According to manipulationist accounts of causal explanation, to explain an event is to show how it could be changed by intervening on its cause. The relevant change must be a ‘serious possibility’ claims Woodward 2003, distinct from mere logical or physical possibility—approximating something I call ‘scientific possibility’. This idea creates significant difficulties: background knowledge is necessary for judgments of possibility. Yet the primary vehicles of explanation in manipulationism are ‘invariant’ generalisations, and these are not well adapted to encoding such knowledge, (...) especially in the social sciences, as some of it is non-causal. Ceteris paribus (CP) laws or generalisations labour under no such difficulty. A survey of research methods such as case and comparative studies, randomised control trials, ethnography, and structural equation modeling, suggests that it would be more difficult and in some instances impossible to try to represent the output of each method in invariant generalisations; and that this is because in each method causal and non-causal background knowledge mesh in a way that cannot easily be accounted for in manipulationist terms. Ceteris paribus-generalisations being superior in this regard, a theory of explanation based on the latter is a better fit for social science. (shrink)

_Abduction of generalizations_ is the process in which explanatory hypotheses are formed for an observed, yet puzzling generalization such as ``pineapples taste sweet" or ``rainbows appear when the sun breaks through the rain". This phenomenon has received little attention in formal logic and philosophy of science. The current paper remedies this lacuna by first giving an overview of some general characteristics of this process, elaborating on its ubiquity in scientific and daily life reasoning. Second, the adaptive logic $\LAG$ is presented (...) to explicate this process formally. (shrink)

Batterman and Rice ([2014]) argue that minimal models possess explanatory power that cannot be captured by what they call ‘common features’ approaches to explanation. Minimal models are explanatory, according to Batterman and Rice, not in virtue of accurately representing relevant features, but in virtue of answering three questions that provide a ‘story about why large classes of features are irrelevant to the explanandum phenomenon’ ([2014], p. 356). In this article, I argue, first, that a method (the renormalization group) they propose (...) to answer the three questions cannot answer them, at least not by itself. Second, I argue that answers to the three questions are unnecessary to account for the explanatoriness of their minimal models. Finally, I argue that a common features account, what I call the ‘generalized ontic conception of explanation’, can capture the explanatoriness of minimal models. (shrink)

The claim of this article is that no event can determine a later event and that in this sense there cannot be sufficient causes. Therefore the causal structure of the world does not exclude free will, even if there are no chance processes.

Theories of explanation seek to tell us what distinctively explanatory information is. The most ambitious ones, such as the DN-account, seek to tell us what an explanation is, tout court. Less ambitious ones, such as causal theories, restrict themselves to a particular domain of inquiry. The least ambitious theories constitute outright skepticism, holding that there is no reasonably unified phenomenon to give an account of. On these views, it is impossible to give any theories of explanation at all. I argue (...) that both the less ambitious and outright skeptical varieties are committed to a certain context-sensitivity of our explanatory discourse. And though this discourse is almost certainly context-sensitive in some respects, it does not exhibit the context-sensitivity less than fully ambitious theories are committed to. Therefore, all accounts that seek to restrict themselves in scope, including causal accounts of explanation, fail. (shrink)

This paper is a sympathetic critique of the argument that Reichenbach develops in Chap. 2 of Experience and Prediction for the thesis that sense experience justifies belief in the existence of an external world. After discussing his attack on the positivist theory of meaning, I describe the probability ideas that Reichenbach presents. I argue that Reichenbach begins with an argument grounded in the Law of Likelihood but that he then endorses a different argument that involves prior probabilities. I try to (...) show how this second step in Reichenbach’s approach can be strengthened by using ideas that have been developed recently for understanding causation in terms of the idea of intervention. (shrink)

While standard procedures of causal reasoning as procedures analyzing causal Bayesian networks are custom-built for (non-deterministic) probabilistic struc- tures, this paper introduces a Boolean procedure that uncovers deterministic causal structures. Contrary to existing Boolean methodologies, the procedure advanced here successfully analyzes structures of arbitrary complexity. It roughly involves three parts: first, deterministic dependencies are identified in the data; second, these dependencies are suitably minimalized in order to eliminate redundancies; and third, one or—in case of ambiguities—more than one causal structure is (...) assigned to the minimalized deterministic dependencies. (shrink)

The purpose of this article is to examine two important issues concerning the agency theory of causality: the charge of anthropomorphism and the relation of simultaneous causation. After a brief outline of the agency theory, sections 2–4 contain the refutation of the three main forms in which the charge of anthropomorphism is to be found in the literature. It will appear that it is necessary to distinguish between the subjective and the objective aspect of the concept of causation. This will (...) lead, in section 5, to contrast two kinds of anthropomorphism, one which has been rightly rejected by modern science and one which is fully compatible with the objective reality of the causal processes. Finally, section 6 will apply the preceding considerations to simultaneous causation. On the one hand, in a basic sense, there can be no simultaneous causal relations. On the other hand, simultaneous causation arises when we consider the natural change by abstracting from the agent and from her/his projects of interven.. (shrink)

Current philosophical accounts of causation suggest that the same causal assertion can have different meanings. Yet, in actual social-scientific practice, the possible meanings of some causal generalisations intended to support policy prescriptions are not always spelled out. In line with a standard referentialist approach to semantics, we propose and elaborate on four questions to systematically elucidate the meaning of causal generalisations. The analysis can be useful to a host of agents, including social scientists, policy-makers, and philosophers aiming at being socially (...) relevant. To illustrate our proposal, we analyse the complexities related to the meaning of causal generalisations in the context of a concrete case of economic research which is explicitly intended to guide public policy, namely, the OECD research on the causes of unemployment. (shrink)

Väitöskirjassani Understanding Interests and Causal Explanation (2001) hahmottelin teoriaa yksittäisten tapahtumien kausaalisesta selittämisestä. Tässä kirjoituksessa tarkastelen niitä haasteita tai vaatimuksia, joihin teoriani yritti vastata. Alustavien huomioiden jälkeen esittelen ensiksi erityisesti selittämisen teoriaan liittyviä haasteita ja sen jälkeen yleisempiä filosofisia vaatimuksia hyväksyttävälle selittämisen teorialle.

Nancy Cartwright begins her recent book, Hunting Causes and Using Them, by noting that while a few years ago real causal claims were in dispute, nowadays “causality is back, and with a vengeance.” In the case of the social sciences, Keith Morrison writes that “Social science asks ‘why?’. Detecting causality or its corollary—prediction—is the jewel in the crown of social science research.” With respect to the health sciences, Judea Pearl writes that the “research questions that motivate most studies in the (...) health sciences are causal in nature.” However, not all data used by people interested in making causal claims come from experiments that use random assignment to control and treatment groups. Indeed, much research in the social and health science depends on non-experimental, observational data. Thus, one of the most important problems in the social and health sciences concerns making warranted causal claims using non-experimental, observational data; viz., “Can observational data be used to make etiological inferences leading to warranted causal claims?” This paper examines one method of warranting causal claims that is especially widespread in epidemiology and the health sciences generally—the use of causal criteria. It is argued that cases of complex causation generally, and redundant causation—both causal overdetermination and causal preemption—specifically, undermine the use of such criteria to warrant causal claims. (shrink)

The dilemma of free will is that if actions are caused deterministically, then they are not free, and if they are not caused deterministically then they are not free either because then they happen by chance and are not up to the agent. I propose a conception of free will that solves this dilemma. It can be called agent causation but it differs from what Chisholm and others have called so.

Backtracking influence is influence that zigzags in time. For example, backtracking influence exists when an event E_1 makes an event E_2 more likely by way of a nomic connection that goes from E_1 back in time to an event C and then forward in time to E_2. I contend that in our local region of spacetime, at least, backtracking influence is redundant in the sense that any existing backtracking influence exerted by E_1 on E_2 is equivalent to E_1's temporally direct (...) influence on E_2. I prove the redundancy of backtracking influence using several plausible physical principles without assuming any fundamental temporal or causal asymmetry. This explanation can play a prominent role in an account of why causation appears to be objectively asymmetric regardless of whether the fundamental laws are symmetric. (shrink)

Neutral monism is a position in metaphysics defended by Mach, James, and Russell in the early twentieth century. It holds that minds and physical objects are essentially two different orderings of the same underlying neutral elements of nature. This paper sets out some of the central concepts, theses and the historical background of ideas that inform this doctrine of elements. The discussion begins with the classic neutral monism of Mach, James, and Russell in the first part of the paper, then (...) considers recent neo-Russellian versions in the second half. The chances for a revival of neutral monism are probably slight; its key ideas and starting points lie far from those in contemporary philosophy of mind. A better route might be through the philosophy of science and a deeper understanding of causation. (shrink)

This essay explains what the Causal Markov Condition says and defends the condition from the many criticisms that have been launched against it. Although we are skeptical about some of the applications of the Causal Markov Condition, we argue that it is implicit in the view that causes can be used to manipulate their effects and that it cannot be surrendered without surrendering this view of causation.

This article defends the use of interventionist counterfactuals to elucidate causal and explanatory claims against criticisms advanced by James Bogen and Peter Machamer. Against Bogen, I argue that counterfactual claims concerning what would happen under interventions are meaningful and have determinate truth values, even in a deterministic world. I also argue, against both Machamer and Bogen, that we need to appeal to counterfactuals to capture the notions like causal relevance and causal mechanism. Contrary to what both authors suppose, counterfactuals are (...) not "unscientific" - a substantial tradition within statistics and the causal modelling literature makes heavy use of them. (shrink)

For a long time, regularity accounts of causation have virtually vanished from the scene. Problems encountered within other theoretical frameworks have recently induced authors working on causation, laws of nature, or methodologies of causal reasoning – as e.g. May (Kausales Schliessen. Eine Untersuchung über kausale Erklärungen und Theorienbildung. Ph.D. thesis, Universität Hamburg, Hamburg, 1999), Ragin (Fuzzy-set social science. Chicago: University of Chicago Press, 2000), Graßhoff and May (Causal regularities. In W. Spohn, M. Ledwig, & M. Esfeld (Eds.), Current issues in (...) causation (pp. 85–114). Paderborn: Mentis, 2001), Swartz (The concept of physical law (2nd ed.). http://www.sfu.ca/philosophy/physical-law/, 2003), Halpin (Erkenntnis, 58, 137–168, 2003) – to direct their attention back to regularity theoretic analyses. In light of the latest proposals of regularity theories, the paper at hand therefore reassesses the criticism raised against regularity accounts since the INUS theory of causation of Mackie (The cement of the universe. A study of causation. Oxford: Clarendon Press, 1974). It is shown that most of these objections target strikingly over-simplified regularity theoretic sketches. By outlining ways to refute these objections it is argued that the prevalent conviction as to the overall failure of regularity theories has been hasty. (shrink)

This is my first professional philosophical essay. I wrote "The twofold meaning of being" in 1996 when I was a student of Nunzio Incardona at University of Palermo (Italy) and before my degree thesis, "The difference in Aristotle’s Metaphysics". It still waits to be published.

In the literature on health, naturalism and normativism are typically characterized as espousing and rejecting, respectively, the view that health is objective and value-free. This article points out that there are two distinct dimensions of disagreement, regarding objectivity and value-ladenness, and thus arranges naturalism and normativism as diagonal opposites on a two-by-two matrix of possible positions. One of the remaining quadrants is occupied by value-dependent realism, holding that health facts are value-laden and objective. The remaining quadrant, which holds that they (...) are non-objective but value-free, is unexplored. The article endorses a view in the latter quadrant, namely, the view that health is a secondary property. The article argues that a secondary property framework provides the resources to respond to the deepest objections to a broadly Boorsean account of natural function, and so preserves the spirit, though not the letter, of that account. Treating health as a secondary property permits a naturalistic explanation—specifically, an evolutionary explanation—of the health concept, in terms of the assistance such a concept might have provided to the survival and reproduction of those organisms that had it. This provides the explanation, missing from Boorse's account, for the fact that function is determined with reference to the contribution to the goals of survival and reproduction, relative to the age of the sex of the species, rather than some other equally natural goals or reference classes. _1_ Introduction _2_ Two Ways to Disagree about Health _3_ Secondary Properties _4_ Health as a Secondary Property _5_ Conclusion. (shrink)

The phrase ‘in virtue of’ is a mainstay of metaphysical discourse. In recent years, many philosophers have argued that we should understand this phrase, as metaphysicians use it, in terms of a concept of metaphysical dependence called ‘grounding’.This dissertation explores a range of central issues in the theory of grounding. Chapter 1 introduces the intuitive concept of grounding and discusses some compulsory questions in the theory of grounding. Chapter 2 focusses on scepticism on grounding, according to which the recent philosophical (...) interest in the topic is misguided. In chapter 3 I discuss grounding’s explanatory roles. Chapter 4 focusses on the claim that if an entity is grounded then it is an ontological free lunch. Chapter 5 discusses and rejects the claim that groundingis a relation between facts. This conclusion raises a problem: if grounding is not a relation between facts it becomes difficult to specify the connections between grounding and explanation and grounding and necessity. But not only is it desirable to specify these relations, it is essential for establishing that grounding is able to play the explanatory roles that are discussed in chapter 3. Chapter 6 responds to this problem by outlining an approach to grounding based on David Lewis’s (2003) theory of truthmaking. Against this backdrop I discuss, in chapter 7, some issues in the logic of grounding. (shrink)

Pluralism with respect to the structure of explanations of facts is not uncommon. Wesley Salmon, for instance, distinguished two types of explanation: causal explanations (which provide insight in the causes of the fact we want to explain) and unification explanations (which fit the explanandum into a unified world view). The pluralism which Salmon and others have defended is compatible with several positions about the exact relation between these two types of explanations. We distinguish four such positions, and argue in favour (...) of one of them. We also compare our results with the views of some authors who have recently written on this subject. (shrink)

Debates about explanation in the social sciences often proceed without any clear idea what an 'account' of explanation should do. In this paper I take a stance - what I will call contextualism - that denies there are purely formal and conceptual constraints on explanation and takes standards of explanation to be substantive empirical claims, paradigmatically claims about causation. I then use this standpoint to argue for position on issues in the philosophy of social science concerning reduction, idealized models, social (...) mechanisms, functional explanations, inference to the best explanation and interpretive understanding. (shrink)

In the recent literature on causal and non-causal scientific explanations, there is an intuitive assumption according to which an explanation is non-causal by virtue of being abstract. In this context, to be ‘abstract’ means that the explanans in question leaves out many or almost all causal microphysical details of the target system. After motivating this assumption, we argue that the abstractness assumption, in placing the abstract and the causal character of an explanation in tension, is misguided in ways that are (...) independent of which view of causation or causal explanation one takes to be most accurate. On major accounts of causation, as well as on major accounts of causal explanation, the abstractness of an explanation is not sufficient for it being non-causal. That is, explanations are not non-causal by dint of being abstract. (shrink)

A theory of causation with ‘tendencies’ as causal con- nections is proposed. Not, however, as ‘necessary connec- tions’: causes are not sufficient, they do not necessitate their effects. The theory is not an analysis of the concept of causation, but a description of what is the case in typical cases of causation. Therefore it does not strictly contradict any analysis of the concept of causation, not even reduct- ive ones. It would even be supported by a counterfactual or a probabilistic (...) analysis. (shrink)

This paper examines the asymmetrical aspect of causal relation, confronting it to Humean and Neo-Humean's view. Following Hausman and Ehring, we favor a situational approach to causal asymmetry. We explore the Hausman's analysis of flagpole's example, clearing the connexions between causation and explanation. Our general diagnosis is that the Neo-humean tradition wrongly supposes that nomic relations, with the exception of minor details, exhaust the causal relations.

For nearly as long as the word “correlation” has been part of statistical parlance, students have been warned that correlation does not prove causation, and that only experimental studies, e.g., randomized clinical trials, can establish the existence of a causal relationship. Over the last few decades, somewhat of a consensus has emerged between statisticians, computer scientists, and philosophers on how to represent causal claims and connect them to probabilistic relations. One strand of this work studies the conditions under which evidence (...) accumulated from non-experimental (observational) studies can be used to infer a causal relationship. In this paper, I compare the typical conditions required to infer that one variable is a direct cause of another in observational and experimental studies. I argue that they are essentially the same. (shrink)

The most common way of analysing the meaning of causal generalisations relies on referentialist semantics. In this article, we instead develop an analysis based on inferentialist semantics. According to this approach, the meaning of a causal generalisation is constituted by the web of inferential connections in which the generalisation participates. We distinguish and discuss five classes of inferential connections that constitute the meaning of causal generalisations produced in policy-oriented economic research. The usefulness of our account is illustrated with the analysis (...) of generalisations about unemployment put forward by the Organisation for Economic Co-operation and Development in its highly influential 1994 OECD Jobs Study. The article ends with a discussion of some crucial philosophical questions about the use of inferentialism in the analysis of causal generalisations. (shrink)

Anti-realists typically contend that truth is epistemically constrained. Truth, they say, cannot outstrip our capacity to know. Some anti-realists are also willing to make a further claim: if truth is epistemically constrained, classical logic is to be given up in favour of intuitionistic logic. Here we shall be concerned with one argument in support of this thesis - Crispin Wright's Basic Revisionary Argument, first presented in his Truth and Objectivity. We argue that the reasoning involved in the argument, if correct, (...) validates a parallel argument that leads to conclusions that are unacceptable to classicists and intuitionists alike. (shrink)

Woodward present an argument for the Causal Markov Condition (CMC) on the basis of a principle they dub ‘modularity’ ([1999, 2004]). I show that the conclusion of their argument is not in fact the CMC but a substantially weaker proposition. In addition, I show that their argument is invalid and trace this invalidity to two features of modularity, namely, that it is stated in terms of pairwise independence and ‘arrow-breaking’ interventions. Hausman & Woodward's argument can be rendered valid through a (...) reformulation of modularity, but it is doubtful that the argument so revised provides any substantially new insight regarding the basis of the CMC. Introduction The CMC versus Hausman & Woodward's conclusion Hausman & Woodward's argument Modularity and independent error terms Conclusion Appendix: D-separation. (shrink)

This thesis studies Judea Pearl’s logic of counterfactuals derived from the causal modeling framework, in comparison to the influential Stanlnaker-Lewis counterfactual logics. My study focuses on a characteristic principle in Pearl’s logic, named reversibility. The principle, as Pearl pointed out, goes beyond Lewis’s logic. Indeed, it also goes beyond the stronger logic of Stanlnaker, which is more analogous to Pearl’s logic. The first result of this thesis is an extension of Stanlnaker’s logic incorporating reversibility. It will be observed that the (...) translation of reversibility from Pearl’s language to the standard language for conditional logic deserves some attention. In particular, a straightforward translation following Pearl’s suggestion would render reversibility incompatible with Stanlnaker’s logic. A new translation of reversibility will be proposed, and an extension of Stanlnaker’s logic with the inclusion of the translated reversibility will be investigated. More importantly, it will be shown that the extended Stanlnaker’s logic is sound and complete with respect to a modified Stanlnaker’s semantics. The extension of Stanlnaker’s logic has an interesting implication. Zhang, Lam, and de Clercq have shown that special case of reversibility, despite its name, actually states an important kind of irreversibility: counterfactual dependence between distinct events is irreversible. In other words, reversibility entails that there is no cycle of counterfactual dependence altogether generalizations of reversibility. However, as shown in Zhang et al., Pearls’ logic does not rule out cycles of counterfactual dependence altogether. It in fact allows cycles that involve three or more distinct events. This is peculiar because the status of cyclic counterfactual dependence seems no more metaphysically secure than that of mutual counterfactual dependence. This consideration leads to an exploration of logics that rule out all cycles of counterfactual dependence. A surprising result is that the extension of Stanlnaker’s logic is precisely a logic of this sort. (shrink)

In the current literature on scientific explanation unification became unfashionable in favour of causal approaches. We want to bring unification back into the picture. In this paper we demonstrate that resemblance questions do occur in scientific practice and that they cannot be properly answered without unification. Our examples show that resemblance questions about particular facts demand what we call causal network unification, while resemblance questions about regularities require what we call mechanism unification. We clarify how these types of unification relate (...) to Philip Kitcher’s account, but also to causal and mechanistic accounts of explanation. (shrink)

Laws of nature take center stage in philosophy of science. Laws are usually believed to stand in a tight conceptual relation to many important key concepts such as causation, explanation, confirmation, determinism, counterfactuals etc. Traditionally, philosophers of science have focused on physical laws, which were taken to be at least true, universal statements that support counterfactual claims. But, although this claim about laws might be true with respect to physics, laws in the special sciences (such as biology, psychology, economics etc.) (...) appear to have—maybe not surprisingly—different features than the laws of physics. Special science laws—for instance, the economic law “Under the condition of perfect competition, an increase of demand of a commodity leads to an increase of price, given that the quantity of the supplied commodity remains constant” and, in biology, Mendel's Laws—are usually taken to “have exceptions”, to be “non-universal” or “to be ceteris paribus laws”. How and whether the laws of physics and the laws of the special sciences differ is one of the crucial questions motivating the debate on ceteris paribus laws. Another major, controversial question concerns the determination of the precise meaning of “ceteris paribus”. Philosophers have attempted to explicate the meaning of ceteris paribus clauses in different ways. The question of meaning is connected to the problem of empirical content, i.e., the question whether ceteris paribus laws have non-trivial and empirically testable content. Since many philosophers have argued that ceteris paribus laws lack empirically testable content, this problem constitutes a major challenge to a theory of ceteris paribus laws. (shrink)

This dissertation starts with a concise overview of what philosophers of science have written about unification and its role in scientific explanation during the last 50 years to provide the reader with some background knowledge. In order to bring unification back into the picture, I have followed two strategies, resulting respectively in Parts I and II of this dissertation. In Part I the idea of unification is used to refine and enrich the dominant causalmechanist and causal-interventionist accounts of scientific explanation. (...) In this part of the dissertation I bracket the classical ideas about unification: deduction and derivation. I do grant, for the sake of argument, that explanations are causal and argue that unification is important from within this causalist perspective. In Part II I continue my strategy of digging into scientific practice to find cases of ontological unification. But here I distance myself from the dominant literature that all explanations must be causal. I will investigate whether explanatory unification is possible in non-causal explanations. Part III contains some further reflections and conclusions. I will formulate my primary results, and I will elaborate on their implications for thinking about unification and explanation. The different forms of ontological unification were quite diverse. This relates to the method I have used. Throughout this dissertation the types of unification that were discussed emerged from digging into scientific practice. This philosophy-of-science-practice approach steered me towards a pluralistic view on unification and on explanation. In this dissertation I do not try to develop a new model of explanation and compare it to existing models. The aim is to show that there are important types of explanatory practice which cannot be properly analyzed if we neglect unification as a desideratum for explanations. (shrink)

In a recent article in this journal, Federica Russo and Jon Williamson argue that an analysis of causality in terms of probabilistic relationships does not do justice to the use of mechanistic evidence to support causal claims. I will present Ronald Giere's theory of probabilistic causation, and show that it can account for the use of mechanistic evidence (both in the health sciences—on which Russo and Williamson focus—and elsewhere). I also review some other probabilistic theories of causation (of Suppes, Eells, (...) and Humphreys) and show that they cannot account for the use of mechanistic evidence. I argue that these theories are also inferior to Giere's theory in other respects. (shrink)

Stemming from the realization of the importance of the role of explanation in the science classroom, the Next Generation Science Standards call for appropriately supporting students to learn science, argue from evidence, and provide explanations. Despite the ongoing emphasis on explanations in the science classroom, there seems to be no well-articulated framework that supports students in constructing adequate scientific explanations, or that helps teachers assess student explanations. Our motivation for this article is twofold: First, we think that the ways in (...) which researchers in science education have studied scientific explanation are, at best, leaves much to be desired and, at worst, simply incomplete. Second, we believe that research about the teaching and learning of explanation in science classrooms must be guided by explicit models or frameworks that specify elements involved in constructing explanations particularly applicable to science. More importantly, we think that the development of such models or guidelines should be based on theoretical and philosophical foundations. In order to develop these frameworks or guidelines, we first outline and clarify models of scientific explanation developed by philosophers of science over the last few decades. In the second section of this article, we present a more recent philosophical work on scientific explanation, the pragmatic approach to studying scientific explanations. This approach suggests a toolbox for analyzing scientists’ scientific explanations, which provides a useful instrument to science education. In Section 3, we discuss the ways by which the previous two sections are useful in developing a K-12 scientific explanation schema. Implications for future research on students’ explanations are discussed. (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)