Intelligent Design or Evolution?
Stuart Pullen, Intelligent Design Press, Raleigh, NC, 2005.
Pullen has a degree in biochemistry from NC State and worked 5 years in that field. Graduate degree in electrical engineering from NC State.
Starts with Darwin's "absolutely break down" quote and goes on to state the two axioms that form the basis of science.
Accepts that the first is self-evident, but that the second is not and is testable. Jumps right in with the claim that science does not understand the origin of life, and that it is beyond chance. Quotes Orgel about not knowing how life originated, and is then critical of scientists who are so completely unwilling to abandon the naturalistic postulate that they must rely on a 'materialism of the gaps': "continue to claim that evolution is a proven fact when in reality they have only assumed that it is true.".
Argues that ID is based on the observable axiom, but does not assume the naturalistic axiom but brings logic to bear on it. "Intelligent design ...assumes that science will not solve the mystery of life's origin. In the 1950s, this would have been a dangerous assumption. ...Not only has science had ample time, but the solutions have become more elusive with time. " Claims creationism is different from ID in that it is based on the existence axiom. Existence axiom: God exists."
Finally says that this book will limit itself to the origin of life problem and not to the inference of design from the subsequent evolution of new classes of animals.
Introduction: Evolution vs Design
p 1 Science with naturalistic assumption is in trouble if a creator exists. ID can follow the evidence where it leads.
p 4 Proposes testing whether evolution is possible, and couches description in terms of "molecular information" and "molecular knowledge". Molecular information is information found in a gene today - an information science concept. Molecular knowledge is defined as the minimum amount of useful information required by a gene to have any function. This seems similar to Johnson's "prescriptive information" in Ch 6 of The Programming of Life.
p 8 Reviews chemical evolution and quotes the researchers who dismiss it as too improbable. Reviews Miller Urey and quotes others to support his judgment of "no way!".
p 11 Comes down to his definition of life:"Life is a system of chemicals possessing molecular knowledge and a mechanism to implement this knowledge in such a way that the system can survive long enough to replicate itself."
p 11 Characterizes simplest living system, or it could be said to be the characterization of what was necessary for life's origin:
This is a classic chicken-and-egg paradox because none of these critical functions can exist without the others.
14 Figure 2 is his summary of the history of evolution, in which he proposes design in four or five places.
I. The Evolution of Knowledge and Information
1. Information vs Knowledge
p 17 Discusses Shannon information. Goes through the reduction in uncertainty, the amount of knowledge gained for coin flip examples.
2. The Evolution of Molecular Knowledge
p 29 Example of information, step in molecular information defined as "infon"
p 31 Complex messages as non-ordered sequences. For proteins they are three-base-acid codons that specify amino acids.
3. Information Storage and Transfer in Life
p43 Bases A,T,G,C like a 4-sided coin. With three such coins, each carrying 2 bits of information, you have 6 bits or 64 possibilities.
p 46 Applies code to DNA
p 48 Useful diagram of DNA replication, DNA polymerase
p 49 The genetic code
p 51 Transcription
p 53 Translation
p 54 Ribosome and translation
p 57 Protein
p 58 Protein folding
p 60 Eukaryotes and prokaryotes - mitochondria in eukaryotes produce ATP but cell-membrane proteins create ATP in prokaryotes (bacteria).
4. Information and Knowledge in the Protein Insulin
p 63 Insulin A chain 21 amino acids, B chain 30 amino acids.
p 68 Protein common ancestor
p 69 Amino acid sequence in insulin useful as evidenced by fact that it is conserved in fish and mammals over 500 million years.
p 69 Conserved amino acids are a measure of information.
p 72 Information in insulin
p 79 Calc 189 bits of information and 127 bits of knowledge in insulin. Works on probability that insulin might have evolved - based on how big the steps are.
p 84 calc vs actual knowledge.
Part II: Chemical Evolution
5. Information & Knowledge before the Genetic Code
p 88 Previous inf and knowledge calcuations assumed genetic code existed. That is, it assumed that life already existed.
p 88 Information theory, not thermodynamics, used to asess information or knowledge in early proteins.
p 90 Some meteorites contain organic carbon, glycine and alanine common. Murchison meteorite had more than 50 non-biological amino acids. Four more aspartate, glutamate and sometimes serine and valine. Missing the other amino acids of life, i.e., 14 of 20 are missing.
p 91 Life has to exclude the non-biological amino acids,
p 92 Discussion of life protein formation, small odds even for non-specific protein.
p 93 Only 4 sequences out of 6 trillion of length 80 would bind with ATP.
p 94 Odds too poor for forming first enzyme by chance.
p 103 "Before life exists, chance will require an incredible number of tries to create knowledge -- Nature simply cannot accumulate enough tries to overcome the poor odds."
p 103 "Any scientist who believes that nature can create molecular knowledge before life exists is relying on faith to justify his opinion because the math just does not support this belief."
6. Introduction to Chemistry and Entropy
p104 "Entropy is often defined as disorder, but this definition is both misleading and incorrect. ... "It is simply a measure of uncertainty that must always increase with time."
p 105 Reviews basic quantum states, ways of representing molecules, review of basic physics of energy and work.
p 113 Graphical approach to representing microstates and entropy.
p 116 Repeats his bashing of disorder as measure of entropy, as chemists do. "Entropy is a measure of available microstates. .... Entropy can also be defined as a measure of uncertainty."
p 116 Second law of thermodynamics discussion
p 118 Applies his 2nd law to heat flow from a hot object to a cold with his stairstep model.
p 121 Discussing entropy and chemical reactions,
p 124 Entropy and energy diagram of forming water molecule.
p 127 Discusses open and closed systems, only closed being capable of chemical equilibrium. Then makes the case that the earth is an open system, so life has to exist far from equilibrium, chemically.
7. Implications of the Second Law
p 129 Life can exist far from equilibrium because of proteins, and in particular enzymes. Enzymes lower the activation energies for reactions that are essential to life.
p 131 Energy from ATP comes into the picture to make possible reactions that won't happen spontaneously.
p 132 Enzymes make possible conditional scenarios - make either A or B depending upon the need. Includes scenarios where multiple enzymes accomplish a result without additional energy.
p 134 Good page to read again and think about. "Hundreds of enzymes make it possible for life to exist in a state of very low entropy." Expresses doubt about origin-of-life scenarios that involve one self-replicating molecule - doesn't have the support staff of hundreds of enzymes, would have to be a perpetual motion machine.
p 134 Photosynthesis and animal metabolism as examples of life directing the flow of entropy.
p 135 "Without a team of enzymes working together with the common goal of self-replication, energy sources do not help. There is simply no way to harness the energy to achieve the goal."
p 136 Interesting discussion of fact that energy sources may actually hinder the origin of life by making it harder for systems to remain in a low entropy state. Abundant energy pushes them past the activation energy thresholds for reactions that would take them apart. And energy doesn't really directly contribute to a self-replicating system unless it knows how to use the energy.
p 136 "unless a self replicator possesses both the knowledge and ability to drive its replication with a plentiful energy source, the molecule's very existence violates the second law."
p 138 After non-equilibrium example of volcano, concludes "Under plausible prebiotic conditions, without molecular knowledge, it is very difficult (if not impossible) to create the complex chemicals used by life today."
p 140 Kauffman and Prigogine's book on chemical oscillators -
p 141 Important page on which he argues that the 2nd Law works against chemical evolution, but not against evolution of existing life by mutation and natural selection. Argues that those who think the 2nd Law acts against evolution are defining entropy as disorder, which is wrong. Defining it correctly as uncertainty removes the conflict.
8. The Structure of DNA, RNA, and Proteins
p 142 DNA Structure
p 144 RNA Structure
p 147 Main functional groups for organic chemistry
p 148 Structure of amino acids
p 149 Condensation reactions to form RNA DNA
p 150 A comment about chirality - L and D-alanine
p 151 Diagrams of 19 of the 20 biological amino acids
9. Prebiotic Synthesis of RNA, DNA, and Peptides
p 157 "Today the most popular theory involves a self-replicating pre-RNA molecule." after recounting failure of protein first and RNA.
p 162 Milller Urey
p 177 Having surveyed the options for the difficulty of developing the precursors for life, still doesn't think it happened without design. Another quote of Orgel.
10. Self Replicating Molecules and Systems
p180 RNA is good at storing information, proteins are good at regulating chemical reactions.
p181 Uses specific example to reinforce his conclusion that proteins do not self-replicate.
p 185 Joyce and Orgel describe difficulties of RNA self replication.
p 186 Another quote of Joyce and Orgel.
p 187 Knowledge to create a ribozyme. Concludes it couldn't happen primordially
11. The Myth of the Primordial Soup
p 196 "Many authors have criticized the concept of the soup. Its resilience in biology textbooks is quite amazing given that so few scientists believe that it ever existed."
p 196 collection of quotes
p 198 summary . Set of 6 difficulties that convince the author that "the first living thing was not a self replicating molecule, but rather a system of chemicals that contained the knowledge required to replicate and the ability to couple this replication systemto an energy source."
III The Evolution of the First Genes
12. Irreducible Complexity
p 200 Refers to Behe's "Darwin's Black Box" and describes the idea of irreducible complexity.
13: Nucleic Acid Synthesis: Adenine
p 203 Given the need for an energy source, discusses the need to find or make adenine and ATP.
p 205 Adenine need tips the balance toward more complex beginning since eleven enzymes are needed to synthesize adanine. List on pg 207.
p Calculates and discusses information needed for adenine synthesis.
p 213 "Adenine synthesis is perhaps the best example of an irreducibly complex system that can be found in life ..." This said after pointing out that the process doesn't work unless all 11 enzymes are present.
14: ATP Synthesis
p218 "All living things use ATP for energy. This means that the capability to synthesize ATP arose before the common ancestor diverged to create all the branches in the tree of life."
p221 builds models to show how oxidation powers things
p222 ATP created by proton gradients
p223 Details of ATP synthesis with G3PD enzyme.
p226 Molecular knowledge in this enzyme G3PD
p234 "ATP Synthase is an incredible enzyme. It is the smallest rotary motor in the world. The protons moved across the cell membrane by the electron donor/acceptor/dehydrogenase complex (figure 14.6) serve as the energy source for ATP synthase."
p235 Assesses knowledge in ATP Synthase
p236 Diagram of ATP Synthase
15. How Many Tries
Does the numbers and concludes that chance is not enough.
p 253 "Science can hide behind the naturalistic axiom for only so long. It does not have a good explanation for the origin of life, and it does not appear that one is forthcoming."
16. Evolution Since the Cambrian Explosion
p 254 Reviews commonality in DNA
p255 Discusses some things that might be explained by gene shuffline, so does not rule out evolutionary mechanism since the Cambrian explosion.
17. Alternatives to Intelligent Design
p 257 Examples to show that we need the observable axiom - alternatives to it are all too far-fetched.
p 258 Some possible variations built on the original design.
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