PHL323 Philosophy of Biology, past assignments

Past Assignments
I. Review of Darwinism

23 January
Review class materials.

What's this?

What's this?
25 January
We're going to review evolutionary theory for a few days, just to make sure we're all clear about the basics. It will be useful even for those who know the theory because it will allow us to raise all the primary philosophical issues of the semester.

Please read from Darwin's The Origin of Species:
  • Chapter 2: the first 2 sections and the last section
  • Chapter 3: the first 3 sections and the last section
  • Chapter 4: the first section

A version of the Origin is available here. (This is not the best version, but most online scholarly versions do not break out the sections, and this one does.)

We'll have a discussion in class about what Darwin is claiming here.

Please also look at Aristotle's De Anima; please read Book II part 1 (this is very short); an online version is this one at MIT. We're going to contrast this with Darwin.

Homework: bring a picture of your dog, if you have one!
27 January
Continuing with Darwin review. Read chapters 1 and 2 of "The Selfish Gene."
30 January
Continuing with Darwin review. Read chapters 3 and 4 of "The Selfish Gene."
February 1
Continuing with our review: what is evolution?
What is the unit of selection? And: is there group selection?

Homework: in developing his theory of evolution, Darwin expressed some concern about how the theory would explain some social organisms, such as some ants and some bees (e.g., honeybees). Given that the females workers of the hive do not have their own young, and given that those females raise the queen's young, and finally given that Darwin knew nothing about genomes (they'd not been discovered yet!), why should he have been worried? Write up in a single page why the behavior of these worker bees might seem like something that should not have evolved. Bring your page to class and I'll collect it, comment on it, and then it can start our conversation later on eusocial species.

II. What gets selected? Is genocentrism sufficient to explain evolution as it occurred?

February 3
What is the unit of selection?

Read in Philosophy of Biology chapter 6, up to but not including the section on genocentrism and genetic information, (this is pages 157-173). Be sure you understand the difference between claiming the unit of selection is the gene, a group, a species; and what (robust) pluralism is.
February 6
Continuing our discussion of challenges to the gene selection theory: death.
February 8
Discussion of eusocial species. Are they an exception to genocentrism, perhaps as an example of group selection?
February 10
Please read the paper by Reeve and Holldobler. This is hard, I know, but if you read the introduction and the conclusion, and struggle a bit but not too hard with the stuff in between, you'll find that you get the main point. We'll discuss it at some length in class as we continue with our topic: models of eusociality, and its relation to the gene-selection view.
February 15
OK, this will take a bit of work on our part, but we'll work together and see if we can't ensure that all of us, with our diverse backgrounds, get what's going on here. Please read Mass Extinctions and Macroevolution. Again, if you focus on the introduction and the conclusion, and do your best with what's in between, you'll be in good shape.

I mentioned that the library has the DVDs of the fine series on evolution, called simply Evolution. Disc three has the portion which describes a nice test of the Red Queen explanation for the evolution of sex. They're on reserve in Penfield; ask at the media reserve desk on the second floor; the call number is Media QH367 .E96 2001. You'll have to watch any of the disks there in the library.

III. Adaptationism under scrutiny. Distinguishing Drift from Selection.

February 20
Read the classic paper by Gould and Lewontin, "The Spandrels of San Marco and the Panglossian Paradigm." I'll email you a copy, but it's available at places like this and this.

This is a good reading to start our writing analyses. The idea is to encourage ourselves to think about the paper a bit before class, so we can talk about it at a more sophisticated level than just me explaining it to you.

Before class write up two copies of answers to the following six questions. One copy I'll collect and grade (generously). The other copy you will read to each other and we'll correct together.
  1. What is a spandrel? Is it designed? What's its significance (if only via analogy) to evolution?
  2. What is adaptationism (as Gould & Lewontin understand it)?
  3. Are the genocentrists adaptationists (as Gould & Lewontin understand adaptationism)?
  4. According to Gould & Lewontin, what strategies do adaptationists use to defend adaptationism when their (first attempts at) explanation fail?
  5. What are "phyletic constraints"?
  6. What are "architectural constraints"?
February 22
Read chapter 3 in Philosophy of Biology. There's some demanding but important philosophy in here, so we'll discuss it at some length.

(Recommended but not required are Philosophy of Biology, chapters 1, 2, and 4; and also chapter 10 (plus the endnotes!) of Dawkins's Selfish Gene reviews eusocials and altruism, so it might be useful to help you review what we've discussed up till now. Otherwise, we're going to discuss this Dawkins chapter again later.)
February 27
We'll continue our discussion of the Beatty problem. Recall that this is described in chapter 3 of Philosophy of Biology. We should discuss also perhaps the question of reduction (which is discussed in chapters 1, 2, and 4 of Philosophy of Biology). We will also briefly discuss the neutral theory. If we have time we'll introduce the Cambrian explosion as the setting for our next topic.

In case you are interested in looking at the original paper, Beatty's paper is available on J-Stor. From campus, you can use this link. Off campus, log into JStor and look for "Chance and Natural Selection," John Beatty, Philosophy of Science, Vol. 51, No. 2 (Jun., 1984), pp. 183-211.

I mentioned that Gould argued most recently that Dennett is an adaptationist. His review of Dennett, which argues Dennett is an adaptationist, is here. Interesting responses to the review are to be found here. (A similar set of exchanges was made between Dennett and the biologist Allen Orr. You can read Orr's review here, and Dennett's reply here.)

IV. Does evolution have a direction?

February 29
OK, we've been reading some demanding papers. Here's an easier read, though it is still very important. Gould & Conway Morris's exchange in Natural History, a relatively mass-audience magazine. It has been collected here.

Reading analysis due. Before class write up two copies of answers to the following six questions. One copy I'll collect and grade (generously). The other copy you will read to each other and we'll correct together.
  1. What does the metaphor of "re-running the tape" mean in this context? What are the different positions that one might take with respect to "re-running the tape"?
  2. What is Conway-Morris's view on the evolution of intelligence? Is intelligence an accident (that is, something that is improbable and might not have evolved)?
  3. In a way your roommate would understand, what are the two key questions of the Cambrian explosion (according to Gould) that Gould explores in A Wonderful Life?
  4. What are Gould's (three) critisms/warnings with respect to our evaluations of the importance of convergence?
Also, please read chapter 5 in Philosophy of Biology.
March 5
Group discussion of drafts for the midterm essay. This will require that you bring to class a draft of your paper. We will discuss how to structure a clear philosophy paper, and then workshop the drafts by sharing your draft with another student who will give you advice. I'll randomly pick the partnerships.

Our midterm paper will be on topics II (genocentrism and its critics), III (adaptationism, role of chance in evolution), or IV (does evolution have a direction?). Write an essay 5 or more pages long, addressing one of the following questions:
  1. What is genocentrism (the selfish gene hypothesis)? How can the genocentrist reply to concerns like the evolution of sex; seemingly unselfish behavior like eusocial insects; or the existence of genes which ultimately kill the organism? Should genocentrism be weakened with any additional explanatory posits -- e.g., like notions of macro-evolutionary forces?
  2. Explain the Beatty problem for distinguishing genetic drift from natural selection. Why is this a problem? What are some potential solutions, and what are the benefits and challenges for those solutions? What answer do you favor?
  3. What is "adaptationism"? What concerns might we have about the stronger forms of adaptationism? How might we distinguish adaptations from constraints? Is (some form of) adaptationism consistent with the existence of genetic drift?
  4. Does evolution have a direction? What are some of the candidates for a direction? What evidence might we have for some of these? Do they have any relation to the kinds of things that we might consider important -- for example to the probability that intelligence would evolve in any given ecosystem?
See my advice on writing philosophy papers; that advice might seem not to apply here, since I recommend that you have a single hypothesis, but it could apply if your answer to one of the primary questions is your focus in the paper. Also, remember that 5 pages is so short that you don't have to attempt to be brilliantly original. You're trying to show that (1) you see the problems clearly and (2) are learning to write well enough to explain complex problems (and perhaps potential solutions) to other people. Just stating the problem so that it cannot be missed is a major accomplishment.

This is not a paper in which you must draw on many sources. You may use the things we've read in class, including class notes -- but of course looking at other sources is good if you cite them correctly.
March 7
Read pages 293-307 of "Possible Largest-Scale Trends in Organismal Evolution." This is demanding, but what we're interested in is primarily understanding the suggested trends. The paper can be found here.
March 9
Your papers are due.

V. Explaining biological purpose

March 9
We will begin our next topic: What is biological purpose?
I will introduce you to the Wright schema. We may finally look back at that selection from Aristotle we read in our first week.
March 12-16
March 19, 21
We'll start on March 19 with some warm up, and then see if you have any questions regarding the papers, and then finally turn to functions.

Read "Functions as Selected Effects: The Conceptual Analyst's Defense," Karen Neander, Philosophy of Science, Vol. 58, No. 2 (Jun., 1991), pp. 168-184.

This is not the first work by Neander on functions, but it clearly separates her view from Millikan's, and so is a good choice for that reason.

This is available on J-Stor. The stable link is Off campus, you will have to log into J-Stor and then search for the file. The off campus J-Stor login should be here.

Millikan and Neander will propose very similar accounts of function (the "etiological" account). Where they differ is on the question of whether this account is a theory (Millikan) or whether it is better understood as describing what biologists really think about functions (Neander).

I'm late posting summary questions, so let's make these due on Wednesday March 21. There are 7 questions. I've appended here some notes also to help you out.
    The main points here of interest to us are in section 3. Read section 3 first. Section 3 lays out her account of functions; the other sections of the paper defend the claim that her account is (to some degree) true to what biologists actually mean when they say "function," and defend her account against the alternatives.

  1. Can you describe Neander's explanation of functions? What does it mean to say, for example, that the purpose of the heart is to pump blood, according to her?

    Part 1 is concerned to briefly set out the worry Neander has for how she understands her account of function as conceptual analysis. (Think of this as worrying about whether it is OK to say that her account of functions is what biologists actually mean when they speak of functions.) Neander also mentions three criticisms of the etiological approach to explaining functions.

  2. What are the three criticisms of the etiological account that she describes?

    Part 2 is concerned to describe a very weak sense of conceptual analysis that hopefully avoids some worries that people have with conceptual analysis.

  3. How does she ultimately define conceptual analysis (she gets around to this on page 171)?

    Parts 4-6 address the three criticisms outlined in part 1.

  4. How does she (in part 4) answer the first criticism?
  5. How does she (in part 5) answer the second criticism?
  6. How does she (in part 6) answer the third criticism?

    Don't worry that the stuff about martians and twin earth may be obscure. Those parts refer to classic ontological and semantic debates. Skip over those parts if they are incomprehensible. Focus on the magically-appearing "instant lion."

    Section 7 considers three alternatives to the standard etiological account. Of special interest to us is subsection (i), which considers the systematic theory (as given in Cummins) as an alternative theory to the etiological account.

  7. What is her objection to the systematic theory?

    Two (I suspect very important) things to think about. First, Neander claims tumors don't have functions. Is this right? What would the genocentrist say if the genocentrist adopted an etiological account of function? Second, what does genetic drift (and the Beatty problem) mean for the etiological account?
March 23
Etiological theories. Read: "In Defense of Proper Functions," Ruth Garrett Millikan, Philosophy of Science, Vol. 56, No. 2 (Jun., 1989), pp. 288-302. Available on jstor here.

Short homework. Take a structural feature of some organism; pick a structural feature that you feel Strongly has a function (that is, don't pick the appendix if you think it's useless, or something like earlobes). Don't pick the heart since everyone uses that. Now, write, as very precisely as you can
  1. What is the exact claim the etiological theory makes about your structure? That is, translate the claim "the structure of the S is to do F" into the etiological theory. (This means your answer should be a technical-looking equation, perhaps supplemented with a bit of just so story about the history assumed.)
  2. What is the difference between this claim that you have now carefully stated as Millikan understands the claim, and as Neander understands the claim.
  3. Would you still want to claim that S did F if it was such a recent innovation that it (perhaps) had not been selected yet? (You are permitted to deny that this question is fair or even makes sense.)
March 28
The systematicists.

If you'll let me assign this, we'll read "Ontology and Teleofunctions: A Defense and Revision of the Systematic Account of Teleological Explanation," Synthese, Volume 150, Issue 1: 69-98. Publication year 2006.

I think you can get it here, but I'll also try to get you an offprint. I won't assign a reading analysis because this guy's such a loser.
April 2, 4
Answering the cross-generational challenge.

Read "Biological Organization and Cross-Generation Functions" by Saborido, Cristian, et al. The British journal for the philosophy of science, 62 (3): 583ff. Published 2011.
April 6
No classes.
April 9 & 11
I'll be giving a talk in Tucson. Write up a brief on your view on how we can best understand purpose talk in biology. Aim for 2-4 pages. Use at least one example drawn from a scientific text (e.g., a textbook) where a teleological description is given, and show how you think we should consider this passage. First, this requires you to answer whether you believe that purpose talk can be reduced, or that it refers to something irreducible, or that instead it is neither reducible nor something irreducible but rather just a mistake (this view is called "eliminativism"). Second, of the reduction views (e.g., historical, systematic) we have seen, which do you think is the most plausible. How should it answer the main criticism(s) of that view? You can adopt a pluralist view, but then defend your choice over the more parsimonious alternative of adopting a single theory. Be sure to use that view (if you endorse one) to translate the passage you have picked.

In addition to the readings we have done already, read carefully Rosenberg and McShea chapters 3 and 4. This will define views like "eliminativism," and also give you a different perspective on teleofunctions.

I want you to write your response up on your own, but you should work together to be sure you know the views. That is, meet during class, and debate your positions, and help each other be sure that you know what each view entails. Make fun of Andy when he comes in late. Expect Sarah and Amber and Kristen to answer all and sundry biological questions. Bring your vampire squid.
April 13
Your short assignment on teleofunctions is due at the beginning of class.

To get started on our new topic, before class Read Rosenberg and McShea Philosophy of Biology chapter 7. Also, start reading Dawkins where we left off -- we will want to read Dawkins chapters 5 through 10 during this section of the course.
VI. Evolutionary psychology; explaining humans with biological theory

April 16
In order to get a sense of the controversy that erupted at the origins of sociobiology, read the (in)famous reviewe of Sociobiology which is available here. It's a quick read.

This week, you should finish reading Dawkins chapters 5-10. These provide the essential background to the debates we'll discuss.

In class, our discussion will turn to evolutionary psychology, and the question, can we explain human behaviors and social customes through biology? We'll look at ultimatum Games as an example.
April 18
April 20 and 23
Please read Archer, "Why Do People Love their Pets?" Write up a brief summary of your answer to the following questions:
  • Why do pets pose a problem to a Darwinian explanation?
  • What explanations for pet ownership does Archer reject?
  • What is Archer's explanation? Is it properly Darwinian? Do you believe it?
  • How should we understand the word "parasite"? Can you define it?
April 25, 27
Read the Cronk paper I sent around. We'll discuss it and also I'll try to make more clear my worry that I voiced last class.
April 27
Ryan mentioned a few times a relevant TED talk. You can find it here: Denis Dutton: A Darwinian theory of beauty.

VII. Are there memes?

April 30
Read Dawkins chapter 11. Here are some answers to which you should write out your answers.
  1. What is a meme?
  2. Why propose memes? What work do they do for our theories?
  3. What is the general feature of all life, according to Dawkins?
  4. What are some of Dawkins's examples of memes? Can you suggest an example of a meme?
  5. Are memes made out of discrete parts?
  6. What do you think? Are there memes?
May 2
Here are TED talks on memes by Daniel Dennett Dan Dennett on dangerous memes and by Susan Blackmore Susan Blackmore on memes and "temes".

An optional reading, sympathetic but critical, is The Trouble with Memes.

VIII. The Big Question.

May 4
Last day of class.

Homework! Research project! Each of you must find a reasonable estimate of the quantity after your name and bring it to class:
  • Andy: how many galaxy superclusters there are
  • Daniel: how many galaxies are in a typical supercluster
  • Steven: how many stars are in our galaxy
  • Cassandra: proportion (fraction) of stars with planets
  • Ryan: proportion (fraction) of planets in an Earth-like orbit
  • Michael: proportion of planets with life (ha ha! you got the hard one!)
  • Amber: how long it took life to evolve on our planet
  • Andrew: how long it took intelligence to evolve on our planet
  • Sarah: how long it took our civilization to make radio
Our topics are: What is life? And why doesn't there seem to be lots of intelligent life around? The Drake Equation. The Fermi Paradox.