Phil 147
Philosophy of Biology
Winter, 2016, Mon. Wed., 5:00-6:20 pm

1. Course Description

The various sciences each have a subject matter—biology, in particular, studies the processes involved in living organisms. Philosophy of biology likewise has a subject matter—biology itself. As a part of philosophy of science, a major part of the goal in philosophy of biology is to understand the ways in which biologists produce knowledge. This inquiry addresses such questions as: What kinds of explanations do biologists provide? How do the explanations of biology relate to those of physics and chemistry? A distinctive feature of biology is that the phenomena it studies have evolved. How can we know about the history of living systems and the processes that shape evolution? Our investigation of biology will look both at its history and its contemporary practice. The reason for turning to its history is that many of the fundamental ideas that guide contemporary biology were developed over the last 200 years and can be identified more crisply during the historical development of modern biology. Thus, we will consider the development of cell theory, physiological chemistry, evolution, and genetics in the 19th century. Many of the same theoretical and conceptual issues that biologists confronted in the 19th century continue to be the focus in contemporary biology, especially those concerned with the mechanisms responsible for biological phenomena and their evolution. We will finish the course by examining recent approaches to understanding biology that emphasize biological systems and consider to what extent do these complement or supplant mechanistic approaches. Students are invited and encouraged to draw upon their own knowledge of biology and its history in class discussions.

Given the nature of the class, substantial material will be presented in lectures that goes beyond what is included in the readings. Also, philosophy is an activity, and learning activities requires active engagement. Accordingly, class attendance and discussion is critical. Although we will have discussions on other occasions as well, several classes are designated as discussion classes and the topics for discussion in these classes will be determined by students.

2. Course Requirements

Class attendance is mandatory. Missing classes more than very occasionally will result in a reduction in your grade. To get the most out of the class, it is absolutely essential that you come to class having read the assigned material and prepared to discuss it. Questions will be posed in each class to be answered using Clickers. Some clicker questions will test basic ideas from the assigned reading. On these questions, one point will be awarded for ansering the question and a second point for answering correctly. Other questions will not have a specific answer designated and will serve to foster discussion. Two points will be awarded for answering each such question. A commulative score based on clicker responses will count for 10% of your final grade.

To promote engagement with the reading and to foster subsequent discussions in class, you will be required to email comments or questions on the reading assigned for those classes marked with an asterisk on the Schedule of Class Meetings and Readings below. These emails should be one medium-length paragraph in length. You can write about anything you found interesting, puzzling, strange, clearly wrong, provocative, etc. These will be graded as acceptable or unacceptable (if I do not tell you that a submission is unacceptable, you can assume that it is acceptable). To ensure that your submission is acceptable, your comment or question must demonstrate that you have read and thought about the assigned material. (Your paragraph should focus on one specific part of the reading--do not try to discuss everything.) Comments must be submitted as email (as plain text, not as attachments) to phil147@mechanism.ucsd.edu by 7AM on days marked with an asterisk in the schedule of classes below. 10% of your final grade will be based on these email comments. You must submit at least eight comments to get full credit.

There will be two exams, a mid-term and a final. The mid-term will count for 25% of your final grade; the final will count for 30%. Exams will include both short answer and essay questions and the complete set of questions from which the actual exam questions will be selected will be distributed approximately one week before the exams. You will also need to write one 3-5 page paper that will count for 25% of your grade. The paper, due by NOON on Wednesday, March 2, must be on one of the topics that will be assigned in class. If possible, the paper should be submitted in Word by email attachment (please be sure to check for viruses before submitting your file!) to papers@mechanism.ucsd.edu.

Above average or below average participation in class discussions can result in a raising or lowering of your final grade from what is determined by the above percentages on these other assignments.

3. Texts

All of the reading assignments can be found by following links on the web site. See the schedule of classes and readings below. Those items that are on license to UCSD may only be available if you are on campus or set up a virtual private network (directions on doing so are avaiable through Academic Computing Services).

If you do not already own one, you will also need to purchase an i>clicker student response transmiter. These transmitters, informally called “clickers,” are available at the UCSD bookstore. Make sure to get an i>clicker and not a different system (e.g., H-ITT or PRS). For more information, visit http://acms.ucsd.edu/services/classroom-support/clickers.html.

4. Academic honesty

Integrity of scholarship is essential for an academic community. The University expects that both faculty and students will honor this principle and in so doing protect the validity of University intellectual work. For students, this means that all academic work must be done by the individual who submits, without unauthorized aid of any kind. This means that on exams you will not use any external resources, including crib sheets, cell phones, etc. All papers, emails, etc., that you submit must be written by you in your own words. If you need to quote someone, be sure to use quotation marks and identify the source. In preparing for exams, papers, etc., you are encouraged to work with your peers. But the actual writing must be yours. You may ask others to read and provide feedback on your writing, but they should not re-write the text for you. Rather, they can provide comments and you undertake the rewriting.

5. Schedule of Classes and Readings

Note: This schedule of reading assignments is tentative and subject to revision. When powerpoints from lectures are available, there will be a link from the lecture title to the pdf file. Dates with asterisks are dates on which comments/question paragraphs on the reading are due. These comments/questions must be sent to phil147@mechanism.ucsd.edu by 7 AM on the dates indicated.

Recommended: William Harvey: On The Motion Of The Heart And Blood In Animals.

January 6: Mechanistic Ideas of Life: The Cell Theory

History of Biology: Cell Theory and Cell Structure: http://www.biologyreference.com/Gr-Hi/History-of-Biology-Cell-Theory-and-Cell-Structure.html

Theodor Schwann (1838), Microscopical Researches into the Accordance in the Structure and Growth of Animals and Plants, Author's Preface and pp. 1-9, 161-168, 186-202.

Useful links: Richard Robinson, Cell theory: http://fig.cox.miami.edu/~cmallery/150/unity/cell.text.htm

*January 11: Mechanistic Ideas of Life: Basic Metabolism

Justig Liebig (1838), Animal Chemistry, or organic chemistry in its application to phyiology and pathology, Preface and pp. 1-23.

Louis Pasteur (1860), “Infusorian Animalcules Living Without Free Oxygen and Determining Fermentation,” pp. 303-307.

Buchner, Eduard (1897). "Alcoholic Fermentation Without Yeast Cells," translation by Herbert C. Friedmann of "Alkoholische Gährung ohne Hefezellen," originally published in Ber. Dt. Chem. Ges. 30, 117-124.

Useful links: John Pebble, History of Biology: Biochemistry http://www.biologyreference.com/Gr-Hi/History-of-Biology-Biochemistry.html

January 13: Vitalism and Organized Mechanisms

Xavier Bichat, Physiological Researches on Life and Death. (Translated by F. Gold. Boston: Richardson and Lord, 1827). Chapter 1.

William Bechtel and Robert C. Richardson, Vitalism, Routledge Encyclopedia of Philosophy.

Claude Bernard, Introduction à l'étude de la médecine expérimentale. (Paris: J.B. Baillière et Fils, 1865, pp. 85-92, 101-4, 107-112, 265-301).

*January 20: Discussion

January 25: Background to Darwin

Charles Darwin (1859), On the origin of species (introduction and chapters 1 and 2).

Useful links: Vassiliki Betty Smocovitis, History of Evolutionary Thought, http://www.biologyreference.com/Gr-Hi/History-of-Evolutionary-Thought.html; 17th-19th Century Discoveries that Led to the Acceptance of Biological Evolution, http://anthro.palomar.edu/evolve/default.htm

*January 27: Darwin's Account of Evolution by Natural Selection

Charles Darwin (1859), On the origin of species (chapters 3, 4, 14).

Phillip Sloan (2008), Evolution, Stanford Encyclopedia of Philosophy, Part 2.

Useful link: About Darwin http://www.aboutdarwin.com/index.html

*February 1: Discussion

February 3: Midterm Exam

February 8: The Reception of Darwin's Origin

Samuel Wilberforce (1860). On Darwin's Origin of Species. Essays Contributed to the Quarterly Review, 2 Vols., (London, 1874), I.92-95.

Huxley, Thomas H. Time and Life: Mr. Darwin's "Origin of Species" Macmillan's Magazine (1859).

Phillip Sloan, Evolution, Stanford Encyclopedia of Philosophy, Part 3.1.

*February 10: Mendel: Darwin’s Savior or Opponent?

Gregor Mendel (1865), Experiments in Plant Hybridization, Verhandlungen des Naturforschenden Vereines in Brüun, 4, 3-47. Sections 1-6, 9, and 11.

Peter J. Bowler (2001). Evolutionary ideas: The Eclipse of Darwinism, eLS

Useful Links: An Introduction to Mendelian Genetics http://anthro.palomar.edu/mendel/default.htm; Lynn Nyhart, History of Biology: Inheritance, http://www.biologyreference.com/Gr-Hi/History-of-Biology-Inheritance.html

*February 17: The Evolutionary Synthesis and Its Critics

Peter J. Bowler (2001). Evolutionary ideas: The Modern Synthesis. eLS

Christopher D. Horvath (2001) Adaptationist claims: Conceptual problems. eLS.

Laland, K., Uller, T., Feldman, M., Sterelny, K., Muller, G. B., Moczek, A., Jablonka, E., Odling-Smee, J., Wray, G. A., Hoekstra, H. E., Futuyma, D. J., Lenski, R. E., Mackay, T. F., Schluter, D., & Strassmann, J. E. (2014). Does evolutionary theory need a rethink? Nature, 514, 161-164.

Luis Boto (2010). Horizontal gene transfer in evolution. eLS

Useful links: Synthetic Theory of Evolution: An Introduction to Modern Evolutionary Concepts and Theories http://anthro.palomar.edu/synthetic/default.htm; Paul Cabe, Population Genetics, http://www.biologyreference.com/Ph-Po/Population-Genetics.html

February 22: Ontology of Evolution: Species and Higher Taxa

Marc Ereshefsky (2010), Species, Stanford Encyclopedia of Philosophy.

Robert N. Brandon (2001), Philosophy of Selection: Units and Levels, eLS

Useful link: Ann E. Kessen and Robert M. Zink, Species, http://www.biologyreference.com/Se-T/Species.html; Defining a Species, http://evolution.berkeley.edu/evosite/evo101/VADefiningSpecies.shtml; Species Problem (Wikipedia), http://en.wikipedia.org/wiki/Species_problem; Unit of Selection (Wikipedia), http://en.wikipedia.org/wiki/Unit_of_selection; Barry Sinervo, Levels of Selection, http://bio.research.ucsc.edu/~barrylab/classes/animal_behavior/LEVELS.HTM

*February 24: Teleology and Function

David Buller (2001), Function and Teleology, eLS.

Colin Allen (2003), Teleological Notions in Biology, Stanford Encyclopedia of Philosophy.

Mossio, M., & Bich, L. (2014). What makes biological organisation teleological? Synthese, 1-26.

*February 29: Discussion

March 2: 3-5 Page paper due by Noon. Email to papers@mechanism.ucsd.edu

March 2: Systems Biology 1: Networks

Barabasi, A.-L., & Oltvai, Z. N. (2004). Network biology: understanding the cell's functional organization. Nature Reviews Genetics, 5, 101-113.

Alon, U. (2007). Network motifs: Theory and experimental approaches. Nature Reviews Genetics, 8, 450-461.

*March 7: Systems Biology 2: Dynamics

Wolkenhauer, O. (2014). Why model? Frontiers in Physiology, 5, 21.

Green, S., Fagan, M., & Jaeger, J. (2014). Explanatory Integration Challenges in Evolutionary Systems Biology. Biological Theory, 1-18.

*March 9: Discussion

March 14 : Final Exam: 7:00-10:00 pm