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.     

The parasitic chytrid, Zygorhizidium, facilitates the growth of the cladoceran zooplankter, Daphnia, in cultures of the inedible alga, Asterionella

In food-web studies, parasites are often ignored owing to their insignificant biomass. We provide evidence that parasites may affect trophic transfer in aquatic food webs. Many phytoplankton species are susceptible to parasitic fungi (chytrids). Chytrid infections of diatoms in lakes may reach epidemic proportions during diatom spring blooms, so that numerous free-swimming fungal zoospores (2-3 microm in diameter) are produced. Analysis shows that these zoospores are rich in polyunsaturated fatty acids and sterols (particularly cholesterol), which indicates that they provide excellent food for zooplankters such as Daphnia. In life-table experiments using the large diatom Asterionella formosa as food, Daphnia growth increased significantly in treatments where a parasite was present. By grazing on the zoospores, Daphnia acquired important supplementary nutrients and were able to grow. When large inedible algae are infected by parasites, nutrients within the algal cells are consumed by these chytrids, some of which, in turn, are grazed by Daphnia. Thus, chytrids transfer energy and nutrients from their hosts to zooplankton. This study suggests that parasitic fungi alter trophic relationships in freshwater ecosystems and may be the important components in shaping the community and the food-web dynamics of lakes.     

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.     

Formation of pyrophosphate,tripolyphosphate, and phosphorylimidazole with the thioester,N, S-diacetylcysteamine,as the condensing agent

Summary Reaction of 0.20M orthophosphate with 0.20M N,S-diacetylcysteamine in 0.40M imidazole at pH 7.0 or 8.0 under drying conditions at 50°C for 6 days yields pyrophosphate and tripolyphosphate in the presence and absence of 0.10M divalent metal ion. The efficiency of utilization of N,S-diacetylcysteamine in the formation of pyrophosphate linkages ranges from 3 – 8% under the above conditions. The thioester, N,S-diacetylcysteamine, and imidazole are required for phosphoanhydride formation.Reaction of 0.40M orthophosphate with 0.20M N, S-diacetylcysteamine in 0.40M imidazole at ambient temperature for 6 days yields phosphorylimidazole in the absence or presence of 0.05M MgCl₂. Phosphorylimidazole and pyrophosphate are formed in the presence of 0.05M CaCl₂; pyrophosphate and tripolyphosphate are formed with 0.15M CaCl₂. The efficiency of utilization of N,S-diacetylcysteamine in the formation of pyrophosphate linkages is roughly 7% at 6 days of reaction with 0.15M CaCl₂. The thioester, N,S-diacetylcysteamine and imidazole are required for the formation of phosphoanhydrides. The significance of these reactions to molecular evolution is discussed.Abbreviations P₁ orthophosphate - P₂ pyrophosphate - P₃ tripolyphosphate - ImP phosphorylimidazole - Ac-Csa(Ac) N, S-diacetylcysteamine - Im imidazole     

On the Position of the Genera Turdoides, Argya, Illadopsis, Neociehla, Ptyrticus, Maerosphenus and Pseudoaleippe in the Timaliidæ

Although in these five genera the long broad first primary and rounded wing agree with Timalia pileata, as does the profile of the bill of Argya fulvus and Argya rubiginosus, they do not do so in any other respect,. neither in their habits, nest and eggs, nor in the scutation of the tarsus. We therefore propose to remove them all from the Timaliidae and place them in two separate families, but leaving them in their present position in the classification as placed by Sclater in Syst. Av. Æthiop. ii. 1930.     

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.     

Expression, localization, structural, and functional characterization of pFGE, the paralog of the Calpha-formylglycine-generating enzyme

pFGE is the paralog of the formylglycine-generating enzyme (FGE), which catalyzes the oxidation of a specific cysteine to Calpha-formylglycine, the catalytic residue in the active site of sulfatases. The enzymatic activity of sulfatases depends on this posttranslational modification, and the genetic defect of FGE causes multiple sulfatase deficiency. The structural and functional properties of pFGE were analyzed. The comparison with FGE demonstrates that both share a tissue-specific expression pattern and the localization in the lumen of the endoplasmic reticulum. Both are retained in the endoplasmic reticulum by a saturable mechanism. Limited proteolytic cleavage at similar sites indicates that both also share a similar three-dimensional structure. pFGE, however, is lacking the formylglycine-generating activity of FGE. Although overexpression of FGE stimulates the generation of catalytically active sulfatases, overexpression of pFGE has an inhibitory effect. In vitro pFGE interacts with sulfatase-derived peptides but not with FGE. The inhibitory effect of pFGE on the generation of active sulfatases may therefore be caused by a competition of pFGE and FGE for newly synthesized sulfatase polypeptides.     

Ethology, Natural History, the Life Sciences, and the Problem of Place

Investigators of animal behavior since the eighteenth century have sought to make their work integral to the enterprises of natural history and/or the life sciences. In their efforts to do so, they have frequently based their claims of authority on the advantages offered by the special places where they have conducted their research. The zoo, the laboratory, and the field have been major settings for animal behavior studies. The issue of the relative advantages of these different sites has been a persistent one in the history of animal behavior studies up to and including the work of the ethologists of the twentieth century. This revised version was published online in July 2006 with corrections to the Cover Date.     

Race,class, politics,and the disappearance of work

“When Work Disappears” has shaped research agendas on poverty, racial hierarchy, and urban social and economic dynamics. That is a lot for one article, yet two issues warrant more analysis. They are the ways in which socially defined “race” – rather than or in combination with class – explains the impact of sustained joblessness, and the political behaviours that may emerge in response to work’s disappearance. I point to evidence showing that both race and class have independent associations with the loss of work in poor African-American communities, as well as interactive effects. In the political arena – too often neglected by sociologists studying poverty – sustained, community-wide joblessness or underemployment are associated both with withdrawal from political engagement and with the recent resurgence of right-wing populism. Even after several decades of intensive research, we have more to learn about the interactions of race, class, politics, and the disappearance of work.     

Morphological properties of the last primaries,the tail feathers,and the alulae of Accipiter nisus,Columba livia,Falco peregrinus,and Falco tinnunculus

We investigated the mechanical properties (Young's modulus, bending stiffness, barb separation forces) of the tenth primary of the wings, of the alulae and of the middle tail feathers of Falco peregrinus. For comparison, we also investigated the corresponding feathers in pigeons (Columba livia), kestrels (Falco tinnunculus), and sparrowhawks (Accipiter nisus). In all four species, the Young's moduli of the feathers ranged from 5.9 to 8.4 GPa. The feather shafts of F. peregrinus had the largest cross‐sections and the highest specific bending stiffness. When normalized with respect to body mass, the specific bending stiffness of primary number 10 was highest in F. tinnunculus, while that of the alula was highest in A. nisus. In comparison, the specific bending stiffness, measured at the base of the tail feathers and in dorso‐ventral bending direction, was much higher in F. peregrinus than in the other three species. This seems to correlate with the flight styles of the birds: F. tinnunculus hovers and its primaries might therefore withstand large mechanical forces. A. nisus has often to change its flight directions during hunting and perhaps needs its alulae for this maneuvers, and in F. peregrinus, the base of the tail feathers might need a high stiffness during breaking after diving. J. Morphol. 276:33–46, 2015. © 2014 Wiley Periodicals, Inc.     

Checklist of the species of the aseptate gregarine families Aikinetocystidae,Diplocystidae, Allantocystidae,Schaudinnellidae, Ganymedidae,and Enterocystidae

The genera and species in six families of the eugregarine suborder Aseptatorina Chakravarty, 1960, are reviewed and the presently accepted ones are listed: Aikinetocystidae Bhatia, 1930 (two genera and two species); Diplocystidae Bhatia, 1930 (one genus and eight species); Allantocystidae tocystidae Bhatia, 1930 (one genus and one species); Schaudinnellidae Poche, 1913 (one genus and one species); Ganymedidae Huxley, 1910 (one genus and one species); and Enterocystidae Codreanu, 1940 (one genus and eight species). A list of 22 synonyms and lapsi calami is also given. Species which might be of value in the biological control of disease vectors are indicated.     

Fate of bacteria, Aeromonas caviae, in the midgut of the housefly, Musca domestica

Abstract. The role of houseflies as agents in the spread of bacterial diseases has been thoroughly investigated, yet the fate of bacteria ingested by flies has not. We examined the physical location of the bacterial enteropathogen Aeromonas caviae in the midgut of laboratory‐reared adult houseflies. Food ingested by houseflies was separated from the midgut epithelium by a double‐layered peritrophic matrix (PM). The inner PM intimately enveloped the food as fecal pellets (food boluses), while the outer PM appeared as a long continuous tube. In flies fed a suspension of A. caviae, live bacteria were not observed within the inner PM, but were compartmentalized between folds of the PM in the inter‐PM space. Similar observations were made for flies fed a suspension of Serratia liquefaciens and for highly contaminated feral flies. Isolates of both A. caviae and S. liquefaciens were chitinolytic (as demonstrated by clearing zones on chitin agar), but the potential role of bacterial enzymes in the alteration of PM morphology or formation needs further investigation.     

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.

     

Quantitation of the involvement of the recA, recB, recC, recF, recJ, recN, lexA, radA, radB, uvrD, and umuC genes in the repair of X-ray-induced DNA double-strand breaks in Escherichia coli

Isogenic Escherichia coli strains carrying single DNA-repair mutations were compared for their capacity for (i) the repair of X-ray-induced DNA double-strand breaks (DSB) as measured using neutral sucrose gradients; (ii) medium-dependent resistance, i.e., a recA-dependent X-ray survival phenomenon that correlates closely with the capacity for repairing DSB; and (iii) the growth medium-dependent, recA-dependent repair of X-ray-induced DNA single-strand breaks (SSB) as measured using alkaline sucrose gradients (about 80% of these SSB are actually parts of DSB). These three capacities were measured to quantitate more accurately the involvement of the various genes in the repair of DSB over a wide dose range. The mutations tested were grouped into five classes according to their effect on the repair of X-ray-induced DSB: (I) the recA, recB, recC, and lexA mutants were completely deficient; (II) the radB and recN mutants were about 90% deficient; (III) the recF and recJ mutants were about 70% deficient; (IV) the radA and uvrD mutants were about 30% deficient; and (V) the umuC mutant resembled the wild-type strains in its capacity for the repair of DSB.     

Arsenic Concentrations in the Surface,Well, and Drinking Waters of the Hisarcik,Turkey, Area

Arsenic is one of the most important water pollutants because of its carcinogenicity. The association between arsenical poisoning and the development of internal malignancies and skin cancer is well known. The U.S. Environmental Protection Agency (USEPA) sets maximum contaminant level goals at zero for carcinogens. In this study are presented groundwater arsenic concentrations in the area of naturally rich boron sources of Turkey. Water samples were collected from the Hisarcik, Turkey, area, which has a large boron mine. An inductively coupled plasma/mass spectrometry method was used to analyze arsenic concentrations in water samples. The arsenic levels in water ranged from no detectable amounts to 3.00 mg As/L (mean: 0.46 ± 0.07SD). This mean As level exceeds by a factor of 10 the USEPA's current Maximum Contaminant Level of 0.05 mgAs/L. Some possible health problems associated with consumption of arsenic-contaminated water are discussed and public health interventions proposed.     

Methane, oxygen, photosynthesis, rubisco and the regulation of the air through time

Rubisco I's specificity, which today may be almost perfectly tuned to the task of cultivating the global garden, controlled the balance of carbon gases and O(2) in the Precambrian ocean and hence, by equilibration, in the air. Control of CO(2) and O(2) by rubisco I, coupled with CH(4) from methanogens, has for the past 2.9 Ga directed the global greenhouse warming, which maintains liquid oceans and sustains microbial ecology.Both rubisco compensation controls and the danger of greenhouse runaway (e.g. glaciation) put limits on biological productivity. Rubisco may sustain the air in either of two permissible stable states: either an anoxic system with greenhouse warming supported by both high methane mixing ratios as well as carbon dioxide, or an oxygen-rich system in which CO(2) largely fulfils the role of managing greenhouse gas, and in which methane is necessarily only a trace greenhouse gas, as is N(2)O. Transition from the anoxic to the oxic state risks glaciation. CO(2) build-up during a global snowball may be an essential precursor to a CO(2)-dominated greenhouse with high levels of atmospheric O(2). Photosynthetic and greenhouse-controlling competitions between marine algae, cyanobacteria, and terrestrial C3 and C4 plants may collectively set the CO(2) : O(2) ratio of the modern atmosphere (last few million years ago in a mainly glacial epoch), maximizing the productivity close to rubisco compensation and glacial limits.     

Species variation in the distribution of cholinesterases in the ovary of the plains viscacha, cat, ferret, rabbit, rat, guinea-pig and roe deer

Synopsis Sections of ovary from plains viscacha, cat, ferret, rabbit, rat, guinea-pig and roe deer have been histochemically processed to demonstrate acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) in nervous and non-nervous tissue. The effects of different reproductive states on enzyme activity were observed in some animals. AChE-containing nerves were sparse in rabbit and rat but plentiful in cat and roe deer. Nerves containing BuChE were not detectable in ferret or guinea-pig and were rare in cat. Species variations in the activity and type of enzyme were also found in non-neuronal tissues. Some blood vessels in the ovaries of guinea-pig and viscacha contained AChE. No other species showed a reaction for AChE in non-neuronal stromal tissue but BuChE was present at this site in all animals except rat. Granulosa cells reacted for AChE only in cat and rabbit while luteal cells were reactive in cat, rabbit and roe deer. Some BuChE activity was present in granulosa and or luteal cells in all species except roe deer. In rat, BuChE activity in luteal cells increased during oregnaney and the early phase of pseudopregnancy. The difficulty of assigning a function to ovarian cholinesterases is discussed.     

Solubility, adsorption, and the thermodynamics of the cutoff effect

For many years, the expression "cutoff effect of anesthesia," has been used to denote the failure of the higher alcohols or paraffins to produce anesthesia. As such, it is used to assess the plausibility of specific models, proposed for anesthesia. However, the uses were shown, in many respects, to be problematic. This article augments the notion of the cutoff to fit for all cases in which only some of the molecules in a homologous series are anesthetics. We find that the location of the cutoff points is affected by three free energy quantities: that of the adsorption of the agent to the anesthetic "site" (f(sl,site)), that of the perturbation of the site (f(ll,site)), and that of the evaporation of the agent from its pure condensed phase (Deltamu degrees (evaporation)). This outcome indicates that the cutoff cannot be attributed to a single parameter. In addition, the analyses that attribute the cutoff to the failure of compounds to obey the much-used Meyer-Overton correlation will have to be amended. This article shows that cutoff results can be used to elucidate the structure of a site.     

Age and growth of the ajime-loach,niwaella delicata, in the yura river, kyoto, japan

The age of the Ajime-loach,Niwaella delicata (a species endemic to Japan), was determined from the number of concentric rings appearing on the cross-sectional surface of the erectile spine (peculiar to Cobitidae). The ages of loaches caught in the Yura River, Kyoto, were determined and growth rates for each sex estimated. It was found that size dimorphism in this species was due to different growth patterns between the sexes, 2.5 years old males being larger than females and usually sexually mature, unlike the latter. Females older than 3.5 years were sexually mature and larger than males of equivalent age.