Evidence, Content and Corroboration and the Tree of Life

Abstract

We examine three critical aspects of Popper's formulation of the 'Logic of Scientific Discovery'-evidence, content and degree of corroborationand place these concepts in the context of the Tree of Life (ToL) problem with particular reference to molecular systematics. Content, in the sense discussed by Popper, refers to the breadth and scope of existence that a hypothesis purports to explain. Content, in conjunction with the amount of available and relevant evidence, determines the testability, or potential degree of corroboration, of a statement; content distinguishes scientific hypotheses from metaphysical assertions. Degree of corroboration refers to the relative and tentative confidence assigned to one hypothesis over another, based upon the performance of each under critical tests. Here we suggest that systematists attempt to maximize content and evidence to increase the potential degree of corroboration in all phylogenetic endeavors. Discussion of this ''total evidence'' approach leads to several interesting conclusions about generating ToL hypotheses.

Never Ending Analysis of a Century Old Evolutionary Debate: “Unringing” the Urmetazoon Bell

“…However, some authors also suggest that data such as morphological, molecular morphological, gene presence or absence, developmental data etc. be concatenated too, (Lienau and DeSalle, 2009;Schierwater et al, 2009). Through concatenation we get a better picture of the overall contribution of different sources of data to a phylogenetic hypothesis, although there is still a major problem of how to adequately partition the data sets and apply appropriate weighting and models of evolutionary change.…”

The series, the network, and the tree: changing metaphors of order in nature

“…This assessment nicely reflects the conflict between pattern analysis and process explanation. Pattern analysts will seek maximal congruence in the distribution of characters (ultimately of any kind) relative to a tree-topology (Lienau and DeSalle 2009); process explainers will call such tree-topologies into question by reference to incompatible evolutionary processes (Doolittle and Bapteste 2007). Pattern analysts will argue that process explanations must not be brought to bear on pattern reconstruction; process explainers will insist that the reconstructed pattern requires a process explanation to become scientifically relevant, i.e., relevant to evolutionary theory.…”

“…To bring assumptions derived from process explanations to bear on pattern reconstruction is considered to invoke the authoritarianism of traditional evolutionary systematists (e.g., Simpson 1961;Mayr 1969) that cladists attempted to overcome with their appeal to Popper's philosophy of science (see above). Whether carried out under parsimony, likelihood models, of Bayes' theorem, pattern reconstruction in terms of a strictly bifurcated branching diagram is still considered by the majority of systematists to provide the necessary scaffold against which evolutionary process explanations can be legitimately inferred (Brady 1985;Rieppel 2004;Lienau and DeSalle 2009). Critics of the 'Tree of Life' metaphor have begun to challenge such logical and epistemological primacy of pattern reconstruction over process explanation, however.…”

“…''In other words, evolution may well be true, but basing one's systematics on that belief will give bad systematics'' (Patterson 2002, p. 31; see also Brower 2000). From a cladist point of view, the prominent analytical issue at stake is to ''eliminate the potentially confounding effects [of] homoplasy'', i.e., of conflicting character distribution (Lienau and DeSalle 2009). The method to do so, discussed above, is a (quasi-)Popperian falsificationism applied to phylogeny reconstruction.…”

Depicting the tree of life in museums: guiding principles from psychological research

“…Particularly among Eubacteria and Archaea, mechanisms such as horizontal gene transfer, hybridization, and lineage merger events mean the inheritance of traits is sometimes reticulate, a pattern that is better represented by a network. There is an ongoing debate among scientists about whether reticulation means that the Tree of Life hypothesis is falsified, obsolete, or should be restricted to a subset of taxa (e.g., Bapteste et al 2009;Doolittle and Bapteste 2007) or whether the Tree remains the best explanation of the graded similarity of all life (e.g., Lienau and DeSalle 2009;Mindell 2013). As Mindell (2013) describes in his thoughtful discussion of the multiple uses of the Tree of Life, reticulate evolution has long been known and accepted as a pattern within the Tree of Life, and the core feature of the Tree, phylogenetic relatedness, remains a valid organizing principle for biological diversity.…”