I analyze the importance of parts in the style of biological theorizing that I call compositional biology. I do this by investigating various aspects, including partitioning frames and explanatory accounts, of the theoretical perspectives that fall under and are guided by compositional biology. I ground this general examination in a comparative analysis of three different disciplines with their associated compositional theoretical perspectives: comparative morphology, functional morphology, and developmental biology. I glean data for this analysis (...) from canonical textbooks and defend the use of such texts for the philosophy of science. I end with a discussion of the importance of recognizing formal and compositional biology as two genuinely different ways of doing biology – the differences arising more from their distinct methodologies than from scientific discipline included or natural domain studied. Ultimately, developing a translation manual between the two styles would be desirable as they currently are, at times, in conflict. (shrink)

There are two fundamentally distinct kinds of biological theorizing. "Formal biology" focuses on the relations, captured in formal laws, among mathematically abstracted properties of abstract objects. Population genetics and theoretical mathematical ecology, which are cases of formal biology, thus share methods and goals with theoretical physics. "Compositional biology," on the other hand, is concerned with articulating the concrete structure, mechanisms, and function, through developmental and evolutionary time, of material parts and wholes. Molecular genetics, biochemistry, developmental (...) class='Hi'>biology, and physiology, which are examples of compositional biology, are in serious need of philosophical attention. For example, the very concept of a "part" is understudied in both philosophy of biology and philosophy of science. ;My dissertation is an attempt to clarify the distinction between formal biology and compositional biology and, in so doing, provide a clear philosophical analysis, with case studies, of compositional biology. Given the social, economic, and medical importance of compositional biology, understanding it is urgent. For my investigation, I draw on the philosophical fields of metaphysics and epistemology, as well as philosophy of biology and philosophy of science. I suggest new ways of thinking about some classic philosophy of science issues, such as modeling, laws of nature, abstraction, explanation, and confirmation. I hint at the relevance of my study of two kinds of biological theorizing to debates concerning the disunity of science. (shrink)

GeneMusiK is an artistic project that puts into play ideas about the capacity of physical morphologies to act as mnemonic systems by using DNA to transcode and remix musical structures. The project suggests that both biological and cultural information can function as both macro- and micro-scale structures arrayed at physical loci to create topologies which function as keys to the mapping of memory.

Aristotle uses two kinds of material cause in his analysis of biological organisms: compositional matter, which persists through their birth and death;and functional matter, which consists of the organs and functional parts out of which biological organisms are made while they are alive. These two kinds of material cause, it has been argued, have quite different explanatory roles: functional matter is required by biological organisms to perform their essential functions,but compositional matter contributes nothing necessary to them and is (...) only responsible for their accidental properties. Against this view, I argue that biological organisms are systematically dependent upon their compositional matter and the latter is responsible for many of their necessary attributes. (shrink)

I motivate the concept of styles of scientific investigation, and differentiate two styles, formal and compositional. Styles are ways of doing scientific research. Radically different styles exist. I explore the possibility of the unification of biology and social science, as well as the possibility of unifying the two styles I identify. Recent attempts at unifying biology and social science have been premised almost exclusively on the formal style. Through the use of a historical example of defenders of (...) compositional biological social science, the Ecology Group at the University of Chicago from, roughly, the 1930s to the 1950s, I attempt to show the coherence and possibility, if not utility, of employing the compositional style to effect the synthesis of biology and social science. I also relate the efforts of the Ecology Group to those of investigators in the Sociology Department of the University of Chicago. In my conclusion, I discuss the usefulness both of employing the category of styles of scientific investigation in historical and philosophical studies of science, as well as the concept of compositionality in scientific studies. I end the paper with some tentative suggestions regarding the importance of compositionality for an analysis of human society. (shrink)

The chapter starts with an exploration of what the family is in order then to move on to look at its parts. The family has been defined in terms of its form (e.g. a mother, a father, and their biological offspring) or its function (e.g. adults taking and/or sharing custodial responsibility for children). In both of these cases, children are a necessary ingredient for a unit to be called a family – but the chapter also briefly reviews proposals to extend (...) the accolade of “family” to beyond child-rearing. From a perspective concerned primarily with family form, biological and more specifically genetic parents have been seen as those to whom children should be born, and by whom they should be raised. From a perspective concerned with family function, this is not necessarily the case. Lastly, the chapter looks at the relation between parents and the requirements that co-parenting may generate in this regard. (shrink)

Since the early twentieth century, the term “chimera” has been used to describe many experimental composite plants and animals. Composite animals and embryos, involving the transfer of cells from different species to make chimeras, continue to be a fundamental cornerstone of biomedical research. However, the twenty‐first century appears to be offering a new role for composite animals. Over the last fifteen to twenty years, composite animals and embryos have taken on a different form of life—an institutional life. With this institutional (...) life, I argue, comes an opportunity to recast differences between humans and other animals and to reconsider how research on human health is governed. (shrink)

While its mechanism and biological significance are unknown, the utility of a short mitochondrial DNA sequence as a “barcode” providing accurate species identification has revolutionized the classification of organisms. Since highest accuracy was achieved with recently diverged species, hopes were raised that barcodes would throw light on the speciation process. Indeed, a failure of a maternally donated, rapidly mutating, mitochondrial genome to coadapt its gene products with those of a paternally donated nuclear genome could result in developmental failure, thus creating (...) a post-zygotic barrier leading to reproductive isolation and sympatric branching into independent species. However, the barcode itself encodes a highly conserved, species-invariant, protein, and the discriminatory power resides in the non-amino acid specific bases of synonymous codons. It is here shown how the latter could register changes in the oligonucleotide frequencies of nuclear DNA that, when they fail to match in pairing meiotic chromosomes, could reproductively isolate the parents so launching a primary divergence into two species. It is proposed that, while not itself contributing to speciation, the barcode sequence provides an index of the nuclear DNA oligonucleotide frequencies that drive speciation. (shrink)

In the New Mechanist literature, most attention has focused on the compositional explanation of processes/activities of wholes by processes/activities of their parts. These are sometimes called “constitutive mechanistic explanations.” In this paper, we defend moving beyond this focus to a Pluralism about compositional explanation by highlighting two additional species of such explanations. We illuminate both Analytic compositional explanations that explain a whole using a compositional relation to its parts, and also Standing compositional explanations that explain (...) a property of a whole using a compositional relation to the properties of its parts. We also highlight how adopting a Pluralism about compositional explanations justifies a more Pluralist view of the ontological posits of such explanations and opens up a range of new research questions. (shrink)

Since the publication of Kuhn’s The Structure of Scientific Revolutions in 1962, the notion of paradigms has shaped the way that philosophy views scientific discovery and how changes in what is regarded as empirical fact occur. This drew heavily on examples from the history of the natural sciences to support Kuhn’s hypothesis. However, some argue that medicine is different from the natural sciences. Gillies has proposed another theory of how paradigms apply to medicine; that of composite paradigms. In doing so, (...) Gillies uses the example of Helicobacter pylori and the shift from the excess-acid theory to the current bacterial-infection theory of gastric ulcers to illustrate these fundamental differences between medicine and the natural sciences.Upon analysis of Gillies’ claim, it is evident that traditional Kuhnian paradigms are also composite and that the manner in which Gillies proposes disease is classified is insufficient in describing medicine. Furthermore, new local paradigms are demonstrably introduced and the change was accompanied by many of the markers of paradigmatic change including changes in worldview, resistance, incommensurability and the introduction of new questions that could not have existed under the previous paradigm. Whilst this change may not be on the scale of the Chemical revolution, it can still be considered paradigm shift.Thagard also proposes an alternate view of discovery using the case of H. pylori. This has much in common with Kuhnian paradigms but Thagard’s theory offers further elucidation and refinement. This allows it to better characterise all of the associated features of discovery relevant in the case of H. pylori, thus provides a preferable tool for examination of this important recent discovery. (shrink)

Homology is a biological sameness relation that is purported to hold in the face of changes in form, composition, and function. In spite of the centrality and importance of homology, there is no consensus on how we should understand this concept. The two leading views of homology, the genealogical and developmental accounts, have significant shortcomings. We propose a new account, the hierarchical-dependency account of homology, which avoids these shortcomings. Furthermore, our account provides for continuity between special, general, and serial homology.

This paper analyzes biological and scientific discourses about the racial composition of the Brazilian population, between 1832 and 1911. The first of these dates represents Darwin’s first arrival in the South-American country during his voyage on H.M.S. Beagle. The study ends in 1911, with the celebration of the First universal Races congress in London, where the Brazilian physical anthropologist J.B. Lacerda predicted the complete extinction of black Brazilians by the year 2012. Contemporary European and North-American racial theories had a profound (...) influence in Brazilian scientific debates on race and miscegenation. These debates also reflected a wider political and cultural concern, shared by most Brazilian scholars, about the future of the Nation. With few known exceptions, Brazilian evolutionists, medical doctors, physical anthropologists, and naturalists, considered that the racial composition of the population was a handicap to the commonly shared nationalistic goal of creating a modern and progressive Brazilian Republic. (shrink)

The biological sciences have always proven a fertile ground for philosophical analysis, one from which has grown a rich tradition stemming from Aristotle and flowering with Darwin. And although contemporary philosophy is increasingly becoming conceptually entwined with the study of the empirical sciences with the data of the latter now being regularly utilised in the establishment and defence of the frameworks of the former, a practice especially prominent in the philosophy of physics, the development of that tradition hasn’t received the (...) wider attention it so thoroughly deserves. This review will briefly introduce some recent significant topics of debate within the philosophy of biology, focusing on those whose metaphysical themes (in everything from composition to causation) are likely to be of wide-reaching, cross-disciplinary interest. (shrink)

Based on sensory integration theory, six fabric samples containing tactile and visual stimuli were selected using the sensory perceptions of designers and combined with balls. Experiments involving these toys were implemented with 15 families with preschool-aged high-functioning autistic children. The results showed that loose sequin, which possessed equal tactile and visual intensities, was strongly correlated with frequent smiling/laughing and high enjoyment levels. The fabric provided a loose tactile sensation regarding surface interweave uniformity and a bright visual sensation regarding visually perceived (...) luster; suede exhibited a greater tactile intensity than visual intensity and was correlated with eye contact and activity response. This fabric possessed a smooth visual sensation regarding visually perceived smoothness; and loose sequin, which possessed equal tactile and visual intensities, was highly correlated with finger pointing and initiation. This fabric offered a thin tactile sensation regarding surface interweave thickness and a bright visual sensation regarding visually perceived luster. We suggest applying fabrics to composite toys. Specifically, loose sequin can be used initially to encourage autistic children to interact; subsequently, suede can enable sustained parent-child interaction. The experimental results provide a reference for establishing an innovative toy-design method for autistic children. Keywords: autism; sensory integration theory; parent-child interaction; toys. (shrink)

A diploid human genome contains approximately six billion nucleotides. This enormous amount of genetic information can be replicated with great accuracy in only a few hours. However, because DNA strands are oriented antiparallel while DNA polymerization only occurs in the 5′ → 3′ direction, semi‐conservative replication of double‐stranded DNA is an asymmetric process, i.e., there is a leading and a lagging strand. This provides a considerable opportunity for non‐random error rates, because the architecture of the two strands as well as (...) the DNA polymerases that replicate them may be different. In addition, the proteins that start or finish chains may well be different from those that perform the bulk of chain elongation. Furthermore, while replication fidelity depends on the absolute and relative concentrations of the four deoxyribonucleotide precursors, these are not equal in vivo, not constant throughout the cell cycle, and not necessarily equivalent in all cell types. Finally, the fidelity of DNA synthesis is sequence‐dependent and the eukaryotic nuclear genome is a heterogeneous substrate. It contains repetitive and non‐repetitive sequences and can actually be considered as two subgenomes that differ in nucleotide composition and gene content and that replicate at different times. The effects that each of these asymmetries may have on error rates during replication of the eukaryotic genome are discussed. (shrink)

This chapter contains sections titled: Introduction Biology and the Theory of Knowledge Biology and Metaphysics Soul, Life, and Reason Conclusion Bibliography.

Although the interdisciplinary nature of contemporary biological sciences has been addressed by philosophers, historians, and sociologists of science, the different ways in which engineering concepts and methods have been applied in biology have been somewhat neglected. We examine - using the mechanistic philosophy of science as an analytic springboard - the transfer of network methods from engineering to biology through the cases of two biology laboratories operating at the California Institute of Technology. The two laboratories study gene (...) regulatory networks, but in remarkably different ways. The research strategy of the Davidson lab fits squarely into the traditional mechanist philosophy in its aim to decompose and reconstruct, in detail, gene regulatory networks of a chosen model organism. In contrast, the Elowitz lab constructs minimal models that do not attempt to represent any particular naturally evolved genetic circuits. Instead, it studies the principles of gene regulation through a template-based approach that is applicable to any kinds of networks, whether biological or not. We call for the mechanists to consider whether the latter approach can be accommodated by the mechanistic approach, and what kinds of modifications it would imply for the mechanistic paradigm of explanation, if it were to address modelling more generally. (shrink)

This study analyzes the influence of grandmothers’ household residency on the presence of low height-for-age and excessive fat, waist circumference, and sum of triceps and subscapular skinfolds in a sample of 247 6- to 8-year-old urban Maya children from Yucatan, Mexico. Between September 2011 and January 2014, we obtained anthropometric and body composition data from children and mothers, as well as socioeconomic characteristics of participants and households. Grandmothers’ place of residence was categorized as either in the same household as their (...) grandchildren or in separate households. Multiple logistic regression models were used to analyze the association between grandmothers’ residency and outcome variables. Models were adjusted for maternal anthropometric characteristics and the following socioeconomic variables: family size, location, maternal education, monthly family income, and household crowding. Models showed that the presence of grandmothers in their grandchildren’s households was not associated with any of the outcome variables. In contrast, larger family size, overcrowding in the household, and lower family income predicted low height-for-age in children. Larger family size decreased the risk for being overweight based on the three parameters of body composition. Overcrowding in the household increased the risk for greater skinfolds thickness, while low family income increased the risk for higher fat mass index. The residency of grandmothers in their adult daughters’ households is not significantly associated with the outcome variables in this sample of urban Maya families. Instead, maternal anthropometric characteristics and socioeconomic conditions of the family have a greater influence on the overall growth of children. (shrink)

Smith gives an excellent overview on research in language evolution, in which he discusses several recent models of how linguistic systems and the cognitive capacities involved in language learning may have co‐evolved. He illustrates how combined pressures on language learning and communication/use produce compositionally structured languages. Once in place, a (culturally transmitted) communication system creates new selection pressures on the capacity for acquiring these systems.

On a common view of evolution, natural selection is the major force that produces evolutionary change. Selection is thought to operate on different types (genotypes or phenotypes) in populations so as to generate differential reproductive survival of these types. This should engender changes in population composition. The conception of selection as a "force" should be considered as a convenient shorthand that easily misleads us. Selection is not a factor over and above items such as temperature regimes, predators, and so forth. (...) These items do causal work in evolutionary processes. The term "selection" is merely an abstract placeholder for them. Differential reproductive survival thus appears to depend on particular environmental items that influence different types in different ways. Such items are properly regarded as the selective agents. On the face of it, selection processes must always be due to the operation of such agents. I argue that this is a mistaken assumption. Processes of selection may well occur in the absence of selective agents. That is because environmental factors may contribute to differential reproductive survival even if they do not affect different genotypes or phenotypes in different ways. Considering the role of the environment in selection, we should distinguish between selective agents and contributive agents. (shrink)

Aristotle insists that the organic matter composing an organism depends for its being and becoming upon the living organism whose organic matter it is. An evolutionary context may at first seem to secure autonomy for an organism’s organic matter: after all, in such a context not only can organisms in divergent taxa have the same trait, but a trait can remain the same through thoroughgoing changes in its form, function, composition, and organismic context over evolutionary time. The biological homology concept (...) attempts to capture this mysterious relationship of trait sameness. However, accounts of biological homology that have dominated the contemporary scene face compelling problems—these problems, I will argue, arise from their exclusion of the organism as an explanatory locus for the being and becoming of biological traits. An evolutionary framework in fact supports an account of homology that retains these two aspects of Aristotle’s views on organic matter. (shrink)

Aristotle insists that the organic matter composing an organism depends for its being and becoming upon the living organism whose organic matter it is. An evolutionary context may at first seem to secure autonomy for an organism’s organic matter: after all, in such a context not only can organisms in divergent taxa have the same trait, but a trait can remain the same through thoroughgoing changes in its form, function, composition, and organismic context over evolutionary time. The biological homology concept (...) attempts to capture this mysterious relationship of trait sameness. However, accounts of biological homology that have dominated the contemporary scene face compelling problems—these problems, I will argue, arise from their exclusion of the organism as an explanatory locus for the being and becoming of biological traits. An evolutionary framework in fact supports an account of homology that retains these two aspects of Aristotle’s views on organic matter. (shrink)

The aim of this paper is to show that biological kinds can be causally homogeneous, although all biological causes are identical with configurations of physical causes. The paper considers two different strategies to establish that result: the first one relies on two different manners of classification (according to function and according to composition); the other one exploits the idea of biological classifications being rather coarse-grained, whereas physical classifications are fine-grained.

The term biology is of Greek origin meaning the study of life. On the other hand, chemistry is the science of matter, which deals with matter and its properties, structure, composition, behavior, reactions, interactions and the changes it undergoes. The theory of abiogenesis maintains that chemistry made a transition to biology in a primordial soup. To keep the naturalistic ‘inanimate molecules to human life’ evolution ideology intact, scientists must assemble billions of links to bridge the gap between the (...) inanimate chemicals that existed in the primordial soup and anatomically modern humans. Even though the proponents of a natural origin of life expressed much optimism for providing their theories, presently there is a detailed compilation of information seriously questioning this doctrine. This reductionistic ideology has always failed to answer two simple questions: (1) What is the minimum number of parts that are essential for a living organism to survive? (2) By what mechanism do these parts get assembled together? Evolutionists say a series of prebiotic processes and developments guide networks of dynamically linked small molecules and amphiphiles to form biological macromolecules, membraneous compartments, and finally primitive cells. However, none of these proposed pathways to life appears to be credible. The continuous advancement in various fields of science are not only providing major challenges to reductionistic ideology but are supplying increasing evidence for a systemic concept of life as an organic whole. Several leading researchers in the field of ‘origin of life’ are continually concluding that there are major scientific problems attached with all existing naturalistic ‘origin of life’ hypothesis. Only by taking into account all biological activities collectively as a system can a satisfactory elucidation of the living state be realized. In this present paper an attempt has been made to present a few significant challenges to the theory of abiogenesis based on the peer reviewed scientific literature. Subsequently, a non-reductionistic concept of life as a system is proposed as an alternative for resolving some of the problems inherent in origin of life research. (shrink)

Apoptosis proteins play an essential role in regulating a balance between cell proliferation and death. The successful prediction of subcellular localization of apoptosis proteins directly from primary sequence is much benefited to understand programmed cell death and drug discovery. In this paper, by use of Chou’s pseudo amino acid composition , a total of 317 apoptosis proteins are predicted by support vector machine . The jackknife cross-validation is applied to test predictive capability of proposed method. The predictive results show that (...) overall prediction accuracy is 91.1% which is higher than previous methods. Furthermore, another dataset containing 98 apoptosis proteins is examined by proposed method. The overall predicted successful rate is 92.9%. (shrink)

The inapplicability of variations on theory reduction in the context of genetics and their irrelevance to ongoing research has led to an anti-reductionist consensus in philosophy of biology. One response to this situation is to focus on forms of reductive explanation that better correspond to actual scientific reasoning (e.g. part–whole relations). Working from this perspective, we explore three different aspects (intrinsicality, fundamentality, and temporality) that arise from distinct facets of reductive explanation: composition and causation. Concentrating on these aspects generates (...) new forms of reductive explanation and conditions for their success or failure in biology and other sciences. This analysis is illustrated using the case of protein folding in molecular biology, which demonstrates its applicability and relevance, as well as illuminating the complexity of reductive reasoning in a specific biological context. (shrink)

What are the conditions under which one biological object is a part of another biological object? This paper answers this question by developing a general, systematic account of biological parthood. I specify two criteria for biological parthood. Substantial Spatial Inclusionrequires biological parts to be spatially located inside or in the region that the natural boundary of t he biological whole occupies. Compositional Relevance captures the fact that a biological part engages in a biological process that must make a necessary (...) contribution to a condition that is minimally sufficient to one or more of the characteristic behaviors of the biological whole. Instead of emphasizing the diversity of part-whole relations in the biological world, this paper asks what biological part-whole relations have in common and what constrains their existence, in general. After presenting the two criteria for biological parthood I discuss in how far my account can cope with hard cases (e.g., redundant parts) and I reveal the merits and limits of monism. (shrink)

How shall we understand apparently teleological systems? What explains their persistence and their plasticity? Here I argue that all seemingly goal-directed systems—e.g., a food-seeking organism, human-made devices like thermostats and torpedoes, biological development, human goal seeking, and the evolutionary process itself—share a common organization. Specifically, they consist of an entity that moves within a larger containing structure, one that directs its behavior in a general way without precisely determining it. If so, then teleology lies within the domain of the theory (...) of compositional hierarchies. (shrink)

German Idealism still dominates most approaches in theoretical biology. This has led to a conception of organisms as tightly regulated self-forming systems where the demands of the whole organism dominate how the parts are coordinated. This article troubles this approach by presenting aspects of biology that refuse to be synthesized into a specific whole. I call this approach “goth biology” as it recognizes the murkiness of systems of knowledge, the loosely composite nature of most living things, and (...) the continual haunting of life by death. Methodologically, I use insights gleaned from the history of post-punk goth music to explore the role of aesthetics, timbres, and forms as elements of lives that bound disparate times and spaces without providing a unified synthesis. A form of biological experience, and a theory of how the body works, goth biology demands that one lose a conception of “self” in order to embrace the complexity of biological interactions. As the goth performance artist Anna-Varney Cantodea recently confessed in an interview: “I have long given up on any goals I might have had,” but this doesn’t keep me from being inspired by everything around me. (shrink)

A mutation alters the hemoglobin in some members of a species of antelope, and as a result the members fare better at high altitudes than their conspecifics do; so high-altitude foraging areas become open to them that are closed to their conspecifics; they thrive, reproduce at a greater rate, and the gene for altered hemoglobin spreads further through the gene pool of the species. That sounds like a classic example (owed to Karen Neander, 1995) of a causal chain traced by (...) evolutionary biology. But a view now nearly universal among philosophers maintains that such biological causation is always shadowed, perhaps even rivaled, by causation on a different level.1 That the subgroup of antelopes forages in areas closed to the conspecifics is a state of affairs embodied or realized, notes this view, in certain movements and state changes done by certain physical microparticles—untold billions of microparticles and movements, but a finite and determinate (more on this below) collection nevertheless. That the subgroup reproduces at a greater rate is likewise realized by a huge collection of microparticle movements, a different collection. And the microparticle happenings comprised in the first collection are causally responsible, strictly in accordance with the laws of microphysics, for the microparticle happenings in the second. Biological causation is always shadowed, perhaps even rivaled, by causation on the level of microphysics. The view I mean is general: any case of causing uncovered by any of the special sciences can be recaptured at the level of microphysics. This view is I think what most philosophers mean by “physicalism”; in any case, “physicalism” is the label I shall use. Physicalism comes in two forms. Modest physicalism holds that any causal transaction reported by the special sciences can be retraced by microphysics.2 Hegemonic physicalism holds that retracing such a transaction at the level of.. (shrink)

With the advent of synthetic biology, scientists are increasingly relying on digital sequence information, instead of physical genetic resources. This article examines the potential impact of this shift on the access and benefit-sharing (ABS) regime of the Convention on Biological Diversity (CBD) and the Nagoya Protocol. These treaties require benefit-sharing with the owners of genetic resources. However, whether “genetic resources” include digital sequence information is unsettled. The CBD conceives genetic resources as genetic material containing functional units of heredity. “Material” (...) implies tangibility, and for some scholars, “functional units of heredity,” undefined in both treaties, mean full-coding sequences. This article argues that digital sequence information obtained from physical genetic resources, full-coding or not, should be treated as genetic resources. Literal construction of the CBD risks eroding its usefulness and the ABS regime. This is because through bioinformatics, sequence information can easily be obtained from genetic resources for utilization, without physically moving them or concluding ABS agreement with owners. The CBD must evolve with scientific progress also because sequence functionality depends on the state of knowledge. These arguments are vindicated by domestic ABS laws equating genetic information with genetic resources; Nagoya Protocol provisions deeming research exploiting the genetic composition of genetic resources as utilization of genetic resources; and CBD provisions requiring the sharing of benefits from the utilization of genetic resources. Moreover, treaty interpretation and case law demand that generic, scientific terms, such as “genetic resources” and “functional units of heredity” be interpreted in an evolutionary manner to capture scientific developments. (shrink)

Many biologists and philosophers have worried that importing models of reasoning from the physical sciences obscures our understanding of reasoning in the life sciences. In this paper we discuss one example that partially validates this concern: part-whole reductive explanations. Biology and physics tend to incorporate different models of temporality in part-whole reductive explanations. This results from differential emphases on compositional and causal facets of reductive explanations, which have not been distinguished reliably in prior philosophical analyses. Keeping these two (...) facets distinct facilitates the identifi cation of two further aspects of reductive explanation: intrinsicality and fundamentality. Our account provides resources for discriminating between different types of reductive explanation and suggests a new approach to comprehending similarities and differences in the explanatory reasoning found in biology and physics. (shrink)

A toy is a valuable medium for promoting parent-child interaction. This study selected six light-emitting or reflective materials to produce composite toy balls, and conducted tests on 15 families with preschool-aged high-functioning autistic children. Quantification method I analysis was employed in the study, and the experimental results indicated that the metal ball was the representative sample that elicited many smiles or laughs and much finger pointing as well as high levels of pleasure and activeness.; the mitball was the representative sample (...) that provoked much eye contact, produced satisfactory reactions to activities,; the quality of fluorescence enhanced the levels of pleasure and the reactions to the activity. We propose that dynamic and reflective materials can be adopted to divert the attention of children, and fluorescent toys can then employed to sustain parent-child interaction. (shrink)

‘When did I, a human person, begin to exist?’ In developing an answer to this question, I utilize a Thomistic framework, which holds that the human person is a composite of a biological organism and an intellective soul. Eric Olson and Norman Ford both argue that the beginning of an individual human biological organism occurs at the moment when implantation of the zygote in the uterus occurs and the ‘primitive streak’ begins to form. Prior to this point, there does not (...) exist an individual human organism, but a cluster of biological cells which has the potential to split and develop as one or more separate human organisms (identical twinning). Ensoulment (the instantiation of a human intellective soul in biological matter) does not occur until the point of implantation. This conception of the beginning of human personhood has moral implications concerning the status of pre‐implantation biological cell clusters. A new understanding of the beginning of human personhood entails a new understanding of the morality of certain medical procedures which have a direct affect on these cell clusters which contain human DNA. Such procedures discussed in this article are embryonic stem cell research, in vitro fertilization, procured abortion, and the use of abortifacient contraceptives. (shrink)

Polger and Shapiro argue that their official recipe, a criterion for judging when the phenomenon of multiple realization exists, renders MR less widespread than its proponents have assumed. I argue that, although Polger and Shapiro’s criterion is a useful contribution, they arrive at their conclusion too hastily. Contrary to Polger and Shapiro, I claim that the phenomenon of multiple realization in the biological world, judged by their criterion, is not as scarce as they suggest. To show this, an updated official (...) recipe, namely a multiple mechanistic realization thesis, integrating Polger and Shapiro’s criterion with a compositional conception of realization, is developed. Then, three examples of varied kinds are examined, showing that cases of MR are not so hard to find in the biological world. (shrink)

A mutation alters the hemoglobin in some members of a species of antelope, and as a result the members fare better at high altitudes than their conspecifics do; so high-altitude foraging areas become open to them that are closed to their conspecifics; they thrive, reproduce at a greater rate, and the gene for altered hemoglobin spreads further through the gene pool of the species. That sounds like a classic example (owed to Karen Neander, 1995) of a causal chain traced by (...) evolutionary biology. But a view now nearly universal among philosophers maintains that such biological causation is always shadowed, perhaps even rivaled, by causation on a different level.1 That the subgroup of antelopes forages in areas closed to the conspecifics is a state of affairs embodied or realized, notes this view, in certain movements and state changes done by certain physical microparticles—untold billions of microparticles and movements, but a finite and determinate (more on this below) collection nevertheless. That the subgroup reproduces at a greater rate is likewise realized by a huge collection of microparticle movements, a different collection. And the microparticle happenings comprised in the first collection are causally responsible, strictly in accordance with the laws of microphysics, for the microparticle happenings in the second. Biological causation is always shadowed, perhaps even rivaled, by causation on the level of microphysics. The view I mean is general: any case of causing uncovered by any of the special sciences can be recaptured at the level of microphysics. This view is I think what most philosophers mean by “physicalism”; in any case, “physicalism” is the label I shall use. Physicalism comes in two forms. Modest physicalism holds that any causal transaction reported by the special sciences can be retraced by microphysics.2 Hegemonic physicalism holds that retracing such a transaction at the level of.. (shrink)

This paper examines the efforts in evolution research to understand form’s structure that developed in Italy during the first half of the twentieth century. In particular, it analyzes how the organic approach in biology and the study of organic form merged in the morphological research agendas of Giuseppe Colosi and Giuseppe Levi. These biologists sought to understand form’s inner composition and structure. First, I will briefly outline the morphological practices and frameworks used to study form changes and structures in (...) the early twentieth century. Second, I will discuss what the Italian biologist Antonio Pensa called the morphological problem. Third, I will examine Colosi’s response to the morphological problem. Fourth, I will analyze Levi’s morphological research program. As a result, this paper paves the way for a more nuanced and varied picture of the so-called “organicism movement” in the first half of the twentieth century by calling attention to morphology as practiced in Italian-speaking biology. In fact, alongside dialectical materialism and holistic biology, two of the main strands within organicism, the architectural approach to evolution as practiced in Italy and elsewhere had a profound impact on twentieth- and twenty-first-century organicism specifically and on evolutionary biology generally. (shrink)

Recently developed super‐resolution microscopy techniques are changing our understanding of lipid rafts and membrane organisation in general. The lipid raft hypothesis postulates that cholesterol can drive the formation of ordered domains within the plasma membrane of cells, which may serve as platforms for cell signalling and membrane trafficking. There is now a wealth of evidence for these domains. However, their study has hitherto been hampered by the resolution limit of optical microscopy, making the definition of their properties problematic and contentious. (...) New microscopy techniques circumvent the resolution limit and, for the first time, allow the fluorescence imaging of structures on length scales below 200 nm. This review describes such techniques, particularly as applied to the study of membrane organisation, synthesising newly emerging facets of lipid raft biology into a state‐of‐the art model.Editor's suggested further reading in BioEssays: Super‐resolution imaging prompts re‐thinking of cell biology mechanisms Abstract and Quantitative analysis of photoactivated localization microscopy (PALM) datasets using pair‐correlation analysis Abstract. (shrink)

The diversity of bone proteoglycan (PG) structure and localisation (pericellular, extracellular in the organic bone matrix) reflects a broad spectrum of biological functions within a unique tissue. PGs play important roles in organizing the bone extracellular matrix, taking part in the structuring of the tissue itself as active regulators of collagen fibrillogenesis. PGs also display selective patterns of reactivity with several constituents including cytokines and growth factors, such as transforming growth factor‐β or osteoprotegerin thereby modulating their bio‐availability and biological activity (...) in the bone tissue. In this review, the complex PG composition in bone will be addressed together with the specific role played by PGs (or their GAGs chains) in bone biology, as regulatory molecules for bone resorption and their involvement in bone tumor development. These roles have been determined after modulation of PG expression or mutations in their corresponding genes, which revealed specific roles for these compounds in bone pathologies (e.g. perlecan or glypican‐3 mutations observed respectively in chondrodysplasia or dysmorphic syndrome). Finally, the potential therapeutic interest of PGs is discussed based on recent data, more particularly on bone tumor‐associated osteolysis as these molecules are involved both in bone resorption and tumor development. BioEssays 29:758–771, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

The ArgumentRecognizing that social Darwinism is an intrinsically varied and composite concept, this essay advocates an approach delineating the various intellectual constituents and sociopolitical contexts. It is argued that German social Darwinism has often had a sophisticated biological content, and that the prevalent notion of the state as a biological organism has drawn on non-Darwinian biological theories. Different social interests and programs, institutional structures, and professional interests have also to be taken into account. Alternative interpretations stressing Nazi vulgarizations of (...) class='Hi'>biology have serious historical flaws. The paper considers the position of the historian Richard J. Evans, who has rejected interpretations of social Darwinism as scientific and medical discourse. While Evans stresses social Darwinism as public rhetoric, I suggest that social-Darwinist ideas have provided rationales for welfare policies and have had institutional, professional, and ideological implications. What occurred in crucial sectors of the emergent German “welfare state” was a shift from the legally trained administrators to specialists in such areas as public health and social work, who frequently looked to biology to legitimate policy. (shrink)

Context: Maturana’s work is not easy to follow. Correct and full understanding of his work has still to be achieved in spite of its importance. Problem: The objective of this paper is to investigate the core logic penetrating Maturana’s wide-ranging work and to place his work in the history of western thought. Method: Through intensive reading of his wide-ranging work, I intended to grasp the core biological structure that he advocates, namely, his core logic. Results: Maturana’s biology is the (...) biology of structural determinism. It is embodied in a composite entity called a “structure-determined system” with two non-intersecting domains - the domain of interactions and the domain of the composition of components – which can be called the core structure or the core logic of his biology. From the perspective of the history of western thought, Aristotle and Schopenhauer can be regarded as good candidates as the precursors of Maturana’s work, and his work can be characterized as an advanced form of Aristotle’s hylomorphism, depicted on the horizon of Schopenhauer’s world of “Vorstellung” (bringing-forth). Implications: This finding will be useful for understanding Maturana’s wide-ranging work and its place in the history of western thought. (shrink)

We demonstrate how different normalization techniques in GC‐MS analysis impart unique properties to the data, influencing any biological inference. Using simulations, and empirical data, we compare the most commonly used techniques (Total Sum Normalization ‘TSN’; Median Normalization ‘MN’; Probabilistic Quotient Normalization ‘PQN’; Internal Standard Normalization ‘ISN’; External Standard Normalization ‘ESN’; and a compositional data approach ‘CODA’). When differences between biological classes are pronounced, ESN and ISN provides good results, but are less reliable for more subtly differentiated groups. MN, TSN, (...) and CODA approaches produced variable results dependent on the structure of the data, and are prone to false positive biomarker identification. In contrast, PQN exhibits the lowest false positive rate, though with occasionally poor model performance. Because ESN requires extensive pre‐planning, and offers only mixed reliability, and ISN, TSN, MN, and CODA approaches are prone to introducing artefactual differences, we recommend the use of PQN in GC–MS research. (shrink)

Sponges branch basally in the metazoan phylogenetic tree and are believed to be composed of four distinct lineages with still uncertain relationships. Indeed, some molecular studies propose that Homoscleromorpha may be a fourth Sponge lineage, distinct from Demospongiae in which they were traditionally classified. They harbour many features that distinguish them from other sponges and are more evocative of those of the eumetazoans. They are notably the only sponges to possess a basement membrane with collagen IV and specialized cell‐junctions, thus (...) possessing true epithelia. Among Homoscleromorphs, we have chosen Oscarella lobularis as a model species. This common and easily accessible sponge is characterized by relatively simple histology and cell composition, absence of skeleton, and strongly pronounced epithelial structure. In this review, we explore the specific features that make O. lobularis a promising homoscleromorph sponge model for evolutionary and developmental researches. (shrink)

The complexity and variation of sound emission by members of the animal kingdom, primarily produced by the orders Passeriformes (songbirds), Cetacea (whales), but also reported in species belonging to the Exopterygota (insects) and Carnivora (mammals), has attracted human attention since the Middle Ages, where birds’ calls were used in compositions of that time. However, the focus of this paper will be on sound productions of birds and whales, as recent scientific and musicological research concentrates on these two animals.

The paper outlines the contours of an organizational perspective on extended inheritance. Based on theoretical studies about biological organization and extended physiology, this perspective allows for the conception of extended biological legacies while keeping a theoretically indispensable distinction between biological systems and their environment. In this context, the line of demarcation between these systems and their surroundings is modelled on an organizational criterion and on the related conceptual distinction between organizational constraints, whose specific role is to harness flows of matter (...) and energy across generations of composite biological systems, and resources exploited by those systems. Biological legacies are restricted to persisting constitutive elements responsible for the reoccurrence of organizational constraints in a given environment. The case of symbiotic transmission is presented as a paradigmatic system illustrating the main proposed conceptual clarifications. (shrink)