Towards an inclusive philosophy for phylogenetic inference

被引:50
作者
Faith, DP
Trueman, JWH
机构
[1] Australian Museum, Sydney, NSW 2000, Australia
[2] Australian Natl Univ, Div Bot & Zool, Canberra, ACT 0200, Australia
关键词
corroboration; likelihood; parsimony; philosophy of science; Popper; PTP; severe test;
D O I
10.1080/106351501300317969
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
We defend and expand on our earlier proposal for an inclusive philosophical framework for phylogenetics, based on an interpretation of Popperian corroboration that is decoupled from the popular falsificationist interpretation of Popperian philosophy. Any phylogenetic inference method can provide Popperian "evidence" or "test statements" based on the method's goodness-of-fit values for different tree hypotheses. Corroboration, or the severity of that test, requires that the evidence is improbable without the hypothesis, given only background knowledge that includes elements of chance. This framework contrasts with attempted Popperian justifications for cladistic parsimony-in which evidence is the data, background knowledge is restricted to descent with modification, and "corroboration," as a by-product of nonfalsification, is to be measured by cladistic parsimony. Recognition that cladistic "corroboration" reflects only goodness-of-fit, not corroboration/severity, makes it clear that standard cladistic prohibitions, such as restrictions on the evolutionary models to be included in "background knowledge," have no philosophical status. The capacity to assess Popperian corroboration neither justifies nor excludes any phylogenetic method, but it does provide a framework in phylogenetics for learning from errors-cases where apparent good evidence is probable even without the hypothesis. We explore these issues in the context of corroboration assessments applied to likelihood methods and to a new form of parsimony. These different forms of evidence and corroboration assessment point also to a new way to combine evidence-not at the level of overall fit, but at the level of overall corroboration/severity. We conclude that progress in an inclusive phylogenetics will be well served by the rejection of cladistic philosophy.
引用
收藏
页码:331 / 350
页数:20
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