bio55: population genetics and evolution

BIO55: Population Genetics and Evolution

I. What is Evolution?

I. What is Evolution?

A. Definitions

"descent with modification"

I. What is Evolution?

A. Definitions

1. Darwin - "descent with modification"

2. Ridley - "change in a lineage of populations between generations"

3. Futuyma - "a change in the properties of populations of organisms, or groups of such populations, over generations"

4. Freeman and Herron - “changes in allele frequencies over time"

I. What is Evolution?

A. Definitions

B. Key Elements1. Populations evolve – individuals develop.

I. What is Evolution?

A. Definitions

B. Key Elements1. Populations evolve – individuals develop.

2. - Evolution is an observable phenomenon:

heritable change in a population over generations. This may be observed at the genetic level, in the genetic structure of the population, or may also be reflected in the physiological, morphological, or behavioral traits affected by this genetic change. We might term this "Lineage Evolution".

I. What is Evolution?

A. Definitions

B. Key Elements1. Populations evolve – individuals develop.

2. - Evolution is an observable phenomenon:

heritable change in a population over generations. This may be observed at the genetic level, in the genetic structure of the population, or may also be reflected in the physiological, morphological, or behavioral traits affected by this genetic change. We might term this "Lineage Evolution".

3. - with known, observable causes:

the genetic structure of a population changes as a function of selection, drift, mutation, migration, and non-random mating.

I. What is Evolution?

A. Definitions

B. Key Elements4. - and known, observable results:

As the genetic structure of a population changes over generations, it can become different (diverge) from other populations. These differences may mean that the populations can no longer breed, and they become biologically distinct entities - different species. We term this "Radiational Evolution".

II. The History of Evolutionary Thought(Mayr, E. 1982. The Growth of Biological Thought)

At one time, there were no scientists, theologians, or historians. There were just philosophers that studied everything, using one way of thinking. That has changed, as we will see....

II. The History of Evolutionary Thought

A. Early GreeksPantheon of meddlesome gods that controlled

every aspect of nature and human experience; even took humans for mating (produced the heroes).

Prometheus fashions humans out of earth and water, and Athena gives humankind a soul

II. The History of Evolutionary Thought

A. Early Greeks B. 2nd Greek School

1. Hippocrates (450-377 bc)

“I swear by Apollo Physician and Asclepius and Hygieia and Panaceia and all the gods and goddesses, making them my witnesses, that I will fulfill according to my ability and judgment this oath and this covenant…”

II. The History of Evolutionary Thought

A. Early Greeks B. 2nd Greek School

1. Hippocrates (450-377 bc)

- Valued an empirical approach… “look and see” rather than a purely philosophical approach to knowledge.

- Believed in use and disuse and inheritance of acquired traits; so accepted change within a "family". - Close to an evolutionary approach

II. The History of Evolutionary Thought

A. Early Greeks B. 2nd Greek School

1. Hippocrates (450-377 bc) 2. Plato (427-347 bc)

II. The History of Evolutionary Thought

A. Early Greeks B. 2nd Greek School

1. Hippocrates (450-377 bc) 2. Plato (427-347 bc) -trained in Pythagorean School; pure philosopher-UNIVERSAL PHILOSOPHY (four dogmas)

II. The History of Evolutionary Thought

A. Early Greeks B. 2nd Greek School

1. Hippocrates (450-377 bc) 2. Plato (427-347 bc) -trained in Pythagorean School; pure philosopher-UNIVERSAL PHILOSOPHY (four dogmas)

Essentialism (unchanging eidos)Plenitude (harmony)Demi-Urge (creative force)Soul (spark of life; most in humans)

The cave

- trained in Pythagorean School; pure philosopher- UNIVERSAL PHILOSOPHY (four dogmas)

Essentialism (unchanging eidos)Plenitude (harmony)Demi-Urge (creative force)Soul (spark of life; most in humans)

Mayr states: "It took more than 2000 years for biology, under the influence of Darwin, to escape the paralyzing grip of essentialism...the rise of modern biology is, in part, the emancipation from Platonic thinking".

II. The History of Evolutionary Thought

A. Early Greeks B. 2nd Greek School

1. Hippocrates (450-377 bc) 2. Plato (427-347 bc) 3. Aristotle (384-322 bc)

II. The History of Evolutionary Thought

A. Early Greeks B. 2nd Greek School

1. Hippocrates (450-377 bc) 2. Plato (427-347 bc) 3. Aristotle (384-322 bc)-Interested in nature-Described 100’s of species-Scala Naturae

II. The History of Evolutionary Thought

A. Early Greeks B. 2nd Greek School

1. Hippocrates (450-377 bc) 2. Plato (427-347 bc) 3. Aristotle (384-322 bc)-Interested in nature-Described 100’s of species-Scala Naturae-Formalized logic, and accepted empirical observations as premises in arguments. But conclusions were drawn from the internal consistency of the argument; they were not tested by observation.

II. The History of Evolutionary Thought

A. Early Greeks B. 2nd Greek School C. The Impact of Christianity

II. The History of Evolutionary Thought

A. Early Greeks B. 2nd Greek School C. The Impact of Christianity

1. Constantine the Great (reign 306-337 ad - First Holy Roman Emporor)

- conversion to Christianity signaled change from to monotheism in west (middle east monotheistic for millenia). -Platonic Dogma’s meshed with Bible:

Single, perfect, harmonious, unchangingcreation

II. The History of Evolutionary Thought

A. Early Greeks B. 2nd Greek School C. The Impact of Christianity

1. Constantine the Great 2. Middle Ages- Fall of Rome (476) to Fall of Constantinople (1453)- Catholic Church as the Political Power

II. The History of Evolutionary Thought

A. Early Greeks B. 2nd Greek School C. The Impact of Christianity

1. Constantine the Great 2. Middle Ages- Fall of Rome (476) to Fall of Constantinople (1453)- Catholic Church as Political Power- The Persians (900-1000ce)

- Ibn a-lHaytham (Alhazen) - al-Biruni - Ibn Sena (Avicenna)

Aristotelian logic and Empiricism!!

II. The History of Evolutionary Thought

A. Early Greeks B. 2nd Greek School C. The Impact of Christianity

1. Constantine the Great 2. Middle Ages- Fall of Rome (476) to Fall of Constantinople (1453)- Catholic Church as Political Power- Thomas Aquinas (1225-1274):

- must be an unmoved mover - must be an initial causality - must be an initial being - must be an ultimate good - the ‘design/purpose’ of nature implies a designer

...yes....

II. The History of Evolutionary Thought

A. Early Greeks B. 2nd Greek School C. The Impact of Christianity

1. Constantine the Great 2. Middle Ages- Fall of Rome (476) to Fall of Constantinople (1453)- Catholic Church as Political Power- Thomas Aquinas (1225-1274):

- must be an unmoved mover - must be an initial causality - must be an initial being - must be an ultimate good - the ‘design/purpose’ of nature implies a designer

- translating the Persians (with Grosseteste and Bacon)

...yes....

II. The History of Evolutionary Thought

A. Early Greeks B. 2nd Greek School C. The Impact of Christianity D. The Renaissance (1400-1700)

II. The History of Evolutionary Thought

A. Early Greeks B. 2nd Greek School C. The Impact of Christianity D. The Renaissance (1400-1700)

1. Voyages of Discovery - 1488 - Dias - Rounds Cape of Good Hope - 1492 - Columbus - "New World"

2. Scientific Revolution a. Astronomy and Physics 1. Nikoli Copernik (1473-1543) 2. Galileo Galilei (1564-1642) 3. Johannes Kepler (1571-1630) 4. Isaac Newton (1642-1727)

Heliocentric solar system - confirmed by Galileo’s observationsPlanets orbit in imperfect ellipses

The motion of planets and other material objects could be explained and predicted based on constant laws of nature

II. The History of Evolutionary Thought

A. Early Greeks B. 2nd Greek School C. The Impact of Christianity D. The Renaissance (1400-1700)

1. Voyages of Discovery 2. Scientific Revolution a. Astronomy and Physics b. The Age of the Earth

II. The History of Evolutionary Thought

A. Early Greeks B. 2nd Greek School C. The Impact of Christianity D. The Renaissance (1400-1700)

1. Voyages of Discovery 2. Scientific Revolution a. Astronomy and Physics b. The Age of the Earth 1. James Ussher (1581-1656): Bishop who Applied logical rigor to the History of the Earth as revealed in the Bible... counted the 'begats'...

- creation began at 9am on October 23, 4004 b.c.

2. Scientific Revolution a. Astronomy and Physics b. The Age of the Earth 1. James Ussher (1581-1656) 2. Nicolaus Steno (1638-1686)- introduced concept of stratigraphy and superposition - sedimentary rocks are layered in order deposited - erosion is continuous and is the primary agent of geology on earth.

2. Scientific Revolution3. Conclusions of the Revolution- Mechanics of Physical Universe were de-deified - Constant, physical laws governed nature. - God as creator (first cause) of universe and laws by which it operates; requires less intervention.

2. Scientific Revolution3. Conclusions of the Revolution- Mechanics of Physical Universe were de-deified - Constant, physical laws governed nature. - God as creator (first cause) of universe and laws by which it operates; requires less intervention. 4. Counter-intuitive Effects on Biology a. constant laws implied stasis since creation b. conflict:

- Deists = secondary laws enough - Natural theologians = diversity and perfection

of life requires a God attending to every detail.

"there is special providence in the fall of a sparrow..." - Shakespeare (1564-1616) - Hamlet

2. Scientific Revolution3. Conclusions of the Revolution- Mechanics of Physical Universe were de-deified - Constant, physical laws governed nature. - God as creator (first cause) of universe and laws by which it operates; requires less intervention. 4. Counter-intuitive Effects on Biology 5. Resolution and Problems-Life was divine and not explicable by natural law-Natural Theology re-emerged-An impressive cataloguing of nature… Botanist John Ray's book (1691) "The Wisdom of God Manifest in the Works of Creation" -How did all these species fit on the ark? Why aren’t they mentioned in the Bible? How did they get to the new world as flood water receded?

II. The History of Evolutionary Thought

A. Early Greeks B. 2nd Greek School C. The Impact of Christianity D. The Renaissance (1400-1700) E. The Enlightenment (1700’s)

E. The Enlightenment (1700’s)

1.Cultural Climate - American, French Revolutions over Monarchy/Authority - reason as a way to solve humanity’s problems

E. The Enlightenment (1700’s)

1.Cultural Climate2. Natural Theology a. Carl Linne (1707-1778) - "Linnaeus" - the great cataloger - latin binomen system -group species based on reproductive structures -created higher taxa order, class, phylum (nested)- Systema Naturae: Creationis telluris est gloria Dei ex opere Naturae per Hominem solum -- "The Earth's creation is the glory of God, as seen from the works of Nature by Man alone." 1758

E. The Enlightenment (1700’s)

1.Cultural Climate2. Natural Theology a. Carl Linne (1707-1778) - "Linnaeus" b. Georges Louis Leclerc, Comte de Buffon (1707-1788)

- the foremost "biologist" of the 18th century- 1749 Histoire Naturelle -emphasized life-history of organisms not their classification (if all are independent creations, what does ‘similarity’ represent, anyway?)-Was aware of evolution as a possibility, but…

"Not only the ass and the horse, but also man, the apes, the quadrupeds, and all the animals might be regarded as constituting but a single family... If it were admitted that the ass is of the family of the horse, and different from the horse only because it has varied from the original form, one could equally well say that the ape is of the family of man, that he is a degenerate man, that man and ape have a common origin; that, in fact, all the families, among plants as well as animals, have come from a single stock, and that all the animals are descended from a single animal, from which have sprung in the course of time, as a result of progress or of degeneration, all the other races of animals. For if it were once shown that we are justified in establishing these families; if it were granted that among animals and plants there has been (I do say several species) but even a single one, which has been produced in the course of direct decent from another species; if, for example, it were true that the ass is but a degeneration from the horse - then there would no longer be any limit to the power of nature, and we should not be wrong in supposing that, with sufficient time, she has been able from a single being to derive all the other organized beings. But this is by no means a proper representation of nature. We are assured by the authority of revelation that all animals have participated equally in the grace of direct Creation and that the first pair of every species issued forth fully formed from the hands of the Creator."

Georges Buffon - Histoire Naturelle (1766)

E. The Enlightenment (1700’s)

1.Cultural Climate2. Natural Theology a. Carl Linne (1707-1778) - "Linnaeus" b. Georges Louis Leclerc, Comte de Buffon (1707-1788)

"it makes no difference which of the authors of the second half of the 18th century one reads - their discussions are, in the last analysis, merely commentaries on Buffon’s work. Except for Darwin and Aristotle, there has been no other student of organisms who has had as far-reaching an influence." Ernst Mayr - Growth of Biological Thought (1982)

E. The Enlightenment (1700’s)

1.Cultural Climate2. Natural Theology a. Carl Linne (1707-1778) - "Linnaeus" b. Georges Louis Leclerc, Comte de Buffon (1707-1788) c. William Paley (1743-1805)

Theologian who restated Aquinas’s “proof of God”, largely using the ‘argument of design’ and the ‘watchmaker’ analogy in his book, Natural Theology (1802).

2. Natural Theology a. Carl Linne (1707-1778) - "Linnaeus" b. Georges Louis Leclerc, Comte de Buffon (1707-1788) c. William Paley (1743-1805) d. James Hutton (1726-1797)- Wrote "Theory of the Earth" in 1795; marks the discovery of "deep time" in English science.

d. James Hutton (1726-1797)

- Wrote "Theory of the Earth" in 1795; marks the discovery of "deep time" in English science.

- Based on two observations:

- 1. granite is an igneous rock, it infuses itself into other rocks (shists) and can only do that when molten.

2. the proper interpretation of “unconformities” - boundaries between cycles of uplift and erosion

d. James Hutton (1726-1797)

- Wrote "Theory of the Earth" in 1795; marks the discovery of "deep time" in English science.

- Based on two observations:

Siccar Point unconformity, observed by Hutton

Process:

1. Initial depositional cycle

Process:

2. uplift (time)

Process:

3. erosion (time)

Process:

4. second depositional cycle (time)

- the crust is recycled - the earth has "no vestige of a beginning - no prospect of an end"

d. James Hutton (1726-1797)

- the crust is recycled - the earth has "no vestige of a beginning - no prospect of an end"

d. James Hutton (1726-1797)

Hadrian’s Wall – 122 a.d. White Cliffs of Dover

Hutton supported the contention that the natural processes of erosion and deposition occur at constant rates over geologic time… so it must take eons for sediments to accumulate to the depth of the cliffs., and natural weathered rock outcrops must be extremely old if rock walls 1500 years old show almost no sign of weathering. = UNIFORMITARIANISM

E. The Enlightenment (1700’s)

1.Cultural Climate2. Natural Theology3. Conclusions of the Period

All were creationists, their discoveries had to be reconciled with their Biblical worldview. But there were conflicts and inconsistencies:

- fossils and extinct species vs. plenitude and universal harmony/perfection - age of earth - 4004 bc? - uh, not likely...- The earth has changed...- How can life remain adapted if earth changes? ...could life change, too?