1. 1 - Darwin's Apple
   1. Purpose of the book is to answer question whether or not God and evolution can coexist
   2. Darwin's arguments in The Origins of Species
      1. Tremendous range of variation exists in nature among plants and animals
      2. All living things are engaged in a struggle for existense
      3. Combination of struggle and variation results in natural selection
   3. The dangerous idea of Darwin is that it gave atheism a rational basis to dismiss God
2. 2 - Eden's Children
   1. In scientific world, belief in God is considered superstition and non-typical among scientists
   2. Scientific Materialism as an assumption and a method can be applied to both distant and ancient objects
   3. Natural history's 2 important features
      1. Emergence of a new group is not the end but the beginning of a new round of evolutionary change
      2. The first members of a major group have characteristics that betray their ancestry
   4. Patters in place and time
      1. Evolution, as a process of descent with modification, links the present to the past
      2. Divergence of species over time can be shown using the fossil record be found in the present-day world around us
   5. Can evolution produce new structures and morphologies using just the mechanism of variation and natural selection, even over million of years? Yes, it can.
      1. Genes encode proteins
      2. Proteins, workhorses of the call, can do everything required to produce an organism
      3. Therefore, mutations and sporadic changes in the genes can change any characteristics of the organism
   6. Can mutations produce beneficial variations for natural selection to work upon? Doesn't they just mess things up?
      1. Bacteria and antibiotics struggle is one of good examples because resistance to antibiotics doesn't preexist in bacteria
   7. Evolution 3-part mechanism as a tool in a laboratory
      1. Mutation
      2. Variation
      3. Natural selection
   8. Evolution is both a fact and a theory
      1. First meaning of evolution as a history connecting past to the present is fact
      2. Second meaning of evolution as a mechanism of change is a theory
   9. The heart of clash between evolution and religion is that they are both a story of origins
3. 3 - God The Charlatan
   1. Anti-evolution strategies and arguments
      1. Evolution might have produced every species except for us
      2. Trying to find something small that must have been only done by Creator, e.g. the biochemical machinery of the living cell
      3. Evolution can't produce change to originate new species
      4. Reject everything that supports evolution
   2. Young earth creationists' claims about the age of the Earth are false
      1. Don't stand against radioisotop methods and nuclids half-lifes
      2. Don't stand against the light coming from stars that are several billion years far from Earth
      3. Therefore, YECs explain that God created everything at once 10,000 years ago but made it appear as if the Earth was 4.5 billion years old!
4. 4 - God The Magician
   1. Controversy around Darwinian Phyletic Gradualism vs. Punctuated Equilibrium
      1. Evolution theory is based on assumption there is gradual change between species, so called phyletic gradualism
      2. According to Stephen J. Gould, fossil record doesn't match Darwinian expected pattern of gradual transformation
      3. So new species might originate in an instantaneous burst of rapid, horizontal genetic change
      4. As such, Creationists claim that microevolution (changes within species) may work, but macroevolution (radical changes required for appearance of new species) doesn't -- therefore intelligent design was at work
   2. Responses to Intelligent Design claims
      1. Why did the designer create species living on islands that resemble those from the nearest mainland?
      2. Why did the designer create all those elephants in between from the original one to the latest ones? Why were the intermediate drafts needed?
      3. Why did the designer create species that were so imperfect that went extinct?
      4. Why did the designer create imperfect organs and bodies?
      5. Why aren't new species designed nowadays?
   3. The "missing" mechanism of evolution is mutation producing variation, upon which natural selection works
   4. Macro and microevolution
      1. Species differ by total sum of differences in their genes
      2. The structural change rate achieved in experiments is enough or even exceeds the pace required to support transitions documented in the the fossil record
      3. Therefore, microevolution processes are sufficient to account for even the fastest transitions documented in the fossil record
   5. The only difference between Punctuated Equlibrium and Darwinian Gradualism is an arbitrary choice of timescale over which to display the data
5. 5 - God The Mechanic
   1. Michael Behe's argument goes like this: Irreducible complexity, e.g., complex biochemical systems (cells), can't be produced by evolution; hence, a designer is required to explain the origin of complex structures.
      1. This argument is an argument from design, and it is quite old and was addressed even by Darwin, using an eye evolving as an example.
      2. It's possible to display how complex organs like eyes or echolocation organs have evolved from simpler forms.
      3. Cell organisms proved to keep working and transforming even when one or more key components were removed in a laboratory experiment.
   2. Can Darwinian evolution explain the development of complex biochemical machines?
      1. First, evolution can fashion new proteins
      2. In one example, reenginnering of an existing protein in a system led to emerging a new complex system (lactose utulization in bacteria) by using mutation and natural selection
      3. It was shown that complex machine appears first as functional units which then are borrowed for other purposes
      4. Evolution produces a biochemical complex structure by modifying existing structures and proteins to produce new organs, new functions, and new biochemistry.
         1. E.g., Krebs cycle of metabolism
         2. and blood clotting
      5. Evolution duplicates and then remodels existing genes to produce novel functions.
   3. If God did work to produce complex systems, he must have done it in a particular time in natural history, meaning that some late complex systems like blood clotting were present at creation but not "turned on" until the time came.
6. 6 - The Gods of Disbelief
   1. There is the hostility prevailing among scientists towards the spiritual culture of religion itself.
   2. Anti-religious claims from Dawkins, Dennet, and others explain the world with explicitly materialistic and naturalistic rules, by which they completely dismiss God, moral principles of good and evil, and the purpose.
   3. Darwinism is dangerous because of the threat it poses to nonmaterialist value systems
      1. Some scientists tried to extrapolate the evolution theory to explain the social relationships and the society fabric (e.g., social Darwinism, sociobiology)
      2. Human mind, any trait, and any behavior are product of natural selection.
      3. Religious belief is also result of the evolution forces because it gives groups advantage.
      4. Evolution has abandoned purpose of life
   4. Science is considered the only source of truth
   5. All that causes reaction in religion circles which in its turn leads them to dismiss science evidence. Hence conflict between religion and science.
   6. Is it possible that evolution materialism is compatible with a religious world of value and meaning?
7. 7 - Beyond Materialism
   1. Science has shown that nature itself is where we can find the explanation for how things work; the only job left for God was a creator of the world and its laws
   2. Problems with deism
      1. Passive, impersonal God that set the universe in motion and then retired doesn't make sense from religious point of view
      2. It is not compatible with dynamic reality of the universe
   3. Classical physics based on Newtonian laws tended to think of physical events as governed by fixed laws
      1. If this were true, every future state of the universe would be predictable (in principle) from the current state
      2. The role of God was finished at the moment the world came into being
   4. Quantum revolution destroyed the Newtonian certainty that physical events are governed by fixed laws
      1. Predictable causality was broken down
      2. Uncertainties are inherent to quantum theory
      3. There is a pattern to these uncertanties, though, at higher level
   5. The indeterminate nature of quantum theory means that the details of the future are not strictly determined by present reality; therefore, clockwork assumptions of extreme materialism are wrong
   6. The fact that mutation and variation are inherently unpredictable means that the course of evolution is, too.
      1. That's why we can't surely say why some some species succeeded while others perished
      2. Any replay of life's tape would lead evolution down a pathway different from the road actually taken
   7. Quantum physics tells us that absolute knowledge, complete understanding of absolute reality will never be ours.
   8. Unpredictability of at the atomic level doesn't mean randomness, though
8. 8 - The Road Back Home
   1. Evolution threatens, first of all, the traditional view of God, described by the great Western monotheistic religions
   2. Core beliefs that share the three great Western religions
      1. Primacy of God in the universe
      2. We exist as the direct result of God's will
      3. God has revealed Himself to us
      4. There is a spiritual reality that surpasses the physical reality of nature.
      5. God is active in the world in a personal sense
   3. What caused the big bang?
      1. Either there is a God and the big bang dates the moment of His creation of the universe
      2. or there is a tendency of matter to create itself from nothingness
   4. Anthropic Principle
      1. Physical constants of the universe - gravity, nuclear force, electromagnetism - were set up in a way that made our existence possible
      2. Dennett refers to multiplying parallel universes and varying physical constants as an explanation of this principle; but we will never be able to find evidence for any of those parallel universes
   5. Compatibility of evolution indeterminacy and divine purpose
      1. Problem: Doesn't randomness of evolution rule out any notion of divine purpose? Or did God rig the evolutionary purpose to produce us in His image?
      2. In traditional religion view, chance is not only consistent with the idea of God, but it is the only way in which a truly independent physical reality can exist
      3. The role of chance in human history is also consistent with the Western conception of God
      4. If we can see God's will in the flow of history and our daily lives, we can certainly see it in the natural history
      5. Therefore, natural laws and chance may equally be instruments of God's intentions
   6. There is notion that evolution, making nature self-sufficient, leaves nothing for God to do
      1. The indeterminate nature of quantum events allows God to influence events in ways that are profound but scientifically undetectable to us
         1. Appearance of mutations
         2. Activation of individual neurons in the brain
         3. Survival of individual cells and organisms
      2. God transcends time so he could easily alter the space-time continuum
      3. God is able to influence the thoughts and actions of individual human beings
      4. Therefore, evolution doesn't weaken the power of God; all it does is to extend natural laws to the novelty of life and to its changes over time
   7. Why would God have bothered with a process that took billions of years if His purpose was to produce human beings?
      1. Evolution is a natural process, and natural processes are undirected
      2. We can't know every details of God's actions.
      3. For eternal being like God, time is of different scale
   8. Evolution history is cruel one, full of struggle and extinction -- so how can it be compatible with a loving God?
      1. Cruelty is relative
      2. The reality of life itself is cruel, so evolution just reflects the objective reality of nature
      3. There is also strong presence of altruistic behaviors and cooperation in nature
      4. The Creator fashioned a self-sufficient world in which matter became the basis of life but the hard determinism doesn't apply due to quantum indeterminacy
         1. So the world is independent and people have free will to choose good or evil
         2. The ultimate purpose of the work of God, though, may never be understood by the mind of man
9. 9 - Finding Darwin's God
   1. There is neither logical nor theological basis for excluding God's use of natural processes to originate species
      1. Religious people trying to refute evolution by referring to lack of scientific understanding of some processes in fact show atheists how to disprove the existence of God by showing that evolution works
      2. Neither the self-sufficiency of nature nor the reality of evil in the world mean God is absent
   2. Faith and Reason
      1. Should play complementary, not conflicting, roles in our struggle to understand the world around us
      2. Science can't assign either meaning or purpose to the world
      3. So our human tendencies to assign meaning and value must transcend science, and ultimately must come outside of it
   3. The issue of historic inevitability
      1. We like to think that evolution's goal was to produce us
      2. But mankind's appearance on this planet was not predetermined
         1. "In a thousand branching pathways, how can we be sure that one of them, historically, unavoidably, would lead for sure to us?"
         2. "What if the comet had missed, and what if out ancestors, not the dinosaurs, turned out to be the ones driven to extinction?"
         3. "Rewind the tape, let it run again, and events might come out differently at every run."
      3. No God would have used such an undetermined process to fashion His prize creatures?
         1. Variability of evolution could lead to human beings appearance at some point anyway - more millions of waiting wouldn't be an issue for eternal God
         2. Another group of animals could have evolved to self-awareness
         3. God who used such a process was clearly even more clever than a designer who had to do it all personally involved, and hence is more worthy of praise and worship
      4. Perceived lack of inevitability doesn't mean that historical contingencies are incompatible with a divine will
         1. Compare to contingencies of human history
         2. Also, contingencies of families producing our lives
         3. The alternative - a strictly determined chain of events - would require a strictly determined physical world, in which we would have no free will
   4. The issue of evil and bad things happening in the world: infanticide, natural disasters, famine, war, etc.
      1. He allows such things because He has made us material creatures, dependent upon the physical world
      2. Consequence of human freedom
      3. Instinctive behaviors, fashioned by evolution process, can get us into trouble sometimes, too
   5. Notion that tendency to believe in God could be explained by natural selection
      1. If religion is just another behavior product of evolution it cannot claim special authority in questions of morals, ethics, and values
      2. But science, being also a product of evolution, could be discredited by exactly the same logic
      3. The evolution helped to create our capacities for both faith and science. To maintain that either is thereby invalidated fails the test of logic
   6. Charles Darwin brought us closer to an understanding of God, and evolution is the key to understanding our relationship with God.