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EVIDENCE
EVIDENCE
Structural and Molecular Evidence of
           Shared Ancestry
PREDICTIONS



Pattern of order that should be observed in fossil record

Homologous structures and shared body plans

Genomic evidence (The Modern Synthesis)
Structural Evidence
Homologous Structures




  Bat Wing   Whale Flipper
The Mechanism of Inheritance:
Family History as Recorded in the
Genome
Genetic Evidence for Shared
         Ancestry
 Junk DNA
Genetic Evidence for Shared
         Ancestry
 Junk DNA

 Fossil DNA
Genetic Evidence for Shared
         Ancestry
 Junk DNA

 Fossil DNA

 Endogenous retroviruses
Genetic Evidence for Shared
         Ancestry
 Junk DNA

 Fossil DNA

 Endogenous retroviruses

 Gene functional redundancy
14
Modern Humans and
           Neanderthals

• Genomes of modern humans and
  Neanderthals are 99.5-percent identical
Mutations:
  A Rich Source Of
Variance But Can They
     Help Explain
     Complexity?
We Are All Mutants!
We Are All Mutants!
Evolution of the Eye
Nature Has a Wild Card Up
        Her Sleeve
Impossibility of building new complex
features if only one gene is available to
perform a vital function
Functionally Redundant Genes - Nature
deals multiple hands to each genome.
Developmental Regulatory Genes
             Human accelerated regions (HARs)

• 49 segments of the human genome there are 18 base
  pair mutations different between humans and
  chimpanzees.
Developmental Regulatory Genes
               Human accelerated regions (HARs)

• 49 segments of the human genome there are 18 base
    pair mutations different between humans and
    chimpanzees.
•   HAR1 (most mutated in humans) is an 118 base pair
    stretch found on the long arm of chromosome 20
Developmental Regulatory Genes
               Human accelerated regions (HARs)

• 49 segments of the human genome there are 18 base
    pair mutations different between humans and
    chimpanzees.
•   HAR1 (most mutated in humans) is an 118 base pair
    stretch found on the long arm of chromosome 20
•    The HAR1 sequence is found (and conserved) in
    chickens and chimpanzees but is not present in fish or
    frogs that have been studied.
Developmental Regulatory Genes
               Human accelerated regions (HARs)

• 49 segments of the human genome there are 18 base
    pair mutations different between humans and
    chimpanzees.
•   HAR1 (most mutated in humans) is an 118 base pair
    stretch found on the long arm of chromosome 20
•    The HAR1 sequence is found (and conserved) in
    chickens and chimpanzees but is not present in fish or
    frogs that have been studied.
•   These highly mutated areas have contributed to the
    development of human brain anatomy.
DARWIN’S WAY
Humility, Dignity, and Patience
Charles Darwin
February 12, 1809 – April 19, 1882
Charles Darwin
         February 12, 1809 – April 19, 1882




“It is an accursed evil to a man to become so absorbed in a subject
     as I am in mine.”
William Paley




Natural Theology; or, Evidences of the Existence and Attributes of the Deity 1802
28
Eye-openers

• Different types of people
Eye-openers

• Different types of people

• Earth Quake in Chile
Eye-openers

• Different types of people

• Earth Quake in Chile

• Tremendous varieties of species
Eye-openers

• Different types of people

• Earth Quake in Chile

• Tremendous varieties of species

• Island ecology
Eye-openers

• Different types of people

• Earth Quake in Chile

• Tremendous varieties of species

• Island ecology

• Species traits coadapted to ecology
After the Beagle
After the Beagle
• 8 books on a variety
  of topics
After the Beagle
• 8 books on a variety
  of topics
• Many scientific
  articles
After the Beagle
• 8 books on a variety
  of topics
• Many scientific
  articles
• Network of
  colleagues
After the Beagle
• 8 books on a variety
  of topics
• Many scientific
  articles
• Network of
  colleagues
• Reef geology of
  islands
After the Beagle
• 8 books on a variety
  of topics
• Many scientific
  articles
• Network of
  colleagues
• Reef geology of
  islands
• Barnacle project
After the Beagle
• 8 books on a variety   • Home Experiments
  of topics               • Dispersal
• Many scientific          • Pigeons
  articles                • Embryology
• Network of
  colleagues
• Reef geology of
  islands
• Barnacle project
After the Beagle
• 8 books on a variety   • Home Experiments
  of topics               • Dispersal
• Many scientific          • Pigeons
  articles                • Embryology
                         • Personal tragedies
• Network of
                           and challenges
  colleagues
                          • Health
• Reef geology of         • Deaths of Annie,
  islands                   Charles, & Mary
• Barnacle project          Eleanor
Species
• Tremendous variety


• Geographical organization of species


• Extinction
Seeds
Seeds
Seeds
Malthus’s Principle
Malthus’s Principle
Malthus’s Principle
Overview of the Principles of
     Natural Selection
Overview of the Principles of
                        Natural Selection
Fact 1
Potential Exponential
Increase of Population



Fact 2
Steady-state stability
of populations




Fact 3
Limitation of resources
Overview of the Principles of
                        Natural Selection
Fact 1
Potential Exponential
Increase of Population



Fact 2                    Inference 1
Steady-state stability    Struggle among
of populations            individuals to survive




Fact 3                    Fact 4
Limitation of resources   Uniqueness of
                          individual



                          Fact 5
                          Heritability of
                          Individual variation
Overview of the Principles of
                        Natural Selection
Fact 1
Potential Exponential
Increase of Population



Fact 2                    Inference 1
Steady-state stability    Struggle among
of populations            individuals to survive




Fact 3                    Fact 4                   Inference 2
Limitation of resources   Uniqueness of            Differential Survival
                          individual



                          Fact 5
                          Heritability of
                          Individual variation
Overview of the Principles of
                        Natural Selection
Fact 1
Potential Exponential
Increase of Population



Fact 2                    Inference 1
Steady-state stability    Struggle among
of populations            individuals to survive




Fact 3                    Fact 4                   Inference 2             Inference 3
Limitation of resources   Uniqueness of            Differential Survival   Gradual Evolution
                          individual



                          Fact 5
                          Heritability of
                          Individual variation
Alfred Wallace
Alfred Wallace
“This view may be true, and yet it may never
be capable of full proof.”
“Well, it is a beginning, and that is
something…..”
Consequences of Darwin’s Theory
Fundamental Unifying
        Law of Biology
n   “All biology is evolutionary biology.”
n   Ecology
n   Population Genetics
n   Comparative Anatomy and Physiology
Medicine
Influences of Darwin’s
       Theory
n Behavior Genetics - Francis Galton
 n The heritability of behavioral
    characteristics
n Freud

n William   James
Sociobiology
n   E.O Wilson

     n   Sociobiology is a synthesis
          of scientific disciplines that
          attempts to explain social
          behavior in all species by
          considering the
          evolutionary advantages
          the behaviors may have.
Behaviorism




n B.F.   Skinner - Selection by Consequences
Cognitive Psychology
DARWIN’S DANGEROUS IDEA


The Classifier’s Conundrum: How to group life forms that
range in similarity across a broad continuum.
DARWIN’S DANGEROUS IDEA


The Classifier’s Conundrum: How to group life forms that
range in similarity across a broad continuum.

Start with a small number of self-replicating systems that
produce imperfect copies resulting in variable traits. Some
replicators gain a reproductive advantage and the traits
possessed by the most successful reproducers will, over
generations, numerically outpace traits of the less adapted
forms. Divergent lineages will naturally emerge when
interbreeding is prohibited.
There is grandeur in this view of life ….
IMPLICATIONS


Biology is a natural science
IMPLICATIONS


Biology is a natural science


Effects in nature have antecedent
causes in nature
On Theological and Metaphysical
           Questions




“I cannot pretend to throw the least light on
         such abstruse problems.”
Evolution: “The Controversy”
Evolution: “The Controversy”
Francis Bacon (1561-1626)




Induction as the Path to Reliable Knowledge
“A wise man proportions his belief to the
evidence.”
                                    David Hume
Reading God’s Thoughts
William Paley

 • Natural Theology
 • Watchmaker Analogy
 • We Recognize Design
    Intuitively



Natural Theology; or, Evidences of the Existence and Attributes of the Deity 1802
William Paley

 • Natural Theology
 • Watchmaker Analogy
 • We Recognize Design
    Intuitively



Natural Theology; or, Evidences of the Existence and Attributes of the Deity 1802
William Paley

 • Natural Theology
 • Watchmaker Analogy




Natural Theology; or, Evidences of the Existence and Attributes of the Deity 1802
William Paley

 • Natural Theology
 • Watchmaker Analogy
 • We Recognize Design
    Intuitively



Natural Theology; or, Evidences of the Existence and Attributes of the Deity 1802
William Behe
• Natural Theology - a.k.a.,
  Intelligent Design

• Irreducible Complexity
  a.k.a., Watchmaker
  Analogy

• We Recognize Design
  Intuitively
William Behe
• Natural Theology - a.k.a.,
  Intelligent Design

• Irreducible Complexity
  a.k.a., Watchmaker
  Analogy

• We Recognize Design
  Intuitively
William Behe
• Natural Theology - a.k.a.,
  Intelligent Design

• Irreducible Complexity
  a.k.a., Watchmaker
  Analogy
William Behe
• Natural Theology - a.k.a.,
  Intelligent Design

• Irreducible Complexity
  a.k.a., Watchmaker
  Analogy

• We Recognize Design
  Intuitively
Are We Really Good at
 Recognizing Design?
Recognizing Intelligence
• As good as we think we are?
Recognizing Intelligence
• As good as we think we are?
• What does Recognition mean?
 • Memory - To Discriminate familiar from unfamiliar
   • Does what I am seeing here resemble other
      designed things in memory?
 • False recognition, overgeneralization, & cognitive
    bias
Recognizing Intelligence
• As good as we think we are?
• What does Recognition mean?
 • Memory - To Discriminate familiar from unfamiliar
   • Does what I am seeing here resemble other
      designed things in memory?
 • False recognition, overgeneralization, & cognitive
    bias
• Later: What is intelligence?
“Evolution’s Nightmare”
“Evolution’s Nightmare”
“Evolution’s Nightmare”
“Salmonella's Nightmare”
“Salmonella's Nightmare”
Interdependent Irreducible Complexity
Interdependent Irreducible Complexity
Tales of Even Tinier Tails
Tales of Even Tinier Tails
Thinking Non-Egocentrically
 Proliferation rate and time
 Variation
 Struggle
 Selection
 Once you get to the single cell stage, you
 are more than halfway to us.
Intelligent Design: What is
        Intelligence?
The Mouse Trap’s Nightmare
The Mouse Trap’s Nightmare
The Mouse Trap’s Nightmare
What you see before you now is a
 state of transition, not The END
               GOAL.

•The struggle continues
•Everything is changing right now and, as
 long as life continues, always will be.
The Property Owner’s Nightmare
The Property Owner’s Nightmare
The Property Owner’s Nightmare
The Property Owner’s Nightmare
Incredulity
Incredulity Creates Mental
                       Blind Spots
"... there are many reasons why you might not understand an explanation of a scientific
     theory ... Finally, there is this possibility: after I tell you something, you just can't
     believe it. You can't accept it. You don't like it. A little screen comes down and you
     don't listen anymore. I'm going to describe to you how Nature is - and if you don't
     like it, that's going to get in the way of your understanding it. It's a problem that
     scientists have learned to deal with: They've learned to realize that whether they
     like a theory or they don't like a theory is not the essential question. Rather, it is
     whether or not the theory gives predictions that agree with experiment. It is not a
     question of whether a theory is philosophically delightful, or easy to understand, or
     perfectly reasonable from the point of view of common sense. A scientific theory
     describes Nature as absurd from the point of view of common sense. And it agrees
     fully with experiment. So I hope you can accept Nature as She is - absurd.


   Please don't turn yourself off because you can't believe Nature is so strange. Just
   hear me all out, and I hope you'll be as delighted as I am when we're through. "


- Richard P. Feynman (1918-1988)
'It is interesting to contemplate a tangled bank, clothed with
many plants of many kinds, with birds singing on the bushes,
with various insects flitting about, and with worms crawling
through the damp earth, and to reflect that these elaborately
constructed forms, so different from each other, and
dependent on each other in so complex a manner, have all
been produced by laws acting around us.'
	 	 	 	 	 	 	 	 	 	 Charles Darwin
There is grandeur in this view of life ….
Evolution part 2

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Evolution part 2

  • 2. EVIDENCE Structural and Molecular Evidence of Shared Ancestry
  • 3. PREDICTIONS Pattern of order that should be observed in fossil record Homologous structures and shared body plans Genomic evidence (The Modern Synthesis)
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  • 7. Homologous Structures Bat Wing Whale Flipper
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  • 16. The Mechanism of Inheritance: Family History as Recorded in the Genome
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  • 23. Genetic Evidence for Shared Ancestry Junk DNA
  • 24. Genetic Evidence for Shared Ancestry Junk DNA Fossil DNA
  • 25. Genetic Evidence for Shared Ancestry Junk DNA Fossil DNA Endogenous retroviruses
  • 26. Genetic Evidence for Shared Ancestry Junk DNA Fossil DNA Endogenous retroviruses Gene functional redundancy
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  • 30. Modern Humans and Neanderthals • Genomes of modern humans and Neanderthals are 99.5-percent identical
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  • 32. Mutations: A Rich Source Of Variance But Can They Help Explain Complexity?
  • 33. We Are All Mutants!
  • 34. We Are All Mutants!
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  • 37. Nature Has a Wild Card Up Her Sleeve Impossibility of building new complex features if only one gene is available to perform a vital function Functionally Redundant Genes - Nature deals multiple hands to each genome.
  • 38. Developmental Regulatory Genes Human accelerated regions (HARs) • 49 segments of the human genome there are 18 base pair mutations different between humans and chimpanzees.
  • 39. Developmental Regulatory Genes Human accelerated regions (HARs) • 49 segments of the human genome there are 18 base pair mutations different between humans and chimpanzees. • HAR1 (most mutated in humans) is an 118 base pair stretch found on the long arm of chromosome 20
  • 40. Developmental Regulatory Genes Human accelerated regions (HARs) • 49 segments of the human genome there are 18 base pair mutations different between humans and chimpanzees. • HAR1 (most mutated in humans) is an 118 base pair stretch found on the long arm of chromosome 20 • The HAR1 sequence is found (and conserved) in chickens and chimpanzees but is not present in fish or frogs that have been studied.
  • 41. Developmental Regulatory Genes Human accelerated regions (HARs) • 49 segments of the human genome there are 18 base pair mutations different between humans and chimpanzees. • HAR1 (most mutated in humans) is an 118 base pair stretch found on the long arm of chromosome 20 • The HAR1 sequence is found (and conserved) in chickens and chimpanzees but is not present in fish or frogs that have been studied. • These highly mutated areas have contributed to the development of human brain anatomy.
  • 43. Charles Darwin February 12, 1809 – April 19, 1882
  • 44. Charles Darwin February 12, 1809 – April 19, 1882 “It is an accursed evil to a man to become so absorbed in a subject as I am in mine.”
  • 45. William Paley Natural Theology; or, Evidences of the Existence and Attributes of the Deity 1802
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  • 58. Eye-openers • Different types of people • Earth Quake in Chile
  • 59. Eye-openers • Different types of people • Earth Quake in Chile • Tremendous varieties of species
  • 60. Eye-openers • Different types of people • Earth Quake in Chile • Tremendous varieties of species • Island ecology
  • 61. Eye-openers • Different types of people • Earth Quake in Chile • Tremendous varieties of species • Island ecology • Species traits coadapted to ecology
  • 63. After the Beagle • 8 books on a variety of topics
  • 64. After the Beagle • 8 books on a variety of topics • Many scientific articles
  • 65. After the Beagle • 8 books on a variety of topics • Many scientific articles • Network of colleagues
  • 66. After the Beagle • 8 books on a variety of topics • Many scientific articles • Network of colleagues • Reef geology of islands
  • 67. After the Beagle • 8 books on a variety of topics • Many scientific articles • Network of colleagues • Reef geology of islands • Barnacle project
  • 68. After the Beagle • 8 books on a variety • Home Experiments of topics • Dispersal • Many scientific • Pigeons articles • Embryology • Network of colleagues • Reef geology of islands • Barnacle project
  • 69. After the Beagle • 8 books on a variety • Home Experiments of topics • Dispersal • Many scientific • Pigeons articles • Embryology • Personal tragedies • Network of and challenges colleagues • Health • Reef geology of • Deaths of Annie, islands Charles, & Mary • Barnacle project Eleanor
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  • 76. Species • Tremendous variety • Geographical organization of species • Extinction
  • 77. Seeds
  • 78. Seeds
  • 79. Seeds
  • 83. Overview of the Principles of Natural Selection
  • 84. Overview of the Principles of Natural Selection Fact 1 Potential Exponential Increase of Population Fact 2 Steady-state stability of populations Fact 3 Limitation of resources
  • 85. Overview of the Principles of Natural Selection Fact 1 Potential Exponential Increase of Population Fact 2 Inference 1 Steady-state stability Struggle among of populations individuals to survive Fact 3 Fact 4 Limitation of resources Uniqueness of individual Fact 5 Heritability of Individual variation
  • 86. Overview of the Principles of Natural Selection Fact 1 Potential Exponential Increase of Population Fact 2 Inference 1 Steady-state stability Struggle among of populations individuals to survive Fact 3 Fact 4 Inference 2 Limitation of resources Uniqueness of Differential Survival individual Fact 5 Heritability of Individual variation
  • 87. Overview of the Principles of Natural Selection Fact 1 Potential Exponential Increase of Population Fact 2 Inference 1 Steady-state stability Struggle among of populations individuals to survive Fact 3 Fact 4 Inference 2 Inference 3 Limitation of resources Uniqueness of Differential Survival Gradual Evolution individual Fact 5 Heritability of Individual variation
  • 90. “This view may be true, and yet it may never be capable of full proof.”
  • 91. “Well, it is a beginning, and that is something…..”
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  • 95. Fundamental Unifying Law of Biology n “All biology is evolutionary biology.” n Ecology n Population Genetics n Comparative Anatomy and Physiology
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  • 106. Influences of Darwin’s Theory n Behavior Genetics - Francis Galton n The heritability of behavioral characteristics n Freud n William James
  • 107. Sociobiology n E.O Wilson n Sociobiology is a synthesis of scientific disciplines that attempts to explain social behavior in all species by considering the evolutionary advantages the behaviors may have.
  • 108. Behaviorism n B.F. Skinner - Selection by Consequences
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  • 112. DARWIN’S DANGEROUS IDEA The Classifier’s Conundrum: How to group life forms that range in similarity across a broad continuum.
  • 113. DARWIN’S DANGEROUS IDEA The Classifier’s Conundrum: How to group life forms that range in similarity across a broad continuum. Start with a small number of self-replicating systems that produce imperfect copies resulting in variable traits. Some replicators gain a reproductive advantage and the traits possessed by the most successful reproducers will, over generations, numerically outpace traits of the less adapted forms. Divergent lineages will naturally emerge when interbreeding is prohibited.
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  • 115. There is grandeur in this view of life ….
  • 116. IMPLICATIONS Biology is a natural science
  • 117. IMPLICATIONS Biology is a natural science Effects in nature have antecedent causes in nature
  • 118. On Theological and Metaphysical Questions “I cannot pretend to throw the least light on such abstruse problems.”
  • 121. Francis Bacon (1561-1626) Induction as the Path to Reliable Knowledge
  • 122. “A wise man proportions his belief to the evidence.” David Hume
  • 124. William Paley • Natural Theology • Watchmaker Analogy • We Recognize Design Intuitively Natural Theology; or, Evidences of the Existence and Attributes of the Deity 1802
  • 125. William Paley • Natural Theology • Watchmaker Analogy • We Recognize Design Intuitively Natural Theology; or, Evidences of the Existence and Attributes of the Deity 1802
  • 126. William Paley • Natural Theology • Watchmaker Analogy Natural Theology; or, Evidences of the Existence and Attributes of the Deity 1802
  • 127. William Paley • Natural Theology • Watchmaker Analogy • We Recognize Design Intuitively Natural Theology; or, Evidences of the Existence and Attributes of the Deity 1802
  • 128. William Behe • Natural Theology - a.k.a., Intelligent Design • Irreducible Complexity a.k.a., Watchmaker Analogy • We Recognize Design Intuitively
  • 129. William Behe • Natural Theology - a.k.a., Intelligent Design • Irreducible Complexity a.k.a., Watchmaker Analogy • We Recognize Design Intuitively
  • 130. William Behe • Natural Theology - a.k.a., Intelligent Design • Irreducible Complexity a.k.a., Watchmaker Analogy
  • 131. William Behe • Natural Theology - a.k.a., Intelligent Design • Irreducible Complexity a.k.a., Watchmaker Analogy • We Recognize Design Intuitively
  • 132. Are We Really Good at Recognizing Design?
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  • 135. Recognizing Intelligence • As good as we think we are?
  • 136. Recognizing Intelligence • As good as we think we are? • What does Recognition mean? • Memory - To Discriminate familiar from unfamiliar • Does what I am seeing here resemble other designed things in memory? • False recognition, overgeneralization, & cognitive bias
  • 137. Recognizing Intelligence • As good as we think we are? • What does Recognition mean? • Memory - To Discriminate familiar from unfamiliar • Does what I am seeing here resemble other designed things in memory? • False recognition, overgeneralization, & cognitive bias • Later: What is intelligence?
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  • 150. Tales of Even Tinier Tails
  • 151. Tales of Even Tinier Tails
  • 152. Thinking Non-Egocentrically Proliferation rate and time Variation Struggle Selection Once you get to the single cell stage, you are more than halfway to us.
  • 153. Intelligent Design: What is Intelligence?
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  • 160. The Mouse Trap’s Nightmare
  • 161. The Mouse Trap’s Nightmare
  • 162. The Mouse Trap’s Nightmare
  • 163. What you see before you now is a state of transition, not The END GOAL. •The struggle continues •Everything is changing right now and, as long as life continues, always will be.
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  • 171. Incredulity Creates Mental Blind Spots "... there are many reasons why you might not understand an explanation of a scientific theory ... Finally, there is this possibility: after I tell you something, you just can't believe it. You can't accept it. You don't like it. A little screen comes down and you don't listen anymore. I'm going to describe to you how Nature is - and if you don't like it, that's going to get in the way of your understanding it. It's a problem that scientists have learned to deal with: They've learned to realize that whether they like a theory or they don't like a theory is not the essential question. Rather, it is whether or not the theory gives predictions that agree with experiment. It is not a question of whether a theory is philosophically delightful, or easy to understand, or perfectly reasonable from the point of view of common sense. A scientific theory describes Nature as absurd from the point of view of common sense. And it agrees fully with experiment. So I hope you can accept Nature as She is - absurd. Please don't turn yourself off because you can't believe Nature is so strange. Just hear me all out, and I hope you'll be as delighted as I am when we're through. " - Richard P. Feynman (1918-1988)
  • 172. 'It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us.' Charles Darwin
  • 173. There is grandeur in this view of life ….