Fitzhugh Kirk
Natural History Museum of Los Angeles County, 900 Exposition Blvd, Los Angeles, CA, 90007, USA.
Acta Biotheor. 2021 Dec;69(4):799-819. doi: 10.1007/s10441-021-09412-4. Epub 2021 May 6.
Three competing 'methods' have been endorsed for inferring phylogenetic hypotheses: parsimony, likelihood, and Bayesianism. The latter two have been claimed superior because they take into account rates of sequence substitution. Can rates of substitution be justified on its own accord in inferences of explanatory hypotheses? Answering this question requires addressing four issues: (1) the aim of scientific inquiry, (2) the nature of why-questions, (3) explanatory hypotheses as answers to why-questions, and (4) acknowledging that neither parsimony, likelihood, nor Bayesianism are inferential actions leading to explanatory hypotheses. The aim of scientific inquiry is to acquire causal understanding of effects. Observation statements of organismal characters lead to implicit or explicit why-questions. Those questions, conveyed in data matrices, assume the truth of observation statements, which is contrary to subsequently invoking substitution rates within inferences to phylogenetic hypotheses. Inferences of explanatory hypotheses are abductive in form, such that some version of an evolutionary theory(ies) is/are included or implied. If rates of sequence evolution are to be considered, it must be done prior to, rather than within abduction, which requires renaming those putatively-shared nucleotides subject to substitution rates. There are, however, no epistemic grounds for renaming characters to accommodate rates, calling into question the legitimacy of causally accounting for sequence data.
有三种相互竞争的“方法”被认可用于推断系统发育假说：简约法、似然法和贝叶斯方法。后两种方法被认为更优越，因为它们考虑了序列替换率。在解释性假说的推断中，替换率本身能站得住脚吗？回答这个问题需要解决四个问题：（1）科学探究的目的，（2）为什么问题的本质，（3）作为对为什么问题的回答的解释性假说，以及（4）承认简约法、似然法和贝叶斯方法都不是导致解释性假说的推断行为。科学探究的目的是获得对效应的因果理解。生物体特征的观察陈述会引发隐含或明确的为什么问题。那些在数据矩阵中传达的问题假定了观察陈述的真实性，这与随后在系统发育假说的推断中调用替换率是相反的。解释性假说的推断在形式上是溯因的，因此某种版本的进化理论被包含或隐含其中。如果要考虑序列进化速率，那就必须在溯因之前而不是在溯因过程中进行，这需要对那些假定共享的、受替换率影响的核苷酸重新命名。然而，没有认识论依据对特征进行重新命名以适应速率，这就质疑了对序列数据进行因果解释的合法性。
