Philosophy of Biology

A year-long debate course for doctoral and postdoctoral researchers

Dynamics of Living Systems — Course Proposal & Protocol

“The growth of knowledge depends entirely on disagreement.” — Karl R. Popper

1. Course Overview

Rationale

Doctoral and postdoctoral researchers in biology and adjacent disciplines are trained to do science, but rarely given the opportunity to examine the philosophical assumptions that underpin their practice. What counts as a good explanation in biology? Are there biological laws? What does it mean to say a trait has a function? These are not idle questions — they shape how research programmes are designed, how evidence is interpreted, and how findings are communicated.

This course provides a structured, year-long forum for early-career researchers to engage with the major debates in the philosophy of biology. Rather than a lecture-based format, the course uses an adversarial debate model in which participants are assigned positions and must argue for views they may not hold. This develops critical thinking, argumentation skills, and a deeper understanding of the conceptual foundations of the life sciences.

Format at a glance

• Duration: 12 monthly sessions (one academic year).
• Frequency: One session per month, approximately 2 hours each.
• Participants: 12–20 doctoral and postdoctoral candidates in biology, ecology, evolution, genetics, neuroscience, or adjacent fields. No prior training in philosophy is required.
• Structure: Each session addresses one major debate. Participants read two short papers (one per side) and are randomly assigned to argue for one position. A structured debate is followed by open discussion.
• Moderation: The course organiser serves as moderator, framing the debate, enforcing time limits, and guiding the open discussion.

Learning objectives

By the end of the course, participants will be able to:

1. Identify and articulate the major philosophical debates relevant to biological research.
2. Construct and defend arguments for positions they may personally disagree with.
3. Critically evaluate the epistemological and metaphysical assumptions underlying their own research.
4. Engage productively with interdisciplinary perspectives on scientific methodology.
5. Read and engage with primary philosophical literature at a level appropriate for informed practitioners.

2. Sequencing Logic

The twelve sessions are organised into three thematic blocks, each building on the last. This progression ensures that participants acquire the conceptual vocabulary needed for later, more applied debates.

Block I — Epistemological Foundations (Months 1–3)

The first block addresses how science works in general before turning to biology specifically. Participants engage with questions about demarcation, explanation, and reduction that will recur throughout the course. These sessions establish a shared philosophical vocabulary.

• Month 1 — Demarcation and Scientific Method (Popper vs. Kuhn / Lakatos)
• Month 2 — Laws in Biology (Nomothetic vs. Contingent)
• Month 3 — Reductionism vs. Emergence

Dependency: Month 1 introduces “falsification” and “paradigm,” which are referenced in every subsequent session. Month 2 connects to debates about explanation that surface in Months 4 and 7. Month 3 sets up the gene-centric debates in Months 5 and 8.

Block II — Core Concepts in Biology (Months 4–7)

The second block turns to the central theoretical concepts of biology itself: natural selection, levels of selection, species, and function. These are the bread-and-butter debates of philosophy of biology, and the ones most directly relevant to participants' research.

• Month 4 — Adaptationism and the Explanatory Power of Natural Selection
• Month 5 — Units and Levels of Selection
• Month 6 — The Species Problem
• Month 7 — Function and Teleology

Dependency: Month 4 requires the epistemological tools from Block I (especially the falsification debate). Months 5 and 6 build on the adaptationism discussion. Month 7 draws on both the reductionism debate (Month 3) and the selection debates (Months 4–5).

Block III — Applied and Contemporary Debates (Months 8–12)

The final block moves outward from theoretical biology into its intersections with society, values, and technology. These sessions are more interdisciplinary and more likely to provoke strong personal reactions — which is why they come last, after participants have developed the argumentative discipline to handle them well.

• Month 8 — Genetic Determinism and Developmental Systems
• Month 9 — Cultural Evolution
• Month 10 — Race and Biology
• Month 11 — Values in Science and Conservation Biology
• Month 12 — Synthetic Biology and the Concept of Life

Dependency: Month 8 draws directly on Months 3 and 5 (reductionism and gene-centrism). Month 10 requires the species concept discussion from Month 6. Month 11 returns to Month 1's demarcation question, now enriched by a full year of context. Month 12 integrates themes from across the course.

Summary of progression

Block	Months	Focus
I — Foundations	1–3	How does science work? What kind of science is biology?
II — Core Concepts	4–7	What are the central concepts and debates in biology?
III — Applications	8–12	Where does biology meet society, values, and technology?

3. Session Protocol

Pre-session (1–2 weeks before)

1. The moderator distributes the two assigned readings via email or a shared platform.
2. Participants are informed of their assigned position (Pro or Con) according to the randomisation scheme (see below).
3. Each participant prepares a brief set of notes (not formally collected) summarising the key arguments of their assigned paper and identifying potential weaknesses in the opposing paper.

Session structure (120 minutes)

Phase	Duration	Description
I. Framing	10 min	Moderator introduces the topic, its historical context, and its relevance to biology. No arguments are presented.
II. Opening statements	20 min	Each side selects a spokesperson (or two) who presents the core argument of their assigned position in 8–10 minutes. No rebuttals yet.
III. Structured rebuttal	20 min	Each side responds to the other's opening statement. The moderator enforces alternation: Pro responds (5 min), Con responds (5 min), then a second round of shorter responses (5 min each).
IV. Open cross-examination	20 min	Any participant may direct a question to the opposing side. The moderator ensures balanced participation and prevents any single speaker from dominating.
V. Closing statements	10 min	Each side gives a 5-minute closing statement, summarising their strongest arguments.
— Break —	5 min
VI. Open discussion	30 min	Participants drop their assigned positions and discuss the topic freely. The moderator poses integrative questions (e.g. “What would change in your research if you adopted position X?”).
VII. Wrap-up	5 min	Moderator summarises key insights and previews the next month's topic.

Ground rules

1. Steelman, don't strawman. Participants must argue for the strongest version of their assigned position, not a caricature.
2. Argue the position, not the person. Ad hominem arguments are not permitted; critique ideas, not authors or fellow participants.
3. Stay in role during Phases II–V. Personal views are reserved for the open discussion in Phase VI.
4. Evidence over rhetoric. Arguments should reference the readings and, where possible, relevant empirical findings from participants' own fields.
5. Respect time limits. The moderator will enforce speaking times strictly.

4. Randomisation Scheme

Design principles

The randomisation scheme is designed to ensure that:

1. Every participant argues Pro and Con an approximately equal number of times over the year.
2. No participant is assigned the same side for more than two consecutive sessions.
3. Assignments are independent of participants' known views, so that everyone argues for positions they may disagree with.
4. Group composition varies across sessions, preventing the formation of fixed coalitions.

Procedure

Let $N$ be the total number of participants (ideally $12 \leq N \leq 20$).

1. Initial assignment (Month 1): Participants are numbered $1$ through $N$. Using a random number generator, each participant is assigned to either Pro or Con, subject to the constraint that each group contains $\lfloor N/2 \rfloor$ or $\lceil N/2 \rceil$ members.
2. Subsequent months: Before each session $t$ (where $t = 2, \ldots, 12$), a new random assignment is generated subject to the following constraints:
   • Balance: after session $t$, participant $i$'s cumulative number of Pro and Con assignments must differ by at most 1.
   • Streak: no participant may be assigned the same side for three or more consecutive sessions.
   • Group diversity: at least two participants beyond what balance alone requires must switch sides from the previous session, so that at each step the overlap between the Pro groups of sessions $t$ and $t-1$ is smaller than $\lceil N/2 \rceil - 1$.
3. Implementation sketch: the moderator generates assignments using a constrained random shuffle. One simple algorithm:
   1. Identify participants who must switch sides to satisfy the streak constraint.
   2. Among remaining participants, identify those for whom switching would improve cumulative balance.
   3. Randomly assign the remaining participants to fill each group to the required size.
   4. Verify the group-diversity constraint; if violated, reshuffle step (c).

Example: 16 participants over 12 sessions

The table below illustrates one possible assignment schedule for 16 participants (P = Pro, C = Con). Each participant ends the year with 6 Pro and 6 Con assignments.

#	M1	M2	M3	M4	M5	M6	M7	M8	M9	M10	M11	M12	P	C
S1	P	C	P	C	P	C	P	C	P	C	P	C	6	6
S2	C	P	C	P	C	P	C	P	C	P	C	P	6	6
S3	P	P	C	C	P	P	C	C	P	P	C	C	6	6
S4	C	C	P	P	C	C	P	P	C	C	P	P	6	6
S5	P	C	C	P	P	C	C	P	P	C	C	P	6	6
S6	C	P	P	C	C	P	P	C	C	P	P	C	6	6
S7	P	C	P	P	C	C	P	P	C	C	P	C	6	6
S8	C	P	C	C	P	P	C	C	P	P	C	P	6	6
S9	P	P	C	P	C	P	C	C	P	C	P	C	6	6
S10	C	C	P	C	P	C	P	P	C	P	C	P	6	6
S11	P	C	P	C	C	P	P	C	C	P	P	C	6	6
S12	C	P	C	P	P	C	C	P	P	C	C	P	6	6
S13	P	P	C	P	C	C	P	C	P	C	P	C	6	6
S14	C	C	P	C	P	P	C	P	C	P	C	P	6	6
S15	P	C	C	P	C	P	P	C	C	P	C	P	6	6
S16	C	P	P	C	P	C	C	P	P	C	P	C	6	6

Note: if the number of participants is odd, one participant will have a 6/5 or 7/5 split. The moderator should track this and ensure fairness across the year. If participants miss a session, their balance should be adjusted in subsequent assignments.

Spokesperson selection

For each session, the spokesperson(s) for each side are selected as follows:

1. In Month 1, spokespeople volunteer or are randomly selected.
2. From Month 2 onward, the moderator selects spokespeople from participants who have not yet served in that role, ensuring that every participant serves as spokesperson at least once during the year. With two spokespeople per side per session (48 spokesperson-slots in total), groups of 12–16 participants allow each person to serve roughly three times; larger groups should rotate so that no participant spokes more often than others by more than one slot.
3. Participants are notified of their spokesperson role at the same time as their side assignment, giving them additional preparation time.

5. Reading List

All readings are journal articles or short book chapters (under 30 pages). Where a key argument originates in a book, a summary article or representative chapter is listed instead. Optional background readings are provided for participants who want additional context.

Month 1 — Demarcation and Scientific Method

Can science be demarcated from non-science? Is falsification the right criterion?

• Pro (Falsificationism): Popper, K. R. (1962). “Science: Conjectures and Refutations.” Chapter 1 of Conjectures and Refutations. Routledge. [pp. 33–65; widely anthologised.]
• Con (Paradigms and Normal Science): Kuhn, T. S. (1970). “Logic of Discovery or Psychology of Research?” In Lakatos & Musgrave (eds.), Criticism and the Growth of Knowledge. Cambridge University Press. [pp. 1–23.]
• Optional background: Godfrey-Smith, P. (2003). Chapters 4–5 of Theory and Reality. University of Chicago Press.

Month 2 — Are There Laws in Biology?

Does biology have genuine laws, or only contingent generalisations?

• Pro (Biological laws exist): Mitchell, S. D. (1997). “Pragmatic Laws.” Philosophy of Science, 64, S468–S479.
• Con (Biology is contingent): Beatty, J. (1995). “The Evolutionary Contingency Thesis.” In Wolters & Lennox (eds.), Concepts, Theories, and Rationality in the Biological Sciences. University of Pittsburgh Press. [pp. 45–81.]
• Optional background: Sober, E. (1997). “Two Outbreaks of Lawlessness in Recent Philosophy of Biology.” Philosophy of Science, 64, S458–S467.

Month 3 — Reductionism vs. Emergence

Can biology be reduced to physics and chemistry, or is it autonomous?

• Pro (Reductionism): Rosenberg, A. (2006). “Reductionism Redux: Computing the Embryo.” Biology & Philosophy, 21(4), 455–468.
• Con (Antireductionism): Kitcher, P. (1984). “1953 and All That: A Tale of Two Sciences.” The Philosophical Review, 93(3), 335–373.
• Optional background: Brigandt, I. & Love, A. (2017). “Reductionism in Biology.” Stanford Encyclopedia of Philosophy.

Month 4 — Adaptationism and Natural Selection

Is natural selection a powerful explanatory framework, or does adaptationism produce unfalsifiable just-so stories?

• Pro (Adaptationism is sound): Orzack, S. H. & Sober, E. (1994). “Optimality Models and the Test of Adaptationism.” The American Naturalist, 143(3), 361–380.
• Con (Critique of adaptationism): Gould, S. J. & Lewontin, R. C. (1979). “The Spandrels of San Marco and the Panglossian Paradigm.” Proceedings of the Royal Society B, 205(1161), 581–598.
• Optional background: Godfrey-Smith, P. (2001). “Three Kinds of Adaptationism.” In Orzack & Sober (eds.), Adaptationism and Optimality. Cambridge University Press.

Month 5 — Units and Levels of Selection

Is the gene the fundamental unit of selection, or does selection operate at multiple levels?

• Pro (Gene-level selection): Dawkins, R. (1982). “Replicators and Vehicles.” In Current Problems in Sociobiology, King's College Sociobiology Group (eds.), Cambridge University Press. [pp. 45–64.]
• Con (Multi-level selection): Sober, E. & Wilson, D. S. (2011). “Adaptation and Natural Selection Revisited.” Journal of Evolutionary Biology, 24, 462–468. Or: Sober & Wilson (1998), “Summary of Unto Others,” in Hull & Ruse (eds.), The Philosophy of Biology.
• Optional background: Okasha, S. (2006). Chapter 1 of Evolution and the Levels of Selection. Oxford University Press.

Month 6 — The Species Problem

Is there a single correct species concept, or should we be pluralists (or anti-realists)?

• Pro (Species realism): Mayr, E. (1996). “What Is a Species, and What Is Not?” Philosophy of Science, 63(2), 262–277.
• Con (Species pluralism / anti-realism): Ereshefsky, M. (1998). “Species Pluralism and Anti-Realism.” Philosophy of Science, 65(1), 103–120.
• Optional background: Richards, R. A. (2010). Chapter 1 of The Species Problem: A Philosophical Analysis. Cambridge University Press.

Month 7 — Function and Teleology

What does it mean to say a biological trait has a function? Is evolutionary history essential?

• Pro (Selected-effects / etiological account): Neander, K. (1991). “The Teleological Notion of `Function'.” Australasian Journal of Philosophy, 69(4), 454–468.
• Con (Causal-role account): Cummins, R. (1975). “Functional Analysis.” The Journal of Philosophy, 72(20), 741–765.
• Optional background: Godfrey-Smith, P. (1993). “Functions: Consensus Without Unity.” Pacific Philosophical Quarterly, 74(3), 196–208.

Month 8 — Genetic Determinism and Developmental Systems

Do genes play a privileged causal role in development, or are they one resource among many?

• Pro (Gene primacy): Waters, C. K. (2007). “Causes That Make a Difference.” The Journal of Philosophy, 104(11), 551–579.
• Con (Developmental Systems Theory): Griffiths, P. E. & Gray, R. D. (1994). “Developmental Systems and Evolutionary Explanation.” The Journal of Philosophy, 91(6), 277–304.
• Optional background: Keller, E. F. (2010). In Ayala & Arp (eds.), Contemporary Debates in Philosophy of Biology. Wiley-Blackwell.

Month 9 — Cultural Evolution

Is cultural change genuinely Darwinian, or does the analogy break down?

• Pro (Cultural evolution is Darwinian): Mesoudi, A., Whiten, A. & Laland, K. N. (2006). “Towards a Unified Science of Cultural Evolution.” Behavioral and Brain Sciences, 29(4), 329–347.
• Con (The analogy fails): Sperber, D. (2000). “An Objection to the Memetic Approach to Culture.” In Aunger (ed.), Darwinizing Culture: The Status of Memetics as a Science. Oxford University Press. [pp. 163–173.]
• Optional background: Lewens, T. (2015). Chapter 1 of Cultural Evolution: Conceptual Challenges. Oxford University Press.

Month 10 — Race and Biology

Is race a biologically meaningful category, or a social construction without coherent biological referent?

• Pro (Biological reality of race): Hardimon, M. O. (2013). “Race Concepts in Medicine.” The Journal of Medicine and Philosophy, 38(1), 6–31.
• Con (Race as social construction): Kaplan, J. M. & Winther, R. G. (2013). “Prisoners of Abstraction? The Theory and Measure of Genetic Variation, and the Very Concept of `Race'.” Biological Theory, 7(4), 401–412.
• Optional background: Spencer, Q. (2018). “A Racial Classification for Medical Genetics.” Philosophical Studies, 175(5), 1013–1037.

Moderator note. This session requires explicit ground rules. The debate concerns the conceptual and empirical question of whether biological population structure maps onto racial categories — not the moral or political status of racial groups. The moderator should frame this clearly at the outset and reserve extra time to re-establish the steelman rule.

Month 11 — Values in Science

Is science (and conservation biology in particular) necessarily value-laden, or should it aspire to value-neutrality?

• Pro (Values are inescapable and legitimate): Elliott, K. C. (2011). “Direct and Indirect Roles for Values in Science.” Philosophy of Science, 78(2), 303–324.
• Con (Value-free ideal): Lacey, H. (1999). Chapter 1 of Is Science Value Free? Values and Scientific Understanding. Routledge. [pp. 1–22.] Or: Douglas, H. (2009), Chapter 1 of Science, Policy, and the Value-Free Ideal.
• Optional background: Sarkar, S. (2005). Chapters 1–2 of Biodiversity and Environmental Philosophy. Cambridge University Press.

Month 12 — Synthetic Biology and the Concept of Life

Does synthetic biology vindicate a mechanistic view of life, or reveal its limits?

• Pro (Life as machine): Endy, D. (2005). “Foundations for Engineering Biology.” Nature, 438(7067), 449–453.
• Con (Beyond the machine metaphor): Nicholson, D. J. (2013). “Organisms ≠ Machines.” Studies in History and Philosophy of Biological and Biomedical Sciences, 44(4), 669–678.
• Optional background: Dupré, J. (2012). Chapters 1–2 of Processes of Life: Essays in the Philosophy of Biology. Oxford University Press.

6. Year at a Glance

Month	Topic	Pro reading	Con reading
1	Demarcation & Method	Popper (1962)	Kuhn (1970)
2	Laws in Biology	Mitchell (1997)	Beatty (1995)
3	Reductionism vs. Emergence	Rosenberg (2006)	Kitcher (1984)
4	Adaptationism	Orzack & Sober (1994)	Gould & Lewontin (1979)
5	Levels of Selection	Dawkins (1982)	Sober & Wilson (2011)
6	The Species Problem	Mayr (1996)	Ereshefsky (1998)
7	Function & Teleology	Neander (1991)	Cummins (1975)
8	Genes & Development	Waters (2007)	Griffiths & Gray (1994)
9	Cultural Evolution	Mesoudi et al. (2006)	Sperber (2000)
10	Race & Biology	Hardimon (2013)	Kaplan & Winther (2013)
11	Values in Science	Elliott (2011)	Lacey (1999)
12	Synthetic Biology & Life	Endy (2005)	Nicholson (2013)

7. Assessment and Outputs (Optional)

If the course is to be credit-bearing or if participants want a more structured output, the following optional components can be added.

Participation record

The moderator keeps a record of each participant's side assignments, spokesperson roles, and attendance. Participants who attend at least 10 of 12 sessions receive a certificate of completion.

Reflection papers

After each session, the side that feels their argument was less successful (informally judged by the moderator and the group) writes a one-page response paper due before the next session. This paper should identify what went wrong and what the strongest counter-argument would have been. These papers are circulated to the group as preparation material.

Capstone essay

At the end of the year, each participant writes a short essay (2,000–3,000 words) on one of the following prompts:

1. Choose one debate from the course and argue that it has direct consequences for how research in your field should be conducted.
2. Identify a philosophical assumption in your own doctoral or postdoctoral research that you had not previously examined. Analyse it using the tools from this course.
3. Propose a 13th session: identify a debate in philosophy of biology not covered in this course, select two readings, and justify its inclusion.

8. Practical Information

Scheduling

Sessions work best on a fixed day of the month (e.g. the third Thursday). Avoiding examination periods, conference season (June–July), and major holidays is advisable. A suggested calendar for an October–September academic year runs from October 2026 through September 2027, one session per month.

Recommended background texts

For participants who want a general introduction to philosophy of biology before or alongside the course:

• Godfrey-Smith, P. (2014). Philosophy of Biology. Princeton University Press. [Short, accessible, excellent.]
• Sober, E. (2000). Philosophy of Biology, 2nd ed. Westview Press. [More technical, very clear.]
• Godfrey-Smith, P. (2003). Theory and Reality: An Introduction to the Philosophy of Science. University of Chicago Press.

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