Quantum microbiology

During his famous 1943 lecture series at Trinity College Dublin, the reknown physicist Erwin Schrodinger discussed the failure and challenges of interpreting life by classical physics alone and that a new approach, rooted in Quantum principles, must be involved. Quantum events are simply a level of organization below the molecular level. This includes the atomic and subatomic makeup of matter in microbial metabolism and structures, as well as the organic, genetic information code of DNA and RNA. Quantum events at this time do not elucidate, for example, how specific genetic instructions were first encoded in an organic genetic code in microbial cells capable of growth and division, and its subsequent evolution over 3.6 to 4 billion years. However, due to recent technological advances, biologists and physicists are starting to demonstrate linkages between various quantum principles like quantum tunneling, entanglement and coherence in biological processes illustrating that nature has exerted some level quantum control to optimize various processes in living organisms. In this article we explore the role of quantum events in microbial processes and endeavor to show that after nearly 67 years, Schr?dinger was prophetic and visionary in his view of quantum theory and its connection with some of the fundamental mechanisms of life.     

Biological adaptabilities and quantum entropies.

The entropy-based theory of adaptability set forth by Michael Conrad in the early 1970s continued to appear in his work for over two decades, and was the subject of the only book he published in his lifetime. He applied this theory to a host of subjects ranging from enzyme dynamics to sociology. This paper reviews the formalism of adaptability theory, clarifying some of its mathematical and interpretive difficulties. The theory frames the computational tradeoff principle, a thesis that was the most frequently recurring claim in his work. The formulation of adaptability theory presented here allows the introduction of quantum entropy functions into the theory, revealing an interesting relationship between adaptability and another one of Conrad's deep preoccupations, the role of quantum processes in life.     

Reflections on a giant of brain science

Walter J. Freeman was a giant of the field of neuroscience whose visionary work contributed various experimental and theoretical breakthroughs to brain research in the past 60 years. He has pioneered a number of Electroencephalogram and Electrocorticogram tools and approaches that shaped the field, while “Freeman Neurodynamics” is a theoretical concept that is widely known, used, and respected among neuroscientists all over the world. His recent death is a profound loss to neuroscience and biomedical engineering. Many of his revolutionary ideas on brain dynamics have been ahead of their time by decades. We summarize his following groundbreaking achievements: (1) Mass Action in the Nervous System, from microscopic (single cell) recordings, through mesoscopic populations, to large-scale collective brain patterns underlying cognition; (2) Freeman–Kachalsky model of multi-scale, modular brain dynamics; (3) cinematic theory of cognitive dynamics; (4) phase transitions in cortical dynamics modeled with random graphs and quantum field theory; (5) philosophical aspects of intentionality, consciousness, and the unity of brain–mind–body. His work has been admired by many of his neuroscientist colleagues and followers. At the same time, his multidisciplinary approach combining advanced concepts of control theory and the mathematics of nonlinear systems and chaos, poses significant challenges to those who wish to thoroughly understand his message. The goal of this commemorative paper is to review key aspects of Freeman’s neurodynamics and to provide some handles to gain better understanding about Freeman’s extraordinary intellectual achievement.     

Is otolith science transformative? New views on fish migration

Publications focused on fish otolith applications grew exponentially from 1981–2000 but have subsequently stabilized, suggesting maturation of otolith applications. Over the past 30 years >3,500 primary journal publications were identified prompting the question, how have otoliths fundamentally changed our understanding of fishes and their environment? Has otolith science in this way been transformative? I use Harden Jones’ 1968 Fish Migration as a benchmark of fish migration concepts prior to Pannella’s 1971 breakthrough paper on otolith microstructure. For case study species I highlight how otolith science has informed migration concepts including, (1) parent stream theory (Atlantic bluefin tuna), (2) adoptive homing (Atlantic herring), and (3) partial migration (European eel). Harden Jones’ overall conclusion that life cycle closure leads to population structure (also known as the migration triangle) is a first principle in fisheries science, but in recent years has been challenged by otolith science. In particular, a transformative discovery attributable to otoliths is that life cycles vary substantially within populations. New avenues of otolith science are now exploring the causes and consequences of this life cycle diversity, and large advances are expected through integration of otolith approaches with electronic tagging, genetics, field manipulations, and modeling that will permit migration concepts to be tested at multiple ecological scales.     

Determinants of time allocation across the lifespan

This paper lays the groundwork for a theory of time allocation across the life course, based on the idea that strength and skill vary as a function of age, and that return rates for different activities vary as a function of the combination of strength and skills involved in performing those tasks. We apply the model to traditional human subsistence patterns. The model predicts that young children engage most heavily in low-strength/low-skill activities, middle-aged adults in high-strength/high-skill activities, and older adults in low-strength/high-skill activities. Tests among Machiguenga and Piro forager-horticulturalists of southeastern Peru show that males and females focus on low-strength/low-skill tasks early in life (domestic tasks and several forms of fishing), switch to higher-strength/higher-skill activities in their twenties and thirties (hunting, fishing, and gardening for males; fishing and gardening for females), and shift focus to high-skill activities late in life (manufacture/repair, food processing). Michael Gurven is an assistant professor of anthropology at the University of California-Santa Barbara. He received his Ph.D. from the University of New Mexico in 2000. He has conducted fieldwork in Paraguay and Bolivia with Ache and Tsimane forager-horticulturalists. His research interests include intragroup cooperation and problems of collective action, and the application of life history theory to explaining human longevity, cognitive development, delayed maturation, and sociality. Since 2002, Gurven and Kaplan have co-directed the Tsimane Health and Life History Initiative, a five-year project to develop theory and test implications of different models of human life history evolution. Hillard Kaplan is a professor of anthropology at University of New Mexico. He received his Ph.D. from the University of Utah in 1983. He has conducted fieldwork in Paraguay, Brazil, Botswana, and Bolivia. His research interests include evolutionary perspectives on life course development and senescence, and brain evolution. He has launched theoretical and empirical investigations into each of these areas, uniting evolutionary and economic approaches. He has applied human capital theory toward explaining human life history evolution, and the proximate physiological and psychological mechanisms governing fertility and parental investment in both traditional, high-fertility, subsistence economies and modern, low-fertility, industrial societies.     

Govindjee,an institution,at his 80th (really 81st) birthday in Třeboň in October, 2013: a pictorial essay

Govindjee (one name only), who himself is an institution, has been recognized and honored by many in the past for he is a true ambassador of “Photosynthesis Research” to the World. He has been called “Mr. Photosynthesis”, and compared to the Great Wall of China. To us in T?eboň, he has been a great research collaborator in our understanding of chlorophyll a fluorescence in algae and in cyanobacteria, and more than that a friend of the Czech “Photosynthesis” group, from the time of Ivan ?etlík (1928–2009) and of Zdeněk ?esták (1932–2008). Govindjee’s 80th (really 81st) birthday was celebrated by the Institute of Microbiology, Laboratory of Photosynthesis, by toasting him with an appropriate drink of a suspension of green algae grown at the institute itself. After my presentation, on October 23, 2013, of Govindjee’s contributions to photosynthesis, and his intimate association with the photosynthetikers (in Jack Myers’s words) of the Czech Republic, Govindjee gave us his story of how he began research in photosynthesis in the late 1950s. This was followed by a talk on October 25 by him on “Photosynthesis: Stories of the Past.” Everyone enjoyed his animated talk—it was full of life and enjoyment. Here, I present a brief pictorial essay on Govindjee at his 80th (really 81st) birthday in T?eboň during October 23–25, 2013.     

Quantum monadology: a consistent world model for consciousness and physics

The NL world model presented in the previous paper is embodied by use of relativistic quantum mechanics, which reveals the significance of the reduction of quantum states and the relativity principle, and locates consciousness and the concept of flowing time consistently in physics. This model provides a consistent framework to solve apparent incompatibilities between consciousness (as our interior experience) and matter (as described by quantum mechanics and relativity theory). Does matter have an inside? What is the flowing time now? Does physics allow the indeterminism by volition? The problem of quantum measurement is also resolved in this model.     

The role of routine serum testosterone testing: routine hormone analysis is not indicated as an initial screening test in the evaluation of erectile dysfunction

A 60-year-old male physician is self-referred to your office for evaluation of his erectile dysfunction, which has been worsening for 5 years. He reports his erections rarely achieve fullness for penetration, and he is unable to ejaculate. He has tried sildenafil citrate (Viagra(R); Pfizer Inc, New York, NY) with mild success in the past. He has a strong libido and feels healthy. He rarely exercises, but is on his feet most of the day at work. He has been healthy his whole life and never seeks a doctor's attention. He has no other medical problems. His only medication is a baby aspirin once a day. His physical examination, including genitalia, is normal. As part of his initial visit, should his serum testosterone level be checked by his urologist?     

Generalized Make and Use Framework for Allocation in Life Cycle Assessment

Allocation in life cycle inventory (LCI) analysis is one of the long‐standing methodological issues in life cycle assessment (LCA). Discussion on allocation among LCA researchers has taken place almost in complete isolation from the series of closely related discussions from the 1960s in the field of input?output economics, regarding the supply and use framework. This article aims at developing a coherent mathematical framework for allocation in LCA by connecting the parallel developments of the LCA and the input?output communities. In doing so, the article shows that the partitioning method in LCA is equivalent to the industry‐technology model in input?output economics, and system expansion in LCA is equivalent to the by‐product‐technology model in input?output output economics. Furthermore, we argue that the commodity‐technology model and the by‐product‐technology model, which have been considered as two different models in input?output economics for more than 40 years, are essentially equivalent when it comes to practical applications. It is shown that the matrix‐based approach used for system expansion successfully solves the endless regression problem that has been raised in LCA literature. A numerical example is introduced to demonstrate the use of allocation models. The relationship of these approaches with consequential and attributional LCA models is also discussed.     

What's in a (Big) Name? The Art and Agency of a Bornean Photographic Collection

This article concerns the photographic collection of Paka anak Otor, the Bidayuh owner of a ‘mini-museum’ in Sarawak, Malaysian Borneo, and how it became entangled in his claims to status within and beyond his village. Superficially, the situation is easily apprehended via two analogous approaches within photographic theory and Southeast Asianist ethnography, which treat objects and images as representations or bearers of power and meaning. Here I suggest that such approaches end up eliding the action-centred nature of Paka's ‘big name’-making ambitions. In response, I approach his photographic collection through an analytical framework deriving from Alfred Gell's seminal theory, Art and Agency (1998), which has hitherto remained marginal to Southeast Asianist anthropology. I argue that, more than merely symbolising or bearing his ‘big name’, Paka's photographs were agentive image-objects that actively instantiated it. I conclude by asking how such an analytical shift might encourage a reconceptualisation of ‘power’ and ‘objecthood’ in Southeast Asianist anthropology.     

Phylogeny of the tribe Fumarieae (Papaveraceae s.l.) based on chloroplast and nuclear DNA sequences: Evolutionary and biogeographic implications

? Premise of the Study: Little research has been done at the molecular level on the tribe Fumarieae (Papaveraceae). Papaveraceae is a model plant group for studying evolutionary patterns despite the lack of a reference phylogeny for this tribe. We investigated the phylogenetic relationships within the tribe to complete the molecular data for this family in order to help understand its character evolution and biogeographic pattern. ? Methods: We used maximum-parsimony and Bayesian approaches to analyze five DNA regions for 25 species representing 10 of the 11 Fumarieae genera and five outgroups. Evolutionary pathways of four characters (habit, life span, type of fruit, and number of seeds per fruit) were inferred on the phylogeny using parsimony. The ancestral distribution areas were reconstructed using dispersal-vicariance analysis. ? Key Results: Fumarieae is monophyletic and includes three groups that agree with the morphology-based subtribes: Discocapninae, Fumariinae, and Sarcocapninae. Within subtribes, the relationships among genera were different from those obtained with morphological data. Annual life span, nonchasmophytic habit, and a several-seeded capsule were the basal character states for the tribe. The ancestor occupied a continuous area between West Eurasia and Africa. Vicariances explain the divergence between lineages Discocapninae (South Africa) and Fumariinae-Sarcocapninae (Mediterranean), and the disjunction of Fumariinae (Mediterranean-Central Asia). ? Conclusions: Molecular phylogeny confirms the subtribal classification of Fumarieae based on morphology. However it provides different results regarding the relationships among genera within each subtribe, which affects the inference of the evolutionary pathway followed by the four selected characters. The disjunct distribution of the tribe is explained by different vicariance scenarios.     

Quantum-dynamical picture of a multistep enzymatic process: reaction catalyzed by phospholipase A(2)

A quantum-classical molecular dynamics model (QCMD), applying explicit integration of the time-dependent Schr?dinger equation (QD) and Newtonian equations of motion (MD), is presented. The model is capable of describing quantum dynamical processes in complex biomolecular systems. It has been applied in simulations of a multistep catalytic process carried out by phospholipase A(2) in its active site. The process includes quantum-dynamical proton transfer from a water molecule to histidine localized in the active site, followed by a nucleophilic attack of the resulting OH(-) group on a carbonyl carbon atom of a phospholipid substrate, leading to cleavage of an adjacent ester bond. The process has been simulated using a parallel version of the QCMD code. The potential energy function for the active site is computed using an approximate valence bond (AVB) method. The dynamics of the key proton is described either by QD or classical MD. The coupling between the quantum proton and the classical atoms is accomplished via Hellmann-Feynman forces, as well as the time dependence of the potential energy function in the Schr?dinger equation (QCMD/AVB model). Analysis of the simulation results with an Advanced Visualization System revealed a correlated rather than a stepwise picture of the enzymatic process. It is shown that an sp(2)--> sp(3) configurational change at the substrate carbonyl carbon is mostly responsible for triggering the activation process.     

Mikhail Khristoforovich Chailakhyan: The fate of the scientist under the sign of florigen

The more significant is a discovery made by the scientist, the greater influence it exerts on the fate of its author. The theory of florigen, a hormone of flowering, put forward by M.Kh. Chailakhyan in 1936 initially was inconvenient for Soviet authorities and brought severe trials to the scientist. However, as distinct from many others, Chailakhyan did not deny his scientific beliefs but continued to defend them in spite of harassment and threats. Later, on the contrary, this theory promoted the worldwide fame of its creator, although during Chailakhyan lifetime florigen has not been definitely identified chemically. Chailakhyan was close to the establishing of florigen protein nature, but even his long life was not enough to identify this elusive substance.     

The Claude Bernard Distinguished Lecture. In pursuit of meaningful learning

The Bernard Distinguished Lecturers are individuals who have a history of experience and expertise in teaching that impacts multiple levels of health science education. Dr. Joel Michael more than meets these criteria. Joel earned a BS in biology from CalTech and a PhD in physiology from MIT following which he vigorously pursued his fascination with the mammalian central nervous system under continuous National Institutes of Health funding for a 15-yr period. At the same time, he became increasingly involved in teaching physiology, with the computer being his bridge between laboratory science and classroom teaching. Soon after incorporating computers into his laboratory, he began developing computer-based learning resources for his students. Observing students using these resources to solve problems led to an interest in the learning process itself. This in turn led to a research and development program, funded by the Office of Naval Research (ONR), that applied artificial intelligence to develop smart computer tutors. The impact of problem solving on student learning became the defining theme of National Science Foundation (NSF)-supported research in health science education that gradually moved all of Dr. Michael's academic efforts from neurophysiology to physiology education by the early 1980's. More recently, Joel has been instrumental in developing and maintaining the Physiology Education Research Consortium, a group of physiology teachers from around the nation who collaborate on diverse projects designed to enhance learning of the life sciences. In addition to research in education and learning science, Dr. Michael has devoted much of his time to helping physiology teachers adopt modern approaches to helping students learn. He has organized and presented faculty development workshops at many national and international venues. The topics for these workshops have included computer-based education, active learning, problem-based learning, and the use of general models in teaching physiology.     

Remembering Our Forebears: Albert Jan Kluyver and the Unity of Life

The Dutch microbiologist/biochemist Albert Jan Kluyver (1888–1956) was an early proponent of the idea of biochemical unity, and how that concept might be demonstrated through the careful study of microbial life. The fundamental relatedness of living systems is an obvious correlate of the theory of evolution, and modern attempts to construct phylogenetic schemes support this relatedness through comparison of genomes. The approach of Kluyver and his scientific descendants predated the tools of modern molecular biology by decades. Kluyver himself is poorly recognized today, yet his influence at the time was profound. Through lens of today however, it has been argued that the focus by Kluyver and others to create taxonomic and phylogenetic schemes using morphology and biochemistry distorted and hindered progress of the discipline of microbiology, because of a perception that the older approaches focused too much on a reductionist worldview. This essay argues that in contrast the careful characterization of fundamental microbial metabolism and physiology by Kluyver made many of the advances of the latter part of the twentieth century possible, by offering a framework which in many respects anticipated our current view of phylogeny, and by directly and indirectly training a generation of scientists who became leaders in the explosive growth of biotechnology.     

Editorial

The Per Brinck Foundation at the editorial office of the journal Oikos and Wiley/Blackwell Publishing annually awards the Per Brinck Oikos Award in honor of the Swedish ecologist Professor Per Brinck, who has played an instrumental role for the development and recognition of the science of ecology in the Nordic countries, especially as serving as the Editor‐in‐Chief for Oikos for many years. The Per Brinck Oikos Award recognizes extraordinary and important contributions to the science of ecology. Particular emphasis is given to scientific work aimed at synthesis that has led to novel and original research in unexplored or neglected fields or to bridging gaps between ecological disciplines. Such achievements typically require theoretical innovation and development as well as imaginative observational or experimental work, all of which will be valid grounds for recognition. The 2012 laureate is Prof. Tim Coulson from Imperial College London for his timely and synthesizing work on linking ecological and evolutionary theory. Instead of treating individual variation in life history as noise, he is embracing individual variation and the mechanisms leading to it. By integrating this variation into models he developed novel theoretical approaches to predict ecological and evolutionary consequences of environmental change on life history, population dynamics and the distribution of quantitative characters and genotypes. In this issue, we publish Tim Coulson’s Per Brinck lecture in which he demonstrates the advantages of integral projection models for the understanding of eco‐evolutionary dynamics in systems that cannot be easily replicated in the field ( Coulson 2012 ). By this hands‐ on paper, Tim advocates the benefits of IPM’s to field biologists who may not have tried to construct models before but might be interested in doing so. Oikos is publishing novel work that aims at synthesis and generalization; for instance recent empirical ( Auld and Charmantier 2011 ) and theoretical work of ( Bårdsen et al. 2011 ) on the linkage of life history and population dynamics to climate change. As evidenced by the per Brinck paper in this issue, real synthesis can be created by the integration of empirical and theoretical approaches in both marine ( Dias and Marshall 2010 ) and terrestrial environments ( Jacquemin et al. 2012 , Rodríguez‐Pérez and Traveset 2012 ). Oikos is aiming to stimulate synthesis in specific fields by bringing together papers from different disciplines and systems into more thematic issues that are centred on key contributions ( Bonte et al. 2012 ). In order to improve our understanding of the wealth of mechanisms determining life history variation, we have compiled such an issue consisting of 17 articles documenting novel insights in life history theory and its relevance for predicting phenomena at higher level of biological organization. We especially would like to highlight the contributions on density dependency in larger herbivores ( Mobæk et al. 2012 ) and novel approaches for testing them in nature ( Simard et al. 2012 ). Equally important is the synthesis created by the compilation of contributions demonstrating the interplay between genetics and environment on floral display and subsequent reproduction ( von Euler et al. 2012 ), its further importance for pollinator fitness ( Cahenzli and Erhardt 2012 ). By means of an elegant experiment, Brody and Irwin (2012) show that variability in plant response to herbivory can be attributed by plant interactions with mutualists and enemies. In a final package of papers, we compile work demonstrating amongst others the importance of stage‐ or age specific life history responses on predation ( Sand et al. 2012 ), phenology ( Briscoe et al. 2012 ) and the importance of overall life history variation on immunology and reservoir competence of infectious diseases ( Previtali et al. 2012 ).     

Climate effects on growth, phenology, and survival of sockeye salmon (Oncorhynchus nerka): a synthesis of the current state of knowledge and future research directions

Sockeye salmon (Oncorhynchus nerka) is one of the most iconic and valued species of Pacific salmon. Various studies have examined the potential effects of future climate change on sockeye salmon, but there is currently no synthesis of the documented effects of climate on this species. In this paper, we present a synthesis of 80 peer-reviewed publications in the English language evaluating the effects of climate on sockeye salmon growth, phenology, and survival. The great majority of studies examined have been conducted with stocks from North America (90?% of studies). Survival (55?%) has been the most frequently studied aspect of the sockeye salmon life history in relation to climate, followed by growth (45?%) and phenology (30?%), with temperature (83.4?%) being the climate-related variable most frequently examined in such studies. Across life stages, the effects of climate-related variables have been most frequently studied on fry (36.3?%) and least studied on spawners (7.5?%). Our synthesis revealed that associations between temperature and growth, phenology, or survival have been uncovered for all the life stages of sockeye salmon, whereas relationships with other climate-related variables have been sparse. There is substantial evidence that sockeye salmon are influenced by thermal conditions experienced at regional, rather than ocean- or continental-wide scales, and that responses to temperature vary among and within stocks. The mechanisms by which climate affect sockeye salmon during the early stages in freshwater and while at sea are still poorly understood and warrant future research. More research on the effects of non-temperature, climate-related variables (e.g. stream flow, ocean pH), inter-generational and carry-over effects of climate, interaction between climate and non-climate stressors, and adaptation to climate change are also needed. Such information will be critical to advance our understanding of how sockeye salmon stocks will fare with future climate change.     

Giovanni Boccaccio's (1313–1375) disease and demise: The final untold tale of liver and heart failure

Giovanni Boccaccio's fatal disease(s) and cause of death have long remained a mystery. Now, for the first time, a thorough multidisciplinary reassessment has finally been carried out. By combining philological and clinical approaches, it is at last possible to suggest a solid retrospective diagnosis based upon a study of his correspondence, poetry and iconography, as well as references to his physical decay in coeval and later sources. It would appear that he suffered over the last three years of his life from hepatic and cardiac failure, conditions that resulted in edema and potentially even hepatic carcinoma. Focusing on an unusually well-documented case from the Middle Ages, this analysis of exceptionally high informative value reconstructs the symptoms of his medical conditions and finally permits us to clarify and explain the historical feaures, presentations and evolutionary history of the case at hand.     

Field theory for biogeography: a spatially explicit model for predicting patterns of biodiversity

Predicting the variation of biodiversity across the surface of the Earth is a fundamental issue in ecology, and in this article we focus on one of the most widely studied spatial biodiversity patterns: the species–area relationship (SAR). The SAR is a central tool in conservation, being used to predict species loss following global climate change, and is striking in its universality throughout different geographical regions and across the tree of life. In this article we draw upon the methods of quantum field theory and the foundation of neutral community ecology to derive the first spatially explicit neutral prediction for the SAR. We find that the SAR has three phases, with a power law increase at intermediate scales, consistent with decades of documented empirical patterns. Our model also provides a building block for incorporating non-neutral biological variation, with the potential to bridge the gap between neutral and niche-based approaches to community assembly.
Ecology Letters (2010) 13: 87–95     

The young Ramón y Cajal as a cell-theory dissenter.

The intellectual development of scientists normally traverses several different phases as they mature in their professions. In many cases, strong support of certain ideas and theories gives way to more critical, productive views that set the stage for major theories and discoveries. This appears to have been the case of Santiago Ramón y Cajal (1852-1934). In his youth, he supported the protoplasmic theory of life, and as he matured he maintained a critical, yet open view of the cell theory, which postulated that life phenomena could not take place below the cellular level. In later years, however, an older and wiser Ramón y Cajal abandoned all traces of dissent and joined in fully supporting a refined version of cell theory, to which his own discoveries significantly contributed.