Philosophy in the biological world

The discussion about construction of how knowledge is built are not new, from Plato and his proposed world of ideas to Kant in his criticism to pure reasons(1) is underlined that the construction of knowledge which we call science is not dogmatic and static, instead it is a non volatile element and  a conditioned subject to time-space paradigm own of humanity, reducing everything to a purely linguistic problem (2). Therefore, syncretism is not a symptom of intellectual immaturity or inferiority of it, but a prudent demonstration against scholastic thought own religious processes, some scholars confused with scientific work.

Added to all this it is important to clarify that, contrary to sciences like mathematics, physics, and chemistry. The theoretical corpus in biological sciences completely lacks axiomatic systems that support the developed theories. While evolution is a fact. The causality of the phenomenon is highly debated due to the number of ad-hoc theories and hypotheses (3, 4). It is in this environment that the phylogenetic theories that attempt to answer the evolutionary relationships of organisms are developed. Therefore this essay  put on the table Bayesian analysis , the likelihood and parsimony as "irreconcilable" philosophical. Trying to approach the reality of evolutionary phenomena (not yet finished to be clear) to consider some as "the best ".

Let's start with the parsimony in which methodologically the tree with fewer transformations is selected, this is derivative of the philosophical principle that the simplest theory must be correct for being the least complex (5). A strongly nominalism position that can result in multiple ad- hoc theories that could never be applied to different events rather than the themselves cases. Following this logic we could generate own theories for each type of phylogenetic relationships of every living form. Which will lead to a greater number of hypotheses the number of species (counting the species already extinct). Which paradoxically ends up being contrary to the principle of parsimony.

In contrast to the  parsimony, the probabilistic models certainly have an advantage developing stochasticity in their methods, thus avoiding a possible fall in phylogenetic Laplace demon advantage. Maximum likelihood analyzes the conditional probability of the observations given the hypothesis, or in more colloquial terms how well the data fit in a given hypothesis. In which each tree is considered a hypothesis generated by choosing the highest likelihood. However likelihood ignores previously gathered evidence about the event at that epistemological terms can only be assigned certain degree of value as truth. By contrast,  Bayesian analysis is an excellent tool for the analysis of phylogenetic hypothesis by quantifying past evidence (prior) and included in the phylogenetic analysis. It is therefore the most appropriate tool to address the problem to elucidate the evolutionary relationships of living forms.

References

1. Kant, Immanuel, and Norman Kemp Smith. 1929. Immanuel Kant's Critique of pure reason. Boston: Bedford.
2. Wittgenstein, Ludwig. 1922. Tractatus logico-philosophicus. London: Routledge & Kegan Paul.
3. Margulis, Lynn; Dorion Sagan (2003). Captando Genomas. Una teoría sobre el origen de las especies. Ernst Mayr (prólogo). David Sempau (trad.) (1ª edición). Barcelona: Editorial Kairós
4. Darwin, Charles Robert. The Origin of Species. Vol. XI. The Harvard Classics. New York: P.F. Collier & Son, 1909–14.
5. Robert Audi, ed., Ockham's razor, The Cambridge Dictionary of Philosophy (2nd Edition), Cambridge University Press.