Uncertainties about 'painless' animals

Macer explores whether it is possible to genetically alter animals to reduce or eliminate their capacity to feel pain, whether it would be ethical to do so, and how we would regard animals that do not feel pain. A possible use for such animals would be as subjects for laboratory research. Among the scientific, philosophical, and ethical uncertainties of pain that Macer considers are: can we define pain? how do we measure pain and anxiety? is pain always related to suffering? what is the minimum level of pain that a being must be able to feel before we reach the conclusion that it should not be used by other beings? are we justified in using beings that do not feel pain when we would not be if they did feel pain and suffer from it?     

What history tells us V. Emile Duclaux (1840–1904)

Conclusion Perhaps we should be more cautions in our vision of how a scientist should behave, a perception closely tied to the present-day organization of scientific research — with its extreme specialization. Is the present situation optimal? And was not the huge spectrum of activities and interests of Emile Duclaux also necessary for the rapid development of microbiology and its general acceptance? We should not reduce the history of medicine to a catalog of the discoverers of diseases. As a scientific organizer, and a prime mover in the development of microbiology, Emile Duclaux deserves a place in our memories.     

Ecology after 100 years: Progress and pseudo-progress

Has the science of ecology fulfilled the promises made by the originators of ecological science at the start of the last century? What should ecology achieve? Have good policies for environmental management flowed out of ecological science? These important questions are rarely discussed by ecologists working on detailed studies of individual systems. Until we decide what we wish to achieve as ecologists we cannot define progress toward those goals. Ecologists desire to achieve an understanding of how the natural world operates, how humans have modified the natural world, and how to alleviate problems arising from human actions. Ecologists have made impressive gains over the past century in achieving these goals, but this progress has been uneven. Some sub-disciplines of ecology are well developed empirically and theoretically, while others languish for reasons that are not always clear. Fundamental problems can be lost to view as ecologists fiddle with unimportant pseudo-problems. Bandwagons develop and disappear with limited success in addressing problems. The public demands progress from all the sciences, and as time moves along and problems get worse, more rapid progress is demanded. The result for ecology has too often been poor, short-term science and poor management decisions. But since the science is rarely repeated and the management results may be a generation or two down the line, it is difficult for the public or for scientists to decide how good or bad the scientific advice has been. In ecology over the past 100 years we have made solid achievements in behavioural ecology, population dynamics, and ecological methods, we have made some progress in understanding community and ecosystem dynamics, but we have made less useful progress in developing theoretical ecology, landscape ecology, and natural resource management. The key to increasing progress is to adopt a systems approach with explicit hypotheses, theoretical models, and field experiments on a scale defined by the problem. With continuous feedback between problems, possible solutions, relevant theory and experimental data we can achieve our scientific goals.     

The Science of Animal Suffering

Can suffering in non‐human animals be studied scientifically? Apart from verbal reports of subjective feelings, which are uniquely human, I argue that it is possible to study the negative emotions we refer to as suffering by the same methods we use in ourselves. In particular, by asking animals what they find positively and negatively reinforcing (what they want and do not want), we can define positive and negative emotional states. Such emotional states may or may not be accompanied by subjective feelings but fortunately it is not necessary to solve the problem of consciousness to construct a scientific study of suffering and welfare. Improvements in animal welfare can be based on the answers to two questions: Q1: Will it improve animal health? and Q2: Will it give the animals something they want? This apparently simple formulation has the advantage of capturing what most people mean by ‘improving welfare’ and so halting a potentially dangerous split between scientific and non‐scientific definitions of welfare. It can also be used to validate other controversial approaches to welfare such as naturalness, stereotypies, physiological and biochemical measures. Health and what animals want are thus not just two of many measures of welfare. They provide the definition of welfare against which others can be validated. They also tell us what research we have to do and how we can judge whether welfare of animals has been genuinely improved. What is important, however, is for this research to be done in situ so that it is directly applicable to the real world of farming, the sea or an animal’s wild habitat. It is here that ethology can make major contributions.     

Integrating scientific guidance into marine spatial planning

Marine spatial planning (MSP), whereby areas of the ocean are zoned for different uses, has great potential to reduce or eliminate conflicts between competing management goals, but only if strategically applied. The recent literature overwhelmingly agrees that including stakeholders in these planning processes is critical to success; but, given the countless alternative ways even simple spatial regulations can be configured, how likely is it that a stakeholder-driven process will generate plans that deliver on the promise of MSP? Here, we use a spatially explicit, dynamic bioeconomic model to show that stakeholder-generated plans are doomed to fail in the absence of strong scientific guidance. While strategically placed spatial regulations can improve outcomes remarkably, the vast majority of possible plans fail to achieve this potential. Surprisingly, existing scientific rules of thumb do little to improve outcomes. Here, we develop an alternative approach in which models are used to identify efficient plans, which are then modified by stakeholders. Even if stakeholders alter these initial proposals considerably, results hugely outperform plans guided by scientific rules of thumb. Our results underscore the importance of spatially explicit dynamic models for the management of marine resources and illustrate how such models can be harmoniously integrated into a stakeholder-driven MSP process.     

Scientific misconduct: more cops, more robbers?

Abandoning an earlier pretense that research misconduct is too rare to matter, the scientific community is trying to figure out how to minimize and police it. Could broadening the definition be the key?     

Overlapping Structures in Sensory-Motor Mappings

This paper examines a biologically-inspired representation technique designed for the support of sensory-motor learning in developmental robotics. An interesting feature of the many topographic neural sheets in the brain is that closely packed receptive fields must overlap in order to fully cover a spatial region. This raises interesting scientific questions with engineering implications: e.g. is overlap detrimental? does it have any benefits? This paper examines the effects and properties of overlap between elements arranged in arrays or maps. In particular we investigate how overlap affects the representation and transmission of spatial location information on and between topographic maps. Through a series of experiments we determine the conditions under which overlap offers advantages and identify useful ranges of overlap for building mappings in cognitive robotic systems. Our motivation is to understand the phenomena of overlap in order to provide guidance for application in sensory-motor learning robots.     

On Disciplinary Fragmentation and Scientific Progress

Why are some scientific disciplines, such as sociology and psychology, more fragmented into conflicting schools of thought than other fields, such as physics and biology? Furthermore, why does high fragmentation tend to coincide with limited scientific progress? We analyzed a formal model where scientists seek to identify the correct answer to a research question. Each scientist is influenced by three forces: (i) signals received from the correct answer to the question; (ii) peer influence; and (iii) noise. We observed the emergence of different macroscopic patterns of collective exploration, and studied how the three forces affect the degree to which disciplines fall apart into divergent fragments, or so-called “schools of thought”. We conducted two simulation experiments where we tested (A) whether the three forces foster or hamper progress, and (B) whether disciplinary fragmentation causally affects scientific progress and vice versa. We found that fragmentation critically limits scientific progress. Strikingly, there is no effect in the opposite causal direction. What is more, our results shows that at the heart of the mechanisms driving scientific progress we find (i) social interactions, and (ii) peer disagreement. In fact, fragmentation is increased and progress limited if the simulated scientists are open to influence only by peers with very similar views, or when within-school diversity is lost. Finally, disciplines where the scientists received strong signals from the correct answer were less fragmented and experienced faster progress. We discuss model’s implications for the design of social institutions fostering interdisciplinarity and participation in science.     

Making Science Accessible: A Semiotics of Scientific Communication

This article serves as a demonstration of how certain models of literary analysis, used to theorize and analyze fiction and narrative, can also be applied to scientific communication in such a manner as to promote the accessibility of science to the general public and a greater awareness of the methodology used in making scientific discovery. The approach of this article is based on the assumption that the principles of structuralism and semiotics can provide plausible explanations for the divide between the reception of science and literature. We provide a semiotic analysis of a scientific article that has had significant impact in the field of molecular biology with profound medical implications. Furthermore, we show how the structural and semiotic characteristics of literary texts are also evident in the scientific papers, and we address how these characteristics can be applied to scientific prose in order to propose a model of scientific communication that reaches the public. By applying this theoretical framework to the analysis of both scientific and literary communication, we establish parallels between primary scientific texts and literary prose.     

Agential autonomy and biological individuality

What is a biological individual? How are biological individuals individuated? How can we tell how many individuals there are in a given assemblage of biological entities? The individuation and differentiation of biological individuals are central to the scientific understanding of living beings. I propose a novel criterion of biological individuality according to which biological individuals are autonomous agents. First, I articulate an ecological–dynamical account of natural agency according to which, agency is the gross dynamical capacity of a goal-directed system to bias its repertoire to respond to its conditions as affordances. Then, I argue that agents or agential dynamical systems can be agentially dependent on, or agentially autonomous from, other agents and that this agential dependence/autonomy can be symmetrical or asymmetrical, strong or weak. Biological individuals, I propose, are all and only those agential dynamical systems that are strongly agentially autonomous. So, to determine how many individuals there are in a given multiagent aggregate, such as multicellular organism, a colony, symbiosis, or a swarm, we first have to identify how many agential dynamical systems there are, and then what their relations of agential dependence/autonomy are. I argue that this criterion is adequate to the extent that it vindicates the paradigmatic cases, and explains why the paradigmatic cases are paradigmatic, and why the problematic cases are problematic. Finally, I argue for the importance of distinguishing between agential and causal dependence and show the relevance of agential autonomy for understanding the explanatory structure of evolutionary developmental biology.     

Mechanisms of muscle dedifferentiation during regeneration

For many years people have known that amphibians have an amazing ability to regenerate lost body parts. In contrast humans have limited regeneration capacity and even simple wound healing results in scarring. Despite more than a century of scientific inquiry, this remarkable phenomenon remains poorly understood. Recent research has begun to provide insight into how this unique process that is now fully accepted to occur via the reversal of cell differentiation is executed at the molecular level. As more and more is known about regeneration and dedifferentiation we can begin to address the question: if given the right signals could mammals also regenerate body structures?     

A natural history of "agonist"

This paper constructs a brief history of the biochemical term agonist by exploring the multiple meanings of the root ag?n in ancient Greek literature and describing how agonist first appeared in the scientific literature of the 20th century in the context of neurophysiologists' debates about the existence and properties of cellular receptors. While the narrow scientific definition of agonist may appear colorless and dead when compared with the web of allusions spun by the ancient Greek ag?n, the scientific power and creativity of agonist actually resides precisely in its exact, restricted meaning for biomedical researchers.     

Modeling the States of Matter in a First-Grade Classroom

ABSTRACT

Scientific modeling along with hands-on inquiry can lead to a deeper understanding of scientific concepts among students in upper elementary grades. Even though scientific modeling involves abstract-thinking processes, can students in younger elementary grades successfully participate in scientific modeling? Scientific modeling, like all other aspects of scientific inquiry, has to be developed. This article clearly outlines how students in a first-grade classroom can develop and use scientific models to explain the properties and behaviors of solids, liquids, and gases in a unit on the states of matter.     

On the Epistemological Crisis in Genomics

There is an epistemological crisis in genomics. At issue is what constitutes scientific knowledge in genomic science, or systems biology in general. Does this crisis require a new perspective on knowledge heretofore absent from science or is it merely a matter of interpreting new scientific developments in an existing epistemological framework? This paper discusses the manner in which the experimental method, as developed and understood over recent centuries, leads naturally to a scientific epistemology grounded in an experimental-mathematical duality. It places genomics into this epistemological framework and examines the current situation in genomics. Meaning and the constitution of scientific knowledge are key concerns for genomics, and the nature of the epistemological crisis in genomics depends on how these are understood.     

Another Crisis in Psychology

A psychologist in Hungary today does not necessarily want to be acknowledged for what he does as a scientist; actually, the number of those who fancy themselves artists or magicians is growing. On the other hand, those of us who make a point of our theoretical or practical work's being of a scientific nature are willing to consider psychology a natural science. But how could something be scientific if not in the same way physics, chemistry, and biology are?     

The cessation of gastrulation

An integral component of gastrulation in all organisms is epithelial-mesenchymal transition (EMT), a fundamental morphogenetic event through which epithelial cells transform into mesenchymal cells. The mesenchymal cells that arise from epithelial cells during gastrulation contribute to various tissue rudiments during subsequent development, including the notochord, somites, heart, gut, kidney, body wall, and lining of the coelom. The process of gastrulation has been the subject of several hundred scientific papers. Despite all that has been written, it is likely that what we currently know about gastrulation is still considerably less than what remains to be learned. One critical remaining question that we consider here is how does gastrulation cease at the right place along the body axis, and at the right time? In this commentary, we focus on the molecular mechanism for the cessation of gastrulation, using the chick embryo as a model system.     

How to write consistently boring scientific literature

Although scientists typically insist that their research is very exciting and adventurous when they talk to laymen and prospective students, the allure of this enthusiasm is too often lost in the predictable, stilted structure and language of their scientific publications. I present here, a top-10 list of recommendations for how to write consistently boring scientific publications. I then discuss why we should and how we could make these contributions more accessible and exciting.     

How can “Super Corals” facilitate global coral reef survival under rapid environmental and climatic change?

Coral reefs are in a state of rapid global decline via environmental and climate change, and efforts have intensified to identify or engineer coral populations with increased resilience. Concurrent with these efforts has been increasing use of the popularized term “Super Coral” in both popular media and scientific literature without a unifying definition. However, how this subjective term is currently applied has the potential to mislead inference over factors contributing to coral survivorship, and the future trajectory of coral reef form and functioning. Here, we discuss that the information required to support a single definition does not exist, and in fact may never be appropriate, i.e. “How Super is Super”? Instead, we advocate caution of this term, and suggest a workflow that enables contextualization and clarification of superiority to ensure that inferred or asserted survivorship is appropriate into future reef projections. This is crucial to robustly unlock how “Super Corals” can be integrated into the suite of management options required to facilitate coral survival under rapid environmental and climate change.     

Toward a cross-species neuroscientific understanding of the affective mind: do animals have emotional feelings?

Do we need to consider mental processes in our analysis of brain functions in other animals? Obviously we do, if such BrainMind functions exist in the animals we wish to understand. If so, how do we proceed, while still retaining materialistic-mechanistic perspectives? This essay outlines the historical forces that led to emotional feelings in animals being marginalized in behavioristic scientific discussions of why animals behave the way they do, and why mental constructs are generally disregarded in modern neuroscientific analyses. The roots of this problem go back to Cartesian dualism and the attempt of 19th century physician-scientists to ground a new type of medical curriculum on a completely materialistic approach to body functions. Thereby all vitalistic principles were discarded from the lexicon of science, and subjective experience in animals was put in that category and discarded as an invalid approach to animal behavior. This led to forms of rigid operationalism during the era of behaviorism and subsequently ruthless reductionism in brain research, leaving little room for mentalistic concepts such as emotional feelings in animal research. However, modern studies of the brain clearly indicate that artificially induced arousals of emotional networks, as with localized electrical and chemical brain stimulation, can serve as "rewards" and "punishments" in various learning tasks. This strongly indicates that animal brains elaborate various experienced states, with those having affective contents being easiest to study rigorously. However, in approaching emotional feelings empirically we must pay special attention to the difficulties and vagaries of human language and evolutionary levels of control in the brain. We need distinct nomenclatures from primary (unconditioned phenomenal experiences) to tertiary (reflective) levels of mind. The scientific pursuit of affective brain processes in other mammals can now reveal general BrainMind principles that also apply to human feelings, as with neurochemical predictions from preclinical animal models to self-reports of corresponding human experiences. In short, brain research has now repeatedly verified the existence of affective experience-various reward and punishment functions-during artificial arousal of emotional networks in our fellow animals. The implications for new conceptual schema for understanding human/primate affective feelings and how such knowledge can impact scientific advances in biological psychiatry are also addressed.