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.     

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.     

Biosynthesis of grandlure,the pheromone of the boll weevil,Anthonomus grandis,from acetate,mevalonate, and glucose

The steam-distilled faeces of adult male boll weevils, Anthonomus grandis, that had been injected with acetate-1¹⁴C, acetate-2¹⁴C, mevalonic acid-2¹⁴C, or glucose¹⁴C(U) showed by column and gas chromatography that approximately 0·02 per cent of the administered radioactivity was incorporated into the volatile fraction. Also, 4 components of the pheromone comprised 57 to 80 per cent of the radioactivity of the volatiles but only 39 per cent of the total content of volatiles. Thus, evidence was obtained for de novo synthesis of the components. Although the boll weevil is essentially an obligate insect of cotton, this insect does not appear to require any specific component in cotton for biosynthesis of the pheromone.     

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.     

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.     

On the ability of four flavonoids, baicilein, luteolin, naringenin, and quercetin, to suppress the fenton reaction of the iron-ATP complex

Four flavonoids, baicilein, luteolin, naringenin, and quercetin were investigated for their ability to suppress the Fenton reaction characteristic of the iron-ATP complex. Absorption spectroscopy indicates that under the conditions of 18.75% aqueous methanol, 0.0625 mM HEPES pH 7.4 buffer and 1.5:1 quercetin/iron-ATP ratio a mix ligand complex formed. All four flavonoids were found to interfere with the voltammetric catalytic wave associated with the iron-ATP complex in the presence of H₂O₂. Quercetin and luteolin were able to completely suppress the catalytic wave of the iron-ATP/H₂O₂ system when a minimum ratio of 1.5:1 of the flavonoid to iron-ATP was reached. At this ratio, the ability of the studied series of flavonoids to suppress the Fenton reaction characteristic of iron-ATP follows as quercetin luteolin > naringenin baicilein. Both quercetin and luteolin contain catechol on the B ring, which may enhance the iron chelation of these species over baicilein and naringenin. The common structural feature of all of these flavonoids is the 4-keto, 5-hydroxy region, which may also contribute to the chelation of iron.     

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.

     

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.     

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.     

Distribution of the chalcone,isosalipurposide, in the onagraceae

Isosalipurposide was present in 13 species and absent from 27 other species of the Onagraceae.