Online research in philosophy

The distinction between phenotype and genotype is fundamental to the understanding of heredity and development of organisms. The genotype of an organism is the class to which that organism belongs as determined by the description of the actual physical material made up of DNA that was passed to the organism by its parents at the organism's conception. For sexually reproducing organisms that physical material consists of the DNA contributed to the fertilized egg by the sperm and egg of its two parents. For asexually reproducing organisms, for example bacteria, the inherited material is a direct copy of the DNA of its parent. The phenotype of an organism is the class to which that organism belongs as determined by the description of the physical and behavioral characteristics of the organism, for example its size and shape, its metabolic activities and its pattern of movement.

In this paper we argue that an operational organism concept can help to overcome the structural deficiency of mathematical models in biology. In our opinion, the structural deficiency of mathematical models lies mainly in our inability to identify functionally relevant biological characters in biological systems, and not so much in a lack of adequate mathematical representations of biological processes. We argue that the problem of character identification in biological systems is linked to the question of a properly formulated organism concept. Lastly, we demonstrate how a decomposition of an organism into independent characters in the context of a specific biological process--such as adaptation by means of natural selection--depends on the dynamical properties and invariance conditions of the equations that describe this process.

What are you and I essentially? When do you and I come into and go out of existence? A common response is that we are essentially organisms, that is, we come into existence as organisms and go out of existence when we cease to be organisms. Jeff McMahan has put forward two arguments against the Organism View: the case of dicephalus and a special case of hemispheric commissurotomy. In this paper, I defend the Organism View against these two cases. Because it is possible to devise more McMahanian-type cases, I also provide a more general solution to these kinds of cases.

The phrase ‘synthetic biology’ is used to describe a set of different scientific and technological disciplines, which share the objective to design and produce new life forms. This essay addresses the following questions: What conception of life stands behind this ambitious objective? In what relation does this conception of life stand to that of traditional biology and biotechnology? And, could such a conception of life raise ethical concerns? Three different observations that provide useful indications for the conception of life in synthetic biology will be discussed in detail: 1. Synthetic biologists focus on different features of living organisms in order to design new life forms, 2. Synthetic biologists want to contribute to the understanding of life, and 3. Synthetic biologists want to modify life through a rational design, which implies the notions of utilising, minimising/optimising, varying and overcoming life. These observations indicate a tight connection between science and technology, a focus on selected aspects of life, a production-oriented approach to life, and a design-oriented understanding of life. It will be argued that through this conception of life synthetic biologists present life in a different light. This conception of life will be illustrated by the metaphor of a toolbox. According to the notion of life as a toolbox, the different features of living organisms are perceived as various rationally designed instruments that can be used for the production of the living organism itself or secondary products made by the organism. According to certain ethical positions this conception of life might raise ethical concerns related to the status of the organism, the motives of the scientists and the role of technology in our society.

Well prior to the invention of the term ‘biology’ in the early 1800s by Lamarck and Treviranus, and also prior to the appearance of terms such as ‘organism’ under the pen of Leibniz in the early 1700s, the question of ‘Life’, that is, the status of living organisms within the broader physico-mechanical universe, agitated different corners of the European intellectual scene. From modern Epicureanism to medical Newtonianism, from Stahlian animism to the discourse on the ‘animal economy’ in vitalist medicine, models of living being were constructed in opposition to ‘merely anatomical’, structural, mechanical models. It is therefore curious to turn to the ‘passion play’ of the Scientific Revolution – whether in its early, canonical definitions or its more recent, hybridized, reconstructed and expanded versions: from Koyré to Biagioli, from Merton to Shapin – and find there a conspicuous absence of worry over what status to grant living beings in a newly physicalized universe. Neither Harvey, nor Boyle, nor Locke (to name some likely candidates, the latter having studied with Willis and collaborated with Sydenham) ever ask what makes organisms unique, or conversely, what does not. In this paper I seek to establish how ‘Life’ became a source of contention in early modern thought, and how the Scientific Revolution missed the controversy.

According to Aristotelian essentialism, the nature of an organism is constituted of a particular goal-directed disposition to produce an organism typical of its kind. This paper argues—against the prevailing orthodoxy—that essentialism of this sort is indispensable to evolutionary biology. The most powerful anti-essentialist arguments purport to show that the natures of organisms play no explanatory role in modern synthesis biology. I argue that recent evolutionary developmental biology provides compelling evidence to the contrary. Developmental biology shows that one must appeal to the capacities of organisms to explain what makes adaptive evolution adaptive. Moreover, the specific capacities in question are precisely those that, according to Aristotle, constitute the nature of an organism. Essentialism 1.1 Aristotelian biological kinds Evolutionary anti-essentialism 2.1 Taxonomic anti-essentialism 2.2 Explanatory anti-essentialism Adaptation 3.1 Stability 3.2 Mutability 3.3 Phenotypic plasticity and adaptive evolution The natures of organisms Conclusion.

Developmental biology has resurfaced in recent years, often without a clearly central role for the organism. The organism is pulled in divergent directions: on the one hand, there is an important body of work that emphasizes the role of the gene in development, as executing and controlling embryological change; on the other hand, there are more theoretical approaches under which the organism disappears as little more than an instance for testing biological generalizations. I press here for the ineliminability of the organism in developmental biology on explanatory grounds. I examine classical work concerned with growth and development, particularly in Drosophila and C. elegans. Some of this work is suggestive of modular development, and accordingly suggests a level below that of the organism as being explanatory. These are not the only type of case. There are other equally well-established results, which indicate greater integration in the developing organism. Though with a modular organization the organism can be thought of as made up of its constituent traits, and though the explanations of these traits may lie in terms of cells or genes, even with modular development the explanations of "genetic" differences require an appeal to the organism. With non-modular organization the organism has an even more central role. This does not mean that these genetic or cellular contributions are unreal in any way, or that development requires some sort of vitalistic contribution; but the genetic contributions make sense only as constituents of the organism, embedded in a larger organic context.

Vere Chappell has pointed out that it is not clear whether Locke has a well-developed ontology or even whether he is entitled to have one.2 Nevertheless, it is clear that Locke believes that there are organisms, and it is clear that he thinks that there are substances. But does he believe that organisms are substances? There are certainly parts of the Essay in which Locke seems unequivocally to state that organisms are substances. For instance, in 2.23.3 Locke uses men and horses as examples of substances. In Locke’s most explicit the account of abstraction, given in 3.3.7-9, organism [vivens] is treated as a sub-species of body and body as a sub-species of substance; so, by transitivity, organism is a kind of substance. Finally, in his discussion of essences in 3.6, Locke uses all of the following organisms as examples of substances: horses, mules, men, sheep, goats, plants, drills, changelings, asses, bulls, cats, and rats. This textual evidence would seem to settle the matter about the ontological status of organisms. However, there are other parts of the Essay in which the ontological status of organisms is less clear, to say the least. In fact, there are texts in which Locke seems to state (or at least to be committed to the..

Despite the radical importance of embryology in the development of organi- cism, developmental biology remains philosophically underexplored as a theoretical and empirical resource to clarify the nature of organisms. This paper discusses how embryology can help develop the organisational definition of the organism as a differentiated, function- ally integrated, and autonomous system. I distinguish two conceptions of development in the organisational tradition that yield two different conceptions of the organism: the life- history view claims that organisms can be considered as such during their whole ontogeny; the constitutive view distinguishes two periods in the life history, a period of generation and a period of self-maintenance of a constitutive organisation. Arguing in favour of the con- stitutive view, it will be claimed that the organisational criteria for the definition of organ- ism (i.e., differentiation, functional integration, and autonomy) can only be applied to the developmental system when it has entered the period of self-maintenance of a constitutive organisation. under the light of current research in developmental biology, it is possible to make explicit how organisms come to be as organisms. To this end, I explore key onto- genetic events that help us clarify the core aspects of animal organisation and allow us to identify the developmental stage that marks the ontological transition between an organism in potency and an organism in actuality. The structure of this ontogenetic unfolding paral- lels the conceptual structure of the very notion of organism; the generation of the being of a particular organism parallels its definition.

Biology lacks a central organism concept that unambiguously marks the distinction between organism and non-organism because the most important questions about organisms do not depend on this concept. I argue that the two main ways to discover useful biological generalizations about multicellular organization--the study of homology within multicellular lineages and of convergent evolution across lineages in which multicellularity has been independently established--do not require what would have to be a stipulative sharpening of an organism concept.