Since most of the functions in cells are mediated by multimeric protein complexes, the determination of protein–protein interactions is an important step in the study of cellular mechanisms. Traditionally, after screening for possible target interactors by means of a yeast two‐hybrid screen, several methods are used to validate the initial result before carrying out functional experiments. Nowadays, non‐invasive fluorescence‐based methods like Bioluminescence Resonance Energy Transfer (BRET) and Fluorescence Resonance Energy Transfer (FRET) are widely used in the (...) study of protein–protein interactions in living cells. In the present review, we address the individual strengths and weaknesses of both RET approaches, providing information on their possible future use in the study of G protein‐coupled receptor oligomerization. BioEssays 30:82–89, 2008. © 2007 Wiley Periodicals, Inc. (shrink)

Conformational changes of proteins and other biomolecules play a fundamental role in their functional mechanism. Single pair Förster resonance energy transfer offers the possibility to detect these conformational changes and dynamics, and to characterize their underlying kinetics. Using spFRET on microscopes with different modes of detection, dynamic timescales ranging from nanoseconds to seconds can be quantified. Confocal microscopy can be used as a means to analyze dynamics in the range of nanoseconds to milliseconds, while total internal reflection fluorescence (...) microscopy offers information about conformational changes on timescales of milliseconds to seconds. While the existence of dynamics can be directly inferred from the FRET efficiency time trace or the correlation of FRET efficiency and fluorescence lifetime, additional computational approaches are required to extract the kinetic rates of these dynamics, a short overview of which is given in this review. The functional mechanism of proteins is often driven by underlying conformational changes. These intramolecular changes and dynamics can be investigated using single pair Förster resonance energy transfer. The kinetic timescales of the dynamics in the range of nanoseconds to seconds is then quantified using different experimental and analytical implementations. (shrink)

Substrate independence and mind-body functionalism claim that thinking does not depend on any particular kind of physical implementation. But real-world information processing depends on energy, and energy depends on material substrates. Biological evidence for these claims comes from ecology and neuroscience, while computational evidence comes from neuromorphic computing and deep learning. Attention to energy requirements undermines the use of substrate independence to support claims about the feasibility of artificial intelligence, the moral standing of robots, the possibility that (...) we may be living in a computer simulation, the plausibility of transferring minds into computers, and the autonomy of psychology from neuroscience. (shrink)

In Newtonian gravity it is a moot question whether energy should be localized in the field or inside matter. An argument from relativity suggests a compromise in which the contribution from the field in vacuum is positive definite. We show that the same compromise is implied by Noether’s theorem applied to a variational principle for perfect fluids, if we assume Dirichlet boundary conditions on the potential. We then analyse a thought experiment due to Bondi and McCrea that gives a (...) clean example of inductive energy transfer by gravity. Some history of the problem is included. (shrink)

The transference theory reduces causation to the transmission of physical conserved quantities, like energy or momenta. Although this theory aims at applying to all felds of physics, we claim that it fails to account for a quantum electrodynamic effect, viz. the Aharonov-Bohm effect. After having argued that the Aharonov-Bohm effect is a genuine counter-example for the transference theory, we offer a new physicalist approach of causation, ontic and modal, in which this effect is embedded.

Following aluminum as part of a material culture of speed and lightness, this article examines how assemblages of energy and metals connect built environments, ways of life, and ideologies of acceleration. Aluminum can be theorized as a circulatory matrix that forms an energy culture. Through a discussion of speed and social justice, the history of aluminium-based socioecologies reveals how the materiality of energy forms assemblages of objects, infrastructures, and practices. The article then traces the aluminum industry’s involvement (...) in the production and distribution of energy itself both at the national scale of power grids and in the emergence of transnational transfers of energy, such as hydropowered smelters in Iceland. Finally, this analysis of deeply embedded energy cultures calls for a transnational approach to the accelerated socioecologies of aluminum production and consumption; and for energy transition theories to pay closer attention to the figured worlds and figuring work of the military-industrial complex. (shrink)

In this paper we study in details a system of two weakly coupled harmonic oscillators from the point of view of Bohm's interpretation of quantum mechanics. This system may be viewed as a simple model for the interaction between a photon and a photodetector. We obtain exact solutions for the general case. We then compute approximate solutions for the case where one oscillator is initially in its first excited state (a single photon) reaching the other oscillator in its ground state (...) (the photodetector). The approximate solutions represent the state of both oscillators after the interaction, which is not an eigenstate of the individual hamiltonians for each oscillator, and therefore the energies for each oscillator do not exist in the Copenhagen interpretation of Quantum Mechanics. We use the approximate solutions that we obtained to compute Bohmian trajectories and to study the energy transfer between the oscillators. We conclude that, even using the Bohmian view, the energy of each individual oscillator is not well defined, as the nonlocal quantum potential is not negligible even after the coupling is turned off. (shrink)

In this paper we study in details a system of two weakly coupled harmonic oscillators from the point of view of Bohm’s interpretation of quantum mechanics. This system may be viewed as a simple model for the interaction between a photon and a photodetector. We obtain exact solutions for the general case. We then compute approximate solutions for the case where one oscillator is initially in its first excited state (a single photon) reaching the other oscillator in its ground state (...) (the photodetector). The approximate solutions represent the state of both oscillators after the interaction, which is not an eigenstate of the individual hamiltonians for each oscillator, and therefore the energies for each oscillator do not exist in the Copenhagen interpretation of Quantum Mechanics. We use the approximate solutions that we obtained to compute Bohmian trajectories and to study the energy transfer between the oscillators. We conclude that, even using the Bohmian view, the energy of each individual oscillator is not well defined, as the nonlocal quantum potential is not negligible even after the coupling is turned off. (shrink)

Stemming from our energy localization hypothesis that energy in general relativity is localized in the regions of the energy-momentum tensor, we had devised a test with the classic Eddington spinning rod. Consistent with the localization hypothesis, we found that the Tolman energy integral did not change in the course of the motion. This implied that gravitational waves do not carry energy in vacuum, bringing into question the demand for the quantization of gravity. Also if information (...) is conveyed by the waves, the traditional view that information transfer demands energy is challenged. Later, we showed that the “body” angular momentum changed at a rate indicating that the moment of inertia increased to higher order, contrary to traditional expectations. We consider the challenges facing the development of a localized expression for the total angular momentum of the body including the contribution from gravity. We find that Komar's expression does not lead to an adequate formulation of localized angular momentum. (shrink)

Quantum measurement is a physical process. A system and an apparatus interact for a certain time period, and during this interaction, information about an observable is transferred from the system to the apparatus. In this study, we quantify the energy fluctuation of the quantum apparatus required for this physical process to occur autonomously. We first examine the so-called standard model of measurement, which is free from any non-trivial energy–time uncertainty relation, to find that it needs an external system (...) that switches on the interaction between the system and the apparatus. In such a sense this model is not closed. Therefore to treat a measurement process in a fully quantum manner we need to consider a “larger” quantum apparatus which works also as a timing device switching on the interaction. In this setting we prove that a trade-off relation, \, holds between the energy fluctuation \ of the quantum apparatus and the measurement time \. We use this trade-off relation to discuss the spacetime uncertainty relation concerning the operational meaning of the microscopic structure of spacetime. In addition, we derive another trade-off inequality between the measurement time and the strength of interaction between the system and the apparatus. (shrink)

A new hypothesis for energy localization in general relativity is introduced which is based upon the fact that the energy-momentum conservation laws are devoid of content in vacuum. The vanishing of pseudotensor components forms the basis of coordinate conditions consistent with the above. The implication is that energy is localized where the energy-momentum tensor is nonvanishing. As a consequence, gravitational waves are not carriers of energy in vacuum. A detailed analysis of a Feynman detector interacting (...) with a plane gravitational wave is consistent with the hypothesis. The fact that there has never been a confirmed direct energy transfer to a detector via gravitational radiation is also consistent with the hypothesis. (shrink)

Derrida’s “What is a ‘Relevant’ Translation?”, first delivered at the fifteenth annual Assises de la Traduction Littéraire à Arles in 1998, is an address that appears at first to speak from the outside and with a certain deference to professional translators. Yet, it quickly becomes apparent that Derrida not only counts himself among them but uses the occasion to reflect on his own surprising success as a translator of Hegel. This success has to do first and foremost with the proven (...) “relevance” of his translation of the notoriously untranslatable term Aufhebung as relève [in English: sublation]. Not a little perplexed by this apparent triumph, Derrida takes up the French term again, this time redeploying it in the translation of a crucial line from Shakespeare’s Merchant of Venice. In doing so, he relaunches his engagement with Hegel, asking what energies bound up in the concept of relève might yet be released, what internal resistances silently at work in it might still be mobilized to take it in an entirely new direction. Such an engagement enables him to explore in turn what resistances may be at work in the notion of translation itself. Inhabited by an internal otherness, by a constitutive resistance to itself, translation must be understood from the very first as transference. While translation studies have long been attentive to the transferential dynamics in which individual translators find themselves enmeshed, Derrida’s text views transference in more impersonal terms as the tenacious grip in which certain structures of thought hold us, structures which also inform our understanding of translation. How to work with and against this structural unconscious? To address this question, it is necessary to examine Derrida’s own translational practice and the privilege he accords to the term trouvaille. (shrink)

The paper is replaced by a new version (12-2019): DOI: 10.5281/zenodo.3572846 -/- Physical phenomena emerge from the quantum fields everywhere in space. However, not only the phenomena emerge from the quantum fields, the law of the conservation of energy must have its origin from the same spatial structure. This paper describes the relations between the main law of physics and the mathematical structure of the “aggregated” quantum fields.

Much has been written about the free energy principle (FEP), and much misunderstood. The principle has traditionally been put forth as a theory of brain function or biological self-organisation. Critiques of the framework have focused on its lack of empirical support and a failure to generate concrete, falsifiable predictions. I take both positive and negative evaluations of the FEP thus far to have been largely in error, and appeal to a robust literature on scientific modelling to rectify the situation. (...) A prominent account of scientific modelling distinguishes between model structure and model construal. I propose that the FEP be reserved to designate a model structure, to which philosophers and scientists add various construals, leading to a plethora of models based on the formal structure of the FEP. An entailment of this position is that demands placed on the FEP that it be falsifiable or that it conform to some degree of biological realism rest on a category error. To this end, I deliver first an account of the phenomenon of model transfer and the breakdown between model structure and model construal. In the second section, I offer an overview of the formal elements of the framework, tracing their history of model transfer and illustrating how the formalism comes apart from any interpretation thereof. Next, I evaluate existing comprehensive critical assessments of the FEP, and hypothesise as to potential sources of existing confusions in the literature. In the final section, I distinguish between what I hold to be the FEP—taken to be a modelling language or modelling framework—and what I term “FEP models.”. (shrink)

By dividing the creation of matter, energy, life, and mind into three big bangs, Holmes Rolston III brings into focus a history of the universe that respects both scientific discovery and the potential presence of an underlying intelligence. Matter-energy appears, initially in simpler forms but with a remarkable capacity for generating heavier elements. The size and expansion rate of the universe, the nature of electromagnetism, gravity, and nuclear forces enable the the explosion of life on Earth. DNA discovers, (...) stores, and transfers information generating billions of species. Cognitive capacities escalate, and with neural sentience this results in human genius. A massive singularity, the human mind gives birth to language and culture, increasing the brain's complexity and promoting the spread of ideas. Ideas generate ideals, which lead life to take on spirit. The nature of matter-energy, genes, and their genesis therefore encourages humans to wonder where they are, who they are, and what they should do. (shrink)

Since the nineteenth century, the problem of the arrow of time has been traditionally analyzed in terms of entropy by relating the direction past-to-future to the gradient of the entropy function of the universe. In this paper, we reject this traditional perspective and argue for a global and non-entropic approach to the problem, according to which the arrow of time can be defined in terms of the geometrical properties of spacetime. In particular, we show how the global non-entropic arrow can (...) be transferred to the local level, where it takes the form of a non-spacelike local energy flow that provides the criterion for breaking the symmetry resulting from time-reversal invariant local laws. (shrink)

Causation has traditionally been analyzed either as a relation of nomic dependence or as a relation of counterfactual dependence. I argue for a third program, a physicalistic reduction of the causal relation to one of energy-momentum transference in the technical sense of physics. This physicalistic analysis is argued to have the virtues of easily handling the standard counterexamples to the nomic and counterfactual analyses, offering a plausible epistemology for our knowledge of causes, and elucidating the nature of the relation (...) between causation and physical science. (shrink)

In this paper I propose a model of the fundamental components of psychoanalytic psychotherapies that I try to explicate with contemporary theories of the Bayesian brain and the Free Energy Principle (FEP). I first show that psychoanalytic therapies require a setting (made up of several envelopes), a particular psychic state and specific processes (transference, free association, dreaming, play, reflexivity and narrativity) in order to induce psychic transformations. I then analyze how these processes of transformations operate and how they can (...) be enlightened by the FEP. I first underline the fact that psychoanalytic therapies imply non-linear processes taking time to unfold and require a setting containing high entropy processes. More precisely, these processes are characterized by an interplay between extension and reduction of free energy. This interplay also favors the emergence of new orders of subjective experience, which occur following states of disorder, according to a certain energetic threshold allowing the modification and improvement of mental functioning. These high entropy states are also characterized by random functioning and psychic malleability which favors the exploration of subjective experience in an original manner. Overall, the approach proposed in this paper support the dialogue between psychoanalysis and other fields of research while underlining how psychoanalytical theoretical and conceptual constructs can also be useful to other disciplines, in particular the neurosciences of subjectivity. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:Climate Justice: Ethics, Energy, and Public PolicyWillis JenkinsClimate Justice: Ethics, Energy, and Public Policy James Martin-Schramm Minneapolis: Fortress Press, 2010. 232 pp. $20.00Religious ethicists are sometimes tempted to interpret climate change as symptomatic of a civilizational corruption so deep that practical responsibility seems nearly impossible. In its considered treatment of energy options and policy responses, [End Page 198] Climate Justice works to make applied Christian (...) ethics competent to address climate change. By interpreting political possibilities with Christian commitments to justice, the book makes a distinctively practical contribution to the literature on Christianity and climate; it lifts an important theological voice in the growing subfield of climate ethics.The book begins by elaborating the general notion of ecological justice into workable criteria. Martin-Schramm describes four basic norms of ecojustice (sustainability, sufficiency, participation, and solidarity), from which he develops twelve energy policy guidelines (e.g., equity, adequacy). He then specifies those guidelines into fourteen criteria by which to assess the justice of climate action (e.g., historical responsibility, emissions verifiability).Subsequent chapters use those criteria to evaluate policy options. A chief difficulty in applying them lies in the tension between intergenerational and intragenerational claims. Global climate negotiations founder on disagreements about these undeveloped, plural dimensions of justice. Martin-Schramm therefore deploys criteria with a balancing objective: to develop obligations to the future while recognizing claims of the present poor and vulnerable, and while keeping the result within the bounds of North American political viability.For example, Martin-Schramm recognizes that the criterion of historical responsibility indicates that the United States should bear about one-third of the costs of climate transition. But he finds that the resulting figure ($331 billion) so outstrips realistic acceptance that he rejects financial transfer in favor of a “national obligation wedge” in which the nation compensates by pledging to reduce future emissions. Since those emission reductions are unlikely apart from a price on carbon, Martin-Schramm argues that justice mandates a fossil fuel tax. With an eye to political viability, he proposes beginning with a modest $5/ton (for comparison, the Stern Report estimates the social costs of carbon at $85/ton).Controversy in the details matters to the whole project because the point of Martin-Schramm’s approach is that a meaningful climate ethic should guide contextual action. Yet other accounts of climate justice will find a scandal of modesty on those contextual points. Martin-Schramm’s climate justice entails less economic transformation than the “Northern structural adjustment” demanded by the Latin American Council of Churches. It is also less ecocentric than accounts from indigenous theologians arguing that justice warrants rights for species at risk of extinction, and perhaps for Earth itself.While Climate Justice is a self-consciously North American account, the criteria it develops would be different and work more critically were the underlying account of justice dialogically constructed across economic, political, and theological borders. Were it pragmatic, in the sense of arising from projects from across those borders, rather than applied deductively, a Christian climate ethic would likely produce an account of justice with more critical demands on industrial infrastructure and on ecological consciousness. [End Page 199]In its self-limitation, however, lies the book’s practical promise. Martin-Schramm wants justice to illuminate effective ways toward real responsibility. His criteria for justice imply that advocating for impossible goals, or for objectives that would imperil other conditions of social justice, would amount to injustice. Making ethics matter for climate change, he shows, requires understanding what justice can do in context.The open question for this book’s project is how a self-limited ethic of applied justice relates to the deeper processes of social transformation obviously needed for adequate response. Martin-Schramm closes with an account of his work reforming the energy economy of Luther College, which should inspire every reader with a sense of what persistent, informed, and contextual action can accomplish.Willis JenkinsYale Divinity SchoolCopyright © 2012 The Society of Christian Ethics... (shrink)

The conservation of energy law, a law of physics that states that the total energy of any closed system is always conserved, is a bedrock principle that has achieved both broad theoretical and experimental support. Yet if interactive dualism is correct, it is thought that the mind can affect physical objects in violation of the conservation of energy. Thus, some claim, the conservation of energy grounds an argument for physicalism. Although critics of the argument focus on (...) the implausibility of causation requiring the transference of energy, I argue that even if causation requires the transference of energy, once we accept the other required premises of the argument that lie behind any supposed argument from the conservation of energy the law of the conservation of energy is revealed as irrelevant to the question of whether the mental is physical. (shrink)

The conservation of energy law, a law of physics that states that the total energy of any closed system is always conserved, is a bedrock principle that has achieved both broad theoretical and experimental support. Yet if interactive dualism is correct, it is thought that the mind can affect physical objects in violation of the conservation of energy. Thus, some claim, the conservation of energy grounds an argument for physicalism. Although critics of the argument focus on (...) the implausibility of causation requiring the transference of energy, I argue that even if causation requires the transference of energy, once we accept the other required premises of the argument that lie behind any supposed argument from the conservation of energy the law of the conservation of energy is revealed as irrelevant to the question of whether the mental is physical. (shrink)

This paper examines the Transference Theory of causation, developed originally by Aronson (1971) and Fair (1979). Three difficulties for that theory are presented: firstly, problems associated with the direction of transference and causal asymmetry; secondly, the case of persistence as causation, for example where a body's own inertia is the cause of its motion; and thirdly the problematic notion of identity through time of physical quantities such as energy or momentum. Finally, the theory is compared with the Conserved Quantity (...) Theory (Dowe 1992c), and it is shown that that account embodies the modifications that the transference theory needs to adopt. (shrink)

Inspired by early-nineteenth-century discoveries about heat transfer, the French physicist Claude Pouillet measured the influx of solar radiation at the earth and, in 1838, asked what these observations revealed about the temperature of the sun and of space itself. At about the same time, the British natural philosophers John Herschel and J. D. Forbes made similar measurements in order to better understand the sun's influence on climate. This paper tells how and why Pouillet, Herschel and Forbes made the first (...) estimates of the solar constant, estimates which would acquire new importance with the discovery of the laws of thermodynamics by the mid century. (shrink)

Gene transcription in eukaryotes is associated with conformational changes of a large area of chromatin adjacent to a gene. This rearrangement may involve the whole loop (topological domain) to which a given gene belongs.Regulatory events associated with activation or inactivation of transcription are found to act through relatively short nucleotide sequences, often located several thousand base pairs apart from gene. These sequences, termed enhancers may act independently on their distance from or orientation with respect to the gene.Both long‐range conformational rearrangements (...) of chromatin and any long distance effects of enhancers may be associated with elastic torsional strain in DNA, arising in transcriptionally active chromatin loops. Enhancer effects, in particular, may be associated with conformational transitions in DNA competing for the energy deposited in the elastic spring of the DNA. (shrink)

The economical/environmental scheduling problem of the ship integrated energy system has high computational complexity, which includes more than one optimization objective, various types of constraints, and frequently fluctuated load demand. Therefore, the intelligent scheduling strategies cannot be applied to the ship energy management system online, which has limited computing power and storage space. Aiming at realizing green computing on SEMS, in this paper a typical SIES-EESP optimization model is built, considering the form of decision vectors, the economical/environmental optimization (...) objectives, and various types of real-world constraints of the SIES. Based on the complexity of SIES-EESPs, a two-stage offline-to-online multiobjective optimization strategy for SIES-EESP is proposed, which transfers part of the energy dispatch online computing task to the offline high-performance computer systems. The specific constraints handling methods are designed to reduce both continuous and discrete constraints violations of SIES-EESPs. Then, an establishment method of energy scheduling scheme-base is proposed. By using the big data offline, the economical/environmental scheduling solutions of a typical year can be obtained and stored with more computing resources and operation time on land. Thereafter, a short-term multiobjective offline-to-online optimization approach by SEMS is considered, with the application of multiobjective evolutionary algorithm and typical schemes corresponding to the actual SIES-EESPs. Simulation results show that the proposed strategy can obtain enough feasible Pareto solutions in a shorter time and get well-distributed Pareto sets with better convergence performance, which can well adapt to the features of real-world SIES-EESPs and save plenty of operation time and storage space for the SEMS. (shrink)

Reasoning about underlying causal relations drives responsibility judgments: agents are held responsible for the outcomes they cause through their behaviors. Two main causal reasoning approaches exist: dependence theories emphasize statistical relations between causes and effects, while transference theories emphasize mechanical transmission of energy. Recently, pluralistic or hybrid models, combining both approaches, have emerged as promising psychological frameworks. In this paper, we focus on causal reasoning as involved in third-party judgements of responsibility and on related judgments of intention and control. (...) In particular, we used a novel visual paradigm to investigate the combined effects of two well-known causal manipulations, namely omission and pre-emption, on these evaluations. Our findings support the view that people apply a pluralistic causal reasoning when evaluating individual responsibility for negative outcomes. In particular, we observed diminished responsibility when dependence, transference, or both fail, compared to when these mechanisms are upheld. Responsibility judgement involves a cognitive hybrid of multiple aspects of causal reasoning. However, important differences exist at the interindividual level, with most people weighting transference more than dependence. (shrink)

Causation is important when considering how an organism maintains health, why disease arises in a healthy person, and how one may intervene to change the course of a disease. This paper explores the form of causative relationships in health, disease and intervention, with particular regard to the pathological and biopsychosocial models. Consistent with the philosophical view of dispositionalism, we believe that objects are the fundamental relata of causation. By accepting the broad scope of the biopsychosocial model, we argue that psychological (...) and social constructs be considered objects. We think that this 'biopsychosocial dispositionalism' offers the flexibility required to describe causation throughout health, disease and intervention pathways. When constructing mechanistic chains to describe causative pathways, we argue that an object will causally connect with others through actions; transfers of energy from one object to another, initiated by the manifestation of one or more dispositional property. Finally, our analysis of causative interactions utilises the concept that a common form of interaction exists between disease and intervention pathways. This common form will always be an object, but the mode of interaction will vary with each disease. We describe how intervention may act through objects being shared between converging mechanistic chains, or through the removal and/or insertion of objects in such chains. We believe that this analysis provides novel insight to the forms of causative transactions that can occur. In addition, we hope that the findings of this analysis represent the first step towards developing a framework for appraising the composition of mechanistic theories. (shrink)

Causation is important when considering: how an organism maintains health; why disease arises in a healthy person; and, how one may intervene to change the course of a disease. This paper explores the form of causative relationships in health, disease and intervention, with particular regard to the pathological and biopsychosocial models. Consistent with the philosophical view of dispositionalism, we believe that objects are the fundamental relata of causation. By accepting the broad scope of the biopsychosocial model, we argue that psychological (...) and social constructs be considered objects. We think that this ‘biopsychosocial dispositionalism’ offers the flexibility required to describe causation throughout health, disease and intervention pathways. When constructing mechanistic chains to describe causative pathways, we argue that an object will causally connect with others through actions; transfers of energy from one object to another, initiated by the manifestation of one or more dispositional property. Finally, our analysis of causative interactions utilises the concept that a common form of interaction exists between disease and intervention pathways. This common form will always be an object, but the mode of interaction will vary with each disease. We describe how intervention may act through objects being shared between converging mechanistic chains, or through the removal and/or insertion of objects in such chains. We believe that this analysis provides novel insight to the forms of causative transactions that can occur. In addition, we hope that the findings of this analysis represent the first step towards developing a framework for appraising the composition of mechanistic theories. (shrink)

The Earth agglomerates and heats. Convection cells within the planetary interior expedite the cooling process. Volcanoes evolve steam, carbon dioxide, sulfur dioxide and pyrophosphate. An acidulous Hadean ocean condenses from the carbon dioxide atmosphere. Dusts and stratospheric sulfurous smogs absorb a proportion of the Sun’s rays. The cooled ocean leaks into the stressed crust and also convects. High temperature acid springs, coupled to magmatic plumes and spreading centers, emit iron, manganese, zinc, cobalt and nickel ions to the ocean. Away from (...) the spreading centers cooler alkaline spring waters emanate from the ocean floor. These bear hydrogen, formate, ammonia, hydrosulfide and minor methane thiol. The thermal potential begins to be dissipated but the chemical potential is dammed. The exhaling alkaline solutions are frustrated in their further attempt to mix thoroughly with their oceanic source by the spontaneous precipitation of biomorphic barriers of colloidal iron compounds and other minerals. It is here we surmise that organic molecules are synthesized, filtered, concentrated and adsorbed, while acetate and methane—separate products of the precursor to the reductive acetyl-coenzyme-A pathway—are exhaled as waste. Reactions in mineral compartments produce acetate, amino acids, and the components of nucleosides. Short peptides, condensed from the simple amino acids, sequester ‘ready-made’ iron sulfide clusters to form protoferredoxins, and also bind phosphates. Nucleotides are assembled from amino acids, simple phosphates carbon dioxide and ribose phosphate upon nanocrystalline mineral surfaces. The side chains of particular amino acids register to fitting nucleotide triplet clefts. Keyed in, the amino acids are polymerized, through acid–base catalysis, to alpha chains. Peptides, the tenuous outer-most filaments of the nanocrysts, continually peel away from bound RNA. The polymers are concentrated at cooler regions of the mineral compartments through thermophoresis. RNA is reproduced through a convective polymerase chain reaction operating between 40 and 100°C. The coded peptides produce true ferredoxins, the ubiquitous proteins with the longest evolutionary pedigree. They take over the role of catalyst and electron transfer agent from the iron sulfides. Other iron–nickel sulfide clusters, sequestered now by cysteine residues as CO-dehydrogenase and acetyl-coenzyme-A synthase, promote further chemosynthesis and support the hatchery—the electrochemical reactor—from which they sprang. Reactions and interactions fall into step as further pathways are negotiated. This hydrothermal circuitry offers a continuous supply of material and chemical energy, as well as electricity and proticity at a potential appropriate for the onset of life in the dark, a rapidly emerging kinetic structure born to persist, evolve and generate entropy while the sun shines. (shrink)

This article examines how local experiments and negotiation processes contribute to social and field-level learning. The analysis is framed within the niche development literature, which offers a framework for analyzing the relation between projects in local contexts and the transfer of local experiences into generally applicable rules. The authors examine 2 case studies drawn from a meta-analysis of 27 new energy projects. The case studies, both pertaining to biogas projects for local municipalities, illustrate the diversity of applications for (...) a technology through processes of local variation and selection. The authors examine the diversity of expectations and the negotiation and alignment of these expectations underlying the diversity of local solutions. Moreover, the authors address how the transfer of lessons from individual local experiments can follow different pathways and yet always require due attention to the social and cultural limits to the transferability of solutions. (shrink)

Summary In this paper we examine the reaction of the Leiden low-temperature laboratory of Heike Kamerlingh Onnes to new ideas in quantum theory. Especially the contributions of Albert Einstein (1906) and Peter Debye (1912) to the theory of specific heat, and the concept of zero-point energy formulated by Max Planck in 1911, gave a boost to solid state research to test these theories. In the case of specific heat measurements, Kamerlingh Onnes's laboratory faced stiff competition from Walter Nernst's Institute (...) of Physical Chemistry in Berlin. In fact, Berlin got the better of it because Leiden lacked focus. After the liquefaction of helium in 1908, Kamerlingh Onnes transformed his laboratory into an international facility for low temperature research, and for this reason it was impossible to make headway with the specific heat measurements. In the case of zero-point energy, Leiden developed a magnetic research programme to test the concept. Initially the balance of evidence seemed to be tipping in favour of zero-point energy. After 1914, however, Leiden would desert the theory in fovour, of a concept from calssical physics. A curious move that illustrates Kamerlingh Onnes's discomfort with the new quantum theory. (shrink)

The discovery and engineering of novel fluorescent proteins (FPs) from diverse organisms is yielding fluorophores with exceptional characteristics for live‐cell imaging. In particular, the development of FPs for fluorescence (or Förster) resonance energy transfer (FRET) microscopy is providing important tools for monitoring dynamic protein interactions inside living cells. The increased interest in FRET microscopy has driven the development of many different methods to measure FRET. However, the interpretation of FRET measurements is complicated by several factors including the high (...) fluorescence background, the potential for photoconversion artifacts and the relatively low dynamic range afforded by this technique. Here, we describe the advantages and disadvantages of four methods commonly used in FRET microscopy. We then discuss the selection of FPs for the different FRET methods, identifying the most useful FP candidates for FRET microscopy. The recent success in expanding the FP color palette offers the opportunity to explore new FRET pairs. (shrink)

Men’s hunting has dominated the discourse on energy capture and flow in the past decade or so. We turn to women’s roles as critical to household formation, pair-bonding, and intergenerational bonds. Their pivotal contributions in food processing and distribution likely promoted kinship, both genetic and affinal, and appear to be the foundation from which households evolved. With conscious recognition of household social units, variable cultural constructions of human kinship systems that were sensitive to environmental and technological conditions could emerge. (...) Kinship dramatically altered the organization of resource access for our species, creating what we term “kinship ecologies.” We present simple mathematical models to show how hunting leads to dependence on women’s contributions, bonds men to women, and bonds generations together. Kinship, as it organized transfers of food and labor energy centered on women, also became integrated with the biological evolution of human reproduction and life history. (shrink)

The concept of time is examined using the second law of thermodynamics that was recently formulated as an equation of motion. According to the statistical notion of increasing entropy, flows of energy diminish differences between energy densities that form space. The flow of energy is identified with the flow of time. The non-Euclidean energy landscape, i.e. the curved space–time, is in evolution when energy is flowing down along gradients and levelling the density differences. The flows (...) along the steepest descents, i.e. geodesics are obtained from the principle of least action for mechanics, electrodynamics and quantum mechanics. The arrow of time, associated with the expansion of the Universe, identifies with grand dispersal of energy when high-energy densities transform by various mechanisms to lower densities in energy and eventually to ever-diluting electromagnetic radiation. Likewise, time in a quantum system takes an increment forwards in the detection-associated dissipative transformation when the stationary-state system begins to evolve pictured as the wave function collapse. The energy dispersal is understood to underlie causality so that an energy gradient is a cause and the resulting energy flow is an effect. The account on causality by the concepts of physics does not imply determinism; on the contrary, evolution of space–time as a causal chain of events is non-deterministic. (shrink)

Insulin is stored within the pancreas in an inactive Zn2+‐bound hexameric form prior to release. Similarly, clinical insulins contain Zn2+ and form multimeric complexes. Upon release from the pancreas or upon injection, insulin only becomes active once Zn2+ disengages from the complex. In plasma and other extracellular fluids, the majority of Zn2+ is bound to human serum albumin (HSA), which plays a vital role in controlling insulin pharmacodynamics by enabling removal of Zn2+. The Zn2+‐binding properties of HSA are attenuated by (...) non‐esterified fatty acids (NEFAs) also transported by HSA. Elevated NEFA concentrations are associated with obesity and type 2 diabetes. Here we present the hypothesis that higher NEFA levels in obese and/or diabetic individuals may contribute to insulin resistance and affect therapeutic insulin dose‐response profiles, through modulation of HSA/Zn2+ dynamics. We envisage this novel concept to have important implications for personalized treatments and management of diabetes‐related conditions in the future. (shrink)

Benjamin Callard has recently suggested that causation between Platonic objects—standardly understood as atemporal and non-spatial—and spatio-temporal objects is not ‘a priori’ unintelligible. He considers the reasons some have given for its purported unintelligibility: apparent impossibility of energy transference, absence of physical contact, etc. He suggests that these considerations fail to rule out a priori Platonic-object causation. However, he has overlooked one important issue. Platonic objects must causally affect different objects differently, and different Platonic objects must causally affect the same (...) objects differently. How are Platonic objects—ones outside space and time—supposed to do that? CiteULike Connotea Del.icio.us What's this? (shrink)

The ganzfeld procedure is a mild sensory isolation technique that was first introduced into experimental psychology during the 1930s and subsequently adapted by parapsychologists to test for the existence of psi--anomalous processes of information or energy transfer such as telepathy or other forms of extrasensory perception that are currently unexplained in terms of known physical or biological mechanisms. Parapsychologists developed the ganzfeld procedure, in part, because they had become dissatisfied the card-guessing methods for testing ESP pioneered by J. (...) B. Rhine at Duke University in the 1930s. In particular, they believed that the repetitive forced-choice procedure in which a participant repeatedly attempts to select the correct "target" symbol from a set of fixed-alternatives failed to capture the circumstances that characterize reported instances of psi in everyday life. (shrink)

Empiricists mostly prefer an epistemic notion of causality intending thereby to avoid metaphysical entanglements. General relativity however provides examples for causality without predictability, i. e. world models in which for geometrical reasons there exist no spacelike hypersurfaces containing traces of all future events. Yet local determinism for every single event remains valid in these cases. Therefore the problem arises how to account for a causal structure that implies local but not global predictability. This problem, it is argued, cannot be solved (...) by characterizing the causal connection of events itself by means of its epistemic aspects. Instead the ontological ground must be emphazised which allows for varying epistemic properties of causal connections according to the space-time structure. This can be done by use of the energy transfer concept of causality which involves no reminiscence of dubious natural necessity. (shrink)

In an earlier paper I suggested that we can solve the Benacerraf Problem – the problem of explaining how mathematical knowledge is possible on the assumption that the objects of mathematics are abstract and immaterial – by positing efficient causal relations between those abstract objects and our brains. The burden of the paper was to remove the appearance that relations between abstracta and concreta, far from being actual, are inconceivable. This alleged inconceivability has been derived from some putative conditions on (...) efficient causation: physical contact, energy transfer, reciprocal effects on the cause, and the idea that the cause must exist in time if its effects do. I argued that none of these conditions are a priori conditions on efficient causation, and thus do not pose an obstacle to the conceivability or metaphysical possibility of efficient causal relations between platonic objects and brains. In this essay I reply to three published challenges to this proposed solution to the Benacerraf Problem. (shrink)

The problem of divine agency and action is analogous to the problem of human agency and action: How is such agency possible in the absence of a dualistic causal interaction between disparate orders of being? This paper explores nondualistic accounts of divine agency that assert the following: (1) physical monism, (2) antireductionism, (3) physical realization, and (4) divine causal realism. I conclude that a robustly causal deity is incompatible with nonddualism's affirmation of physical monism. Specifically, I argue the incoherence of (...) nondualistic strategies that advocate divine information transfer without energy transfer or the divine downward causation of physical events. Furthermore, I claim that the principle of explanatory exclusion makes any nondualistic, noninterventionist account of divine agency highly dubious. Finally, I suggest that Judaism, Christianity, and Islam can avoid a causally inert deity only if they are willing to deny the current presumption of the causal closure of the physical. (shrink)

Quantum Counterfactual Communication is the recently-proposed idea of using quantum physics to send messages between two parties, without any matter/energy transfer associated with the bits sent. While this has excited massive interest, both for potential ‘unhackable’ communication, and insight into the foundations of quantum mechanics, it has been asked whether this process is essentially quantum, or could be performed classically. We examine counterfactual communication, both classical and quantum, and show that the protocols proposed so far for sending signals (...) that don’t involve matter/energy transfer associated with the bits sent must be quantum, insofar as they require wave-particle duality. (shrink)

Relative distance and velocity magnitudes between two arbitrarily moving particles are independent of an observer's reference frame, and may be used to construct theoretically a clock whose rate is Lorentz-invariant. This result is in accord with the principle of relativity, using the interaction interpretation: Relativistic changes arise in association with momentum-energy transfer, rather than in consequence of velocity-induced changes in measuring clocks and rods.

Philosophical accounts of causation have traditionally been framed as attempts to analyze the concept of a cause. In recent years, however, a number of philosophers have proposed instead that causation be empirically reduced to some relation uncovered by the natural sciences: e.g., a relation of energy transfer. This paper argues that the project of empirical analysis lacks a clearly defined methodology, leaving it uncertain how such views are to be evaluated. It proposes several possible accounts of empirical analysis (...) and argues that the most promising approach would treat it as a contingent identity discovered by identifying the relation (or relations) that most nearly approximate the inferential role of causal concepts in a psychological theory of causal judgment. (shrink)

We here review primary methods used in quantifying and mapping 5‐hydroxymethylcytosine (5hmC), including global quantification, restriction enzyme‐based detection, and methods involving DNA‐enrichment strategies and the genome‐wide sequencing of 5hmC. As discovered in the mammalian genome in 2009, 5hmC, oxidized from 5‐methylcytosine (5mC) by ten‐eleven translocation (TET) dioxygenases, is increasingly being recognized as a biomarker in biological processes from development to pathogenesis, as its various detection methods have shown. We focus in particular on an ultrasensitive single‐molecule imaging technique that can detect (...) and quantify 5hmC from trace samples and thus offer information regarding the distance‐based relationship between 5hmC and 5mC when used in combination with fluorescence resonance energy transfer. (shrink)

By melodic landscape, this paper points to natural milieus such as mountains whose motifs are caught up in contrapuntal relations. With Merleau-Ponty, the structure of the world is a symphony, and the production of life which implicates both organism and environment as unfurling of Umwelt is ‘a melody that sings itself’. For the Chinese culture, mountains have been deemed virtuous in Confucianism, immortal by Daoists, and spiritual for a Buddhist to reach a substrate level of pure stream of a-subjective consciousness. (...) A Chinese painter-poet within the ‘mountain-water’ genre would consider mountains as performance of events, a concert of vibration of light, shape and sound, movement and rest. Insofar as art is to create energy transfer, Chinese artists of mountains aim at concerting with nature as organised by rhythms and conspecifics, unfolding contrapuntal melodies with all kinds of counterpoints. As Deleuze and Guattari's notion of refrains are the three forces or tempos of chaos, earth and world confronting/converging one another, this paper endeavours to find out, first, how Deleuze and Guattari's geological, organic and alloplastic stratifications can be put alongside mountains, animals, plants and arts, and second, how this notion can contribute to our new appreciation of the way Chinese mountains in arts can give out music. (shrink)