Time, from psychology to neurophysiology: a historical view

Two aspects of psychology and physiology of time are dealt with in this paper: the way time perception was increasingly studied during the 19th century by scientists, including many physicists, and the way the temporal properties of the nervous system were discovered and explored by physiologists. The neurophysiological correlation between both aspects still remains to be explained. The relationship between time consciousness and consciousness mechanisms was often guessed by philosophers and looked for by scientists. It remains a major subject of investigation in neuroscience as well as a philosophical puzzle.     

Individual essentialism in biology

A few philosophers of biology have recently explicitly rejected Essential Membership, the doctrine that if an individual organism belongs to a taxon, particularly a species, it does so essentially. But philosophers of biology have not addressed the broader issue, much discussed by metaphysicians on the basis of modal intuitions, of what is essential to the organism. In this paper, I address that issue from a biological basis, arguing for the Kripkean view that an organism has a partly intrinsic, partly historical, essence. The arguments appeal to the demands of biological explanation and are analogous to arguments that I have given elsewhere that a taxon has a partly intrinsic, partly historical, essence. These conclusions about the essences of individuals and taxa yield an argument for Essential Membership. Finally, I cast doubt on LaPorte’s objection to that doctrine arising from the view that a species cannot survive having a daughter.     

The role of theology in current evolutionary reasoning

A remarkable but little studied aspect of current evolutionary theory is the use by many biologists and philosophers of theological arguments for evolution. These can be classed under two heads: imperfection arguments, in which some organic design is held to be inconsistent with God's perfection and wisdom, and homology arguments, in which some pattern of similarity is held to be inconsistent with God's freedom as an artificer. Evolutionists have long contended that the organic world falls short of what one might expect from an omnipotent and benevolent creator. Yet many of the same scientists who argue theologically for evolution are committed to the philosophical doctrine of methodological naturalism, which maintains that theology has no place in science. Furthermore, the arguments themselves are problematical, employing concepts that cannot perform the work required of them, or resting on unsupported conjectures about suboptimality. Evolutionary theorists should reconsider both the arguments and the influence of Darwinian theological metaphysics on their understanding of evolution.     

What is life?

Background

Many traditional biological concepts continue to be debated by biologists, scientists and philosophers of science. The specific objective of this brief reflection is to offer an alternative vision to the definition of life taking as a starting point the traits common to all living beings.

Results and Conclusions

Thus, I define life as a process that takes place in highly organized organic structures and is characterized by being preprogrammed, interactive, adaptative and evolutionary. If life is the process, living beings are the system in which this process takes place. I also wonder whether viruses can be considered living things or not. Taking as a starting point my definition of life and, of course, on what others have thought about it, I am in favor of considering viruses as living beings. I base this conclusion on the fact that viruses satisfy all the vital characteristics common to all living things and on the role they have played in the evolution of species. Finally, I argue that if there were life elsewhere in the universe, it would be very similar to what we know on this planet because the laws of physics and the composition of matter are universal and because of the principle of the inexorability of life.

     

Gender differences in body build and physiological functions in the adult population of Yucatan, Mexico

This study, conducted in 1994-95, evaluates differences in body build, blood pressure and respiratory functions between sexes and age groups of low socioeconomic strata individuals living in Merida, Yucatan, Mexico. The cross-sectional sample includes 344 males and 320 females, 20-98 years of age divided into six age groups (20-29, 30-39, 40-49, 50-59, 60-69 and 70+ years) by sex. Differences between age cohorts in height, weight, fatness, systolic blood pressure, and most respiratory variables (excluding expiratory reserve volume, minute ventilation and respiration rate) are greater among women than in men. The more marked secular trend in stature and bigger biological differences between age cohorts in women might have its beginning in 19th century when living conditions of women were worse than those of men. Only since the last decades of 20th century, migrations and improvements in living conditions might caused more drastic changes in women of low social strata than in men. Results of regression analysis show a greater relationship between studied variables in women than in men what confirms that women are less sensitive to environmental factors. A pattern of changes in minute ventilation (MV) with rising age of the cohorts differs between men and women (smaller differences appear in the women's cohort) Also a different pattern (MV) is seen in European populations. The latter may suggest existence of some adaptational phenomena to the local environment.     

The doctrine of specific etiology

Modern medicine is often said to have originated with nineteenth century germ theory, which attributed diseases to bacterial contagions. The success of this theory is often associated with an underlying principle referred to as the “doctrine of specific etiology”. This doctrine refers to specificity at the level of disease causation or etiology. While the importance of this doctrine is frequently emphasized in the philosophical, historical, and medical literature, these sources lack a clear account of the types of specificity that it involves and why exactly they matter. This paper argues that nineteenth century germ theory involves two types of specificity at the level of etiology. One type receives significant attention in the literature, but its influence on modern medicine has been misunderstood. A second type is present in this model, but it has been completely overlooked in the extant literature. My analysis clarifies how these types of specificity led to a novel conception of etiology that continues to figure in medicine today.     

Cells as irreducible wholes: the failure of mechanism and the possibility of an organicist revival

According to vitalism, living organisms differ from machines and all other inanimate objects by being endowed with an indwelling immaterial directive agency, ‘vital force,’ or entelechy. While support for vitalism fell away in the late nineteenth century many biologists in the early twentieth century embraced a non vitalist philosophy variously termed organicism/holism/emergentism which aimed at replacing the actions of an immaterial spirit with what was seen as an equivalent but perfectly natural agency—the emergent autonomous activity of the whole organism. Organicists hold that organisms unlike machines are ‘more than the sum of their parts’ and predict that the vital properties of living things can never be explained in terms of mechanical analogies and that the reductionist agenda is doomed to failure. Here we review the current status of the mechanist and organicist conceptions of life particularly as they apply to the cell. We argue that despite the advances in biological knowledge over the past six decades since the molecular biological revolution, especially in the fields of genetics and cell biology the unique properties of living cells have still not been simulated in mechanical systems nor yielded to reductionist—analytical explanations. And we conclude that despite the dominance of the mechanistic–reductionist paradigm through most of the past century the possibility of a twentyfirst century organicist revival cannot be easily discounted.     

Problems in the Integrated Study of Individual Differences

The properties of all the stages of evolution of matter, from the chemical to the sociohistorical, are part of man as well. In each of these properties, in addition to what is common and typical for groups of people, there is something that is unique to the individual and irreproducible. One characteristic noted in theoretical conceptions of individual differences is that they tend to study properties relating to different stages in the development of matter in isolation from one another. In most studies of differential psychophysiology, the biochemical and endocrine properties of the organism and the bioelectric properties of the nervous system are examined as if they had nothing to do with individual characteristics in the formation of classical Pavlovian conditioned reflexes. The psychological properties of the personality are examined in the Vygotsky and Leont'ev school independently of their relationship to somatic, neurophysiological, and psychodynamic properties (the properties of temperament).     

The history of Hayek’s theory of cultural evolution

This paper traces the historical origins of Friedrich A. Hayek’s theory of cultural evolution, and argues that Hayek’s evolutionary thought was significantly inspired by Alexander M. Carr-Saunders and Oxford zoology. While traditional Hayek scholarship emphasizes the influence of Carl Menger and the British eighteenth-century moral philosophers, I claim that these sources underdetermine what was most characteristic of Hayek’s theory, viz. the idea that cultural evolution is a matter of group selection, and the idea that natural selection operates on acquired as well as on inherited properties.     

Living matter—nexus of physics and biology in the 21st century

Cells are made up of complex assemblies of cytoskeletal proteins that facilitate force transmission from the molecular to cellular scale to regulate cell shape and force generation. The “living matter” formed by the cytoskeleton facilitates versatile and robust behaviors of cells, including their migration, adhesion, division, and morphology, that ultimately determine tissue architecture and mechanics. Elucidating the underlying physical principles of such living matter provides great opportunities in both biology and physics. For physicists, the cytoskeleton provides an exceptional toolbox to study materials far from equilibrium. For biologists, these studies will provide new understanding of how molecular-scale processes determine cell morphological changes.The distinction between being “alive” or “not alive” has been a long-standing question for those interested in our natural world. In many ancient cultures, the difference between living organisms and inorganic matter was thought to be due to innate differences arising from a “vital force,” such that biology operated with different fundamental properties than the physical world. The ability to disprove such theories came about over the course of the 17th to the 19th centuries, as scientists developed theories of atoms and were able to synthesize organic matter from inorganic constituents. Over the past 100 years, developments in molecular biology and biochemistry have provided a wealth of information on the structure and function of biological molecules, much of which was acquired in collaborations between physical and biological scientists. Application of X-ray–scattering techniques first developed to study metals enabled discovery of the structure of complicated biological molecules ranging from DNA to ion channels. Use of laser trapping techniques first developed to trap and cool atoms enabled precise force spectroscopy measurements of single molecular motors. We now know that biological molecules, while more complicated than their inorganic counterparts, must obey the rules of physics and chemistry.This wealth of molecular-scale information does not directly inform the behaviors of living cells. The organelles within cells are made up of complex and dynamic assemblies of proteins, lipids, and nucleic acids, all immersed within an aqueous environment. These assemblies are somehow able to build materials that can robustly facilitate the plethora of morphological and physical behaviors of cells at the subcellular (intracellular transport), cellular (division, adhesion, migration), and multicellular (tissue morphogenesis, wound healing) length scales. The dynamic cytoskeleton transmits information and forces from the molecular to the cellular length scales. But what is it about the behaviors of biological molecules that endow cells with the ability to respirate, move, and replicate themselves robustly—all qualities we consider essential to “life”? For these questions, understanding of the physics and chemistry of systems of biological molecules is needed. Interactions that occur within ensembles of molecules lead to emergent properties and behaviors that cannot be predicted at the single-molecule level. These emergent chemical and physical properties of living matter are likely fundamentally different from inorganic or “dead” materials. Discovering the underlying principles of living matter provides fantastic opportunities to learn new physics and biology.The fields of condensed matter physics and materials science study the physical properties that emerge when objects (e.g., atoms, molecules, grains of sand, or soap bubbles) are placed in sufficiently close proximity, such that interactions between them cannot be ignored. Interatomic or intermolecular interactions give rise to emergent properties that are not seen in isolated species. Familiar examples involve electron transport across a material or a material''s response to externally applied magnetic fields or mechanical forces. These emergent properties, such as conductivity, elasticity, and viscosity, enable us to predict the behavior of a collection of objects in these condensed phases. In this paper, I will focus on my perspective of how approaches to understanding the mechanical properties of physical materials can inform understanding of the mechanical properties of living matter found within cells.In a crystal of metal, precisely organized atoms are located nanometers apart, and the energies of their interactions are on the scale of an electron volt (40-fold larger than thermal energy or twice the energy released on the hydrolysis of a single ATP molecule). These give rise to an energy density, or elastic modulus, on the order of gigapascals, which underlies the rigidity of metals. For small deformations, the restoring force between atoms means that this metal behaves like an elastic spring: after a force is applied, the metal returns to its original shape. Understanding force transmission through crystalline metals was facilitated by the development of elasticity theory in the 16th and 17th centuries. Fluids, such as water, lack crystalline order, but predictive understanding of fluid flows and forces was captured through development of theories of fluid dynamics. Now think of another material, Silly Putty, which behaves elastically at short timescales (it bounces like a rubber ball) but then oozes and flows at long timescales, acting like a viscous fluid. Silly Putty is made of long polymers that are trapped by one another at short timescales, but thermal energy is sufficient to allow them to diffuse and translocate at long timescales. Silly Putty is also a “soft material,” in that the polymer''s interaction energies are at the thermal energy level, and its length scale is at the micrometer level. Materials like Silly Putty were thought to be too complicated for analytical theory. It was only in the middle of the 20th century that the theoretical framework to understand these “messy” and “disorganized” polymer-based materials was developed.The most powerful theories for understanding these vastly different forms of physical matter were developed in the absence of even the simplest of computers. The theories relied on developing physical properties or parameters to describe the material with a “mean field,” a type of coarse-graining that identifies the essential properties of individual constituents and interactions but ignores many other details. These mean fields give us new intuitions concerning the origin of material properties and give rise to definitions of physical parameters, such as elasticity and viscosity. However, these theories also require materials that do not jostle around a lot and remain close to equilibrium. In fact, understanding materials “far from equilibrium” has been identified as a major challenge in physics for the next century (National Research Council, 2007) .Materials formed by dynamic protein assemblies in the cytoskeleton are disorganized, heterogeneous, and driven far from equilibrium. Motor proteins generate local stresses, and their activity is spatially modulated. The polymerization and depolymerization of cytoskeletal polymers is controlled by a myriad of regulatory proteins. All these dynamic molecular processes endow the cytoskeletal assemblies with unique behaviors that enable them to support complex physiological tasks. It is likely these dynamics also provide underlying robustness of the cells in response to fluctuating and changing environments. These properties make living cells exquisite materials that cannot be captured by existing frameworks of physical matter. I suspect that we have not yet identified the important parameters needed to characterize their properties. The rich dynamics created by active biological matter present a formidable challenge in the area of materials science.How do we hope to understand the properties of these complex cytoskeletal assemblies and materials? It may seem as though understanding cytoskeletal machinery is an insurmountable feat, the approaches that have been successful for physical materials will not work, and we must rely on complex simulations that require modeling of all individual components. This may be true. However, I think that this is a pessimistic view. Just consider how complicated physical materials would be if we did not have the appropriate parameters to describe the macroscopic responses and had instead became obsessed about knowing the details of all the interactions between underlying atoms and molecules? In the same vein, I believe that predictive insights into biological matter will emerge through development of new physical theories that use mean-field approaches to understanding materials that contain active components and are driven far from equilibrium. The burgeoning field of active-matter physics is currently considering these questions (Ramaswamy, 2010) . However, these theoretical approaches require physical measurements of cells and cellular proteins that may not be clearly linked to a physiological process or have a clear biological context. Materials built from cytoskeletal proteins in vitro should also provide an excellent source of experimental measurements, but closer collaboration with theorists working in this field and collaboration between biochemists and experimental physical scientists is needed to develop control over such materials. Developing predictive physical theories of the cytoskeleton will elucidate principles of why “the whole is more than the sum of its parts” that will provide greater control and design over living matter, in the same way that engineering has provided great advances in applications of materials from the physical world.What do biologists gain from theories of living matter? These theories will provide a crucial link between molecular and cellular length scale behaviors and will provide insight into the mechanisms of why specific molecular perturbations alter cell behavior. Moreover, they should provide us with general design principles of living matter. What are the basic aspects of a machine needed to separate chromosomes, establish polarity, or generate contractile forces that is utilized across different cell types? Can knowing these aspects provide insight into the evolution of cellular machines and the robustness of cell behavior? Thus, study of cellular materials both provides new opportunities for physicists and will provide crucial predictive understanding of cell physiology.Open in a separate windowMargaret L. Gardel     

Finding simplicity in complexity: general principles of biological and nonbiological organization

What differentiates the living from the nonliving? What is life? These are perennial questions that have occupied minds since the beginning of cultures. The search for a clear demarcation between animate and inanimate is a reflection of the human tendency to create borders, not only physical but also conceptual. It is obvious that what we call a living creature, either bacteria or organism, has distinct properties from those of the normally called nonliving. However, searching beyond dichotomies and from a global, more abstract, perspective on natural laws, a clear partition of matter into animate and inanimate becomes fuzzy. Based on concepts from a variety of fields of research, the emerging notion is that common principles of biological and nonbiological organization indicate that natural phenomena arise and evolve from a central theme captured by the process of information exchange. Thus, a relatively simple universal logic that rules the evolution of natural phenomena can be unveiled from the apparent complexity of the natural world.     

Is information a proper observable for biological organization?

In the last century, jointly with the advent of computers, mathematical theories of information were developed. Shortly thereafter, during the ascent of molecular biology, the concept of information was rapidly transferred into biology at large. Several philosophers and biologists have argued against adopting this concept based on epistemological and ontological arguments, and also, because it encouraged genetic determinism. While the theories of elaboration and transmission of information are valid mathematical theories, their own logic and implicit causal structure make them inimical to biology, and because of it, their applications have and are hindering the development of a sound theory of organisms. Our analysis concentrates on the development of information theories in mathematics and on the differences between these theories regarding the relationship among complexity, information and entropy.     

Ecological aspects of the surface microlayer. I. ATP,ADP, AMP contents,and energy charge ratios of microplanktonic communities

Forty samples of both the surface microlayer (60 to 100 μm) and underlying waters (0.5 m), were collected in a neritic area (Gulf of Marseilles, France) and their microplanktonic composition studied by adenosine, pigment, and organic carbon content. In the surface film, the accumulation of the living fraction was weaker than for inert organic matter; this phenomenon was more marked in the hydrological structures which are named “slicks”. The relationship between nucleotides and chlorophyll provided evidence for a substantial participation of heterotrophic organisms, such as bacteria, in the living biomass of the surface film. In this layer, lower values of the energy charge, as compared with those of water from 0.5 m may indicate the presence of stressed microorganisms. Nevertheless, as was shown by ATP data, part of hyponeustonic microbiomass was alive, and not killed by severe ecological conditions of this biotope. High AMP concentrations may be partially explained by a contribution of non-living organic matter, as was proved by the high enrichment factor for this adenosine form, higher than those of ATP and ADP, closer to those of phaeophytins, degrading products from chlorophylls. Adenylic nucleotide measurements in the paniculate matter of the surface microlayer, as their ratios and relations with chlorophyll, seem to be a practical tool for investigating the sea-air interface, from an ecological point of view.     

Hebrew and Latin astrology in the twelfth century: the example of the location of pain

The formative period of Latin and Hebrew astrology occurred virtually simultaneously in both cultures. In the second quarter of the twelfth century the terminology of the subject was established and the textbooks which became authoritative were written. The responsibility for this lay almost entirely with two scholars: John of Seville for the Latins, and Abraham ibn Ezra for the Jews. It is unlikely to have been by coincidence that the same developments in astrology occurred in these two cultures. John of Seville and Abraham ibn Ezra were both brought up within the Islamic culture of Spain, and their astrology was Arabic astrology. Moreover, some scholars have thought that John’s origins were Jewish, while Ibn Ezra is known to have collaborated with Latin scholars (whose names are not recorded). It cannot be a coincidence that they forged the science of astrology for their respect co-religionists at almost the same time. Yet, very little research has been done on the possible relations between the two scholars. The purpose of this paper is to begin to explore this relationship, and to illustrate it in particular by their shared doctrine concern the location of pain.     

Trophic structure,available resources and population density in terrestrial vs. aquatic ecosystems

The relationship between available resources and the level at which density is regulated may not be obvious where direct inter- or intraspecific competition for available resources is absent. Interpretation of such cases requires that a distinction be made between organisms ingesting living material (biophages) and those subsisting on dead organic matter (saprophages).     

Origin of European rabbit (Oryctolagus cuniculus) in a Mediterranean island: Zooarchaeology and ancient DNA examination

Mammalian species presently living on Mediterranean islands have been brought in by man. The question of their geographical origin and of the time of their introduction is often a matter of debate. We studied this problem using a population of rabbits (European rabbit: Oryctolagus cuniculus) living in Zembra, an island off Tunisia. Archaeological surveys show that rabbit has been introduced to the island by Bronze Age or Roman people, between the IIIrd Millenium B.C. and the IIIrd century A.D. Part of the 16S-rRNA gene of mitochondrial DNAs from fossil bones of different ages (dated back to 130–390 A.D.) was characterized and compared to that of present day rabbits of differing geographical origin. The data suggest that animals present on Zembra in late Roman times belonged to the same maternal lineage as present populations from Northern Spain and Southern France.     

Molecular evidence for a terrestrial origin of snakes

Biologists have debated the origin of snakes since the nineteenth century. One hypothesis suggests that snakes are most closely related to terrestrial lizards, and reduced their limbs on land. An alternative hypothesis proposes that snakes are most closely related to Cretaceous marine lizards, such as mosasaurs, and reduced their limbs in water. A presumed close relationship between living monitor lizards, believed to be close relatives of the extinct mosasaurs, and snakes has bolstered the marine origin hypothesis. Here, we show that DNA sequence evidence does not support a close relationship between snakes and monitor lizards, and thus supports a terrestrial origin of snakes.     

Where the wild things are: environmental preservation and human nature

Environmental philosophers spend considerable time drawing the divide between humans and the rest of nature. Some argue that humans and our actions are unnatural. Others allow that humans are natural, but maintain that humans are nevertheless distinct. The motivation for distinguishing humans from the rest of nature is the desire to determine what aspects of the environment should be preserved. The standard view is that we should preserve those aspects of the environment outside of humans and our influence. This paper examines the standard view by asking two questions. First, are the suggested grounds for distinguishing humans from the rest of the environment viable? Second, is such a distinction even needed for determining what to preserve? The paper concludes that debates over whether humans are natural and whether humans are unique are unhelpful when deciding what to preserve.