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. (shrink)

Framing systematics as a field consistent with scientific inquiry entails that inferences of phylogenetic hypotheses have the goal of producing accounts of past causal events that explain differentially shared characters among organisms. Linking observations of characters to inferences occurs by way of why-questions implied by data matrices. Because of their form, why-questions require the use of common-cause theories. Such theories in phylogenetic inferences include natural selection and genetic drift. Selection or drift can explain ‘morphological’ characters but selection cannot be causally (...) applied to sequences since fitness differences cannot be directly associated with individual nucleotides or amino acids. The relation of selection to sequence data is by way of downward or top-down causation from those phenotypes upon which selection occurs. The application of phylogenetic inference to explain sequence data is thus restricted to instances where drift is the relevant theory; those nucleotides or amino acids that can be explained via downward causation are precluded from inclusion in the data matrix. The restrictions on the inclusion of sequence data in phylogenetic inferences equally apply to species hypotheses, precluding the more restrictive approach known as DNA barcoding. Not being able to discern drift and selection as relevant causal mechanisms can severely constrain the inclusion and explanations of sequence data. Implications of such exclusion are discussed in relation to the requirement of total evidence. (shrink)

Поняття «філософія науки» незаперечно увійшло до сучасного філософського дискурсу. У філо- софському та науковому середовищах є різні тлумачення філософії науки. Власне науку тради- ційно вважають суспільною інституцією, створеною з метою здобуття та застосування знань про природні та штучні реалії. Водночас введення поняття «філософія науки» було б три віальним, якби його обсяг зводився до перетину обсягів понять «наука» і «філософія». Пе ре- хід від тлумачення науки загалом до її розуміння як сукупності конкретних наук з особ ливими предметними галузями викликає виокремлення із (...) загальної філософії науки групоцентрованих філософій наук на кшталт філософії біології, філософії психології, філософії технічних наук, філософії медицини, філософії соціальних наук, філософії інформаційних наук, філософії фізи- ки, філософії математики, філософії філософії тощо. У статті виокремлено різновиди сучас- ної філософії математичних та природничих наук. Специфічні ознаки цих наук аналізовано за допомоги графових класифікацій відповідних філософій. Підкреслено важливість для всіх різ- новидів філософії науки використовуваних ними реконструкцій практичних теорій. У першій частині окреслено мету статті й розглянуто предметні та теоретичні класифікації філосо- фій науки, у другій — оцінні, називні, теоретико-реконструктивні та мовно-реконструктив ні, а також зроблено висновки щодо доцільності застосування цих класифікацій до філософій суспільних та гуманітарних наук. В підсумку автори висновують, що, незважаючи на попу- лярність у філософсько-науковому середовищі різкого протиставлення класичної та некласич- ної фізики, для цього немає ґрунтовних об’єктивних підстав. (shrink)

In this paper, I focus on life-threatening medical conditions and argue that from the point of view of natural properties, induction(s), and participation in laws, at least some of the ill organisms dealt with in somatic medicine form natural kinds in the same sense in which the kinds in the exact sciences are thought of as natural. By way of comparing two ‘divisions of nature’, viz., a ‘classical’ exact science kind (gold) and a kind of disease (Graves disease), I show (...) that there is no justifiable ‘ontological gap’ between disease kinds and exact sciences kinds. We have instead a difference of degree. (shrink)

Abstract In this paper I offer an anti-Humean interpretation of the causal interactions in somatic medicine. I focus on life-threatening pathological states and show how Nancy Cartwright’s capacities can offer a plausible epistemology for medical processes and the singular causal claims advanced in medical diagnoses. I argue that the capacities manifested in the emergence of symptoms and signs could be tracked down if healthy organisms are construed as nomological machines and suggest that the causal reasoning from current medical practice bears (...) a tacit adherence to anti-Humean assumptions. Content Type Journal Article Pages 1-28 DOI 10.1007/s12136-011-0141-1 Authors Stefan Dragulinescu, Drumul Taberei 20, Bucharest, Romania Journal Acta Analytica Online ISSN 1874-6349 Print ISSN 0353-5150. (shrink)

Suppose that an informant (test, expert, device, perceptual system, etc.) is unlikely to err when pronouncing on a particular subject matter. When this is so, it might be tempting to defer to that informant when forming beliefs about that subject matter. How is such an inferential process expected to fare in terms of truth (leading to true beliefs) and evidential fit (leading to beliefs that fit one’s total evidence)? Using a medical diagnostic test as an example, we set out a (...) formal framework to investigate this question. We establish seven results and make one conjecture. The first four results show that when the test’s error probabilities are low, the process of deferring to the test can score well in terms of (i) both truth and evidential fit, (ii) truth but not evidential fit, (iii) evidential fit but not truth, or (iv) neither truth nor evidential fit. Anything is possible. The remaining results and conjecture generalize these results in certain ways. These results are interesting in themselves—especially given that the diagnostic test is not sensitive to the target disease’s base rate—but also have broader implications for the more general process of deferring to an informant. Additionally, our framework and diagnostic example can be used to create test cases for various reliabilist theories of inferential justification. We show, for example, that they can be used to motivate evidentialist process reliabilism over process reliabilism. (shrink)

According to a recent suggestion, the names of gene taxa should be conceived of as referring to individuals with concrete genes as their parts, just as the names of biological species are often understood as denoting individuals with organisms as their parts. Although prima facie this suggestion might advance the debate on gene concepts in a similar way as the species-are-individuals thesis advanced the debate on species concepts, I argue that the principal arguments in support of the gene-individuality thesis are (...) much less compelling than the parallel arguments in the species case. In addition, I argue that the notion of biological function invoked in the gene-individuality thesis (selected effect) is not the one that biologists actually use when individuating genes. Contra the gene-individuality thesis, I argue that gene names refer to kinds, defined primarily (though not exclusively) by causal-role functions. (shrink)

This thesis has two goals. Firstly, we consider the problem of model selection for the purposes of prediction. In modern science predictive mathematical models are ubiquitous and can be found in such diverse fields as weather forecasting, economics, ecology, mathematical psychology, sociology, etc. It is often the case that for a given domain of inquiry there are several plausible models, and the issue then is how to discriminate between them – this is the problem of model selection. We consider approaches (...) to model selection that are used in classical [also known as frequentist] statistics, and fashionable in recent years methods of Akaike Information Criterion [AIC] and Bayes Information Criterion [BIC], the latter being a part of a broader Bayesian approach. We show the connection between AIC and BIC, and provide comparison of performance of these methods. Secondly, we consider some philosophical arguments that arise within the setting of the model selection approaches investigated in the first part. These arguments aim to provide counterexamples to the epistemic thesis of scientific realism, viz., that predictively successful scientific theories are approximately true, and to the idea that truth and predictive accuracy go together. We argue for the following claims: 1) that none of the criticisms brought forward in the philosophical literature against the AIC methodology are devastating, and AIC remains a viable method of model selection; 2) that the BIC methodology likewise survives the numerous criticisms; 3) that the counterexamples to scientific realism that ostensibly arise within the framework of model selection are flawed; 4) that in general the model selection methods discussed in this thesis are neutral with regards to the issue of scientific realism; 5) that a plurality of methodologies should be applied to the problem of model selection with full awareness of the foundational issues that each of these methodologies has. (shrink)