Me and the comparative biology

Systematics as a discipline, plays an important role in comparative biology, it allows us to understand species phylogenetic history, taking into account their evolutionary processes and patterns¹. There is a universe of philosophical ideas discussed in the systematic literature, where even the reasoning process from data, to the final tree hypothesis can have a direct impact on our phylogenetic analyzes^1-2. Hence, having a philosophical position should be the beginning to our study², how we know what we know and how we decided to address that knowledge has been debated along history³. 

knowledge understood as the data obtained from the evidence, made me choose an induction approach, where multiple instances observed of a phenomenon will lead us to a more general view, in spite of deductivism, that falls into a syllogism². The contemporary systematics employs different forms of logic in combined forms nowadays^2,4. Therefore, the method that best fits my scientific inference is a Bayesian approach, the analyzes can rarely be sure of a result, but they can be very safe. Its inference differs from traditional statistical inference in preserving uncertainty^5-7.

First, in order to carry out the respective phylogenetic analyzes, it’s necessary to define the research question of interest. The conceptual framework needs to be clarified and subsequently, generate a quantifiable hypothesis^6-7, the probability of how possible it’s depends on all previous information available. Observation alone can not give a posterior probability, we need to have a prior probability as well^3,6-7. Also, it’s necessary the establishment of interest parameters given our current data and models. The choice of a prior is based on how much information we believe we have prior to the data, and how accurate we believe that information to be^6-7. Therefore, the posterior distribution reflects our updated knowledge, balancing prior knowledge with observed data⁷. 

The use of Bayesian statistics allows us, to update knowledge instead of testing a null hypothesis over and over again. If the evidence changes, knowledge will also change or be more reliable^3,6,8-9, thus that’s why I prefer it.

References

1. Funk, V. & Brooks, D. Phylogenetic systematics as the basis of comparative biology. (Smithsonian Institution Press, 1993). 

2. Wiley, E. & Lieberman, B. Phylogenetics: Theory and Practice of Phylogenetic Systematics. (John Wiley & Sons, 2011).

3. Sober, E. Evidence and Evolution: The Logic Behind the Science. 3-107 (Cambridge University Press, 2008).

4. Hume, D. 1748. An Enquiry concerning Human Understanding, T. Cadell, London.

5. Glickman, M. & Dyk, D. Basic Bayesian Methods. Topics in Biostatistics 319-338 (2007). doi:10.1007/978-1-59745-530-5_16

6. Van de Schoot, R. et al. A Gentle Introduction to Bayesian Analysis: Applications to Developmental Research. Child Development 85, 842-860 (2013).

7. Smith, A., Skene, A., Shaw, J., Naylor, J. & Dransfield, M. The implementation of the bayesian paradigm. Communications in Statistics - Theory and Methods 14, 1079- 1102 (1985).

8. Gelman, A. Simulation of a Statistics Blogosphere - Statistical Modeling, Causal Inference, and Social Science. (2010). At https://andrewgelman.com/2010/03/22/simulation_of_a/ 

9. Cameron, D.Bayesian Methods for Hackers: Probabilistic Programming and Bayesian Inference (Addison-Wesley Data & Analytics). (Addison-Wesley Professional, 2015).