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.     

Checkpoints and restriction points in bacteria and eukaryotic cells

Bacterial checkpoints, analogous to those proposed to exist in eukaryotic cells, offer insights into the definition of a checkpoint. Examination of bacterial "checkpoint" or arrest phenomena illustrate problems with a too-casual application of the checkpoint idea to eukaryotic phenomena. The question raised here is whether there are cellular processes that "check" whether a cellular process is completed. It is possible that many eukaryotic "checkpoints" may not have "checking" functions. Some of the ubiquitous checkpoint phenomena widely described may be merely the result of the inherent incompleteness of earlier events preventing the initiation of subsequent events.     

Is Life Law-Like?

Genes are generally assumed to be primary biological causes of biological phenotypes and their evolution. In just over a century, a research agenda that has built on Mendel's experiments and on Darwin's theory of natural selection as a law of nature has had unprecedented scientific success in isolating and characterizing many aspects of genetic causation. We revel in these successes, and yet the story is not quite so simple. The complex cooperative nature of genetic architecture and its evolution include teasingly tractable components, but much remains elusive. The proliferation of data generated in our "omics" age raises the question of whether we even have (or need) a unified theory or "law" of life, or even clear standards of inference by which to answer the question. If not, this not only has implications for the widely promulgated belief that we will soon be able to predict phenotypes like disease risk from genes, but also speaks to the limitations in the underlying science itself. Much of life seems to be characterized by ad hoc, ephemeral, contextual probabilism without proper underlying distributions. To the extent that this is true, causal effects are not asymptotically predictable, and new ways of understanding life may be required.     

Comparing healthcare systems: outcomes, ethical principles, and social values

The question of how healthcare should be structured has been at the forefront of public debate for quite some time. In particular, debate has raged over the acceptability of socialized and rights-oriented approaches to healthcare as opposed to privatized and commodity-oriented approaches. The present discussion looks at the underlying logic of the debate and at the use of outcome measures as a primary determinant. It suggests that outcome measures are of limited use in deciding the issue because they ignore important variables and further suggests that outcome measures are inappropriate tools when comparing distinct healthcare systems because they ignore valuational components that are integral to deciding whether a healthcare system is consistent with a society's principles and values.     

A direct advance on advance directives

Advance directives (ADs), which are also sometimes referred to as 'living wills', are statements made by a person that indicate what treatment she should not be given in the event that she is not competent to consent or refuse at the future moment in question. As such, ADs provide a way for patients to make decisions in advance about what treatments they do not want to receive, without doctors having to find proxy decision-makers or having recourse to the doctrine of necessity. While patients can request particular treatments in an AD, only refusals are binding. This paper will examine whether ADs safeguard the autonomy and best interests of the incompetent patient, and whether legislating for the use of ADs is justified, using the specific context of the legal situation in the United Kingdom to illustrate the debate. The issue of whether the law should permit ADs is itself dependent on the issue of whether ADs are ethically justified; thus we must answer a normative question in order to answer the legislative one. It emerges that ADs suffer from two major problems, one related to autonomy and one to consent. First, ADs' emphasis on precedent autonomy effectively sentences some people who want to live to death. Second, many ADs might not meet the standard criteria for informed refusal of treatment, because they fail on the crucial criterion of sufficient information. Ultimately, it transpires that ADs are typically only appropriate for patients who temporarily lose physical or mental capacity.     

Physics,biology, and sociology: A reappraisal

To the extent that all biological phenomena are perceivable only through their physical manifestations, it may be justified to assume that all biological phenomena will be eventually represented in terms of physics; perhaps not of present day physics, but of some “extended” form of it. However, even if this should be correct, it must be kept in mind that representing individual biological phenomena in terms of physics is not the same as deducing from known physical laws the necessity of biological phenomena. Drawing an analogy from pure mathematics, it is possible that while every biological phenomenon may be represented in terms of physics, yet biological statements represent a class of “undecidable” statements within the framework of physics. Such a conjecture is reinforced by the history of physics itself and illustrated on several examples. The 19th century physicists tried in vain todeduce electromagnetic phenomena from mechanical ones. A similar situation may exist in regard to biological and social sciences. Quite generally, the possibility of representing a class B phenomena in terms of class A phenomena does not imply that the phenomena of class B can be deduced from those of class A. The consequences of the above on the relation between physics, biology, and sociology are studied. A tentative postulational formulation of basic biological principles are given and some consequences are discussed. It is pointed out that not only can the study of biological phenomena throw light on some physical phenomena, but that the study of social phenomena may be of value for the understanding of the structures and functions of living organisms. The possibility of a sort of “socionics” is indicated.     

The prevention and repair of large abdominal-wall defects by muscle transposition: a preliminary communication

Abdominal-wall defects, whether occurring as perioperative or postoperative phenomena, have been variously managed. Where the defect cannot be repaired by the use of the patient's own tissues, synthetic material is commonly utilized. Where both the preceding are unsuccessful, closure by means of muscles transferred from the thigh should be considered. Muscles have distinct advantages over fascial grafts or synthetic materials: they are dynamic structures that are effective in controlling herniae, may relieve symptoms in the case of symptomatic scoliosis resulting from the muscle loss, and may improve bowel action by improving expulsive abdominal efforts. Preliminary experience with for patients is presented, together with details of the operative technique. Since this report was submitted, a fifth patient suffering from a congenital "prune belly" syndrome has been treated.     

Neural oscillations are a start toward understanding brain activity rather than the end

Does rhythmic neural activity merely echo the rhythmic features of the environment, or does it reflect a fundamental computational mechanism of the brain? This debate has generated a series of clever experimental studies attempting to find an answer. Here, we argue that the field has been obstructed by predictions of oscillators that are based more on intuition rather than biophysical models compatible with the observed phenomena. What follows is a series of cautionary examples that serve as reminders to ground our hypotheses in well-developed theories of oscillatory behavior put forth by theoretical study of dynamical systems. Ultimately, our hope is that this exercise will push the field to concern itself less with the vague question of “oscillation or not” and more with specific biophysical models that can be readily tested.     

Induced pluripotent stem cells: past, present, and future

The development of iPSCs reflected the merging of three major scientific streams and has in turn led to additional new branches of investigation. However, there is still debate about whether iPSCs are functionally equivalent to ESCs. This question should be answered only by science, not by politics or business.     

Recursive evolution.

In evolutionary systems in which the units (individuals) are generated by a morphogenetic process, unbiased "mosaic type" mutability of the phenotype is not possible (Waddington's principle). The question is whether this unavoidable "channeling" can itself be made plastic through provision of alternative morphogeneses possessing differing "hot spots." If so, plasticity would not only be reestablished, but be established at a higher level. Plasticity itself would be plastic. The property of ultrasplasticity is evolutionarily necessary and stable, but perhaps not possible. Ultraplastic systems form a subclass of "temporal brains" as described in deductive biology. Many of their properties have yet to be discovered.     

Organisms or biological individuals? Combining physiological and evolutionary individuality

The definition of biological individuality is one of the most discussed topics in philosophy of biology, but current debate has focused almost exclusively on evolution-based accounts. Moreover, several participants in this debate consider the notions of a biological individual and an organism as equivalent. In this paper, I show that the debates would be considerably enriched and clarified if philosophers took into account two elements. First, physiological fields are crucial for the understanding of biological individuality. Second, the category of biological individuals should be divided into two subcategories: physiological individuals and evolutionary individuals, which suggests that the notions of organism and biological individual should not be used interchangeably. I suggest that the combination of an evolutionary and a physiological perspective will enable biologists and philosophers to supply an account of biological individuality that will be both more comprehensive and more in accordance with scientific practices.     

Beneficence, determinism and justice: an engagement with the argument for the genetic selection of intelligence

In 2001, Julian Savulescu wrote an article entitled 'Procreative Beneficence: Why We Should Select the Best Children', in which he argued for the genetic selection of intelligence in children. That article contributes to a debate on whether genetic research on intelligence should be undertaken at all and, if so, should intelligence selection be available to potential parents. As such, the question of intelligence selection relates to wider issues concerning the genetic determinism of behavioural traits, i.e. alcoholism. This article is designed as an engagement in the intelligence selection debate using an analysis of Savulescu's arguments to raise a series of problematic issues in relation to the ethics of parental selection of intelligence. These problematic issues relate to wider assumptions that are made in order to put forward intelligence selection as a viable ethical option. Such assumptions are more generic in character, but still relate to Savulescu's article, concerning issues of genetic determinism, private allocation and inequality, and, finally, individual versus aggregate justice. The conclusion focuses on what the implications are for the question of agency, especially if intelligence selection is allowed.     

What systems biology can tell us about disease

A recent debate has touched upon the question of whether diseases can be understood as dysfunctional mechanisms or whether there are "pathological" mechanisms that deserve to be investigated and explained independently (Nervi 2010; Moghaddam-Taaheri 2011). Here I suggest that both views tell us something important about disease but that in many instances only a systemic view can shed light on the relationship between physiology and pathology. I provide examples from the literature in systems biology in support of my position. As a result of my analysis, I conclude that a perspective narrowly focusing on mechanisms is insufficient if the goal is to get a comprehensive picture of disease.     

Live Better by Consuming Less?: Is There a "Double Dividend" in Sustainable Consumption?

Industrial ecology has mainly been concerned with improving the efficiency of production systems. But addressing consumption is also vital in reducing the impact of society on its environment. The concept of sustainable consumption is a response to this. But the debates about sustainable consumption can only really be understood in the context of much wider and deeper debates about consumption and about consumer behavior itself. This article explores some of these wider debates. In particular, it draws attention to a fundamental disagreement that runs through the literature on consumption and haunts the debate on sustainable consumption: the question of whether, or to what extent, consumption can be taken as "good for us." Some approaches assume that increasing consumption is more or less synonymous with improved well-being: the more we consume the better off we are. Others argue, just as vehemently, that the scale of consumption in modern society is both environmentally and psychologically damaging, and that we could reduce consumption significantly without threatening the quality of our lives. This second viewpoint suggests that a kind of "double dividend" is inherent in sustainable consumption: the ability to live better by consuming less and reduce our impact on the environment in the process. In the final analysis, this article argues, such "win-win" solutions may exist but will require a concerted societal effort to realize.     

Photorefractoriness in Japanese quail: possible involvement of the thyroid gland

Quail have a form of refractoriness to long daylengths that is relative and not absolute. The properties of "relative refractoriness" are compared with the more typical "absolute" form seen in starlings and the question is posed as to whether the two types represent the extremes of a single underlying process or are quite separate phenomena. A model is offered that assumes that a single process is involved, and some tests of the hypothesis, notably the involvement of the thyroid gland, are described.     

Molecular mechanisms of action of the soy isoflavones includes activation of promiscuous nuclear receptors. A review

Consumption of soy has been demonstrated to reduce circulating cholesterol levels, most notably reducing low-density lipoprotein (LDL) cholesterol levels in hypercholesterolemic individuals. The component or components that might be responsible for this effect is still a matter of debate or controversy among many researchers. Candidate agents include an activity of soy protein itself, bioactive peptides produced during the digestive process, or the soy isoflavones. Although soy intake may provide other health benefits including preventative or remediative effects on cancer, osteoporosis and symptoms of menopause, this review will focus on isoflavones as agents affecting lipid metabolism. Isoflavones were first discovered as a bioactive agent disrupting estrogen action in female sheep, thereby earning the often-used term 'phytoestrogens'. Subsequent work confirmed the ability of isoflavones to bind to estrogen receptors. Along with the cholesterol-lowering effect of soy intake, research that is more recent has pointed to a beneficial antidiabetic effect of soy intake, perhaps mediated by soy isoflavones. The two common categories of antidiabetic drugs acting on nuclear receptors known as peroxisome proliferator activated receptors (PPARs) are the fibrates and glitazones. We and others have recently asked the research question 'do the soy isoflavones have activities as either "phytofibrates" or "phytoglitazones"?' Such an activity should be able to be confirmed both in vivo and in vitro. In both the in vivo and in vitro cases, this action has indeed been confirmed. Further work suggests a possible action of isoflavones similar to the nonestrogenic ligands that bind the estrogen-related receptors (ERRs). Recently, these receptors have been demonstrated to contribute to lipolytic processes. Finally, evaluation of receptor activation studies suggests that thyroid receptor activation may provide additional clues explaining the metabolic action of isoflavones. The recent advances in the discovery and evaluation of the promiscuous nuclear receptors that bind many different chemical ligands should prove to help explain some of the biological effects of soy isoflavones and other phytochemicals.     

Testing the validity of comparisons between the rheological and the calorimetric glass transition temperatures

Dynamic mechanical techniques are used increasingly in the investigation of vitrification phenomena in biological materials, thus posing the question of whether the rheological T(g) should be compared with the established practice of obtaining T(g) values from differential scanning calorimetry. The nature of the rheological T(g) is discussed and its frequency dependence is established with a view to facilitating comparisons with calorimetric data. Despite claims made in the literature, results on high sugar-kappa-carrageenan mixtures, hydrated gelatin films, and thermoset epoxy resins demonstrate that there is no clear reference point for comparison of the glass transition temperatures derived with the two techniques. Furthermore, the structure-forming ability of kappa-carrageenan and other biopolymers impacts primarily upon the mechanical manifestation of vitrification and contributes to the state of complexity of comparisons between thermal and mechanical data.     

Is a gene‐centric human proteome project the best way for proteomics to serve biology?

With the recent developments in proteomic technologies, a complete human proteome project (HPP) appears feasible for the first time. However, there is still debate as to how it should be designed and what it should encompass. In “proteomics speak”, the debate revolves around the central question as to whether a gene‐centric or a protein‐centric proteomics approach is the most appropriate way forward. In this paper, we try to shed light on what these definitions mean, how large‐scale proteomics such as a HPP can insert into the larger omics chorus, and what we can reasonably expect from a HPP in the way it has been proposed so far.     

Insulin-like growth factor binding protein-2 as a regulator of IGF actions in CNS: implications in multiple sclerosis

Insulin-like growth factors (IGFs) are indispensable peptide hormones for proper development of the central nervous system (CNS). Because IGF-1 exhibits neuroprotective and myelinogenetic effects, it possesses therapeutic potential in treating neurodegenerative demyelinating diseases such as multiple sclerosis (MS). However, IGF actions are largely dependant on high-affinity regulatory IGF binding proteins (IGFBPs), which are likely to interfere with therapeutic attempts at elevating IGF-1 levels in the CNS. In particular, IGFBP-2 plays a dominant role in IGF regulation in the CNS and is upregulated in several pathological conditions, including MS. The question remains as to whether IGFBPs should be considered "interfering" components of IGF treatment strategies or might possibly be utilized to clinical advantage. This review discusses our current understanding of biological functions of IGFBP-2 in the CNS and its implications in the demyelinating disease MS.     

Microbial deterioration of cultural heritage and works of art — tilting at windmills?

Microorganisms (bacteria, archaea and fungi), in addition to lichens and insect pests, cause problems in the conservation of cultural heritage because of their biodeteriorative potential. This holds true for all types of historic artefacts, and even for art made of modern materials, in public buildings, museums and private art collections. The variety of biodeterioration phenomena observed on materials of cultural heritage is determined by several factors, such as the chemical composition and nature of the material itself, the climate and exposure of the object, in addition to the manner and frequency of surface cleaning and housekeeping in museums. This study offers a review of a variety of well-known biodeterioration phenomena observed on different materials, such as stone and building materials, objects exhibited in museums and libraries, as well as human remains and burial-related materials. The decontamination of infected artefacts, exhibition rooms and depots incurs high expenditure for museums. Nevertheless, the question has to be raised: whether the process of biodeterioration of cultural heritage can or should be stopped under all circumstances, or whether we have to accept it as a natural and an implicit consecution of its creation. This study also highlights critically the pros and cons of biocide treatments and gives some prominent examples of successful and unsuccessful conservation treatments. Furthermore, an outlook on the future research needs and developments in this highly interesting field is given.