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Previous BIG discussion topics

Discussion Topics for Spring 2014

January 24: Muraille, Eric. 2013. "Redefining the Immune System as a Social Interface for Cooperative Processes" PLoS Pathog 9 (3):e1003203.
January 31: "The Metabolism of Philosophy, in Three Parts," pp. 193–-224 in " Dialectic and Paradox: Configurations of the Third in Modernity", B. Malkmus and I. Cooper, eds., Bern: Peter Lang, 2013. (pdf) Hannah Landecker will be visiting.
February 7: Sepkoski, D. (forthcoming)" Extinction, Diversity, and Endangerment" in Catastrophic Thinking: Extinction and the Value of Diversity. D. Sepkoski will be visiting.
February 14: Sterner, B. (forthcoming) "Material Overlap, Scaffolding, And the Diversity of Individuality" Beckett Sterner (Field Museum, Chicago) will be visiting.
February 21: Harms, M.J., and J.W. Thornton. 2013. Evolutionary biochemistry: revealing the historical and physical causes of protein properties. Nature Reviews Genetics 14(8): 559–571.
February 28: Lynch, M. 2012. Evolutionary layering and the limits to cellular perfection. PNAS 109 (46):18851-18856.
March 7: Stoltzfus, A. 2012. "Constructive neutral evolution: exploring evolutionary theory's curious disconnect." Biology Direct 7(1): 35. http://www.biology-direct.com/content/7/1/35
March 14: Spring Break No meeting
March 21: Spring Break No meeting
March 28: Mitman, G. (2013) "Ecological Imperialism Revisited: Entanglements of Disease, Commerce, and Knowledge in a Global World" Globalizing Histories of Science,Technology,and Medicine conference, May 19–21,2013, NYU, Abu Dhabi
Gregg Mitman (University of Wisconsin, Madison) will be visiting.
April 4: Fehr, C. 2012. "Feminist Engagement with Evolutionary Psychology", Hypatia Volume 27, Issue 1, pages 50–72. Carla Fehr (University of Waterloo, Canada) will be visiting.
April 11: Lange, M. 2013. Really Statistical Explanations and Genetic Drift. Philosophy of Science 80: 169–188
April 18: May, G. and Nelson, P. 2013."Defensive mutualisms: do microbial interactions within hosts drive the evolution of defensive traits?" Functional Ecology
doi: 10.1111/1365-2435.12166
April 25: Waters, C. Kenneth. 1994. Genes made molecular. Philosophy of Science 61: 163–185.
May 2: Waters, C. Kenneth. 2004. What was classical genetics? Studies in the History and Philosophy of Science 35: 783–809.
May 9: Waters, C. Kenneth. Forthcoming. Shifting Attention From Theory to Practice in Philosophy of Biology.

Discussion Topics for Fall 2013

September 6, 2013 W. F. Doolittle "Is Junk DNA bunk? A critiquie of ENCODE " PNAS Published online before print March 11, 2013 www.pnas.org/cgi/doi/10.1073/pnas.1221376110
September 13, 2013 Kültz, D. et al. 2013. New Frontiers for Organismal Biology. BioScience 63(6): 464-471
September 20, 2013 Leonelli, S. 2013. Classificatory Theory in Biology. Biological Theory 7: 338–345
September 27, 2013 Desjardins, E. 2012 "Path Dependence, Ecology and Restoration" PSA
October 4, 2013 Guerrini, A. 2013. Experiments, Causation, and the Uses of Vivisection in the First Half of the Seventeenth Century. Journal of the History of Biology 46: 227–254. DOI 10.1007/s10739-012-9319-7
October 11, 2013 Marshall Abrams (University of Alabama at Birmingham) will be visiting.
Steiner, U.K. and Tuljaiurka, S.R. 2012 "Neutral theory for life histories and individual variability in fitness components" PNAS 109(12) 4684–4689
October 18, 2013 Fridolin Gross (European School of Molecular Medicine (SEMM) in Milan) will be visiting.
Gross. F. (preprint) "The Sum of the Parts: Mycoplasma genitalium and the Future of Systems Biology"
Optional background reading. The following article includes information about the case study discussed in Gross' paper. Participants may find it helpful as background, but it will not be presupposed in our discussion.
Karr, J. R., Sanghvi, J. C., Macklin, D. N., Gutschow, M. V,. Jacobs, J. M., Bolival Jr., B., Assad-Garcia, N., Glass, J. I. and Covert, M. W. 2012. "A Whole-Cell Computational Model Predicts Phenotype from Genotype" Cell 150: 389–401
October 25, 2013 Weisberg, M. (draft) "Remeasuring Man"
November 1, 2013 Millstein, R.L. (manuscript) "Populations in Homogeneous and Heterogeneous Environments"
November 8, 2013 Theme: Model Organisms versus Model Taxa or Model Systems
Griesemer, J.R. (forthcoming)."What Salamander Biologists Have Taught Us About Evo-devo. In Conceptual Change in Biology: Scientific and Philosophical Perspectives on Evolution and Development" ed. A.C. Love. Berlin: Springer
Lanyon, S. and T. Gamble (work in progress) "An Evolutionary Perspective on the Value of Model Systems"
November 15, 2013 Mehmet Elgin (Mugla University, Turkey) will be visiting.
Sella, G. and Hirsh, A.E. 2005. "The application of statistical physics to evolutionary biology" PNAS 102(27): 9541–9546. www.pnas.orgcgidoi10.1073pnas.0501865102
November 22, 2013 Luke Premo (Washington State University) will be visiting.
Premo, L. S., 2012. "Local extinctions, connectedness, and cultural evolution in structured populations" Advances in Complex Systems 15:1150002:1–18.
December 6, 2013 Shaw, R.G. and Etterson, J.R. 2012. "Rapid climate change and the rate of adaptation: insight from experimental quantitative genetics" Tansley Review New Phytologist 195: 752–765. doi: 10.1111/j.1469-8137.2012.04230.x

Discussion topics for Spring 2013

January 25: Zuk, M. 2013. "Paleofantasy: What Evolution Really Tells Us about Sex, Diet, and How We Live" Introduction and Chapter 10
February 1: Wagner, A. 2012. "The role of randomness in Darwinian evolution"
Philosophy of Science 79: 95-119.
February 8: Hopkins, M.J. and S. Lidgard. 2012. "Evolutionary mode routinely varies among morphological traits within fossil species lineages" PNAS 109: 20520–20525.
February 15: Woodward, J . 2010 “Causation in Biology: Stability, Specificity, and the Choice of Levels of Explanation” Biology and Philosophy 25: 287–318.
February 22: Fawcett, T.W. and A.D. Higginson. 2012 ."Heavy use of equations impedes communication among biologists" PNAS 109: 11735–11739.
doi: 10.1073/pnas.1205259109
March 1: Chris Pincock (Ohio Sate) visiting.
Pincock, C. 2012."Mathematical models of biological patterns: Lessons from Hamilton’s selfish herd" Biology & Philosophy 27(4): 481–496.
March 8: Niklas, K.J. and S.A. Newman. 2013. "The origins of multicellular
organisms" Evolution & Development 15: 41–52.
March 15: No Meeting
March 22: No Meeting SPRING BREAK
March 29: Frank, S.A. and M.R. Rosner. 2012 "Nonheritable Cellular Variability Accelerates the Evolutionary Processes of Cancer" PLoS Biology 10(4):e1001296. doi:10.1371/journal.pbio.1001296
April 5: Marie Kaiser (Geneva) visiting
Kaiser, M.I. "An Ontic Account of Reductive Explanation in Biology" (draft paper)
April 12: Marie Kaiser (Geneva) visiting
Knuuttila, Tarj and Loettgers, Andrea. 2011 "The productive tension. Mechanisms vs. templates in modeling the phenomenon", in: Paul Humphreys and Cyrille Imbert, Models, Simulations, and Representations, Routledge: New York/London.
April 19: Joyce Havstad (UCSD) visiting
Havstad, Joyce C. "The Classification of Proteins" draft paper.
April 26: Rinaldi, A. 2007. "Naturally better" EMBO reports 8: 995-999;
Ball, P. 2001." Life’s lessons in design" Nature 409: 413-416.
May 3: Crabtree, G.R. 2013. Our fragile intellect. Part I. Trends in Genetics 29: 1–3; http://dx.doi.org/10.1016/j.tig.2012.10.002
Crabtree, G.R. 2013. Our fragile intellect. Part II. Trends in Genetics 29: 3–5.http://dx.doi.org/10.1016/j.tig.2012.10.003


Discussion topics for Fall 2012

September 7: Teaching Genetics
Redfield, R.J. 2012. “Why Do We Have to Learn This Stuff?”—A New Genetics for 21st Century Students. PLoS Biol 10(7): e1001356. (http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001356)
September 14: Sterner, B. "Warranting Causal Generalizations in Systems Biology" (forthcoming)
Guest: Beckett Sterner (MCPS visiting fellow)
September 21: Darwin's Beagle Voyage
Guest: Paul Brinkman North Carolina Museum of Natural History
Darwin, C. 1845. Journal of Researches (or Voyage of the Beagle); chapters 5 (pp. 81–105) and 7 (pp.123–141) . Available online: http://darwin-online.org.uk/content/frameset?itemID=F14&viewtype=side&pageseq=1
(also available from Google books)
Optional: Brinkman, P. 2010. Charles Darwin’s Beagle Voyage, Fossil Vertebrate Succession, and ‘‘The Gradual Birth & Death of Species’’Journal of the History of Biology 43: 363–399. (This article is what his HST talk at 3:35 pm in 131 Tate will be based upon.)
September 28: Human egalitarianism
Gavrilets, Sergey 2012. On the evolutionary origins of the egalitarian syndrome. Proceedings of the National Academy of Sciences 109: 14069-14074.
October 5: Behavioral biology
Guest: Marta Halina (MCPS visiting graduate student)
Halina, M. (draft paper) "Animal Mindreading: Moving Beyond the Theoretician’s Dilemma"
To celebrate the 50th anniversary of the publication of Thomas Kuhn's The Structure of Scientific Revolutions the group will take two weeks during the semester to explore how Kuhn’s ideas apply to different eras and areas of interest to the Biological Interest Group.
October 12: Kuhnfest event: Darwinian Revolution
Smocovitis, V.B. 2005. ‘‘It Ain’t Over ‘til it’s Over’’: Rethinking the Darwinian Revolution. JHB 38: 33–49 ( http://www.jstor.org/stable/4331918)
Ruse, M. 2009. The Darwinian revolution: Rethinking its meaning and significance. PNAS 106: 10040–10047 (http://www.pnas.org/content/106/suppl.1/10040.full)
October 19: Kuhnfest event: Darwinian Revolution
Bellon, R. 2011. "Inspiration in the Harness of Daily Labor: Darwin, Botany, and the Triumph of Evolution, 1859-1868." Isis 102: 393–420. (http://www.jstor.org/stable/full/10.1086/661591)
October 26: 5-275 Moos Tower (Developmental Biology Center)
*** Note change of location***
Matson, Clinton K. and Zarkower, David (2012) "Sex and the singular DM domain: insights into sexual regulation, evolution and plasticity" Nature Reviews: Genetics 13: 163–174.
November 2: Modeling
Two chapters from Long, J. 2012. Darwin's Devices: What Evolving Robots Can Teach us about the History of Life and the Future of Technology. New York: Basic Books. (ch1pdf, ch3pdf)
November 9: Molecular Genetics and Morality
McKaughan, D.J. 2012. "Voles, vasopression, and infidelity: a molecular basis for monogamy, a platform for ethics, and more?" Biology & Philosophy 27: 521-543.
November 16: NO MEETING
November 23: THANKSGIVING NO MEETING
November 30: Meyer, J.R. et al. 2012. Repeatability and Contingency in the Evolution of a Key Innovation in Phage Lambda. Science 335: 428–432. DOI: 10.1126/science.1214449
December 7: Murmann, J. P. (forthcoming) "Scaffolding in Economics, Management, and the Design of Technologies"
Guest: Peter Murmann (The Wharton School, University of Pennsylvania, & Australian School of Business, University of New South Wales, Sydney, NSW 2052, Australia)

Discussion Topics for Spring 2012

January 20: Frédéric Bouchard (2011) “Darwinism without populations: a more inclusive understanding of the “Survival of the Fittest”” Studies in History and Philosophy of Biological and Biomedical Sciences 42: 106–114 http://www.sciencedirect.com/science/article/pii/S1369848610000956

January 27: 10 am. Note earlier start time. Frédéric Bouchard (University of Montreal) visiting. Bouchard, F. (2010) “Symbiosis, Lateral Function Transfer and the (many) saplings of life” Biol. Philos. 25: 623–641 DOI 10.1007/s10539-010-9209-3
http://www.springerlink.com/content/07207v2700814650/

February 3:
Zuk, M. (2009) The evolutionary search for our perfect past. New York Times, January 19. http://www.nytimes.com/2009/01/20/health/views/20essa.html
Bailey, N.W. and Zuk, M. (2008) Acoustic experience shapes female mate choice in field crickets. Proceedings of the Royal Society of London, B 275: 2645–2650.
Bailey, N.W., McNabb, J.R. and Zuk, M. (2008) Pre-existing behavior facilitated the loss of a sexual signal in the field cricket Teleogryllus oceanicus. Behavioral Ecology 19: 202–207. 10.1093/beheco/arm123
available from www.beheco.oxfordjournals.org
Zuk, M. and Bailey, N.W. (2008) Birds gone wild: same-sex parenting in albatross.Trends in Ecology and Evolution 23: 658–660.
http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347%2808%2900298-X
Zuk, M., Rotenberry, J.T., and Tinghitella, R.M. (2006) Silent night: Adaptive disappearance of a sexual signal in a parasitized population of field crickets. Biology Letters 2: 521–524. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1834006/
Zuk, M. (2006) Family values in black and white. Nature 439: 917.
http://www.nature.com/nature/journal/v439/n7079/full/439917a.html
Zuk, M. (2004) Birds do it, bonobos do it (opinion). Los Angeles Times, March 7, M3. http://articles.latimes.com/2004/mar/07/opinion/op-zuk7

February 10: Ratcliff, W.C., R.F. Denison, M. Borrello, M. Travisano (2012) "Experimental evolution of multicellularity" www.pnas.org/cgi/doi/10.1073/pnas.1115323109.

February 17: Gasman, D. (2004) The Scientific Origins of National Socialism. New Brunswick: Transaction Publishers. pp. xi–xxxi (Introduction to the Transaction Edition) and pp. 1–30 (Chapter 1. Ernst Haeckel and the Monist League)

February 24: 10 am. Note earlier start time. Robert Richards (Fishbein Center for the History of Science and Medicine, University of Chicago) visiting.
Richards, R. (2008) The Tragic Sense of Life: Ernst Haeckel and the Struggle over Evolutionary Thought. Chicago: University of Chicago Press. pp. 223–232, 244–276. (selections from Chapter 7. The Popular Presentation of Evolution) and pp. 489–512. (Appendix 2. The Moral Grammar of Narratives in the History of Biology—the Case of Haeckel and Nazi Biology)

March 2: Evolutionary Psychology. Bolhuis, J., G. Brown, R. Richardson and K. Laland. (2011). Darwin in Mind: New Opportunities for Evolutionary Psychology .PLoS Biology 9 (7): e1001109. (OPEN ACCESS)

March 23: Philosophy of Science from a Scientist. Peter Truran

March 30: Mayr's Proximate-Ultimate Distinction. Mayr, E. (1961) Cause and Effect in Biology. Science 134: 1501-1506.

April 6: Revisiting Mayr's Proximate-Ultimate Distinction. Laland, K.N.et al. (2011) Cause and Effect in Biology Revisited: Is Mayr's Proximate-Ultimate Dichotomy Still Useful? Science 334: 1512–1516. doi: 10.1126/science.1210879

April 13: Travisano, M., Shaw, R, (draft manuscript) Genotype-phenotype mapping: reconsidering a research program

April 20: Plasticity. Schwander, T. and Leimar, O. (2011) "Genes as leaders and followers in evolution" Trends in Ecology and Evolution, March 2011, Vol. 26, No. 3 143–151. doi:10.1016/j.tree.2010.12.010

April 27: Nathan, M.J. (2012) "The Varieties of Molecular Explanation" Philosophy of Science, 79(2): 233–254. http://www.jstor.org/stable/10.1086/664791

Discussion Topics for Fall 2011

September 9: Schiener, S. (2010) "Toward a Conceptual Framework for Biology", The Quarterly Review of Biology 85: 293-318.
September 16: Tsou, J. "Intervention, Causal Reasoning, and the Neurobiology of Mental Disorders: Pharmacological Drugs as Experimental Instruments" (working paper).
September 23: Gerson, E. (2007) "The Juncture of Evolutionary and Developmental Biology", In: From Embryology to Evo-devo: A History of Developmental Evolution. M.D. Laubichler and J. Maienschein (eds.). Cambridge, MA: MIT Press, pp. 435-463.
September 30: MacLeod, M. (draft) "Limitations of natural-­talk in the life sciences: Homology and other cases"
Miles MacLeod will be attending the meeting.
Optional background reading
Hacking, I (2007) “Natural Kinds: Rosy Dawn, Scholastic Twilight” Royal Institute of Philosophy Supplement 61(1): 203–239. DOI: 10.1017/S1358246107000203
October 7: 10:00 am Karl Niklas (Cornell University) attended the meeting. Note early start time.
William L. Crepet and Karl J. Niklas (2009) "Darwin's second 'abominable mystery': Why are there so many angiosperm species?" American Journal of Botany 96:366-381.
October 14: Lidgard, S. & L.H. Liow "Living fossils and evolutionary stasis - a framework" (working paper). Scott Lidgard attended the meeting.
October 21: Emilie C. Snell-Rood, James David Van Dyken, Tami Cruickshank, Michael J. Wade, and Armin P. Moczek (2010) “Toward a population genetic framework of developmental evolution: the costs, limits, and consequences of phenotypic plasticity” BioEssays 32:71–81. DOI 10.1002/bies.200900132
Ben Lehner, Kunihiko Kaneko (2011) “Fluctuation and response in biology” Cell. Mol. Life Sci. 68:1005–1010. DOI 10.1007/s00018-010-0589-y
October 28: Manganaro, C. (forthcoming, PhD thesis) Assimilation Nation: Human Science and Racial Destiny in Hawai‘i, 1919–1939, Chapter 1
November 4: Evan Weiher, Deborah Freund, Tyler Bunton, Artur Stefanski, Tali Lee and Stephen Bentivenga (2011) "Advances, challenges and a developing synthesis of ecological community assembly theory" Phil. Trans. R. Soc. B 366: 2403-2413
doi: 10.1098/rstb.2011.0056
November 11: O’Malley, M.A., K.C. Elliott, C. Haufe, and R.M. Burian (2009) "Philosophies of Funding" Cell 138: 611-615
Haufe, C. "The Good, The Bad, and the Exploratory" (working paper)
Chris Haufe (Case Western Reserve University) attended the meeting.
November 18: Leonelli, S. (2009) "On the Locality of Data and Claims About Phenomena." Philosophy of Science 76(5): 737–749
December 2: Meeting will start early at 10:00 am. Sabina Leonelli attended the meeting.
Leonelli, S. (forthcoming) "Classificatory Theory in Data-Intensive Science: The Case of Open Biomedical Ontologies" International Studies in the Philosophy of Science
December 9: Douglas H. Erwin, Marc Laflamme, Sarah M. Tweedt, Erik A. Sperling, Davide Pisani, Kevin J. Peterson (2011) “The Cambrian Conundrum: Early Divergence and Later Ecological Success in the Early History of Animals” Science 334, 1091 DOI: 10.1126/science.1206375

Discussion Topics for Spring 2011

January 21: Lehrer, J. (2010) "The Truth Wears Off: Is there something wrong
with the scientific method?" (Annals of Science) New Yorker. (Dec. 13th, 2010
issue)

January 28: Ioannidis, J. P. (2005) "Why most published research findings
are false." PLoS Medicine 2:e124. (Open Access:
http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124)

February 4: Turner, D. (2011) "Gould's Replay Revisited." Biology & Philosophy
26:65–79.

February 11: Lynch, M. (2007) "The frailty of adaptive hypotheses for the origins of organismal complexity". PNAS 104: 8597–8604.

February 18: Reiss, J. O. (2009) "Not by Design: Retiring Darwin's Watchmaker" Berkeley: University of California Press ISBN-10: 052025893 ISBN-13: 978-0520258938 Chapters 1 and 2, The Problem and Philosophical Background pp 3–27.

February 25: Reiss, J. O. (2009) "Not by Design: Retiring Darwin's Watchmaker" Chapter 6, Darwin, Natural Theology, and the Principle of Natural Selection, pp 121–149.

March 4: Reiss, J. O. (2009) "Not by Design: Retiring Darwin's Watchmaker" Chapter 10, Adaptedness, Natural Selection, and the Conditions for Existence, pp 257–277.

March 25: Note that the meeting will begin at 10 am and that John Reiss will be joining the group. Reiss, J. O. (2009) "Not by Design: Retiring Darwin's Watchmaker" Chapters 11 and 12, How to Talk about Macroevolution and The Conditions for Existence as a Unifying Concept in Evolutionary Biology, pp 279–352.

April 1: Crowe, Nathan "Embodying Conflict: Robert Briggs and the Potential of Nuclear Transplantation" dissertation chapter, work in progress

April 8: Meeting Canceled.
Haufe, Chris "The Good, the Bad, and the Exploratory" work in progress

April 15: Raff, Rudolf A. (1996) "The Shape of Life" Chicago: University of Chicago Press ISBN-10: 9780226702667, ISBN-13: 978-0226702667 Chapter 6, pp. 173–210.
Slack, J.M.W. et al. (1993) "The zootype and the phylotypic stage." Nature 361:490–492.

April 22: Bininda-Edmonds O.R.P. et al. (2003) "Inverting the hourglass: quantitative evidence against the phylotypic stage in vertebrate development." Proceedings of the Royal Society B: Biological Sciences 270:341–346.
*Optional/Background reading
Richardson, M.K. et al. (1997) "There is no highly conserved embryonic stage in the vertebrates: implications for current theories of evolution and development." Anatomy and Embryology 196:91–106.

April 29: Prud’homme, B. and N. Gompel (2010) "Genomic Hourglass." Nature 468: 768–769.
Schmidt, K. and J. M. Starck (2011) "Testing evolutionary hypotheses about the phylotypic period of zebrafish." Journal of Experimental Zoology Part B, Molecular and Developmental Evolution.
*Optional/Background reading
Kalinka, A.T. et al. (2010) "Gene expression divergence recapitulates the developmental hourglass model." Nature 468:811–814.
Domazet-Lošo, T. and D. Tautz, (2010) "A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns."Nature 468:815–818.

Discussion Topics for Fall 2010

September 10: Wald, C. and C. Wu (2010) "Of Mice and Women: The Bias in Animal Models", Science 327: 1571-2; Kim, A.M. et al. (2010) "Sex bias in trials and treatment must end", Nature 465: 688-9; Baylis, F. (2010) "Pregnant women deserve better", Nature 465: 689-90; Zucker, I. and A.K. Berry (2010) "Males still dominate animal studies", Nature 465: 690.

September 17: Beery, A.K., and I. Zucker. (in press) “Sex bias in neuroscience and biomedical research” Neuroscience & Biobehavioral Reviews.
September 24: Behavioral Biology - Owens, I. P. (2006) "Where is behavioural ecology going?" Trends in Ecology & Evolution 21:356–61

October 1: Penrose, L. S. (1959) "Self Reproducing Machines" Scientific American June 1959 200(6): 105–114.

October 8: Gánti, T. (1997) "Biogenesis Itself" J. Theor. Biol. 187: 583–593.

October 15: Jablonka, E. and Raz, G. (2009) "Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution" The Quarterly Review of Biology 84(2): 131–176.

October 22: Nowak, M. A., C. E. Tarnita, and E. O. Wilson (2010) "The evolution of
eusociality" Nature 466:1057–1062.
Background reading: Maynard Smith, J. (1964) "Group Selection and Kin Selection" Nature 201:1145–1147; Hamilton, W. D. (1963) "The Evolution of Altruistic Behavior" American Naturalist 97:354–356

October 29: Replies to Nowak et al. (2010)
Joan E. Strassmann, Robert E. Page, Jr., Gene E. Robinson, & Thomas D. Seeley "Kin Selection and Eusociality" manuscript (password protected:
David Sloan Wilson's blog: http://scienceblogs.com/evolution/2010/09/what_does_it_mean_for_a_theory.php
Ford Denison's blog: http://blog.lib.umn.edu/denis036/thisweekinevolution/2010/08/theres_much_more_to_hamiltons.html
Jerry Coyne's blog: http://jerrycoyne.uchicago.edu/about.html
Richard Dawkins' blog: http://richarddawkins.net/articles/508102-a-misguided-attack-on-kin-selection

November 5: No meeting (HSS/PSA)

November 12: Prum, R.O. (in press) "The Lande–Kirkpatrick Mechanism is the Null Model of Evolution by Intersexual Selection: Implications for Meaning, Honesty, and Design in Intersexual Signals" Evolution.
Background reading: Kokko, H. et al. (2006) "Unifying and Testing Models of Sexual Selection" Annu. Rev. Ecol. Evol. Syst. 37:43–66.

November 19: Prum, R.O. (in press) "The Lande–Kirkpatrick Mechanism is the Null Model of Evolution by Intersexual Selection: Implications for Meaning, Honesty, and Design in Intersexual Signals" Evolution.
Background reading: Kokko, H. et al. (2006) "Unifying and Testing Models of Sexual Selection" Annu. Rev. Ecol. Evol. Syst. 37:43–66.

November 26: THANKSGIVING - No meeting

December 3: Roughgarden, J. (2009) "The Genial Gene: Deconstructing Darwinian Selfishness" Berkeley: University of California Press. Chapter 1, pp17–22, Chapter 2, pp 23–60.

December 10: Miller, G. (2010) "The Seductive Allure of Behavioral Epigenetics", Science 329: 24-27

Discussion Topics for Spring 2010

January 22: Perini, Laura (2005) “Explanation in two dimensions: diagrams and biological explanation” Biology and Philosophy 20(2-3) pp 257–269 DOI: 10.1007/s10539-005-2562-y

January 29: Perini, Laura (2005) “Visual Representations and Confirmations” Philosophy of Science 72(5) pp 913–926

February 5: 10 am ** Note start time ** Perini, Laura "Diagrammatic Reasoning in Biology" (forthcoming in Knowledge Engineering Review) Laura Perini will be visiting the group.

February 12: Michon, F., and M. Tummers (2009), "The dynamic interest in topics within the biomedical scientific community" PLoS ONE 4(8):e6544.

February 19: Weiss, K. (2005) "The phenogenetic logic of life" Nat. Rev. Genet. 6: 36–45

February 26: Buchanan, A, Weiss, K, Fullerton, SM (2006) "Dissecting complex disease: the quest for the philosopher’s stone?" (a forum article with commentary and our reply) International J. Epidemiol. 35: 562-596.Commentary and reply can be found at http://ije.oxfordjournals.org/content/vol35/issue3/index.dtl

March 5: 10 am ** Note start time ** Ken Weiss will be joining the group to discuss his work. Buchanan, A, Sholtis, S, Richtsmeier, J, Weiss, K. (2009) "What are genes for? How are traits made? What is the question?" Bioessays 31: 198-208.

March 12: NO MEETING

March 19: Spring Break

March 26: Denison, R. Ford, "Darwinian agriculture: where does nature's wisdom lie?" Preface & Chapter 1

April 2: Denison, R. Ford, "Darwinian agriculture: where does nature's wisdom lie?" Chapter 6

April 9: Denison, R. Ford, "Darwinian agriculture: where does nature's wisdom lie?" Chapter 8

April 16: Reydon, T. (2009), "Gene Names as Proper Names of Individuals: An
Assessment" British Journal for the Philosophy of Science 60:409-432

April 23: Cain, J. (2009) "Rethinking the Synthesis Period in Evolutionary Studies"
Journal of the History of Biology 42: 621-648

April 30: Borrello, M. E. (2009) "Shifting Balance and Balancing Selection: A Group Selectionist’s Interpretation of Wright and Dobzhansky" chapter 15 in Descended from Darwin Insights into the History of Evolutionary Studies, 1900–1970 Cain, J. and Ruse, M. (eds) Transactions of the American Philosophical Society Volume 99 Part 1 pp 323–344.

May 7: Macilwain, C. (2009) "Watching science at work" Nature 462: 840-842

Discussion Topics for Fall 2009

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September 11: "Environmental Standardization: Cure or Cause of Poor Reproducibility in Animal Experiment?" Richter et al. (2009) Nature Methods 6:257-261

September 18: "The Principle of Drift: Biology's First Law." Brandon, R.N. (2006) The Journal of Philosophy 102(7): 319-335

September 25: "Style, Function, and Cultural Evolutionary Processes" Bettinger, R.L., Boyd, R., Richerson, P.J. Chapter 8 in Darwinian Archaeologies Maschner, D.H.G. (ed) New York: Plenum, 1996 pp. 133-164
Chapter 1 of Testing for Cultural Transmission in the Pleistocene: The Middle to Upper Paleolithic transition from the Near East to Europe Tostevin, G.B. (in preparation)

October 2: Seminar discussion with Gil Tostevin.
Chapter. 3 of Testing for Cultural Transmission in the Pleistocene: The Middle to Upper Paleolithic transition from the Near East to Europe Tostevin, G.B. (in preparation) pp. 54-89 (starting at '3.2 Culture History as Evolutionary Process')

October 9: Chapter 3 of Representation and Productive Ambiguity in Mathematics and the Sciences Emily Grosholz. Oxford University Press, 2007

October 16: Chapter 4 of Representation and Productive Ambiguity in Mathematics and the Sciences Emily Grosholz. Oxford University Press, 2007

October 23: Note 10 am start time BIG Seminar Discussion with Emily Grosholz

October 30: "Size, Shape, and Asymmetry in Fossil Hominins: The Status of the LB1 Cranium Based on 3D Morphometric Analyses" K. L. Baab and K.P. McNulty (2009) Journal of Human Evolution doi:10.1016/j.jhevol.2008.08.011

November 6: "Darwin's Achievement" Philip Kitcher (Philosophical perspective inspired by Darwin)?

November 13: "Mind the Gap: Did Darwin Avoid Publishing his Theory for Many Years?" John van Wyhe Notes Rec. R. Soc. (2007) 61, 177–205.doi:10.1098/rsnr.2006.0171

November 20: Readings in preparation for Joan Strassmann and David Queller visit. "Sociobiology Goes Micro: Long used for studying development, Dictyostelium now also provides a model for analyzing social interactions" Joan E. Strassmann and David C. Queller ASM News (2004) 70(11) 526–532.
"Facultative cheater mutants reveal the genetic complexity of cooperation in social amoebae" Lorenzo A. Santorelli, Christopher R. L. Thompson, Elizabeth Villegas, Jessica Svetz, Christopher Dinh, Anup Parikh, Richard Sucgang, Adam Kuspa, Joan E. Strassmann, David C. Queller & Gad Shaulsky, Nature (February 2008) 451(28) 1107–1111.
"Cheater-resistance is not futile" Anupama Khare, Lorenzo A. Santorelli, Joan E. Strassmann, David C. Queller, Adam Kuspa & Gad Shaulsky, Nature (2009) 461, 980–982 doi:10.1038/nature08472

December 4: Readings in preparation for Joan Strassmann and David Queller visit.
"Kin Discrimination Increases with Genetic Distance in a Social Amoeba" Elizabeth A. Ostrowsk*, Mariko Katoh, Gad Shaulsky, David C. Queller and Joan E. Strassmann, PLoS Biology (2008) 6(11): e287 doi:10.1371/journal.pbio.0060287 or at http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0060287
"Polymorphic Members of the lag Gene Family Mediate Kin Discrimination in Dictyostelium" Rocio Benabentos, Shigenori Hirose, Richard Sucgang, Tomaz Curk, Mariko Katoh, Elizabeth A. Ostrowski, Joan E. Strassmann, David C. Queller, Blaz Zupan, Gad Shaulsky, and Adam Kuspa, Current Biology (2009) 19, 567–572
doi: 10.1016/j.cub.2009.02.037

December 11: Note 10 am start time BIG Seminar Discussion with Joan Strassmann and David Queller on "Beyond society: the evolution of organismality" David C. Queller and Joan E. Strassmann, Phil. Trans. R. Soc. B (2009) 364, 3143–3155
doi: 10.1098/rstb.2009.0095

Discussion Topics for Spring 2009

January 23: "Migration: An Engine for Social Change" by Peter Richerson and Robert Boyd. Discussion of BIG plans for upcoming semester

January 30: David Sepkoski visits: discuss Punk Eke paper

February 6: "Evolution on a restless planet: Were environmental variability and environmental change major drivers of human evolution?", Robert L. Bettinger and Robert Boyd. Handbook of Evolution Vol. 2 edited by Franz M. Wuketits and Francisco J. Ayala, pp. 223-242. 2005

February 13: "Cultural innovations and demographic change", Peter J. Richerson and Robert Boyd. Submitted to Demographic Processes and Cultural Change, James Steele, editor.

February 20: (early 10 AM start time) Peter Richerson visits the group, discuss Restless Planet and Demographic Change papers (Peter Richerson will present a talk entitled "Darwinian Evolutionary Ethics: Between Patriotism and Sympathy" at the SST symposium at 3:35pm in 131 Phys)

February 27: "The Many Faces of Fitness and the Structure of Natural Selection Theory" by Marcel Weber

March 6: Meet with Ruth Shaw's group in room 342 Gortner on the St. Paul Campus to discuss fitness. Ruth G. Shaw, Charles J. Geyer, Stuart Wagenius, Helen H. Hangelbroek, and Julie R. Etterson "Unifying Life-History Analyses for Inference of Fitness and Population Growth" vol. 172, no. 1 The American Naturalist E3–E47 July 2008.

March 13: Prelims and Part I (Chapters 1-3) from Re-engineering Philosophy for Limited Beings by William Wimsatt
Chapter 1 Myths of LaPlacean Omniscience
Chapter 2 Normative Idealizations versus the Metabolism of Error
Chapter 3 Toward a Philosophy for Limited Beings

March 20: Spring Break

March 27: Chapter 4 (introduction), chapters 5, 7, 8 from Re-engineering Philosophy for Limited Beings by William Wimsatt
Part 2: Problem-Solving Strategies for Complex Systems
Chapter 4 Robustness, Reliability, and Overdetermination
Chapter 5 Heuristics and the Study of Human Behavior
Chapter 7 Robustness and Entrenchment: How the Contingent Becomes Necessary
Chapter 8 Lewontin's Evidence (That There Isn't Any)

April 3: Introduction to Part III "Reductionism(s) in Practice", pp. 159 - 178.
Chapter 11 "Reductive Explanation: A Functional Account", pp. 241 - 273 from Re-engineering Philosophy by for Limited Beings William Wimsatt

April 10: Introduction to Part IV "Engineering an Evolutionary View of Science", pp. 313 - 318.
Chapter 13 "Epilogue: On the Softening of the Hard Sciences", pp. 319 - 342 from Re-engineering Philosophy by for Limited Beings William Wimsatt

April 17: William Wimsatt visits. The meeting will begin at 10 AM. There will be an opportunity for graduate students to lunch with Professor Wimsatt after the group meeting.

April 24: Alan Love, "Temporal Dimensions of Reductionism in Biology"

May 1: Alex Rosenberg "Reductionism in a Historical Science" Phil. Sci. 68(2) 135 - 163

May 8: "Species, Genes, and the Tree of Life" Joel Velasco talk in 737 Heller Hall
Abstract: A common view is that species occupy a unique position on the Tree of Life. For this they must be genealogically exclusive groups. In this paper I argue that exclusivity could represent facts about gene genealogies. Here, an exclusive group is a group of organisms that forms a clade for a higher proportion of the genome than any conflicting clade. Taxa occupy a unique position in what can be called the "primary concordance tree". But each gene has its own historical "tree of life". I conclude by arguing that both organismal pedigrees with the corresponding Tree of Life as well as gene genealogies and their trees are objectively real and play important, but different, roles in biological practice.

Discussion topics for Fall 2008:

Topic 1: Evolution and the Levels of Selection by Samir Okasha Oxford University Press (2006) ISBN 0199267979 and related articles
BIG decided to begin the year by reading and discussing Samir Okasha's Evolution and the Levels of Selection (Oxford University Press, 2005). Samir will be visiting the BIG Seminar on Friday, October 31st. He will also give an SST talk at 3:30. His book is one of the most important works in the philosophy of biology in recent years. It not only provides a fresh look at one of the central topics in the philosophy of biology (in part by introducing important recent work from evolutionary biology), but he also critically examines (and improves upon) the conceptual analysis of evolutionary theory that forms the basis of work on many topics in the philosophy of biology.

The first four chapters of Samir's book build upon one another to provide a common basis from which each of the following four chapters independently follow. So we will begin by discussing the four chapters in turn, and then decide how to proceed with the remainder of the book. Here is our initial schedule:

September 12: Introduction (pp. 1–9) 

"Natural Selection in the Abstract" (Ch. 1, pp. 10–39)
September 18: talk by Greg Velicer (Indiana University) "The Evolution of Sociality" Thursday, 3:30 PM, 239 Gortner (St Paul campus) come a few minutes early and score some cookies and coffee (and a chair)
September 19: "Strategies of Microbial Cheater Control" by Michael Travisano and Greg Velicer Trends in Microbiol. (2004) 12(2) 72–78
September 26: "Selection at Multiple Levels: Concepts and Methods" (Ch. 2, pp. 40–75)
October 3: "Causality and Multi-level Selection" (Ch. 3, pp. 76–111)
October 10: "Philosophical Issues in the Levels-of Selection Debate" (Ch. 4, pp. 112–142)
October 17: "The Gene's-Eye View and its Discontents" (Ch. 5, pp. 143–172)

Discussion topics for Spring 2008:

Topic 1: Laws in Biological Sciences (with Center visitor Michael Strevens)
January 18: Michael Strevens (manuscript) "Physically Contingent Laws and Counterfactual Support"
January 25: We will meet with Michael Strevens to discuss his views on laws in biological sciences

Topic 2: Evolutionary Psychology
February 1: Leda Cosmides & John Tooby, "Evolutionary Psychology: A Primer" online publication, http://www.psych.ucsb.edu/research/cep/primer.html.
February 8: John Dupré, "The Evolutionary Psychology of Sex and Gender", chapter 3 of Human Nature and the Limits of Science, Oxford: Oxford University Press 2001, pp. 44 - 69.
February 15: John Dupré, "The Charms and Consequences of Evolutionary Psychology", chapter 4 of Human Nature and the Limits of Science, Oxford: Oxford University Press 2001, pp. 70 - 92.
February 22: Martie G. Haselton et al., "Ovulatory shifts in human female ornamentation: Near ovulation, women dress to impress", Hormones and Behavior 51 (2007) 40 - 45.

Topic 3: Chance and Contingency in Evolutionary Biology
February 29: Beatty, John (2006) "Replaying Life's Tape", Journal of Philosophy, Volume CIII, Number 7, pp. 336 - 62.

Topic 4: Downward Causation
March 7: Carl F. Craver and William Bechtel, “Downward Causation and Biological Mechanisms”, Biology and Philosophy 22 (2007) 547–563.
March 14: Spring Break
March 21: Spring Break

Topic 5: William Harvey's Epistemology
March 28: William Harvey and Descartes—Philosophical Perspectives (1)
J. A. Passmore “William Harvey and the Philosophy of Science”, The Australasian Journal of Philosophy, 36(2) (1958) 85–94.
Also: John P. McCaskey “Regula Socratis: The Rediscovery of Ancient Induction in Early Modern England”, PhD Thesis, Stanford University 2006 (excerpt) pp. 314–333.
April 4: William Harvey and Descartes—Philosophical Perspectives (2)
Geoffrey Gorham “Mind-Body Dualism and the Harvey–Descartes Controversy”, Journal of the History of Ideas, 55(2) (1994) 211–234.
April 11: William Harvey's Embryology
James G. Lennox “The Comparative Study of Animal Development: William Harvey’s Aristotelianism”, chapter 1 of The Problem of Animal Generation in Early Modern Philosophy Justin E. H. Smith (ed), Cambridge: Cambridge University Press 2006, pp. 21–46.
April 18: Jason Clark (manuscript) "Relations of Homology Between Basic and Higher-Cognitive Emotions: Steps Toward a Unified Theory of Emotion"

Topic 6: Alan's Big Adventure (prefaced by Ken introduction of Reichenbach's version of the distinction between the contexts of discovery and justification)
April 25: Alan C. Love et al. “Co-option and Dissociation in Larval Origins and Evolution: the Sea Urchin Larval Gut”, Evolution & Development, 10(1) (2008) 74–88.
May 2: Alan C. Love et al. “Co-option and Dissociation in Larval Origins and Evolution: the Sea Urchin Larval Gut”, Evolution & Development, 10(1) (2008) 74–88.
May 9: Michael Root "The Use of Race in Medicine as a Proxy for Genetic Differences", Philosophy of Science 70(5) (2003) 1173–1183.

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