Control of DNA supercoiling by the free-energy of hydrolysis of ATP that involves gene expression is analyzed in terms of three levels of unconnected metabolic pathways. These are synthesis and breakdown of topoisomerase mRNAs, synthesis and breakdown of topoisomerase proteins and supercoiling and relaxation of DNA. The so-called square-matrix method previously developed for the control of metabolic pathways, is extended to deal with this hierarchical control system. It turns out that also in this case, the matrix of control coefficients is (...) equal to the inverse of the so-called elasticity matrix, which contains all relevant elasticity coefficients as well as information about the structure and connectedness of the pathways involved. For a simpler case of a hierarchy of two systems, we demonstrate that the explicit matrix inversion method may be replaced by an implicit method in which the regulatory effects that run through the other level are described by an additional elasticy coefficient which may then be treated as if local. (shrink)

The concepts of regulation and homeostasis are of frequent use but lack a single universally accepted definition. Here we propose a definition of theregulatory strength andhomeostatic strength, which allow to assess the importance of a regulatory pathway in a quantitative fashion.

We will show that there is a strong form of emergence in cell biology. Beginning with C.D. Broad’s classic discussion of emergence, we distinguish two conditions sufficient for emergence. Emergence in biology must be compatible with the thought that all explanations of systemic properties are mechanistic explanations and with their sufficiency. Explanations of systemic properties are always in terms of the properties of the parts within the system. Nonetheless, systemic properties can still be emergent. If the properties of the components (...) within the system cannot be predicted, even in principle, from the behavior of the system’s parts within simpler wholes then there also will be systemic properties which cannot be predicted, even in principle, on basis of the behavior of these parts. We show in an explicit case study drawn from molecular cell physiology that biochemical networks display this kind of emergence, even though they deploy only mechanistic explanations. This illustrates emergence and its place in nature. (shrink)

Systems biology is a vigorous and expanding discipline, in many ways a successor to genomics and perhaps unprecendented in its combination of biology with a ...

Biochemistry and molecular biology have been focusing on the structural, catalytic, and regulatory proper- ties of individual macromolecules from the perspective of clarifying the mechanisms of metabolism and gene expression. Complete genomes of ‘primitive’ living organisms seem to be substantially larger than necessary for metabolism and gene expression alone. This is in line with the findings of silent phenotypes for supposedly important genes, apparent redundancy of functions, and variegated networks of signal transduction and transcription factors. Here we propose that evolutionary (...) optimization has been much more intensive than to lead to the bare minima necessary for autonomous life. Much more complex organisms prevail. Much of this complexity arises in the nonlinear interactions between cellular macromolecules and in subtle differences between paralogs (isoenzymes). The complexity can only be understood when analyzed quantitatively, for which quantitative experimentation is needed in living systems that are as simple and manipulatable as possible, yet complex in the above sense. We illustrate this for the glutamine synthetase cascade in Escherichia coli. By reviewing recent molecular findings, we show that this cascade is much more complex than necessary for simple regulation of ammonia assimilation. Simulations suggest that the function of this complexity may lie in quasi-intelligent behavior, including conditioning and learning. (shrink)

This paper is a report of a pilot study of how candidates argue when they are running for political office. The election studied was the provincial election in Ontario, Canada, in the fall of 2011. Having collected about 250 arguments given during the election from newspaper media, we sought answers to the following questions, among others: which argumentation schemes have the greatest currency in political elections? Is a list of the best known argumentation schemes sufficient to classify the arguments given (...) in elections? What schemes should be added to the familiar list to make it more adequate for studying elections? Is it useful to classify arguments as being used for positive, policy-critical, person-critical and defensive purposes? Can political parties be usefully characterized by noting their preferred kinds of arguments and their most frequent uses of arguments? What lessons can be learned from this study to better design future studies of the same kind? (shrink)

This presentation seeks to understand informal logic as a set of methods for the logical evaluation of natural language arguments. Some of the methods identified are the fallacies method, deductivism, warrantism and argument schemes. A framework for comparing the adequacy of the methods is outlined consisting of the following categories: learner- and user-efficiency, subjective and objective reliability, and scope. Within this framework, it is also possible to compare informal and formal logic.

Abstract Much has been written about the socio-cultural functions of religion. It is equally important to discuss the role and impact of religion and ethics on development and promoting reform in civil society. In today's South Asian context it is necessary to analyse religion both as a tradition and a representation of modernity. Otherwise it is difficult to clearly understand not only the relationship of domination-subordination, together with processes of exclusions and violence prevalent in the sub-continent but also the emerging (...) perspectives, lineages and languages of sociology in general and religion in particular. An attempt is made in this paper to examine the relationship and to evaluate the processes in the evolving discourse of sociology. It also analyses the 'moral' as embedded in religion and as an autonomous category emerging with secularisation. The subtleties of rights and righteousness in the method and metamorphosis of development are also dealt with in this paper. -/- . (shrink)

Richard Whately’s views of arguments involving authority are very different in his Elements of Rhetoric and his Elements of Logic. This essay begins by documenting these differences and wondering why they are. It then proceeds to take a broader and more historical view of Whately’s discussions of authority and finds him occupying an important developmental ground between his predecessor Locke and contemporary views of the argument from authority. In fact, some of the things we now think are important in a (...) good argument from authority are anticipated by Whately. (shrink)

This bibliography of literature on the fallacies is intended to be a resource for argumentation theorists. It incorporates and sup- plements the material in the bibliography in Hansen and Pinto’s Fallacies: Classical and Contemporary Readings, and now includes over 550 entries. The bibliography is here present- ed in electronic form which gives the researcher the advantage of being able to do a search by any word or phrase of interest.

I begin by looking at passages in Mill's System of Logic that circumscribe the range of logic as he understood the subject. His logic is clearly too narrow to be the arbiter of the extended arguments presented in his Utilitarianism, On Liberty, and The Subjection of Women. Looking at Mill's argumentative practice in those works we see that he is noticeably concerned to deal with objections, more so even than in giving arguments for his position. His practice is shown to (...) be consistent with his professed views about how opinions outside science and mathematics are to be justified. These views are stated primarily in On Liberty where Mill gives a standard of justification and proclaims the importance of dealing with objections as part of that standard. Given Mill's characterization of an art, or practice - also found in the Logic - it turns out that a case can be made that Mill's views on argumentation fit the criteria for an art, pretty much on a par with ethics as an art. In the sense that I give to 'argumentation theory' it seems entirely appropriate to say that implicitly Mill held a theory of argumentation, a theory distinct from other proposed theories of argumentation, and a theory worth further study and development. (shrink)

This appearance condition of fallacies refers to the phenomenon of weak arguments, or moves in argumentation, appearing to be okay when really they aren’t. Not all theorists agree that the appearance condition should be part of the conception of fallacies but this essay explores some of the consequences of including it. In particular, the differences between committing a fallacy, causing a fallacy and observing a fallacy are identified. The remainder of the paper is given over to discussing possible causes of (...) mistakenly perceiving weak argumentation moves as okay. Among these are argument caused misperception, perspective caused misperception, discursive environment caused misperception and perceiver caused misperception. The discussion aims to be sufficiently general so that it can accommodate different models and standards of argumentation that make a place for fallacies. (shrink)

This short essay is an introduction to the essays included in this special issue of Argumentation devoted to fallacies.

This essay studies an argumentative practice in eighteenth-century France by exploring the persuasiveness of some petitions to obtain printer licences. Those who wanted to enter the printing business in eighteenth-century France had to obtain licences from the King to do so. The French government had established limits to the number of printers it would permit to operate in the realm; hence, there was competition for any vacancy that became open. Thus, the context is that of trained printers in provincial towns, (...) most of them with their own printing equipment, applying to the government in Paris for the highly valued licences to run printing businesses. We examine a small number of the original petitions and give an account of their persuasive capacity by (a) noticing the narrative character of the letters and (b) distinguishing between propositional and affective attitudes. Our view is that a reconstruction of the petitions as reasonable persuasive discourse is possible when it is noticed how the two kinds of attitudes can be combined to promote the same end. (shrink)

In a recent paper, “One Logician’s Perspective on Argumentation”, van Benthem expressed his reservations on Toulmin’s diagnosis and abandonment of formal logic, and argued that Toulmin was wrong for leading the study of argumentation apart from formal approach. In this paper we will try to reveal two se-rious misunderstandings of Toulmin’s ideas in his discussions, and thereby make an apology for Toulmin.

The biological sciences study (bio)complex living systems. Research directed at the mechanistic explanation of the "live" state truly requires a pluralist research program, i.e. BioComplexity research. The program should apply multiple intra-level and inter-level theories and methodologies. We substantiate this thesis with analysis of BioComplexity: metabolic and modular control analysis of metabolic pathways, emergence of oscillations, and the analysis of the functioning of glycolysis.

What I will aim for in answering the title question is extensional adequacy, that is, I will try to formulate an account that captures as much of the extension as possible of what we ordinarily think counts as a portrait. Two philosophers have recently and independently from one another embarked on the same project. Cynthia Freeland’s theory of portraiture, as it is developed in her book, Portraits and Persons, is discussed in Sections 1 and 2 of this paper. Sections 3 (...) and 4 offer a critical exploration of Paolo Spinicci’s phenomenological study of portraiture. Finally, in Sections 5 and 6, I present an alternative account of portraiture, one that will hopefully address all the objections raised against the two competing theories. (shrink)

activity” has been considered to play a major role in the short-term maintenance of memories. Many studies since then have provided support for this view and greatly advanced our knowledge of the effects of stimulus type and modality on delay activity and its temporal dynamics. In humans, working memory has also been a subject of intense investigation using scalp and intracranial electroencephalography as well as magnetoencephalography, which provide estimates of local population activity. The published findings include reports of systematic changes (...) in signal amplitude during working memory in the theta, alpha, beta. (shrink)

We comment on the proposition “that lower temperatures and especially greater seasonal variation in temperature call for individuals and societies to adopt … a greater degree of self-control” (Van Lange et al., sect. 3, para. 4) for which we cannot find empirical support in a large data set with data-driven analyses. After providing greater nuance in our theoretical review, we suggest that Van Lange et al. revisit their model with an eye toward the social determinants of self-control.