Delusional beliefs have sometimes been considered as rational inferences from abnormal experiences. We explore this idea in more detail, making the following points. Firstly, the abnormalities of cognition which initially prompt the entertaining of a delusional belief are not always conscious and since we prefer to restrict the term “experience” to consciousness we refer to “abnormal data” rather than “abnormal experience”. Secondly, we argue that in relation to many delusions (we consider eight) one can clearly identify what the abnormal cognitive (...) data are which prompted the delusion and what the neuropsychological impairment is which is responsible for the occurrence of these data; but one can equally clearly point to cases where this impairments is present but delusion is not. So the impairment is not sufficient for delusion to occur. A second cognitive impairment, one which impairs the ability to evaluate beliefs, must also be present. Thirdly (and this is the main thrust of our chapter) we consider in detail what the nature of the inference is that leads from the abnormal data to the belief. This is not deductive inference and it is not inference by enumerative induction; it is abductive inference. We offer a Bayesian account of abductive inference and apply it to the explanation of delusional belief. (shrink)

I provide an analysis of Hegel's interpretation of the faith exemplified in Abraham's journey to Mt. Moriah to sacrifice his son. I do so by looking at changes in Hegel's discussion of this episode in the Lectures on the Philosophy of Religion that were given over the last decade of his career. In the process of tracing the contours of the development of Hegel's thinking on this issue I argue that his social philosophy, on which persons are first and foremost (...) creatures of rational self-determination, is informed by his understanding of logic and metaphysics, and I suggest some of the rationalist and romantic elements animating Hegel's thought remain viable today. (shrink)

The present paper proposes a route to modal claims that allows us to infer to certain possibilities even if they are sensorily unimaginable and beyond the evidential capacity of stipulative imagining. After a brief introduction, Sect. 2 discusses imaginative resistance to help carve a niche for the kinds of inferences about which this essay is chiefly concerned. Section 3 provides three classic examples, along with a discussion of their similarities and differences. Section 4 recasts the notion of potential explanation in (...) Lipton’s (Inference to the best explanation, Routledge, Abingdon, 2004) in order to accommodate inferences to possibility claims; Sect. 5 then attempts to characterise a principle underlying such inferences. Section 6 concludes by discussing how the proposal relates to other modal epistemologies, with emphasis on the potential of such inferences to produce genuinely new ideas. (shrink)

The relationship between Peircean abduction and the modern notion of Inference to the Best Explanation is a matter of dispute. Some philosophers, such as Harman :88–95, 1965) and Lipton, claim that abduction and IBE are virtually the same. Others, however, hold that they are quite different :503, 1998; Minnameier in Erkenntnis 60:75–105, 2004) and there is no link between them :419–442, 2009). In this paper, I argue that neither of these views is correct. I show that abduction and IBE (...) have important similarities as well as differences. Moreover, by bringing a historical perspective to the study of the relationship between abduction and IBE—a perspective that is lacking in the literature—I show that their differences can be well understood in terms of two historic developments in the history of philosophy of science: first, Reichenbach’s distinction between the context of discovery and the context of justification—and the consequent jettisoning of the context of discovery from philosophy of science—and second, underdetermination of theory by data. (shrink)

Inference to the Best Explanation (IBE) is widely criticized for being an unreliable form of ampliative inference – partly because the explanatory hypotheses we have considered at a given time may all be false, and partly because there is an asymmetry between the comparative judgment on which an IBE is based and the absolute verdict that IBE is meant to license. In this paper, I present a further reason to doubt the epistemic merits of IBE and argue that (...) it motivates moving to an inferential pattern in which IBE emerges as a degenerate limiting case. Since this inferential pattern is structurally similar to an argumentative strategy known as Inferential Robustness Analysis (IRA), it effectively combines the most attractive features of IBE and IRA into a unified approach to non-deductive inference. (shrink)

Tomis Kapitan’s work on Peirce’s conception of abduction was instrumental for our coming to see how Peircean abduction both relates to and is importantly different from inference to the best explanation (IBE). However, he ultimately concluded that Peirce’s conception of abduction was a muddle. Despite the deeply problematic nature of Peirce’s theory of abduction in these respects, Kapitan’s work on Peircean abduction offers insight into the nature of abductive inquiry that is importantly relevant to the task of making (...) sense of explanatory inquiry in the sciences in general. The view developed here stems from his work and involves disambiguating three forms of inference involved in Peircean abduction in terms of Reichenbach’s and Laudan’s context models of inquiry. Importantly, this includes understanding that abduction involves the context of pursuit. (shrink)

I examine and resolve an exegetical dichotomy between two main interpretations of Peirce’s theory of abduction, namely, the Generative Interpretation and the Pursuitworthiness Interpretation. According to the former, abduction is the instinctive process of generating explanatory hypotheses through a mental faculty called insight. According to the latter, abduction is a rule-governed procedure for determining the relative pursuitworthiness of available hypotheses and adopting the worthiest one for further investigation—such as empirical tests—based on economic considerations. It is shown that the Generative Interpretation (...) is inconsistent with a fundamental fact of logic for Peirce—i.e., abduction is a kind of inference—and the Pursuitworthiness Interpretation is flawed and inconsistent with Peirce’s naturalistic explanation for the possibility of science and his view about the limitations of classical scientific method. Changing the exegetical locus classicus from the logical form of abduction to insight and economy of research, I argue for the Unified Interpretation according to which abduction includes both instinctive hypotheses-generation and rule-governed hypotheses-ranking. I show that the Unified Interpretation is immune to the objections raised successfully against the Generative and the Pursuitworthiness interpretations. (shrink)

Abduction* is the genus with deduction and induction as species. Modus tollens is backward reasoning as an unknown proposition is inferred from a known proposition. Reductio ad absurdum is abductive because the conclusion is inferred by deriving a contradiction from an assumption. Inductive reasoning from effect to cause is also backward reasoning. But abduction* consists of forward reasoning as well. The generic structure of abductive* argumentation is universal among all cultures, occupations and disciplines.

This chapter presents a typology of the different kinds of inductive inferences we can draw from our evidence, based on the explanatory relationship between evidence and conclusion. Drawing on the literature on graphical models of explanation, I divide inductive inferences into (a) downwards inferences, which proceed from cause to effect, (b) upwards inferences, which proceed from effect to cause, and (c) sideways inferences, which proceed first from effect to cause and then from that cause to an additional effect. I further (...) distinguish between direct and indirect forms of downwards and upwards inferences. I then show how we can subsume canonical forms of inductive inference mentioned in the literature, such as inference to the best explanation, enumerative induction, and analogical inference, under this typology. Along the way, I explore connections with probability and confirmation, epistemic defeat, the relation between abduction and enumerative induction, the compatibility of IBE and Bayesianism, and theories of epistemic justification. (shrink)

Epistemic two-dimensional semantics, advocated by Chalmers and Jackson, among others, aims to restore the link between necessity and a priority seemingly broken by Kripke, by showing how armchair access to semantic intensions provides a basis for knowledge of necessary a posteriori truths. The most compelling objections to E2D are that, for one or other reason, the requisite intensions are not accessible from the armchair. As we substantiate here, existing versions of E2D are indeed subject to such access-based objections. But, we (...) moreover argue, the difficulty lies not with E2D but with the typically presupposed conceiving-based epistemology of intensions. Freed from that epistemology, and given the right alternative—one where inference to the best explanation provides the operative guide to intensions—E2D can meet access-based objections, and fulfill its promise of restoring the desirable link between necessity and a priority. This result serves as a central application of Biggs and Wilson, according to which abduction is an a priori mode of inference. (shrink)

A reorientation is needed in methodological debate about the role of intuitions in philosophy. Methodological debate has lost sight of the reason why it makes sense to focus on questions about intuitions when thinking about the methods or epistemology of philosophy. The problem is an approach to methodology that focuses almost exclusively on questions about some evidential role that intuitions may or may not play in philosophers’ arguments. A new approach is needed. Approaching methodological questions about the role of intuitions (...) in philosophy with an abductive model of philosophical inquiry in mind will help ensure the debate doesn't lose sight of what motivates the debate. (shrink)

Charles S. Peirce (1839-1914) made relevant contributions to deductive logic, but he was primarily interested in the logic of science, and more especially in what he called 'abduction' (as opposed to deduction and induction), which is the process whereby hypotheses are generated in order to explain the surprising facts. Indeed, Peirce considered abduction to be at the heart not only of scientific research, but of all ordinary human activities. Nevertheless, in spite of Peirce's work and writings in the field of (...) methodology of research, scarce attention has been paid to the logic of discovery over the last hundred years, despite an impressive development not only of scientific research but also of logic. -/- Having this in mind, the exposition is divided into five parts: 1) a brief presentation of Peirce, focusing on his work as a professional scientist; 2) an exposition of the classification of inferences by the young Peirce: deduction, induction and hypothesis; 3) a sketch of the notion of abduction in the mature Peirce; 4) an exposition of the logic of surprise; and finally, by way of conclusion, 5) a discussion of this peculiar ability of guessing understood as a rational instinct. -/- . (shrink)

In this article, I will provide a critical overview of the form of non-deductive reasoning commonly known as “Inference to the Best Explanation” (IBE). Roughly speaking, according to IBE, we ought to infer the hypothesis that provides the best explanation of our evidence. In section 2, I survey some contemporary formulations of IBE and highlight some of its putative applications. In section 3, I distinguish IBE from C.S. Peirce’s notion of abduction. After underlining some of the essential elements of (...) IBE, the rest of the entry is organized around an examination of various problems that IBE confronts, along with some extant attempts to address these problems. In section 4, I consider the question of when a fact requires an explanation, since presumably IBE applies only in cases where some explanation is called for. In section 5, I consider the difficult question of how we ought to understand IBE in light of the fact that among philosophers, there is significant disagreement about what constitutes an explanation. In section 6, I consider different strategies for justifying the truth-conduciveness of the explanatory virtues, e.g., simplicity, unification, scope, etc., criteria which play an indispensable role in any given application of IBE. In section 7, I survey some of the most recent literature on IBE, much of which consists of investigations of the status of IBE from the standpoint of the Bayesian philosophy of science. (shrink)

In this paper art history and visual studies, the disciplines that study visual culture, are presented as a field whose conjectural paradigm can be used to understand the epistemic problems associated with abduction. In order to do so, significant statements, concepts and arguments from the work of several specialists in this field have been highlighted. Their analysis shows the fruitfulness and potential for understanding the study of visual culture as a field that is interwoven with the assumptions of abductive (...) cognition. (shrink)

Christian apologists, like Willian Lane Craig and Stephen T. Davis, argue that belief in Jesus’ resurrection is reasonable because it provides the best explanation of the available evidence. In this article, I refute that thesis. To do so, I lay out how the logic of inference to the best explanation (IBE) operates, including what good explanations must be and do by definition, and then apply IBE to the issue at hand. Multiple explanations—including (what I will call) The Resurrection Hypothesis, (...) The Lie Hypothesis, The Coma Hypothesis, The Imposter Hypothesis, and The Legend Hypothesis—will be considered. While I will not attempt to rank them all from worst to best, what I will reveal is how and why The Legend Hypothesis is unquestionably the best explanation, and The Resurrection Hypothesis is undeniably the worst. Consequently, not only is Craig and Davis’ conclusion mistaken, but belief in the literal resurrection of Jesus is irrational. In presenting this argument, I do not take myself to be breaking new ground; Robert Cavin and Carlos Colombetti have already presented a Bayesian refutation of Craig and Davis’ arguments. But I do take myself to be presenting an argument that the average person (and philosopher) can follow. It is my goal for the average person (and philosopher) to be able to clearly understand how and why the hypothesis “God supernaturally raised Jesus from the dead” fails utterly as an explanation of the evidence that Christian apologist cite for Jesus’ resurrection. (shrink)

From the perspective of distributed cognition I will stress how abduction is essentially multimodal, in that both data and hypotheses can have a full range of verbal and sensory representations, involving words, sights, images, smells, etc., but also kinesthetic – related to the ability to sense the position and location and orientation and movement of the body and its parts – and motor experiences and other feelings such as pain, and thus all sensory modalities. The presence of kinesthetic and motor (...) aspects demonstrates that abductive reasoning can be manipulative. We can also see, in this regard, how implicit factors take part in the abductive procedure, which consequently acquires the character of a kind of “thinking through doing”. This paper further describes 1) the fact that hypotheses in science can be built through different cognitive mediators and so they can also model the same cognitive aspect in different ways; how they can be carriers/ producers of knowledge in a multimodal way; 2) the problem of the possible non-explanatory and instrumental nature of abductive reasoning and the analysis of the consequences for induction; 3) the role of manipulative abduction in building new evidence/ experiments and how they trigger smart inductive inferences. (shrink)

Reasoning over our knowledge bases and theories often requires non-deductive inferences, especially – but by no means only – when commonsense reasoning is the case, i.e. when practical agency is called for. This kind of reasoning can be adequately formalized via the notion of supraclassical consequence, a non-deductive consequence tightly associated with default and non-monotonic reasoning and featuring centrally in abductive, inductive, and probabilistic logical systems. In this paper, we analyze core concepts and problems of these systems in the (...) light of supraclassical consequence. (shrink)

This monograph is an in-depth and engaging discourse on the deeply cognitive roots of human scientific quest. The process of making scientific inferences is continuous with the day-to-day inferential activity of individuals, and is predominantly inductive in nature. Inductive inference, which is fallible, exploratory, and open-ended, is of essential relevance in our incessant efforts at making sense of a complex and uncertain world around us, and covers a vast range of cognitive activities, among which scientific exploration constitutes the pinnacle. (...) Inductive inference has a personal aspect to it, being rooted in the cognitive unconscious of individuals, which has recently been found to be of paramount importance in a wide range of complex cognitive processes. One other major aspect of the process of inference making, including the making of scientific inferences, is the role of a vast web of beliefs lodged in the human mind, as also of a huge repertoire of heuristics, that constitute an important component of ‘unconscious intelligence’. Finally, human cognitive activity is dependent in a large measure on emotions and affects, that operate mostly at an unconscious level. Of special importance in scientific inferential activity is the process of hypothesis making, which is examined in this book, along with the above aspects of inductive inference, at considerable depth. The book focuses on the inadequacy of the viewpoint of naive realism in understanding the contextual nature of scientific theories, where a cumulative progress towards an ultimate truth about Nature appears to be too simplistic a generalization. It poses a critique to the commonly perceived image of science which is seen as the last word in logic and objectivity, the latter in the double sense of being independent of individual psychological propensities and, at the same time, approaching a correct understanding of the workings of a mind-independent nature. Adopting the naturalist point of view, it examines the essential tension between the cognitive endeavours of individuals and scientific communities, immersed in belief systems and cultures, on the one hand, and the engagement with a mind-independent reality on the other. In the end, science emerges as an interpretation of nature, which is perceived by us only contextually, as successively emerging cross-sections of limited scope and extent. Successive waves of theory building in science appear as episodic and kaleidoscopic changes in perspective as certain in-built borders are crossed, rather than as a cumulative progress towards some ultimate truth. While written in an informal and conversational style, the book raises a number of deep and intriguing questions located at the interface of cognitive psychology and philosophy of science, meant for both the general lay reader and the specialist. Of particular interest is the way it explores the role of belief (aided by emotions and affects) in making the process of inductive inference possible since belief is a subtle though all-pervasive cognitive factor not adequately investigated in the current literature. (shrink)

Proponents of the explanatory indispensability argument for mathematical platonism maintain that claims about mathematical entities play an essential explanatory role in some of our best scientific explanations. They infer that the existence of mathematical entities is supported by way of inference to the best explanation from empirical phenomena and therefore that there are the same sort of empirical grounds for believing in mathematical entities as there are for believing in concrete unobservables such as quarks. I object that this (...) class='Hi'>inference depends on a false view of how abductive considerations mediate the transfer of empirical support. More specifically, I argue that even if inference to the best explanation is cogent, and claims about mathematical entities play an essential explanatory role in some of our best scientific explanations, it doesn’t follow that the empirical phenomena that license those explanations also provide empirical support for the claim that mathematical entities exist. (shrink)

What is an inference and when is an inference deductive rather than inductive, abductive, etc. The goal of this paper is precisely to determine what is that we, humans, do when we engage in deduction, i.e., whether there is something that satisfies both our pre-theoretical intuitions and theoretical presuppositions about deduction, as a cognitive process. The paper is structured in two parts: the first one deals with the issue of what is an inference. There, I will (...) defend the hypothesis that an inference is a causal process where an initial cognitive state causes another in such a way that the causal translation depends essentially on the content of the involved states. In other words, in an inference, a mental state A causes another B, partially because they have the content they have. Based on the conclusion from the first part, I will develop an account of deductive inference in the second part of the article. In order to achieve this, I will start by setting the stage and developing four constraints that an adequate account of deductive inference ought to satisfy. Then, I will present six different hypotheses that one might propose to characterize inferences of this kind. I have divided the proposals in two groups, the first one – which I will call the “logical proposals” – assume that whether an inference is a deduction or not depends exclusively on the content of the mental states involved in the inference, while the second – which I will call the “cognitive proposals” – reject the aforementioned assumption and instead recognize that extra cognitive information is required to determine whether an inference is a deduction or not. I will evaluate each proposal in turn, according to whether they satisfy the constraints introduced at the beginning of this second part. As a result of such evaluation, I will conclude that only one of the cognitive proposals actually satisfies the four constraints and therefore should be considered to give an adequate characterization of deductive inference. (shrink)

Nonindexical Context-Dependence and the Interpretation as Abduction Approach Inclusive nonindexical context-dependence occurs when the preferred interpretation of an utterance implies its lexically-derived meaning. It is argued that the corresponding processes of free or lexically mandated enrichment can be modeled as abductive inference. A form of abduction is implemented in Simple Type Theory on the basis of a notion of plausibility, which is in turn regarded a preference relation over possible worlds. Since a preordering of doxastic alternatives taken for (...) itself only amounts to a relatively vacuous ad hoc model, it needs to be combined with a rational way of learning from new evidence. Lexicographic upgrade is implemented as an example of how an agent might revise his plausibility ordering in light of new evidence. Various examples are given how this apparatus may be used to model the contextual resolution of context-dependent or semantically incomplete utterances. The described form of abduction is limited and merely serves as a proof of concept, but the idea in general has good potential as one among many ways to build a bridge between semantics and pragmatics since inclusive context-dependence is ubiquitous. (shrink)

One of the many notable virtues of Igor Douven's The Art of Abduction is that it is open access. Since a well-written chapter-by-chapter overview of the book is.

We contend that it is possible to argue reasonably for and against arguments from classifications and definitions, provided they are seen as defeasible (subject to exceptions and critical questioning). Arguments from classification of the most common sorts are shown to be based on defeasible reasoning of various kinds represented by patterns of logical reasoning called defeasible argumentation schemes. We show how such schemes can be identified with heuristics, or short-cut solutions to a problem. We examine a variety of arguments of (...) this sort, including argument from abductive classification, argument from causal classification, argument from analogy-based classification and arguments from classification based on generalizations. (shrink)

In a series of papers over the past twenty years, and in a new book, Igor Douven has argued that Bayesians are too quick to reject versions of inference to the best explanation that cannot be accommodated within their framework. In this paper, I survey their worries and attempt to answer them using a series of pragmatic and purely epistemic arguments that I take to show that Bayes’ Rule really is the only rational way to respond to your evidence.

It is usually accepted that deductions are non-informative and monotonic, inductions are informative and nonmonotonic, abductions create hypotheses but are epistemically irrelevant, and both deductions and inductions can’t provide new insights. In this article, I attempt to provide a more cohesive view of the subject with the following hypotheses: (1) the paradigmatic examples of deductions, such as modus ponens and hypothetical syllogism, are not inferential forms, but coherence requirements for inferences; (2) since any reasoner aims to be coherent, any (...) class='Hi'>inference must be deductive; (3) a coherent inference is an intuitive process where the premises should be taken as sufficient evidence for the conclusion, which on its turn should be viewed as necessary evidence for the premises in some modal range; (4) inductions, properly understood, are abductions, but there are no abductions beyond the fact that in any inference the conclusion should be regarded as necessary evidence for the premises; (5) monotonicity is not only compatible with the retraction of past inferences given new information, but it is a requirement for it; (6) this explanation of inferences holds true for discovery processes, predictions and trivial inferences. (shrink)

The phenomenon of presupposition suspension can be analyzed in terms of explicatures and the corresponding non-presumptive interpretative reasoning underlying it. On the view presented in this paper, the polyphonic articulation of an utterance at different levels can be used to explain cases in which presuppositions are suspended. Presuppositional suspensions indicate that the presumptive reading does not hold and a different interpretation is needed. Utterances can display various types of polyphonic structures, accounting for the speaker’s and the hearer’s commitments. A speaker (...) can be held directly responsible for what he says, but he is committed only indirectly to what he presupposes, i.e. what is uttered by a second voice (the second utterer or enunciator) representing what the common opinion accepts to be true. The reconstruction of the pragmatic structure of an utterance is guided by a complex type of reasoning, which can be represented as an argumentative abductive pattern, grounded on hierarchies of presumptions. By comparing the possible presumptions associated with the explicit meaning and the contextual information, the hearer can find a best possible explanation of the intended effect of the utterance. (shrink)

IBE ('Inference to the best explanation' or abduction) is a popular and highly plausible theory of how we should judge the evidence for claims of past events based on present evidence. It has been notably developed and supported recently by Meyer following Lipton. I believe this theory is essentially correct. This paper supports IBE from a probability perspective, and argues that the retrodictive probabilities involved in such inferences should be analysed in terms of predictive probabilities and a priori probability (...) ratios of initial events. The key point is to separate these two features. Disagreements over evidence can be traced to disagreements over either the a priori probability ratios or predictive conditional ratios. In many cases, in real science, judgements of the former are necessarily subjective. The principles of iterated evidence are also discussed. The Sceptic's position is criticised as ignoring iteration of evidence, and characteristically failing to adjust a priori probability ratios in response to empirical evidence. (shrink)

Dans cet article, nous examinerons le thème de la découverte en science. Nous soutiendrons qu’il est possible de définir une stratégie rationnelle soutenant la découverte au moyen du principe de l’abduction. Afin de démontrer cette thèse, il s’agira d’abord de diagnostiquer le problème de la complexité et de l’irrationalité de la découverte scientifique et de considérer la position néo-positiviste endossée par Karl Popper et Hans Reichenbach, selon laquelle la découverte ne peut faire l’objet d’une étude proprement logique ou épistémologique. Par (...) la suite, l’analyse se concentrera sur la position de Norwood R. Hanson qui, répondant et contredisant celle de Popper et de Reichenbach, affirme qu’il existe une « logique de la découverte », fondée sur le principe de l’abduction. Après avoir déployé l’argument de Hanson et explicité sa conception du principe de l’abduction, nous montrerons, en nous appuyant sur la vision d’Atocha Aliseda, comment l’abduction est liée à la découverte en science. Finalement, nous examinerons la notion d’inférence à la meilleure explication et le concept « d’hypothèse explicative » de Peter Lipton, ce qui permettra d’expliquer dans quelle mesure cette variante de l’abduction nous permet de comprendre les éléments et conditions qui favorisent la génération de découvertes en science. (shrink)

This paper deals with Peirce’s understanding of perceptual judgment, relating it to the conditions for the use of language defined by Michael Dummett. Namely, drawing on Dummett’s requirement for harmony between descriptive and evaluative aspects of our linguistic practice, we will try to give an interpretation of Peirce’s view of perception that implies rejecting the idea that the formation of a perceptual judgment has an inferential structure. On the other hand, since it is, in Peirce’s opinion, the structure of (...) class='Hi'>abductive inference, this approach should enable us to draw some conclusions related to abduction in general. (shrink)

This paper proceeds in two parts. In the first part, I set out Fodor’s concerns about abduction in his recent books, The Mind Doesn’t Work That Way and In Critical Condition. In the second part, I attempt to meet these concerns by suggesting how - within the framework of the Massive Modularity Hypothesis - abduction functions, specifically in the context of means-end reasoning to connect Input Modules and Output Modules. My suggestion will be that natural selection is the Mother of (...) Abductive Inference and that it is evidenced in all sorts of sub-doxastic Means-End Reasoning contexts and for a variety of species. I will eventually discuss two representative cases to illustrate this suggestion: namely, dead reckoning and spatial reorientation. (shrink)

During the last quarter of a century, a number of philosophers have become attracted to the idea that necessity can be analyzed in terms of a hyperintensional notion of essence. One challenge for proponents of this view is to give a plausible explanation of our modal knowledge. The goal of this paper is to develop a strategy for meeting this challenge. My approach rests on an account of modality that I developed in previous work, and which analyzes modal properties in (...) terms of the notion of a metaphysical law. I discuss what information about the metaphysical laws is required for modal knowledge. Moreover, I describe two ways in which we might be able to acquire this information. The first way employs inference to the best explanation. The metaphysical laws, including the essential truths, play a crucial role in causal and grounding explanations and we can gain knowledge of these laws by abductive inferences from facts of which we have perceptual or a priori knowledge. The second way of gaining information about the metaphysical laws rests on knowledge that is partly constitutive of competence with the concepts that are needed to express the relevant information. Finally, I consider how knowledge of the metaphysical laws can be used to establish modal claims, paying special attention to the much-discussed connection between conceiving and possibility. (shrink)

This essay (a revised version of my undergraduate honors thesis at Stanford) constructs a theory of analogy as it applies to argumentation and reasoning, especially as used in fields such as philosophy and law. The word analogy has been used in different senses, which the essay defines. The theory developed herein applies to analogia rationis, or analogical reasoning. Building on the framework of situation theory, a type of logical relation called determination is defined. This determination relation solves a puzzle about (...) analogy in the context of logical argument, namely, whether an analogous situation contributes anything logically over and above what could be inferred from the application of prior knowledge to a present situation. Scholars of reasoning have often claimed that analogical arguments are never logically valid, and that they therefore lack cogency. However, when the right type of determination structure exists, it is possible to prove that projecting a conclusion inferred by analogy onto the situation about which one is reasoning is both valid and non-redundant. Various other properties and consequences of the determination relation are also proven. Some analogical arguments are based on principles such as similarity, which are not logically valid. The theory therefore provides us with a way to distinguish between legitimate and illegitimate arguments. It also provides an alternative to procedures based on the assessment of similarity for constructing analogies in artificial intelligence systems. (shrink)

Advancement in cognitive science depends, in part, on doing some occasional ‘theoretical housekeeping’. We highlight some conceptual confusions lurking in an important attempt at explaining the human capacity for rational or coherent thought: Thagard & Verbeurgt’s computational-level model of humans’ capacity for making reasonable and truth-conducive abductive inferences (1998; Thagard, 2000). Thagard & Verbeurgt’s model assumes that humans make such inferences by computing a coherence function (f_coh), which takes as input representation networks and their pair-wise constraints and gives as (...) output a partition into accepted (A) and rejected (R) elements that maximizes the weight of satisfied constraints. We argue that their proposal gives rise to at least three difficult problems. (shrink)

In the words of Charles Peirce from 1901, “man is but a degenerate monkey, with a paranoic talent for self-satisfaction, no matter what scrapes he may get himself into, calling them ‘civilization…’” Peirce’s concept of degenerate monkey draws attention both to our neotenous or prolonged newborn-like nature as “degenerate” in the mathematical sense of a genetic falling away from more mature genomes of other primates, and also to our monkeying around with the long evolutionary narrative of foraging, through the advent (...) of agriculture, settlement, and civilization. -/- Homo sapiens, man the knower, is the way we humans like to distinguish ourselves from the rest of nature. But if we consider ourselves as degenerate monkeys, perhaps homo errans, man the blunderer, would have been a better term, calling attention to our softened instinctive intelligence, in contrast to the “unerring instincts of other races,” as Peirce put it. -/- I take Peirce’s term “degenerate monkey” as not limited to moderns, but applicable to homo sapiens sapiens, anatomically modern humans, generally. Considering humans as degenerate monkeys is a key to understanding human development, in my view, precisely because we need to attune ourselves to the instinctive intelligence of the environment, drawing its intelligence into our dematured, blundering selves through abductive inference, and therein finding our maturity. Without that attunement to the Others, monkey goes mad, monkeying in its mirror of itself, fatally fixated, like Narcissus, and with similar results: planet of the degenerate monkeys, monkeying to mayhem. -/- As Cornelius, the ape archaeologist and historian in The Planet of the Apes stated it, reading from the sacred scrolls: “Beware the beast Man, for he is the Devil's pawn. Alone among God's primates, he kills for sport or lust or greed. Yea, he will murder his brother to possess his brother's land. Let him not breed in great numbers, for he will make a desert of his home and yours. Shun him; drive him back into his jungle lair, for he is the harbinger of death.” Or as Ralph Waldo Emerson put it: “The end of the human race will be that it will eventually die of civilization.” . (shrink)

Benjamin Libet's celebrated experiments concerning freedom elicited numerous attempts of _philosophical_ repudiation. Ten years ago, however, Judy Trevena and Jeff Miller published a _technical_ objection; they claim to have detected a,,smearing artifact" in Libet's calculations. This rests on a misunderstanding of Libet's methodology. In my reconstruction of Libet's argument, he draws an abductive inference to the best explanation. Now, Trevena's and Miller's objection does indeed lead to alternative explanations of Libet's measurements. These alternatives are _ad hoc_ and extremely (...) improbable. They constitute worse explanations than the explanation offered by Libet. _German_ Benjamin Libets bahnbrechende Experimente zur Willensfreiheit aus den Achtziger Jahren des vorigen Jahrhunderts gehören längst zu den Klassikern der Experimentalkunst. Aus _philosophischer_ Perspektive sind sie oft kritisiert worden; unabhängig davon ist zu Beginn des neuen Jahrtausends ein _technischer_ Einwand gegen Libet prominent geworden, der von Freiheitsfreunden gerne zitiert wird. Er geht auf Judy Trevena und Jeff Miller zurück und besteht in dem Vorwurf, dass Libet mit seiner Berechnung der _gemittelten_ Bereitschaftspotential-Kurven die wahren Verhältnisse verschmiere und dabei aus mathematischen Gründen den Anstiegs-Zeitpunkt des Bereitschaftspotentials künstlich nach vorne verschiebe – das ist der Vorwurf des sog. Verschmierungsartefakts. Ich zeige, dass der Vorwurf nicht sticht. Er beruht auf einem Missverständnis der Schlussmethode Libets. Laut meiner wissenschaftstheoretischen Rekonstruktion zieht Libet weder deduktive noch induktive Schlüsse aus seinen Einzelbeobachtungen; er schließt abduktiv, d.h. er schließt auf die beste Erklärung seiner Einzelbeobachtungen. Wie eine genaue arithmetische Analyse zeigt, bieten die Alternativ-Erklärungen, unter denen sich das Verschmierungsartefakt bewahrheiten würde, schlechtere Erklärungen als Libets Erklärung – sie sind an den Haaren herbeigezogen und extrem unwahrscheinlich. (shrink)

In this paper, we set out to investigate the following question: if science relies heavily on induction, does philosophy of science rely heavily on induction as well? Using data mining and text analysis methods, we study a large corpus of philosophical texts mined from the JSTOR database (n = 14,199) in order to answer this question empirically. If philosophy of science relies heavily on induction, just as science supposedly does, then we would expect to find significantly more inductive arguments than (...) deductive arguments and abductive arguments in the published works of philosophers of science. Using indicator words to classify arguments by type (namely, deductive, inductive, and abductive arguments), we search through our corpus to find patterns of argumentation. Overall, the results of our study suggest that philosophers of science do rely on inductive inference. But induction may not be as foundational to philosophy of science as it is thought to be for science, given that philosophers of science make significantly more deductive arguments than inductive arguments. Interestingly, our results also suggest that philosophers of science do not rely on abductive arguments all that much, even though philosophers of science consider abduction to be a cornerstone of scientific methodology. (shrink)

This thesis develops and defends a Peircean conception of the task of metaphysics and critically compares it with recent anti-metaphysical forms of pragmatism. Peirce characterises metaphysics in terms of its place within his hierarchical classification of the sciences. According to the classification, metaphysics depends on logic for principles and provides principles to the natural and social sciences. This arrangement of the sciences is defended by appeal to Peirce's account of philosophy as 'cenoscopy'. The dependence of the natural and social sciences (...) on cenoscopy is then argued for on the basis of Peirce's rejection of psychologism and in terms of the necessity of abductive inference. Peirce's position is then compared with recent forms of pragmatism. While it is less naturalistic, Peirce's position is defended on pragmatist grounds. An account of Peirce on truth is then developed. Peirce's account of truth in terms of an ideal limit of inquiry is defended as consistent with recent, more deflationary, approaches. The truth of 'abstract propositions' is a matter of local indefeasibility. These abstract propositions are related to the 'absolute truth', understood as a single non-abstract proposition. The truth of this proposition is then understood in terms of an identity theory. Two conceptions of Peircean metaphysics are presented. Both are 'abductive'. Their task is to explain the possibility of success in inquiry. However, only one proposal accepts the notion of an absolute truth. The 'absolutist' proposal is defended as an interpretation of Peirce and as a contemporary option for pragmatist philosophers. The thesis concludes by comparing recent anti-metaphysical arguments due to Huw Price with the Peircean position. Room for the absolutist proposal is defended by means of an account of recent exchanges between Price and Robert Brandom on dispositional modality. (shrink)

The aim of this study is to justify the belief that there are biological normative mechanisms that fulfill non-trivial causal roles in the explanations (as formulated by researchers) of actions and behaviors present in specific systems. One example of such mechanisms is the predictive mechanisms described and explained by predictive processing (hereinafter PP), which (1) guide actions and (2) shape causal transitions between states that have specific content and fulfillment conditions (e.g. mental states). Therefore, I am guided by a specific (...) theoretical goal associated with the need to indicate those conditions that should be met by the non-trivial theory of normative mechanisms and the specific models proposed by PP supporters. In this work, I use classical philosophical methods, such as conceptual analysis and critical reflection. I also analyze selected studies in the field of cognitive science, cognitive psychology, neurology, information theory and biology in terms of the methodology, argumentation and language used, in accordance with their theoretical importance for the issues discussed in this study. In this sense, the research presented here is interdisciplinary. My research framework is informed by the mechanistic model of explanation, which defines the necessary and sufficient conditions for explaining a given phenomenon. The research methods I chose are therefore related to the problems that I intend to solve. In the introductory chapter, “The concept of predictive processing”, I discuss the nature of PP as well as its main assumptions and theses. I also highlight the key concepts and distinctions for this research framework. Many authors argue that PP is a contemporary version of Kantianism and is exposed to objections similar to those made against the approach of Immanuel Kant. I discuss this thesis and show that it is only in a very general sense that the PP framework is neo-Kantian. Here we are not dealing with transcendental deduction nor with the application of transcendental arguments. I argue that PP is based on reverse engineering and abduction inferences. In the second part of this chapter, I respond to the objection formulated by Dan Zahavi, who directly accuses this research framework of anti-realistic consequences. I demonstrate that the position of internalism, present in the so-called conservative PP, does not imply anti-realism, and that, due to the explanatory role played in it by structural representations directed at real patterns, it is justified to claim that PP is realistic. In this way, I show that PP is a non-trivial research framework, having its subject, specific methods and its own epistemic status. Finally, I discuss positions classified as the socalled radical PP. In the chapter “Predictive processing as a Bayesian explanatory model” I justify the thesis according to which PP offers Bayesian modeling. Many researchers claim that the brain is an implemented statistical probabilistic network that is an approximation of the Bayesian 7 rule. In practice, this means that all cognitive processes are to apply Bayes' rule and can be described in terms of probability distributions. Such a solution arouses objections among many researchers and is the subject of wide criticism. The purpose of this chapter is to justify the thesis that Bayesian PP is a non-trivial research framework. For this purpose, I argue that it explains certain phenomena not only at the computational level described by David Marr, but also at the level of algorithms and implementation. Later in this chapter I demonstrate that PP is normative modeling. Proponents of the use of Bayesian models in psychology or decision theory argue that they are normative because they allow the formulation of formal rules of action that show what needs to be done to make a given action optimal. Critics of this approach emphasize that such thinking about the normativity of Bayesian modeling is unjustified and that science should shift from prescriptive to descriptive positions. In a polemic with Shira Elqayam and Jonathan Evans (2011), I show that the division they propose into prescriptivism and Bayesian descriptivism is apparent, because, as I argue, there are two forms of prescriptivism, i.e. the weak and the strong. I argue that the weak version is epistemic and can lead to anti-realism, while the strong version is ontic and allows one to justify realism in relation to Bayesian models. I argue that a weak version of prescriptivism is valid for PP. It allows us to adopt anti-realism in relation to PP. In practice, this means that you can explain phenomena using Bayes' rule. This does not, however, imply that they are Bayesian in nature. However, the full justification of realism in relation to the Bayesian PP presupposes the adoption of strong prescriptivism. This position assumes that phenomena are explained by Bayesian rule because they are Bayesian as such. If they are Bayesian in nature, then they should be explained using Bayesian modeling. This thesis will be substantiated in the chapters “Normative functions and mechanisms in the context of predictive processing” and “Normative mechanisms and actions in predictive processing”. In the chapter “The Free Energy Principle in predictive processing”, I discuss the Free Energy Principle (hereinafter FEP) formulated by Karl Friston and some of its implications. According to this principle, all biological systems (defined in terms of Markov blankets) minimize the free energy of their internal states in order to maintain homeostasis. Some researchers believe that PP is a special case of applying this principle to cognition, and that predictive mechanisms are homeostatic mechanisms that minimize free energy. The discussion of FEP is important due to the fact that some authors consider it to be important for explanatory purposes and normative. If this is the case, then FEP turns out to be crucial in explaining normative predictive mechanisms and, in general, any normative biological mechanisms. To define the explanatory possibilities of this principle, I refer to the discussion of its supporters on the issue they define as the problem of continuity and discontinuity between life and mind. A critical analysis of this discussion and the additional arguments I have formulated have allowed me to revise the explanatory ambitions of FEP. I also reject the belief that this principle is necessary to explain the nature of predictive mechanisms. I argue that the principle formulated and defended by Friston is an important research heuristic for PP analysis. 8 In the chapter “Normative functions and mechanisms in predictive processing”, I start my analyzes by formulating an answer to the question about the normative nature of homeostatic mechanisms. I demonstrate that predictive mechanisms are not homeostatic. I defend the view that a full explanation of normative mechanisms presupposes an explanation of normative functions. I discuss the most important proposals for understanding the normativity of a function, both from a systemic and teleosemantic perspective. I conclude that the non-trivial concept of a function must meet two requirements which I define as explanatory and normative. I show that none of the theories I have invoked satisfactorily meets both of these requirements. Instead, I propose a model of normativity based on Bickhard's account, but supplemented by a mechanistic perspective. I argue that a function is normative when: (1) it allows one to explain the dysfunction of a given mechanism; (2) it contributes to the maintenance of the organism's stability by shaping and limiting possible relations, processes and behaviors of a given system; and when (3) (according to the representational and predictive functions) it enables explaining the attribution of logical values of certain representations / predictions. In such an approach, a mechanism is normative when it performs certain normative functions and when it is constitutive for a specific action or behavior, despite the fact that for some reason it cannot realize it either currently or in the long-term. Such an understanding of the normativity of mechanisms presupposes the acceptance of the epistemic hypothesis. I argue that this hypothesis is not cognitively satisfactory, and therefore the ontic hypothesis should be justified, which is directly related to adopting the position of ontic prescriptivism. For this reason, referring to the mechanistic theory of scientific explanations, I formulate an ontical interpretation of the concept of a normative mechanism. According to this approach, a mechanism or a function is normative when they perform such and such causal roles in explaining certain actions and behaviors. With regard to the normative properties of predictive mechanisms and functions, this means that they are the causes of specific actions an organism carries out in the environment. In this way, I justify the necessity of accepting the ontic hypothesis and rejecting the epistemic hypothesis. The fifth chapter, “Normative mechanisms and actions in predictive processing”, is devoted to the dark room problem and the related exploration-exploitation trade-off. A dark room is the state that an agent could be in if it minimized the sum of all potential prediction errors. I demonstrate that, in accordance with the basic assumption of PP about the need for continuous and long-term minimization of prediction errors, such a state should be desirable for the agent. Is it really so? Many authors believe it is not. I argue that the test of the value of PP is the possibility of a non-trivial solution of this problem, which can be reduced to the choice between active and uncertainty-increasing exploration and safe and easily predictable exploitation. I show that the solution proposed by PP supporters present in the literature does not enable a fully satisfactory explanation of this dilemma. Then I defend the position according to which the full explanation of the normative mechanisms, and, subsequently, the solution to the dilemma of exploration and exploitation, involves reference to the existence of constraints present in the environment. The constraints 9 include elements of the environment that make a given mechanism not only causal but also normative. They are therefore key to explaining the predictive mechanisms. They do not only play the role of the context in which the mechanism is implemented, but, above all, are its constitutive component. I argue that the full explanation of the role of constraints in normative predictive mechanisms presupposes the integration of individual models of specific cognitive phenomena, because only the mechanistic integration of PP with other models allows for a non-trivial explanation of the nature of normative predictive mechanisms that would have a strong explanatory value. The explanatory monism present in many approaches to PP makes it impossible to solve the problem of the dark room. Later in this chapter, I argue that the Bayesian PP is normative not because it enables the formulation of such and such rules of action, but because the predictive mechanisms themselves are normative. They are normative because they condition the choice of such and such actions by agents. In this way, I justify the hypothesis that normative mechanisms make it possible to explain the phenomenon of agent motivation, which is crucial for solving the dark room problem. In the last part of the chapter, I formulate the hypothesis of distributed normativity, which assumes that the normative nature of certain mechanisms, functions or objects is determined by the relations into which these mechanisms, functions or objects enter. This means that what is normative (in the primary sense) is the relational structure that constitutes the normativity of specific items included in it. I suggest that this hypothesis opens up many areas of research and makes it possible to rethink many problems. In the “Conclusion”, I summarize the results of my research and indicate further research perspectives. (shrink)

Medical diagnosis has been traditionally recognized as a privileged field of application for so called probabilistic induction. Consequently, the Bayesian theorem, which mathematically formalizes this form of inference, has been seen as the most adequate tool for quantifying the uncertainty surrounding the diagnosis by providing probabilities of different diagnostic hypotheses, given symptomatic or laboratory data. On the other side, it has also been remarked that differential diagnosis rather works by exclusion, e.g. by modus tollens, i.e. deductively. By drawing on (...) a case history, this paper aims at clarifying some points on the issue. Namely: 1) Medical diagnosis does not represent, strictly speaking, a form of induction, but a type, of what in Peircean terms should be called ‘abduction’ (identifying a case as the token of a specific type); 2) in performing the single diagnostic steps, however, different inferential methods are used for both inductive and deductive nature: modus tollens, hypothetical-deductive method, abduction; 3) Bayes’ theorem is a probabilized form of abduction which uses mathematics in order to justify the degree of confidence which can be entertained on a hypothesis given the available evidence; 4) although theoretically irreconcilable, in practice, both the hypothetical- deductive method and the Bayesian one, are used in the same diagnosis with no serious compromise for its correctness; 5) Medical diagnosis, especially differential diagnosis, also uses a kind of “probabilistic modus tollens”, in that, signs (symptoms or laboratory data) are taken as strong evidence for a given hypothesis not to be true: the focus is not on hypothesis confirmation, but instead on its refutation [Pr (¬ H/E1, E2, …, En)]. Especially at the beginning of a complicated case, odds are between the hypothesis that is potentially being excluded and a vague “other”. This procedure has the advantage of providing a clue of what evidence to look for and to eventually reduce the set of candidate hypotheses if conclusive negative evidence is found. 6) Bayes’ theorem in the hypothesis-confirmation form can more faithfully, although idealistically, represent the medical diagnosis when the diagnostic itinerary has come to a reduced set of plausible hypotheses after a process of progressive elimination of candidate hypotheses; 7) Bayes’ theorem is however indispensable in the case of litigation in order to assess doctor’s responsibility for medical error by taking into account the weight of the evidence at his disposal. (shrink)

This presentation discusses a notion encountered across disciplines, and in different facets of human activity: autonomous activity. We engage it in an interdisciplinary way. We start by considering the reactions and behaviors of biological entities to biotechnological intervention. An attempt is made to characterize the degree of freedom of embryos & clones, which show openness to different outcomes when the epigenetic developmental landscape is factored in. We then consider the claim made in programming and artificial intelligence that automata could show (...) self-directed behavior as to the determination of their step-wise decisions on courses of action. This question remains largely open and calls for some important qualifications. We try to make sense of the presence of claims of freedom in agency, first in common sense, then by ascribing developmental plasticity in biology and biotechnology, and in the mapping of programmed systems in the presence of environmental cues and self-referenced circuits as well as environmental coupling. This is the occasion to recall attempts at working out a logical and methodological approach to the openness of concepts that are still to be found, and assess whether they can operate the structuring intelligibility of a yet undeveloped or underdeveloped field of study, where a “bisociation" and a unification of knowledge might be possible. (shrink)

I defend external world realism. I assume that the principle of inference to the best explanation is justified: roughly, a hypothesis that provides a better explanation of the total evidence is more probable than one that does not. I argue that the existence of a world of spatial objects provides a systematic explanation of the spatial contents of visual experience, and that it provides a better explanation than traditional skeptical hypotheses. This paper thus pursues the explanationist strategy of Laurence (...) BonJour and Jonathan Vogel. It is an improved, more compelling defense, for at least two reasons. First, the attention to spatial properties, and in particular to what I call perspectival projections, makes the explanatory power of the realist hypothesis much more vivid and concrete. Second, the argument preserves and elucidates much that seems correct in the explanationist arguments others have offered while avoiding significant problems and shortcomings. (shrink)

[English in PhilArchive, unpublished]. Ruđer Bošković's (Rogerius Joseph Boscovich, 1711-1787) induction is described as a reasoning procedure that combines abductive, generalizing and deductive forms of inference. According to Bošković, the application of inductive reasoning extends beyond natural science. Bošković's critique of the use of the principle of sufficient reason is discussed, and constructive rules of Bošković's inductive logic are proposed from the standpoint of contemporary justification logic. To that end, justification logic could be extended with Bošković's typology of (...) reasons. Hunter's result (1965) is conceived as a confirmation that the inference from the constructive defectus rationis is a necessary component of Bošković's induction. - English version in _PhilArchive_. (shrink)

This paper shows how reasoning from best explanation combines with linguistic and factual presumptions during the process of retrieving a speaker’s intention. It is shown how differences between presumptions need to be used to pick the best explanation of a pragmatic manifestation of a dialogical intention. It is shown why we cannot simply jump to an interpretative conclusion based on what we presume to be the most common purpose of a speech act, and why, in cases of indirect speech acts, (...) we need to depend on an abductive process of interpretation. (shrink)

Some adaptationist explanations are regarded as maximally solid and others fanciful just-so stories. Just-so stories are explanations based on very little evidence. Lack of evidence leads to circular-sounding reasoning: “this trait was shaped by selection in unseen ancestral populations and this selection must have occurred because the trait is present.” Well-supported adaptationist explanations include evidence that is not only abundant but selected from comparative, populational, and optimality perspectives, the three adaptationist subdisciplines. Each subdiscipline obtains its broad relevance in evolutionary biology (...) via assumptions that can only be tested with the methods of the other subdisciplines. However, even in the best-supported explanations, assumptions regarding variation, heritability, and fitness in unseen ancestral populations are always present. These assumptions are accepted given how well they would explain the data if they were true. This means that some degree of “circularity” is present in all evolutionary explanations. Evolutionary explanation corresponds not to a deductive structure, as biologists usually assert, but instead to ones such as abduction or induction. With these structures in mind, we show the way to a healthier view of “circularity” in evolutionary biology, and why integration across the comparative, populational, and optimality approaches is necessary. (shrink)

this article provides a response to David Hume’s argument against the plausibility of miracles as found in Section 10 of his An enquiry concerning human understanding by means of Charles Sanders Peirce’s method of retroduction, hypothetic inference, and abduction, as it is explicated and applied in his article entitled A Neglected Argument for the Reality of God, rather than fo‐ cusing primarily on Peirce’s explicit reaction to Hume in regard to miracles, as found in Hume on miracles. the main (...) focus will be on Peirce’s neglected argument rather than his explicit con ontation with Hume on the issue of miracles, because his criticisms of Hume demands a methodological approach appropriate for scienti cally analysing surprising phenomena or outliers, of which miracles or the reality of god would be but two examples amongst many. this article, then, consists of an attempt to construct this method as one that draws inferences neither a priori nor a posteriori, but per posterius, because such a method is capable of rigorously questioning rogue or surprising phenomena, e.g. miracles. (shrink)

In this critical notice, I focus my attention on the chapters that deal with the explanationist response to skepticism.

Cosmological models that invoke a multiverse - a collection of unobservable regions of space where conditions are very different from the region around us - are controversial, on the grounds that unobservable phenomena shouldn't play a crucial role in legitimate scientific theories. I argue that the way we evaluate multiverse models is precisely the same as the way we evaluate any other models, on the basis of abduction, Bayesian inference, and empirical success. There is no scientifically respectable way to (...) do cosmology without taking into account different possibilities for what the universe might be like outside our horizon. Multiverse theories are utterly conventionally scientific, even if evaluating them can be difficult in practice. (shrink)

Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery-driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential in biological (...) research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from ‘the sequence tells the structure tells the function’ fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader. (shrink)