Philosofical Posture

 

PHILOSOPHICAL POSTURE

Iver Leandro Daza

Traditionally the objective of parsimony has been reduced to the expression of William de Ockham: "it is useless to do with more what can be done with less", and this in essence has been said to be the principle of parsimony [1]. Parsimony, among other principles for inference, have been proposed to reach conclusions about phylogenetic relationships [2]. Maximum parsimony (MP), seeks to find the tree topology that requires the least amount of changes in the state of the character to produce the characteristics of the terminals present in the tree and build said phylogenetic relationships and, additionally, provides an ordering of the trees produced from "best" to “worst” [3]. This inference method requires that the researcher distinguish between antetral and derived characters, plesiomorphies of apomorphies, in the data set to be used [4]. With this said, the best genealogy is the one that contains the least homoplasy [2].

Among the main arguments against the use of parsimony, it is found that parsimony implicitly assumes doubtful propositions about evolutionary processes [3]. For authors who propose against the use of parsimony, such as Felsenstein, this may be inconsistent under a simplified process model and also consider that in empirical data it has a higher probability of failure [5]. Another argument mentions that it tries to estimate too many parameters, this comes from the fact that, if each character of the data is allowed its own branch length vector, the parsimony results are similar to Maximum likelihood [6]. Parsons also argues against it, mentioning that the simplest explanation is not always correct, and there is no prima facie reason to believe that a theory is correct because of the number of objects or entities it contains [7].

Despite the opposition against this approach, there are others who favor this perspective. Platnick and Gaffne in a discussion of Popper and systematics suggested that the best method for phylogenetic inferences is the one on which strong proofs can be developed in the Popperian sense, which could offer a justification for the use of cladistic parsimony [8]. In fact, Sober maintains that phylogenetic reconstructions are better interpreted from the Popperian corroboration [5]. Even when it’s generally accepted that for molecular analyzes likelihood is more appropriate, as well as inference by parsimony is more appropriate for morphological data, it has not been proven and in fact it is more “a social fact and not something logically inevitable", in other words, the data does not have an explicit indicator of which method is better for the analysis [3]

It seems the homoplasy interference while trying to study the phylogenetic relationship in the clade caudata has not been fully resolved using these approaches, that’s why the implied weighing method of the MP has a certain appeal given the fact that no other research (not even the amphibian tree of life phylogeny [9]) has tried to reweight characters given the rampant homoplasy some authors claim have found [10,11]. The justification for the use of parsimony is quite dependent on philosophical and statistical inference [1] just as corroboration and probability both are linked, as discussed by popper [8]. In the maximum parsimony the implied weighing method follows the inverse ratio path that the corroboration and probability have, as the more homoplasy found in a tree’s character, the less impact it has on the subsequent construction of the trees.

The ongoing debate on which method might be better will continue, but I am not going to say that future works using Bayesian inference or maximum likelihood methods will not be helpful. The current approach is a proposal to resolve the current situation and try to emphasize the important of parsimony method among the family-level relationship of the salamanders

Bibliography

1.Sober E. 2004 The contest between parsimony and likelihood. Syst. Biol. 53, 644–653.

2.Rodríguez A et al. 2017 Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches. Mol. Phylogenet. Evol. 115, 16–26.

3.Coelho MTP, Diniz-Filho JA, Rangel TF. 2019 A parsimonious view of the parsimony principle in ecology and evolution. Ecography (Cop.). 42, 968–976.

4.Sober E. 1983 Parsimony in Systematics. Ann. Rev. Ecol. Syst. 14, 335–357.

5.Popper K. 2005 The logic of scientific discovery. Routledge.

6.Daniel F, Peter C. 2016 Probability , Parsimony , and Popper . Cranston Published by : Oxford University Press for the Society of Systematic Biologists Stable Pa. Syst. Biol. 41, 252–257.