A contribution to the search of general mathematical principles in biology

A somewhat different approach to the principle of biotopological mapping, discussed in previous publications, is given. The organism is considered as a set of properties, each of which is in its turn a set of numerous subproperties which are logically included in the corresponding properties. Topology is introduced by an appropriate definition of neighborhoods, and four postulates are stated which concern the mapping of the spaces corresponding to higher organisms on those of lower ones. A number of conclusions are drawn from the postulates. Some of them correspond to well-known facts. For example, in man and some higher organisms appropriate emotional stimuli should produce gastrointestinal or cardiovascular disturbances; or some microorganisms should produce substances harmful to other microorganisms (antibiotics). Some other conclusions are still awaiting verification. One of them is, for example, that there must exist unicellular organisms which produce antibodies to appropriate antigens.     

On some theoretical grounds for an organism-centered biology: Property emergence, supervenience, and downward causation

In this paper, we investigate some theoretical grounds for bridging the gap between an organism-centered biology and the chemical basis of biological explanation, as expressed in the prevailing molecular perspective in biological research. First, we present a brief survey of the role of the organism concept in biological thought. We advance the claim that emergentism (with its fundamental tenets: ontological physicalism, qualitative novelty, property emergence, theory of levels, irreducibility of the emergents, and downward causation) can provide a metaphysical basis for a coherent sort of organicism. Downward causation (DC) is the key notion in emergentist philosophy, as shown by the tension between the aspects of dependence and nonreducibility in the concept of supervenience, preferred by many philosophers to emergence as a basis for nonreductive physicalism. As supervenience physicalism does not lead, arguably, to a stable nonreductive physicalist account, we maintain that a philosophical alternative worthy of investigation is that of a combination of supervenience and property emergence in the formulation of such a stance. Taking as a starting-point O’Connor’s definition of an emergent property, we discuss how a particular interpretation of downward causation (medium DC), inspired by Aristotelian causal modes, results in an explanation of property emergence compatible with both physicalism and non-reductionism. In this account of emergence, one may claim that biology, as a science of living organization, is and remains a science of the organism, even if completely explained by the laws of chemistry. We conclude the paper with a new definition of an emergent property.     

Corrigendum: The smooth and stable operation of centromeres [Genes Genet. Syst. (2012) 87, p. 63-73

In this Review, Takahashi et al. (2000) was mistakenly cited in the wrong context (page 64, right column, line 25). Conclusion of the reference was rather that centromere deposition of CENP-A was affected by the kinetochore component Mis6 in fission yeast, which is an intriguing property of this organism.     

Diversity of nitrite reductase genes in "Candidatus Accumulibacter phosphatis"-dominated cultures enriched by flow-cytometric sorting

"Candidatus Accumulibacter phosphatis" is considered a polyphosphate-accumulating organism (PAO) though it has not been isolated yet. To reveal the denitrification ability of this organism, we first concentrated this organism by flow cytometric sorting following fluorescence in situ hybridization (FISH) using specific probes for this organism. The purity of the target cells was about 97% of total cell count in the sorted sample. The PCR amplification of the nitrite reductase genes (nirK and nirS) from unsorted and sorted cells was performed. Although nirK and nirS were amplified from unsorted cells, only nirS was detected from sorted cells, indicating that "Ca. Accumulibacter phosphatis" has nirS. Furthermore, nirS fragments were cloned from unsorted (Ba clone library) and sorted (Bd clone library) cells and classified by restriction fragment length polymorphism analysis. The most dominant clone in clone library Ba, which represented 62% of the total number of clones, was not found in clone library Bd. In contrast, the most dominant clone in clone library Bd, which represented 59% of the total number of clones, represented only 2% of the total number of clones in clone library Ba, indicating that this clone could be that of "Ca. Accumulibacter phosphatis." The sequence of this nirS clone exhibited less than 90% similarity to the sequences of known denitrifying bacteria in the database. The recovery of the nirS genes makes it likely that "Ca. Accumulibacter phosphatis" behaves as a denitrifying PAO capable of utilizing nitrite instead of oxygen as an electron acceptor for phosphorus uptake.     

Life,information theory,and topology

The information content of an organism determines to a large extent its ability to perform the basic vital functions: selection of food, breaking up of the food molecules into appropriate parts, selection of those parts, and their assimilation. The information content needed is very large and requires a sufficiently large complexity of the organism. The information content of an organism is largely determined by the information content of the constituent organic molecules. The information content of the latter is in its turn determined by the number of physically distinguishable atoms or radicals of which the molecule is composed. The different arrangements of atoms in a molecule are represented by the structural formula, which is basically a graph. It is shown that the topology of this graph also determines to a large extent the information content. Different points of a graph may be physically indistinguishable; in general, however, they are different in regard to their topological properties. A study of the relations between the topological properties of graphs and their information content is suggested, and several theorems are demonstrated. A relation between topology and living processes is thus found also on the molecular level.     

The sense of consciousness

I propose that consciousness might be understood as the property of a system that functions as a sense in the biological meaning of that term. The theory assumes that, as a complex system, the sense of consciousness is not a fixed structure but implies structure with variations and that it evolved, as many new functions do, through the integration of simpler systems. The recognized exteroceptive and enteroceptive senses provide information about the organism's environment and about the organism itself that are important to adaptation. The sense of consciousness provides information about the brain and thus about the organism and its environment. It senses other senses and processes in the brain, selecting and relating components into a form that "makes sense"-where making sense is defined as being useful to the organism in its adaptation to the environment. The theory argues that this highly adaptive organizing function evolved with the growing complexity of the brain and that it might have helped resolve discrepancies created at earlier stages. Neural energies in the brain that are the input to the sense of consciousness, along with the processing subsystem of which they are a part, constitute the base of consciousness. Consciousness itself is an emergent effect of an organizing process achieved through the sense of consciousness. The sense of consciousness thus serves an organizing function although it is not the only means of organization in the brain. Its uniqueness lies in the character of the organization it creates with consciousness as a property of that organization. The paper relates the theory to several general conceptions-interactionism, epiphenomenalism and identity theory-and illustrates a number of testable hypotheses. Viewing consciousness as a property of a sense provides a degree of conceptual integration. Much of what we know about the evolution and role of the conventionally recognized senses should help us understand the evolution and role of the sense of consciousness, and of consciousness itself.     

ENERGY,QUANTA, AND VISION

1. Direct measurements of the minimum energy required for threshold vision under optimal physiological conditions yield values between 2.1 and 5.7 x 10^–10 ergs at the cornea, which correspond to between 54 and 148 quanta of blue-green light. 2. These values are at the cornea. To yield physiologically significant data they must be corrected for corneal reflection, which is 4 per cent; for ocular media absorption, which is almost precisely 50 per cent; and for retinal transmission, which is at least 80 per cent. Retinal transmission is derived from previous direct measurements and from new comparisons between the percentage absorption spectrum of visual purple with the dim-vision luminosity function. With these three corrections, the range of 54 to 148 quanta at the cornea becomes as an upper limit 5 to 14 quanta actually absorbed by the retinal rods. 3. This small number of quanta, in comparison with the large number of rods (500) involved, precludes any significant two quantum absorptions per rod, and means that in order to produce a visual effect, one quantum must be absorbed by each of 5 to 14 rods in the retina. 4. Because this number of individual events is so small, it may be derived from an independent statistical study of the relation between the intensity of a light flash and the frequency with which it is seen. Such experiments give values of 5 to 8 for the number of critical events involved at the threshold of vision. Biological variation does not alter these numbers essentially, and the agreement between the values measured directly and those derived from statistical considerations is therefore significant. 5. The results clarify the nature of the fluctuations shown by an organism in response to a stimulus. The general assumption has been that the stimulus is constant and the organism variable. The present considerations show, however, that at the threshold it is the stimulus which is variable, and that the properties of its variation determine the fluctuations found between response and stimulus.     

Clutch size, offspring performance, and intergenerational fitness

It is now generally recognized that clutch size affects morethan offspring number. In particular, clutch size affects asuite of traits associated with offspring reproductive performance.Optimal clutch size is therefore determined not by the numericallymost productive clutch but by the clutch that maximizes collectiveoffspring reproductive success. Calculation of optimal clutchsize thus requires a consideration of ecological factors operatingduring an intergenerational time frame, spanning the lifetimeof the egglaying adult and the lifetimes of her offspring. Theoptimal clutch cannot define reproductive values in advance,but instead requires that the strategy chosen is the best responseto the set of reproductive values that it itself generates.In this article, we introduce methods for solving this problem,based on an iterative solution of the equation characterizingexpected lifetime reproductive success. We begin by consideringa semelparous organism, in which case lifetime reproductivesuccess is a function only of the state of the organism. Foran iteroparous organism, lifetime reproductive success dependsupon both state and time, so that our methods extend the usualstochastic dynamic programming approach to the evaluation oflifetime reproductive success. The methods are intuitive andeasily used. We consider both semelparous and iteroparous organisms,stable and varying environments, and describe how our methodscan be employed empirically.     

A note on the nature and origin of life

Some relational aspects of the property of self-reproduction of biological systems are studied. If in addition to the requirement of the property of self-reproduction we add also the requirement of adaptability of the organism to changing environment, this imposes certain conditions on the topology of the graphs which represent such systems. A further study of the relational properties of such systems seems to offer the possibility of deriving the principle of biological mapping from the requirement of self-reproduction and adaptability. An examination of the problem of the original formation of such self-reproducing systems in connection with the established fact of impossibility of spontaneous generation leads to the conclusion that an organism must inhibit such processes which, in the absence of organisms, would lead to spontaneous generation.     

Formation of fluorine technogenic anomalies in above-ground ecosystems of Siberia: Biological sorption,monitoring, possibility of lowering the negative impact

This paper studies how aluminum smelter emissions into the atmosphere affect the accumulation of fluorine by soil and plants, as well as change the chemical composition in leaves of woody plants. The ratio between total and extractable fluorine is ascertained to vary widely depending on the plant species. Meanwhile, gas resistant plants are characterized by an increased ash content in leaves (at the expense of K, P, Ca, etc.) and growth in the ratio between total and water-soluble fluorine. Plant resistance to fluorine that enters tissues depends on the capability of an organism to transform the toxicant into insoluble forms, which are not involved in physiological processes, i.e., on the presence of tissue elements with high precipitating capability. The gas-resistant species are ascertained to be characterized by high capability of limiting the intake of fluorine through roots, as well as its migration through a plant (especially to the organs that determine the further development of an organism).     

Near Homogeneity of PR2-Bias Fingerprints in the Human Genome and Their Implications in Phylogenetic Analyses

Genes of a multicellular organism are heterogeneous in the G+C content, which is particularly true in the third codon position. The extent of deviation from intra-strand equality rule of A = T and G = C (Parity Rule 2, or PR2) is specific for individual amino acids and has been expressed as the PR2-bias fingerprint. Previous results suggested that the PR2-bias fingerprints tend to be similar among the genes of an organism, and the fingerprint of the organism is specific for different taxa, reflecting phylogenetic relationships of organisms. In this study, using coding sequences of a large number of human genes, we examined the intragenomic heterogeneity of their PR2-bias fingerprints in relation to the G+C content of the third codon position (P ₃ ). Result shows that the PR2-bias fingerprint is similar in the wide range of the G+C content at the third codon position (0.30–0.80). This range covers approximately 89% of the genes, and further analysis of the high G+C range (0.80–1.00), where genes with normal PR2-bias fingerprints and those with anomalous fingerprints are mixed, shows that the total of 95% of genes have the similar finger prints. The result indicates that the PR2-bias fingerprint is a unique property of an organism and represents the overall characteristics of the genome. Combined with the previous results that the evolutionary change of the PR2-bias fingerprint is a slow process, PR2-bias fingerprints may be used for the phylogenetic analyses to supplement and augment the conventional methods that use the differences of the sequences of orthologous proteins and nucleic acids. Potential advantages and disadvantages of the PR2-bias fingerprint analysis are discussed. Received: 21 December 2000 / Accepted: 16 February 2001     

生长的冗余—作物对于虫害超越补偿作用的一种解释

本文阐述了作物在株高、叶面积、分枝或分蘖数、繁殖器官数量、生育期长度及生物产量对经济产量的比例等方面常存在大量冗余。这种冗余随着辅助能量输入的增加而增大。生长冗余本是生物适应波动环境的一种生态对策,以便增大稳定性,减小绝种的风险。但当环境条件改善或经人类支持与保护后,作物的这种固有的冗余特性变成了一种浪费和负担,对高产不利。通过栽培或育种手段减少冗余便可高产。在一些情形下,昆虫取食能减少作物的冗余。这便是作物对虫害的超越补偿的基本原因。     

Organizational invariance in (M,R)-systems

Robert Rosen's concept of (M,R)-systems was a fundamental advance in our understanding of the essential nature of a living organism as a self-organizing system, one that is closed to efficient causation, synthesizing, and maintaining all of the catalysts necessary for sustained operation during the whole period of its lifetime. Although it is not difficult to construct a model metabolic system to represent an (M,R)-system, such a model system will typically appear to lack organizational invariance, an essential property of a living (M,R)-system. To have this property, an (M,R)-system must not only be closed to external causation, it must also have its organization coded within itself, i.e., the knowledge of which components are needed for which functions must not be defined externally. In this paper, we discuss how organizational invariance may be achieved, and we argue that the apparent failure of previous models to be organizationally invariant is an artifact of the usual practice of treating catalytic cycles as 'black boxes'. If all of the steps in such a cycle are written as uncatalyzed chemical reactions, then it becomes clear that the organization of the system is fully defined by the chemical properties of the molecules that compose it.     

Development of the appendicularian Oikopleura dioica: Culture, genome, and cell lineages

Appendicularians are planktonic tunicates (urochordates), and retain a swimming tadpole shape throughout their life. Together with ascidians, they are the closest relatives of the vertebrates. Oikopleura dioica is characterized by its simplified life habit and anatomical organization. It has a tiny genome, the smallest ever found in a chordate. Its life cycle is extremely short – about 5 days – and it can be maintained in the laboratory over many generations. Embryos and adults are transparent and consist of a small number of cells. The anatomy of juveniles and adults has been described in detail. Cleavage pattern, cell lineages, and morphogenetic movements during embryogenesis have also been comprehensively documented. A draft genome sequence is now available. These features make this organism a suitable experimental model animal in which genetic manipulations would be feasible, as in Drosophila and Caenorhabditis elegans . In this review, I summarize a hundred years' knowledge on the development throughout the life cycle of this organism. Oikopleura is an attractive organism for developmental and evolutionary studies of chordates. It offers considerable promise for future genetic approaches.     

Plasmid-encoded lysostaphin endopeptidase resistance of Staphylococcus simulans biovar staphylolyticus

Staphylococcus simulans biovar staphylolyticus, the lysostaphin-producing organism, secretes a staphylolytic endopeptidase (EC 3.4.99.17) that is encoded on plasmid pACK1. Susceptibility of pACK1-cured strains to lysis by endopeptidase established that resistance to this enzyme is not an inherent property of the organism but rather is encoded on this dispensable plasmid. Furthermore, the enzyme is not an autolysin that is essential for cell wall synthesis because strains lacking the endopeptidase gene grew normally.     

Helicobacter pylori expresses an autolytic enzyme: gene identification,cloning, and theoretical protein structure

Helicobacter pylori is an important pathogen of the gastric system. The clinical outcome of infection is thought to be correlated with some genetic features of the bacterium. However, due to the extreme genetic variability of this organism, it is hard to draw definitive conclusions concerning its virulence factors. Here we describe a novel H. pylori gene which expresses an autolytic enzyme that is also capable of degrading the cell walls of both gram-positive and gram-negative bacteria. We designated this gene lys. We found this gene and observed its expression in a number of unrelated clinical strains, a fact that suggests that it is well conserved in the species. A comparison of the nucleotide sequences of lys and the hypothetical gene HP0339 from H. pylori strain ATCC 26695 revealed almost total identity, except for the presence of an insertion consisting of 24 nucleotides in the lys sequence. The coding sequences of lys and HP0339 show a high degree of homology with the coding sequence of bacteriophage T4 lysozyme. Because of this similarity, it was possible to model the three-dimensional structures of both the lys and HP0339 products.     

Phosphoglycerol substituents present on the cyclic beta-1,2-glucans of Rhizobium meliloti 1021 are derived from phosphatidylglycerol.

The synthesis of periplasmic cyclic beta-1,2-glucans is a property unique to species of the family Rhizobiaceae. For this reason, it is generally believed that these molecules may play an important role in the plant infection process. In the present study, we determined that the cyclic beta-1,2-glucans produced by Rhizobium meliloti 1021 were predominantly anionic in character and contained both phosphoglycerol and succinic acid substituents. In addition, we demonstrated that phosphatidylglycerol was the source of the phosphoglycerol substituents present on these oligosaccharides and that greater than 60% of the total phospholipid turnover in this organism involved this substitution reaction.     

The conservation of redundancy in genetic systems: effects of sexual and asexual reproduction

The relationship between probability of survival and the number of deleterious mutations in the genome is investigated using three different models of highly redundant systems that interact with a threatening environment. Model one is a system that counters a potentially lethal infection; it has multiple identical components that act in sequence and in parallel. Model two has many different overlapping components that provide three-fold coverage of a large number of vital functions. The third model is based on statistical decision theory: an ideal detector, following an optimum decision strategy, makes crucial decisions in an uncertain world. The probability of a fatal error is reduced by a redundant sampling system, but the chance of error rises as the system is impaired by deleterious mutations. In all three cases the survival profile shows a synergistic pattern in that the probability of survival falls slowly and then more rapidly. This is different than the multiplicative or independent survival profile that is often used in mathematical models. It is suggested that a synergistic profile is a property of redundant systems. Model one is then used to study the conservation of redundancy during sexual and asexual reproduction. A unicellular haploid organism reproducing asexually retains redundancy when the mutation rate is very low (0001 per cell division), but tends to lose high levels of redundancy if the mutation rate is increased (001 to 01 per cell division). If a similar unicellular haploid organism has a sexual phase then redundancy is retained for mutation rates between 0001 and 01 per cell division. The sexual organism outgrows the asexual organism when the above mutation rates apply. If they compete for finite resources the asexual organism will be extinguished. Variants of the sexual organism with increased redundancy will outgrow those with lower levels of redundancy and the sexual process facilitates the evolution of more complex forms. There is a limit to the extent that complexity can be increased by increasing the size of the genome and in asexual organisms this leads to progressive accumulation of mutations with loss of redundancy and eventual extinction. If complexity is increased by using genes in new combinations, the asexual form can reach a stable equilibrium, although it is associated with some loss of redundancy. The sexual form, by comparison, can survive, with retention of redundancy, even if the mutation rate is above one per generation. The conservation and evolution of redundancy, which is essential for complexity, depends on the sexual process of reproduction.     

The individuality of artifacts and organisms

Is there any genuine difference between organisms and artifacts? Where and how would we identify such a difference? This paper argues the difference involves the character of their individuality. Unlike an organism, an artifact's individuality is (for the most part) determined by the function that the designer selected in the artifact's production rather than the functional interdependence of its parts. In both cases, individuality is a historical property and in both cases the parts may be functionally interdependent to some extent. However, for artifacts, this interdependence is not what makes it the individual that it is. Instead, the interdependence of its parts is in the service of the functions for which the spear was designed. No such additional purpose or function exists for an organism.     

TOR, a central controller of cell growth

Cell growth (increase in cell mass) and cell proliferation (increase in cell number) are distinct yet coupled processes that go hand-in-hand to give rise to an organ, organism, or tumor. Cyclin-dependent kinase(s) is the central regulator of cell proliferation. Is there an equivalent regulator for cell growth? Recent findings reveal that the target of rapamycin TOR controls an unusually abundant and diverse set of readouts all of which are important for cell growth, suggesting that this conserved kinase is such a central regulator.