Philosophy in phylogenetic analysis
To speak of philosophy in phylogenetic analysis it is important to know several positions on the subject, some authors favor methods with good philosophical support (coherence with the theory of epistemology), others leave these in the background and are more interested by the performance of the methods (simulations of real well-supported phylogenies to then evaluate the methods that best "reconstruct", based on probability).
Siddall & Kluge (1997) argued that parsimony fits the theory of epistemology developed by Karl Popper, while probability does not. On the other hand, they presented parsimony better than probability based on Popper's concept of corroboration. For Popper, testing a theory means trying to refute it by means of a counterexample. If it is not possible to refute it, this theory is corroborated, and it can be accepted provisionally, but not verified; that is, no theory is absolutely true, but not refuted.
The principle of parsimony, known as the Ockham knife proposed by the Franciscan William Ockham. This principle establishes that entities should not be multiplied beyond necessity, which is often interpreted as implying that when alternative hypotheses explain data equally well, the simplest is preferred4. This principle principle is not the same as the parsimony method used for phylogenetic reconstruction, which classifies phylogenetic trees in a variable way according to the minimum number of character transformations among the taxa. The method of parsimony is a set of methods, this method is adjusted to the principle of parsimony in which the transformations of a hypothetical nature is not multiplied beyond the need (dependent on the costs assigned to different kinds of transformations).4
On the other hand probabilistic models have the advantage of developing stochasticity (Process whose behavior is non-deterministic) in their methods. The maximum likelihood analyzes how much the data fits to a given hypothesis; where a tree is considered a hypothesis when choosing the highest probability for that event; In the Bayesian analysis it is quantified that both a previous test (Prior) is adjusted to a later one.
De Queiroz & Poe 2001 say that contrary to the views of the authors who have criticized the likelihood approach to phylogenetic inference as incompatible with Karl Popper's degree of corroboration, an examination of Popper's own writings reveals that the concept general likelihood is the basis of its degree of corroboration. Consequently, it is not surprising that phylogenetic inference probability methods are fully compatible with Popper's corroboration and that methods of cladistic parsimony are compatible with corroboration only if they are interpreted as incorporating probabilistic assumptions. But if parsimony methods are interpreted as incorporating probabilistic assumptions, these assumptions are models that can be used in the context of probability, and the non-probabilistic implementations of those methods are simply approximations for their probabilistic counterparts. Interpreted in this way, there is no conflict between parsimony and maximum likelihood, because the general statistical perspective of maximum likelihood and popperian corroboration summarizes all the individual methods and models that can be applied within the context of that perspective, including those that of cladistic parsimony. 2, 5, 6
Other authors such as Brooks et. al., 2007 speak of a new strategy in which neither Popper's philosophy nor statistical coherence can give priority to a method of quantitative phylogenetic analysis; It is common for an author to present parsimony, maximum likelihood and Bayesian inference and then have a preference for some of them. 1
Personally I agree with what De Queiroz & Poe 2001 proposes, since they are based on methods with good philosophical support, and corroborations, not on finding the absolute truth. Phylogenetic analyzes should be based on corroborations and not absolute truths; Independent of the method, each one presents a hypothesis that can be corroborated.
1 Brooks, D; Bilewitch, J; Condy, C; Evans, D; Folinsbee, K; Fröbisch, J; Halas, D; Hill, S; McLennan, D; Mattern, M; Tsuji, L; Ward, L; Wahlberg, N; Zamparo, D & David Zanatta, D. 2007. Quantitative Phylogenetic Analysis in the 21 st Century.Análisis Filogenéticos Cuantitativos en el siglo XXI.Revista Mexicana de Biodiversidad 78: 225- 252, 2007
2 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(3):305–321, 2001
3 Siddall , M & Kluge, A . 1997. Probabilism and phylogenetic inference. Cladistics 13:313–336.
4 Sober , E. 1994. From a biological point of view. Cambridge Univ. Press, Cambridge, England.
5 Popper K. R. 1968. The logic of scientifi c discovery. Harper and Row, New York. 544 p.
6 Popper K. R. 1997. The demarcation between science and metaphysics. In The philosophy of Rudolph Carnap, P. A. Schilpp (ed.). Open Court, La Salle. p. 183-22