Coherent phenomena in photosynthetic light harvesting: part one—theory and spectroscopy

The role of non-trivial quantum mechanical effects in biology has been the subject of intense scrutiny over the past decade. Much of the focus on potential “quantum biology” has been on energy transfer processes in photosynthetic light harvesting systems. Ultrafast laser spectroscopy of several light harvesting proteins has uncovered coherent oscillations dubbed “quantum beats” that persist for hundreds of femtoseconds and are putative signatures for quantum transport phenomena. This review describes the language and basic quantum mechanical phenomena that underpin quantum transport in open systems such as light harvesting and photosynthetic proteins, including the photosystem reaction centre. Coherent effects are discussed in detail, separating various meanings of the term, from delocalized excitations, or excitons, to entangled states and coherent transport. In particular, we focus on the time, energy and length scales of energy transport processes, as these are critical in understanding whether or not coherent processes are important. The role played by the protein in maintaining chromophore systems is analysed. Finally, the spectroscopic techniques that are used to probe energy transfer dynamics and that have uncovered the quantum beats are described with reference to coherent phenomena in light harvesting.     

Coherent phenomena in photosynthetic light harvesting: part two—observations in biological systems

Considerable debate surrounds the question of whether or not quantum mechanics plays a significant, non-trivial role in photosynthetic light harvesting. Many have proposed that quantum superpositions and/or quantum transport phenomena may be responsible for the efficiency and robustness of energy transport present in biological systems. The critical experimental observations comprise the observation of coherent oscillations or “quantum beats” via femtosecond laser spectroscopy, which have been observed in many different light harvesting systems. Part Two of this review aims to provide an overview of experimental observations of energy transfer in the most studied light harvesting systems. Length scales, derived from crystallographic studies, are combined with energy and time scales of the beats observed via spectroscopy. A consensus is emerging that most long-lived (hundreds of femtoseconds) coherent phenomena are of vibrational or vibronic origin, where the latter may result in coherent excitation transport within a protein complex. In contrast, energy transport between proteins is likely to be incoherent in nature. The question of whether evolution has selected for these non-trivial quantum phenomena may be an unanswerable question, as dense packings of chromophores will lead to strong coupling and hence non-trivial quantum phenomena. As such, one cannot discern whether evolution has optimised light harvesting systems for high chromophore density or for the ensuing quantum effects as these are inextricably linked and cannot be switched off.     

The semantic approach to evolutionary theory

Paul Thompson, John Beatty, and Elisabeth Lloyd argue that attempts to resolve certain conceptual issues within evolutionary biology have failed because of a general adherence to the received view of scientific theories. They maintain that such issues can be clarified and resolved when one adopts a semantic approach to theories. In this paper, I argue that such conceptual issues are just as problematic on a semantic approach. Such issues arise from the complexity involved in providing formal accounts of theoretical laws and scientific explanations. That complexity is due to empirical and pragmatic considerations, not one's adherence to a particular formal approach to theories. This analysis raises a broader question. How can any formal account properly represent the complex nature of empirical phenomena?     

(Extra)thermodynamics of the drug-receptor interaction.

A core concept in pharmacology is drug-receptor affinity, i.e., the tendency of a drug molecule to bind to one or more receptors due to the collective influence of multiple molecular forces. The estimation of affinity as a dissociation constant (reciprocal of the equilibrium constant) is extraordinarily valuable. However, elucidation of the nature of the underlying concept--i.e., what accounts for affinity--is not achievable using such a static measure. Observing how the system responds to a perturbation (e.g., to a change in temperature) reveals more fundamental information. The present review summarizes the general concepts of thermodynamic analysis applied to drug-receptor interactions and discusses 'extrathermodynamic' phenomena, such as enthalpy-entropy 'compensation'. Together, these concepts may provide insight into the nature of drug-receptor interactions, begin to elucidate the forces that underlie such interactions--and begin to define and refine more nebulous terms such as affinity.     

The fine structure of ‘homology’

There is long-standing conflict between genealogical and developmental accounts of homology. This paper provides a general framework that shows that these accounts are compatible and clarifies precisely how they are related. According to this framework, understanding homology requires both (a) an abstract genealogical account that unifies the application of the term to all types of characters used in phylogenetic systematics and (b) locally enriched accounts that apply only to specific types of characters. The genealogical account serves this unifying role by relying on abstract notions of ‘descent’ and ‘character’. As a result, it takes for granted the existence of such characters. This requires theoretical justification that is provided by enriched accounts, which incorporate the details by which characters are inherited. These enriched accounts apply to limited domains (e.g. genes and proteins, or body parts), providing the needed theoretical justification for recognizing characters within that domain. Though connected to the genealogical account of homology in this way, enriched accounts include phenomena (e.g. serial homology, paralogy, and xenology) that fall outside the scope of the genealogical account. They therefore overlap, but are not nested within, the genealogical account. Developmental accounts of homology are to be understood as enriched accounts of body part homology. Once they are seen in this light, the conflict with the genealogical account vanishes. It is only by understanding the fine conceptual structure undergirding the many uses of the term ‘homology’ that we can understand how these uses hang together.     

Prokaryotic systematics in the genomics era

As an essential and basic biological discipline, prokaryotic systematics is entering the era of genomics. This paradigmatic shift is significant not only for understanding molecular phylogeny at the whole genome level but also in revealing the genetic or epigenetic basis that accounts for the phenotypic criteria used to classify and identify species. These developments provide an opportunity and a challenge for systematists to reanalyze the molecular mechanisms underlying the taxonomic characteristics of prokaryotes by drawing the knowledge from studies of genomics and/or functional genomics employing platform technologies and related bioinformatics tools. It is expected that taxonomic books, such as Bergey’s Manual of Systematic Bacteriology may evolve into a systematics library indexed by phylogenomic information with an comprehensive understanding of prokaryotic speciation and associated increasing knowledge of biological phenomena.     

A Role for the Endothelial Glycocalyx in Regulating Microvascular Permeability in Diabetes Mellitus

Diabetic angiopathy is a major cause of morbidity and mortality in diabetes mellitus. Endothelial dysfunction and associated alterations in blood flow, pressure and permeability are widely accepted phenomena in the diabetic milieu and are understood to lead to microangiopathy. Despite the clinical importance of diabetic microangiopathy, the mechanisms of pathogenesis remain elusive. In particular, much is yet to be understood about the nature of the putative increased permeability with respect to diabetes. Microvessel permeability is intrinsically difficult to measure and a surrogate (solute or solvent flux) is usually reported, the measurement of which is hampered by haemodynamic factors, such as flow rate, hydrostatic pressure gradient, solute concentration and surface area available for exchange. Very few studies describing the measurement of permeability with respect to diabetes have controlled for all these factors. As a result, the nature of the increased microvessel permeability in diabetes mellitus and indeed its causes are poorly understood. Recent studies have shown that hyperglycaemia can alter the glycocalyx structure, and parallel findings have shown that the apparent increase in permeability demonstrated in hyperglycaemia may be due to an increase in the permeability of the vessels to water, and not an increase in protein permeability, an effect attributable to altered glycocalyx. This review focuses on the current understanding of microvascular permeability in terms of the endothelial glycocalyx- fibre-matrix theory, those methods used to determine permeability in the context of diabetes, and the more recent developments in our understanding of elevated microvascular permeability in the diabetic circulation.     

Chromosomal rearrangements,genome reorganization,and speciation

Historical analysis of studying chromosome changes in evolution allows better understanding of the current level of research in this area. Reorganizations of the genetic system due to chromosomal rearrangements have important evolutionary consequences and may lead to speciation. Despite the complexity of evaluating the primacy of chromosome changes in speciation events, such phenomena are possible and occur in nature, as recent studies have demonstrated.     

Cultural Rules, Rituals, and Behavior Regulation

While it is generally agreed that culture and biology are both relevant to an understanding of human behavior, there is little consensus about the appropriate use of reductionist procedures. Disagreement abounds concerning the nature of the interaction and the relative contribution of distal and proximal mechanisms. An understanding of such issues may emerge only with long study of the interaction of variables at different conceptual levels of organization that intervene between the genes and culture. It is toward this larger end that the limited efforts of this paper are directed. Two cultural phenomena are considered: Murdoch's "social laws of sexual choice," and aspects of human ritual behavior. Although these constitute a unique organization of cultural items, I attempt to show how they are influenced by underlying biopsychological processes. I specifically reject, however, the view that cultural phenomena are isomorphic with, or can be completely reduced to, such processes. Emergent novelty and multiple possibilities are always present at more inclusive levels of organization. I argue that the relationship between the different sets of system variables is based on homologous functions and not merely on analogies.
SEYMOUR PARKER is Professor, Department of Anthropology, University of Utah, Salt Lake City. UT 84112     

A Biomechanical Model of Tumor-Induced Intracranial Pressure and Edema in Brain Tissue

Brain tumor growth and tumor-induced edema result in increased intracranial pressure (ICP), which, in turn, is responsible for conditions as benign as headaches and vomiting or as severe as seizures, neurological damage, or even death. Therefore, it has been hypothesized that tracking ICP dynamics may offer improved prognostic potential in terms of early detection of brain cancer and better delimitation of the tumor boundary. However, translating such theory into clinical practice remains a challenge, in part because of an incomplete understanding of how ICP correlates with tumor grade. Here, we propose a multiphase mixture model that describes the biomechanical response of healthy brain tissue—in terms of changes in ICP and edema—to a growing tumor. The model captures ICP dynamics within the diseased brain and accounts for the ability/inability of healthy tissue to compensate for this pressure. We propose parameter regimes that distinguish brain tumors by grade, thereby providing critical insight into how ICP dynamics vary by severity of disease. In particular, we offer an explanation for clinically observed phenomena, such as a lack of symptoms in low-grade glioma patients versus a rapid onset of symptoms in those with malignant tumors. Our model also takes into account the effects tumor-derived proteases may have on ICP levels and the extent of tumor invasion. This work represents an important first step toward understanding the mechanisms that underlie the onset of edema and ICP in cancer-afflicted brains. Continued modeling effort in this direction has the potential to make an impact in the field of brain cancer diagnostics.     

The visual system as a constraint on the survival and success of specific artworks

Why should vision science turn its gaze towards artworks? One possibility is that understanding visual processing might yield some fundamental insight into the nature of art. However, there are many examples of phenomena that can be seen - such as automobiles, clouds or leaves - but which are not explained in any deep sense by the properties of human visual perception. We examine one art historical question that might benefit from knowledge about the visual system: why do some artworks 'survive' historically while others fade into the dustbin of time? One possible reason, suggested by studies of rapid visual categorization, is that some objects are recognized more quickly and easily than others and thus are less culturally specific in terms of pictorial representation. A second, related, explanation is that many artistic techniques use the eyes as a channel to evoke other senses, cognition, emotions and the motor system. 'Art' is a social and historical construct - after all, the concept of 'fine art' was invented in the 18th century - and thus many aspects of artistic appreciation are specific to particular cultural and historical contexts. Some great works, however, may be adopted by successive generations because of an ability to appeal to a shared perceptual system.     

Randomness and multilevel interactions in biology

The dynamic instability of living systems and the “superposition” of different forms of randomness are viewed, in this paper, as components of the contingently changing, or even increasing, organization of life through ontogenesis or evolution. To this purpose, we first survey how classical and quantum physics define randomness differently. We then discuss why this requires, in our view, an enriched understanding of the effects of their concurrent presence in biological systems’ dynamics. Biological randomness is then presented not only as an essential component of the heterogeneous determination and intrinsic unpredictability proper to life phenomena, due to the nesting of, and interaction between many levels of organization, but also as a key component of its structural stability. We will note as well that increasing organization, while increasing “order”, induces growing disorder, not only by energy dispersal effects, but also by increasing variability and differentiation. Finally, we discuss the cooperation between diverse components in biological networks; this cooperation implies the presence of constraints due to the particular nature of bio-entanglement and bio-resonance, two notions to be reviewed and defined in the paper.     

Synthesizing insight: artificial life as thought experimentation in biology

What is artificial life? Much has been said about this interesting collection of efforts to artificially simulate and synthesize lifelike behavior and processes, yet we are far from having a robust philosophical understanding of just what Alifers are doing and why it ought to interest philosophers of science, and philosophers of biology in particular. In this paper, I first provide three introductory examples from the particular subset of artificial life I focus on, known as ‘soft Alife’ (s-Alife), and follow up with a more in-depth review of the Avida program, which serves as my case study of s-Alife. Next, I review three well-known accounts of thought experiments, and then offer my own synthesized account, to make the argument that s-Alife functions as thought experimentation in biology. I draw a comparison between the methodology of the thought-experimental world that yields real-world results, and the s-Alife research that informs our understanding of natural life. I conclude that the insights provided by s-Alife research have the potential to fundamentally alter our understanding of the nature of organic life and thus deserve the attention of both philosophers and natural scientists.     

Polymicrobial challenges to Koch's postulates: Ecological lessons from the bacterial vaginosis and cystic fibrosis microbiomes

Koch's postulates have shaped our understanding of infectious diseases; however, one of the tangential consequences of them has been the emergence of a predominantly monomicrobial perspective concerning disease aetiology. This orthodoxy has been undermined by the growing recognition that some important infectious diseases have a polymicrobial aetiology. A significant new development in our understanding of polymicrobial infections is the recognition that they represent functional ecosystems and that to understand such systems and the outcome and impact of therapeutic interventions requires an understanding of how these communities arise and develop. Therefore, it is timely to explore what we can learn from other fields. In particular, ecological theory may inform our understanding of how polymicrobial communities assemble their structure and their dynamics over time. Such work may also offer insights into how such communities move from stable to unstable states, as well as the role of invasive pathogens in the progression of the disease. Ecological theory offers a theoretical framework around which testable hypotheses can be developed to clarify the polymicrobial nature and dynamics of such infections in the face of environmental change and therapeutic interventions.     

Selfish altruism,fierce cooperation and the predator*

This paper suggests a new way to think about a famous question: what explains cooperation in nature and in particular in humans? I argue that, for an evolutionary biologist as well as a quantitative social scientist, the triangle of two ‘teammates’ in the presence of a predator (passing and shooting in two-on-one situations) is one of the fundamental conceptual building-blocks for understanding these phenomena because in such a situation the fact that life is packaged in many distinct enclosures (and not in one big monolithic blob) can unfold its comparative advantage. I show how, in the presence of a predator, cooperative equilibria emerge among entirely selfish teammates if we infinitesimally bias the lead player in the selfish direction or assign a computational burden on the predator due to the presence of a teammate. I argue that ‘predators’ are common in the biological jungle but also in everyday human settings. Intuitively, this paper builds on the simple idea – a familiar one to a biologist observing the natural world but perhaps less so to social scientists – that everybody has enemies.     

Group behaviour in physical,chemical and biological systems

Groups exhibit properties that either are not perceived to exist, or perhaps cannot exist, at the individual level. Such ‘emergent’ properties depend on how individuals interact, both among themselves and with their surroundings. The world of everyday objects consists of material entities. These are, ultimately, groups of elementary particles that organize themselves into atoms and molecules, occupy space, and so on. It turns out that an explanation of even the most commonplace features of this world requires relativistic quantum field theory and the fact that Planck’s constant is discrete, not zero. Groups of molecules in solution, in particular polymers (‘sols’), can form viscous clusters that behave like elastic solids (‘gels’). Sol-gel transitions are examples of cooperative phenomena. Their occurrence is explained by modelling the statistics of inter-unit interactions: the likelihood of either state varies sharply as a critical parameter crosses a threshold value. Group behaviour among cells or organisms is often heritable and therefore can evolve. This permits an additional, typically biological, explanation for it in terms of reproductive advantage, whether of the individual or of the group. There is no general agreement on the appropriate explanatory framework for understanding group-level phenomena in biology.     

Classical versus stochastic kinetics modeling of biochemical reaction systems

We study fundamental relationships between classical and stochastic chemical kinetics for general biochemical systems with elementary reactions. Analytical and numerical investigations show that intrinsic fluctuations may qualitatively and quantitatively affect both transient and stationary system behavior. Thus, we provide a theoretical understanding of the role that intrinsic fluctuations may play in inducing biochemical function. The mean concentration dynamics are governed by differential equations that are similar to the ones of classical chemical kinetics, expressed in terms of the stoichiometry matrix and time-dependent fluxes. However, each flux is decomposed into a macroscopic term, which accounts for the effect of mean reactant concentrations on the rate of product synthesis, and a mesoscopic term, which accounts for the effect of statistical correlations among interacting reactions. We demonstrate that the ability of a model to account for phenomena induced by intrinsic fluctuations may be seriously compromised if we do not include the mesoscopic fluxes. Unfortunately, computation of fluxes and mean concentration dynamics requires intensive Monte Carlo simulation. To circumvent the computational expense, we employ a moment closure scheme, which leads to differential equations that can be solved by standard numerical techniques to obtain more accurate approximations of fluxes and mean concentration dynamics than the ones obtained with the classical approach.     

'WHY ARE WE CURSED?': WRITING HISTORY AND MAKING PEACE IN NORTH WEST UGANDA

This article examines the nature of peacemaking and social reconstruction in Arua district, a marginalized border area of Uganda, in the late 1990s. After considering other recent accounts of violence and peacemaking, it focuses on the roles of local history writing and other forms of historical narrative in coming to terms with past violence. Local historians had two main aims: to maintain a particular understanding of the past within the local community itself, and to present themselves to others as the victims, rather than the perpetrators, of the violence in their past, as part of a wider process of mending relationships with both neighbouring groups and the Ugandan state. In attempting this, they deployed a variety of media that may be understood as historical narratives, from the performance of ritual healing ceremonies to writing conventional local histories.     

Coupling the cell cycle to cell growth

In order to multiply, both prokaryotic and eukaryotic cells go through a series of events that are collectively called the cell cycle. However, DNA replication, mitosis and cell division may also be viewed as having their own, in principle independent, cycles, which are tied together by mechanisms extrinsic to the cell cycle—the checkpoints—that maintain the order of events. We propose that our understanding of cell-cycle regulation is enhanced by viewing each event individually, as an independently regulated process. The nature of the parameters that regulate cell-cycle events is discussed and, in particular, we argue that cell mass is not such a parameter.     

Bayesian inference in populations of cortical neurons: a model of motion integration and segmentation in area MT

A major issue in cortical physiology and computational neuroscience is understanding the interaction between extrinsic signals from feedforward connections and intracortical signals from lateral connections. We propose here a computational model for motion perception based on the assumption that the local cortical circuits in the medio-temporal area (area MT) implement a Bayesian inference principle. This approach establishes a functional balance between feedforward and lateral, excitatory and inhibitory, inputs. The model reproduces most of the known properties of the neurons in area MT in response to moving stimuli. It accounts for important motion perception phenomena including motion transparency, spatial and temporal integration/segmentation. While integrating several properties of previously proposed models, it makes specific testable predictions concerning, in particular, temporal properties of neurons and the architecture of lateral connections in area MT. In addition, the proposed mechanism is consistent with the known properties of local cortical circuits in area V1. This suggests that Bayesian inference may be a general feature of information processing in cortical neuron populations. Received: 3 December 1997 / Accepted in revised form: 21 July 1998