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This chapter explores the history of an interdisciplinary research program on the social, economic, cultural, and psychological determinants of health and the biological pathways by which they operate. The study dealt with the inevitable resistance to interdisciplinary research by, initially, breaking it up into small nonthreatening chunks and only later attempting to prove that the whole was greater than the sum of parts. A particular problem was that the research was addressing social inequalities in health. When the political climate was unfavorable, such research was seen to be, at best, irrelevant and, at worst, threatening. When the political climate in Britain changed, yesterday's pure academic research became today's applied science.

“Darwinian” approaches to epistemic normativity, which is explain epistemic normativity in terms of the biological function of belief, are articulated and criticized. A “biological” conception of belief, on which the biological function of belief is to be true, is considered. It is argued that Darwinian approaches depend on the problematic assumption that biological functioning is valuable, and that the plausibility of these approaches depends on empirical knowledge about the natural history of human cognition that we presently do not possess. The possibility of non-epistemic biological functions of belief is considered.

Of all the shifts in psychological opinion in the period covered by this book, probably the most far-reaching was the remodeling of it in the light of evolutionary theories. The evolutionary paradigm placed the mind in the general analysis of nature and the biological functions. This chapter examines the development of ‘materialist’, evolutionary psychological theory in the work of one of its leading writers, Herbert Spencer, in detail and in context. Spencer's new psychology, launched in 1855, was portrayed by both radicals and conservatives as marking a fresh and strikingly original turn in the development of psychological theory. The first section describes the changes in models of the mind in the second half of the nineteenth century. The second section discusses Spencer's psychology from associationism to evolutionary theory. The third examines the varying responses to psychological theory. The last section discusses epistemology and evolutionary psychology.

This introductory chapter explains the objective of this book, which is to offer a theory of intentional content and to provide an account of what it is meant when people say that a person is musing about something. This book attempts to develop a theory of biological functions and an account of how we ascribe content to intentional systems. It also discusses a more sophisticated intentional system called a doxastic system and it also looks at simple system referred to as special-purpose systems.

This chapter describes the gap between biological and artifactual functions. It questions whether there is a conceptually clear distinction between both domains that needs to be bridged at all. It suggests that artifact functions are not as easy to analyze as one might have first thought. It examines what is going on with biological and artifactual functions at three decisive points: when the artifactual encounters the biological; when new functions become culturally established; and c) when new artifacts are invented. This chapter shows mixed functions, functions that were crossing boundaries, and mixing elements of various sorts.

This chapter focuses on another aspect that divides biological from artifactual functions. It describes how theories that analyze functions of technical artifacts in terms of beliefs of agents can be transposed into theories in which artifacts have functions as properties. The new approach toward understanding malfunctioning is provided. It deals with the constructed theory to a uniform “ICE-like” function theory, and indicates its similarities with Cummins's theory. This chapter shows that in etiological theories, malfunctioning biological items may be items that are irreversibly malformed, whereas in the proposed approach, an artifact may be taken as malfunctioning only if it can reasonably be brought back into a state in which it stops malfunctioning.

Many contemporary thinkers see a challenge to teleology that accompanied Darwin’s proposal of modern evolutionary theory. This chapter articulates this challenge, and reviews the two primary contemporary approaches to teleology: etiological versus causal role accounts of biological function. Both approaches attempt to naturalize teleology—to analyze teleology in a way consistent with the natural sciences, especially biological science. While this is an enormously productive endeavor, there are some reasons to be skeptical about the ultimate success of this approach to teleology.

Life and death are matters that concern children at a very young age. The death of a loved one or a pet can be very disturbing. At some point, children inevitably need to confront the issue of the prerequisites for life and the causes of death. This chapter addresses the question of the extent to which young children in different countries such as America, Ecuador, and Germany understand the creation of life and the permanence of death. It examines whether they understand the finality of death in a material sense as the cessation of biological functioning and whether they understand that things that are no longer alive stop eating, sleeping, and breathing.

It is by no means clear what the biological function of disgust might be. The Darwinian taste-toxicity theory runs into obvious trouble: disgust cannot be viewed simply as a protection against the ingestion of unhealthy substances. This is connected to the obscure origin of disgust in the human species: how can we speculate about the origin of disgust if we don't know what its purpose is? Only if we know its function can be know why it arises. What kind of adaptation is it? Is it perhaps a by-product of some other direct adaptation? Nor should we expect that its function, assuming it has one, is anything simple—as fear has the simple function of motivating the animal to avoid danger. Disgust might play a more complex role in the overall human psychological and biological economy. This chapter proposes to make some exploratory remarks about this very difficult question.

People start out on the fertility journey wanting to be a normal family. Those who are faced with giving up the idea of a biological child are still concerned with being a normal family; indeed, they become more concerned with this issue than they were before. This chapter appraises the difficulties entailing an alternative parenthood, specifically in the form of the cultural ideology of a non-biological offspring. The issue of achieving/projecting normalcy assumes paramountcy in the concerns of the incumbent parents. When people are able to consider non-biological alternatives, it is because they have ceased to equate gender identity with biological functions. Three issues assume importance in resorting to an alternative route to parenthood: making peace with a non-biogenetic issue; incorporating normalcy in and around the family and the child; dealing with the fact that the family will not embody the cultural ideology of biological parenthood.

This essay applies Kant’s account of organisms as purposes to recent debates about the notion of function in biology. It claims that the notion of a function in both organisms and artefacts is simply the notion of what something ‘ought to’ or ‘should’ or ‘is meant to’ do. It defends this claim in terms of the idea of ‘primitive’ normativity. This is not a normativity based on reasons, but a more fundamental normativity, implicit in our natural perceptual and imaginative responses to the world, which is required for intentionality as such. The acceptance of human nature as involving normativity in this primitive sense shows that there is no obstacle in principle to ascribing normativity to natural phenomena in general, giving us license to use our everyday notion of function to help us make sense of biological phenomena.

Recognizing specific biological concepts described in text is an important task that is receiving increasing attention in bioinformatics. To leverage the literature effectively, sophisticated data analysis algorithms must be able to identify key biological concepts and functions in text. However, biomedical text is complex and diverse in subject matter and lexicon. Very specialized vocabularies have been developed to describe biological complexity. In addition, using computational approaches to understand text in general has been a historically challenging subject (Rosenfeld 2000). In this chapter we will focus on the basics of understanding the content of biological text. We will describe common text classification algorithms. We demonstrate how these algorithms can be applied to the specific biological problem of gene annotation. But text classification is also potentially instrumental to many other areas of bioinformatics; we will see other applications in Chapter 10. There is great interest in assigning functional annotations to genes from the scientific literature. In one recent symposium 33 groups proposed and implemented classification algorithms to identify articles that were specifically relevant for gene function annotation (Hersh, Bhuporaju et al. 2004). In another recent symposium, seven groups competed to assign Gene Ontology function codes to genes from primary text (Valencia, Blaschke et al. 2004). In this chapter we assign biological function codes to genes automatically to investigate the extent to which computational approaches can be applied to identify relevant biological concepts in text about genes directly. Each code represents a specific biological function such as ‘‘signal transduction’’ or ‘‘cell cycle’’. The key concepts in this chapter are presented in the frame box. We introduce three text classification methods that can be used to associate functional codes to a set of literature abstracts. We describe and test maximum entropy modeling, naive Bayes classification, and nearest neighbor classification. Maximum entropy modeling outperforms the other methods, and assigns appropriate functions to articles with an accuracy of 72%. The maximum entropy method provides confidence measures that correlate well with performance.

Due to the finite number of dynamic behaviours that can be implemented by regulatory systems, it should be possible to enumerate and classify different developmental mechanisms that can achieve the same biological function. For example, there are only a small number of ways by which small regulatory networks can create a stripe of gene expression in a static or growing tissue. By comparing these different mechanisms, we can discover the design principles of stripe-producing regulatory networks. Such a rigorous and mechanistic classification scheme would constitute the basis for a theory of development that characterizes and explains the regularities and recurring motifs observed in organismal morphology. This tackles a central question in biology, which has fascinated numerous researchers since the rational taxonomists first raised it in the 19th century. This chapter introduces and defines a concept of developmental mechanism suitable for this endeavour, based on the conceptual framework of dynamical systems theory, which characterizes the dynamical repertoire of regulatory networks. Equivalent mechanisms are defined as sharing the same topology of their phase portraits: they have the same number and geometrical arrangement of attracting states, saddle points, and basins of attraction, and undergo structurally stable bifurcations as systems parameters change over time. These abstract concepts and their application are illustrated using specific examples such as simulated stripe-forming networks, vertebrate limb development, and the segmentation gene network in insects. This constitutes a first, tentative step towards a more general geometrical theory of developmental mechanisms and the complex map from genotype to phenotype.

Any argument to substantiate the ethical salience of the distinction between being healthy and being diseased must consist of two steps. First, an account must be offered of how to draw the distinction between the two conditions; and second, it must be shown why that distinction marks an important boundary. Naturalistic theories, according to which diseases are understood as biologically malfunctioning traits, fail to make the health/disease distinction ethically salient in itself because of a set of problems involved in trying to derive appropriate goals for medical care from facts about biological goals and the typical effects by which traits contribute to them.

The February 16th, 2001 issue of Science magazine announced the completion of the human genome project—making the entire nucleotide sequence of the genome available (Venter, Adams et al. 2001). For the first time a comprehensive data set was available with nucleotide sequences for every gene. This marked the beginning of a new era, the ‘‘genomics’’ era, where molecular biological science began a shift from the investigation of single genes towards the investigation of all genes in an organism simultaneously. Alongside the completion of the genome project came the introduction of new high throughput experimental approaches such as gene expression microarrays, rapid single nucleotide polymorphism detection, and proteomics methods such as yeast two hybrid screens (Brown and Botstein 1999; Kwok and Chen 2003; Sharff and Jhoti 2003; Zhu, Bilgin et al. 2003). These methods permitted the investigation of hundreds if not thousands of genes simultaneously. With these high throughput methods, the limiting step in the study of biology began shifting from data collection to data interpretation. To interpret traditional experimental results that addressed the function of only a single or handful of genes, investigators needed to understand only those few genes addressed in the study in detail and perhaps a handful of other related genes. These investigators needed to be familiar with a comparatively small collection of peer-reviewed publications and prior results. Today, new genomics experimental assays, such as gene expression microarrays, are generating data for thousands of genes simultaneously. The increasing complexity and sophistication of these methods makes them extremely unwieldy for manual analysis since the number and diversity of genes involved exceed the expertise of any single investigator. The only practical solution to analyzing these types of data sets is using computational methods that are unhindered by the volume of modern data. Bioinformatics is a new field that emphasizes computational methods to analyze such data sets (Lesk 2002). Bioinformatics combines the algorithms and approaches employed in computer science and statistics to analyze, understand, and hypothesize about the large repositories of collected biological data and knowledge.

According to Philippa Foot, judgements of good or evil are the same in kind as judgements about the goodness or badness of the parts and behaviours of plants or animals. In both cases the judgements in question are purely factual ones concerning defective functional performance. Foot’s case gains prima facie plausibility from the apparently factual nature of judgements regarding the flourishing of plants and animals. Here it is argued that the existence of trade-offs between individual survival and reproduction undermines the equation of flourishing with proper organic functioning. These trade-offs present a general challenge for efforts to naturalize ethics by means of naturalized theories of function.

This chapter stipulates that race is not a “scientific” or biologically coherent category, emphasizing the notion that there is no allele for race. It considers race as a hierarchical social construct that assigns human value and group power. Throughout the ages, the concept of race developed to the point that it has underlying consequences for biological functions, including gene expression. The notion affects material conditions of survival, such as relative respect and privilege, education, and medical and dental care. However, the absence of an allele, such as skin color, proves that race has no scientific basis. As a sociological matter, skin color is a presumptive indicator but historically it is not the exclusive marker. And as a biological matter, melanin concentration merely reveals how one's ancestors adapted to more or less sunny climates—and dark skin is more or less distributed around the equator, no matter which continent.

This chapter challenges the assumption of attention functioning as a means of preventing consciousness from getting overloaded, and also challenges the assumption of any relationships between management of scarce resources and the original biological function of attention. It emphasizes that attention is directly derived from mechanisms governing the control of basic movements. The author establishes the theoretical stage through discussions on the implications of the brain’s preference to stimulus events and action plans in a feature-based manner and processing information through different mechanisms. The chapter also discusses many empirical findings supporting the conception of action planning and action control having the potential to determine perception and attention.

When is it rational to suppose that a creature is a zombie, that it has no inner life or experiences? Plausibly, Mother Nature gave humans the capacity to have experiences so that they could cope with their surroundings and exhibit complex behavior in response to an ever-changing environment. This suggests a test for zombiehood. Where there is no (or very little) flexibility in behavior in response to the same stimulus, that is evidence that no experiences are operative in the production of the behavior. With this test in hand, the question of whether very simple creatures––such as caterpillars, protozoa, and plants—are the subjects of experience is addressed.