sábado, 16 de febrero de 2019

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 analyzes1-2. 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 nowadays2,4. 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 uncertainty5-7.

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 hypothesis6-7, 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 well3,6-7. 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 be6-7. 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 reliable3,6,8-9, 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). 


1 comentario:

Andres Ordoñez dijo...

Dear Liz,

I like your writing, however, in a matter of content I am missing the part of Bayes in systematics.