On the nature and origin of cellular complexity: The combinatorial–eukaryogenetic scenario

The ideas on the nature and origin of the cell nucleus published by K.S. Merezhkowsky in his book The Theory of Two Plasms as the Basis of Symbiogenesis, a New Study on the Origins of Organisms (1909) are still relevant. In this book, Merezhkowsky (1909, p. 86) wrote, “Part of my theory related to the nucleus, its nature and origin will be the subject of a separate paper, which will present facts serving as the basis for the ideas, which are here only touched upon briefly.” For various reasons, he was not able to publish the paper intended. Therefore, I here attempt to interpret Merezhkowsky’s original concepts on the nature and origin of the cell nucleus in a modern context.     

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.     

Where We Used to Live: Validating Retrospective Measures of Childhood Neighborhood Context for Life Course Epidemiologic Studies

Early life exposures influence numerous social determinants of health, as distal causes or confounders of later health outcomes. Although a growing literature is documenting how early life socioeconomic position affects later life health, few epidemiologic studies have tested measures for operationalizing early life neighborhood context, or examined their effects on later life health. In the Life-course Influences on Fetal Environments (LIFE) Study, a retrospective cohort study among Black women in Southfield, Michigan (71% response rate), we tested the validity and reliability of retrospectively-reported survey-based subjective measures of early life neighborhood context(N=693). We compared 3 subjective childhood neighborhood measures (disorder, informal social control, victimization), with 3 objective childhood neighborhood measures derived from 4 decades of historical census tract data 1970-2000, linked through geocoded residential histories (tract % poverty, tract % black, tract deprivation score derived from principal components analysis), as well as with 2 subjective neighborhood measures in adulthood. Our results documented that internal consistency reliability was high for the subjective childhood neighborhood scales (Cronbach’s α =0.89, 0.93). Comparison of subjective with objective childhood neighborhood measures found moderate associations in hypothesized directions. Associations with objective variables were strongest for neighborhood disorder (rhos=.40), as opposed to with social control or victimization. Associations between subjective neighborhood context in childhood versus adulthood were moderate and stronger for residentially-stable populations. We lastly formally tested for, but found little evidence of, recall bias of the retrospective subjective reports of childhood context. These results provide evidence that retrospective reports of subjective neighborhood context may be a cost-effective, valid, and reliable method to operationalize early life context for health studies.     

The Proverbial Bourdieu: Habitus and the Politics of Representation in the Ethnography of Kabylia

Since the 1970s, anthropologists have been centrally concerned with the relationship of ethnographic representation to political and historical context. Interestingly, the work of Pierre Bourdieu has largely escaped such contextualization, despite the significance of Bourdieu's ideas to anthropological theorizing. Today, many of Bourdieu's central concepts float free from the context out of which they arose—the Kabyle region of Algeria. This article addresses this omission by reading Bourdieu's early works against each other to reconstitute aspects of his methodology and fieldwork. Focusing on his choice to represent the Kabyles of his early work in prose, and those in his later work via proverbs, I suggest that key premises of Bourdieu's theory may not be supported by historical and ethnographic evidence. I consider how Bourdieu's position as a young social scientist grappling with ethnographic responsibilities in colonial wartime led him to privilege his interlocutors' accounts in some studies while expunging them from others. [Keywords: Bourdieu, represented speech, literacy, Algeria, Berbers]     

Cytogerontology since 1881: A reappraisal of August Weismann and a review of modern progress

Summary Cytogerontology, the science of cellular ageing, originated in 1881 with the prediction by August Weismann that the somatic cells of higher animals have limited division potential. Weismann's prediction was derived by considering the role of natural selection in regulating the duration of an organism's life. For various reasons, Weismann's ideas on ageing fell into neglect following his death in 1914, and cytogerontology has only reappeared as a major research area following the demonstration by Hayflick and Moorhead in the early 1960s that diploid human fibroblasts are restricted to a finite number of divisions in vitro.In this review we give a detailed account of Weismann's theory, and we reveal that his ideas were both more extensive in their scope and more pertinent to current research than is generally recognised. We also appraise the progress which has been made over the past hundred years in investigating the causes of ageing, with particular emphasis being given to (i) the evolution of ageing, and (ii) ageing at the cellular level. We critically assess the current state of knowledge in these areas and recommend a series of points as primary targets for future research.     

‘The vagaries of a Rafinesque’: imagining and classifying American nature

Some early nineteenth-century American naturalists condemned their contemporary, Constantine Samuel Rafinesque (1783–1840), as ‘eccentric’, or worse. Both during his life and long after his death, his botanical work in particular was criticised, even ridiculed. However, in recent years, attempts have been made to restore his reputation and the term ‘genius’ has even been used to describe him. This paper examines this continuing fascination with this strange, disturbing figure and argues that in the competing interpretations of his life and work, Rafinesque has generally been used to typify bad classification; he is perhaps better understood in a broader, literary context as embodying a particular kind of American national identity.     

A dispersal-limited sampling theory for species and alleles

The importance of dispersal for biodiversity has long been recognized. However, it was never advertised as vigorously as Stephen Hubbell did in the context of his neutral community theory. After his book appeared in 2001, several scientists have sought and found analytical expressions for the effect of dispersal limitation on community composition, still in the neutral context. This has been done along two relatively independent lines of research that have a different mathematical approach and focus on different, yet related, types of results. Here, we study both types in a new framework that makes use of the sampling nature of the theory. We present sampling distributions that contain binomial or hypergeometric sampling on the one hand, and dispersal limitation on the other, and thus views dispersal limitation as ubiquitous as sampling effects. Further, we express the results of one line of research in terms of the other and vice versa, using the concept of subsamples. A consequence of our findings is that metacommunity size does not independently affect the outcome of neutral models in contrast to a previous assertion (Ecol. Lett., 7, 2004, p. 904) based on an incorrect formula (Phys. Rev. E, 68, 2003, p. 061902, eqns 11-14). Our framework provides the basis for development of a dispersal-limited non-neutral community theory and applies in population genetics as well, where alleles and mutation play the roles of species and speciation respectively.     

Fashioning the Immunological Self: The Biological Individuality of F. Macfarlane Burnet

During the 1940s and 1950s, the Australian microbiologist F. Macfarlane Burnet sought a biologically plausible explanation of antibody production. In this essay, we seek to recover the conceptual pathways that Burnet followed in his immunological theorizing. In so doing, we emphasize the influence of speculations on individuality, especially those of philosopher Alfred North Whitehead; the impact of cybernetics and information theory; and the contributions of clinical research into autoimmune disease that took place in Melbourne. We point to the influence of local experimental and intellectual currents on Burnet’s work. Accordingly, this essay describes an arc distinct from most other tracings of Burnet’s conceptual development, which focus on his early bacteriophage research, his fascination with the work of Julian Huxley and other biologists in the 1920s, and his interest in North Atlantic experimental investigations in the life sciences. No doubt these too were potent influences, but they seem insufficient to explain, for example, Burnet’s sudden enthusiasm in the 1940s for immunological definitions of self and not-self. We want to demonstrate here how Burnet’s deep involvement in philosophical biology – along with attention to local clinical research – provided him with additional theoretic tools and conceptual equipment, with which to explain immune function.     

Origins of Life: Chemical and Philosophical Approaches

In this article we address selected important milestones of chemical evolution that led to life. The first such milestone could be achieved by Oparin’s model, which accounts for the early stages of chemical evolution. These occurred at the dawn of development of primitive chemical systems that were pre-RNA. Oparin’s model consists of spontaneous formation of coacervates that encapsulate chemical matter, undergo primitive self-replication, and provide a pathway to a primitive metabolism. We review the experimental updates of his model from our laboratory and discuss types of selection that could have occurred in these primitive systems. Another major milestone in chemical evolution is the transition from abiotic to biotic. This has occurred later, after the RNA world evolved. A controversy of what life is interferes with the efforts to elucidate this transition. Thus, we present various definitions of life, some of which specifically include the requirements and mechanisms for this transition. Self-replication is one of the major requirements for life. In this context we re-examine the question if viruses, which do not have capability to self-replicate, are alive. We draw on philosophy of Hegel, Aristotle, Rescher, Priest, and Fry to guide us in our endeavors. Specifically, we apply Hegel’s law on quantity-to-quality transition to abiotic-to-biotic transition, Aristotle’s philosophy to the definition of life, Priest’s dialetheism to the question if viruses are alive or not, Fry’s philosophy to the beginning of natural selection in chemical evolution, and Rescher’s philosophy to the possible cognitive bias toward simple definitions of life.     

Chloroplast two-component systems: evolution of the link between photosynthesis and gene expression

Two-component signal transduction, consisting of sensor kinases and response regulators, is the predominant signalling mechanism in bacteria. This signalling system originated in prokaryotes and has spread throughout the eukaryotic domain of life through endosymbiotic, lateral gene transfer from the bacterial ancestors and early evolutionary precursors of eukaryotic, cytoplasmic, bioenergetic organelles—chloroplasts and mitochondria. Until recently, it was thought that two-component systems inherited from an ancestral cyanobacterial symbiont are no longer present in chloroplasts. Recent research now shows that two-component systems have survived in chloroplasts as products of both chloroplast and nuclear genes. Comparative genomic analysis of photosynthetic eukaryotes shows a lineage-specific distribution of chloroplast two-component systems. The components and the systems they comprise have homologues in extant cyanobacterial lineages, indicating their ancient cyanobacterial origin. Sequence and functional characteristics of chloroplast two-component systems point to their fundamental role in linking photosynthesis with gene expression. We propose that two-component systems provide a coupling between photosynthesis and gene expression that serves to retain genes in chloroplasts, thus providing the basis of cytoplasmic, non-Mendelian inheritance of plastid-associated characters. We discuss the role of this coupling in the chronobiology of cells and in the dialogue between nuclear and cytoplasmic genetic systems.     

Are aposematic signals honest? A review

We explore the relevance of honest signalling theory to the evolution of aposematism. We begin with a general consideration of models of signal stability, with a focus on the Zahavian costly signalling framework. Next, we review early models of signalling in the context of aposematism (some that are consistent and some inconsistent with costly honest signalling). We focus on controversies surrounding the idea that aposematic signals are handicaps in a Zahavian framework. Then, we discuss how the alignment of interests between signaller and predator influences the evolution of aposematism, highlight the distinction between qualitative and quantitative honesty and review theory and research relevant to these categories. We also review recent theoretical treatments of the evolution of aposematism that have focused on honest signalling as well as empirical research on a variety of organisms, including invertebrates and frogs. Finally, we discuss future directions for empirical and theoretical research in this area.     

The Context of Ecosystem Theory

Arthur George Tansley's paper “The Temporal Genetic Series as a Means of Approach to Philosophy,” published here for the first time, provides the philosophical context for the development of his ecosystem theory. His rejection of idealist reasoning, his concern with ethics, and his long standing interest in Freudian psychology as well as mechanistic reasoning comprised the intellectual underpinnings for his thinking on systems and ecosystem theory.     

Georgy Gause’s shift from ecology and evolutionary biology to antibiotics research: reasons,objectives, circumstances

Georgy Gause (1910–1986) is best known for his contribution to ecology and evolutionary theory. His book “The Struggle for Existence” (1934) inspired generations of ecologists. Yet his scientific interests were diverse, embracing many aspects of the life sciences and medicine. The most notable shift in his research took place in the early 1940s when he began to study antibiotics and discovered Gramicidin S. Superficially, this shift looked like an attempt to switch from purely theoretical to applied research during the years of World War II, but Gause’s decision may also have been seriously affected by the “Great Purge” and the growth of Lysenkoism. Personal factors played a significant role in his career too. In this article, we propose four factors which drove Gause to switch his focus from ecology to antibiotics: the inner logic of his scientific research, Stalin’s science policy and the growth of Lysenkoism, the sociopolitical influence of World War II, and personal relationships. We will also show how all these factors are interdependent to some extent.     

Wilhelm Ludwig and his contributions to population genetics

This article reviews the life and work of the German biologist Wilhelm Ludwig (1901-1959), whose contributions to population genetics have been largely ignored. Ludwig's work was a rich tapestry of population biology, spanning investigations into population growth, biological asymmetries, sex ratio, and paternity analysis. He was ahead of his time in explicitly combining the theory of population ecology and population genetics. His classic paper on annidation showed the possibility of population differentiation in the face of gene flow, and his early studies demonstrated the importance of selection in evolutionary change. Much of his work spanned the period of the Second World War in Germany, and interesting questions remain about his life during this turbulent period.     

The Darwin of pangenesis

The Darwin of pangenesis is very much another Darwin. Pangenesis is Darwin's comprehensive theory of generation, his theory about all sexual and asexual modes of reproduction and growth. He never explicitly integrated pangenesis with his theory of natural selection. He first formulated pangenesis in the 1840s and integrated it with the physiology, including the cytology, of that era. It was, therefore, not consilient with the newer cytology of the 1860s when he published it in 1868. By reflecting on the role of pangenesis in Darwin's life and work, we can learn to take a wider view of his most general theorising about animal and plant life.     

THE RPS12 GENE IN SPROGYRA MAXIMA (CHLOROPHYTA) AND ITS EVOLUTIONARY SINGNIFICANCE1

The str operon consists fo four genes in eubacteria. Portions of his operon are conserved in the chloroplast genomes of green algae and land plants. In land plant chloroplasts, the str operon comprises only two genes, rps12 and rps7, and is arranged in a trans-spliced state. Since no other previously studied chloroplast genome contains this arrangement, and because the charophyte lineage is the sister group of land plants, we chose to look for this arrangement in the Charophyceae. The two str genes, rps12 and rps7, present in the chloroplasts of Spirogyra maxima Hanssall, were identified by hybridization of a Southern blot and requenced. The results indicate that Spirogyra contains a str operon almost identical to that of land plant chloroplasts. Based upon the structure of the operon in other chloroplasts and eubacterial genomes, the trans-spliced state most likely evolved early within the charophyte lineage.     

Accumulation response of chloroplasts induced by mechanical stimulation in bryophyte cells

Chloroplast movement has been studied in many plants but mainly as a model system for light signaling. However, we recently showed that the avoidance response of chloroplasts is also induced by mechanical stimulation in fern protonemal cells. Here we report the discovery of a mechanically induced accumulation response of chloroplasts in bryophytes. When mechanical stimulation was directly applied with a capillary to a part of a cell, chloroplasts moved towards and accumulated at the pressed site within 30 min after the onset of stimulation in all species tested. The accumulation movement of chloroplasts was inhibited by Cremart but not by cytochalasin B in red-light-grown protonemata of Physcomitrella patens (Hedw.) B., S. & G. To determine the contribution of external Ca(2+) to the response, we examined the effects on the accumulation movement of gadolinium (Ga(3+)), an inhibitor of stretch-activated ion channels, and lanthanum (La(3+)), a potent inhibitor of calcium channels. Mechano-relocation of chloroplasts was abolished by these drugs, but no effects were observed on photo-relocation of chloroplasts, irrespective of light colors and intensity. These results suggest that influx of external Ca(2+) through the plasma membrane is essential for the early steps in signaling of mechano-relocation of chloroplasts whose motility system is dependent on microtubules.     

Determinants of time allocation across the lifespan

This paper lays the groundwork for a theory of time allocation across the life course, based on the idea that strength and skill vary as a function of age, and that return rates for different activities vary as a function of the combination of strength and skills involved in performing those tasks. We apply the model to traditional human subsistence patterns. The model predicts that young children engage most heavily in low-strength/low-skill activities, middle-aged adults in high-strength/high-skill activities, and older adults in low-strength/high-skill activities. Tests among Machiguenga and Piro forager-horticulturalists of southeastern Peru show that males and females focus on low-strength/low-skill tasks early in life (domestic tasks and several forms of fishing), switch to higher-strength/higher-skill activities in their twenties and thirties (hunting, fishing, and gardening for males; fishing and gardening for females), and shift focus to high-skill activities late in life (manufacture/repair, food processing). Michael Gurven is an assistant professor of anthropology at the University of California-Santa Barbara. He received his Ph.D. from the University of New Mexico in 2000. He has conducted fieldwork in Paraguay and Bolivia with Ache and Tsimane forager-horticulturalists. His research interests include intragroup cooperation and problems of collective action, and the application of life history theory to explaining human longevity, cognitive development, delayed maturation, and sociality. Since 2002, Gurven and Kaplan have co-directed the Tsimane Health and Life History Initiative, a five-year project to develop theory and test implications of different models of human life history evolution. Hillard Kaplan is a professor of anthropology at University of New Mexico. He received his Ph.D. from the University of Utah in 1983. He has conducted fieldwork in Paraguay, Brazil, Botswana, and Bolivia. His research interests include evolutionary perspectives on life course development and senescence, and brain evolution. He has launched theoretical and empirical investigations into each of these areas, uniting evolutionary and economic approaches. He has applied human capital theory toward explaining human life history evolution, and the proximate physiological and psychological mechanisms governing fertility and parental investment in both traditional, high-fertility, subsistence economies and modern, low-fertility, industrial societies.     

Dynamic changes in the organization of microfilaments associated with the photocontrolled motility of chloroplasts in epidermal cells ofVattisneria

Summary Using time-lapse video microscopy, we performed a semiquantitative investigation of the movement of chloroplasts on the cytoplasmic layer that faces the outer periclinal wall (P side) of epidermal cells of leaves of the aquatic angiospermVallisneria gigantea Graebner. Under continuous irradiation with red light (650 nm, 0.41 W/m²), the movement of chloroplasts on the P side was transiently accelerated within 5 min. The increased movement began to decrease at around 20 min and fell below the original level after 40 to 60 min of irradiation with red light. The acceleration and deceleration of movement of chloroplasts on the P side seemed to lead directly to the increase and the subsequent decrease in the rate of migration of chloroplasts from the P side to the anticlinal layers of cytoplasm, which are responsible for the accumulation of chloroplasts on the P side, as we demonstrated previously. In the presence of inhibitors of photosynthesis, the accelerated movement of chloroplasts was maintained for as long as the chloroplasts were irradiated with red light. The rapid acceleration and deceleration of the movement of chloroplasts could be observed repeatedly with sequential irradiation with red and then far-red light (746 nm, 0.14 W/m²). Concomitantly with the loss of motility of chloroplasts on the P side, a dynamic change in the configuration of microfilaments, from a network to a honeycomb, occurred on the P side.Abbreviations APW artificial pond water - A side cytoplasmic layer that faces the anticlinal wall - ATP adenosine triphosphate - DCMU 3-(3,4-dichlorophenyl)-1,1-dimethylurea - F-actin fibrous actin - FITC fluorescein isothiocyanate - PBS phosphate-buffered saline - Pfr farred-light-absorbing form of phytochrome - Pr red-light-absorbing form of phytochrome - P side cytoplasmic layer that faces the outer periclinal wall Dedicated to Professor Eldon H. Newcomb in recognition of his contributions to cell biology     

Biological adaptabilities and quantum entropies.

The entropy-based theory of adaptability set forth by Michael Conrad in the early 1970s continued to appear in his work for over two decades, and was the subject of the only book he published in his lifetime. He applied this theory to a host of subjects ranging from enzyme dynamics to sociology. This paper reviews the formalism of adaptability theory, clarifying some of its mathematical and interpretive difficulties. The theory frames the computational tradeoff principle, a thesis that was the most frequently recurring claim in his work. The formulation of adaptability theory presented here allows the introduction of quantum entropy functions into the theory, revealing an interesting relationship between adaptability and another one of Conrad's deep preoccupations, the role of quantum processes in life.