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Australian Systematic Botany Australian Systematic Botany Society
Taxonomy, biogeography and evolution of plants
RESEARCH ARTICLE (Open Access)

Popper and phylogenetics, a misguided rendezvous

Lars Vogt
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Institut für Evolutionsbiologie und Ökologie, Universität Bonn, An der Immenburg 1, D-53121 Bonn, Germany. Email: lars.m.vogt@gmail.com

Australian Systematic Botany 27(2) 85-94 https://doi.org/10.1071/SB14025
Submitted: 14 August 2014  Accepted: 14 August 2014   Published: 6 October 2014

Journal Compilation © CSIRO Publishing 2014 Open Access CC BY-NC-ND

Abstract

Popper’s falsificationism is frequently referred to as a general normative reference system in phylogenetics. Referring to falsificationism, phylogeneticists have made four central claims, including that frequency probabilities (1) cannot be used for inferring degrees of corroboration and (2) cannot be used in phylogenetics because phylogeny is a unique process, (3) likelihood methods represent verificationist approaches, and (4) the congruence test is a Popperian test. However, these claims are inconsistent with Popper’s theory. Moreover, phylogeneticists have proposed four strategies for dealing with the unfalsifiability of cladograms, including (1) interpreting re-interpretations of putative synapomorphy as homoplasy as Popperian ad hoc manoeuvres, (2) decoupling corroboration from falsification, (3) interpreting the tree with the highest likelihood as the most corroborated tree, and (4) interpreting tree hypotheses as Popperian probabilistic hypotheses that do not have to be falsifiable. These strategies are also inconsistent with Popper’s theory. Four fundamental problems and a problem with Popper’s formula for measuring degree of corroboration demonstrate that Popper’s theory does not live up to its own claims. Moreover, neither historical nor experimental sciences can be conducted in a way that is consistent with the principles of falsificationism. Therefore, phylogeneticists should stop referring to falsificationism when defending a specific methodological position.

Additional keywords: corroboration, falsificationism, likelihood, parsimony, testability.


References

Andersson G (1998) Basisprobleme. In ‘Karl Popper: Logik der Forschung. Klassiker Auslegen. Vol. 12’. (Ed. H Keuth) pp. 145–164. (Akademie Verlag: Berlin)

Bock WJ (1973) Philosophical foundations of classical evolutionary classification. Systematic Zoology 22, 375–392.
Philosophical foundations of classical evolutionary classification.Crossref | GoogleScholarGoogle Scholar |

Cleland CE (2001) Historical science, experimental science, and the scientific method. Geology 29, 987–990.
Historical science, experimental science, and the scientific method.Crossref | GoogleScholarGoogle Scholar |

Cleland CE (2002) Methodological and epistemic differences between historical science and experimental science*. Philosophy of Science 69, 474–496.
Methodological and epistemic differences between historical science and experimental science*.Crossref | GoogleScholarGoogle Scholar |

Cracraft J (1978) Science, philosophy, and systematics. Systematic Zoology 27, 213–216.
Science, philosophy, and systematics.Crossref | GoogleScholarGoogle Scholar |

de Queiroz K, Poe S (2001) Philosophy and phylogenetic inference: a comparison of likelihood and parsimony methods in the context of Karl Popper’s writings on corroboration. Systematic Biology 50, 305–321.
Philosophy and phylogenetic inference: a comparison of likelihood and parsimony methods in the context of Karl Popper’s writings on corroboration.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BD38zntVOgug%3D%3D&md5=c6c63694cf5cf6913dfa39d0276e8cefCAS | 12116577PubMed |

de Queiroz K, Poe S (2003) Failed refutations: further comments on parsimony and likelihood methods and their relationship to Popper’s degree of corroboration. Systematic Biology 52, 352–367.

Earman J, Salmon WC (1992) The confirmation of scientific hypotheses. In ‘Introduction to the Philosophy of Science’. (Eds MH Salmon, J Earman, C Glymour, JG Lennox, P Machamer, JE McGuire, JD Norton, WC Salmon, KF Schaffner) pp. 42–103. (Prentice Hall: Englewood Cliffs, NJ)

Faith DP (1992) On corroboration: a reply to Carpenter. Cladistics 8, 265–273.
On corroboration: a reply to Carpenter.Crossref | GoogleScholarGoogle Scholar |

Faith DP (1999) Error and the growth of experimental knowledge Systematic Biology 48, 675–679. [Review]

Faith DP (2004) L.A.S. Johnson Review No. 1. From species to supertrees: Popperian corroboration and some current controversies in systematics. Australian Systematic Botany 17, 1–16.
L.A.S. Johnson Review No. 1. From species to supertrees: Popperian corroboration and some current controversies in systematics.Crossref | GoogleScholarGoogle Scholar |

Faith DP (2006) Science and philosophy for molecular systematics: which is the cart and which is the horse? Molecular Phylogenetics and Evolution 38, 553–557.
Science and philosophy for molecular systematics: which is the cart and which is the horse?Crossref | GoogleScholarGoogle Scholar | 16230031PubMed |

Faith DP, Cranston PS (1992) Probability, parsimony, and Popper. Systematic Biology 41, 252–257.
Probability, parsimony, and Popper.Crossref | GoogleScholarGoogle Scholar |

Faith DP, Trueman JWH (2001) Towards an inclusive philosophy for phylogenetic inference. Systematic Biology 50, 331–350.
Towards an inclusive philosophy for phylogenetic inference.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BD38zntVOnsg%3D%3D&md5=702ed20380225ba5d08390b30d5b3517CAS | 12116579PubMed |

Farris JS (1983) The Logical Basis of Phylogenetic Analysis. In ‘Advances in Cladistics 2’. (Eds NI Platnick, VA Funk) pp. 7–36. (Columbia University Press: New York)

Farris JS (2000) Corroboration versus ‘strongest evidence’. Cladistics 16, 385–393.

Farris JS (2013) Popper: not Bayes or Rieppel. Cladistics 29, 230–232.
Popper: not Bayes or Rieppel.Crossref | GoogleScholarGoogle Scholar |

Farris JS (2014) Popper with probability. Cladistics 30, 5–7.
Popper with probability.Crossref | GoogleScholarGoogle Scholar |

Farris JS, Kluge AG, Carpenter JM (2001) Popper and likelihood versus ‘Popper*’. Systematic Biology 50, 438–444.
Popper and likelihood versus ‘Popper*’.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BD38zntVOntA%3D%3D&md5=63ed57f618a2416dcd46d738fdba3fd9CAS | 12116585PubMed |

Fisher RA (1922) On the mathematical foundations of theoretical statistics. Philosophical Transaction of the Royal Society of London A 222, 309–368.
On the mathematical foundations of theoretical statistics.Crossref | GoogleScholarGoogle Scholar |

Franklin J (2001) Resurrecting logical probabilities. Erkenntnis 55, 277–305.
Resurrecting logical probabilities.Crossref | GoogleScholarGoogle Scholar |

Gee H (1999) ‘In Search of Deep Time.’ (The Free Press: New York)

Gillies DA (1971) A falsifying rule for probability statements. The British Journal for the Philosophy of Science 22, 231–261.
A falsifying rule for probability statements.Crossref | GoogleScholarGoogle Scholar |

Grant T, Kluge AG (2003) Data exploration in phylogenetic inference: scientific, heuristic, or neither. Cladistics 19, 379–418.
Data exploration in phylogenetic inference: scientific, heuristic, or neither.Crossref | GoogleScholarGoogle Scholar |

Grünbaum A (1976) Is the method of bold conjectures and attempted refutations justifiably the method of science. The British Journal for the Philosophy of Science 27, 105–136.
Is the method of bold conjectures and attempted refutations justifiably the method of science.Crossref | GoogleScholarGoogle Scholar |

Helfenbein KG, DeSalle R (2005) Falsifications and corroborations: Karl Popper’s influence on systematics. Molecular Phylogenetics and Evolution 35, 271–280.
Falsifications and corroborations: Karl Popper’s influence on systematics.Crossref | GoogleScholarGoogle Scholar | 15737596PubMed |

Howson C, Urbach P (1989) ‘Scientific Reasoning: the Bayesian Approach.’ (Open Court Publishing Company: La Salle, IL)

Hoyningen-Huene P (2006) Context of discovery versus context of justification and Thomas Kuhn. In ‘Revisiting Discovery and Justification: Historical and Philosophical Perspectives on the Context Distinction’. (Eds J Schickore, F Steinle) pp. 119–131. (Springer: Dordrecht, the Netherlands)

Hull DL (1983) Karl Popper and Plato’s metaphor. In ‘Advances in Cladistics 2’. (Eds NI Platnick, VA Funk) pp. 177–189. (Columbia University Press: New York)

Hume D (1993) ‘An Enquiry Concerning Human Understanding.’ (Hackett Publishing: Indianapolis, IN)

Kitts DB (1977) Karl Popper, verifiability, and systematic zoology. Systematic Zoology 26, 185–194.
Karl Popper, verifiability, and systematic zoology.Crossref | GoogleScholarGoogle Scholar |

Kluge AG (1997a) Testability and the refutation and corroboration of cladistic hypotheses. Cladistics 13, 81–96.
Testability and the refutation and corroboration of cladistic hypotheses.Crossref | GoogleScholarGoogle Scholar |

Kluge AG (1997b) Sophisticated falsification and research cycles: consequences for differential character weighting in phylogenetic systematics. Zoologica Scripta 26, 349–360.
Sophisticated falsification and research cycles: consequences for differential character weighting in phylogenetic systematics.Crossref | GoogleScholarGoogle Scholar |

Kluge AG (2001) Philosophical conjectures and their refutation. Systematic Biology 50, 322–330.
Philosophical conjectures and their refutation.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BD38zntVOguw%3D%3D&md5=b48f853d8e731ee69ab0f7310da34cb2CAS | 12116578PubMed |

Kluge AG (2002) Distinguishing ‘or’ from ‘and’ and the case for historical identification. Cladistics 18, 585–593.

Kluge AG (2003) The repugnant and the mature in phylogenetic inference: atemporal similarity and historical identity. Cladistics 19, 356–368.
The repugnant and the mature in phylogenetic inference: atemporal similarity and historical identity.Crossref | GoogleScholarGoogle Scholar |

Kuhn TS (1970) Logic of discovery or psychology of research? In ‘Criticism and the Growth of Knowledge’. (Eds I Lakatos, A Musgrave) pp. 1–23. (Cambridge University Press: Cambridge, UK)

Lakatos I (1968) Changes in the problem of inductive logic. In ‘The Problem of Inductive Logic’. (Ed. I Lakatos) pp. 315–417. (North-Holland Pub. Co.: Amsterdam, the Netherlands)

Lakatos I (1970) Falsification and the methodology of scientific research programmes. In ‘Criticism and the Growth of Knowledge. Vol. 4’. (Eds I Lakatos, I A Musgrave) pp. 91–96. (Cambridge University Press: Cambridge, UK)

Mackie JL (1985) ‘Logic and Knowledge.’ (Clarendon Press: Oxford, UK)

McGuire JE (1992) Scientific change: perspectives and proposals. In ‘Introduction to the Philosophy of Science’. (Eds MH Salmon, J Earman, C Glymour, JG Lennox, P Machamer, JE McGuire, JD Norton, WC Salmon, KF Schaffner) pp. 132–178. (Prentice Hall: Englewood Cliffs, NJ)

Platnick NI, Gaffney ES (1978) Systematics and the Popperian paradigm. Systematic Zoology 27, 381–388.
Systematics and the Popperian paradigm.Crossref | GoogleScholarGoogle Scholar |

Popper KR (1983) ‘Realism and the Aim of Science; From the Postscript to the Logic of Scientific Discovery.’ (Routledge: London)

Popper KR (1994) ‘Logik der Forschung, 10. Auflage.’ (J.C.B. Mohr (Paul Siebeck): Tübingen, Germany)

Popper KR (2005) ‘The Logic of Scientific Discovery.’ (Routledge: London)

Putnam H (1974) The ‘corroboration’ of theories. In ‘The Philosophy of Karl Popper’. (Ed. PA Schilpp) pp. 221–240. (Open Court Publishing Company: La Salle, IL)

Randle CP, Pickett KM (2010) The conflation of ignorance and knowledge in the inference of clade posteriors. Cladistics 26, 550–559.
The conflation of ignorance and knowledge in the inference of clade posteriors.Crossref | GoogleScholarGoogle Scholar |

Reichenbach H (1938) ‘Experience and Prediction.’ (University of Chicago Press: Chicago, IL)

Rieppel O (2003) Popper and systematics. Systematic Biology 52, 259–271.
Popper and systematics.Crossref | GoogleScholarGoogle Scholar | 12746152PubMed |

Rowbottom DP (2013) Popper’s measure of corroboration and p(h|b). The British Journal for the Philosophy of Science 64, 739–745.
Popper’s measure of corroboration and p(h|b).Crossref | GoogleScholarGoogle Scholar |

Salmon WC (1967) ‘The Foundations of Scientific Inference.’ (University of Pittsburgh Press: Pittsburgh, PA)

Salmon WC (1968) The justification of inductive rules of inference. In ‘The Problem of Inductive Logic’. (Ed. I Lakatos) pp. 24–43. (North-Holland Pub. Co.: Amsterdam, the Netherlands)

Salmon WC (1998) Rational prediction. In ‘Philosophy of Science: The Central Issues’. (Eds M Curd, JA Cover) pp. 433–444. (W.W. Norton and Company Inc.: New York)

Schroeder-Heister P (1998) Wahrscheinlichkeit. In ‘Klassiker Auslegen: Karl Popper, Logik der Forschung’. (Ed. H Keuth) pp. 185–213. (Akademie Verlag: Berlin)

Schurz G (1998) Das Problem der Induktion. In ‘Karl Popper: Logik der Forschung’, Klassiker Auslegen, Vol. 12. (Ed. H Keuth) pp. 25–40. (Akademie Verlag: Berlin)

Siddall ME, Kluge AG (1997) Probabilism and phylogenetic inference. Cladistics 13, 313–336.
Probabilism and phylogenetic inference.Crossref | GoogleScholarGoogle Scholar |

Sober E (1983) Parsimony in systematics: philosophical issues. Annual Review of Ecology and Systematics 14, 335–357.
Parsimony in systematics: philosophical issues.Crossref | GoogleScholarGoogle Scholar |

Sober E (1988) ‘Reconstructing The Past – Parsimony, Evolution, and Inference.’ A Bradford book. (The MIT Press: Cambridge, MA)

Sober E (2000) ‘Philosophy of Biology’, 2nd edn. (Westview Press: Oxford, UK)

Spohn W (2001) Vier Begründungsbegriffe. In ‘Erkenntnistheorie – Positionen zwischen Tradition und Gegenwart’. (Ed. T Grundmann) pp. 33–52. (Mentis: Paderborn, Germany)

Stamos DN (1996) Popper, falsifiability, and evolutionary biology. Biology and Philosophy 11, 161–191.
Popper, falsifiability, and evolutionary biology.Crossref | GoogleScholarGoogle Scholar |

Thornton S (2009) Karl Popper. In ‘The Stanford Encyclopedia of Philosophy’. (Ed. EN Zalta) (The Metaphysics Research Lab, Stanford University: Standford, CA) Available at http://plato.stanford.edu/archives/win2011/entries/popper [Verified July 2014]

Vogt L (2002) Testing and weighting characters. Organisms, Diversity & Evolution 2, 319–333.
Testing and weighting characters.Crossref | GoogleScholarGoogle Scholar |

Vogt L (2007) A falsificationist perspective on the usage of process frequencies in phylogenetics. Zoologica Scripta 36, 395–407.
A falsificationist perspective on the usage of process frequencies in phylogenetics.Crossref | GoogleScholarGoogle Scholar |

Vogt L (2008) The unfalsifiability of cladograms and its consequences. Cladistics 24, 62–73.
The unfalsifiability of cladograms and its consequences.Crossref | GoogleScholarGoogle Scholar |

Vogt L (2014) Why phylogeneticists should care less about Popper’s falsificationism. Cladistics 30, 1–4.
Why phylogeneticists should care less about Popper’s falsificationism.Crossref | GoogleScholarGoogle Scholar |

Wiley EO (1975) Karl R. Popper, systematics, and classification : a reply to Walter Bock and other evolutionary taxonomists. Systematic Zoology 24, 233–243.
Karl R. Popper, systematics, and classification : a reply to Walter Bock and other evolutionary taxonomists.Crossref | GoogleScholarGoogle Scholar |