The progress of the molecular biosciences has been so enormous that a discipline studying how cellular functioning emerges out of the behaviors of their molecular constituents has become reality. Systems biology studies cells as spatiotemporal networks of interacting molecules using an integrative approach of theory , experimental biology , and quantitative network-wide analytical measurement . Its aim is to understand how molecules jointly bring about life. Systems biology is rapidly discovering principles governing the functioning of molecular networks and methods to (...) model and measure them. The application of the conceptual strength of systems sciences such as physics and engineering are opening up new ways of experimentally studying the design and functioning of molecular networks. Typically, in such studies models are used to highlight principles, design experiments, or to act in a predictive mode to specifically modify cellular behavior. In this trend article, theoretical approaches being applied in systems biology will be discussed. A number of books have recently appeared that deal with theoretical aspects of systems biology. In this article they are highlighted to facilitate the communication of systems biology to a broader audience. (shrink)

Microbial systems biology has made enormous advances in relating microbial physiology to the underlying biochemistry and molecular biology. By meticulously studying model microorganisms, in particular Escherichia coli and Saccharomyces cerevisiae, increasingly comprehensive computational models predict metabolic fluxes, protein expression, and growth. The modeling rationale is that cells are constrained by a limited pool of resources that they allocate optimally to maximize fitness. As a consequence, the expression of particular proteins is at the expense of others, causing trade‐offs between cellular objectives (...) such as instantaneous growth, stress tolerance, and capacity to adapt to new environments. While current computational models are remarkably predictive for E. coli and S. cerevisiae when grown in laboratory environments, this may not hold for other growth conditions and other microorganisms. In this contribution, we therefore discuss the relationship between the instantaneous growth rate, limited resources, and long‐term fitness. We discuss uses and limitations of current computational models, in particular for rapidly changing and adverse environments, and propose to classify microbial growth strategies based on Grimes's CSR framework. (shrink)

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)

Mechanistic models in molecular systems biology are generally mathematical models of the action of networks of biochemical reactions, involving metabolism, signal transduction, and/or gene expression. They can be either simulated numerically or analyzed analytically. Systems biology integrates quantitative molecular data acquisition with mathematical models to design new experiments, discriminate between alternative mechanisms and explain the molecular basis of cellular properties. At the heart of this approach are mechanistic models of molecular networks. We focus on the articulation and development of mechanistic (...) models, identifying five constraints which guide the articulation of models in molecular systems biology. These constraints are not independent of one another, with the result that modeling becomes an iterative process. We illustrate the use of these constraints in the modeling of the mechanism for bistability in the lac operon. (shrink)

After more than a century of research on glycolysis, we have detailed descriptions of its molecular organization, but despite this wealth of knowledge, linking the enzyme properties to metabolic pathway behavior remains challenging. These challenges arise from multi‐layered regulation and the context and time dependence of component functions. However, when viewed as a system that functions according to the principles of supply and demand, a simplifying theoretical framework can be applied to study its regulation logic and to assess the coherence (...) of experimental interpretations. These principles are universally applicable, as they emphasize the common metabolic tasks of glycolysis: the provision of free‐energy carriers, and precursors for biosynthesis and stress‐related compounds. Here we will review the regulation of multi‐tasking by glycolysis and consider how an understanding of this central metabolic pathway can be pursued using general principles, rather than focusing on the biochemical details of constituent components. (shrink)

"You will learn powerful exercises and techniques that are simple to do and immediately effective, helping you quiet emotional upsets in seconds, remove physical pain in yourself and others in minutes, lay the foundation for a perfect relationship, remove the anxiety and frustration of financial difficulties, and much, much more"-- Back cover.

For years people have been waiting for a book that merges the abstract Eastern philosophy of inner peace with the scientific applications of quantum physics. Well, that book has finally arrived! The Secret of Quantum Living is a straightforward guide that offers profound spiritual insights and a practical, easy-to-apply process for healing and harmonious living. Join Dr. Frank Kinslow on a journey to deep inner peace through what quantum physics calls the "implicate order." Within the pages of this powerful (...) book, you will learn Dr. Kinslow's process of Quantum Entrainment® (QE) and discover how to enrich and enliven all areas of your life. You'll be able to resolve problems or challenges you face by applying QE to your finances, your relationships, your sex life . . . and even your eating, sleeping, and exercising habits. You will also uncover ways to dissolve anger issues, negative thinking, physical pain, and emotional discord. And the great news is that anyone can practice QE! It doesn't require previous training, and it's so simple that a child can do it. The Secret of Quantum Living is fun to read and exciting to apply. You'll begin seeing results from your very first session. Give it a try . . . you'll be surprised how quickly the process works for you! (shrink)

Who am I? -- How to see with new eyes -- How the mind works -- How time works -- Self-awareness -- How to fix the future -- Your problems are not the problem -- How to overcome happiness -- Memory is not intelligent -- Fixing a broken mind -- Overcoming psychological pain -- Overcoming physical pain -- The perfect relationship -- How to not-know -- When you become enlightened.

Global justice is one of the most important subjects in law and political theory today. What principles of justice might tell us about the actual practices of the WTO and other international economic institutions is of vital importance to states and their citizens. This volume reflects the results of a symposium held at Tillar House, the ASIL headquarters in Washington, DC, in November 2008 which brought together philosophers, legal scholars, and economists to discuss the problems of understanding international economic law (...) from the standpoint of rights, justice, and economic efficiency. The book makes advances in developing the normative criterion for ecaluation and justifying the international economic legal order. (shrink)

This paper argues that God may create and exist in any possible world, no matter how much suffering of any sort that world includes. It combines the traditional free will defence with the notion of an ‘occasion’ for good or evil action and limits God's responsibility to the creation of these occasions. Since no possible world contains occasions for more evil than good action, God is morally permitted to create any possible world. With regard to suffering that is not due (...) to free will, namely the suffering of beings who are not moral agents, the paper questions the idea that the relief of such suffering is a moral perfection. (shrink)

In what follows I argue for two interrelated theses: that early Buddhism is not a form of empiricism, and that consequently there is no basis for an early Buddhist apologetic which contrasts an empirical early Buddhism with either a metaphysical Hinduism on the one hand, or with a baseless Christianity on the other.

I present an outline of the Omega Point theory, which is a model for an omnipresent, omniscient, omnipotent, evolving, personal God who is both transcendent to spacetime and immanent in it, and who exists necessarily. The model is a falsifiable physical theory, deriving its key concepts not from any religious tradition but from modern physical cosmology and computer science; from scientific materialism rather than revelation. Four testable predictions of the model are given. The theory assumes that thinking is a purely (...) physical process of the brain, and that personality dies with the brain. Nevertheless, I show that the Omega Point theory suggests a future universal resurrection of the dead very similar to the one predicted in the Judeo‐Christian‐Islamic tradition. The notions of “grace” and the “beatific vision” appear naturally in the model. (shrink)

“Dissecting Bioethics,” edited by Tuija Takala and Matti Häyry, welcomes contributions on the conceptual and theoretical dimensions of bioethics.The section is dedicated to the idea that words defined by bioethicists and others should not be allowed to imprison people's actual concerns, emotions, and thoughts. Papers that expose the many meanings of a concept, describe the different readings of a moral doctrine, or provide an alternative angle to seemingly self-evident issues are therefore particularly appreciated.The themes covered in the section so far (...) include dignity, naturalness, public interest, community, disability, autonomy, parity of reasoning, symbolic appeals, and toleration. (shrink)

The emerging new multidisciplinary and crosscultural field of bioethics will require sen sitive, open-minded professionals to take the lead in hospital ethics, in genetic coun selling, and in the teaching of bioethics to students in nursing, medicine and the basic sciences. Nurses with ward experience who return to university to gain an MA or PhD in bioethics are eminently suited for this leadership role, for they may be more likely than physicians to study for a liberal education to supplement their (...) professional know ledge ; their first-hand experience in nursing is an antidote to the pointless subtleties into which philosophical ethics so often degenerates. When teaching ethics to nurses one must remember that, while some will simply use this knowledge in their own clinical work, others will go on to be teachers and researchers in bioethics. Their training must therefore be broad and interdisciplinary, including real substantive philosophy (as opposed to philosophical ethics), as well as mystical bioethics, religious law, ethics of genetic counselling, clinical approaches to ethical pseudo prob lems, research skills, etc. (shrink)

This paper argues that God may create and exist in any possible world, no matter how much suffering of any sort that world includes. It combines the traditional free will defence with the notion of an 'occasion' for good or evil action and limits God's responsibility to the creation of these occasions. Since no possible world contains occasions for more evil than good action, God is morally permitted to create any possible world. With regard to suffering that is not due (...) to free will, namely the suffering of beings who are not moral agents, the paper questions the idea that the relief of such suffering is a moral perfection. (shrink)

Chapter 4 MIND AND REBIRTH I The argument of the first three chapters is essentially that the study of early Buddhism is neither methodologically, logically, nor emotively flawed. These chapters argue for the rationality of.

Why was it that, with belief in the old gods discredited and scepticism spreading widely, Stoic ideals attracted the attention and ultimately won the adhesion of the most thoughtful Romans?Mr. Moellering traces this, first, to Stoicism's appeal to the Roman religious sense, and, secondly, to the Roman character itself. Aeneas, he believes, is the very embodiment of Roman Stoicism.

In lieu of an abstract, here is a brief excerpt of the content:Hume Against Spinoza and Aristotle1 Frank J. Leavitt It is always good to try to make peace, to try to resolve differences between whatsomebelieveare conflictingpoints ofview. Nevertheless, sometimes the points ofview which are believed to be opposed to each other really do oppose one another and so the most ingenious attempts at reconciliation turn out to have been ill-conceived. Wim Klever has brought considerable scholarship to bear in (...) his attempt to show that Hume and Spinoza were not so far apart as we thought.2 It was an especially pleasant surprise to see the comparison of their views on personal identity,3 for example. And he has made a convincing case for doubt that Hume's "sharp anti-Spinözistic utterings"4 in Treatise 1.4.5 were really sincere. In my opinion, however, Klever has gone too farin trying to bring together what should have been left asunder. Some ofhis points ofthe purportedly common ground shared by Hume and Spinoza are based on what I believe to be a blatant misreading ofSpinoza. Other points show a failure to appreciate a fundamental disagreement between Hume and Spinoza on central issues in the old Aristotelian tradition. Hume and Spinoza, like other philosophersofthe seventeenth and eighteenth centuries, can be best understood when one is aware ofthe Aristotelian background against which they were writing and with which they expected their readers to be familiar. Hume shows familiarity with Aristotelianism in his discussion of the "antient philosophy" at Treatise 1.4.3 as well as in his various remarks about scholasticism.6Spinoza'srelationshipto ChristianAristotelianism has been discussed by Wolfson6 and by myself,7 among others. And his relationship to Maimonides, who was his link to Jewish Aristotelianism, has been discussed by Harvey.8 1 shall base my claim that Hume and Spinoza were much further apart than Klever makes them out to be upon an attempt to identify some scholastic and Aristotelian issues and doctrines with respect to which Hume and Spinoza took very different stands. The firstthing which I wanttodraw attention toisKlever'sreading ofthe scholia to 2 Ethics 40, which bears on medieval disputes over the nominalistic, conceptualistic and realistic approaches to Aristotle's treatment of the problem of the universels. Since Spinoza allows that universal notions "are notformed by all men in the same way,"9 Klever Volume XVII Number 2 203 FRANK J. LEAVITT makes him out to be holding the same position which Hume expresses when he adopts Berkeley's opinion that "all general ideas are nothing but particular ones, annexed to a certain term" (T 17). And Klever claims "Hume and Spinoza are both thorough nominalists."10 But Klever misses the point that Hume denies that there are, in addition to particular ideas, universal ones, that is, common notions, while Spinoza clearly admits, in the second scholium to 11 Ethics 40, the difference which Hume denies. According to Spinoza we have (1> confused representations of particular things, and (2) remembered ideas which are "similar to those through which we imagine things." These latter are ideas of the sort which Hume recognized. But in addition tothese two, which Spinoza calls "opinion" and "imagination," Spinoza claims that we have (3) "notions common to all men, and adequate ideas ofthe properties ofthings." These are notions of"those things which are common to all, and which are equallyin a part and in the whole [and which] cannotbe conceived exceptadequately"(2Ethics 38). These notions, which parallel Descartes' "clear and distinct ideas" are the general abstract ideas which Hume denies in Treatise 1.1.7. There Hume denies that ideas can be general "in their nature" but allows that they can be general "in their representation." To the extent to which Hume's position can be called "nominalism," the passages to which I have referred show that Spinoza, who basically accepted the Cartesian doctrine ofclear and distinct ideas, was not a nominalist. Aristotle drew a sharp distinction between imagination and thought in De anima 2.3. Descartes preserved the distinction between imagination and intellection at the beginningofthe fourth Meditation, among other places. The passage from the second scholium to 2 Ethics 40, which I have already cited adheres to this distinction, which was already... (shrink)

The Experience of Human Communication approaches everyday communication as a philosophical and psychological matter. Using insights from Merleau-Ponty, Heidegger, and Foucault, Frank Macke stresses that human communication—and with it, the human body—is, first and foremost, a relational phenomenon involving friends and family.