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.     

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.     

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.     

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.     

Botulism: the agent,mode of action of the botulinum neurotoxins,forms of acquisition,treatment and prevention

The botulinum neurotoxins are produced by anaerobic, spore-forming bacteria belonging to the Clostridium genus. They are synthesised as a single chain protein (150 kDa), which is not or weakly active. The active form results from a proteolysis cleaving the precursor in a light chain (about 50 kDa) and a heavy chain (about 100 kDa), which are linked by a disulfide bridge. The heavy chain is involved in the recognition of a specific neuronal surface receptor and mediates the internalization of the light chain into the cytosol. The light chain is responsible for the intracellular activity. It catalyses the proteolysis of SNARE proteins, which are involved in the exocytosis of synaptic vesicles containing acetylcholine. Hence, the release of acetylcholine at the neuromuscular junction is blocked, leading to a flaccid paralysis. Human botulism, usually type A, B or E, is associated with intoxination, ingestion of preformed toxin in food, with digestive toxi-infection, mainly in newborns (infant botulism), or with wound contamination (wound botulism). The treatment of botulism is usually symptomatic. The specific treatment is based on the serotherapy or on the use of purified specific antibodies. The vaccination against botulism is efficient. However, since the botulinum neurotoxins are widely used for the treatment of numerous dystonias, a generalised vaccination is not conceivable.     

Non-progressive evolution,the red queen hypothesis,and the balance of nature

The Red Queen hypothesis, or the ability organisms have to control and regulate the available trophic energy, is a recently proposed parameter for measuring fitness. Firstly, this hypothesis is analysed in terms of its heuristic power. Secondly, the claimed causal dependence between this parameter and a, still controversial, law of constant extinction is judged to be unjustified, however reasonable such a claim appears to be. Finally, the ubiquity of competition in nature which is seemingly required by the Red Queen and supposedly realized at the expense of a mutualistic alternative, is deemed to be a questionable assumption.     

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.     

Onto-Tools,the toolkit of the modern biologist: Onto-Express,Onto-Compare,Onto-Design and Onto-Translate

Onto-Tools is a set of four seamlessly integrated databases: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Onto-Express is able to automatically translate lists of genes found to be differentially regulated in a given condition into functional profiles characterizing the impact of the condition studied upon various biological processes and pathways. OE constructs functional profiles (using Gene Ontology terms) for the following categories: biochemical function, biological process, cellular role, cellular component, molecular function and chromosome location. Statistical significance values are calculated for each category. Once the initial exploratory analysis identified a number of relevant biological processes, specific mechanisms of interactions can be hypothesized for the conditions studied. Currently, many commercial arrays are available for the investigation of specific mechanisms. Each such array is characterized by a biological bias determined by the extent to which the genes present on the array represent specific pathways. Onto-Compare is a tool that allows efficient comparisons of any sets of commercial or custom arrays. Using Onto-Compare, a researcher can determine quickly which array, or set of arrays, covers best the hypotheses studied. In many situations, no commercial arrays are available for specific biological mechanisms. Onto-Design is a tool that allows the user to select genes that represent given functional categories. Onto-Translate allows the user to translate easily lists of accession numbers, UniGene clusters and Affymetrix probes into one another. All tools above are seamlessly integrated. The Onto-Tools are available online at http://vortex.cs.wayne.edu/Projects.html.     

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.     

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.     

Regulation,necessity, and the misinterpretation of knockouts

Much contemporary biology consists of identifying the molecular components that associate to perform biological functions, then discovering how these functions are controlled. The concept of control is key to biological understanding, at least of the physiological kind; identifying regulators of processes underpins ideas of causality and allows complicated, multicomponent systems to be summarized in relatively simple diagrams and models. Unfortunately, as this article demonstrates by drawing on published articles, there is a growing tendency for authors to claim that a molecule is a ‘regulator’ of something on evidence that cannot support the conclusion. In particular, gene knockout experiments, which can demonstrate only that a molecule is necessary for a process, are all too frequently being misinterpreted as revealing regulation. This logical error threatens to blur the important distinction between regulation and mere necessity and therefore to weaken one of our strongest tools for comprehending how organisms work.     

Association,ranging, and the social unit in chimpanzees of the Mahale Mountains,Tanzania

In order to characterize the social unit in chimpanzees, about which several conflicting views have been proposed, the proximity matrix among 55 recognized chimpanzees and the range covered by each of them are examined, on the basis of data obtained at the Mahale Mountains during 12 months in 1978–1979. It is shown once again that chimpanzees have a bisexual social unit (unit-group). Two such unit-groups were detected in the study area. All animals belonged to one of the two unit-groups except a few cycling females (and a juvenile male accompanied by his cycling mother) which were seen to associate alternately with members of two neighboring unit-groups, covering a whole range of one or even two unit-groups. The problem of such females is discussed in relation to the spatial relationships between the two unit-groups. Reexamining the membership of a unit-group, it is demonstrated that a unit-group was most likely patrilineal. While nulliparous females transferred between unit-groups, parous females tended to remain in a unit-group where they first gave birth to infants and to have several offspring therein. This appeared significant for ensuring recruitment of members of the next generation to a patrilineal unit-group. Although some adult males left their natal unit-group, they never joined the other. Male departure from a unit-group seemed to be forced by the other males and to be the sociological equivalent of going into exile, which is unique in nonhuman primates.     

Count data, detection probabilities, and the demography, dynamics, distribution, and decline of amphibians

The evidence for amphibian population declines is based on count data that were not adjusted for detection probabilities. Such data are not reliable even when collected using standard methods. The formula C = Np (where C is a count, N the true parameter value, and p is a detection probability) relates count data to demography, population size, or distributions. With unadjusted count data, one assumes a linear relationship between C and N and that p is constant. These assumptions are unlikely to be met in studies of amphibian populations. Amphibian population data should be based on methods that account for detection probabilities.     

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 effects of the glucocorticoid,dexamethasone, on the development of the Drosophila embryo

We have investigated the effects of the glucocorticoid, dexamethasone, and five structural analogs on Drosophila development in an effort to identify steroid ligands that may play a role in the embryogenesis of this organism. Embryos were exposed to glucocorticoids either by direct culture in supplemented medium, or by examining embryos from adult flies raised on supplemented fly food. After exposure, embryos were examined for developmental defects. At a morphological level, exposure to dexamethasone disrupts the dorsolateral folding of the amnioserosa during germ band extension. In addition, germ band retraction and dorsal closure is also disrupted. The phenocritical period of these effects is within the first 4 h of embryogenesis. This response is dosage sensitive, with embryos responding to concentrations of dexamethasone ranging from 10^–6 to 10^–3M. Furthermore, glucocorticoids which are closely related structural analogs of dexamethasone also disrupt germ band retraction and dorsal closure, while other tested steroids had no effect on embryonic development. At a molecular level, expression of the gene, Krüppel, is absent from the amnioserosa of dexamethasone-treated embryos. The cuticular phenocopy resulting from exposure to dexamethasone and related glucocorticoids is morphologically similar to the mutant phenotype associated with four genes required for germ band retraction, namely hindsight, serpent, tail-up and u-shaped. The results of this study represent the first association of a glucocorticoid with dose, stage and tissue specific effects on Drosophila development at both morphological and molecular levels.     

Partition structures, Polya urns, the Ewens sampling formula, and the ages of alleles

It has recently been shown that the Ewens sampling formula may be generated by a Polya-like urn model. A genealogical proof of this result equates the labelling of balls in the urn to the partition by age of alleles in the sample. This urn construction is shown to be equivalent to the construction of Kingman (Proc. Roy. Soc. London Ser. A 361 (1978), 1-20) using a Poisson-Dirichlet "paintbox" and as a consequence, the partition by ages is seen to be equivalent to the size biased permutation of the Poisson-Dirichlet distribution. This approach unifies and extends many results on ages of alleles, the Polya urn, and the Poisson-Dirichlet distribution. Furthermore the Ewens sampling formula is characterized as being the only partition structure which may be generated by an urn-like mechanism.     

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.     

acon-3, the Neurospora crassa ortholog of the developmental modifier, medA, complements the conidiation defect of the Aspergillus nidulans mutant

Aspergillus nidulans and Neurospora crassa are ascomycetes that produce asexual spores through morphologically distinct processes. MedA, a protein with unknown function, is required for normal asexual and sexual development in A. nidulans. We determined that the N. crassa ortholog of medA is acon-3, a gene required for early conidiophore development and female fertility. To test hypotheses about the evolutionary origins of asexual development in distinct fungal lineages it is important to understand the degree of conservation of developmental regulators. The amino acid sequences of A. nidulans MedA and N. crassa ACON-3 shared 37% identity and 51% similarity. acon-3 is induced at late time points of conidiation. In contrast, medA is constitutively expressed and MedA protein localizes to nuclei in all tissue types. Nonetheless, expression of acon-3 using its native promoter complemented the conidiation defects of the A. nidulans ΔmedA and medA15 mutants. We conclude that the biochemical activity of the medA orthologs is conserved for conidiation.