Transformational and taxic homology revisited

Usages and meanings of the terms “taxic” and “transformational homology” are reviewed from 1982 to the present. While “taxic homology” has been relatively invariant in its connotation, “transformational homology” as employed by different authors refers to at least three different concepts. This has resulted in confusion.     

Logical-Semantic Analysis and the Development of L.S. Vygotsky's Ideas About “Units” and “Elements” of Psychological Systems

Based on an analysis of L.S. Vygotsky's concepts of “units” and “elements” of psychological systems, this article highlights five of their attributes. It shows that these attributes are logically symmetrical, since in their wording they can be converted into one another by negation or by replacing some words with their opposites. This suggests that the concepts of the “unit” and “element” of a system are different poles of one theoretical construct of the activity of human psychology. Thus methods for the study of psychological systems by breaking them down into elements or by separating them into units can be seen as complementary. The article describes differences among the concepts of “unit,” “minimal unit,” and “cell” of a psychological system. It reviews several problems that are solvable using the “method of units,” as well as some concepts of the theory of psychological systems that are understood as holistic, conceptual, and active processes and/or results of human interaction with the world. Among the examples of such systems are “systems of psychological functions” (according to Vygotsky), as well as separate activities (according to A.N. Leontiev), human actions and operations (interactions with the world on the level of objects and mental or physical means). The “component” of a psychological system is defined as any “something” that in some sense belongs to or is included in human interaction with the world. A component that belongs to the system is called an “element” of it, but a component that is included in the functioning and development of the system is called a “part” of it. The article presents the mathematical and psychological foundation of these definitions. It identifies and discusses the substantial (independently existing) components of psychological systems and their attributes (properties and conditions). It describes the relationships between them using the bipolar theoretical constructs “part-element” and “substantial-attributive” component of a system.     

Do women have evolved mate preferences for men with resources?: A reply to Smuts

Research by more than 50 scientists studying more than 10,000 individuals inhabiting 33 countries, six continents, and five islands supports the hypothesis that women have evolved mate preferences for men who show cues of resource possession or resource acquisition potential. Smuts' (1991) apparent view that these species-typical preferences do not exist is contravened by the scientific evidence. Repeated assertions that “behaviors depends on context” do not illuminate our understanding in the absence of specifying which behaviors, which contexts, and which evolved mechanisms are activated by the relevant contextual input. Progress in the study of evolution and human behavior depends on using key terms in consensually defined rather than idiosyncratic ways, on distinguishing evolved psychological mechanisms from manifest behavior, and on giving greater weight to cumulative scientific evidence than to subjective impressions.     

Characterizing the Data in Online Companion-dog Obituaries to Assess Their Usefulness as a Source of Information about Human–Animal Bonds

Online pet obituary sites host hundreds of obituaries regarding the passing of companion animals. Often composed by the owner or primary caretaker of the animal, they are a potential source of data about human–animal bonds where there were strong positive human emotions surrounding the animal at point of death. The aim of the present study was to characterize on-line pet obituaries and to evaluate their usefulness as a source of information on the human–animal bond. One hundred and thirty full obituaries of dogs were studied. Where the role of the writer could be identified, the majority of obituary writers identified themselves as a female parental figure to the dog (34.6%); however, obituaries were also written by male parental figures (7.7%) and children (5.4%). Most obituaries (60%) fell within the 100-400 words length range. Obituaries were seen to express several key concepts. For instance, dogs were described as “child-like,” “part of the family,” showing “sympathy” and/or “gratitude” to the owner, and having a “sense of humor.” For their part, writers expressed “guilt” over the dog’s death, discussed a concept of the “afterlife” and noted an “instant connection” between themselves and the dog. A high proportion of the obituaries discussed the afterlife (51%) and indicated that the dog was considered part of the family (49%). There were some significant associations between concept usage within obituaries. Dogs that were described as “child-like” were more often perceived to be in an “afterlife” and to have had an “instant connection” with obituary writers (x² = 38.08, p < 0.001). We conclude that online pet obituaries can be a valuable source of information on human feelings surrounding a companion animal death.     

PERSPECTIVE: THE PACE OF MODERN LIFE: MEASURING RATES OF CONTEMPORARY MICROEVOLUTION

We evaluate methods for measuring and specifying rates of microevolution in the wild, with particular regard to studies of contemporary, often deemed “rapid,” evolution. A considerable amount of ambiguity and inconsistency persists within the field, and we provide a number of suggestions that should improve study design, inference, and clarity of presentation. (1) Some studies measure change over time within a population (allochronic) and others measure the difference between two populations that had a common ancestor in the past (synchronic). Allochronic studies can be used to estimate rates of “evolution,” whereas synchronic studies more appropriately estimate rates of “divergence.” Rates of divergence may range from a small fraction to many times the actual evolutionary rates in the component populations. (2) Some studies measure change using individuals captured from the wild, whereas others measure differences after rearing in a common environment. The first type of study can be used to specify “phenotypic” rates and the later “genetic” rates. (3) The most commonly used evolutionary rate metric, the darwin, has a number of theoretical shortcomings. Studies of microevolution would benefit from specifying rates in standard deviations per generation, the haldane. (4) Evolutionary rates are typically specified without an indication of their precision. Readily available methods for specifying confidence intervals and statistical significance (regression, bootstrapping, randomization) should be implemented. (5) Microevolutionists should strive to accumulate time series, which can reveal temporal shifts in the rate of evolution and can be used to identify evolutionary patterns. (6) Evolutionary rates provide a convenient way to compare the tempo of evolution across studies, traits, taxa, and time scales, but such comparisons are subject to varying degrees of confidence. Comparisons across different time scales are particularly tenuous. (7) A number of multivariate rate measures exist, but considerable theoretical development is required before their utility can be determined. We encourage the continued investigation of evolutionary rates because the information they provide is relevant to a wide range of theoretical and practical issues.     

Gorilla adaptations to naturalistic environments

In the past few decades there have been increased investigations into the effects of captive environments on behavior. Simultaneously, zoological gardens have undergone a revolution in philosophy and design, resulting in a proliferation of “naturalistic” habitats. Complex environments such as these have been found to affect the behavior of captive animals favorably, including increasing reproductive and rearing success, encouraging the expression of species-typical behavior patterns, and decreasing abnormal behaviors. In June 1988, Zoo Atlanta completed four naturalistic habitats for western lowland gorillas (Gorilla gorilla gorilla). These new habitats afforded a unique opportunity to study the adaptation of lowland gorillas to novel, naturalistic habitats. During the first year of habitation, a total of 451 hours of data were collected on 11 gorillas housed in three harem groups. Focal animal sampling with a behavioral change scoring system was used to obtain information on behavior, substrate, environmental components utilized, and location in sun or shade. Instantaneous scans at 15 minute intervals provided information on location and behavior of all individuals. Adaptation to the environments was assessed by using the indices of: time spent manipulating objects across the course of the study, the percent of the habitats utilized, and the dispersal of individual animals over the habitats. Trends in these behaviors indicated that exploration of the environments significantly decreased, but that this decline in exploration took over six months to occur. Several interpretations of these findings are presented including the unfamiliarity of these naturalistic habitats to these subjects.     

Orthogonal Invariant Sets of the Diffusion Tensor and the Development of a Curvilinear Set Suitable for Low-Anisotropy Tissues

We develop a curvilinear invariant set of the diffusion tensor which may be applied to Diffusion Tensor Imaging measurements on tissues and porous media. This new set is an alternative to the more common invariants such as fractional anisotropy and the diffusion mode. The alternative invariant set possesses a different structure to the other known invariant sets; the second and third members of the curvilinear set measure the degree of orthotropy and oblateness/prolateness, respectively. The proposed advantage of these invariants is that they may work well in situations of low diffusion anisotropy and isotropy, as is often observed in tissues such as cartilage. We also explore the other orthogonal invariant sets in terms of their geometry in relation to eigenvalue space; a cylindrical set, a spherical set (including fractional anisotropy and the mode), and a log-Euclidean set. These three sets have a common structure. The first invariant measures the magnitude of the diffusion, the second and third invariants capture aspects of the anisotropy; the magnitude of the anisotropy and the shape of the diffusion ellipsoid (the manner in which the anisotropy is realised). We also show a simple method to prove the orthogonality of the invariants within a set.     

Kinetochore fiber formation in animal somatic cells: dueling mechanisms come to a draw

The attachment to and movement of a chromosome on the mitotic spindle are mediated by the formation of a bundle of microtubules (MTs) that tethers the kinetochore on the chromosome to a spindle pole. The origin of these “kinetochore fibers” (K fibers) has been investigated for over 125 years. As noted in 1944 by Schrader [Mitosis, Columbia University Press, New York, 110 pp.], there are three possible ways to form a K fiber: (a) it grows from the pole until it contacts the kinetochore, (b) it grows directly from the kinetochore, or (c) it forms as a result of an interaction between the pole and the chromosome. Since Schrader's time, it has been firmly established that K fibers in centrosome-containing animal somatic cells form as kinetochores capture MTs growing from the spindle pole (route a). It is now similarly clear that in cells lacking centrosomes, including higher plants and many animal oocytes, K fibers “self-assemble” from MTs generated by the chromosomes (route b). Can animal somatic cells form K fibers in the absence of centrosomes by the “self-assembly” pathway? In 2000, the answer to this question was shown to be a resounding “yes.” With this result, the next question became whether the presence of a centrosome normally suppresses K fiber self-assembly or if this route works concurrently with centrosome-mediated K-fiber formation. This question, too, has recently been answered: observations on untreated live animal cells expressing green fluorescent protein-tagged tubulin clearly show that kinetochores can nucleate the formation of their associated MTs in a unique manner in the presence of functional centrosomes. The concurrent operation of these two “dueling” routes for forming K fibers in animal cells helps explain why the attachment of kinetochores and the maturation of K fibers occur as quickly as they do on all chromosomes within a cell.     

Estimating resource selection with count data

Resource selection functions (RSFs) are typically estimated by comparing covariates at a discrete set of “used” locations to those from an “available” set of locations. This RSF approach treats the response as binary and does not account for intensity of use among habitat units where locations were recorded. Advances in global positioning system (GPS) technology allow animal location data to be collected at fine spatiotemporal scales and have increased the size and correlation of data used in RSF analyses. We suggest that a more contemporary approach to analyzing such data is to model intensity of use, which can be estimated for one or more animals by relating the relative frequency of locations in a set of sampling units to the habitat characteristics of those units with count‐based regression and, in particular, negative binomial (NB) regression. We demonstrate this NB RSF approach with location data collected from 10 GPS‐collared Rocky Mountain elk (Cervus elaphus) in the Starkey Experimental Forest and Range enclosure. We discuss modeling assumptions and show how RSF estimation with NB regression can easily accommodate contemporary research needs, including: analysis of large GPS data sets, computational ease, accounting for among‐animal variation, and interpretation of model covariates. We recommend the NB approach because of its conceptual and computational simplicity, and the fact that estimates of intensity of use are unbiased in the face of temporally correlated animal location data.     

Kinematics of metachronous walking. III. Invariants]

The concept of a kinematic space for a locomotor system is introduced and regime of locomotion is defined as a continued one-dimensional manifold of this space. The problem of describing of locomotion is set (settled) by kinematic invariants. It is shown that metachrony of such millipedes as Scolopendra and Julus can be considered as a special case of some "relativity principle", on the basis of which the expression of metachrony invariant has come out. The attempt is made to use this principle for the determination of step's invariants of each individual leg too.     

Levels or Domains of Life?

In the case of living beings – the very concept of “level” of organization becomes obscure: it suggests a value-based assessment, assigning notions like “lower” and “higher” with rather vague criteria for constructing the ladder of perfection, complexity, importance, etc. We prefer therefore the term “domain”, entities ranking equal. Domains may represent natural entities as well as purely human constructs developed in order to gain understanding of some facets of living things; living, evolved beings (e.g. viviparous animals, eukaryotic cells, etc.) as well as those abstract constructs, such as genotype and ‘niche’ which have been developed in the search for better understanding of such living things. Delimitation of such domains is sometimes a question of the dexterity of the researcher, and sometimes draws from the tradition in a given field. Such domains are not completely (canonically) translatable to each other. Rather, they interact by a process that we call here reciprocal formation. Life (including the biosphere and human cultures which are emergent within the frame of the biosphere) is unique among multi-domain systems. In contrast to purely physical systems, life is a semiotic system driven by the historical experience of lineages, interpreted and re-interpreted by the incessant turnover of both individuals and their communities. This paper provides cases of domain interrelations, and addresses two questions: (1) How do new qualities of inter-domain interaction emerge historically? (2) How do new domains (ways of understanding the world) emerge in evolution. Two approaches, physical and biosemiotic, are discussed as we seek to get a better understanding of the overarching tasks.     

An algebraic-combinatorial model for the identification and mapping of biochemical pathways

We develop the mathematical machinery for the construction of an algebraic-combinatorial model using Petri nets to construct an oriented matroid representation of biochemical pathways. For demonstration purposes, we use a model metabolic pathway example from the literature to derive a general biochemical reaction network model. The biomolecular networks define a connectivity matrix that identifies a linear representation of a Petri net. The sub-circuits that span a reaction network are subject to flux conservation laws. The conservation laws correspond to algebraic-combinatorial dual invariants, that are called S-(state) and T-(transition) invariants. Each invariant has an associated minimum support. We show that every minimum support of a Petri net invariant defines a unique signed sub-circuit representation. We prove that the family of signed sub-circuits has an implicit order that defines an oriented matroid. The oriented matroid is then used to identify the feasible sub-circuit pathways that span the biochemical network as the positive cycles in a hyper-digraph.     

Principles of organization of polistinae (Hymenoptera,Vespidae) population

The paper describes some invariant relations of the Polistinae population structure, including resistance to abiotic and biotic factors that occurs against the background of the hierarchy of biological systems and increasing autonomy of their functioning. A decrease in the dependence on the hostile environment is shown to be due to the activity of foundresses and workers adjusting to external rhythms, developing specialized responses to predators and parasites (predictable external noise of biotic nature), and creating new information. The population organization of Polistinae wasps is considered in the framework of Anokhin’s theory of functional systems and systemogenesis. There are specific processes in the population that unite individual colonies and their reproduction; they are accompanied by the formation of an advanced feedback and functional systems. Systemic processes can be simultaneously regarded as “adaptation” (reflecting the organization of environmental elements) and as “adaptiveness” (reflecting the organization of the activity of intra-colony processes and the organization of reproduction). The organization of the colony activity and reproduction in functional systems reflects the future survival rather than the preceding phenomena and events. The behavior of individuals in a colony is determined not only by the effects of abiotic and biotic factors (via transformation of cues into behavioral programs), but also by previous adaptations (stored in the “memory” as images of still absent events). General progress, limited or partial progress, and narrow specialization in the organization of polistine colonies and populations are considered using the examples of morphofunctional, environmental, energy and information criteria. The emphasis on invariant relations makes it possible to more fully describe biological systems in terms of such general categories as isomorphism, homeostasis or self-organization, and also enables us to use more effectively the theory of general functional systems in studying social insects.     

Dimensional Analysis Using Toric Ideals: Primitive Invariants

Classical dimensional analysis in its original form starts by expressing the units for derived quantities, such as force, in terms of power products of basic units etc. This suggests the use of toric ideal theory from algebraic geometry. Within this the Graver basis provides a unique primitive basis in a well-defined sense, which typically has more terms than the standard Buckingham approach. Some textbook examples are revisited and the full set of primitive invariants found. First, a worked example based on convection is introduced to recall the Buckingham method, but using computer algebra to obtain an integer matrix from the initial integer matrix holding the exponents for the derived quantities. The matrix defines the dimensionless variables. But, rather than this integer linear algebra approach it is shown how, by staying with the power product representation, the full set of invariants (dimensionless groups) is obtained directly from the toric ideal defined by . One candidate for the set of invariants is a simple basis of the toric ideal. This, although larger than the rank of , is typically not unique. However, the alternative Graver basis is unique and defines a maximal set of invariants, which are primitive in a simple sense. In addition to the running example four examples are taken from: a windmill, convection, electrodynamics and the hydrogen atom. The method reveals some named invariants. A selection of computer algebra packages is used to show the considerable ease with which both a simple basis and a Graver basis can be found.     

Trivaline Molecular Complexes with Trinucleotides Form in Solution the Extended,about 1000 Å in Length Structures

Abstract

The fluorescence, flow linear dichroism and electron microscopy (EM) have shown the trivaline ability to interact in solution with certain molecules of trinucleotides. This interaction results in formation of extended structures up to several. thousand angstroms in length. Such structures were observed for trivaline complexes with homopurine, homopyrimidine or random sequences of deoxyribo- and ribonucleotides, independently of the presence or absence of the terminal 5′-phosphate residue. A model of such a structural organization is proposed. An elementary structural unit consists of a trivaline β-dimer and adsorbed trinucleotide. So, “dimeric” complex is formed. Two such “dimeric” complexes combine with each other by means of peptide-peptide contacts (as with β-sandwich). So, “tetrameric” complex is formed It has a dyad axis. Two such structural units combine with each other by means of Hoogsteen's hydrogen bonds. So, “octamreic” complex is formed. It has three mutually perpendicular dyad axes. The “octameric” complexes appear to be able to combine with each other by means of stacking interactions, and to form the regular organized aggregates consisting of many dozens of elementary units. So, “stacking” structure is formed. The “octameric” complex is the symmetry translational unit of such a stucture. The spatial position of the bases in all these structures is additionally fixed by the nucleo-peptide interactions. These aggregates have the appearance of extended structures on electron micrographs.     

The dietary patterns are a modifying risk factor for breast cancer: An ecological study

A comparative study of dietary patterns (DPs) with breast cancer (BC) incidence in different countries has been performed. It was established that in the countries with a high incidence of BC (76 per 100 000 people) the levels of consumption of the “nutrients of animal foods,” “fruits and beverages,” and “alcoholic drinks” are 1.5–2 times higher and that of “cereals and vegetables” is 1.5 times lower than in the countries with a low incidence of BC (35 per 100 000). In Mediterranean countries, where incidence of BC is 51 per 100 000, the levels of consumption of “animal foods” is two times lower than the levels of consumption of “cereals and vegetables.” A method of assessing the impact of DPs on the incidence of BC has been proposed.     

Male–male relationships in chimpanzees and the evolution of human pair bonds

The evolution of monogamy has been a central question in biological anthropology. An important avenue of research has been comparisons across “socially monogamous” mammals, but such comparisons are inappropriate for understanding human behavior because humans are not “pair living” and are only sometimes “monogamous.” It is the “pair bond” between reproductive partners that is characteristic of humans and has been considered unique to our lineage. I argue that pair bonds have been overlooked in one of our closest living relatives, chimpanzees. These pair bonds are not between mates but between male “friends” who exhibit enduring and emotional social bonds. The presence of such bonds in male–male chimpanzees raises the possibility that pair bonds emerged earlier in our evolutionary history. I suggest pair bonds first arose as “friendships” and only later, in the human lineage, were present between mates. The mechanisms for these bonds were co-opted for male-female bonds in humans.     

Orchids,bilateral symmetry and insect perception

The basic characteristics of orchids, possessing the greatest number of complex floral images of any Angiosperm family, are reviewed. Bilateral symmetry (zygomorphy) is shown by use of information theory techniques to give much greater possibilities for the transmission of visually mediated information than radial symmetry. The difference in information content is further enhanced by motion. The analysis is offered as evidence that the evolution of diversity in complex images, if effected by the unique behavioral specificity of pollinators known as “flower constancy”, is most economically explained by hypothesizing recognition and storage of the total image (“gestalt”) in the agents of natural selection.