Seminar
Yale University, Fall 2019
E&EB 321
E&EB 621
HUMS tbd
Time: Tuesday 1:30-3:20
Location: OML 201
Instructors: Casey Dunn, Gunter Wagner
Office hours: Casey Dunn Tuesday 3:30-5:00 pm; Gunter Wagner TBD
This course is an introduction to the Philosophy of Biology, with application to specific current problems.
It will focus on two major strands of thinking seeking answers to two fundamental and to some extend complementary questions: “How do we know?” (epistemology) and “What things really exist in the world?” (ontology). These two themes have the most important impact on the practice of science, as they pertain to the nature of the scientific enterprise and how it works [epistemology and philosophy of science], as well as what scientists consider part of reality. In each of these fields of philosophy we will outline the main positions and then discuss how they apply to past and current debates in biology, in particular, but not exclusively, evolutionary biology.
This course assumes that the student is familiar with core concepts in Biology, but does not assume a background in philosophy.
The prerequisites for E&EB 321 are either a semester of biology or a semester of philosophy.
There are no prerequisites for E&EB 621.
If interest in the course exceeds capacity for productive and participatory discussion, the enrollment of this course will be limited. Please check Canvas for an assigned question that must be submitted by the end of the day of the first class. We will use your answers to this question to make enrollment decisions.
There are two sites relevant to the course:
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The Canvas site is where we post the syllabus and readings, post assignments, and post course communications.
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The github respository is where we edit the syllabus. This is also a way to publicly share the course contents. Please submit suggestions and corrections for the class via the issue tracker.
Classes will consist of lectures, student led discussions, and project presentations.
The course grade for E&EB 321 will be based on the following:
- 20% Responses to prompts
- 25% Midterm paper
- 40% Final paper
- 15% Class participation
There will be 2 prompts for questions throughout the course. See details below about responding to these prompts.
The midterm paper will be 6-8 pages, with the focus on describing multiple perspectives on a previously addressed problem in the Philosophy of Biology. The final paper will be 10-12 pages, and will provide a synthesis and novel approach to a different problem. An abstract will be submitted two weeks before the deadline for each.
The papers are to be double spaced 12 point font. They must be fully cited (references do not count toward the page limit).
The assignments and evaluation for E&EB 621 will be as follows:
- 35% Class presentation
- 40% Responses to prompts
- 25% Presentation
The presentation will be 20 minutes (including questions) on a topic relevant to the graduate student's research. It will be in the last class, or in the preceding two weeks depending on enrollment.
There will be 4 prompts for questions throughout the course. See details below about responding to these prompts.
Place your name and the text of the prompt at the top of your submission. Your response is to be 400-500 words, excluding citations. Stay within this range - part of the challenge is to be concise.
Please keep the following in mind as you write your response:
- These are short, so they should have a sharp point - get right to the meat of the issue and address it as directly as possible. Do not have long expository intros (eg causality is…) that chew into the space available to address the specifics of the prompt.
- Be sure to read the prompt closely before writing, then after you have written revisit the prompt to confirm that your text addresses it as directly as possible.
- Address the prompt as directly as possible. Prompts may be multi-part, so you need to make sure you are addressing each component of what is being asked for. Stay focused on the request of the prompt. For example, if the question is about how causality can be misleading in the study of biology, don't focus on how the inference of causality can be misled.
- Do use citations. They help make the biology specific and concrete, and they connect the philosophical perspectives to ideas in the philosophical literature.
Most readings will come from:
Peter Godfrey-Smith. 2013. Philosophy of Biology. Princeton University Press. ISBN:978-0691174679. Link from Yale Library to digital edition: https://muse.jhu.edu/book/36379/
This required text is abbreviated as PGS in the schedule below.
Additional readings will be drawn from the literature, and provided at least 5 days before each class.
All students are expected to:
- Complete the assigned readings in full before class, and come to class prepared to discuss them in detail.
- Cite all sources in papers, including drafts, every time they use a source. This isn't just for attribution, it is so that your reader understands the foundations of your assertions and knows where to look for more information on a topic.
- Place quotation marks around any cited or cut-and-pasted materials, in addition to footnoting or otherwise marking the source.
- Mark each paraphrased source, as though it were quoted.
- List all sources consulted for the draft or paper in the closing materials, such as a bibliography or roster of sources consulted.
- Do not collaborate unless explicitly allowed.
- Do not submit another person's solution to a problem, including a solution found online.
- Do not submit or reuse material from the same paper in multiple courses unless both instructors provide written permission to do so.
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Laplane L, Mantovani P, Adolphs R, Chang H, Mantovani A, McFall-Ngai M, Rovelli C, Sober E, Pradeu T: Opinion: Why science needs philosophy. Proc. Natl. Acad. Sci. 2019, 116:3948–3952. http://dx.doi.org/10.1073/pnas.1900357116
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PGS Chapters 1-2
- Pearl, J. (2002). Reasoning with Cause and Effect. AI Magazine, 23(1), 95. https://doi.org/10.1609/aimag.v23i1.1612
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The Wikipedia article on ontology - https://en.wikipedia.org/wiki/Ontology
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Chapter 1 (A Manifesto for a Processual Philosophy of Biology) from: Nicholson and Dupre. 2018. Everything Flows: Towards a Processual Philosophy of Biology. Oxford. doi:10.1093/oso/9780198779636.003.0001
- PGS Chapters 3, 4
Response due for prompt on causation (E&EB 621): Discuss how the concept of causality may be helpful or misleading in biological research, with reference to at least one specific topic.
- PGS Chapter 5
- PGS Chapter 6
Response due for prompt on natural selection (E&EB 321 and E&EB 621): Why has the concept of fitness been so challenging for biologists, and how can philosophy help address the challenge?
Gunter away
- PGS Chapter 7
E&EB 321 Midterm paper due
Arendt, D., Musser, J. M., Baker, C. V. H., Bergman, A., Cepko, C., Erwin, D. H., et al. (2016). The origin and evolution of cell types. Nature Reviews Genetics, 17(12), 1–14. http://doi.org/10.1038/nrg.2016.127
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Ghiselin, M. T. (2005). Homology as a relation of correspondence between parts of individuals. Theory in Biosciences = Theorie in Den Biowissenschaften, 124(2), 91–103. http://doi.org/10.1007/BF02814478
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Wagner, G. P. (2007). The developmental genetics of homology. Nature Reviews Genetics, 8(6), 473–479. http://doi.org/10.1038/nrg2099
Response due for prompt on cell types (E&EB 621): What do you think of the ontological status of cell types? Does it fit into a process ontology?
- PGS Chapter 9
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Jablonski, D. (2007). Scale and hierarchy in macroevolution. Palaeontology, 50(1), 87–109. http://doi.org/10.1111/j.1475-4983.2006.00615.x
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Dietrich, M. Chapter 9: Microevolution and Macroevolution Are Governed by the Same Processes. in: Ayala, F. J., & Arp, R. (Eds.). (2009). Contemporary Debates in Philosophy of Biology. Oxford, UK: Wiley-Blackwell. http://doi.org/10.1002/9781444314922 . (also in canvas)
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Erwin, DH. Chapter 10: Microevolution and Macroevolution Are Not Governed by the Same Processes. in: Ayala, F. J., & Arp, R. (Eds.). (2009). Contemporary Debates in Philosophy of Biology. Oxford, UK: Wiley-Blackwell. http://doi.org/10.1002/9781444314922 . (also in canvas)
Response due for prompt on homology (E&EB 321 and E&EB 621): How can a process ontology enlighten the ontological status of homologous elements?
E&EB 321 Final paper due
A list of texts for background reading, and from which some of the assigned readings will be drawn.
Bueno et al. 2018. Individuation, Process, and Scientific Practices. Oxford. https://global.oup.com/academic/product/individuation-process-and-scientific-practices-9780190636814?cc=us&lang=en&
Cartwright. 1983. How the laws of physics lie. Oxford.
Godfrey-Smith, Peter. 2013. Philosophy of Biology (Princeton Foundations of Contemporary Philosophy Book 8). Princeton University Press. https://press.princeton.edu/titles/10273.html, https://muse.jhu.edu/book/36379/
Nicholson and Dupre. 2018. Everything Flows: Towards a Processual Philosophy of Biology. Oxford. http://search.library.yale.edu/catalog/13672921
Pearl, Judea. 2009. Causality: Models, Reasoning and Inference (2nd Edition). Cambridge University Press. http://search.library.yale.edu/catalog/12582524
Sterelny and Griffiths. 1999. Sex and Death. University of Chicago Press. https://www.press.uchicago.edu/ucp/books/book/chicago/S/bo3638489.html An introduction to the philosophy of biology