We know that animals are harmed in plant production. Unfortunately, though, we know very little about the scale of the problem. This matters for two reasons. First, we can’t decide how many resources to devote to the problem without a better sense of its scope. Second, this information shortage throws a wrench in arguments for veganism, since it’s always possible that a diet that contains animal products is complicit in fewer deaths than a diet that avoids them. In this (...) paper, then, we have two aims: first, we want to collect and analyze all the available information about animal death associated with plant agriculture; second, we try to show just how difficult it’s to come up with a plausible estimate of how many animals are killed by plant agriculture, and not just because of a lack of empirical information. Additionally, we show that there are significant philosophical questions associated with interpreting the available data—questions such that different answers generate dramatically different estimates of the scope of the problem. Finally, we document current trends in plant agriculture that cause little or no collateral harm to animals, trends which suggest that field animal deaths are a historically contingent problem that in future may be reduced or eliminated altogether. (shrink)

According to a rich tradition in philosophy of action, intentional action requires practical knowledge: someone who acts intentionally knows what they are doing while they are doing it. Piñeros Glasscock argues that an anti-luminosity argument, of the sort developed in Williamson, can be readily adapted to provide a reductio of an epistemic condition on intentional action. This paper undertakes a rescue mission on behalf of an epistemic condition on intentional action. We formulate and defend a version of an epistemic condition (...) that is free from any luminosity commitments. While this version of an epistemic condition escapes reductio, it comes with substantive commitments of its own. In particular, we will see that it forces us to deny the existence of any essentially intentional actions. We go on to argue that this consequence should be embraced. On the resulting picture, intentional action is not luminous. But it still entails practical knowledge. (shrink)

In the future, when we compare the welfare of a being of one substrate (say, a human) with the welfare of another (say, an artificial intelligence system), we will be making an intersubstrate welfare comparison. In this paper, we argue that intersubstrate welfare comparisons are important, difficult, and potentially tractable. The world might soon contain a vast number of sentient or otherwise significant beings of different substrates, and moral agents will need to be able to compare their welfare levels. However, (...) this work will be difficult, because we lack the same kinds of commonalities across substrates that we have within them. Fortunately, we might be able to make at least some intersubstrate welfare comparisons responsibly in spite of these issues. We make the case for cautious optimism and call for more research. (shrink)

According to many philosophers, belief is a settling state. On this view, someone who believes p is disposed to take p for granted in practical and theoretical reasoning. This paper presents a simple objection to this settling conception of belief: it conflicts with our ordinary patterns of belief ascription. I show that ascriptions of unsettled beliefs are commonplace, and that they pose problems for all of the most promising ways of developing the settling conception. I proceed to explore the implications (...) of my argument for the relation between belief and credence, and for the relative importance of belief in psychological explanation. (shrink)

One leading account of justification comes from the evidentialist tradition. According to evidentialists, whether a doxastic attitude is justified depends on whether that attitude is supported by the believer’s evidence. This chapter assesses the prospects for evidentialism, focusing on the question of whether evidentialists can provide a satisfactory account of their key notions – evidence possession and evidential support – without helping themselves to the notion of justification.

This essay defends a novel form of virtue epistemology: Modal Virtue Epistemology. It borrows from traditional virtue epistemology the idea that knowledge is a type of skillful performance. But it goes on to understand skillfulness in purely modal terms — that is, in terms of success across a range of counterfactual scenarios. We argue that this approach offers a promising way of synthesizing virtue epistemology with a modal account of knowledge, according to which knowledge is safe belief. In particular, we (...) argue that the modal elements of the view offer important advantages over traditional virtue epistemology, which assigns a central explanatory role to aptness. At the same time, the virtue epistemological elements of the theory reveal new avenues for overcoming obstacles to traditional modal accounts of knowledge. Finally, we highlight the advantages of Modal Virtue Epistemology over alternative syntheses, such as Pritchard's (2012) hybrid approach. (shrink)

This paper argues that we should assign certainty a central place in epistemology. While epistemic certainty played an important role in the history of epistemology, recent epistemology has tended to dismiss certainty as an unattainable ideal, focusing its attention on knowledge instead. I argue that this is a mistake. Attending to certainty attributions in the wild suggests that much of our everyday knowledge qualifies, in appropriate contexts, as certain. After developing a semantics for certainty ascriptions, I put certainty to explanatory (...) work. Specifically, I argue that by taking certainty as our central epistemic notion, we can shed light on a variety of important topics, including evidence and evidential probability, epistemic modals, and the normative constraints on credence and assertion. (shrink)

One attractive feature of process reliabilism is its reductive potential: it promises to explain justification in entirely non-epistemic terms. In this paper, I argue that the phenomenon of epistemic defeat poses a serious challenge for process reliabilism’s reductive ambitions. The standard process reliabilist analysis of defeat is the ‘Alternative Reliable Process Account’ (ARP). According to ARP, whether S’s belief is defeated depends on whether S has certain reliable processes available to her which, if they had been used, would have resulted (...) in S not holding the belief in question. Unfortunately, ARP proves untenable. I show, by way of counterexample, that ARP fails to articulate either necessary or sufficient conditions on defeat. Process reliabilists must either provide an alternative reductive account of defeat or renounce their reductive aspirations. (shrink)

Quasi-realists face the challenge of providing a plausible analysis of acknowledgments of moral fallibility. This paper devel...

What is it to believe something might be the case? We develop a puzzle that creates difficulties for standard answers to this question. We go on to propose our own solution, which integrates a Bayesian approach to belief with a dynamic semantics for epistemic modals. After showing how our account solves the puzzle, we explore a surprising consequence: virtually all of our beliefs about what might be the case provide counterexamples to the view that rational belief is closed under logical (...) implication. (shrink)

When is it permissible to rely on a proposition in practical reasoning? Standard answers to this question face serious challenges. This paper uses these challenges to motivate a certainty norm of practical reasoning. This norm holds that one is permitted to rely on p in practical reasoning if and only if p is epistemically certain. After developing and defending this norm, I consider its broader implications. Taking a certainty norm seriously calls into question traditional assumptions about the importance of belief (...) and knowledge. In particular, it raises the possibility that many epistemological jobs that are usually assigned to belief and knowledge should be reallocated to two related but importantly different states: psychological and epistemic certainty. (shrink)

The past decade has seen a protracted debate over the semantics of epistemic modals. According to contextualists, epistemic modals quantify over the possibilities compatible with some contextually determined group’s information. Relativists often object that contextualism fails to do justice to the way we assess utterances containing epistemic modals for truth or falsity. However, recent empirical work seems to cast doubt on the relativist’s claim, suggesting that ordinary speakers’ judgments about epistemic modals are more closely in line with contextualism than relativism (...) (Knobe & Yalcin 2014; Khoo 2015). This paper furthers the debate by reporting new empirical research revealing a previously overlooked dimension of speakers’ truth-value judgments concerning epistemic modals. Our results show that these judgments vary systematically with the question under discussion in the conversational context in which the utterance is being assessed. We argue that this ‘QUD effect’ is difficult to explain if contextualism is true, but is readily explained by a suitably flexible form of relativism. (shrink)

We often claim to know what might be—or probably is—the case. Modal knowledge along these lines creates a puzzle for information-sensitive semantics for epistemic modals. This paper develops a solution. We start with the idea that knowledge requires safe belief: a belief amounts to knowledge only if it could not easily have been held falsely. We then develop an interpretation of the modal operator in safety that allows it to non-trivially embed information-sensitive contents. The resulting theory avoids various paradoxes that (...) arise from other accounts of modal knowledge. It also delivers plausible predictions about modal Gettier cases. (shrink)

One leading approach to justification comes from the reliabilist tradition, which maintains that a belief is justified provided that it is reliably formed. Another comes from the ‘Reasons First’ tradition, which claims that a belief is justified provided that it is based on reasons that support it. These two approaches are typically developed in isolation from each other; this essay motivates and defends a synthesis. On the view proposed here, justification is understood in terms of an agent’s reasons for belief, (...) which are in turn analyzed along reliabilist lines: an agent's reasons for belief are the states that serve as inputs to their reliable processes. I show that this synthesis allows each tradition to profit from the other's explanatory resources. In particular, it enables reliabilists to explain epistemic defeat without abandoning their naturalistic ambitions. I go on to compare my proposed synthesis with other hybrid versions of reliabilism that have been proposed in the literature. (shrink)

This paper develops a question-sensitive theory of intention. We show that this theory explains some puzzling closure properties of intention. In particular, it can be used to explain why one is rationally required to intend the means to one’s ends, even though one is not rationally required to intend all the foreseen consequences of one’s intended actions. It also explains why rational intention is not always closed under logical implication, and why one can only intend outcomes that one believes to (...) be under one’s control. (shrink)

According to expressivists, normative language expresses desire‐like states of mind. According to noncognitivists, normative beliefs have a desire‐like functional role. What is the relation between these two doctrines? It is widely assumed that expressivism commits you to noncognitivism, and vice versa. This paper opposes that assumption. I advance a view that combines a noncognitivist psychology with a descriptivist semantics for normative language. While this might seem like an ungainly hybrid, I argue that it has important advantages over more familiar metaethical (...) positions. The noncognitivist aspect of the theory captures all of the explanatory benefits standardly associated with expressivism. At the same time, the descriptivist element allows us to avoid the semantic headaches for expressivism. (shrink)

Relativism and expressivism offer two different semantic frameworks for grappling with a similar cluster of issues. What is the difference between these two frameworks? Should they be viewed as rivals? If so, how should we choose between them? This chapter sheds light on these questions. After providing an overview of relativism and expressivism, I discuss three potential choice points: their relation to truth conditional semantics, their pictures of belief and communication, and their explanations of disagreement.

Why engage in inquiry? According to many philosophers, the goal of inquiring into some question is to come to know its answer. While this view holds considerable appeal, this paper argues that it stands in tension with another highly attractive thesis: knowledge does not require absolute certainty. Forced to choose between these two theses, I argue that we should reject the idea that inquiry aims at knowledge. I go on to develop an alternative view, according to which inquiry aims at (...) maximizing the epistemic value of our credences. This alternative view makes room for knowledge that falls shy of certainty, and it coheres nicely with a rich body of work in epistemic decision theory. I proceed to highlight the implications of this replacement for some important topics in epistemology, including the dogmatism paradox, the nature of interrogative attitudes, and the norm of practical reasoning. (shrink)

According to noncognitivism, normative beliefs are just desire-like attitudes. While noncognitivists have devoted great effort to explaining the nature of normative belief, they have said little about all of the other attitudes we take towards normative matters. Many of us desire to do the right thing. We sometimes wonder whether our conduct is morally permissible; we hope that it is, and occasionally fear that it is not. This gives rise to what Schroeder calls the 'Many Attitudes Problem': the problem of (...) developing a plausible noncognitivist account of the full range of attitudes that we take towards normative matters. This paper explores the problem and proposes a solution. (shrink)

According to deontological approaches to justification, we can analyze justification in deontic terms. In this paper, I try to advance the discussion of deontological approaches by applying recent insights in the semantics of deontic modals. Specifically, I use the distinction between weak necessity modals and strong necessity modals to make progress on a question that has received surprisingly little discussion in the literature, namely: ‘What’s the best version of a deontological approach?’ The two most obvious hypotheses are the Permissive View, (...) according to which justified expresses permission, and the Obligatory View, according to which justified expresses some species of obligation. I raise difficulties for both of these hypotheses. In light of these difficulties, I propose a new position, according to which justified expresses a property I call faultlessness, defined as the dual of weak necessity modals. According to this view, an agent is justified in phi-ing iff it’s not the case that she should [/ought] not phi. I argue that this ‘Faultlessness View’ gives us precisely what’s needed to avoid the problems facing the Permissive and Obligatory Views. (shrink)

According to the dogmatist, knowing p makes it rational to disregard future evidence against p. The standard response to the dogmatist holds that knowledge is defeasible: acquiring evidence against something you know undermines your knowledge. However, this response leaves a residual puzzle, according to which knowledge makes it rational to intend to disregard future counterevidence. I argue that we can resolve this residual puzzle by turning to an unlikely source: Kavka’s toxin puzzle. One lesson of the toxin puzzle is that (...) it is irrational to intend to do that which you know will be irrational. This yields a simple reply to the dogmatist: it is irrational to intend to disregard future evidence because you can know in advance that it will be irrational to do so. (shrink)

Research into two-stage models of “free will” – first “free” random generation of alternative possibilities, followed by “willed” adequately determined decisions consistent with character, values, and desires – suggests that William James was in 1884 the first of a dozen philosophers and scientists to propose such a two-stage model for free will. We review the later work to establish James’s priority. By limiting chance to the generation of alternative possibilities, James was the first to overcome the standard two-part argument against (...) free will, i.e., that the will is either determined or random. James gave it elements of both, to establish freedom but preserve responsibility. We show that James was influenced by Darwin’s model of natural selection, as were most recent thinkers with a two-stage model. In view of James’s famous decision to make his first act of freedom a choice to believe that his will is free, it is most fitting to celebrate James’s priority in the free will debates by naming the two-stage model – first chance, then choice -“Jamesian” free will. (shrink)

This paper develops a new challenge for moral noncognitivism. In brief, the challenge is this: Beliefs — both moral and non-moral — are epistemically evaluable, whereas desires are not. It is tempting to explain this difference in terms of differences in the functional roles of beliefs and desires. However, this explanation stands in tension with noncognitivism, which maintains that moral beliefs have a desire-like functional role. After critically reviewing some initial responses to the challenge, I suggest a solution, which involves (...) rethinking the functional relationship between desire and belief. (shrink)

Philosophical Perspectives, Volume 35, Issue 1, Page 23-49, December 2021.

A survey of popular textbooks and websites on philosophy produces a ­remarkable consensus on the great problems facing philosophers from ­ancient to modern times. They typically include metaphysics - what is there?, the problem of knowledge - how do we know what exists?, the mind/body problem - can an immaterial mind move the material body?, the “hard problem” of consciousness, freedom of the will, theories of ethics - is there an objective universal Good?, and problems from theology - does God (...) exist?, is God responsible for evil? This book introduces the Information Philosopher website, a work in progress on several classic questions in philosophy that ­logical positivists and analytic language philosophers thought they could ­­dis-solve as logical puzzles, pseudo-problems, or conceptual errors. (shrink)

Are all epistemic notions – including evidence and rational credence – sensitive to practical considerations? A number of philosophers have argued that the answer must be ‘No’, since otherwise rational agents would be susceptible to diachronic Dutch books. After unpacking this challenge, I show how it can be resisted by appealing to an analogy between shifting stakes and memory loss. The upshot: pervasive epistemic shiftiness may be tenable after all.

Vaccination can protect vaccinated individuals and often also prevent them from spreading disease to other people. This opens up the possibility of getting vaccinated for the sake of others. In fact, altruistic vaccination has recently been conceptualized as a kind of vaccination that is undertaken primary for the benefit of others. In order to better understand the potential role of altruistic motives in people’s vaccination decisions, we conducted two focus group studies with a total of 37 participants. Study 1 included (...) three focus groups on the subject of HPV vaccination for boys. Study 2 included three focus groups on the subject of pertussis and measles vaccination for childcare workers. We found substantial evidence of other-regarding motives across all focus groups, which suggests that altruistic motives could be an important factor when it comes to people’s vaccination decisions. We address the significance of these findings for vaccination policy surrounding HPV vaccination for boys and vaccination for childcare workers. We also extend the findings to normative work on vaccination for the sake of others more generally. (shrink)

1. What is the relation between skilful action and knowledge? According to most philosophers, the two have little in common: practical intelligence and theoretical intelligence are largely separate...

It is common for conservationists to refer to non-native species that have undesirable impacts on humans as “invasive”. We argue that the classification of any species as “invasive” constitutes wrongful discrimination. Moreover, we argue that its being wrong to categorize a species as invasive is perfectly compatible with it being morally permissible to kill animals—assuming that conservationists “kill equally”. It simply is not compatible with the double standard that conservationists tend to employ in their decisions about who lives and who (...) dies. (shrink)

We should disassociate ourselves from wrongdoing. If Hobby Lobby is against LGBTQ rights, we shouldn’t shop there. If Old Navy sources their clothing from sweatshops, we shouldn’t buy them. If animals are treated terribly in factory farms, we shouldn’t eat the meat, eggs, and dairy products that come from them. Let’s call these disassociation intuitions. What explains the existence and force of disassociation intuitions? And based on that explanation, are they intuitions worth taking seriously? In other words, depending on the (...) etiology of these intuitions, should we accept that you ought to dissociate yourself from wrongdoing? Our aim here is to outline a hypothesis that would, if true, answer the first question, and which suggests a way to vindicate some disassociation intuitions as morally correct. (shrink)

Agnieszka Jaworska and Julie Tannenbaum recently developed the ingenious and novel person‐rearing account of moral status, which preserves the commonsense judgment that humans have a higher moral status than nonhuman animals. It aims to vindicate speciesist judgments while avoiding the problems typically associated with speciesist views. We argue, however, that there is good reason to reject person‐rearing views. Person‐rearing views have to be coupled with an account of flourishing, which will (according to Jaworska and Tannenbaum) be either a species norm (...) or an intrinsic potential account of flourishing. As we show, however, person‐rearing accounts generate extremely implausible consequences when combined with the accounts of flourishing Jaworska and Tannenbaum need for the purposes of their view. (shrink)

There are long-standing doubts about whether data from subjective scales—for instance, self-reports of happiness—are cardinally comparable. It is unclear how to assess whether these doubts are justified without first addressing two unresolved theoretical questions: how do people interpret subjective scales? Which assumptions are required for cardinal comparability? This paper offers answers to both. It proposes an explanation for scale interpretation derived from philosophy of language and game theory. In short: conversation is a cooperative endeavour governed by various maxims (Grice 1989); (...) because subjective scales are vague and individuals want to make themselves understood, scale interpretation is a search for a focal point (Schelling 1960). A specific focal point it hypothesised; if this hypothesis is correct, subjective data will be cardinally comparable. Four individually necessary and jointly sufficient conditions for cardinal comparability are specified. The paper then argues this hypothesis can be empirically be tested, makes an initial attempt to do so using subjective well-being data, and concludes it is supported. Numerous areas for further research are identified including, at the end of the paper, how certain tests could be used to ‘correct’ subjective data if they are not cardinal. (shrink)

While life satisfaction theories (LSTs) of well-being are barely discussed in philosophy, they are popular among social scientists and wider society. When philosophers have discussed LSTs, they are taken to be a distinct alternative to the three canonical accounts of well-being—hedonism, desire theories, the objective list. This essay makes three main claims. First, on closer inspection, LSTs are indistinguishable from a type of desire theory—the global desire theory. Second, the life satisfaction/global desire theories are the only subjectivist accounts of well-being (...) in the sense that they maintain individuals decide what makes their lives go well for them; hedonism and other desire theories are subjectivist only in some alternative senses. Third, subjectivism is implausible, although for different reasons from those that are usually given. I examine what I take to be the two main current objections to LSTs and argue that they are unproblematic. I then raise two different, challenging objections. The first is novel. The second has been noted in passing, but its seriousness underestimated. I close by sketching some non-obvious difficulties that subjectivists will face if they attempt to show rival objectivist theories suffer even more counterintuitive implications. Although subjectivism has a strong intuitive pull, we should be ready to abandon it in favour of an objectivist theory—although it is not my purpose here to say which one. (shrink)

Suppose you want to do as much good as possible. What should you do? According to members of the effective altruism movement—which has produced much of the thinking on this issue and counts several moral philosophers as its key protagonists—we should prioritise among the world’s problems by assessing their scale, solvability, and neglectedness. Once we’ve done this, the three top priorities, not necessarily in this order, are (1) aiding the world’s poorest people by providing life-saving medical treatments or alleviating poverty (...) itself, (2) preventing global catastrophic risks, such as those posed by nuclear war or rogue artificial intelligence, and (3) ending factory farming. These claims are both plausible and striking. If correct, they should prompt a stark revision of how we approach our altruistic activities. However, the project of determining how to do the most good—as opposed to say, whether we should do the most good—has only recently, within the last ten years, become the subject of serious academic attention. Many key claims have not yet been carefully scrutinised. This is a cause for concern: are effective altruists doing good badly? In this thesis, I critique and develop some of the latest claims about how individuals can do the most good. I do this in three areas: the value of saving lives (preventing premature deaths), how best to improve lives (making people happier during their lives), and cause prioritisation methodology (frameworks for determining which problems are the highest priorities). In each case, I raise novel theoretical considerations that, when incorporated, change the analysis. Roughly speaking, my main conclusions are (1) saving lives is not as straightforwardly good we tend to suppose, may not be good at all, and is not clearly a priority; (2) happiness can be measured through self-reports and, based on the self-reported evidence, treating mental health stands out as an overlooked problem that may be an even more cost-effective way to improve lives than alleviating poverty; (3) the cause prioritisation methodology proposed by effective altruists needs to be moderately reconceptualised and, when it is, it turns out it is not as illuminating a tool as we might have thought and hoped. (shrink)

As well as disagreeing about how much one should donate to charity, moral theories also disagree about where one should donate. In light of this disagreement, how should the morally uncertain philanthropist allocate her donations? In many cases, one intuitively attractive option is for the philanthropist to split her donations across all of the charities that are recommended by moral views in which she has positive credence, with each charity’s share being proportional to her credence in the moral theories that (...) recommend that particular charity. Despite the fact that something like this approach is already being used by real-world philanthropists to distribute billions of dollars of donations, it is not supported by any of the approaches to moral uncertainty that have been proposed thus-far in the philosophical literature. In this paper, we will develop a bargaining-based approach to moral uncertainty that honors the proportionality intuition in favor of splitting one’s donations. We also show how this bargaining-based approach has several further advantages over the best alternative proposals. (shrink)

Epistemologists have long believed that epistemic luck undermines propositional knowledge. Action theorists have long believed that agentive luck undermines intentional action. But is there a relationship between agentive luck and epistemic luck? While agentive luck and epistemic luck have been widely thought to be independent phenomena, we argue that agentive luck has an epistemic dimension. We present several thought experiments where epistemic luck seems to undermine both knowledge-how and intentional action and we report experimental results that corroborate these judgments. These (...) findings have implications for the role of knowledge in a theory of intentional action and for debates about the nature of knowledge-how and the significance of knowledge representation in folk psychology. (shrink)

This is a pdf of a Mathematica calculation that supplements the paper "Presentist Fragmentalism and Quantum Mechanics" forthcoming in Foundations of Physics. In that paper the Born rule (or at least a progenitor) is derived from experimental conditions on the mutual observations of two fragments. In this pdf the experimental conditions are applied to Hilbert space dimensions 3, 4, and 5. It turns out each of these have a 1-dimensional solution space which, it is hoped, can be interpretated as the (...) phase. (shrink)

Suicide among college students is a major public health problem. Research has confirmed that negative focused disposition had a significant effect on suicidal ideation. This study aims to evaluate somatic anxiety, general distress and depression as mediators of the relationship between negative focused disposition and suicidal ideation.

According to F. Adams [this journal, vol. 68, 2018] cognition cannot be realized in plants or bacteria. In his view, plants and bacteria respond to the here-and-now in a hardwired, inflexible manner, and are therefore incapable of cognitive activity. This article takes issue with the pursuit of plant cognition from the perspective of an empirically informed philosophy of plant neurobiology. As we argue, empirical evidence shows, contra Adams, that plant behavior is in many ways analogous to animal (...) behavior. This renders plants suitable to be described as cognitive agents in a non-metaphorical way. Sections two to four review the arguments offered by Adams in light of scientific evidence on plant adaptive behavior, decision-making, anticipation, as well as learning and memory. Section five introduces the ‘phyto-nervous’ system of plants. To conclude, section six resituates the quest for plant cognition into a broader approach in cognitive science, as represented by enactive and ecological schools of thought. Overall, we aim to motivate the idea that plants may be considered genuine cognitive agents. Our hope is to help propel public awareness and discussion of plant intelligence once appropriately stripped of anthropocentric preconceptions of the sort that Adams' position appears to exemplify. (shrink)

Bob Solomon enjoyed humor, a good laugh. He was not a teller and collector of jokes or of humorous stories, as Ted Cohen and Noël Carroll are. He did not cultivate clever witticisms. Rather, his interest was in viewing life’s contingency and absurdity for the humor that can be found there, and the target of this humor was as likely to be himself or his friends as it was to be strangers. Bob also displayed philosophical courage. He once argued before (...) an incredulous audience of philosophers that the Three Stooges are funny, and admitted unashamedly to being a life-long devotee. In the published version of that talk he observes: “few adults in their chosen professions would dare attempt a Stooges gesture at risk of being terminally dismissed, but most men carry the secret knowledge around with them, and, in a wild fit of catharsis, display a tell-tale Stooges gesture when the door closes and the boss is out of view. I only hesitate to suggest that it is one of the most basic bonds between men, and perhaps the fact that it mystifies and sometimes horrifies women is far more elemental than the mere phrase ‘a sense of humor’ could ever suggest”. (shrink)

All living things have sensory capacities. Plants, in particular, have sensory receptors, transduce the activations of these receptors, and process these outputs in order to manage actions that demand sensory integration. However, there is a kind of sensory function that plants cannot perform. They cannot sense something as other than themselves. Animals, by contrast, perceive. They experience two kinds of "othering impressions"—impressions of entities as located outside and available for interaction, and hence as distinct from the perceiving subject. First, they (...) represent external entities in a "body scheme" that enables sensorimotor interaction with these entities. Second, higher animals such as mammals and birds and possibly fish, represent these entities as located relative to a "cognitive map." These othering impressions are very important because they are the foundation for the human conceptions of the self and other. (shrink)

The problem of plant individuality is something which has vexed botanists throughout the ages, with fashion swinging back and forth from treating plants as communities of individuals (Darwin 1800 ; Braun and Stone 1853 ; Münch 1938 ) to treating them as organisms in their own right, and although the latter view has dominated mainstream thought most recently (Harper 1977 ; Cook 1985 ; Ariew and Lewontin 2004 ), a lively debate conducted mostly in Scandinavian journals proves that the (...) issues are far from being resolved (Tuomi and Vuorisalo 1989b ; Fagerström 1992 ; Pan and Price 2001 ). In this paper I settle the matter once and for all, by showing which elements of each side are correct. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for (...) all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide (...) significant new insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth (...) and developmental stages across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of (...) the PO has been expanded to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)