1. The Nature of Science and Evolution, and Evolution as Science
Chapter 1
The Nature of Science and Evolution, and Evolution as Science

2. Every Primitive Person Was a Biologist
For at least 2 million years of human prehistory

3. Agriculture Arose 13,000 to 15,000 Years Ago
From foraging to farming and in the late 20th century to factory food feeding

4. Impact of Agriculture Relatively permanent villages
Reduced contact with wildlife
Division of labor in the community
Shift to a hierarchical culture: headmen, chiefs, kings
Fewer individuals are experienced with or understand the natural world

5. Most Cultures Have Creation Myths
Atun, the Sun God (Egypt)
Unkulunkulu (Zulu)
Pan Gu (China)
Eden (Judeo-Christian)
Link for more
Creation Myths
Plumed Serpent God (Maya)

6. Judeo-Christian & Islamic Theory of Special Creation
All living “kinds” were created in a series of separate special supernatural creations during the six days of creation described in the Book of Genesis.
This creation preceded recorded history by only a few centuries at most.

7. Explanations based on authority or revelation

8. Two Pairs of Related Ancient World Views
Fixity of Species versus Evolution
And
A Young versus an Old Age for the Earth

9. Greek Natural Philosophers
Aristotle (384 – 322 B.C.E.)

10. Founders of Biological Thought
Anaximander ( B.C.E.) imagined a transition from fish to reptiles to mammals and birds
Empedocles ( B.C.E.) imagined a type of spontaneous generation from an assemblage of parts; only certain successful combinations survived
Heraclitus (5th century B.C.E.) imagined change as the fundamental principal of the universe

11. Aristotle (384 – 322 B.C.E.)
Aristotle carried out dissections of animals but not humans
Aristotle made collections of natural objects and creatures from the land and seas
He recognized different kinds of organisms and, for example, appreciated that sea mammals were distinct from fish as were sharks and rays
He studied fertilized chicken eggs and noted the sequence of organ development over time

12. Aristotle
Aristotle imagined the world could be understood by the combination of observation and reason
Aristotle’s own observations were quite good, but he was also naïve about accepting fabulous tales about nature from others
Aristotle wrote many books about many topics, most of which are now lost
Aristotle began as a gifted amateur but his legacy was as an unquestioned authority, holding back scientific progress for centuries

13. Some Mysteries Addressed by the Natural Philosophers
Cosmogenesis
Where did the universe come from?
Biogenesis
Where did life come from?
Evolution
How do you explain the diversity of life?
Humanity
What does it mean to be human?

14. Theory of Special Creation
James Usher/Ussher (1581 – 1656), Bishop of Armagh in Ireland, was one of the leading biblical scholars of the early seventeenth century.
Usher/Ussher is best known today for his detailed and influential chronology of the world, which he argued began in 4004 B.C.E. (on Sunday the 23rd of October to be precise!).

15. Ibn al-Haytham (“Alhacen”) (965 -~1040)
Alhacen, a father figure for Islamic science, made significant contributions optics, physics, anatomy, astronomy, engineering, mathematics, medicine, ophthalmology, philosophy, psychology, visual perception, and to science in general with his early application of the scientific method

16. St. Thomas Aquinas ( )
Scholasticism was the dominant form of theology and philosophy in the Latin West in the Middle Ages, particularly in the 12th, 13th, and 14th centuries.
It was both a method and a system which aimed to reconcile the Christian theology of the Church Fathers with the Greek philosophy of Aristotle and his commentators.
Aquinas was the foremost classical proponent of Natural Theology.

17. The Renaissance and the Great Voyages of Discovery
Christopher Columbus
( )

18. The Renaissance and the Great Voyages of Discovery
Ferdinand Magellan
( )

19. Sir Francis Bacon (1561 – 1626)
The modern scientific method crystallized in the 17th and 18th centuries
Francis Bacon outlined a new system of logic to improve on the old philosophical process of syllogism [deductive reasoning] in his work Novum Organum (1620) — a reference to Aristotle's Organon
The philosopher should instead proceed through inductive reasoning from fact to axiom to physical law

20. René Descartes ( )
In 1637, René Descartes established the framework for the scientific method's guiding principles in his treatise, Discourse on Method
A rationalist and mathematician, Descartes is remembered for “Cogito ergo sum” – [ “I think, therefore I am.” ]
Descartes studied animal physiology through vivisection, believing animals could not feel pain

21. The Emergence of Science From the Renaissance to the Age of Enlightenment
Observation of the Natural World
Collection of Data
Hypothesis Formation
Hypothesis Testing
experiment – experimental sciences
data comparison – historical sciences
Formation of Laws and Theories

22. Hypotheses for the Orbits of the Planets of our Solar System
Claudius Ptolemy proposed a geocentric universe ~150 A.D.
Nicolaus Copernicus ( ) shifted the paradigm to a heliocentric universe in the early 1500s

23. The Age of Reason
The Age of Reason or The Enlightenment arose during the 17th century (~ ~1800)
The Enlightenment gave birth to critical ideas, such as the centrality of freedom, democracy, and reason as primary values for society

24. The Enlightenment and More Great Voyages of Discovery
Captain James Cook
( )

25. The Age of Reason
The Enlightenment’s emphasis on rational thought and behavior led to the market mechanism and capitalism, the scientific method, religious tolerance, and the organization of states into self-governing republics through democratic means
This world view nurtured the birth of modern western science, in its descriptive, experimental and historical modes

26. Historical Sciences and Events in the Past
Careful observations and comparative studies are important tools in disciplines with historical elements, e.g.:
Astronomy
Geology
Paleontology
Evolution
(human history)

27. Evolution as a Science
Evolution has been criticized as unscientific because past events cannot be tested in the laboratory
Evolution that occurred in the past can be observed, documented, studied and tested, e.g.
the sequence of the fossil record
the adaptation of organisms to their environments
the geographic distribution of organisms
the comparison of DNA sequences

28. Evolution as “Only” a Theory
Evolution by means of Natural Selection (Darwinism) is among the foundational theories in science — along with the atomic theory, the theory of relativity, the universal theory of gravitation
A theory does not become a “fact”
A scientific theory organizes and explains collections of observations and facts!
Evolution as a process is a fact

29. Evolution: an Overview of the Term and the Concept
The word evolution had different meanings in the past compared to the way we use the word today
Evolution as the development of an individual
Evolution as the transformation of populations between generations
Transformation of populations (species) and descent with modification: 1859 – the present
Now we say individuals develop and populations evolve

30. Evolution as the Development of an Individual
Original 17th century definition
From the Latin evolutio, unrolling
18th century theory of preformation or encapsulation (emboitement)

31. Figure 03A: Adult humans as preformed within sperm, or within egg of the female

32. Evolution as the Transformation of Populations over Generations
In the 19th century, evolution came to mean transformation of a species or the transformation of the features of organisms

33. Evolutionary Predecessors
In the years before Darwin, many biologists attempted to solve the mystery of the “species question”
A species definition is still a contentious issue today

34. Carl von Linné = Carolus Linnaeus (1707—1778)
This Swedish biologist established the system still used today for naming organisms”: binomial nomenclature (genus + species)
He was also a Biblical creationist who initially abided by and promoted the view that species do not change
“God created, Linnaeus organized”

35. Historical Footnote
Although Linnaeus has been credited with inventing the use of binomials for species names, the idea did not originate with him
It originated with Gaspard Bauhin, a Swiss botanist, and was first used in 1623, in his Pinax Theatri Botanici
However, the idea of the binomial species name did not catch on then
Linnaeus actually reintroduced the use of binomials for species names and popularized it among naturalists
Solanum tuberosum G Bauhin (1591) 

36. Carolus Linnaeus
“The WORLD is the Almighty’s theater each object ought to be clearly grasped and clearly named, for if one neglects this, the great amount of things will necessary overwhelm us and, lacking a common language, all exchange of knowledge will be in vain.” (1753)

37. Georges Louis Leclerc, comte de Buffon (1707-1788)
Buffon is best remembered for his great work Histoire naturelle, générale et particulière (1749–1778: in 36 volumes, 8 additional volumes published after his death by Lacépède). It included everything known about the natural world up until that date.
Buffon noted that despite similar environments, different regions have distinct plants and animals, a concept later known as Buffon's Law, widely considered the first principle of Biogeography.

38. Georges Louis Leclerc, comte de Buffon (1707-1788)
Buffon drew the radical conclusion that species must have both "improved" and "degenerated" (evolved) after dispersing away from a center of creation
He also asserted that climate change must have facilitated the worldwide spread of species from their center of origin
Darwin later said that "the first author who in modern times has treated [evolution] in a scientific spirit was Buffon"

39. Jean-Baptiste de Lamarck (1744 - 1829)
J-B. de Lamarck worked most of his life at the Muséum d’Histoire Naturelle in Paris
His academic position gave him a chance to promote the idea that species change

40. Lamarck’s World View
Lamarck believed that all living things are endowed with a vital force that controls their development and functioning and enables them to overcome handicaps in the environment: Vitalism
Vitalism, in one form or another, goes back to the ancient Greek naturaI philosophers and continued to have advocates into the 19th and early 20th centuries

41. Scala Naturae
Lamarck and essentially all European naturalists before him accepted the idea of a scale or ladder of nature, scala naturae, which derives from Aristotle
Characters and species were viewed on a scale from primitive or lower to advanced or higher on the ladder of life
This progressive view of evolution remains in the mind of the general public but has been abandoned by science

42. Lamarck’s World View
In 1809, Lamarck published his four main principles:
The first organisms arose by abiogenesis
Organisms have an innate power to progress toward more complex and perfect forms (later termed orthogenesis)
Organisms have an inner disposition to adapt their characteristics in response to changes in the environment (an aspect of vitalism for Lamarck but similar to the modern term developmental adaptation)
Characters acquired during an individual’s life in response to changes in the environment were passed on to offspring (the inheritance of acquired traits)

43. Lamarckism: The Inheritance of Acquired Characteristics
blacksmiths
weavers
A regular and sustained program of weightlifting yields enlarged muscles, an immediate physiological response of muscles to the increased effort
However, these big muscles (somatic trait) remain with the individual that endured the regular exercises, and are not passed to their offspring
This is because the enlarged characteristics result from individual effort, not from an inheritable genetic change (genetic trait)

44. Giraffe Necks
Applied to giraffes, Lamarck’s view (top) would expect that in stretching for leaves giraffes lengthened their necks to reach tree-top vegetation, and this acquired characteristics was passed to offspring
In Darwin’s view (bottom), giraffes with long necks out competed those with short necks who died for lack of vital resources

45. Adaptation to Life in the Dark
Figure 02A: Surface-dwelling and cave fish
Figure 02C: Mexican axolotl
Figure 02B: Blind and non-pigmented (albino) cave-dwelling axolotl
How could an organism behave differently to acquire the loss of a pigment, even if not synthesizing it reduces energy costs?

46. William Paley ( )
Paley’s Natural Theology; or, Evidences of the Existence and Attributes of the Deity (1802) was a major influence on the young Charles Darwin

47. “Intelligent Design” Is Nothing New
(1986)

48. Contemporary Evolutionary Biology Responds to Intelligent Design
“All appearances to the contrary, the only watchmaker in nature is the blind forces of physics, albeit deployed in a very special way. A true watchmaker has foresight: he designs his cogs and springs, and plans their interconnections, with a future purpose in his mind's eye. Natural selection, the blind, unconscious automatic process which Darwin discovered, and which we now know is the explanation for the existence and apparently purposeful form of all life, has no purpose in mind. It has no mind and no mind's eye. It does not plan for the future. It has no vision, no foresight, no sight at all. If it can be said to play the role of watchmaker in nature, it is the blind watchmaker.” 
Richard Dawkins
( )
“The Bishop goes on to the human eye, asking rhetorically, and with the implication that there is no answer, 'How could an organ so complex evolve?' This is not an argument, it is simply an affirmation of incredulity.” ― Richard Dawkins, The Blind Watchmaker (1986)

49. The End of Vitalism
Friedrich Wöhler synthesizes urea by the reaction of potassium cyanate with ammonium sulfate
Although Wöhler was attempting to prepare ammonium cyanate, not urea
Thus, Wöhler inadvertently discredited Vitalism, the theory that the chemicals of living organisms are fundamentally different from inanimate matter, thereby starting the discipline of organic chemistry

50. Evolution as the Transformation of Populations between Generations
Robert Edmond Grant ( )
One of Darwin’s professors and mentors
Described the evolution of invertebrate groups in 1826, one of the first published uses of the word “evolution” for the transformation of organisms

51. Transformation and Descent with Modification: 1859–Now
From the publication of On the Origin of Species in 1859 until 1900, evolution was understood as:
the origination and transformation of species (one species of horse → another species of horse)
the transformation of major groups/lineages of organisms and the search for ancestors (invertebrates → vertebrates; fish → amphibians
the transformation of features such as jaws, limbs, kidneys, nervous systems within lineages of organisms

52. Transformation and Descent with Modification: 1859–Now
Figure 04: Progressive divergence within individual species
Darwin’s own diagram, from The Origin of Species (1859), illustrating a hypothetical phylogeny

53. Individuals, Populations and Evolution
Organisms exist as individuals
Natural selection acts on individuals but individuals do not evolve (they develop)
Individuals exist in populations that inhabit discrete ecological niches
Sexually reproducing individuals exhibit variation
Limited resources leads to differential survival

54. Individuals, Populations and Evolution
Populations do not reproduce, individuals reproduce
Variation is an essential prerequisite for natural selection
Genetic composition of a population will change due to drift (random forces) and to (nonrandom) natural selection
Populations may subdivide
Populations or subsets of populations may “crash” or become extinct

55. Figure T01: Comparison of Characteristics of Individuals and Populations
We’ll talk about these Life Characteristics in later chapters.

56. Individuals Exist in Populations that Inhabit Discrete Ecological Niches
It is primarily the action of natural selection which allows species to be successful in their specific ecological niches
We’ll look at the connections between ecology and evolution throughout this course

57. Different Lichen Species Occupy Slightly Different Niches
© Popovici loan/ShutterStock, Inc.
Figure B01: Lichens
(A superorganism?)

58. Chapter 1 End

59. The Scientific Method 1. Produce a hypothesis
2. Design and perform controlled experiments or make observations that allow data relevant to the hypothesis to be collected
3. Analyze the data in an objective way against the background of existing knowledge
4. Draw conclusions that support or refute the hypothesis