Causality, randomness, intelligibility, and the epistemology of the cell

Because the basic unit of biology is the cell, biological knowledge is rooted in the epistemology of the cell, and because life is the salient characteristic of the cell, its epistemology must be centered on its livingness, not its constituent components. The organization and regulation of these components in the pursuit of life constitute the fundamental nature of the cell. Thus, regulation sits at the heart of biological knowledge of the cell and the extraordinary complexity of this regulation conditions the kind of knowledge that can be obtained, in particular, the representation and intelligibility of that knowledge. This paper is essentially split into two parts. The first part discusses the inadequacy of everyday intelligibility and intuition in science and the consequent need for scientific theories to be expressed mathematically without appeal to commonsense categories of understanding, such as causality. Having set the backdrop, the second part addresses biological knowledge. It briefly reviews modern scientific epistemology from a general perspective and then turns to the epistemology of the cell. In analogy with a multi-faceted factory, the cell utilizes a highly parallel distributed control system to maintain its organization and regulate its dynamical operation in the face of both internal and external changes. Hence, scientific knowledge is constituted by the mathematics of stochastic dynamical systems, which model the overall relational structure of the cell and how these structures evolve over time, stochasticity being a consequence of the need to ignore a large number of factors while modeling relatively few in an extremely complex environment.     

DNA-damage repair; the good, the bad, and the ugly

Organisms have developed several DNA-repair pathways as well as DNA-damage checkpoints to cope with the frequent challenge of endogenous and exogenous DNA insults. In the absence or impairment of such repair or checkpoint mechanisms, the genomic integrity of the organism is often compromised. This review will focus on the functional consequences of impaired DNA-repair pathways. Although each pathway is addressed individually, it is essential to note that cross talk exists between repair pathways, and that there are instances in which a DNA-repair protein is involved in more than one pathway. It is also important to integrate DNA-repair process with DNA-damage checkpoints and cell survival, to gain a better understanding of the consequences of compromised DNA repair at both cellular and organismic levels. Functional consequences associated with impaired DNA repair include embryonic lethality, shortened life span, rapid ageing, impaired growth, and a variety of syndromes, including a pronounced manifestation of cancer.     

On the distribution of the Slow Worm,Anguis fragilis,and the European Glass Lizard,Ophisaurus apodus,in Turkey

Abstract

The two subspecies of Ophisaurus apodus represent different ecotypes: thracicus is a coastal type, which occurs in Turkey along all coasts (but only local along the Black Sea coast), whereas nominate apodus is an inland type which is found in Turkey only in the extreme east. Anguis fragilis is confined to areas in which the monthly mean precipitation is above 20 mm.     

The tree, the network, and the species

To enrich the Hennigian internodal conception of species, a new formalization of the definition of the species concept is proposed. This rigorous definition allows for considerable unification of the various, and sometimes conflicting, techniques of species delimitation used in practice. First, the domain of such a definition is set out, namely, the set of all organisms on Earth, past, present, and future. Next, the focus is on the genealogical relationship among organisms, which provides the key to analysing the giant or global genealogical network (GGN) connecting all these organisms. This leads to the construction of an algorithm revealing the topological structure of the GGN, from families to lineages, ending up with a definition of species as equivalence classes of organisms corresponding to branches of the 'tree of life'. Such a theoretical definition of the species concept must be accompanied by various recognition criteria to be operational. These criteria are, for example, the ill-named 'biological species concepts', 'phylogenetic species concepts', etc., usually, but wrongly, presented as definitions of the species concept. Besides clarifying this disputed point, the definition in the present study displays the huge diversity of the scales (time-scale and population size) involved in actual species, thus explaining away the classical problems raised by previous attempts at defining the species concept (uniparental reproduction, temporal depth of species, and hybridization).  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 509–521.     

Parallelism,parsimony, and the phytogeny of the lemuridae

In spite of the increasing popularity of cladistic methods in studies of primate systematics, few authors have investigated the effects of parallel evolution when such methods are applied to empirical data. To counter the effects of parallelism, cladistic techniques rely on the principle of evolutionary parsimony. When parsimony procedures are used to reconstruct the phylogeny of the Lemuridae, nine highly parsimonious phylogenies can be deduced. Further choice among these competing hypotheses of relationship is determined by the extent to which one embraces the parsimony principle. The phylogeny obtained by the most rigorous adherence to the parsimony principle is one which is wholly consistent with traditional evolutionary classifications of the Lemuridae. Moderate levels of parallelism can lead to the generation of several plausible, alternative phylogenetic hypotheses; less than 25% of the characters analyzed here need have evolved in parallel, yet they are largely responsible for the ambiguity of the nine different lemurid phylogenies. This suggests that phylogeny reconstructions based entirely on cladistic methods do not provide a suitable basis for the construction of classifications for groups such as the order Primates, where the degree of parallelism is likely to be quite high.     

Bonding, biophilia, biosynergy, and the future of primates in the wild

Human and nonhuman primates bond with one another in countless ways, and the results are varied and vital to the individuals and species involved. The manifesto that is the basis for the collection of essays in which this commentary is included proposes that the "human/nonhuman bonds that arise in primatological research and practice deserve and demand study and research." An essential corollary of this proposal is that the primatologists themselves must be studied. The aim of this essay is to explore the influence of human/nonhuman primate bonding on conservation practice and on the future of primates in the wild. This commentary applies the author's professional experience as a conservation psychologist and his research on the impact of profound interspecies bonds on human worldviews, attitudes, and behavior. It examines two general categories of bonds: those driven by Biophilia (human fascination with life) and those influenced by Biosynergy (mutual enrichment of life). It is the author's premise that biosynergy promotes complex collaborative interspecies bonds that broaden the conservationist's desire to enhance synergy among all organisms in an ecosystem. Conversely, biophilia induces relatively simple unidirectional bonds between humans and other animals that deepen the conservationist's desire to understand and protect certain species. This contrast raises some crucial questions. Do biophilia-driven bonds between conservationists and their favorite primates blind them to the synergistic needs of all species and impair their ability to work for sustained preservation of threatened habitat? Does biosynergy-based human/nature bonding enhance focus on conservation as an ecological science and thus ignore species-specific factors crucial to assure survival of endangered primates? How can both types of bonds be optimally applied to the conservation of wildlife and wilderness?     

Genes, exercise, growth, and the sedentary, obese child.

It is still not possible to provide an evidence-based answer to the question of whether regular exercise is essential for normal growth. It is also unclear whether very low levels of exercise result in growth deficits. Regular exposure to exercise is characterized by heterogeneity in responsiveness, with most individuals experiencing improvements in fitness traits but a significant proportion showing only very minor gains. Whether a sedentary mode of life during the growing years results in a permanent deficit in cardiorespiratory fitness or a diminished ability to respond favorably to regular exercise later in life remains to be investigated. Although several genes have been associated with fitness levels or response to regular exercise, the quality of the evidence is weak mainly because studies are statistically underpowered. The special case of the obese, sedentary child is discussed, and the importance of the "energy gap" in the excess weight gain during growth is highlighted. Obese, sedentary children have high blood pressure, dyslipidemia, elevated glycemia and type 2 diabetes, hepatic steatosis, respiratory problems, orthopedic complications, and other health disorders more frequently than normal weight, physically active children. The role of genetic differences in the inclination to be sedentary or physically active is reviewed. An understanding of the true role of genetic differences and regular exercise on the growth of children will require more elaborate paradigms incorporating not only DNA sequence variants and exercise exposure but also information on nutrition, programming, and epigenetic events during fetal life and early postnatal years.     

Sir2 and the acetyltransferase, Pat, regulate the archaeal chromatin protein, Alba

The DNA binding affinity of Alba, a chromatin protein of the archaeon Sulfolobus solfataricus P2, is regulated by acetylation of lysine 16. Here we identify an acetyltransferase that specifically acetylates Alba on this residue. The effect of acetylation is to lower the affinity of Alba for DNA. Remarkably, the acetyltransferase is conserved not only in archaea but also in bacteria where it appears to play a role in metabolic regulation. Therefore, our data suggest that S. solfataricus has co-opted this bacterial regulatory system to generate a rudimentary form of chromatin regulation.     

Diacylglycerol, phosphatidic acid, and the converting enzyme, diacylglycerol kinase, in the nucleus

There exists phosphoinositide (PI) cycle in the nucleus, which is operated differentially from the classical PI cycle at the plasma membrane. Evidence has been accumulated that nuclear PIs and the related enzymes are closely involved in a variety of nuclear processes, although the details remain to be elucidated. In this mini review, some components of PI cycle, i.e., diacylglycerol, phosphatidic acid, and the converting enzyme, diacylglycerol kinase, in the nucleus are discussed with focusing on the lipid metabolism, cell cycle regulation, and animal models.     

Galactic Factors,the Young Sun,the Earth,and the Biophysics of Living Systems

The effects of radiation from the young Sun and galactic cosmic rays on the physical conditions on the early Earth are significantly underestimated in studies of the problems related to the origin and evolution of the biosphere. This review considers the dynamics of solar and galactic processes over the 4.56 billion years of the existence of the Solar System. These factors substantially affected the development of adaptive technologies in ancient and modern living systems. The features of biosphere development are considered for the early Earth under the young Sun, which was fainter, but more flare active. The radiation spectrum of the young Sun is discussed together with the paradoxical mismatch between the solar radiation spectrum and the chlorophyll adsorption spectrum. Ways of solving the paradox are proposed. The role of solar radiation is important when studying models of the early biosphere of the Earth and hypothetical biospheres of giant planet satellites and exoplanets.

     

Ultrastructure,Behavior, and Algal Flagellate Affinities of the Helioflagellate Ciliophrys marina,and the Classification of the Helioflagellates (Protista,Actinopoda, Heliozoea)1

Ciliophrys marina is a small marine helioflagellate, with a central nucleus, which is capable of reversibly transforming from a rapidly swimming flagellate cell with no axopodia to the structure of a heliozoan with a flagellum that beats only a few times a minute. When in the flagellate form, the flagellum acts as a tractellum due to the tubular mastigonemes found along its length. When the rapidly swimming flagellate strikes a piece of debris, the flagellum goes through a very characteristic shock-induced avoidance reaction. Similarly, when a mechanical shock is delivered to the cell in its heliozoan form, the axopodia are contracted in less than 20 msec. Both reactions are inhibited in low calcium seawater. Transformation from the heliozoan to the flagellate form is accomplished by slow retraction and absorbance of the axopodia and activation of the flagellum. Ultrastructurally, each axopodium is found to contain three microtubules which attach to the outer nuclear membrane of the central nucleus at sites that this study characterizes by electron microscopy of thin sections and freeze fracture preparations. The mitochondria have tubular cristae, each containing an intracristal filament. Finally, a taxonomic review of the helioflagellates is presented, and it is suggested that C. marina is derived from the chrysomonads. An argument is also made for classifying C. marina with the heliozoan order Actinophryida, as a recently published classification of the protozoa does.     

Bioethics,children, and the environment

Queer perspectives have typically emerged from sexual minorities as a way of repudiating flawed views of sexuality, mischaracterized relationships, and objectionable social treatment of people with atypical sexuality or gender expression. In this vein, one commentator offers a queer critique of the conceptualization of children in regard to their value for people's identities and relationships. According to this account, children are morally problematic given the values that make them desirable, their displacement of other beings and things entitled to moral protection, not to mention the damaging environmental effects that follow in the wake of population growth. Objectionable views of children are said even to have colonized the view of lesbian, gay, bisexual, and trans (LGBT) people who – with the enthusiastic endorsement of bioethics – increasingly turn to assisted reproductive treatments to have children. In the face of these outcomes, it is better – according to this account – that people reconsider their interest in children. This account is not, however, ultimately strong enough to override people's interest in having children, relative to the benefits they confer and relative to the benefits conferred on children themselves. It is certainly not strong enough to justify differential treatment of LGBT people in matters of assisted reproductive treatments. Environmental threats in the wake of population growth might be managed in ways other than devaluing children as such. Moreover, this account ultimately damages the interests of LGBT people in matters of access, equity, and children, which outcome is paradoxical, given the origins of queer perspectives as efforts to assert and defend the social interests of sexual and gender minorities.     

Cholinesterases and arylesterase in the umbilical cord, the placenta, and the amniotic membrane, in the female at term]

Cholinesterasic activity of umbilical cord (tissue), completely bloodless, is exclusively due to pseudocholinesterase. Cholinesterase is more active in placenta than in cord; it is an acetylcholinesterase at 80 per cent. Both forms coexist, about equally, in amniotic membrane. A considerable arylesterasic activity is proved in cord, placenta and membrane, the greatest activity being in placenta. Comparing the greater activity in maternal plasma and cord blood's plasma to the very weak activity in amniotic fluid, it is possible to think that cork, membrane, placenta and also amniotic fluid pseudocholinesterase and arylesterase, come from plasma. On the contrary, placental acetylcholinesterase seems original and probably is the source of this enzyme activity in amniotic fluid.     

Dark adaptation,sensitivity, and rhodopsin level in the eye of the lobster,Homarus

Summary Dark adaptation of living lobsters was measured by recording the ERG at several temperatures in the range 5–20 °C following adapting flashes that convert about 70% of the rhodopsin to metarhodopsin. Recovery of log threshold is rapid, and at 10–20° is nearly complete in 10 min. Only at 5 °C is dark adaptation significantly slowed. Comparison of dark adaptation with data on regeneration of pigment (Bruno et al., 1977) is consistent with the hypothesis that as rhodopsin concentration rises and falls, its only effect on sensitivity is to alter the probability of quantum catch. This interpretation is further bolstered by observations on winter lobsters that have a 70% deficiency of rhodopsin without the concomitant increase in metarhodopsin that accompanies light adaptation. No effect of metarhodopsin on sensitivity was detected. These experiments support the growing body of evidence indicating that the relationship between rhodopsin concentration and log threshold is fundamentally different in the rhabdomeric photoreceptors of invertebrates and the rods and cones of vertebrates.This work was supported by USPHS research grant EY 00222 to Yale University. S.N.B. was aided by NIH Postdoctoral Fellowship EY 52378, by funds made available through the Unidel Foundation, and by a grant from the University of Delaware Research Foundation.     

Making Forest of Bliss: The Film, the Book, the DVD, and the Breakthrough

Robert Gardner's and Àkos Östör's Making of Forest of Bliss (2002) is a combination book and DVD that contains eight teaching tools for better understanding Gardner's celebrated film Forest of Bliss. After the film was shot in 1985, filmmaker Gardner and anthropologist Östör recorded a conversation about each image and sound of the film while they screened it again in 1987, and remembered their filmmaking process on location in Benares, India. The feature length (89 minute) documentary about death ritual, reincarnation, the sacred Ganges River, and the very atmosphere of Benares is included as DVD, as are teaching tools such as frame grabs (still images from the film), a mathematically precise shot list, bibliography, important criticism and essays about the film, and the featured in-depth conversation between filmmaker Gardner and anthropological advisor Östör. This essay articulates the unique breakthroughs in pedagogy, cross-cultural studies, and multidisciplinary analysis such hybrid technology provides.     

Carnosine, the Protective, Anti-aging Peptide

Carnosine attenuates the development of senile features when used as a supplement to a standard diet of senescence accelerated mice (SAM). Its effect is apparent on physical and behavioral parameters and on average life span. Carnosine has a similar effect on mice of the control strain, but this is less pronounced due to the non-accelerated character of their senescence processes.     

Fear, faces, and the human amygdala

The amygdala's historical role in processing stimuli related to threat and fear is being modified to suggest a role that is broader and more abstract. Amygdala lesions impair the ability to seek out and make use of the eye region of faces, resulting in impaired fear perception. Other studies in rats and humans revive earlier proposals that the amygdala is important not only for fear perception as such, but also for detecting saliency and biological relevance. Debates about some features of this processing now suggest that while the amygdala can process fearful facial expressions in the absence of conscious perception, and while there is some degree of preattentive processing, this depends on the context and is not necessarily more rapid than cortical processing routes. A large current research effort extends the amygdala's putative role to a number of psychiatric illnesses.     

Neurology, technology, and the diagnostic imperative

Advancements in diagnostic technologies have revolutionized the field of neurology. The use of these tools in the course of neurological evaluations is driven by a strong version of the diagnostic imperative, with the goal of precisely identifying the locus and extent of disease processes. Because of the discrepancy between the sophistication of these technologies and the availability of therapeutic interventions, there is active debate regarding the appropriate use of these tools when the diagnosis is clear, or when no change is made to the therapeutic management. A narrow view of management that is bounded by the availability of pharmacological or surgical interventions results in a more rigid dichotomy between the needs of doctors and patients. A broader view that relaxes the constraint between diagnostic procedures and interventions is more in keeping with the observation that many acts are performed for the benefit of doctors and patients alike. An historical and ethical analysis of the diagnostic imperative, with attention to the rise of innovative medical technologies and current concepts of therapeutic intervention, can help clarify the principles of medical paternalism and beneficence that guide current models of decision making in the neurological sciences.     

Phosphorylation of the Na,K-ATPase and the H,K-ATPase

Phosphorylation is a widely used, reversible means of regulating enzymatic activity. Among the important phosphorylation targets are the Na⁺,K⁺- and H⁺,K⁺-ATPases that pump ions against their chemical gradients to uphold ionic concentration differences over the plasma membrane. The two pumps are very homologous, and at least one of the phosphorylation sites is conserved, namely a cAMP activated protein kinase (PKA) site, which is important for regulating pumping activity, either by changing the cellular distribution of the ATPases or by directly altering the kinetic properties as supported by electrophysiological results presented here. We further review the other proposed pump phosphorylations.