Abstract
Framing systematics as a field consistent with scientific inquiry entails that inferences of phylogenetic hypotheses have the goal of producing accounts of past causal events that explain differentially shared characters among organisms. Linking observations of characters to inferences occurs by way of why-questions implied by data matrices. Because of their form, why-questions require the use of common-cause theories. Such theories in phylogenetic inferences include natural selection and genetic drift. Selection or drift can explain ‘morphological’ characters but selection cannot be causally applied to sequences since fitness differences cannot be directly associated with individual nucleotides or amino acids. The relation of selection to sequence data is by way of downward or top-down causation from those phenotypes upon which selection occurs. The application of phylogenetic inference to explain sequence data is thus restricted to instances where drift is the relevant theory; those nucleotides or amino acids that can be explained via downward causation are precluded from inclusion in the data matrix. The restrictions on the inclusion of sequence data in phylogenetic inferences equally apply to species hypotheses, precluding the more restrictive approach known as DNA barcoding. Not being able to discern drift and selection as relevant causal mechanisms can severely constrain the inclusion and explanations of sequence data. Implications of such exclusion are discussed in relation to the requirement of total evidence.
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References
Achinstein P (1970) Inference to scientific laws. In: Stuewer RH (ed) Volume V: historical and philosophical perspectives of science. Minnesota studies in the philosophy of science. University of Minnesota Press, Minneapolis, pp 87–111
Aliseda A (2006) Abductive reasoning: logical investigations into discovery and explanation. Springer, Dordrecht
Auletta G, Ellis GFR, Jaeger L (2008) Top-down causation by information control: from a philosophical problem to a scientific research programme. J R Soc Interface 5:1159–1172
Baker VR (1996) Hypotheses and geomorphological reasoning. In: Rhoads BL, Thorn CE (eds) The scientific nature of geomorphology: proceedings of the 27th Binghamton symposium in geomorphology held 27–29 September 1996. Wiley, New York, pp 57–85
Baldwin CC, Weigt LA (2012) A new species of soapfish (Teleostei: Serranidae: Rypticus), with redescription of R. subbifrenatus and comments on the use of DNA barcoding in systematic studies. Copeia 2012:23–36
Barker SF (1957) Induction and hypothesis. Cornell University Press, New York
Barnes E (1994) Why P rather than Q? The curiosities of fact and foil. Philos Stud 73:35–53
Baum DA, Smith SD (2013) Tree thinking: an introduction to phylogenetic biology. Roberts and Company Publishers, Greenwood Village
Biswas S, Akey JM (2006) Genomic insights into positive selection. Trends Genet 22:437–446
Bromberger S (1966) Why-questions. In: Colodny RG (ed) Mind and cosmos: essays in contemporary science and philosophy. University of Pittsburgh series in the philosophy of science, 3. University of Pittsburgh Press, Pittsburgh, pp 86–111
Burton RB (2000) The problem of control in abduction. Trans Charles S. Peirce Soc 36:149–156
Campbell DT (1974) Downward causation in hierarchically organized biological systems. In: Ayala FJ, Dobzhansky T (eds) Studies in the philosophy of biology: reduction and related problems. University of California Press, Berkeley, pp 179–186
Carnap R (1950) Logical foundations of probability. University of Chicago Press, Chicago
Castalanelli MA, Teale R, Rix MG, Kennington WJ, Harvey MS (2014) Barcoding of mygalomorph spiders (Araneae: Mygalomorphae) in the Pilbara bioregion of Western Australia reveals a highly diverse biota. Invertebr Syst 28:375–385
Cleland CE (2001) Historical science, experimental science, and the scientific method. Geology 29:987–990
Cleland CE (2002) Methodological and epistemic differences between historical science and experimental science. Philos Sci 69:474–496
Cleland CE (2009) Philosophical issues in natural history and its historiography. In: Tucker A (ed) A companion to the philosophy of history and historiography. Wiley-Blackwell, Oxford, pp 44–62
Cleland CE (2011) Prediction and explanation in historical natural science. Br J Philos Sci 62:551–582
Cleland CE (2013) Common cause explanation and the search for a smoking gun. Geol Soc Spec Pap 502:1–9
Curd MV (1980) The logic of discovery: an analysis of three approaches. In: Nickles T (ed) Scientific discovery, logic and rationality. D. Reidel Publishing Company, Dordrecht, pp 201–219
Davies PCW (2012) The epigenome and top-down causation. Interface Focus 2:42–48
de Regt HW, Leonelli S, Eigner K (2009) Focusing on scientific understanding. In: de Regt H, Leonelli S, Eigner K (eds) Scientific understanding: philosophical perspectives. University of Pittsburgh Press, Pittsburgh, pp 1–17
DeBry RW (1992) The consistency of several phylogeny-inference methods under varying evolutionary rates. Mol Biol Evol 9:537–551
Ellis GFR (2008) On the nature of causation in complex systems. Trans R Soc S Afr 63:69–84
Ellis GFR (2012) Top-down causation and emergence: some comments on mechanisms. Interface Focus 2:126–140
Ellis G (2013) Time to turn cause and effect on their heads. New Sci 2930:28–29
Ellis GFR, Noble D, O’Connor T (2011) Top-down causation: An integrating theme within and across the sciences? Interface Focus 2:1–3
Fann KT (1970) Peirce’s theory of abduction. Martinus Nijhoff, The Hague
Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27:401–410
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376
Felsenstein J (2004) Inferring phylogenies. Sinauer Associates Inc, Sunderland
Fetzer JH (1993) Philosophy of science. Paragon House, New York
Fetzer JH, Almeder RF (1993) Glossary of epistemology/philosophy of science. Paragon House, New York
Fitzhugh K (2005a) Les bases philosophiques de l’inférence phylogénétique: une vue d’ensemble. Biosystema 24:83–105
Fitzhugh K (2005b) The inferential basis of species hypotheses: the solution to defining the term ‘species’. Mar Ecol 26:155–165
Fitzhugh K (2006a) The abduction of phylogenetic hypotheses. Zootaxa 1145:1–110
Fitzhugh K (2006b) The ‘requirement of total evidence’ and its role in phylogenetic systematics. Biol Philos 21:309–351
Fitzhugh K (2006c) The philosophical basis of character coding for the inference of phylogenetic hypotheses. Zool Scr 35:261–286
Fitzhugh K (2008a) Fact, theory, test and evolution. Zool Scr 37:109–113
Fitzhugh K (2008b) Abductive inference: implications for ‘Linnean’ and ‘phylogenetic’ approaches for representing biological systematization. Evol Biol 35:52–82
Fitzhugh K (2008c) Clarifying the role of character loss in phylogenetic inference. Zool Scr 37:561–569
Fitzhugh K (2009) Species as explanatory hypotheses: refinements and implications. Acta Biotheor 57:201–248
Fitzhugh K (2010) Evidence for evolution versus evidence for intelligent design: parallel confusions. Evol Biol 37:68–92
Fitzhugh K (2012) The limits of understanding in biological systematics. Zootaxa 3435:40–67
Fitzhugh K (2013) Defining ‘species’, ‘biodiversity’, and ‘conservation’ by their transitive relations. In: Pavlinov IY (ed) The species problem—ongoing problems. InTech, New York, pp 93–130
Fitzhugh K (2014) Character mapping and cladogram comparison versus the requirement of total evidence: Does it matter for polychaete systematics? Mem Mus Vic 71:67–78
Fitzhugh K (2015) What are species? Or, on asking the wrong question. Festivus 47:229–239
Fitzhugh K (in press) Dispelling five myths about hypothesis testing in biological systematics. Org Divers Evol
Godfrey-Smith P (2003) Theory and reality: an introduction to the philosophy of science. University of Chicago Press, Chicago
Graybeal A (1998) Is it better to add taxa or characters to a difficult phylogenetic problem? Syst Biol 47:9–17
Griffiths P, Stotz K (2013) Genetics and philosophy: an introduction. Cambridge University Press, New York
Hacking I (2001) An introduction to probability and inductive logic. Cambridge University Press, New York
Hanson NR (1958) Patterns of discovery: an inquiry into the conceptual foundations of science. Cambridge University Press, New York
Hausman DM (1998) Causal asymmetries. Cambridge University Press, New York
Heath TA, Hedtke SM, Hillis DM (2008) Taxon sampling and the accuracy of phylogenetic analyses. J Syst Evol 46:239–257
Hebert PDN, Cywinska A, Ball SL, DeWaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc B 270:313–321
Hebert PDN, Penton EH, Burns JM, Janze DH, Hallwachs W (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Acad Sci USA 101:14812–14817
Hedtke SM, Morgan MJ, Cannatella DC, Hillis DM (2013) Targeted enrichment: maximizing orthologous gene comparisons across deep evolutionary time. PLoS ONE 8:e67908. doi:10.1371/journal.pone.0067908
Hempel CG (1962) Deductive nomological vs. statistical explanation. In: Feigl H, Maxwell G (eds) Minnesota studies in the philosophy of science, vol 3. University of Minnesota Press, Minneapolis, pp 98–169
Hempel CG (1965) Aspects of scientific explanation and other essays in the philosophy of science. The Free Press, New York
Hempel CG (1966) Recent problems of induction. In: Colodny RG (ed) Mind and cosmos. University of Pittsburgh Press, Pittsburgh, pp 112–134
Hempel CG (2001) The philosophy of Carl G. Hempel: studies in science, explanation, and rationality. In: Fetzer JH (ed). Oxford University Press, New York
Hennig W (1966) Phylogenetic systematics. University of Illinois Press, Urbana
Hey J (1999) The neutralist, the fly and the selectionist. TREE 14:35–38
Hillis DM (1995) Approaches for assessing phylogenetic accuracy. Syst Biol 44:3–16
Hoekstra HE, Hirschmann RJ, Bundey RA, Insel PA, Crossland JP (2006) A single amino acid mutation contributes to adaptive beach mouse color pattern. Science 313:101–104
Hoffmann M (1999) Problems with Peirce’s concept of abduction. Found Sci 4:271–305
Hoyningen-Huene P (2013) Systematicity: the nature of science. Oxford University Press, New York
Hurst LD (2002) The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet 18:486–487
Jaeger L, Calkins ER (2011) Downward causation by information control in micro-organisms. Interface Focus 2:26–41
Jeffares B (2008) Testing times: regularities in the historical sciences. Stud Hist Philos Biol Biomed Sci 39:469–475
Josephson JR, Josephson SG (eds) (1994) Abductive inference: computation, philosophy, technology. Cambridge University Press, New York
Kelly T (2008) Common sense as evidence: against revisionary ontology and skepticism. Midwest Stud Philos 32:53–78
Koonin EV (2012) The logic of chance: the nature and origin of biological evolution. FTS Press, Upper Saddle River
Laland KN, Sterelny K, Odling-Smee J, Hoppitt W, Uller T (2011) Cause and effect in biology revisited: is Mayr’s proximate-ultimate dichotomy still useful? Science 334:1512–1516
Lavelle JS, Botterill G, Lock S (2013) Contrastive explanation and the many absences problem. Synthese 190:3495–3510
Lipton P (2004) Inference to the best explanation. Routledge, New York
Lloyd EA (1988) The structure and confirmation of evolutionary theory. Princeton University Press, Princeton
Magnani L (2001) Abduction, reason, and science: processes of discovery and explanation. Kluwer Academic, New York
Mahner M, Bunge M (1997) Foundations of biophilosophy. Springer, New York
Martínez M, Moya A (2011) Natural selection and multi-level causation. Philos Theory Biol 3:e202
Martínez M, Esposito M (2014) Multilevel causation and the extended synthesis. Biol Theory 9:209–220
Marwick P (1999) Interrogatives and contrasts in explanation theory. Philos Stud 96:183–204
McDonald JH, Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652–654
McLaughlin A (1970) Rationality and total evidence. Philos Sci 37:271–278
Mitchell A (2011) DNA barcoding is useful for taxonomy: a reply to Ebach. Zootaxa 2772:67–68
Neta R (2008) What evidence do you have? Br J Philos Sci 59:89–119
Nickles T (1980) Introductory essay: scientific discovery and the future of philosophy of science. In: Nickles T (ed) Scientific discovery, logic and rationality. D. Reidel Publishing Company, Dordrecht, pp 1–59
Nola R, Sankey H (2007) Theories of scientific method: an introduction. McGill-Queen’s University Press, Ithaca
Norton JD (2003) A material theory of induction. Philos Sci 70:647–670
Okasha S (2006) Evolution and the levels of selection. Oxford University Press, New York
Okasha S (2012) Emergence, hierarchy and top-down causation in evolutionary biology. Interface Focus 2:49–54
Peirce CS (1878) Illustrations of the logic of science. Sixth paper.—Deduction, induction, and hypothesis. Pop Sci Mon 13:470–482
Peirce CS (1902) Reasoning. In: Baldwin JA, Rand B (eds) Dictionary of philosophy and psychology: prefatory note. Text, Le-Z. Addenda: indices. I. Greek terms. II. Latin terms. III. German terms. IV. French terms. V. Italian terms. The Macmillan Company, New York, pp 426–428
Peirce CS (1931) Collected papers of Charles Sanders Peirce, volume 1, principles of philosophy. In: Hartshorne C, Weiss P, Burks A (eds). Harvard University Press, Cambridge
Peirce CS (1932) Collected papers of Charles Sanders Peirce, volume 2, elements of logic. In: Hartshorne C, Weiss P, Burks A (eds). Harvard University Press, Cambridge
Peirce CS (1933a) Collected papers of Charles Sanders Peirce, volume 3, exact logic. In: Hartshorne C, Weiss P, Burks A (eds). Harvard University Press, Cambridge
Peirce CS (1933b) Collected papers of Charles Sanders Peirce, volume 4, the simplest mathematics. In: Hartshorne C, Weiss P, Burks A (eds). Harvard University Press, Cambridge
Peirce CS (1934) Collected papers of Charles Sanders Peirce, volume 5, pragmatism and pragmaticism. In: Hartshorne C, Weiss P, Burks A (eds). Harvard University Press, Cambridge
Peirce CS (1935) Collected papers of Charles Sanders Peirce, volume 6, scientific metaphysics. In: Hartshorne C, Weiss P, Burks A (eds). Harvard University Press, Cambridge
Peirce CS (1958a) Collected papers of Charles Sanders Peirce, volume 7, science and philosophy. In: Hartshorne C, Weiss P, Burks A (eds). Harvard University Press, Cambridge
Peirce CS (1958b) Collected papers of Charles Sanders Peirce, volume 8, correspondence and bibliography. In: Burks A (ed). Harvard University Press, Cambridge
Petrov DA (2014) Searching for adaptation in the genome. In: Losos JB, Baum DA, Futuyma DJ, Hoekstra HE, Lenski RE, Moore AJ, Peichel CL, Schluter D, Whitlock MC (eds) The Princeton guide to evolution. Princeton University Press, Princeton, pp 466–474
Philippe H, Brinkmann H, Lavrov DV, Littlewood DTJ, Manuel M (2011) Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol 9:e1000602
Popper KR (1983) Objective knowledge: an evolutionary approach. Oxford University Press, New York
Popper KR (1992) Realism and the aim of science. Routledge, New York
Psillos S (2002) Simply the best: a case for abduction. In: Kakas AC, Sadri F (eds) Computational logic: logic programming and beyond. Springer, New York, pp 605–625
Psillos S (2007) Philosophy of science A-Z. University Press, Edinburgh
Psillos S (2011) An explorer upon untrodden ground: Peirce on abduction. In: Gabbay D, Hartmann S, Woods J (eds) The handbook of the history of logic, vol 10., inductive logicElsevier B. V, Oxford, pp 117–151
Reilly FE (1970) Charles Peirce’s theory of scientific method. Fordham University Press, New York
Rescher N (1970) Scientific explanation. The Free Press, New York
Rescher N (1978) Peirce’s philosophy of science: critical studies in his theory of induction and scientific method. University of Notre Dame Press, Notre Dame
Ronquist F, van der Mark P, Huelsenbeck JP (2009) Bayesian phylogenetic analysis using MrBayes. In: Lemey P, Salemi M, Vandamme A-M (eds) The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing. Cambridge University Press, New York, pp 210–266
Salmon WC (1967) The foundations of scientific inference. University of Pittsburgh Press, Pittsburgh
Salmon WC (1984a) Scientific explanation and the causal structure of the world. Princeton University Press, Princeton
Salmon WC (1984b) Logic. Prentice-Hall Inc, Englewood Cliffs
Salmon WC (1989) Four decades of scientific explanation. In: Kitcher P, Salmon WC (eds) Scientific explanation. Minnesota studies in the philosophy of science, vol XIII. University of Minnesota Press, Minneapolis, pp 3–219
Salmon WC (1998) Causality and explanation. Oxford University Press, New York
Salthe SN (1985) Evolving hierarchical systems: their structure and representation. Columbia University Press, New York
Sawyer SA (1994) Inferring selection and mutation from DNA sequences: the McDonald–Kreitman test revisited. In: Golding B (ed) Non-neutral evolution: theories and molecular data. Springer, Dordrecht, pp 77–87
Schmidt HA, von Haeseler A (2009) Phylogenetic inference using maximum likelihood methods. In: Lemey P, Salemi M, Vandamme A-M (eds) The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing. Cambridge University Press, New York, pp 181–198
Schurz G (2005) Explanations in science and the logic of why-questions: discussion of the Halonen–Hintikka-approach and alternative proposal. Synthese 143:149–178
Schurz G (2008) Patterns of abduction. Synthese 164:201–234
Sintonen M (2004) Reasoning to hypotheses: Where do questions come? Found Sci 9:249–266
Smith MA, Bertrand C, Crosby K, Eveleigh ES, Fernandez-Triana J, Fisher BL, Gibbs J, Hajibabaei M, Hallwachs W, Hind K, Hrcek J, Huang D-W, Janda M, Janzen DH, Li Y, Miller SE, Packer L, Quicke D, Ratnasingham S, Rodriguez J, Rougerie R, Shaw MR, Sheffield C, Stahlhut JK, Steinke D, Whitfield J, Wood M (2012) Wolbachia and DNA barcoding insects: patterns, potential, and problems. PLoS ONE 7:e36514
Sober E (1975) Simplicity. Oxford University Press, New York
Sober E (1984) The nature of selection: evolutionary theory in philosophical focus. The MIT Press, Cambridge
Sober E (1986) Explanatory presupposition. Aust J Philos 64:143–149
Sober E (1988) Reconstructing the past: parsimony, evolution, and inference. The MIT Press, Cambridge
Sober E (1994) From a biological point of view: essays in evolutionary biology. Cambridge University Press, New York
Strahler AN (1992) Understanding science: an introduction to concepts and issues. Prometheus Books, Buffalo
Swofford DL, Olsen GJ, Waddell PJ, Hillis DM (1996) Phylogenetic inference. In: Hillis DM, Moritz C, Mable BK (eds) Molecular systematics. Sinauer Associates, Sunderland, pp 407–514
Thagard P (1988) Computational philosophy of science. The MIT Press, Cambridge
Thagard P (2004) Rationality and science. In: Mele A, Rawlings P (eds) Handbook of rationality. Oxford University Press, Oxford, pp 363–379
Tucker A (2004) Our knowledge of the past: a philosophy of historiography. Cambridge University Press, New York
Tucker A (2011) Historical science, over- and underdetermined: a study of Darwin’s inference of origins. Br J Philos Sci 62:805–829
Turner D (2007) Making prehistory: historical science and the scientific realism debate. Cambridge University Press, New York
Van Fraassen BC (1990) The scientific image. Clarendon Press, New York
Vrba E, Eldredge N (1984) Individuals, hierarchies and processes: towards a more complete evolutionary theory. Paleobiology 10:146–171
Walker SI (2014) Top-down causation and the rise of information in the emergence of life. Information 5:424–439
Walker SI, Cisneros L, Davies PCW (2012) Evolutionary transitions and top-down causation. Proc Artif Life 13:283–290
Walton D (2004) Abductive reasoning. The University of Alabama Press, Tuscaloosa
Wheeler WC (2012) Systematics: a course of lectures. Wiley-Blackwell, Oxford
Whitlock MC (2014) From DNA to phenotypes. In: Losos JB, Baum DA, Futuyma DJ, Hoekstra HE, Lenski RE, Moore AJ, Peichel CL, Schluter D, Whitlock MC (eds) The Princeton guide to evolution. Princeton University Press, Princeton, pp 40–46
Wiley EO, Lieberman BS (2011) Phylogenetics: theory and practice of phylogenetic systematics. Wiley-Blackwell, Oxford
Zhang Z, Yu J (2006) Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates. Genomics Proteomics Bioinform 4:173–181
Zwickl DJ, Hillis DM (2002) Increased taxon sampling greatly reduces phylogenetic error. Syst Biol 51:588–598
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Fitzhugh, K. Sequence Data, Phylogenetic Inference, and Implications of Downward Causation. Acta Biotheor 64, 133–160 (2016). https://doi.org/10.1007/s10441-016-9277-0
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DOI: https://doi.org/10.1007/s10441-016-9277-0