The theory of organism and the culturalist foundation of biology

Summary After the disappearance of organism was diagnosed, the discussion about the role of a theory of organism in biology is characterised by a significant contradiction. On the one hand, the importance of a theory of organism is stated. Particularly developmental biology demands organism-centred approaches as a basis for conceptual integration. On the other hand, several modern biological disciplines such as genetics and molecular biology simply don’t need a theory of organism for their work. Consequently, the determination of the status of the organism and its relevance for biology at all is an unsolved problem. In order to clarify the methodological status of the organism in biology we start with the reconstruction of three important propositions. A life oriented approach and a hierarchy concept - which both are from a neo-Darwinian origin - are confronted with a structuralist approach of organism, that can be characterised as a non-Darwinist approach. Our own attempt for the solution of the organism problem applies the tools of culturalist methodology. In accordance to this pragmatic approach, the term organism is introduced as a concept of notion. A constructional morphological case study exemplifies the applicability of this concept. From the culturalist point of view a methodological foundation of biology can be achieved, that provides a consistent basis for a comprehensive integration of biological knowledge.     

Hierarchical modelling of acclimatory processes

The term acclimation has been used with several connotations in the field of acclimatory physiology. An attempt has been made, in this paper, to define precisely the term “acclimation” for effective modelling of acclimatory processes. Acclimation is defined with respect to a specific variable, as cumulative experience gained by the organism when subjected to a step change in the environment. Experimental observations on a large number of variables in animals exposed to sustained stress, show that after initial deviation from the basal value (defined as “growth”), the variables tend to return to basal levels (defined as “decay”). This forms the basis for modelling biological responses in terms of their growth and decay.Hierarchical systems theory as presented by Mesarovic, Macko & Takahara (1970) facilitates modelling of complex and partially characterized systems. This theory, in conjunction with “growth-decay” analysis of biological variables, is used to model temperature regulating system in animals exposed to cold. This approach appears to be applicable at all levels of biological organization. Regulation of hormonal activity which forms a part of the temperature regulating system, and the relationship of the latter with the “energy” system of the animal of which it forms a part, are also effectively modelled by this approach. It is believed that this systematic approach would eliminate much of the current circular thinking in the area of acclimatory physiology.     

Protein utilization in correlation to protein intake

In a 14-day experiment, weaned and adult rats were given ad libitum isocaloric diets with a mounting casein content (5, 10, 15, 25 and 40% by weight) and growth parameters of protein biological value, PER and NPR, and the utilization parameters NPU (body protein) and LPU (liver protein) were determined together with phosphoenolpyruvate carboxykinase (gluconeogenetic enzyme) and pyruvate kinase (glycolytic enzyme) activity in the animals' liver. The decrease in all the biological value parameters in weaned rats on 25% and 40% casein diets and in adult rats on 15%, 25% and 40% casein diets shows that these concentrations are too high for the organism. The decrease in PER and diminished weight and body and liver nitrogen increments in both age groups in animals with a low protein intake is evidence that 5% casein is an inadequate concentration. The optimum diet for weaned rats is thus a 15% casein diet and for adult rats a 10% casein diet, as confirmed by the linear correlation between weight increments, body and liver nitrogen and protein intake and also by gluconeogenetic enzyme activity. Under the given experimental conditions the study is a contribution to the determination of optimum physiological doses of proteins.     

Estimation of fetal weight by ultrasound.

Estimation of fetal size by ultrasound has supported two recent concepts of fetal growth. Firstly, the normal weight gain is constant from 28 weeks of gestation until several weeks after term; about 27 g/day. Secondly, the average weight of fetuses born preterm is lower than the average weight of fetuses of the same gestational age who remain in utero. This means that up to 40% of infants born at 28-30 weeks of gestation are small-for-gestational age, when related to the biological optimum. Unfortunately, the test-retest variation of fetal weight estimation is as much as 50% of the standard deviation of the gestational-age-specific fetal weight distribution. This means that fetal growth has to be followed for many weeks to document statistically significant deviations. No study has, as yet, demonstrated the value of this approach to distinguish between intrauterine growth retardation and growth along low centiles by fetuses of reduced growth potential.     

Stochastic von Bertalanffy models, with applications to fish recruitment

We consider three individual-based models describing growth in stochastic environments. Stochastic differential equations (SDEs) with identical von Bertalanffy deterministic parts are formulated, with a stochastic term which decreases, remains constant, or increases with organism size, respectively. Probability density functions for hitting times are evaluated in the context of fish growth and mortality. Solving the hitting time problem analytically or numerically shows that stochasticity can have a large positive impact on fish recruitment probability. It is also demonstrated that the observed mean growth rate of surviving individuals always exceeds the mean population growth rate, which itself exceeds the growth rate of the equivalent deterministic model. The consequences of these results in more general biological situations are discussed.     

Kinetics of polyol oxidation with Gluconobacter oxydans

Summary The influence of culture pH on the metabolism of Gluconobacter oxydans was determined. An acidic milieu during growth of the organism enhances the oxidation rate. The CO₂ evolution rate representing the assimilation of the product is inhibited by a low pH value. Growth of the bacteria is possible both on glycerol and DHA in separate phases, which is not a controlled as diauxic growth. Product formation follows Luedeking-Piret kinetics.now: Institut für Biotechnologie, TU Graz, Petersgasse 12, 8010 Graz, Austria     

A model for the age-dependent dynamics of growth of terrestrial mammals

Two hypothetical biological mechanisms were proposed that largely determine the dynamics of growth of overland mammals. The first mechanism is the maintenance of a spatial similarity of the anatomy of the organism during its growth, and the second is the maintenance of the stability of the internal environment of the organism. On the basis of the advanced hypothesis, a model of age-dependent dynamics of growth was constructed, and a differential equation describing the changes in the body mass with time was derived. According to this model, the dynamics of growth and the mass of an adult individual are determined by two energy constants that characterize the mechanism of food assimilation and the energy expenditures for the movement of the individual in space. The deviation between the solution obtained and the experimental data on age-dependent changes in the mass of the human body was on the average 6%. These insignificant deviations were explained in the framework of the proposed hypothesis, which indicates its validity.     

Length–weight relationships of fish species caught in a mangrove swamp in the Gulf of California (Mexico)

The relation between length (L) and weight (W) was estimated for 33 species representing 14 families of fishes from El Conchalito mangrove swamp, Gulf of California (Mexico). The parameter b estimated by nonlinear least squares of weight and length data, ranged from 1.41 to 3.68. Length ‐ weight parameters can be used for several biological or fishery purposes to enable the derivation of weight estimates from given a value of length or vice versa.     

Four notions of biological function

I argue that there are at least four different ways in which the term ‘function’ is used in connection with the study of living organisms, namely: (1) function as (mere) activity, (2) function as biological role, (3) function as biological advantage, and (4) function as selected effect. Notion (1) refers to what an item does by itself; (2) refers to the contribution of an item or activity to a complex activity or capacity of an organism; (3) refers to the value for the organism of an item having a certain character rather than another; (4) refers to the way in which a trait acquired and has maintained its current share in the population. The recognition of a separate notion of function as biological advantage solves the problem of the indeterminate reference situation that has been raised against a counterfactual analysis of function, and emphasizes the importance of counterfactual comparison in the explanatory practice of organismal biology. This reveals a neglected problem in the philosophy of biology, namely that of accounting for the insights provided by counterfactual comparison.     

Biological indicators for low temperature steam and formaldehyde sterilization: the effect of defined media on sporulation, growth index and formaldehyde resistance of spores of Bacillus stearothermophilus strains

Preliminary screening was carried out on spores of 29 strains of Bacillus stearothermophilus to determine their potential as biological indicator organisms for low temperature steam and formaldehyde sterilization. Each strain was sporulated on four chemically defined media. Fourteen strains produced satisfactory sporulation on one or more of the media but there was considerable variation in the extent of sporulation. The growth index of the spores, which was dependent on both the strain of organism and the sporulation medium, ranged from 1% to 90%. The spores were appraised on the basis of their resistance to inactivation by 0.5% w/v formaldehyde in aqueous solution at 70°C. The survivor curves obtained could be characterized into five types on the basis of the shape of the curve. Only five strains of Bacillus stearothermophilus produced spores with the characteristics of high resistance, linear semi-logarithmic survivor curve and high growth index that would be required of a potential biological indicator organism.     

A concept of relation between physical and biological time in animals

A definition is proposed for biological ("internal") time tau(t) for a growing organism whose weight variation obeys the law w(t): tau(t) = 1/c(w) (t) = w(t)/w'(t), where t is physical ("external") time, w'(t) is weight increase rate, and c(w) (t) = w'(t)/w(t) is specific growth rate. Properties of functions tau(t) and w(tau) were studied for those cases when growth curves w(t) were described by Bertalanffy's or logistic equations.     

What is an "organism"? On the occurrence of a new term and its conceptual transformations 1680-1850

The essay reconstructs the occurrence of the term "organism" and the transformations of its concept from around 1680 to the middle of the nineteenth century. The different sections refer to individual authors who used the word "organism" and situate its usage in specific historical contexts. After earlier uses of the word in medieval sources, the Latin word "organismus" appeared in 1684 in Stahl's medico-physiological writings. Around 1700, it can be found in French (organisme), English (organism), Italian (organismo) and later also in German (Organismus). During the eighteenth century, the word "organism" generally referred to a specific principle or form of order, often in opposition to the order of "mechanism," that could be applied to plants, animals or the entire world. At the end of the eighteenth century, the term became a generic name for individual living entities with inside-outside-interfaces and an inner "organization" of parts. From around 1830, the word "organism" replaced the expressions "organic" or "organized body" as a recurrent technical term in the emerging biological disciplines.     

Accumulation of polyhydroxyalkanoates by Microlunatus phosphovorus under various growth conditions

Microlunatus phosphovorus is an activated-sludge bacterium with high levels of phosphorus-accumulating activity and phosphate uptake and release activities. Thus, it is an interesting model organism to study biological phosphorus removal. However, there are no studies demonstrating the polyhydroxyalkanoate (PHA) storage capability of M. phosphovorus, which is surprising for a polyphosphate-accumulating organism. This study investigates in detail the PHA storage behavior of M. phosphovorus under different growth conditions and using different carbon sources. Pure culture studies in batch-growth systems were conducted in shake-flasks and in a bioreactor, using chemically defined growth media with glucose as the sole carbon source. A batch-growth system with anaerobic–aerobic cycles and varying concentrations of glucose or acetate as the sole carbon source, similar to enhanced biological phosphorus removal processes, was also employed. The results of this study demonstrate for the first time that M. phosphovorus produces significant amounts of PHAs under various growth conditions and with different carbon sources. When the PHA productions of all cultivations were compared, poly(3-hydroxybutyrate) (PHB), the major PHA polymer, was produced at about 20–30% of the cellular dry weight. The highest PHB production was observed as 1,421 mg/l in batch-growth systems with anaerobic–aerobic cycles and at 4 g/l initial glucose concentration. In light of these key results regarding the growth physiology and PHA-production capability of M. phosphovorus, it can be concluded that this organism could be a good candidate for microbial PHA production because of its advantages of easy growth, high biomass and PHB yield on substrate and no significant production of fermentative byproducts.     

New principles in determining the biological value of proteins

Some new principles are suggested in determination of the protein biological values that take into account the amino acid composition and the processes occurring in the course of protein assimilation. Food proteins have a significant effect on the protein-amino acid metabolism of the organism by reducing oxidative catabolism of essential amino acids which are deficient in the utilized protein, i.e. they have a compensating effect on the deficiency of exogenous essential amino acids. The understanding of the process allowed the author to approach the solution of the problem of the replacement of the amino acid score with the biological value. For this purpose two new parameters which determine the quality and the second phase of protein assimilation have been introduced, i.e. potential biological value (BVp) and compensation coefficient (C), respectively. The experimental biological value (BV) is determined as the sum of the two parameters: BV = BVp + C.     

The Biokinetic Spectrum for Temperature

We identify and describe the distribution of temperature-dependent specific growth rates for life on Earth, which we term the biokinetic spectrum for temperature. The spectrum has the potential to provide for more robust modeling in thermal ecology since any conclusions derived from it will be based on observed data rather than using theoretical assumptions. It may also provide constraints for systems biology model predictions and provide insights in physiology. The spectrum has a Δ-shape with a sharp peak at around 42°C. At higher temperatures up to 60°C there was a gap of attenuated growth rates. We found another peak at 67°C and a steady decline in maximum rates thereafter. By using Bayesian quantile regression to summarise and explore the data we were able to conclude that the gap represented an actual biological transition between mesophiles and thermophiles that we term the Mesophile-Thermophile Gap (MTG). We have not identified any organism that grows above the maximum rate of the spectrum. We used a thermodynamic model to recover the Δ-shape, suggesting that the growth rate limits arise from a trade-off between activity and stability of proteins. The spectrum provides underpinning principles that will find utility in models concerned with the thermal responses of biological processes.     

Metabolic Adaptation Processes That Converge to Optimal Biomass Flux Distributions

In simple organisms like E.coli, the metabolic response to an external perturbation passes through a transient phase in which the activation of a number of latent pathways can guarantee survival at the expenses of growth. Growth is gradually recovered as the organism adapts to the new condition. This adaptation can be modeled as a process of repeated metabolic adjustments obtained through the resilencings of the non-essential metabolic reactions, using growth rate as selection probability for the phenotypes obtained. The resulting metabolic adaptation process tends naturally to steer the metabolic fluxes towards high growth phenotypes. Quite remarkably, when applied to the central carbon metabolism of E.coli, it follows that nearly all flux distributions converge to the flux vector representing optimal growth, i.e., the solution of the biomass optimization problem turns out to be the dominant attractor of the metabolic adaptation process.     

Relationship between fetal weight and malformation in developmental toxicity studies

Exposure to developmental toxicants may cause fetal malformations, increase prenatal death rates and reduce fetal weight at term. However, there has been little formal study of the relationship among these effects. Certainly, no statistical methods are currently available to jointly analyze these effects of exposure. As a preliminary step in developing such methods, simple exploratory analyses were conducted using a series of ten studies conducted for the National Toxicology Program. Because fetal weight and malformation status were both reported for all live fetuses, the data permitted an exploration of the correlation between these two outcomes. The data show a clear pattern wherein malformed fetuses tended to be lighter at term than nonmalformed fetuses. While these patterns cannot be used to draw inferences regarding the biological relationship between fetal weight and malformation, they do suggest the potential value in developing statistical models for the joint effect of exposure on fetal weight and malformations.     

THE NATURE OF THE GROWTH RATE

1. The growth rate of organisms may be considered as a chemical reaction which gives the mature organism as its end-product. The organism grows at a definite rate which is, at any moment, proportional to the amount of growth yet to be made. 2. Shoots of young pear trees measured at weekly intervals during the growing season showed a rate similar to that of an autocatalytic reaction. 3. Young walnut trees showed distinct cycles of growth in a single season, but the growth in each cycle proceeded at a rate corresponding to an autocatalytic reaction. 4. The growth rate follows a definite, quantitative course though judged by different criteria. Data are presented for maize in which green weight, dry weight, and height of the plant are used. Data for cattle show that either weight or height of the animal may be used as a criterion.     

Exclusion processes on a growing domain

A discrete model provides a useful framework for experimentalists to understand the interactions between growing tissues and other biological mechanisms. A cellular automata (CA) model with domain growth, cell motility and cell proliferation, based on cellular exclusion processes, is developed here. Average densities can be defined from the CA model and a continuum representation can be determined. The domain growth mechanism in the CA model gives rise to a Fokker-Planck equation in the corresponding continuum model, with a diffusive and a convective term. Deterministic continuum models derived from conservation laws do not include this diffusive term. The new diffusive term arises because of the stochasticity inherited from the CA mechanism for domain growth. We extend the models to multiple species and investigate the influence of the flux terms arising from the exclusion processes. The averaged CA agent densities are well approximated by the solution of nonlinear advection-diffusion equations, provided that the relative size of the proliferation processes to the diffusion processes is sufficiently small. This dual approach provides an understanding of the microscopic and macroscopic scales in a developmental process.     

蜜蜂——新兴的模式生物

蜜蜂作为具有重要经济价值和生态价值的社会性昆虫, 在诸如神经生物学和社会生物学等研究领域也具有很高的模型价值。蜜蜂基因组工程为深入认识蜜蜂的生物学特点,进一步发挥其在多个研究领域的模型价值奠定了分子基础。本文基于蜜蜂的生物学特点,介绍了蜜蜂作为模式生物所具备的优势,及其在学习和记忆、劳动分工、级型分化、免疫等热点领域的研究价值。通过总结和展望国内外蜜蜂生物学研究形势,呼吁国内相关各学科开展合作研究。