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.     

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.     

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.     

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?     

Preparation, Properties, and Composition of Nereis vitellin, the Yolk Protein of the Annelid, Nereis virens

In the literature, oogenesis in nereid annelids is considered to be a model system because, unlike other system studied, nereid oocytes are thought to synthesize the bulk of their yolk protein themselves. As the first step to test the validity of this hypothesis, nereid yolk protein was characterized biochemically. Vitellin, the main fraction of the soluble yolk proteins, was prepared from Nereis virens oocytes. Preparation, purification, and some physical characteristics of this green-colored protein Nereis vitellin are described. The molecular weight was determined by gel chromatography as 420,000 daltons. With regard to the amino acid composition, Nereis vitellin was found to resemble both insect vitellins and an average protein, as defined by other authors. Methionine and cysteine were found in traces only. By staining procedures, Nereis vitellin was characterized as lipoglycoprotein. Nereis vitellin was also prepared from the coelomic fluid of gravid females of Nereis virens .     

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.     

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.     

Functional characterization of the promoter of the vitellogenin gene, AsVg1, of the malaria vector, Anopheles stephensi

Some genetic strategies for controlling transmission of mosquito-borne diseases call for the introgression of antipathogen effector genes into vector populations. Endogenous mosquito promoter and other cis-acting DNA sequences are needed to direct the expression of the effector molecules to maximize their efficacy. Vitellogenin (Vg)-encoding gene control sequences are candidates for driving tissue-, stage- and sex-specific expression of exogenous genes. One of the Anopheles stephensi Vg genes, AsVg1, was cloned and a full-length cDNA, as well as 850 base pairs adjacent to the 5'-end, were sequenced and characterized. Expression of AsVg1 is restricted to the fat body tissues of blood-fed females, and the amino acid sequence of the conceptual translation product is >85% identical to those of other anopheline Vgs. These characteristics support the conclusion that AsVg1 is a Vg-encoding gene. Functional analyses of the AsVg1 putative cis-regulatory sequences were performed using transgenic mosquitoes. The results showed that DNA fragments encompassing the 850 base pairs immediately adjacent to the 5'-end of the gene and the 3'-end untranslated region are sufficient to direct sex-, stage- and tissue-specific expression of a reporter gene. These data indicate that the AsVg1 promoter is a good candidate for controlling the expression of anti-pathogen effector molecules in this malaria vector mosquito.     

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.     

Crystal structure of the heterodimeric complex of the adaptor,ClpS, with the N-domain of the AAA+ chaperone,ClpA

Substrate selectivity and proteolytic activity for the E. coli ATP-dependent protease, ClpAP, is modulated by an adaptor protein, ClpS. ClpS binds to ClpA, the regulatory component of the ClpAP complex. We report the crystal structure of ClpS in complex with the isolated N-terminal domain of ClpA in two different crystal forms at 2.3- and 3.3-A resolution. The ClpS structure forms an alpha/beta-sandwich and is topologically analogous to the C-terminal domain of the ribosomal protein L7/L12. ClpS contacts two surfaces on the N-terminal domain in both crystal forms; the more extensive interface was shown to be favored in solution by protease protection experiments. The N-terminal 20 residues of ClpS are not visible in the crystal structures; the removal of the first 17 residues produces ClpSDeltaN, which binds to the ClpA N-domain but no longer inhibits ClpA activity. A zinc binding site involving two His and one Glu residue was identified crystallographically in the N-terminal domain of ClpA. In a model of ClpS bound to hexameric ClpA, ClpS is oriented with its N terminus directed toward the distal surface of ClpA, suggesting that the N-terminal region of ClpS may affect productive substrate interactions at the apical surface or substrate entry into the ClpA translocation channel.     

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.     

A comparative histochemical study of the masseter muscle of the cattle,sheep, swine,dog, guinea pig,and rat

Summary The masseter muscles of different mammals were studied by means of histochemical reactions: NADH: Nitro BT oxidoreductase (NADHOX), 3-hydroxybutyrate: NAD⁺ oxidoreductase (HBOX), glycerol-3-phosphate: menadione oxidoreductase (GPOX), and acid-stable and alkali-stable myosin adenosine triphosphatase (ATPase). The masseter muscles of cattle and sheep consisted only of the fibres that reacted moderately for GPOX and strongly for NADHOX, HBOX, and the acid-stable ATPase. The masseter fibres of rats and guinea pigs reacted uniformly and strongly for GPOX and the alkali-stable ATPase. The fibres of the rats showed a weak to strong reaction for NADHOX and mostly a negative reaction for HBOX, whereas those of the guinea pigs reacted uniformly and strongly for NADHOX and HBOX. The masseter fibres of swine and dogs showed a weak or strong reaction for the alkali-stable and a negative or weak reaction for HBOX. The fibres of the swine were weak to strong in NADHOX activity and those of the dogs uniformly strong; the fibres of the two species gave a moderate to strong reaction for GPOX. The masseter fibres of the ruminant differed from those of the other species in histochemical properties, and appeared to have the histochemical characteristics that meed functional demands for slow, long-term exercise.     

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.     

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.     

Age, growth, maturity, and mortality of the Alaska skate, Bathyraja parmifera, in the eastern Bering Sea

The Alaska skate, Bathyraja parmifera, is the most abundant species of skate on the eastern Bering Sea shelf, accounting for over 90% of total skate biomass. However, little is known regarding the life history of this species despite its common occurrence as bycatch in several Bering Sea fisheries. This is the first study to focus on the age and growth of B. parmifera. From 2003 to 2005, more than one thousand specimens were collected by fisheries observers and on scientific groundfish surveys. Annual banding patterns in more than 500 thin sections of vertebral centra were examined for age determination. Caudal thorns were tested as a potentially non-lethal ageing structure. Annual band pair deposition was verified through edge and marginal increment analyses. A three-parameter von Bertalanffy growth function and a Gompertz growth function were fit to observed length-at-age data. Both models provided significant fits, although the Gompertz function best described the overall pattern of growth in both males and females, based upon statistical criteria and parameter estimates. Age and size at 50% maturity were 9 years and 92 cm TL for males and 10 years and 93 cm TL for females. The maximum observed ages for males and females were 15 years and 17 years, respectively. Estimates of natural mortality (M) ranged from 0.14 to 0.28, and were based on published relationships between M and longevity, age at maturity, and the von Bertalanffy growth coefficient. Due to these life history characteristics and a lack of long-term species-specific stock data, a conservative management approach would be appropriate for B. parmifera.     

Fecundity,autogeny, and the larval environment of the pitcher-plant mosquito,Wyeomyia smithii

Summary Pupae and fourth instar larvae of a southern (30°N, Alabama, USA) population of Wyeomyia smithii Coq. (Diptera: Culicidae) were collected from pitcher plants. Adults which emerged were maintained without food then dissected to determine their egg clutch size. Among females which matured eggs, fecundities were negatively correlated with larval densities in individual pitchers. The mean autogenous fecundity of the overwintering generation did not differ from a summer sample. Adults unable to mature eggs comprised 6–39% of samples, depending on whether collected as pupae or fourth instar larvae. Fecundity was negatively correlated with time to adult eclosion among larvae maintained on unrenewed pitcher contents in the laboratory.Cohorts from this population were reared in artificial containers from egg hatch to adulthood at a single density and a superior or inferior diet. On the superior larval diet, all females survived to reproductive age, and all but one (>99%) produced eggs autogenously. On the inferior diet, survivorship to adult eclosion was significantly less, a high proportion of females died before reaching reproductive age, and only 19% of survivors matured eggs without blood. Protracted larval development induced by the inferior diet did not influence the probability of autogeny among females that survived to reproductive maturity.The relationship between larval environment and reproductive strategies is contrasted across the geographic range of W. smithii. Bloodfeeding occurs among southern populations where density dependent constraints on preimaginal growth are constantly severe. The loss of hematophagy among northern populations may have been facilitated by periods of density independent larval growth.Institute of Food and Agricultural Sciences, University of Florida, Experimental Station Journal Series No. 3645