1.  Assigned reading: chapter 2 of text

2. Natural vs. Supernatural explanations  All societies have or had creation myths that invoke the action of supernatural forces to explain the origins of life and the history of the earth.  Ideas invoking the role of gods and divine actions are supernatural (i.e. beyond nature).

3. In 1859 Charles Darwin published “On the origin of species.”

4. Darwin and the origin  In “The Origin” Darwin presented a detailed strongly, supported argument, that life had originated naturally and that over time organisms had evolved by means of a mechanism he called natural selection.  How did this transition from supernatural to a natural explanation for the diversity of life occur?

5. Development of Natural Philosophy  The early Greeks were among the first to develop natural philosophy to explain the world.  Natural philosophers aimed to develop sets of physical laws to explain the world around them and how it worked.

6. Methodological Naturalism  The Greeks’ approach of trying to explain the world using only natural phenomena is sometimes called Methodological Naturalism.  Methodological because this strategy provides a procedure or method for scientifically explaining the world and natural because it focused on nature.

7. Anaximander’s cosmology  An early example of methodological naturalism is Anaximander’s cosmology (p. 31 of text). He proposed the earth is a disk surrounded by huge wheels on which the moon and sun rotate around the earth.  His explanation is mechanistic because it invokes a natural (although incorrect) mechanism to explain the presence and motion of celestial objects.

8. Aristotle (384-322 BC)  Aristotle was the first Greek philosopher to emphasize observation and the testing of ideas to explain those observations (i.e., hypothesis testing).  Supernatural explanations are inherently untestable.  The Greeks also emphasized the importance of logic in moving from observations to general principles.

9. An ancient and ever-changing earth  That the earth is old and undergoes constant change was not widely accepted until recently in western thought.  Most of Darwin’s contemporaries considered the earth to be young (only thousands of years old rather than 4.6 billion).

10. An ancient and ever-changing earth  By time Darwin was a young man the idea that the Earth was young was being challenged.  Opposition based on principle of Uniformitarianism.  Idea that geological processes happening today are the same as have operated in the past.

11. An ancient and ever-changing earth  Uniformitarianism contrasted with Catastrophism which proposed that current geological formations had resulted from catastrophic events (such as biblical flood) which occurred on scale unknown today.  Uniformitarianism first proposed by James Hutton and championed by Charles Lyell in his books Principles of Geology.

12. An ancient and ever-changing earth  Hutton and Lyell inferred the Earth must be very old based on measurements of rates of ongoing rock forming processes (e.g. deposition of mud and sand).  These developments in geology focused Darwin on the potential importance of gradual change in shaping structures.

13. The intellectual environment  In the early 1800’s the world was primed for a comprehensive theory of evolution to be developed.  Multiple people put forward the idea that evolution had taken place, what was lacking was a workable mechanism.  One influential scientist is this period was Jean-Baptiste Lamarck.

14. Jean-Baptiste Lamarck  In 1809 Lamarck suggested that organisms descended gradually from older less complex species. He considered lineages of organisms had an inherent tendency to become more complex over time and transformed over time.  His primary mechanism was called the Inheritance of Acquired Characteristics (IAC).

15. Inheritance of Acquired Characteritics  IAC suggested that traits an organism acquired during its life could be passed on to its offspring. By this process of transformation lineages would change over time.  For example, a giraffe stretching its neck during its life would become slightly longer necked and pass this slightly longer neck to its offspring.

16. Inheritance of Acquired Characteristics  Lamarck’s ideas were widely discussed and influential in his time as there was no understanding of how heredity occurs.  Obviously, Lamarck’s ideas about mechanism of evolution contradict current biological knowledge.  Information flows from DNA to phenotype not in the reverse direction

17. Charles Darwin (1809-1882)  Was the son of a wealthy doctor, but he himself dropped out of medical school.  Studied theology at university, but was more interested in natural history.  After graduation signed on as the Captain’s companion for a round the world voyage aboard the surveying ship HMS Beagle.

18. The Beagle Voyage  On the voyage Darwin read Lyell’s Principles of Geology and was greatly influenced by Lyell’s emphasis of two major points.  1. The Earth is very old.  2. Geological features we see around us can be explained by the action of the slow, gradual processes we can observe every day (e.g. the eroding of rock by waves and wind; the slow deposition of sediment).

19. The Beagle Voyage  Darwin was Captain Fitzroy’s companion during the voyage (1831-1836).  The Beagle mapped the coast of South America and circled the globe.  Visited South America, Australia, Pacific Islands and South Africa.  Famously visited the Galapagos Islands a group of volcanic (hence quite young islands) off the coast of Ecuador.

21. Galapagos Giant Tortoise Unique animals on Galapagos include giant tortoises, marine iguanas, and Darwin’s finches.

23. Sharp- beaked Ground Finch

24. The Beagle Voyage  On the voyage Darwin noted many things that were puzzling from the point of view of a creationist explanation for the diversity of life.

25. What Darwin observed  1. South American fossils resembled living animals. . Parts of the world with similar climates and habitats  2. Parts of the world with similar climates and habitats (e.g. Australia, South America) populated by very different organisms (e.g. Australia, South America) populated by very different organisms.  3. Plants and animals on each continent are distinctive.  4. Many species on oceanic islands are found only there (endemic).  5. Endemic species on islands closely resemble species on adjacent mainland.

26. What Darwin observed  These observations taken together don’t make sense if organisms are specially created. Why should similar habitats in different parts of the world have completely different faunas? Why should remote islands have unique faunas that differ from, but resemble, those on adjacent land masses?  Togetherthese observations suggested to Darwin that species change over time i.e., evolution occurs.  Together these observations suggested to Darwin that species change over time i.e., evolution occurs.

27. Natural Selection  Convinced by the time he returned to England that evolution occurs, Darwin needed a mechanism to explain how evolution happens.  His mechanism is the process of natural selection.

28. Natural selection  An important event in developing natural selection was when Darwin read Thomas Malthus’ “Essay on population.”  Malthus emphasized that the reproductive potential of animals and the rate at which populations could increase in size was much greater than the rate at which food resources might increase.

29. Natural selection  Darwin realized that most organisms that were born could not survive to reproduce. There just were not enough resources.  Thus, there must be “a struggle for existence” in which only some organisms survived to reproduce and the remainder did not.

30. Natural Selection  Darwin knew that individuals in populations are different from each other (there is variation).  His insight was in realizing that if success in surviving and reproducing was related to variation (i.e. to the traits individuals possessed) that beneficial traits would become more common and populations would change over time.

31. Darwinian Natural Selection Artificial Selection  Artificial Selection. Humans have selectively bred for desirable traits in domestic animals and plants for millenia.  Process has produced our crop plants, garden plants, pets, and domestic animals.  Darwin closely studied pigeon breeding.

32. Pigeon breeding  Pigeon fanciers by selecting for particular traits among Common Rock Doves by breeding from only certain individuals had been able to produce a huge variety of different breeds of domestic pigeons.  These varieties were so different in appearance that they would have been considered to be different species if encountered in the wild.

33. Common Rock Dove http://ibc.lynxeds.com/photo/rock-dove- columba-livia/perched-my-balcony

34. Hungarian Buga www.PigeonBreed.com

35. Holle Cropper www.PigeonBreed.com

36. Pomeranian Pouter www.PigeonBreed.com

37. Frillback Crested www.PigeonBreed.com

38. Evolution by Natural Selection  Darwin envisaged a process similar to artificial selection that had produced organisms we see today. He called it Natural Selection.  Instead of humans deciding who would breed, nature would.

39.  Darwin proposed evolution was the inevitable outcome of 4 postulates:   1. There is variation in populations. Individuals within populations differ.  2. Variation is heritable. Evolution by Natural Selection

40.  3. In every generation some organisms are more successful at surviving and reproducing than other. There is differential reproductive success.  4. Survival and reproduction are not random, but are related to variation among individuals. Organisms with best characteristics are ‘naturally selected.’

41. Evolution by Natural Selection  If these 4 postulates are true then the population will change from one generation to the next.  Evolution will occur.

42. Darwin and Wallace  Darwin realized his ideas would be controversial and delayed publishing them for fear of the backlash that would result. Instead he continued to gather evidence to support his ideas.  It was not until he received a letter from Alfred Russel Wallace in 1858 in which Wallace outlined the idea of natural selection was Darwin finally prompted to publish his work.

43. Darwin and Wallace  1858 Charles Darwin and Alfred Russel Wallace jointly proposed natural selection as the mechanism of evolution in a paper presented to the Royal Society.  1859 Origin of Species published

44. The Modern Synthesis The Modern Synthesis  Idea of evolution accepted rapidly  Lack of understanding of heredity and population genetics prevented natural selection being accepted as mechanism until 1930’s.  “Modern Synthesis” of population genetics and natural selection to explain gradual evolution, speciation, and macroevolution.

45. Evidence for Evolution  Evidence of change in organisms over time  Living species: evolution of beak length in soapberry bugs. evolution of beak length in soapberry bugs. Soapberry bugs use long beak to penetrate seeds in fruits and eat them. Soapberry bugs use long beak to penetrate seeds in fruits and eat them. Native host plant is balloon vine which has thick fruits. Native host plant is balloon vine which has thick fruits.

46. Evolution of Soapberry Bugs  In 1926 flat-podded Golden rain tree introduced to Florida. Has thin fruits.  Today soapberry bugs feeding on Golden rain trees have much shorter beaks than those living on balloon vines.

47. Comparison of beak lengths in areas with and without golden rain trees

48. Data from museum specimens documents change in beak length over time.

49. Vestigial organs  Many organisms possess rudimentary or functionless versions of body parts that function in close relatives/ancestors  Cave populations of Mexican tetra fish have eye sockets but no eyes.  Kiwis have tiny, stubby wings  Boas have tiny remnant hind limbs

50. Human vestigial structures  Coccyx: vestigial tailbone at base of spine.  Arrector pili muscle at base of hair follicles makes hair stand up.  Appendix: reduced in size. Used in digestion of cellulose in herbivores e.g. rabbits.

51. Vestigial developmental trait  Adult chickens: three bones in forefoot (wing), four in hindfoot.  However, digit 5 appears briefly during embryonic development before disappearing.

52. Molecular vestigial traits  Human genome contains large numbers of pseudogenes that do not code for functional RNA or proteins.  E.g. several pseudogenes of hemoglobin. May be as many as 6,000 pseudogenes in human genome.

53. Fossil evidence of evolution  Clear from fossil evidence that many (in fact almost all that have ever existed) species have become extinct.

54. Fossil evidence of evolution  Law of Succession: Fossil and living organisms in same area related to each other and differ from organisms in other areas.  E.g. Australia filled with marsupials, fossils are of similar marsupial forms.  South America contains both fossil and living armadillos

55. Extinct glyptodont (2,000 kg) resembles modern-day armadillo (2 kg).

56. Fossil evidence of evolution  Transitional forms  If fossil organisms ancestral to modern organisms then there should be transitional fossils that show characteristics intermediate between the older and more recent groups.

57. Archaeopteryx  Archaeopteryx the oldest known fossil bird (name means “ancient wing) has mix of reptilian and avian features.  Reptilian: long tail, teeth, long clawed fingers  Avian: feathers, ribs with uncinate processes, avian shoulder girdle.

58. Archaeopteryx (oldest known fossil bird) Jurassic 180mya

60. Evidence of common ancestry. Homologous structures  Structures constructed from the same basic components.  Forelimbs of human, mole, horse, dolphin and bat constructed from same bones, but used in radically different ways.  Makes no sense if organisms specially created, but logical if organisms share a common ancestor.

61. FIG 2.11 Homologous structures (i.e. derived from a common ancestor). Even though the forelimbs have evolved to carry out very different tasks they are all constructed from the same bones.

62. Developmental Homology  Embryos of diverse array of vertebrates very similar in early development

64.  Not all similarities due to homology.  Streamlined shapes of fish and whale not a result of common ancestry but convergent evolution. FIG 2.12.

65. Molecular Homology  With few exceptions all organisms use same genetic code.  Genetic flaws shared by species.

66. Molecular Homology  Chromosome 17 in humans PMP22 gene has duplicate sequence of DNA (CMT1A repeat) on either side of it.  Result of duplication and insertion of DNA.  Occasionally causes inaccurate crossing over during meiosis.

67. Molecular Homology  Humans share CMT1A repeat with bonobos and chimpanzees, but not gorillas, orang-utans or other primates.  Suggests CMT1A derived from common ancestor of bonobos, chimps and humans.

68. Other evidence for evolution  Jerry-rigged structures e.g. The Panda’s thumb.

70. Panda’s Thumb  In Pandas, a wrist bone modified as tool to strip bamboo.  Panda’s “thumb” not very efficient solution to Bamboo-stripping problem.  Natural selection must work with the material available.  “Thumb” implies pandas not designed, but evolved.

71. Other evidence for evolution  Adaptive radiation and clusters of species.  Many remote islands populated by diverse, but closely related species.

72. Adaptive radiation  Ancestral colonist arrives on island.  Shortage of resident species means many niches are unfilled.  Ancestral species give rise to many species that occupy unfilled niches.

73. Adaptive radiation  Examples: Darwin’s finches on Galapagos Island, Drosophila on Hawaiian Islands.

74. Darwin’s Finches  On Galapagos Islands there are 13 species of anatomically very different, but closely related species of finch.  They differ greatly in beak size and diet having evolved very different lifestyles.

76. Hawaiian Drosophila  More than 25% of the world’s 1,250 species of Drosophila fruit flies found on Hawaiian Islands.  Few insect competitors so Drosophila have diversified to fill large number of niches.

78. If faunas created, why are woodpecker finches, but not woodpeckers found on the Galapagos?

79. Creationism and “Intelligent Design”  The idea of evolution has been harshly criticized by religious fundamentalists since the publication of the Origin in 1859.  This has been especially true in the U.S.  Repeatedly, believers in the literal truth of the Bible have attempted to have alternatives to evolution (i.e., creationism) taught in the public schools and to have the teaching of evolution either banned or restricted.

80. Creationism and “Intelligent Design”  The U.S. Supreme Court has prohibited the teaching of creationism in public schools as a violation of the establishment of religion clause of the Constitution.  Latest attempt to insert creationism into schools is the idea of “Intelligent Design.”

81. Creationism and “Intelligent Design”  The concept of “intelligent design” is outlined most clearly in Michael Behe’s book “Darwin’s Black Box.”  The central idea in “intelligent design” is that some structures in the body are so complex that they could not possibly have evolved by a gradual process of natural selection. These structures are said to “irreducibly complex.”

82. Creationism and “Intelligent Design”  By “irreducibly complex” Behe means that a complex structure cannot be broken down into components that are themselves functional and that the structure must have come into existence in its complete form.

83. Creationism and “Intelligent Design”  If structures are “irreducibly complex” Behe claims that they cannot have evolved. Thus, their existence implies they must have been created by a designer (i.e. God, although the designer is not explicitly referred to as such).

84. Creationism and “Intelligent Design”  Behe’s main examples are various biochemical pathways in the body, the blood clotting system, and structures such as the bacterial flagellum.

85. Creationism and “Intelligent Design”  Since the publication of Behe’s book, it has been demonstrated repeatedly that things he has claimed to be irreducibly complex are not in fact so.  E.g. the flagellum in eel sperm lacks several of the components found in other flagella, yet the flagellum functions well.

86. Creationism and “Intelligent Design”  The blood clotting system in dolphins lacks at least one component that the human system has, yet it too is functional.  In addition, plausible gradual scenarios for the evolution of biochemical pathways including the Kreb’s cycle have been documented.

87. Evolution of complex structures  The evolution of complex structures, such as the eye, appears difficult, but natural selection achieves this by the slow accumulation of minor improvements from one generation to the next.

88. Evolution of complex structures  Each step on the evolutionary pathway from a simple light sensing cell to a complex eye capable of focusing and producing color vision, must be beneficial to the organism that possess it and a slight improvement on earlier versions.  It is not necessary for a structure to be perfect or even very good it just needs to be better than the alternatives to be favored by selection.

89. Variation in mollusc eyes from (a) pigment spot to (b) pigment cup to (c) simple optic cup in abalone to (d) complex lensed eyes in a marine snail and octopus.

90. Evolution of complex structures  Computer simulations suggest that eyes can evolve easily and in nature eyes have evolved independently more than 40 times.