The Impact of Lamarck’s Theory of Evolution Before Darwin’s Theory

This paper analyzes the impact that Lamarckian evolutionary theory had in the scientific community during the period between the advent of Zoological Philosophy and the publication Origin of Species. During these 50 years Lamarck’s model was a well known theory and it was discussed by the scientific community as a hypothesis to explain the changing nature of the fossil record throughout the history of Earth. Lamarck’s transmutation theory established the foundation of an evolutionary model introducing a new way to research in nature. Darwin’s selectionist theory was proposed in 1859 to explain the origin of species within this epistemological process. In this context, Charles Lyell’s Principles of Geology and Auguste Comte’s Cours de Philosophie Positive appear as two major works for the dissemination of Lamarck’s evolutionary ideology after the death of the French naturalist in 1829.     

Reconstituting Corticostriatal Network on-a-Chip Reveals the Contribution of the Presynaptic Compartment to Huntington’s Disease

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Endless Urban Growth? On the Mismatch of Population,Household and Urban Land Area Growth and Its Effects on the Urban Debate

In European cities, the rate of population growth has declined significantly, while the number of households has increased. This increase in the number of households is associated with an increase in space for housing. To date, the effects of both a declining population and decreasing household numbers remain unclear. In this paper, we analyse the relationship between population and household number development in 188 European cities from 1990–2000 and 2000–2006 to the growth of urban land area and per capita living space. Our results support a trend toward decreasing population with simultaneously increasing household number. However, we also found cites facing both a declining population and a decreasing household number. Nevertheless, the urban land area of these “double-declining” cities has continued to spread because the increasing per capita living space counteracts a reduction in land consumption. We conclude that neither a decline in population nor in household number “automatically” solve the global problem of land consumption.     

Taking the ‘Error’ Out of Ruse‘s Error Theory

Michael Ruses Darwinian metaethics has come under just criticism from Peter Woolcock (1993). But with modification it remains defensible. Ruse (1986) holds that people ordinarily have a false belief that there are objective moral obligations. He argues that the evolutionary story should be taken as an error theory, i.e., as a theory which explains the belief that there are obligations as arising from non-rational causes, rather than from inference or evidential reasons. Woolcock quite rightly objects that this position entails moral nihilism. However, I argue here that people generally have justified true beliefs about which acts promote their most coherent set of moral values, and hence, by definition, about which acts are right. What the evolutionary story explains is the existence of these values, but it is not an error theory for moral beliefs. Ordinary beliefs correspond to real moral properties, though these are not objective or absolute properties independent of anyones subjective states. On its best footing, therefore, a Darwinian metaethics of the type Ruse offers is not an error theory and does not entail moral nihilism.     

Sources of Wilhelm Johannsen’s Genotype Theory

This paper describes the historical background and early formation of Wilhelm Johannsen’s distinction between genotype and phenotype. It is argued that contrary to a widely accepted interpretation (For instance, W. Provine, 1971. The Origins of Theoretical Population Genetics. Chicago: The University of Chicago Press; Mayr, 1973; F. B. Churchill, 1974. Journal of the History of Biology 7: 5–30; E. Mayr, 1982. The Growth of Biological Thought, Cambridge: Harvard University Press; J. Sapp, 2003. Genesis. The Evolution of Biology. New York: Oxford University Press) his concepts referred primarily to properties of individual organisms and not to statistical averages. Johannsen’s concept of genotype was derived from the idea of species in the tradition of biological systematics from Linnaeus to de Vries: An individual belonged to a group – species, subspecies, elementary species – by representing a certain underlying type (S. Müller-Wille and V. Orel, 2007. Annals of Science 64: 171–215). Johannsen sharpened this idea theoretically in the light of recent biological discoveries, not least those of cytology. He tested and confirmed it experimentally combining the methods of biometry, as developed by Francis Galton, with the individual selection method and pedigree analysis, as developed for instance by Louis Vilmorin. The term “genotype” was introduced in W. Johannsen’s 1909 (Elemente der Exakten Erblichkeitslehre. Jena: Gustav Fischer) treatise, but the idea of a stable underlying biological “type” distinct from observable properties was the core idea of his classical bean selection experiment published 6 years earlier (W. Johannsen, 1903. Ueber Erblichkeit in Populationen und reinen Linien. Eine Beitrag zur Beleuchtung schwebender Selektionsfragen, Jena: Gustav Fischer, pp. 58–59). The individual ontological foundation of population analysis was a self-evident presupposition in Johannsen’s studies of heredity in populations from their start in the early 1890s till his death in 1927. The claim that there was a “substantial but cautious modification of Johannsen’s phenotype–genotype distinction” (Churchill, 1974, p. 24) from a statistical to an individual ontological perspective derives from a misreading of the 1903 and 1909 texts. The immediate purpose of this paper is to correct this reading of the 1903 monograph by showing how its problems and results grow out of Johannsen’s earlier work in heredity and plant breeding. Johannsen presented his famous selection experiment as the culmination of a line of criticism of orthodox Darwinism by William Bateson, Hugo de Vries, and others (Johannsen, 1903). They had argued that evolution is based on stepwise rather than continuous change in heredity. Johannsen’s paradigmatic experiment showed how stepwise variation in heredity could be operationally distinguished from the observable, continuous morphological variation. To test Galton’s law of partial regression, Johannsen deliberately chose pure lines of self-fertilizing plants, a pure line being the descendants in successive generations of one single individual. Such a population could be assumed to be highly homogeneous with respect to hereditary type, and Johannsen found that selection produced no change in this type. Galton, he explained, had experimented with populations composed of a number of stable hereditary types. The partial regression which Galton found was simply an effect of selection between types, increasing the proportion of some types at the expense of others.     

Exploring Twitter to Analyze the Public’s Reaction Patterns to Recently Reported Homicides in London

Crime is an ubiquitous part of society. The way people express their concerns about crimes has been of particular interest to the scientific community. Over time, the numbers and kinds of available communication channels have increased. Today, social media services, such Twitter, present a convenient way to express opinions and concerns about crimes. The main objective of this study is to explore people’s perception of homicides, specifically, how the characteristics and proximity of the event affect the public’s concern about it. The analysis explores Twitter messages that refer to homicides that occurred in London in 2012. In particular, the dependence of tweeting propensity on the proximity, in space and time, of a crime incident and of people being concerned about that particular incident are examined. Furthermore, the crime characteristics of the homicides are analysed using logistic regression analysis. The results show that the proximity of the Twitter users’ estimated home locations to the homicides’ locations impacts on whether the associated crime news is spread or not and how quickly. More than half of the homicide related tweets are sent within the first week and the majority of them are sent within a month of the incident’s occurrence. Certain crime characteristics, including the presence of a knife, a young victim, a British victim, or a homicide committed by a gang are predictors of the crime-tweets posting frequency.     

Gene Network and Database for Genes of Wheat’s Resistance to Pathogenic Fungi

An overview describing a gene network that controls the formation of plant responses to diseases caused by pathogenic fungi (http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet//viewer/Plant%20fungus%20pathogen.html) is presented. The gene network represents the coordinated interactions of genes, proteins, and regulatory molecules, including integrated defense mechanisms that prevent the development of infection, localize the lesion, and minimize damage. The gene network was reconstructed on the basis of literature data, and the elements of the gene network were associated with the records of the PGR database (Pathogenesis-Related Genes, http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?-page+top+-newId), where information on plant genes resistant to pathogenic fungi is accumulated. Reconstruction of the gene network allows us to formalize, visualize, and systematize possible mechanisms for the response of plant cells to fungal infection, which may be useful for the planning of experiments and interpretation of experimental data in this field of science.     

Extension of Shafranov’s Equilibrium Theory to the Description of Current Quenches Affected by Resistive Wall Dissipation in Tokamaks

Plasma Physics Reports - An equation for the plasma column position in a tokamak is derived with account of the resistive wall reaction on the changes in the plasma. A similar problem was...     

Methodology in Aristotle’s Theory of Spontaneous Generation

Aristotle’s theory of spontaneous generation offers many puzzles to those who wish to understand his theory both within the context of his biology and within the context of his more general philosophy of nature. In this paper, I approach the difficult and vague elements of Aristotle’s account of spontaneous generation not as weaknesses, but as opportunities for an interesting glimpse into the thought of an early scientist struggling to reconcile evidence and theory. The paper has two goals: (1) to give as charitable and full an account as possible of what Aristotle’s theory of spontaneous generation was, and to examine some of its consequences; and (2) to reflect on Aristotle as a scientist, and what his comments reveal about how he approached a difficult problem. In particular, I propose that the well-recognized problem of the incompatibility between Aristotle’s concept of spontaneity and his theory of spontaneous generation presents an opportunity for insight into his scientific methodology when approaching ill-understood phenomena.     

Current approaches to the treatment of Parkinson’s Disease

Parkinson’s Disease (PD) is the second most common neurodegenerative disorder. Clinical approaches to manage PD include symptomatic therapies, serving to compensate for the effects of dopaminergic neuronal deficits, as well as more recently a move toward disease modification, with the goal of slowing or stopping disease progression. This perspective surveys the approved therapies for PD treatment as well as provides a view of the ongoing clinical approaches aimed at improving outcomes for PD patients.     

Call Characteristic Network Reveal Geographical Patterns of Call Similarity:Applying Network Analysis to Frog’s Call Research

Individual’s phenotypic traits are the results of adaptation to ecological conditions.Therefore,different selection pressures caused by heterogeneous environments may result in phenotypic difference,especially for individuals in different geographical populations.Here,we illustrated for the first time to use social network analysis(SNA)for examining whether geographical proximity predicts the similarity patterns in call characteristics among populations of an anuran species.We recorded calls from 150 male dorsal-striped opposite-fingered treefrogs(Chiromantis doriae)at 11 populations in Hainan Province and one population in Guangdong Province in China's Mainland,and we measured eight acoustic variables for each male.Mantel test didn’t show a correlation between geographical proximity and the similarity in call characteristics among populations.In addition,we failed to find correlations between a population’s eigenvector centrality and the distance to its nearest neighbor,nor between the coefficient of variation of similarity in call characteristics of a population and the average distance to all other populations.Nevertheless,three acoustic clusters were identified by the Girvan-Newman algorithm,and clustering was partially associated with geography.Furthermore,the most central populations were included in the same cluster,but the top betweenness populations were located within different clusters,suggesting that centrality populations are not necessary bridging between clusters.These results demonstrate the potential usefulness of the SNA toolbox and indicate that SNA helps to uncover the patterns that often overlooked in other analytical methods.By using SNA in frog’s call studies,researchers could further uncover the potential relationship in call characteristics between geographical populations,further reveal the effects of ecological factors on call characteristics,and probably enhance our understanding of the adaptive evolution of acoustic signals.     

A Multi-Marker Genetic Association Test Based on the Rasch Model Applied to Alzheimer’s Disease

Results from Genome-Wide Association Studies (GWAS) have shown that the genetic basis of complex traits often include many genetic variants with small to moderate effects whose identification remains a challenging problem. In this context multi-marker analysis at the gene and pathway level can complement traditional point-wise approaches that treat the genetic markers individually. In this paper we propose a novel statistical approach for multi-marker analysis based on the Rasch model. The method summarizes the categorical genotypes of SNPs by a generalized logistic function into a genetic score that can be used for association analysis. Through different sets of simulations, the false-positive rate and power of the proposed approach are compared to a set of existing methods, and shows good performances. The application of the Rasch model on Alzheimer’s Disease (AD) ADNI GWAS dataset also allows a coherent interpretation of the results. Our analysis supports the idea that APOE is a major susceptibility gene for AD. In the top genes selected by proposed method, several could be functionally linked to AD. In particular, a pathway analysis of these genes also highlights the metabolism of cholesterol, that is known to play a key role in AD pathogenesis. Interestingly, many of these top genes can be integrated in a hypothetic signalling network.     

Strasburger’s legacy to mitosis and cytokinesis and its relevance for the Cell Theory

Eduard Strasburger was one of the most prominent biologists contributing to the development of the Cell Theory during the nineteenth century. His major contribution related to the characterization of mitosis and cytokinesis and especially to the discovery of the discrete stages of mitosis, which he termed prophase, metaphase and anaphase. Besides his observations on uninucleate plant and animal cells, he also investigated division processes in multinucleate cells. Here, he emphasised the independent nature of mitosis and cytokinesis. We discuss these issues from the perspective of new discoveries in the field of cell division and conclude that Strasburger's legacy will in the future lead to a reformulation of the Cell Theory and that this will accommodate the independent and primary nature of the nucleus, together with its complement of perinuclear microtubules, for the organisation of the eukaryotic cell.     

Ecology of Children’s Growth: An Example from Transitional Populations of the Brazilian Amazon

The intense environmental and social changes taking place in Amazonia make this a key area for health studies of populations transitioning to a cosmopolitan lifestyle and market economy. Caboclos are among those populations. They comprise the majority of rural Brazilian Amazon peoples. At present there is limited information about their patterns of growth and health. In this paper, anthropometric data on Caboclo children from three groups living in different environments are presented and discussed within a bioanthropological framework. Caxiuanã, Aracampina, and Santana have a combined population of 1,069 people. Caxiuanã relies more on subsistence activities for survival and Santana more on commerce, while Aracampina uses both subsistence strategies. Compared to US children, Caboclo are generally shorter and lighter in all age groups. However, their weight-for-height is above the 50th percentile. In relation to skinfolds, age groups 0–2, 6–8, and 9–11 years present statistically significant differences among the three communities. Caxiuanã children have the smallest and Aracampina children have the largest skinfolds. While seasonal and environmental differences may account for some of the observed variation in growth and fatness patterns, socioeconomic factors also play a key role in the trends observed. Thus, an ecological model provides the best framework for explaining these findings. Caxiuanã children are small and thin as a result of their combined poor environment and limited access to cash, western goods, and health care. Aracampina and Santana’s fuller access to such socioeconomic influences and richer ecology results in taller and fatter children. Understanding similar interactions between ecology and social factors will be fundamental to developing sustainable health initiatives among rural Amazonian populations.     

What are the Evolutionary Origins of Mitochondria? A Complex Network Approach

Mitochondria originated endosymbiotically from an Alphaproteobacteria-like ancestor. However, it is still uncertain which extant group of Alphaproteobacteria is phylogenetically closer to the mitochondrial ancestor. The proposed groups comprise the order Rickettsiales, the family Rhodospirillaceae, and the genus Rickettsia. In this study, we apply a new complex network approach to investigate the evolutionary origins of mitochondria, analyzing protein sequences modules in a critical network obtained through a critical similarity threshold between the studied sequences. The dataset included three ATP synthase subunits (4, 6, and 9) and its alphaproteobacterial homologs (b, a, and c). In all the subunits, the results gave no support to the hypothesis that Rickettsiales are closely related to the mitochondrial ancestor. Our findings support the hypothesis that mitochondria share a common ancestor with a clade containing all Alphaproteobacteria orders, except Rickettsiales.     

Dynamics of the Subthalamo-pallidal Complex in Parkinson’s Disease During Deep Brain Stimulation

The dynamics of the subthalamo-pallidal complex in Parkinson’s disease during deep brain stimulation (DBS) were studied using two models, a simple firing-rate model and a population-based model. We extended the simple firing-rate model of the complex formed by the subthalamic nucleus (STN) and the external segment of the Globus Pallidus (GPe) to explore its dynamical regime during DBS. More specifically, the modulation of neuronal activity (i.e., pattern and amplitude) during DBS was studied. A similar approach was used with the population-based model. Simulation results revealed a gradual decrease in bursting activity in STN cells when the DBS frequency increased. In addition, the contribution of the stimulation current type (mono- or biphasic) to the results was also examined. A comparison of the two models indicated that the population-based model was more biologically realistic and more appropriate for exploring DBS mechanisms. Understanding the underlying mechanisms of DBS is a prerequisite for developing new stimulation protocols.     

Targeting the mTOR Signaling Network for Alzheimer’s Disease Therapy

The mammalian target of rapamycin (mTOR) is a highly conserved serine/threonine kinase that can sense environmental stimuli such as growth factors, energy state, and nutrients. It is essential for cell growth, proliferation, and metabolism, but dysregulation of mTOR signaling pathway is also associated with a number of human diseases. Encouraging data from experiments have provided sufficient evidence for the relationship between the mTOR signaling pathway and Alzheimer’s disease (AD). Upregulation of mTOR signaling pathway is thought to play an important role in major pathological processes of AD. The mTOR inhibitors such as rapamycin have been proven to ameliorate the AD-like pathology and cognitive deficits effectively in a broad range of animal models. Application of mTOR inhibitors indicates the potential value of reducing mTOR activity as an innovative therapeutic strategy for AD. In this review, we will focus on the recent process in understanding mTOR signaling pathway and the vital involvement of this signaling pathway in the pathology of AD, and discuss the application of mTOR inhibitors as potential therapeutic agents for the treatment of AD.