A relic of design: against proper functions in biology
Tóm tắt
The notion of biological function is fraught with difficulties—intrinsically and irremediably so, we argue. The physiological practice of functional ascription originates from a time when organisms were thought to be designed and remained largely unchanged since. In a secularized worldview, this creates a paradox which accounts of functions as selected effect attempt to resolve. This attempt, we argue, misses its target in physiology and it brings problems of its own. Instead, we propose that a better solution to the conundrum of biological functions is to abandon the notion altogether, a prospect not only less daunting than it appears, but arguably the natural continuation of the naturalisation of biology.
Tài liệu tham khảo
Amundson R, Lauder GV (1994) Function without purpose: the uses of causal role functions in evolutionary biology. Biol Philos 9:443–470
Beadle GW, Tatum EL (1941) Genetic control of biochemical reactions in neurospora. Proc Natl Acad Sci 27:499–506. https://doi.org/10.1073/pnas.27.11.499
Bechtel W, Richardson R (2010) Discovering Complexity - Decomposition and Localization as Strategies in Scientific Research. The MIT Press, Cambridge
Bernard C (1863) Nouvelle fonction du foie considéré comme organe producteur de matière sucrée chez l’homme et les animaux. Baillière, Paris
Bigelow J, Pargetter R (1987) Functions. J Philos 84(4):181–196. https://doi.org/10.2307/2027157
Birney E (2012) Lessons for big-data projects. Nature 489:49
Blekhman R, Man O, Herrmann L, Boyko AR, Indap A, Kosiol C, Bustamante CD, Teshima KM, Przeworski M (2008) Natural selection on genes that underlie human disease susceptibility. Curr Biol 18(12):883–889. https://doi.org/10.1016/j.cub.2008.04.074
Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ et al (2012) Annotation of functional variation in personal genomes using regulomeDB. Genome Res 22(9):1790–1797. https://doi.org/10.1101/gr.137323.112
Brunet TDP, Doolittle WF (2014) Getting “function” right. Proc Natl Acad Sci USA 111(33):3365. https://doi.org/10.1073/pnas.1409762111
Brunet TDP, Doolittle F, Bielawski JP (2021) The role of purifying selection in the origin and maintenance of complex function. Stud Hist Philos Sci 11:125
Brzovi Z, Sustar P (2020) Postgenomics function monism. Stud Hist Phil Biol Biomed Sci 101. https://doi.org/10.1016/j.shpsc.2019.101243
Buller DJ (1998) Etiological theories of function: a geographical survey. Biol Philos 13(4):505–527. https://doi.org/10.1023/A:1006559512367
Ciccarelli FD (2010) The (R)evolution of cancer genetics. BMC Biol 2–5
Craver CF (2006) When mechanistic models explain. Synthese 153(3):355–376. https://doi.org/10.1007/s11229-006-9097-x
Craver C, Darden L (2013) In search of mechanisms. The University of Chicago Press, Chicago
Cummins R (1975) Functional analysis. J Philos 72(20):741–765
Domazet-Lošo T, Tautz D (2010) Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa. BMC Biol 8:1–10. https://doi.org/10.1186/1741-7007-8-66
Doolittle WF (2013) Is junk DNA bunk? A critique of ENCODE. Proc Natl Acad Sci USA 110(14):5294–5300. https://doi.org/10.1073/pnas.1221376110
Doolittle WF, Brunet TDP (2017) On causal roles and selected effects: our genome is mostly junk. BMC Biol 15(1):1–9. https://doi.org/10.1186/s12915-017-0460-9
Doolittle F, Brunet TDP, Linquist S, Ryan Gregory T (2014) Distinguishing between ‘Function’ and ‘Effect’ in genome biology. Genome Biol Evol 6(5):1234–1237. https://doi.org/10.1093/gbe/evu098
Duschesneau F (2010) “Rôle du couple « structure/fonction » dans la constitution de la biologie comme science.” In: Gayon J, de Ricqlès A (eds.) Les fonctions: des organismes aux artefacts. Paris: Presses Universitaires de France
Eddy SR (2012) The C-value paradox, junk DNA and ENCODE. Curr Biol. https://doi.org/10.1016/j.cub.2012.10.002
Eddy SR (2013) The ENCODE project: missteps overshadowing a success. Curr Biol. https://doi.org/10.1016/j.cub.2013.03.023
Garson J (2019) There are no ahistorical theories of function. Philos Sci 86(5):1146–1156. https://doi.org/10.1086/705472
Germain P-L (2012) Cancer cells and adaptive explanations. Biol Philos 27:785–810. https://doi.org/10.1007/s10539-012-9334-2
Germain PL, Ratti E, Boem F (2014) Junk or functional DNA? ENCODE and the function controversy. Biol Philos 29(3):807–831
Ginger RS, Askew SE, Ogborne RM, Wilson S, Ferdinando D, Dadd T, Smith AM, Kazi S, Szerencsei RT, Winkfein RJ, Schnetkamp PPM, Green MR (2008) SLC24A5 encodes a trans-golgi network protein with potassium-dependent sodium-calcium exchange activity that regulates human epidermal melanogenesis. J Biol Chem 283:5486–5495. https://doi.org/10.1074/jbc.M707521200
Godfrey-Smith P (1999) Adaptationism and the power of selection. Biol Phil 14:181–194. https://doi.org/10.1023/A:1006630232690
Godfrey-Smith P (2001) Three kinds of adaptationism. In: Orzack SH, Sober E (eds) Adaptationism and optimality. Cambridge University Press, Cambridge, pp 335–57
Godfrey-Smith P (2009) Darwinian populations and natural selection. Oxford University Press
Gould SJ, Lewontin RC (1979) The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. JSTOR 205(1161):581–598
Graur D (2016) Molecular and genome evolution. Sinauer Associates, Inc.
Graur D, Zheng Y, Price N, Azevedo RRBR, Zufall R, Elhaik E (2013) On the immortality of television sets: ‘function’ in the human genome according to the evolution-free Gospel of ENCODE. Genome Biol Evol 5(3):578–90. https://doi.org/10.1093/gbe/evt028
Griffiths PE (1996) The historical turn in the study of adaptation. Br J Philos Sci 47:511–532. https://doi.org/10.1093/bjps/47.4.511
Griffiths PE (2009) In what sense does ‘nothing make sense except in the light of evolution’? Acta Biotheor 57(1–2):11–32. https://doi.org/10.1007/s10441-008-9054-9
Guyton AC, Hall JE (2000) Textbook of medical physiology, 10th edn. W.B. Saunders Company, Philadelphia
Heilbrunn LV (1937) An outline of general physiology. W.B. Saunders Company.
Holmes FL (1963) Elementary analysis and the origins of physiological chemistry. Isis 54:50–81. https://doi.org/10.1086/349664
Keller EF (2000) The century of the gene. Harvard University Press, Cambridge
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Hardison RC (2014) Defining functional DNA elements in the human genome. Proc National Acad Sci 111(17):6131–6138. https://doi.org/10.1073/pnas.1318948111
Kohler R (1982) From medical chemistry to biochemistry: the making of a biomedical discipline. Cambridge University Press, Cambridge
Laland KN, Odling-Smee J, Hoppitt W, Uller T (2013) More on how and why: cause and effect in biology revisited. Biol Philos 28:719–745. https://doi.org/10.1007/s10539-012-9335-1
Lamason RL, Mohideen M-APK, Mest JR, Wong AC, Norton HL, Aros MC, Jurynec MJ, Mao X, Humphreville VR, Humbert JE, Sinha S, Moore JL, Jagadeeswaran P, Zhao W, Ning G, Makalowska I, McKeigue PM, O’Donnell D, Kittles R, Parra EJ, Mangini NJ, Grunwald DJ, Shriver MD, Canfield VA, Cheng KC (2005) SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science 310:1782–1786. https://doi.org/10.1126/science.1116238
Lavoisier AL (1780) Expériences sur la respiration des animaux, et sur les changemens qui arrivent à l'air en passant par leur poumon. Académie des sciences
Lennox JG (2010) La fonction biology: phylogénie d'un concept. In: Gayon J, de Ricqlès A (eds.) Les fonctions: des organismes aux artefacts. Paris: Presses Universitaires de France
Lenoir T (2011) The strategy of life: teleology and mechanics in nineteenth century German biology
Levins R, Lewontin RC (1985) The dialectical biologist. Harvard University Press
Lewens T (2004) Organisms and artifacts: Design in nature and elsewhere. MIT Press
Lewontin RC, Kamin LJ, Rose SP (1984) Not in our genes biology, ideology, and human nature. Pantheon Books, New York
Linquist S, Doolittle WF, Palazzo AF (2020) Getting clear about the F-word in genomics. PLoS Genet. https://doi.org/10.1371/journal.pgen.1008702
Lloyd EA (2015) Adaptationism and the logic of research questions: how to think clearly about evolutionary causes. Biol Theory 10(4):343–62. https://doi.org/10.1007/s13752-015-0214-2
Magendie F (1816) Note sur les gaz intestinaux de l’homme sain. Annales de Chimie et de Physique 2:292–296
Matthen M (1997) Teleology and the product analogy. Australas J Philos 75:21–37. https://doi.org/10.1080/00048409712347651
Mayr E (1961) Cause and effect in biology. Science 134:1501
Mayr E (1974) Teleological and teleonomic, a new analysis. In: Cohen RS, Wartofsky MW (eds.) Methodological and historical essays in the natural and social sciences Boston studies in the philosophy of science. Dordrecht, Springer. https://doi.org/10.1007/978-94-010-2128-9_6
Mayr E (1992) The idea of teleology. J Hist Ideas 53(1):117–135. https://doi.org/10.2307/2709913
Millikan R (1989) In defense of proper functions. Philos Sci 56(2):288–302
Morange M (1997) The transformation of molecular biology on contact with higher organisms, 1960–1980: from a molecular description to a molecular explanation. Hist Philos Life Sci 19(3):369–393
Morange M (2010) “L'attribution de fonctions aux macromolécules individuelles : une histoire complexe, qui reflète les transformations de la biologie. In: Gayon J, de Ricqlès A (eds.) Les fonctions: des organismes aux artefacts. Paris: Presses Universitaires de France
Morange M (2021) The black box of biology. Harvard University Press, Cambridge
Mossio M, Bich L (2017) What makes biological organisation teleological? Synthese 194(4):1089–1114. https://doi.org/10.1007/s11229-014-0594-z
Mossio M, Saborido C, Moreno A (2009) An organizational account of biological functions. British J Phil Sci 60(4):813–841. https://doi.org/10.1093/bjps/axp036
Nagel E (1977) Goal-directed processes in biology. J Philos 74:261. https://doi.org/10.2307/2025745
Neander K (1991) Functions as selected effects. Philos Sci 58(2):168–184
Neander K (1995) Explaining complex adaptations: a reply to Sober’s ‘reply to Neander.’ Br J Philos Sci 46:583–587
Neander K (2006) Moths and metaphors. review essay on organisms and artifacts: design in nature and elsewhere by Tim Lewens. Biol Philos 21(4):591–602. https://doi.org/10.1007/s10539-005-9006-6
Neandert K (2018) Does biology need teleology? In: Joyce R (ed) The Routledge handbook of evolution and philosophy. Routledge, Oxford
Nicholson DJ (2013) Organisms ≠ machines. Stud Hist Philos Sci C 44:669–678. https://doi.org/10.1016/j.shpsc.2013.05.014
Nicholson DJ (2014) The machine conception of the organism in development and evolution: a critical analysis. Stud Hist Philos Sci C 48:162–174. https://doi.org/10.1016/j.shpsc.2014.08.003
Nicholson DJ (2019) Is the cell really a machine? J Theor Biol 477:108
Niu D-K, Jiang L (2013) Can ENCODE tell us how much junk DNA we carry in our genome? Biochem Biophys Res Commun 430(4):1340–43. https://doi.org/10.1016/j.bbrc.2012.12.074
Nobeli I, Favia AD, Thornton JM (2009) Protein promiscuity and its implications for biotechnology. Nat Biotechnol 27:157–167. https://doi.org/10.1038/nbt1519
Olby R (1974) The path to the double helix. University of Washington Press, Seattle
Pennisi E (2012) ENCODE project writes eulogy for junk DNA. Science 337:1159
Piantadosi ST, Tily H, Gibson E (2012) The communicative function of ambiguity in language. Cognition 122(3):280–291. https://doi.org/10.1016/j.cognition.2011.10.004
Robinson A (2010) The virtue of vagueness. Nature 463(7282):736–736. https://doi.org/10.1038/463736a
Ruse M (2003) Darwin and design: does evolution have a purpose? Harvard University Press, Cambridge
Searle J (1995) The construction of social reality. Simon & Schuster, New York
Sloan P (1985) The question of natural purpose. In McMuulin E (ed) Evolution and creation. University of Notre Dame Press
Stamatoyannopoulos JA (2012) What does our genome encode? Genome Res 22:1602–1611. https://doi.org/10.1101/gr.146506.112
Starr et al (2018) Pervasive contingency and entrenchment in a billion years of Hsp90 evolution. PNAS 115(17):4453–4458
The ENCODE Project Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447(7146):799–816
The ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57–74. https://doi.org/10.1038/nature11247
Tinbergen N (1963) On aims and methods of ethology. Z Tierpsychol 20(4):410–433. https://doi.org/10.1111/j.1439-0310.1963.tb01161.x
Vierstra et al (2020) Global reference mapping of human transcription factor footprints. Nature 584(7818):729–736
Walsh DM (2007) The pomp of superfluous causes: the interpretation of evolutionary theory. Philos Sci 74:281–303. https://doi.org/10.1086/520777
Walsh D, Lewins T, Ariew A (2002) The trials of life: natural selection and random drift. Philos Sci 69:429–446. https://doi.org/10.1086/342454
Weber M (2005) Philosophy of experimental biology. Cambridge University Press, Cambridge
Weber M (2017) How objective are biological functions? Synthese 194(12):4741–4755. https://doi.org/10.1007/s11229-017-1483-z
Wouters AG (2003) Four notions of biological function. Stud Hist Philos Sci C 34(4):633–668. https://doi.org/10.1016/j.shpsc.2003.09.006
Wouters A (2005) The function debate in philosophy. Acta Biotheoretica 123–151
Wright L (1973) Functions. Philos Rev 82:139–168
Wright L (1976) Teleological explanations: An etiological analysis of goals and functions. University of California Press