 90 percent of the American public does not accept the full-fledged neo-Darwinian account of evolution with its denial of any role for a purposeful creator." Includes again the Crick quote.

p 21 "Metaphors reign where mystery resides."

p 21 University of Chicago cell biologist James Shapiro describes the integrated system of proteins that constitutes the mammalian blood-clotting system "as a powerful real-time distributed computing system."

p 22 Eloquent musing about purpose or no purpose, includes the line "Yet the persistence of dissenting scientific opinion and the inability of biologists to avoid the language of purpose raise a pardonable curiosity."

p 22-23 Presents a segment of the genetic code in base language compared to the first lines of the Declaration of Independence written in ASCII code.

p 26 Describes the conference where Thaxton, Bradley and Olsen presented the ideas from their book "The Mystery of Life's Origin" where the group conceded their lack of progress on explaining life's origin but reacted strongly against their proposal of intelligent design.

p 29 Discusses "origins sciences" as distinct from "operations sciences".

2. The Evolution of a Mystery and Why It Matters

p 33 Wohler and the synthesis of urea. Wohler's "Urea!" moment. Actually had major impact on the development of biology since it showed that the chemicals of life can be synthesized from ordinary chemistry -- very much counter to the culture of the time which held that the matter of life and non-life were separated by an unbridgeable gap.

p 36 Discusses idealism where mind is considered to be the ultimate reality, Plato to Aquinas.

p 37 Discusses materialism, matter first and mind derivative. Hobbes to Hume and naturalism or materialism.

p 37 "The age-old conflict between the mind-first and matter-first worldviews cuts right through the heart of the mystery of life's origin."

p 38 In a section title "The Mystery of the Missing Mystery" he wonders about the acceptance of the "matter first" position by many scientists whereas the founders of modern science like Kepler, Boyle and Newton had been "men of deep religious conviction who believed that scientific evidence pointed to a rational mind behind the order and design they perceived in nature."

p 38 He attributes this flight to materialism to a number of models and discoveries - Laplace and his nebular hypothesis gave a naturalistic explanation for the formation of stars, Charles Lyell and his uniformitarianism model for long slow geological formation processes, and physics and astronomy seeing the universe's history as infinite so that no matter how slow, a naturalistic development seemed feasible. Then Darwin's theory of evolution gave a mechanism for the development of life so the collective worldview being developed could accept the position that "an undirected process could account for the origin of new forms of life without divine intervention, guidance, or design."

p 39 "But the origin of the first life remained a small hole in this elaborate tapestry of naturalistic explanation."

p 39 The models suggested that Earth had once been too hot to sustain life, so "life had not existed eternally, but instead had appeared at a definite time in earth's history. To scientific materialists, life might be regarded as an eternal given, a self-existent reality, like matter itself. But this was no longer a credible explanation for life on earth. There was a time when there was no life on earth. And then life appeared."

p 39 Darwin himself in 1866 "Though I expect that at some future time the [origin] of life will be rendered intelligible, at present it seems to me beyond the confines of science."

p 39 Pasteur and the demise of vitalism.

p 40 Story of the lack of curiosity about origin of life in the Victorian age because of the demise of vitalism. Meyer's comment "From my vantage point in 1986, having just learned about the current impasse in contemporary origin-of-life research, the nonchalance of the Victorians seemed itself a bit mysterious." He attributes it to Wohler's "Urea!" moment and the synthesis of a substance that is a part of life gave biologists the confidence that the synthesis of all of life's substances would be forthcoming.

p 40 Helmholtz enters the picture with his thermodynamic experiments with living organisms and his demonstration that they satisfy the First Law of Thermodynamics" or conservation of energy.

p 41 Ernst Haeckel enters the picture. As a German materialist, he "denied any qualitative distinction between life and nonliving matter:'We can no longer draw a fundamental distinction between organisms and anorgana [i.e., the nonliving].'"

p 42 Another German, Rudolf Virchow, boldly asserted the materialistic credo "Everywhere there is mechanistic process only, with the unbreakable necessity of cause and effect."

p 42 Meyer has carefully built the picture of how scientific materialism became entrenched. The materialists viewed it as inevitable that the beginning of life would be explained with reference to materialistic processes only. "For Haeckel, finding a materialistic explanation for the origin of life was not just a scientific possibility; it was a philosophical imperative."

p 42 Explaining the origin of life was "extending evolution backward".

p 46 Comparison of Huxley and Haeckel. The first abiogenesis proposals.

p 49 Interesting story of Marx and Engels' interest in abiogenesis as an evolutionary mechanism and its parallel to revolutionary birth of the "classless society". Oparin was in that mix. Life as a "sudden spurt" and communist revolution as a "sudden spurt", creating a new society.

p 50 Again points to Wohler's "Urea!" moment as profoundly influencing thought.

p 51 Oparin's "building blocks" 1936. Oxygen-free early atmosphere, N & C in compounds, building of amino acids

p 53 Oparin - cell walls, proteins - hydrophobic lipids form enclosures in prebiotic ocean. So Oparin lay groundwork for Miller-Urey.

p 54 Miller-Urey

3. The Double Helix

p 57 By the Darwin centennial in 1959 "A seamless and fully naturalistic account of the origin and development of life-forms appeared, if not complete, then at least sketched in enough detail to preclude anachronistic speculations about a designing hand."

p 61 Mendel's peas - recessive genes implied a hereditary map.

p 66 Avery took Griffiths study of bacteria and mice and deduced that DNA was the agent of hereditary transfer.

p 73 Rosalind Franklin and the maltese cross x-ray pattern, indications of a helix with dimensions 20A by 34A.

p 77 Converging on the double helix with phosphates on outside and antiparallel strands

p 82 AT GC insight . Gave regular helix even when sequence was random.

p 83 "Thus, it had an impressive potential for variability and complexity of sequence as required by any potential carrier of hereditary information."

p 83 Watson and Crick's explanation "The phosphate-sugar backbone of our model is completely regular, but any sequence fo the pairs of bases can fit into the structure. It follows that in a long molecule, many different permutations are possible, and it therefore seems likely that the precise sequence of the bases is the code which carries the genetic information."

4. Signature in the Cell

p 85 Information in DNA

p 85 "At some point in the history of the universe, biological information came into existence."

p 86 "DNA contains 'alternative sequences' of nucleotide bases and can produce a specific effect." This to make the case that the DNA contains information, even though it is not conscious.

p 88 Shannon's information theory

p 92 "Proteins build cellular machines and structures, they carry and deliver cellular materials, and they catalyze chemical reactions that the cell needs to stay alive. Proteins also process genetic information. To accomplish this critical work, a typical cell uses thousands of different kinds of proteins. And each protein has a distinctive shape related to its function, just as the different tools in a carpenter's toolbox have different shapes related to their functions."

p 94 Sanger's determination that insulin had a highly irregular sequence of amino acids that defies description by simple rules.

p 95f shape and specificity of proteins

p 98 "Chromosomes are made of DNA spooled on histones."

p 99 Amino acid chain is a polypeptide, and when it is folded into a specific functional shape it is a protein.

p 100 protein characterized by "sequence specificity" like software, like language.

• Sequence hypothesis - DNA - Crick
• DNA structure - Watson and Crick
• Structure of insulin, very irregular - Sanger
• 3D structure of myoglobin - Kendrew
• Link between genes and proteins - Beadle and Tatum who irradiated molds and found that it broke things- they were missing parts in subsequent generations.

p 102 Genetic code, early 1960's

p 103 Gene expression system -transcription-mRNA-ribosome-codons-helped by tRNA.

p schematic of gene expression.

p 106 Good example and discussion of "specified complexity".

p 110 "biochemist Leslie Orgel observes 'Living organisms are distinguished by their specified complexity. Crystals ... fail to qualify as living because the lack complexity; mixtures of random polymers fail to qualify because they lack specificity."

p 110 "oddly, at nearly the same time that computer scientists were beginning to develop machine languages, molecular biologists were discovering that living cells had been using something akin to machine code or software all along."

p 110 "Like software, the coding regions of DNA direct operations within a complex material system via highly variable and improbable, yet also precisely specified, sequences of chemical characters. "

5. The Molecular Labyrinth

p 116 Crick's code hypothesis

p 119 Zanecnik's discovery that ribosomes make the proteins. Ribosomes are far from the nucleus and contain no DNA. Discovery of tRNA

p 119 Ochoa and the deciphering of the genetic code

p 122 Gene expression - transcription - conditions - introns. schematic of transcription. "RNA polymerase is an extraordinarily complex protein machine of great specificity." Some nice detail about it there.

p 123 Sketch of transcription that I might model after. Includes the DNA, RNA and RNA polymerase.

p 124 A brief version of the 'lactose or no lactose' story that I have read elsewhere. Even in simple prokaryotes, an inhibitor that prevents protein formation when no lactose is present, and produces the necessary proteins to use it when it is present - a sophisticated capability in very primitive life.

p 125 Another sketch of RNA polymerase and its multiple parts - not so familiar to me.

p 126 Initiation phase and the TATA sequence. Illustration.

p 127 Translation from a 4 character base alphabet to a 20 character amino acid alphabet

p 127 "transcription constitutes a complex, functionally integrated process involving several specialized and individually necessary proteins. Yet production of each of these separate proteins is itself dependent on the very process of transcription that they make possible."

p 128 Detailed description of protein building in the ribosome.

p 128 Uracil on mRNA substitutes for Thymine. A binds to T, C binds to G. Need to sort out the details of this

p 131 Replicating DNA. Get into a lot of chicken and egg scenarios.

p 132 Not only complexity but integrated complexity.

p 133 Interesting quote of Lewontin

p 133 Goodsell "The key molecular process that makes modern life possible is protein synthesis, since proteins are used in nearly every aspect of living. The synthesis of proteins requires a tightly integrated sequence of reactions, most of which are themselves performed by proteins."

p 133 Monod "The code is meaningless unless translated. The modern cell's translating machinery consists of at least fifty macromolecular components which are themselves coded in DNA: the code cannot be translated otherwise than by products of translation." Meyer notes that the number is too small - translation requires more than a hundred proteins.

p 134 Lewontin "What makes the proteins that are necessary to make the protein?"

p 134 Goodsell "is one of the unanswered riddles of biochemistry: which came first, proteins or protein synthesis? If proteins are needed to make protein, how did the whole thing get started?"

p 134 "scientists investigating the origin of life must explain the origin of at least three key features:"

• origin of the system for storing and encoding digital inforrmation in the cell, DNA's capacity to store digitally encoded information.
• origin of the large amount of specified complexity or functionally specified information in DNA
• origin of the integrated complexity - the functional interdependence of parts - of the cell's information system.

6. The Origin of Science and the Possibility of Design

p 141 After defending the "detective" approach to origin of life issues, sort of like Watson and Crick pursued the story of DNA, Meyer tells of an interview with Eugene Wigner. "he explained why he thought the odds were overwhelmingly against any process of undirected chemical evolution producing life." Wigner was sympathetic with the intelligent source idea.

p 142 Interesting interactions with Bondi and Hoyle, both early advocates of the steady state theory - Hoyle was at Cambridge to discuss origin of life, and was not unsympathetic with Meyer's ideas about intelligent design.

p 142

Western science is grounded in "the belief that the natural order is the product of a single intelligence from which our own intelligence descends." "Science vs Religion? Intelligent Design and the Problem of Evolution", Oxford: Polity, 2007, p15

Scientists have the job of "thinking God's thoughts after Him".

"According to Judeo-Christian beliefs the world is the free creation of God from nothing. The structure of the world cannot therefore be deduced from first principles; we have to look at it, to make observations and experiments fo find out how God made it. This reinforces the Aristotelian principle that all knowledge comes through the senses, but requires that it be situated within a wider set of beliefs concerning the nature of the world that is implicit in the doctrine of creation. " "The Christian Origin of Science", Logos 4, 2001, p 138-159. (p145)

Hodgson notes that early scientists assumed that the world was both rational - because it was created by a Mind -- and contingent -- because that Mind had acted freely. These assumptions led to "a fresh style of scientific thinking," one that "was made possible by the Judeo-Christian vision of the world."(p142)

p 147 In the remainder of this chapter Meyer muses about the fact that the history of Cambridge itself and a long list of early scientists were firmly on the side of design while many modern scientists consider design a "science stopper".

7. Of Clues to Causes

p 153-4 Interesting discussion of the science of past events and the idea of abductive reasoning. Though subject to the dangers of syllogisms and the logical fallacy of "affirming the consequent", there is plausibility in the situation where "we cannot explain what we have seen without the hypothesis ...". The "method of multiple working hypotheses" and the "inference to the best explanation".

p 155 Peter Lipton and his treatise "Inference to the Best Explanation".

p 159-160 Discusses Lyell and Darwin and their efforts to explain the past by "causes now in operation."

p 161 Scriven adds the strengthening feature that independent evidence supports the claim that the given cause can produce the effect.

p 161 "causal adequacy as the main criterion by which competing hypotheses are adjudicated .." "affirming the consequent - the error of ignoring other possibile causes with the power to produce the same effect."

p 166 In addition to causal adequacy, one must show that the cause was actually present "causal existence criterion".

p 168 Scriven "absence of evidence (despite a thorough search) of ... other possible causes"

p 169 Darwin's use of Scriven's condition.

p 170 Discusses further the "causes now in operation" and "vera causa" ideas and muses that intelligence is known to produce complex specifiec information. Faces the difficulty of showing that it was the "only known cause"

8. Chance Elimination and Pattern Recognition

This is the best treatment of this subject that I have seen. Outcomes for which "chance" is a reasonable hypothesis are not those things that have no cause, but those for which the relevant causes allow several possible outcomes. When chance is invoked, you are still looking at causes, and may be able to precisely state the probability of a certain outcome.

p 173 Jacques Monod and "Chance and Necessity" Monod was a colleague of Crick and posited that the combination of chance variation and lawlike processes of necessity could explain the history of life.

p 174 Monod did not try to explain the origin of the information in the cell. But he took the position that scientists can, and should, explain all phenomena by reference to chance, necessity, or a combination of the two.

p 175 Takes on the questions "When is it reasonable to invoke chance ...?" and "what justifies excluding such and explanation from consideration?". Uses Tacoma Narrows Bridge as example of inappropriate use of chance to cover ignorance.

p 175 Legitimate to attribute an event to chance when "there is a known process... which can generate the event ...with some regular or predictable frequency."

p 176 "When scientists say that something happened by chance, they do not usually mean to deny that something caused the event in question. ...they mean that there is a process in play that produces a range of outcomes each of which has a chance or probability of occurring .."

p 177 "When scientists attribute an event to chance, they also usually mean there is no good reason to think the event happened either by design or because of a known physical process that must, of necessity, generate only one possible outcome."

p 177 The chance hypothesis, when justified, serves to negate the alternative hypothesis of bias or design - it is also commonly called the null hypothesis. It nullifies design or necessity as causes.

p 178 Discussion of the contributions of Dembski and Fisher.

p 180 Discussion of Fisher's approach to eliminating chance alone from consideration as the best explanation. Fisher's method involved a probability curve and a predecided rejection region.

p 183 Noting that 100 heads in a row has the same probability of any other distribution of heads and tails, Dembski recognizing that if one could identify a pattern or a goal that is being served by that particular outcome then chance alone could be reasonably rejected.

p 188 Ex post facto pattern recognition can negate chance.

p 189 "the occurrence of an improbable event alone does not justify eliminating the chance hypothesis .." "both the occurrence of an improbable event and the recognition of a pattern are necessary ..."

p 190 Invokes Christian de Duve to define probabilistic resources "What counts [in assessing the probability of a chance hypothesis] is the number of opportunities provided for a given event to happen, relative to the event's probability."

9. Ends and Odds

p 195 Notes most scientists' skepticism about chance alone in life, even with the presumption of a rich prebiotic soup.

p 197 Uses specified information in a telephone number to suggest that you're not going to get it by chance. Also used Scrabble letters and blind draw to illustrate the idea.

p 198 Quotes Alexander Cairns-Smith on limitations of blind chance.

p 201 Discusses minimum complexity for cell - experiments - 250-400 genes for simplest cell, simplest present cell 482 proteins, 562,000 bases .

p 202 Over 100 specific proteins in translation.

p 204 Wistar conference, Peter Medawar, mentions Victor Weisskopf as one of initial skeptics of chance hypothesis, "combinatorial problem".

p 206 brief discussion of chirality problem.

p 208 MIT biochemist Robert Sauer - 100 amino acid by chance 1 in 10⁶³ compared to 10⁶⁵ atoms in galaxy.

p 209 Douglas Axe extend Sauer's research. Pretty well axed the possibility of proteins arising by chance.

10. Beyond the Reach of Chance

p 216 To get an idea of probabilistic resources, Dembski calculated 10⁸⁰ particles in observable universe, 10¹⁶ seconds since the big bang. Used Planck length and Planck time to assess total number of events at 10¹³⁹.

p 217 Other estimates of number of chances, but none renders plausible the chance construction of a 150 amino acid functional protein.

p 223 P T Mora's 1963 quote on insufficiency of the chance hypothesis.

p 224 More skepticism about the pre-biotic soup.

p 227 Interesting that de Duve dumps chance, but presumes a law-like inevitability of life "A string of improbable events - drawing the same lottery number twice, or the same bridge hand twice in a row - does not happen naturally. All of which lead me to conclude that life is an obligatory manifestation of matter, bound to arise where conditions are appropriate."

11. Self-Organization and Biochemical Predestination

p 229 Introduces Dean Kenyon, PhD Stanford, worked under Melvin Calvin who received the Nobel Prize for the discovery of the Calvin cycle.

p 230 1969 Kenyon & Steinman wrote book Biochemical Predestination. Best selling graduate-level text on origin of life in 70s and 80s. Promoted self-organization, an appeal to a kind of necessity. Took inspiration from Oparin.

p 234 In 1975 Kenyon began to doubt that self-organization could give rise to the information in DNA. Saw proteins as poor templates for the transfer of information.

p 237 Polanyi and a seminal article.

p 238 "Polanyi argued that even if living organisms function like machines, they cannot be fully explained by reference to the laws of physics and chemistry."

p 239 gives example of computer which cannot be reduced to its hardware components because of the programming and communication aspects. "Polanyi demonstrated that the same thing was true of living things. ... communication systems, like machines, defy reduction to physical and chemical law and by showing further that living organisms contain a communications system, namely, the gene-expression system in which DNA stores information for building proteins."

p 239 "Polanyi argued that, in the case of communications systems, the laws of physics and chemistry do not determine the arrangements of the characters that convey information. The laws of acoustics and the properties of air do not determine which sounds are conveyed by speakers of natural languages. Neither do the chemical properties of ink determine the arrangements of letters on a printed page. Instead, the laws of physics and chemistry allow a vast array of possible sequences of sounds, characters, or symbols in any code or language. Which sequence of characters is used to convey a message is not determined by physical law, but by the choice of the users of the communications system in accord with the established conventions fo vocabulary and grammar .."

p 240 "DNA base sequencing cannot be explained by lower-level chemical laws or properties any more than the information in a newspaper headline can be explained by reference to the chemical properties of ink. Nor can the conventions of the genetic code that determine the assignments between nucleotide triplets and amino acids during translation be explained in this manner. Instead, the genetic code functions as a higher-level constraint distinct from the laws fo physics and chemistry, much like a grammatical convention in a human language.

p 240 "DNA's capacity to convey information actually requires a freedom from chemical determinism or constraint, in particular, in the arrangement of the nucleotide bases. He argued that if the bonding properties fo nucleotides determined their arrangement, the capacity of DNA to convey information would be destroyed."

p 240 Polyanyi "Whatever may be the origin of a DNA configuration, it can function as a code only if its order is not due to the forces of potential energy. It must be as physically indeterminate as the sequence of words is on a printed page."

p 241 "To say that the information in DNA does not reduce to or derive from physical and chemical forces implied that the information in DNA did not originate from such forces. If so, then there was nothing Kenyon could do to salvage his self-organizational model. "

p 242 Figure 11.2 illustrates the key fact that there are no chemical bonds between the bases along the longitudinal axis in the center of the helix. "Yet it is precisely along this axis of the DNA molecule tht the genetic information is stored."

p 244 "In sum, two features of DNA ensure that "self-organizing" bonding affinities cannot explain the specific arrangement of nucleotide bases in the molecule: (1) There are no bonds between bases along the information-bearing axis of the molecule and (2) there are no differential affinities between the backbone and the specific bases that could account for variations in sequence."

p 244 Used a set of magnetic letters on a magnetized board to illustrate the fact that the laws of attraction that held the letters on the board did nothing to limit his rearrangement of the letters.

p 246 The mystery of the code. Information in DNA and code or translation system imbedded in tRNA molecule with its associated synthetase protein.

p 247 Diagram of tRNA emphasizing that there is no direct chemical interaction between the end with the anticodon and the end to which the amino acid bonds.

p 248 17 variant genetic codes

p 248 20 aminoacyl-tRNA synthetases

p 250 "MIT philosopher Robert Stalnaker puts it, information content 'requires contingency'"

12. Thinking Outside the Bonds

p 254 Prigogine Nobel Prize for showing that energy into non-equilibrium systems could lead to self-organization. But their self-organization led to a type of order, not the unconstrained framework that can handle information.

p 257 Tornado through junkyard assembling a 747 story attributed to Fred Hoyle.

p 260 Kauffman model. Self-organization from smaller molecules.

p 267 Discusses the displacement problem - just shifting the origin of information problem backward.

13. Chance and Necessity, or the Cat in the Hat Comes Back

p 271 Using the Cat In the Hat as a metaphor - after covering the house with pink, the Cat employs a "voom!" to make all the pink disappear. Meyer says "Origin of life researchers have been looking for their 'Voom' for over 50 years" to clean up the problem of the origin of the information.

p 272-275 General discussion of Oparin's original model, his revised model presuming natural selection acting on molecules, Muller's criticism, Pattee's assertion that natural selection works only on cells that already have DNA, de Duves' assertion that prebiotic natural selection fails because they "need information which implies they have to presuppose what is to be explained in the first place."(275)

p 276 John von Neumann's mathematical approach 1966 showed "that any system capable of self-replication would require subsystems that were functionally equivalent to the information storage, replicating, and processing systems found in extant cells."

p 277 Quastler 1964 DNA first scenario for the origin of information in polynucleotides as an "accidental choice remembered".

p 279 Eigen, a Nobel laureate German biophysicist, produced the hypercycle model of multiple simpler molecules in a grouping which led to progressive development. John Maynard Smith, Freeman Dyson, Robert Shapiro criticized on the basis of higher likelihood of degradation, lack of an error-free replication system, and the "error catastrophe".

p 281-290 Computer algorithms Ev and Avida, both of which have an information problem.

p 290 The conservation of information.

14. The RNA World

p296 Pegs RNA world efforts in mid 80s.

p297 Interaction with Kenneth Miller.

p 298 Brief statement of the RNA world scenario

p 299 Sketch of RNA world scenario.

1. RNA building blocks are hard to synthesize and easy to destroy
2. Ribozymes are poor substitutes for proteins
3. An RNA-based translation and coding system is implausible
4. The RNA world doesn't explain the origin of genetic information
5. Ribozyme engineering does not simulate undirected chemical evolution.

p321 "An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going." Crick, "Life Itself", Simon and Schuster, 1981, p88.

p 322 "Theories relying on necessity awaited the discovery of an oxymoron, namely, 'a law capable of producing information' - a regularity that could generate specified irregularity"

15. The Best Explanation

p325 Proposes a rubric for approaching the best explanation.

• Is the proposed cause known to be adequate?
• Is there evidence that the cause was in fact present?
• Which hypothesis best explains the evidence?

He proposes this in a setting of comparing historical science to the activity of a detective trying to solve a crime mystery.

p 326 The effect to be characterized is the origin of complex specified information in DNA. This characterization must distinguish

• "information content" from mere "information-carrying capacity".
• "specified information" from mere "Shannon information"
• "specified complexity" from mere "complexity"

p 330ff His reasons for choosing ID as the "inference to the best explanation"

1. No other causally adequate explanations
2. Experimental evidence confirms causal adequacy of ID
3. ID is the only known cause of specified information.

16. Another Road to Rome

p 351 Dembski's method of design inference, referencing "The Design Inference".

p 355 Diagram of the process "from chance elimination to intelligent design".

p 356 The importance of independent tests to distinguish lawlike necessity from intelligent design. Recognizing patterns from an independent realm of experience.

p 357 "Dembski theorized that we reliably detect intelligent activity when we observe events that are both improbable and specified, where events are specified when they conform to a particular kind of pattern, namely, a pattern that can be recognized independently of the occurrence of the event in question."

p 359 Recognizing Mt. Rushmore as intelligent design as example of independent criteria.

p 359 Two types of specifications: when we recognize a

• "complex pattern of events matches or conforms to a pattern that we know from something else we have witnessed."
• "complex pattern of events has a functional significance because of some functional knowledge that we possess"

p 362 Diagram of using the functional criterion.

p 366 Diagram of applying the functional criterion to DNA

17. But Does It Explain?

p 373 Uses some hypothetical cave markings which point to communication and therefore to an intelligent source.

p 374 "The markings reveal a sophisticated system for conveying information, and the only known cause for such a thing is intelligence - conscious rational activity. "

p 374 He uses this setting to outline the various objections to the intelligent design hypothesis:

• based on ignorance of any known natural process capable of producing such information
• since we don't know of any non-human examples of intelligent activity, we can't say anything about the origin
• can't invoke intelligent cause, because that would imply an intelligent cause of that cause and therefore infinite regress

p 375 Responds to the charge that ID is an "argument from ignorance", a kind of argument that says cause X cannot produce result E, therefore cause Y produces result E without giving positive evidence that cause Y can in fact produce result E.

p 376 A more specific statement of the charge: "They claim that design advocates use our present ignorance of any natural or material cause of specified information as the sole basis for inferring and intelligent cause for the origin of biological information."

p 377 Argues that ID is not an "argument from ignorance" but rather an "inference to the best explanation" based on the best available information. Refers back to Ch 7 and Ch 15 for his steps in building the basis for this position. A key sentence is "Instead, it asserts the superior explanatory power of a proposed cause based upon its proven - its known - causal adequacy and based upon a lack of demonstrated efficacy among the competing proposed causes."

p 379-381 Argues that we should not be deterred from an inference to the best explanation by the possibility that future investigations might prove it wrong. "As physicists John Barrow and Frank Tipler note, to criticize design arguments, as Hume did, simply because they assume the uniformity and normative character of natural law cuts just as deeply against 'the rational basis of any form of scientific inquiry.'"

p 383 Takes on Hume's argument against design.

p 389 Takes on Dawkins' central argument in "The God Delusion" that seeks to invalidate a proposed cause because it has an infinite regress of prior causes.

p 391 After blasting Dawkins' infinite regress arguments for a couple of pages, this is an interesting discussion of mind with the suggestion that in the materialist's view it is "either an illusion or a temporary 'epiphenomenon' that has no ability to affect the material world."

p 393 Continues the discussion of Dawkins down to the point of the basic idealism vs materialism dichotomy with the question "What is a better candidate to be the first cause of this phenomenon: mind or matter?"

p 395 Very interesting conclusion to this chapter. In making the comparison to SETI's efforts to detect intelligent signals, he concludes "few would question the premise of the search, namely, that we should treat information-rich radio signals as a signature of intelligence. The discovery of specified information alone would suggest antecedent intelligence as the best explanation for the origin of that information, without independent evidence of designing agents existing in the relevant places or times , remote though they might be. Nor when we detect intelligence in more ordinary situations do we worry about making arguments from ignorance, or generating infinite regresses, or running afoul of Hume's critique of analogical reasoning."

18. But Is It Science?

p 396 Criticizes Judge Jones of the Dover case which turned on the notion that ID "is not science" but which took a good bit of the statement in the opinion from the ACLU's brief. Reflected "an entrenched view common not only among members of the media, but within the scientific establishment at large."

p 397 Story of Dean Kenyon's treatment at San Francisco State University.

p 399 About the charge that ID is "not science"... "The argument shifts the focus from an interesting question of truth to a trivial question of definition."

p 399-402 Discusses the difficulty of defining "science" and the great variety of practices used in different kinds of scientific investigations. Classifies ID with the historical sciences.

p 403 Defense of ID as a historically scientific theory.

1. The case for ID is based on empirical evidence
2. Advocates of ID use established scientific methods
3. ID is a testable theory
   • p 406 Includes discussion of junk DNA
4. The case for ID exemplifies historical scientific reasoning
5. ID addresses a specific question in evolutionary biology
6. ID is supported by peer-reviewed scientific literature

19. Sauce for the Goose

p 416 Takes on Michael Ruse, whom he characterizes as "an archnemesis of young-earth creationism".

p Ruse's testimony in the Arkansas creationism suit brought by the ACLU was based on his definition of science:

1. guided by natural law
2. explanatory by reference to natural law
3. testable against the empirical world
4. tentative in its conclusions
5. falsifiable

p 417 Discusses "defeaters" in the form of "demarcation issues" which seek to exclude ID as science.

p 418 Summarizes Ruse's arguments - science must explain by reference to natural law, and ID suggests intelligent agents break natural laws, intelligent designer violates the rules of science

p 419 Meyer's response, intelligent designer does not necessarily break the rules of nature, alter the conditions under which the laws act, natural laws describe but do not explain at times, works against Darwinism as much as against ID, historical science often explains in terms of events rather than the underlying laws.

p 422 Argues against the demarcation gambit, claiming that any definition of science so restrictive as to eliminate ID would also eliminate its materialistic competitors, whereas broadening the definition of science to include them would also include ID.

p 423 Deals with the "unobservable agent" charge, and on p424 has a good discussion of how the same charge could be leveled against the whole Darwinian framework.

p 428 Discusses the objections of Pennock and Miller

p 433 In discussing "How Dover Was Decided" he has an interesting discussion of methodological naturalism. I was a little surprised at how strongly he came down against methodological naturalism - I see it as the mindset in most science experiments, recognizing that if non-naturalistic causes are present in a laboratory experiment, the experiment is not going to elucidate them. But I suppose it is because that was the foil used in the Dover case.

20. Why It Matters

p 439 Tells of his experience on a talk show in the Dover frenzy in 2005, where he was pressed hard to call ID a religion and to assert that he was religious in order to justify dismissing ID as science.

p 440 The first time in the book that he states that he is a Christian.

p 441 Asserts that ID is not religion. Concedes that it has implications for metaphysical questions, but so do its materialistic counterparts.

p 443 Not either-or: theories of origins can be both scientific and religious.

p 444 "Contrary to the 'just the facts' stereotype of science, many scientific theories have larger ideological, metaphysical, or religious implications. Origins theories in particular have such implications since they make claims about the causes that brought life or humankind or the universe into existence."

p 445 George Gaylord Simpson "Man is the result of a purposeless and materialistic process that did not have him in mind. He was not planned. "

p 444-446 A major barrage making the point that many evolutionary biologists have made categorical statements in favor of blind materialism and antagonistic to faith that are blatantly philosophical and not scientific.

p 447 Again owns up to being a Christian theist, in the context of saying that does not validate or invalidate ID.

p 450 Quote of Bertrand Russell to point up the hopelessness of materialism.

p 450-451 His response to the hopelessness and pessimism of Russell and the philosophical materialists. He doesn't try to persuade the reader to agree with the details of his personal faith, but to take hope from the evidence for intelligent design to ask the deeper questions about purpose and not conclude with Russell that they are not worth asking.

p 450 "Though the theory of intelligent design does not identify the agent responsible for the information - the signature - in the cell, it does affirm that the ultimate cause of life is personal. By personal I mean a self-conscious, deliberative mind in possession of thoughts, will, and intentions. Only persons have such minds and only minds of this kind can create complex specified information. If we know anything we know this. Thus, while the theory of intelligent design does not prove the existence of God or answer all of our existential questions, it does reestablish the conditions of a meaningful 'search for meaning.' The case for intelligent design challenges the premise of the materialist credo and holds out the possibility of reversing the philosophy of despair that flows from it. Life is the product of mind; it was intended, purposed, 'previsioned.' Hence, there may be a reality behind matter that is worth investigating. "

p 451 The feeling of this discussion is that of a stubborn resistance to someone telling you that there is nothing to investigate past materialism and defining all questions of purpose as being out of bounds in science.

p 451 After discussing the deeper philosophical questions that men ask, and have always asked, he summarizes with: "What excites me about intelligent design and the compelling evidence now on display in its favor is not that the theory answers these questions, but instead that it provides a reason for thinking that they are once again worth asking."

p 451 "chance and necessity", happenstance and law, won't do it, because they fail to explain the existence of complex specified information.

p 452 After pointing to obvious examples of inferring mind from the objects created by man, he summarizes. "But to detect the presence of mind, to detect the activity of intelligence in the echo of its effects, requires a mode of reasoning - indeed a form of knowledge - that science, or at least official biology, has long excluded. If living things - things that we manifestly did not design ourselves - bear the hallmarks of design, if they exhibit a signature that would lead us to recognize intelligent activity in any other realm of experience, then perhaps it is time to rehabilitate this lost way of knowing and to rekindle our wonder in the intelligibility and design of nature that first inspired the scientific revolution. "

Epilogue: A Living Science

p 453 Comments that ID is often dismissed as lacking utility for setting a research agenda.

p 454 Comments on Philip Kitcher's "Living With Darwin" . Detailed comments but bottom line is that ID is declared to be a "dead science" because it cannot explain junk DNA.

p 456 Argues that we know a lot about what to expect from "chance & natural selection" and intelligently designed processes, so that there can be some discrimination about which is the better explanation when new information is found.

p 459 Much has been learned from the new genomics in the last 15 years, and he argues that it is more consistent with expectations from ID than from strictly chance processes.

1. The concentration of information in DNA
   • Genetic signal dwarfs noise in junk dna, contrary to what chance would lead one to expect.
   • Distributed data sets in genes, with same segment used for different proteins.
   • Organized like heirarchical file folders
   • Multilevel coding, codes within codes.
   • Functional logic and design patterns similar to a computer operating system.
2. Heirarchial arrangement, optimized for access and retrieval
   • Different kinds of genes and gene groupings are arranged in non-random groupings.
   • Gene folders themselves are grouped in superfolders with LINES, SINES, according to function
   • Superfolders grouped into "isochores"
3. Informational context - genomic and extragenomic
   • Context-dependent modularity indicates a larger informational context than just the DNA
   • Evolutionary models are bottom-up, but function of many genes and proteins appears to be top-down.
   • 474 'body-plan' information appears to be outside DNA

Appendix A: Some Predictions of Intelligent Design

p 485 Possible role of the centrioles in cancer, discussion of centrioles.

p 492 Comments about Behe and Miller and the bacterial flagellum

Appendix B: Multiverse Cosmology and the Origin of Life

p 499 Koonin and a proposal of chance-based life development with an infinite number of universes.

p 500 Discussion of cosmological ideas: homogeneity, flatness, inflation

p 502 Vilenken and endless bubble universes, "many worlds in one". Koonin's chance development of life follows Vilenken's model.