Science through the internet: Researching, evaluating and citing websites

This article attempts to convey the joys and frustrations of skimming the Internet trying to find relevant information concerning an academic’s work as a scientist, a student or an instructor. A brief overview of the Internet and the “do’s and don’ts” for the neophyte as well for the more seasoned “navigator” are given. Some guidelines of “what works and what does not” and “what is out there” are provided for the scientist with specific emphasis for biologists, as well as for all others having an interest in science but with little interest in spending countless hours “surfing the net”. An extensive but not exhaustive list of related websites is provided.     

Dynamic palaeoredox and exceptional preservation in the Cambrian Spence Shale of Utah

Garson, D.E., Gaines, R.R., Droser, M.L., Liddell, W.D. & Sappenfield, A. 2011: Dynamic palaeoredox and exceptional preservation in the Cambrian Spence Shale of Utah. Lethaia, Vol. 45, pp. 164–177. Burgess Shale‐type faunas provide a unique glimpse into the diversification of metazoan life during the Cambrian. Although anoxia has long been thought to be a pre‐requisite for this particular type of soft‐bodied preservation, the palaeoenvironmental conditions that regulated extraordinary preservation have not been fully constrained. In particular, the necessity of bottom water anoxia, long considered a pre‐requisite, has been the subject of recent debate. In this study, we apply a micro‐stratigraphical, ichnological approach to determine bottom water oxygen conditions under, which Burgess Shale‐type biotas were preserved in the Middle Cambrian Spence Shale of Utah. Mudstones of the Spence Shale are characterized by fine scale (mm‐cm) alternation between laminated and bioturbated intervals, suggesting high‐frequency fluctuations in bottom water oxygenation. Whilst background oxygen levels were not high enough to support continuous infaunal activity, brief intervals of improved bottom water oxygen conditions punctuate the succession. A diverse skeletonized benthic fauna, including various polymerid trilobites, hyolithids, brachiopods and ctenocystoids suggests that complex dysoxic benthic community was established during times when bottom water oxygen conditions were permissive. Burgess Shale‐type preservation within the Spence Shale is largely confined to non‐bioturbated horizons, suggesting that benthic anoxia prevailed in intervals, where these fossils were preserved. However, some soft‐bodied fossils are found within weakly to moderately bioturbated intervals (Ichnofabric Index 2 and 3). This suggests that Burgess Shale‐type preservation is strongly favoured by bottom water anoxia, but may not require it in all cases. □Anoxia, Burgess Shale, Burgess Shale type‐preservation, Langston Formation, Spence Shale Member, Utah.     

Marvelling at the Marvel: The Supposed Conversion of A.D. Darbishire to Mendelism

The so-called “biometric-Mendelian controversy” has received much attention from science studies scholars. This paper focuses on one scientist involved in this debate, Arthur Dukinfield Darbishire, who performed a series of hybridization experiments with mice beginning in 1901. Previous historical work on Darbishire’s experiments and his later attempt to reconcile Mendelian and biometric views describe Darbishire as eventually being “converted”' to Mendelism. I provide a new analysis of this episode in the context of Darbishire’s experimental results, his underlying epistemology, and his influence on the broader debate surrounding the rediscovery and acceptance of Mendelism. Iinvestigate various historiographical issues raised by this episode in order to reflect on the idea of “conversion” to a scientific theory. Darbishire was an influential figure who resisted strong forces compelling him to convert prematurely due to his requirements that the new theory account for particularly important anomalous facts and answer the most pressing questions in the field. This revised version was published online in July 2006 with corrections to the Cover Date.     

What would T. H. Huxley have made of prion diseases?

T. H. Huxley was “Darwin’s bulldog,” and took the offensive in championing the cause of evolution against skeptical scientists and outraged theologians. As such, he took part in one of the great “paradigm shifts” of biology, at the end of the nineteenth century. Huxley was a rigorous scientist and wrote important articles on scientific method, as well as publishing extensively on a wide range of subjects in natural history. In the second half of the twentieth century, the “prion hypothesis” was put forward to explain the pathogenesis of a curious group of diseases known as the transmissible spongiform encephalopathies. This also involved a “paradigm shift” because the prion hypothesis postulated that biologically relevant information could be enciphered in protein conformation (rather than encoded in nucleic acid base sequences), and could be transmitted from one molecule to another, thereby causing infectious disease. This article examines a few of Huxley’s remarks to speculate on how he might have responded to the scientific debate about prion disease had he lived a century later.     

Chronic Homework in Emerging Borderlands of Healthcare

The task of caring for those with chronic illnesses has gained a new centrality in health care at a global level. We introduce the concept of “chronic homework” to offer a critical reflection on the treatment of chronic illnesses in three quite different national and local contexts: Uganda, Denmark, and the United States. A major challenge for clinicians, patients, and family caregivers is how to navigate the task of moving health care from clinic to home. By “chronic homework,” we refer to the work patients and families are expected to carry out in their home contexts as part of the treatment of chronic conditions. Families and patients spend time receiving training by clinical experts in the various tasks they are to do at home. While this “colonization” of the popular domain could easily be understood from a Foucauldian perspective as yet another emerging mode of governmentality, this a conceptualization can oversimplify the way specific practices of homework are re-imagined and redirected by patients and significant others in their home surroundings. In light of this re-invention of homework in local home contexts, we foreground another conceptual trope, describing chronic homework as a borderland practice.     

Pyramid power: Principal cells of the hippocampus unite!

Electrical transmission in the mammalian brain is now well established. A new study by Thomson and colleagues elegantly demonstrates coupling between CA1 hippocampal pyramidal cells, which is far more common than previously supposed. Although the history of coupling is extensive, doubt, predjudice, and technical issues long kept it from wide acceptance. Here “spikelets” or “fast prepotentials” are found when two cells are coupled and in this situation result from electrical transmission of impulses from one coupled cell to the other. Interesting questions remain as to whether connexin or pannexin gap junctions serve as the molecular substrate of transmission, and the role of electrical transmission in hippocampal physiology is uncertain. Increased coupling could well contribute to the known tendency of the hippocampus to exhibit seizure activity.     

A century of oceanographic and fisheries exploration on the continental shelf off Argentina

A detailed analysis is presented of the main contributions, both local and international, to the fields of oceanography and fishery sciences resulting from exploratory cruises carried out on the continental shelf off Argentina over the last 100 years. The end of the 19th century is chosen as a starting point for this analysis as it marks the beginning of active marine research by Argentinian scientists and an accumulation of information on Antarctic and Subantarctic organisms in foreign journals. Mention is also made of previous contributions derived from the classic expeditions and global circumnavigational voyages during the 18th and 19th centuries. Although the aims of those were not always strictly oceanographic, they rendered significant information to this field of knowledge. In the early years, references arose mainly from the particular geographic situation of the Argentinian shelf, a necessary passage in the navigation routes to the Pacific Ocean, and later on the way to Antarctica. Sources of information are divided into four categories: (a) foreign scientific projects in the area; (b) investigation by Argentinian scientists and research vessels; (c) joint projects between Argentinian and foreign institutions; and (d) contributions from sources other than oceanographic cruises (commercial navigation, maritime weather reports, satellite images, etc.). The analysis includes an updated and classified bibliographical list of the main contributions to the fields of oceanography and fishery sciences derived from those sources, published either in international or local journals or appearing as technical and internal reports. The motivations, objectives and main achievements of foreign surveys and programmes in the area and their impact on local scientific progress are discussed. The early sixties mark a turning point in the evolution of international research in the area. The creation of biological stations along the Argentinian coast, and the support given to the pooling of human resources set the basis for the development of bilateral programmes. Similar progress in Brazil and Uruguay led to the outgrowth of regional activities. Joint scientific efforts described in this analysis include the programmes carried out by the research vessels of Germany (“Walther Herwig”, “Meteor”), Japan (“Kaiyo Maru”, “Orient Maru”, “Shinkai Maru”), Poland (“Professor Siedlecki”), Russia (“Evrika”, “Dimitry Stefanov”) and the USA (“Vema”, “Atlantis II”), the achievements of which are a landmark in the evolution of marine science in the aea.     

Biosemiosis and the Cellular Basis of Mind

The human brain is a complex organ made up of neurons and several other cell types, and whose role is processing information for use in elicitation of behaviors. To accomplish this, the brain requires large amounts of energy, and this energy is obtained by the oxidation of glucose (Glc). However, the question of how the oxidation of Glc by individual neurons in brain results in their collective ability to rapidly generate feats of cognition that allow them to recognize the nature of the universe in which they live and to communicate this information remains unclear. In this article, insights into this process are provided by first considering the brain’ s homeostatic “operating system” for supply of energy to stimulated neurons, and how this system defines the basic unit of brain “structure”. This is followed by consideration of the brain’s “two-cell” neuronal communication mechanism which defines the basic unit of brain “function”. Finally, an analysis of the nature of frequency-encoded “neuronal languages” that enable ensembles of neurons to translate energy derived from the oxidation of Glc into a collective “mind”, the aggregate of all brain processes including those involving perception, thought, insight, foresight, imagination and behavior.     

Animat navigation using a cognitive graph

 This article describes a computational model of the hippocampus that makes it possible for a simulated rat to navigate in a continuous environment containing obstacles. This model views the hippocampus as a “cognitive graph”, that is, a hetero-associative network that learns temporal sequences of visited places and stores a topological representation of the environment. Calling upon place cells, head direction cells, and “goal cells”, it suggests a biologically plausible way of exploiting such a spatial representation for navigation that does not require complicated graph-search algorithms. Moreover, it permits “latent learning” during exploration, that is, the building of a spatial representation without the need of any reinforcement. When the rat occasionally discovers some rewarding place it may wish to rejoin subsequently, it simply records within its cognitive graph, through a series of goal and sub-goal cells, the direction in which to move from any given start place. Accordingly, the model implements a simple “place-recognition-triggered response” navigation strategy. Two implementations of place cell management are studied in parallel. The first one associates place cells with place fields that are given a priori and that are uniformly distributed in the environment. The second one dynamically recruits place cells as exploration proceeds and adjusts the density of such cells to the local complexity of the environment. Both implementations lead to identical results. The article ends with a few predictions about results to be expected in experiments involving simultaneous recordings of multiple cells in the rat hippocampus. Received: 25 June 1999 / Accepted in revised form: 20 March 2000     

<Emphasis Type="Italic">Physisporinus vitreus</Emphasis>: a versatile white rot fungus for engineering value-added wood products

The credo of every scientist working in the field of applied science is to transfer knowledge “from science to market,” a process that combines (1) science (fundamental discoveries and basic research) with (2) technology development (performance assessment and optimization) and (3) technology transfer (industrial application). Over the past 7 years, we have intensively investigated the potential of the white rot fungus, Physisporinus vitreus, for engineering value-added wood products. Because of its exceptional wood degradation pattern, i.e., selective lignification without significant wood strength losses and a preferential degradation of bordered pit membranes, it is possible to use this fungus under controlled conditions to improve the acoustic properties of tonewood (i.e., “mycowood”) as well as to enhance the uptake of preservatives and wood modification substances in refractory wood species (e.g., Norway spruce), a process known as “bioincising.” This minireview summarizes the research that we have performed with P. vitreus and critically discusses the challenges encountered during the development of two distinct processes for engineering value-added wood products. Finally, we peep into the future potential of the bioincising and mycowood processes for additional applications in the forest and wood industry.     

Engineering aspects of biological ion channels—from biosensors to computational models for permeation

Molecular sequencing has helped resolve the phylogenetic relationships amongst the diverse groups of algal, fungal-like and protist organisms that constitute the Chromalveolate “superkingdom” clade. It is thought that the whole clade evolved from a photosynthetic ancestor and that there have been at least three independent plastid losses during their evolutionary history. The fungal-like oomycetes and hyphochytrids, together with the marine flagellates Pirsonia and Developayella, form part of the clade defined by Cavalier-Smith and Chao (2006) as the phylum “Pseudofungi”, which is a sister to the photosynthetic chromistan algae (phylum Ochrophyta). Within the oomycetes, a number of predominantly marine holocarpic genera appear to diverge before the main “saprolegnian” and “peronosporalean” lines, into which all oomycetes had been traditionally placed. It is now clear that oomycetes have their evolutionary roots in the sea. The earliest diverging oomycete genera so far documented, Eurychasma and Haptoglossa, are both obligate parasites that show a high degree of complexity and sophistication in their host parasite interactions and infection structures. Key morphological and cytological features of the oomycetes will be reviewed in the context of our revised understanding of their likely phylogeny. Recent genomic studies have revealed a number of intriguing similarities in host–pathogen interactions between the oomycetes with their distant apicocomplexan cousins. Therefore, the earlier view that oomycetes evolved from the largely saprotrophic “saprolegnian line” is not supported and current evidence shows these organisms evolved from simple holocarpic marine parasites. Both the hyphal-like pattern of growth and the acquisition of oogamous sexual reproduction probably developed largely after the migration of these organisms from the sea to land.     

Influence of landscape on the spread of an infection

The influence of topographical situation on the spread of infection is studied. The investigation is based on a multigroup model. The population under consideration is thought to be divided into subpopulations living in regions that are separated from each other by natural barriers (mountains). Infection is carried from one region to another by migrating infectives. Migration is possible only along the river system so that the structure of the epidemiological network is that of a symmetric tree. The results allow comparison of the velocity of propagation of the epidemic for different geographical situations and allow quantification of the “channel-effect”, according to which mountainous regions are channels rather than barriers to the spread of an epidemic.     

The Preface to Darwin’s <Emphasis Type="Italic">Origin of Species</Emphasis>: The Curious History of the “Historical Sketch” *

Almost any modern reader’s first encounter with Darwin’s writing is likely to be the “Historical Sketch,” inserted by Darwin as a preface to an early edition of the Origin of Species, and having since then appeared as the preface to every edition after the second English edition. The Sketch was intended by him to serve as a short “history of opinion” on the species question before he presented his own theory in the Origin proper. But the provenance of the “Historical Sketch” is somewhat obscure. Some things are known about its production, such as when it first appeared and what changes were made to it between its first appearance in 1860 and its final form, for the fourth English edition, in 1866. But how it evolved in Darwin’s mind, why he wrote it at all, and what he thought he was accomplishing by prefacing it to the Origin remain questions that have not been carefully addressed in the scholarly literature on Darwin. I attempt to show that Darwin’s various statements about the “Historical Sketch,” made primarily to several of his correspondents between 1856 and 1860, are somewhat in conflict with one another, thus making problematic a satisfactory interpretation of how, when, and why the Sketch came to be. I also suggest some probable resolutions to the several difficulties. How Darwin came to settle on the title “Historical Sketch” for the Preface to the Origin is not certain, but a guess may be ventured. When he first submitted the text to Asa Gray in February 1860 he called it simply “Preface Contributed by the Author to this American Edition” (Burkhardt et al., eds., vol. 8, 1993, p. 572; the collected correspondence is hereafter cited as CCD). In fact he had thought of it as being properly called a Preface much earlier, perhaps as early as 1856, as will be seen in what follows. It came to be called “An Historical Sketch of the Recent Progress of Opinion on the Origin of Species” only in the third English edition, April 1861. This is the title it retained thereafter, with the exception of an addition to the title in the sixth English edition, “Previously to the Publication of the First Edition of this Work” (Peckham, 1959, pp. 20, 59). The word “sketch,” on the other hand was one of two words Darwin commonly used in private correspondence to refer to the book that would later become the Origin, the other word being “Abstract,” and both signifying that Darwin thought of the work as being a resume rather than a full-fledged study (e.g., letter to J.D. Hooker, May 9 1856, CCD vol. 6 p. 106; letter to Baden Powell January 18 1860, CCD vol. 8 p. 41; letter to Lyell 25 June 1858, CCD v. 7, 1991, pp. 117–8; letter to Lyell May 1856, CCD, v. 6 p. 100). The most likely source of the title “Historical Sketch” for Darwin’s Preface is Charles Lyell’s Principles of Geology in which, beginning with the third edition (1834), Lyell added titles to his chapters, calling chapters 2–4 “Historical Sketch of the Progress of Geology” (Secord, in Lyell [1997], p. xlvii; for other uses by Lyell of this expression, cf. Porter, 1976, p. 95; idem 1982, p. 38; and Lyell, 1830 [1990], p. 30). Further parallels between Lyell’s Introduction and Darwin’s “Historical Sketch” in terms of content and strategy are suggested below.     

Redefining the X Axis: “Professionals,” “Amateurs” and the Making of Mid-Victorian Biology – A Progress Report

A summary of revisionist accounts of the contextual meaning of`“professional” and “amateur,” as applied to the mid-Victorian X Club, is followed by an analysis of the liberal goals and inner tensions of this coalition of gentlemen specialists and government teachers. The changing status of amateurs is appraised, as are the new sites for the emerging laboratory discipline of “biology.” Various historiographical strategies for recovering the women’s role are considered. The relationship of science journalism to professionalization, and the constructive engagement of X Club publicists with their empowering audiences, are discussed. Finally, the article assesses how far the content and boundary closure of ``biology,' forged by Thomas Henry Huxley, were related to `professional' and political goals. Purebiology’s social and medical roots are examined, and the way inter-professional and wider Darwinian conflicts resulted in anew lexicon of words for the X Clubbers around 1870, including“evolution” and “agnosticism,” as well as “biology.” Biology’srole in the forging of British national identity is discussed, as are its relationship to the social strategies of liberal, Dissenting, and industrial groups in the country, whose authority sustained the new laboratory rhetoric. This revised version was published online in July 2006 with corrections to the Cover Date.     

Autophagolysosomes exhibiting lysosomophagy in the granular lymphocytes of patients with granular lymphocyte-proliferative disorders

The ultrastructure of granular lymphocytes (GLs) in the peripheral blood of 12 patients with granular lymphocyte-proliferative disorders (GLPDs) was studied. Autophagolysosomes exhibiting so-called “lysosomophagy” were seen in the GLs of four of these patients but not in normal individuals. Because rod-shaped lysosomes beginning to enclose other lysosomes were seen, the autophagolysosomes exhibiting lysosomophagy in GLs were thought to be formed by the same wrapping mechanism. As far as we know, this is the first report of lysosomophagy in lymphocytes.     

Gametophytic self-incompatibility: understanding the cellular mechanisms involved in “self” pollen tube inhibition

Self-incompatibility (SI) prevents the production of “self” seed and inbreeding by providing a recognition and rejection system for “self,” or genetically identical, pollen. Studies of gametophytic SI (GSI) species at a molecular level have identified two completely different S-genes and SI mechanisms. One GSI mechanism, which is found in the Solanaceae, Rosaceae and Scrophulariaceae, has S-RNase as the pistil S-component and an F-box protein as the pollen S-component. However, non-S-locus factors are also required. In an incompatible situation, the S-RNases degrade pollen RNA, thereby preventing pollen tube growth. Here, in the light of recent evidence, we examine alternative models for how compatible pollen escapes this cytotoxic activity. The other GSI mechanism, so far found only in the Papaveraceae, has a small secreted peptide, the S-protein, as its pistil S-component. The pollen S-component remains elusive, but it is thought to be a transmembrane receptor, as interaction of the S-protein with incompatible pollen triggers a signaling network, resulting in rapid actin depolymerization and pollen tube inhibition and programmed cell death (PCD). Here, we present an overview of what is currently known about the mechanisms involved in regulating pollen tube inhibition in these two GSI systems.     

From “Us vs. Them” to “Shared Risk”: Can Animals Help Link Environmental Factors to Human Health?

Linking human health risk to environmental factors can be a challenge for clinicians, public health departments, and environmental health researchers. While it is possible that nonhuman animal species could help identify and mitigate such linkages, the fields of animal and human health remain far apart, and the prevailing human health attitude toward disease events in animals is an “us vs. them” paradigm that considers the degree of threat that animals themselves pose to humans. An alternative would be the development of the concepts of animals as models for environmentally induced disease, as well as potential “sentinels” providing early warning of both noninfectious and infectious hazards in the environment. For such concepts to truly develop, critical knowledge gaps need to be addressed using a “shared risk” paradigm based on the comparative biology of environment–host interactions in different species.     

Statistical Study of Protective and Risk Factors Assessed on Adolescents from South Eastern Europe and Italy, Attending High Schools in Apulia (Italy)*

This research is part of a European project in which particular attention was dedicated to “refugee” adolescents (whose migration occurred after traumatic socio-political and economic events in their country of origin). The purpose of this research was to provide a better understanding of the psychological risks and protective factors linked to the socio-cultural integration of refugee adolescents from countries with serious socio-economic difficulties. Another goal of the research was to contribute to the programmes which favour the psychophysical recovery of these adolescents from South-East Europe, with the target of attaining a normal and, as far as possible, healthy integration. The overall results obtained from the investigation form the basis for attempts to provide new models for the future creation of better policies of integration.*A collaborative project (conducted by University of Bari, Johannes Kepler Univesity in Linz, University of Tuzla, University of Prishtina, University of Tirana, Institute for Anthropological Research in Zagreb), supported by the European Commission 5th Framework specific research and technological development programme “Confirming the International Role of Community Research” – INCO – Copernicus (ICA2-CT-2002-10006).     

Reactions chimiques couplees considerees en tant que filtres passe-bande

An investigation is made as to whether or not the existence of a band-pass filter function, analogous to that in electronics, can be proved from the fundamental laws of chemical kinetics. The problem is important for better understanding of the preference of certain biological rhythms to others. It is shown with simple examples that such behavior is possible for a number of systems of coupled chemical reactions far enough from the thermodynamic equilibrium. It is of interest to generalize this behavior since it could conceivably play a role in the transmission of “usable information” in biology.      

Is there a Real Nexus Between Ethics and Aesthetics?

Aesthetics is a vexed topic in philosophy, with a long history. For my purposes, an aesthetic experience is a foundational affective response to an object, to which terms such as “ugly”, “beautiful”, “pretty” or “harmonious” are applied. These terms are derived from a Discourse of aesthetics; some remain constant, others change from generation to generation. Aesthetics and ethics have been linked in Western thought since the days of Plato and Aristotle. This essay examines what is happening to that link in contemporary experience. It emphasises the ways in which the popular media exploit aesthetic appeal to penetrate their market, and to exploit and frame intuitive responses to current and past events. Production values, the artfulness of editors and the financial interests of producers and directors thus do much to determine contemporary aesthetic and ethical judgements. That which is beautifully presented invites the ethical involvement of the audience. Events whose images are beautifully presented constitute “hyperevidence”, a pre-judged, reinforced and amplified illusion of reality and participation. Understanding how aesthetic excellence draws audiences into ethical relationship with what is presented becomes an important part of education in ethics, including bioethics.