Practice-oriented controversies and borrowed epistemic credibility in current evolutionary biology: phylogeography as a case study

Although there is increasing recognition that theory and practice in science are intimately intertwined, philosophy of science perspectives on scientific controversies have been historically focused on theory rather than practice. As a step in the construction of frameworks for understanding controversies linked to scientific practices, here we introduce the notion of borrowed epistemic credibility (BEC), to describe the situation in which scientists, in order to garner support for their own stances, exploit similarities between tenets in their own field and accepted statements or positions properly developed within other areas of expertise. We illustrate the scope of application of our proposal with the analysis of a heavily methods-grounded, recent controversy in phylogeography, a biological subdiscipline concerned with the study of the historical causes of biogeographical variation through population genetics- and phylogenetics-based computer analyses of diversity in DNA sequences, both within species and between closely related taxa. Toward this end, we briefly summarize the arguments proposed by selected authors representing each side of the controversy: the ‘nested clade analysis’ school versus the ‘statistical phylogeography’ orientation. We claim that whereas both phylogeographic ‘research styles’ borrow epistemic credibility from sources such as formal logic, the familiarity of results from other scientific areas, the authority of prominent scientists, or the presumed superiority of quantitative vs. verbal reasoning, ‘theory’ plays essentially no role as a foundation of the controversy. Besides underscoring the importance of strictly methodological and other non-theoretical aspects of controversies in current evolutionary biology, our analysis suggests a perspective with potential usefulness for the re-examination of more general philosophy of biology issues, such as the nature of historical inference, rationality, justification, and objectivity

Reasoning about Minimal Belief and Negation as Failure

We investigate the problem of reasoning in the propositional fragment of MBNF, the logic of minimal belief and negation as failure introduced by Lifschitz, which can be considered as a unifying framework for several nonmonotonic formalisms, including default logic, autoepistemic logic, circumscription, epistemic queries, and logic programming. We characterize the complexity and provide algorithms for reasoning in propositional MBNF. In particular, we show that entailment in propositional MBNF lies at the third level of the polynomial hierarchy, hence it is harder than reasoning in all the above mentioned propositional formalisms for nonmonotonic reasoning. We also prove the exact correspondence between negation as failure in MBNF and negative introspection in Moore's autoepistemic logic

Rich Counter-Examples for Temporal-Epistemic Logic Model Checking

Model checking verifies that a model of a system satisfies a given property, and otherwise produces a counter-example explaining the violation. The verified properties are formally expressed in temporal logics. Some temporal logics, such as CTL, are branching: they allow to express facts about the whole computation tree of the model, rather than on each single linear computation. This branching aspect is even more critical when dealing with multi-modal logics, i.e. logics expressing facts about systems with several transition relations. A prominent example is CTLK, a logic that reasons about temporal and epistemic properties of multi-agent systems. In general, model checkers produce linear counter-examples for failed properties, composed of a single computation path of the model. But some branching properties are only poorly and partially explained by a linear counter-example. This paper proposes richer counter-example structures called tree-like annotated counter-examples (TLACEs), for properties in Action-Restricted CTL (ARCTL), an extension of CTL quantifying paths restricted in terms of actions labeling transitions of the model. These counter-examples have a branching structure that supports more complete description of property violations. Elements of these counter-examples are annotated with parts of the property to give a better understanding of their structure. Visualization and browsing of these richer counter-examples become a critical issue, as the number of branches and states can grow exponentially for deeply-nested properties. This paper formally defines the structure of TLACEs, characterizes adequate counter-examples w.r.t. models and failed properties, and gives a generation algorithm for ARCTL properties. It also illustrates the approach with examples in CTLK, using a reduction of CTLK to ARCTL. The proposed approach has been implemented, first by extending the NuSMV model checker to generate and export branching counter-examples, secondly by providing an interactive graphical interface to visualize and browse them.Comment: In Proceedings IWIGP 2012, arXiv:1202.422

The Role of Deontic Logic in the Specification of Information Systems

In this paper we discuss the role that deontic logic plays in the specification of information systems, either because constraints on the systems directly concern norms or, and even more importantly, system constraints are considered ideal but violable (so-called `soft¿ constraints).\ud To overcome the traditional problems with deontic logic (the so-called paradoxes), we first state the importance of distinguishing between ought-to-be and ought-to-do constraints and next focus on the most severe paradox, the so-called Chisholm paradox, involving contrary-to-duty norms. We present a multi-modal extension of standard deontic logic (SDL) to represent the ought-to-be version of the Chisholm set properly. For the ought-to-do variant we employ a reduction to dynamic logic, and show how the Chisholm set can be treated adequately in this setting. Finally we discuss a way of integrating both ought-to-be and ought-to-do reasoning, enabling one to draw conclusions from ought-to-be constraints to ought-to-do ones, and show by an example the use(fulness) of this

Positive Logic with Adjoint Modalities: Proof Theory, Semantics and Reasoning about Information

We consider a simple modal logic whose non-modal part has conjunction and disjunction as connectives and whose modalities come in adjoint pairs, but are not in general closure operators. Despite absence of negation and implication, and of axioms corresponding to the characteristic axioms of (e.g.) T, S4 and S5, such logics are useful, as shown in previous work by Baltag, Coecke and the first author, for encoding and reasoning about information and misinformation in multi-agent systems. For such a logic we present an algebraic semantics, using lattices with agent-indexed families of adjoint pairs of operators, and a cut-free sequent calculus. The calculus exploits operators on sequents, in the style of "nested" or "tree-sequent" calculi; cut-admissibility is shown by constructive syntactic methods. The applicability of the logic is illustrated by reasoning about the muddy children puzzle, for which the calculus is augmented with extra rules to express the facts of the muddy children scenario.Comment: This paper is the full version of the article that is to appear in the ENTCS proceedings of the 25th conference on the Mathematical Foundations of Programming Semantics (MFPS), April 2009, University of Oxfor