Meaning in Nature: Organic Manufacture?

The paper examines Marcello Barbieri’s (2007) Introduction to Biosemiotics. Highlighting debate within the biosemiotic community, it focuses on what the volume offers to those who explain human intellect in relation to what Turing called our ‘physical powers.’ In scrutinising the basis of world-modelling, parallels and contrasts are drawn with other work on embodied-embedded cognition. Models dominate biology. Is this a qualitative fact or does it point to biomechanisms? In evaluating the 18 contributions, it is suggested that the answers will shape the field. First, they will decide if biochemistry and explanatory reduction can be synergised by biosemantics. Second, they will show if our intellectual powers arise from biology. Does thinking use—not a language faculty—but what Marko? and colleagues call semiosis by the living? Resolution of such issues, it is suggested, can change how we view cognition. Above all, if the biomechanists win the day, cultural models can be regarded as extending natural meaning. On such a view, biomechanisms prompt us to act and perceive as we model our own natural models. This fits Craik’s vision: intellect gives us the alphanumerical ‘symbols’ that allow thoughts to have objective validity. For the biomechanist, this is explained—not by brains alone—but, rather, by acting under the constraints of historically extended sensoria.     

Genomic instability, bystander effects and radiation risks: implications for development of protection strategies for man and the environment

The last few years has seen what people are now referring to as a "shifting Paradigm" in our way of thinking about radiation effects on biological systems. The concept of the central role of DNA damage due to double strand breaks induced by a radiation "hit" has been itself hit by many studies showing persistent effects in the distant progeny of radiation exposed cells. This phenomenon is known as radiation induced genomic instability. More recently evidence has been accumulating that not even the parent cell need be exposed to radiation (the bystander effect). The new paradigm suggests that cellular stress responses or damage signalling through a range of signal transduction pathways are involved and that cell-cell contact or secretion of damage signalling molecules can induce responses in undamaged and unirradiated cells. Are these new effects relevant to risk assessment, or does it matter HOW radiation affects cells if we have good epidemiological evidence of which to base our risk estimates? The aim of this paper is to introduce the new concepts and to consider reasons why they might alter our methods of risk estimation. The paper also considers the impact of the new concepts on environmental protection and discusses the need for research in the field of comparative radiobiology if we are to develop policies which can adequately protect biodiversity.     

Ecology's dark matter: The elusive and enigmatic niche

Ecologists are often frustrated that their universe, populated by strange and wilful creatures, seems fuzzy and unpredictable. Physicists, in contrast, seem to have it much better. But that's because we usually focus on Newtonian physics. In fact, physicists seem happy to live with all kinds of strange beasts, including dark matter, something they have never seen, but which they nevertheless believe makes up most of the matter in the universe. Here I argue that niches are ecology's dark matter. We are embarrassed by them, because we do not quite know what they are, and yet their presence can be universally felt; otherwise, ecological communities, like galaxies without dark matter, would simply collapse. I describe how we could potentially better describe these dark shapes that haunt our science and why this is important. In particular, I present the outline of a method for demonstrating whether or not plant species have complementary resource-use niches; something that has been difficult to show unequivocally. The presence of such resource-use niches would put to rest once and for all the notion of species equivalence and the neutral world that this assumption entails. I conclude that ecologists should take a leaf out of the physicists’ book and accept that the continued search for the esoteric niche is a legitimate and central (if frustrating) part of ecology.     

Significance of Polarization Charges and Isomagnetic Surface in Magnetohydrodynamics

From the frozen-in field lines concept, a highly conducting fluid can move freely along, but not traverse to, magnetic field lines. We discuss this topic and find that in the study of the frozen-in field lines concept, the effects of inductive and capacitive reactance have been omitted. When admitted, the relationships among the motional electromotive field, the induced electric field, the eddy electric current, and the magnetic field becomes clearer. We emphasize the importance of isomagnetic surfaces and polarization charges, and show analytically that whether a conducting fluid can freely traverse magnetic field lines or not depends solely on the magnetic gradient along the path of the fluid. If a fluid does not change its density distribution and shape (can be regarded as a quasi-rigid body) and moves along isomagnetic surface, it can freely traverse magnetic field lines without any magnetic drag, no matter how strong the magnetic field is. Besides theoretical analysis, we also present experimental results to support our analysis. The main purpose of this work is to correct a fallacy among some astrophysicists.     

The effect of attractant lures in camera trapping: a case study of population estimates for the Iberian lynx (Lynx pardinus)

Capture–recapture analysis of camera trap data is a conventional method to estimate the abundance of free-ranging wild felids. Due to notorious low detection rates of felids, it is important to increase the detection probability during sampling. In this study, we report the effectiveness of attractants as a tool for improving the efficiency of camera trap sampling in abundance estimation of Iberian lynx. We developed a grid system of camera stations in which stations with and without attractant lures were spatially alternated across known Iberian lynx habitat. Of the ten individuals identified, five were detected at stations with no attractant (blind sets), and nine, at the lured stations. Thirty-eight percent of blind set station’s independent captures and 10?% of lured station’s independent captures resulted in photographs unsuitable for correct individual identification. The total capture probability at lured stations was higher than that obtained at blind set stations. The estimates obtained with blind set cameras underestimated the number of lynxes compared to lured cameras. In our study, it appears that the use of lures increased the efficiency of trail camera captures and, therefore, the accuracy of capture–recapture analysis. The observed failure to detect known individuals at blind set camera stations may violate capture–recapture assumptions and bias abundance estimates.     

Development of molecular biology at the University of Wisconsin, Madison.

Dramatic changes in the foundation of academic departments in our universities are uncommon. With the demonstration that DNA was the cellular source of genetic information, and that this information could be regulated, the field of molecular biology was born. Later, when scientists found that they could tinker with this information, the field matured. In an unusually rapid manner, molecular biology was integrated into the University of Wisconsin, Madison, in the late 1950s and early 1960s. This present article is a chronology of how it happened. What are the factors that made this transition possible in the University of Wisconsin? What lessons have we learned from this experience?     

Development of molecular biology at the University of Wisconsin, Madison

Dramatic changes in the foundation of academic departments in our universities are uncommon. With the demonstration that DNA was the cellular source of genetic information, and that this information could be regulated, the field of molecular biology was born. Later, when scientists found that they could tinker with this information, the field matured. In an unusually rapid manner, molecular biology was integrated into the University of Wisconsin, Madison, in the late 1950s and early 1960s. This present article is a chronology of how it happened. What are the factors that made this transition possible in the University of Wisconsin? What lessons have we learned from this experience?     

A simple and inexpensive method for investigating microbiological,enzymatic, or inorganic catalysis using standard histology and microbiology laboratory equipment: assembly,mass transfer properties,hydrodynamic conditions and evaluation

We introduce a generic, simple, and inexpensive method for performing microbiological, enzymatic, or inorganic catalysis with solids using standard histology and microbiology laboratory equipment. Histology cassettes were used to standardize hydrodynamic conditions and to protect the catalysts and their solid supports. Histology cassettes have the following advantages: they are readily available, inexpensive, solvent and acid resistant, automatable, and the slots in the cassette walls allow liquid to circulate freely. Standard Erlenmeyer flasks were used as reaction vessels. We developed a new camera to observe the movement and position of the histology cassettes as well as the liquid in the Erlenmeyer flasks. The camera produces a stable image of the rotating liquid in the Erlenmeyer flask. This visualization method revealed that in a 250?ml Erlenmeyer flask, stable operating conditions are achieved at a shaking frequency of 300?rpm and a fill volume of 30?ml. In vessels with vertical walls, such as beakers or laboratory bottles, the movement of the histology cassette is not reproducible. Mass transfer characterization using a biological model system and the chemical sulfite-oxidation method revealed that the histology cassette does not influence gas-liquid mass transfer.     

How much the eye tells the brain

In the classic "What the frog's eye tells the frog's brain," Lettvin and colleagues showed that different types of retinal ganglion cell send specific kinds of information. For example, one type responds best to a dark, convex form moving centripetally (a fly). Here we consider a complementary question: how much information does the retina send and how is it apportioned among different cell types? Recording from guinea pig retina on a multi-electrode array and presenting various types of motion in natural scenes, we measured information rates for seven types of ganglion cell. Mean rates varied across cell types (6-13 bits . s(-1)) more than across stimuli. Sluggish cells transmitted information at lower rates than brisk cells, but because of trade-offs between noise and temporal correlation, all types had the same coding efficiency. Calculating the proportions of each cell type from receptive field size and coverage factor, we conclude (assuming independence) that the approximately 10(5) ganglion cells transmit on the order of 875,000 bits . s(-1). Because sluggish cells are equally efficient but more numerous, they account for most of the information. With approximately 10(6) ganglion cells, the human retina would transmit data at roughly the rate of an Ethernet connection.     

Open systems living in a closed biosphere: a new paradox for the Gaia debate

While energetically open, the biosphere is appreciably closed from the standpoint of matter exchange. Matter cycling and recycling is hence a necessary and emergent property of the global-scale system known as Gaia. But how can an aggregate of open-system life forms have evolved and persisted for billions of years within a planetary system that is largely closed to matter influx and outflow? The puzzling nature of a closed yet persistent biosphere draws our attention to the course of evolution of fundamental metabolic strategies and matter-capture techniques. It suggests a facet of the Gaia hypothesis, framed in terms of persistence. The oceans, atmosphere, soils and biota constitute a complex system which maintains and adjusts matter cycling and recycling within the constraints of planetary closure such that open-system forms of life can persist. This weaker version of the Gaia hypothesis may be useful because it readily lends itself to at least one form of test. What is the solution to the closed biosphere puzzle, and does it indicate that Gaia merits status as a discrete entity? We suggest several disciplines within the field of biology that might provide tools and perspectives toward reaching a solution. These disciplines include artificial closed ecosystems, prokaryote evolution, the nexus of thermodynamics and evolutionary biology, and hierarchy theory in ecosystem modeling and evolution theory.     

What are 60 warblers worth? Killing in the name of conservation

Ecological research sometimes entails animal suffering and even animal killing. The ethical appropriateness of animal suffering and killing in conservation research may entail considerations that differ from many other kinds of research. This is true, insomuch as conservation research is specifically motivated by an ethical premise: an appreciation for non-human life. In striking contrast with other academic fields (e.g. medicine), however, the ethical dimension of conservation research is only rarely discussed. When it is discussed, it tends to be characterized by logical errors. These errors are important because they are general (i.e. both common and with far-reaching implications), and they are easily made by intelligent people; especially those with no formal training in ethics or logic. Failure to recognize these errors could stymie efforts to increase the ethical quality of ecological research conducted in the name of conservation.
We take advantage of a recently published dialogue concerning the ethical appropriateness of a specific field experiment that entailed killing black-throated blue warblers, Dendroica caerulescens . Both sides of this debate exemplify the kinds of errors to which we refer. In this paper we briefly review the arguments presented on each side of this debate, highlight their mistakes, and indicate necessary corrections. We argue that: (1) compliance with animal research regulations, while important, inadequately accommodates the ethical aspects of animal research, and (2) individual ecologists ought to understand themselves what does and does not represent sound and valid arguments for ethical decisions. Finally, we discuss how any ecological researcher might begin to apply our analysis to his or her own research.     

What animals do not do or fail to find: A novel observational approach for studying cognition in the wild

To understand how our brain evolved and what it is for, we are in urgent need of knowledge about the cognitive skills of a large variety of animal species and individuals, and their relationships to rapidly disappearing social and ecological conditions. But how do we obtain this knowledge? Studying cognition in the wild is a challenge. Field researchers (and their study subjects) face many factors that can easily interfere with their variables of interest. Although field studies of cognition present unique challenges, they are still invaluable for understanding the evolutionary drivers of cognition. In this review, I discuss the advantages and urgency of field‐based studies on animal cognition and introduce a novel observational approach for field research that is guided by three questions: (a) what do animals fail to find?, (b) what do they not do?, and (c) what do they only do when certain conditions are met? My goal is to provide guidance to future field researchers examining primate cognition.     

OUGHT WE TO ENHANCE OUR COGNITIVE CAPACITIES?1

Ought we to improve our cognitive capacities beyond the normal human range? It might be a good idea to level out differences between peoples cognitive capacities; and some people's reaching beyond normal capacities may have some good side‐effects on society at large (but also bad side‐effects, of course). But is there any direct gain to be made from having ones cognitive capacities enhanced? Would this as such make our lives go better? No, I argue; or at least there doesn't seem to be any evidence suggesting that it would. And it doesn't matter whether we consider the question from a narrow hedonistic perspective, from a more refined hedonistic perspective, from a desire‐satisfaction view, or from some reasonable objective list view of what makes a life go well. Only an extremely perfectionist – and implausible – view of what makes our lives go well could support any direct value in cognitive enhancement. Finally, our sense of identity gives us no good reasons to enhance even our capacity to remember. So, cognitive enhancement as such would not improve our lives.     

Interaction of retinal image and eye velocity in motion perception

When we move our eyes, why does the world look stable even as its image flows across our retinas, and why do afterimages, which are stationary on the retinas, appear to move? Current theories say this is because we perceive motion by summation: if an object slips across the retina at r degrees/s while the eye turns at e degrees/s, the object's perceived velocity in space should be r + e. We show that activity in MT+, the visual-motion complex in human cortex, does reflect a mix of r and e rather than r alone. But we show also that, for optimal perception, r and e should not summate; rather, the signals coding e interact multiplicatively with the spatial gradient of illumination.     

A Brief History of De Novo Protein Design: Minimal,Rational, and Computational

Protein design has come of age, but how will it mature? In the 1980s and the 1990s, the primary motivation for de novo protein design was to test our understanding of the informational aspect of the protein-folding problem; i.e., how does protein sequence determine protein structure and function? This necessitated minimal and rational design approaches whereby the placement of each residue in a design was reasoned using chemical principles and/or biochemical knowledge. At that time, though with some notable exceptions, the use of computers to aid design was not widespread. Over the past two decades, the tables have turned and computational protein design is firmly established. Here, I illustrate this progress through a timeline of de novo protein structures that have been solved to atomic resolution and deposited in the Protein Data Bank. From this, it is clear that the impact of rational and computational design has been considerable: More-complex and more-sophisticated designs are being targeted with many being resolved to atomic resolution. Furthermore, our ability to generate and manipulate synthetic proteins has advanced to a point where they are providing realistic alternatives to natural protein functions for applications both in vitro and in cells. Also, and increasingly, computational protein design is becoming accessible to non-specialists. This all begs the questions: Is there still a place for minimal and rational design approaches? And, what challenges lie ahead for the burgeoning field of de novo protein design as a whole?     

Conclusion: Energy ethics and ethical worlds

What happens when the effects of our ethical actions stretch beyond, often far beyond, first- and second-person phenomena? What happens when one person's richly textured ethical world is another's profound violation? Energy offers a particularly useful empirical terrain on which to think through the questions posed by ethical worlds. Ethical worlds gesture both to the supra-individual, supra-present contexts in which we all craft quotidian ethics, and to the expansive geographies and timescapes in which the effects of our ethical practices ramify. Ethical worlds, fields, or landscapes are not bordered by first- or second-person experiences, but rather they intersect and interfere with one another often at great distance, often over multiple generations, and certainly not equally. Ethical practices in more powerful fields spill out, invade, and give shape to ethical practices in other ethical fields. What does it mean to start to see and feel and analyse at these ethical crossroads? In particular, what might it mean to acknowledge that structure, power, and interest – which are too often arrayed against close ethnographic attention to individual and shared experience – are not ‘larger forces’ but other ethical worlds, equally amenable to ethnographic attention?     

Meteorite or gemstone? Dreaming as one end of a continuum of functioning: Implications for research and for the use of dreams in therapy and self-knowledge.

Is a dream a meteorite—a bit of material arriving from a distant place that needs to be carefully analyzed to give us knowledge about that place (outside or inside us)? Is it a strange text which has come to us in a foreign language, that needs to be translated into our own? This “meteorite view” is held by some religious and spiritual persons, by many orthodox psychoanalysts and other therapists, and implicitly by many researchers. They all see the dream as something alien, something totally different from our ordinary mental functioning. This paper presents a great deal of research favoring an alternate view—that the dream is an earth-stone, not an alien stone. It may be impressive and beautiful (gemstone), but it's still an earth-stone. The dream is part of our mental functioning. It is one end of a continuum, running from focused waking thought, through looser thought, fantasy, daydreaming, reverie and dreaming. We review reasons why dreams are often considered “totally different”: they're perceptual, not conceptual; they're bizarre; they are “so real”; they're so easily forgotten; they're involuntary; they occur in REM sleep—a totally different state. We demonstrate that none of these reasons are persuasive. In each sense, there is overlap between dreams and other forms of functioning. The continuum view leads to different kinds of research and a different style of dreamwork. It also helps answer questions the field has long struggled with including: Should we study “a dream” or “dreaming”? Are dreams meaningful or meaningless? (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

The Effect of Perceived Regional Accents on Individual Economic Behavior: A Lab Experiment on Linguistic Performance,Cognitive Ratings and Economic Decisions

Does it matter if you speak with a regional accent? Speaking immediately reveals something of one’s own social and cultural identity, be it consciously or unconsciously. Perceiving accents involves not only reconstructing such imprints but also augmenting them with particular attitudes and stereotypes. Even though we know much about attitudes and stereotypes that are transmitted by, e.g. skin color, names or physical attractiveness, we do not yet have satisfactory answers how accent perception affects human behavior. How do people act in economically relevant contexts when they are confronted with regional accents? This paper reports a laboratory experiment where we address this question. Participants in our experiment conduct cognitive tests where they can choose to either cooperate or compete with a randomly matched male opponent identified only via his rendering of a standardized text in either a regional accent or standard accent. We find a strong connection between the linguistic performance and the cognitive rating of the opponent. When matched with an opponent who speaks the accent of the participant’s home region—the in-group opponent –, individuals tend to cooperate significantly more often. By contrast, they are more likely to compete when matched with an accent speaker from outside their home region, the out-group opponent. Our findings demonstrate, firstly, that the perception of an out-group accent leads not only to social discrimination but also influences economic decisions. Secondly, they suggest that this economic behavior is not necessarily attributable to the perception of a regional accent per se, but rather to the social rating of linguistic distance and the in-group/out-group perception it evokes.     

Adaptation genomics: the next generation

Understanding the genetics of how organisms adapt to changing environments is a fundamental topic in modern evolutionary ecology. The field is currently progressing rapidly because of advances in genomics technologies, especially DNA sequencing. The aim of this review is to first briefly summarise how next generation sequencing (NGS) has transformed our ability to identify the genes underpinning adaptation. We then demonstrate how the application of these genomic tools to ecological model species means that we can start addressing some of the questions that have puzzled ecological geneticists for decades such as: How many genes are involved in adaptation? What types of genetic variation are responsible for adaptation? Does adaptation utilise pre-existing genetic variation or does it require new mutations to arise following an environmental change?     

Neuronal mechanisms for visual stability: progress and problems

How our vision remains stable in spite of the interruptions produced by saccadic eye movements has been a repeatedly revisited perceptual puzzle. The major hypothesis is that a corollary discharge (CD) or efference copy signal provides information that the eye has moved, and this information is used to compensate for the motion. There has been progress in the search for neuronal correlates of such a CD in the monkey brain, the best animal model of the human visual system. In this article, we briefly summarize the evidence for a CD pathway to frontal cortex, and then consider four questions on the relation of neuronal mechanisms in the monkey brain to stable visual perception. First, how can we determine whether the neuronal activity is related to stable visual perception? Second, is the activity a possible neuronal correlate of the proposed transsaccadic memory hypothesis of visual stability? Third, are the neuronal mechanisms modified by visual attention and does our perceived visual stability actually result from neuronal mechanisms related primarily to the central visual field? Fourth, does the pathway from superior colliculus through the pulvinar nucleus to visual cortex contribute to visual stability through suppression of the visual blur produced by saccades?