Phil 147
Philosophy of Biology
Ridge Walk Academic Complex 0426
Winter, 2022, Tuesdays and Thursday, 2:00-3:20 pm

Alternate beginning of quarter plan:

Classes will be conducted on Zoom for at least the first two weeks. The meeting room is: 981 9236 7288. Please make sure you join using your first and last name. As a default, please keep yourself muted. To participate in class discussion, please use the raise hand function. When I call upon you, unmute yourself.

Instead of clickers, during this period we will use the polling function on zoom. Your participation will be recorded using the name you show on zoom. You will not need to purchase a clicker until we return to in-person classes.

Office hours for this period will be by request. Please send email with the header OFFICE HOUR REQUEST to phil147@mechanism.ucsd.edu. I will send you a link to the zoom room for the meeting. I will regularly be available for appointments during scheduled office hours and will make appointments for other times if those are not suitable.

If we do not return to in person learning after two weeks, alterations to the syllabus may be required. I will not increase the number or difficulty assignments, but they may need to be handled in a different manner.

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. 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. Students are invited and encouraged to draw upon their own knowledge of biology and its history in class discussions.

Since biology is the subject matter for the course, we will be covering a fair amount of biology in readings and in class. This, however, is not a biology course. The goal is not for you to learn all of the biological content, but to gain an appreciation for how biologists pursue their craft and how it gives rise to philosophical questions. So, when reading biological texts, don't try to master all the details but to develop a general understanding of the nature of the research biologists were or are engaged in.

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 participation in 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 the questions students submit in advance.

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 answering 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 cumulative 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. If there are no readings for that day (it is listed as a discussion class), then comment or raise a question about something covered since the last discussion class. You are encouraged on those classes to raise questions you would like to discuss with others in the class. These emails should be one medium-length paragraph in length (a one-liner is too short, more than one screen is too much). You can write about anything you found interesting, puzzling, strange, clearly wrong, provocative, etc. I will respond to each email that is submitted on time. 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.) On days marked with an asterisk in the schedule of classes below, comments must be submitted as email (as plain text, not as attachments) to phil147@mechanism.ucsd.edu by 4PM on the day before.  10% of your final grade will be based on these email comments.

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 (900 to 1500 words) that will count for 25% of your grade. The paper, due by NOON on Friday, February 25, 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 participation in class discussions can result in a raising 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 transmitter. 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). I will arrange a procedure for registering your clicker after the first two weeks.

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 slides 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 4PM on the day before the class.

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

Unit 1: Mechanistic Cell Biology

January 6: The Emergence of Cell Theory

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

Bechtel, W., & Bollhagen, A. (2019). Philosophy of cell biology. In E. N. Zalta (Ed.), Stanford Encyclopedia of Philosophy. Stanford: Metaphysics Research Lab, Stanford University. Parts 1 and 2

Useful link: Robinson, Richard, Cell Theory and Cell Structure

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

January 13: From Physiological Chemistry to Biochemistry

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.

Bechtel, W. (1986). Building interlevel pathways:  The discovery of the Embden-Meyerhof pathway and the phosphate cycle. In J. Dorn & P. Weingartner (Eds.), Foundations of Biology (pp. 68-87 only). Vienna: Holder-Pichlert-Tempsky.

*January 18: Modern Cell and Molecular Biology

Bechtel, W., & Bollhagen, A. (2019). Philosophy of cell biology. In E. N. Zalta (Ed.), Stanford Encyclopedia of Philosophy. Stanford: Metaphysics Research Lab, Stanford University. Parts 4 and 5

Morange, M. (2016) History of Molecular Biology. In eLS

Brigandt, I. (2019) Philosophy of Molecular Biology. In eLS

Useful link: Sara E. Miller and Kenneth S. Saladin, Electron microscopy

*January 20: Discussion Class

Unit 2: The Development of Evolutionary Ideas

January 25: Background to Darwin

Bowler, P. J. (2021). Evolutionary Ideas: Darwin. In eLS

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

Useful links Vassiliki Betty Smocovitis, History of Evolutionary Thought

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

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

*February 1: Discussion

February 3: Midterm Exam

Unit 3: Evolution, Genetics, and Development

February 8: 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

*February 10: The Evolutionary Synthesis and Its Challenges

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

Luis Boto (2015). Horizontal gene transfer in evolution. eLS

Useful link: Paul Cabe, Population Genetics

February 15: The Broadening of the Synthesis: Evolutionary-Developmental Biology (Evo-Devo)

Gould, S. J., & Lewontin, R. C. (1979). The spandrels of San Marco and the Panglossian paradigm:  A critique of  the adaptationist programme. Proceedings of the Royal Society of London, Series B, 205, 581-598.

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

Brigandt, I. (2015). From Developmental Constraint to Evolvability: How Concepts Figure in Explanation and Disciplinary Identity. In A. C. Love (Ed.), Conceptual Change in Biology: Scientific and Philosophical Perspectives on Evolution and Development (pp. 305-325). Dordrecht: Springer Netherland [Through section 14.3 only]

Useful link: Arthur, W. Evolutionary Developmental Biology: Developmental Bias and Constraint. In eLS.

*February 17: The Ontology of Evolution: Species and Higher-Taxa

Marc Ereshefsky (2017), Species, Stanford Encyclopedia of Philosophy. [Sections 1-2 only]

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

Crespi, B. J. (2001). Selection: Units and Levels. In eLS.

*February 22: Discussion Class

February 24: Maintaining Balance: Homeostasis and Cybernetics

Cannon, W. B. (1929). Organization of physiological homeostasis. Physiological Reviews, 9, 399-431.

Rosenblueth, A., Wiener, N., & Bigelow, J. (1943). Behavior, purpose, and teleology. Philosophy of Science, 10, 18-24. [Emphasize 399-410 and 424-427]

Useful links: Billman, G. E. (2020). Homeostasis: The Underappreciated and Far Too Often Ignored Central Organizing Principle of Physiology. Frontiers in physiology, 11, 200. http://europepmc.org/abstract/MED/32210840, Emphasize pages 1-9. and Goldstein, D. S., & Kopin, I. J. (2017). Homeostatic systems, biocybernetics, and autonomic neuroscience. Autonomic Neuroscience, 208, 15-28. doi:https://doi.org/10.1016/j.autneu.2017.09.001

February 25: 3-5 page paper due by Noon. Email to papers@mechanism.ucsd.edu

March 1: Life Far From Equilibrium: Autopoiesis and Autonomy

Varela, F. J., Maturana, H. R., & Uribe, R. (1974). Autopoiesis: The organization of living systems, its characterization and a model. BioSystems, 5, 187-196. [Sections 1-5 and 8 only]

Varela, F. J. (1981). Autonomy and autopoiesis. In G. Roth & H. Schwegler (Eds.), Self-organizing systems: An interdisciplinary approach (pp. 14-24). Frankfurt: Campus Verlag. [Emphasize pp. 14-18]

Ruiz-Mirazo, K., & Moreno, A. (2004). Basic autonomy as a fundamental step in the synthesis of life. Artificial Life, 10, 235-259. [up to 247]

*March 3: Teleology and Function

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

Colin Allen (2003), Teleological Notions in Biology, Stanford Encyclopedia of Philosophy. [Sections 3 and 4]

March 8: Bridging Mechanism and Autonomy: The Centrality of Control

Bich, L. and Bechtel, W. (forthcoming). Organization needs organization: Understanding integrated control in living organisms.

*March 10: Discussion Class

March 17: Final Exam