Cogprints: No conditions. Results ordered -Date, Title.

English Surnames: DNA, plural origins and emigration

2014-08-24T21:04:39Z

Since the turn of the millennium, DNA testing has helped with establishing the sizes of biological descent families within surnames. Some surnames have a dominant family: their remaining populations can be ascribed either to NPEs (non paternity events)or to smaller separate-origin families. Previously, there was no direct evidence as to how large each male-line family could grow within a surname, considering that real-life plural-origin surnames could contain a few or many separate-origin families of various sizes. However, DNA testing is providing evidence to help indicate in particular the size of the largest male-line medieval descent family in a surname. We here perform statistical analyses of some relevant DNA results. This allows us to compare the DNA results with some predicted findings from our computer simulations.

Getting the most from a surname study: semantics, DNA and computer modelling (third edition)

2014-02-25T12:50:26Z

We here address such questions as: what does a surname mean;is it single origin;and,why do some surnames grow abnormally large? Though most surnames are rare, most people have populous surnames. In this article, we consider in particular the evidence that some frequent surnames could be completely or nearly single origin; this would imply that the whole surname relates to a single family that has grown abnormally large. Some populous surnames have a geographical distribution that might be thought to be consistent with a single origin. As yet, such supposition generally lacks support from adequate DNA evidence. Guided by the empirical evidence, our computer simulations identify various possible reasons for a surname family’s unusually prolific growth. In particular, chance is a main factor. Also, overall population growth conditions vary widely between different counties. This can go a long way towards explaining the large population of Plant, which is apparently the second largest single-family contender in the favourable growing conditions of Staffordshire. This surname shows relatively little evidence of a significant living population that stems from origins other than that of its dominant family. The initial semblance that Sykes could be the second largest single-family contender in West Yorkshire is more open to debate, since there might be more substantial other origins. To explain its dominant family, it seems necessary to invoke some exceptional characteristics such as more favourable growth factors for its homeland than those pertaining in the available data for the whole county. Also, for the computer modelling, we consider the effects of additional factors such as polygyny, resilience to plague,Y-chromosome linked fecundity, or an early start to an hereditary surname. Such factors can be beneficial in seeing a family through initial precarious times, sustaining its survival through to a small but real chance of subsequent proliferation in more favourable Industrial Age growth conditions.

Getting the most from a surname study: semantics, DNA and computer modelling

2012-11-09T19:41:09Z

We here address such questions as: what does a surname mean; is it single origin; and, why do some surnames grow abnormally large? Though most surnames are rare, most people have populous surnames. In 1881 for example, 90% of the population of England and Wales had the most populous 4% of surnames; and, in 1998, 80% had the 1% most populous. In this paper, we consider the evidence that some frequent surnames could be single source; this would imply that a single family has grown abnormally large. For some populous surnames, they have a geographical distribution that might be thought to be consistent with a single origin though, as yet, such supposition generally lacks support from adequate DNA evidence. With the onset of DNA testing, some scientists are becoming more active in surname studies and they might be more reluctant than some traditionalists to infer too much from categories of surname meaning. Instead, they are likely to maintain that statistical analyses of the data should be properly performed. For example, King and Jobling (2009) considered forty English surnames and found no statistically significant correlation between the supposed semantic category of a surname and its degree of DNA matching into single male-line families. As a specific example that we here describe in some detail, little can be deduced about the inter-relatedness of those called Plant from the assumption of a semantic category, such as by arguing that it is locative and hence single-origin, or occupational and hence multi-origin. By comparison, more surely, we discuss the DNA evidence that this name’s main family grew unusually. Though motivated initially by the evidence of unusual growth for Plant, we extend our deliberations more generally to other surnames. Guided by the empirical evidence, our computer simulations identify various reasons for a surname family’s prolific growth. In particular, chance is a main factor, along with favourable conditions during the Industrial Age when overall population growth took off, evidently earlier in some regions than in others. Also, the modelling suggests that some additional factor such as polygyny or resilience to plague or favourable economic circumstance, after an early start to a hereditary surname, is beneficial in seeing a family through initial precarious times, sustaining its survival through to a small but real chance of subsequent proliferation in favourable Industrial Age conditions.

Quantum Genetics and Quantum Automata Models of Quantum-Molecular Selection Processes Involved in the Evolution of Organisms and Species

2012-04-25T12:30:10Z

Previous theoretical or general approaches (Rosen, 1960; Shcherbik and Buchatsky, 2007) to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 (Baianu,1971a, b) , and further developed in several recent articles (Baianu, 1977, 1983, 1987, 2004, 2011).The representation of genomes and Interactome networks in categories of many-valued logic LMn –algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata. Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an internal re-structuring of major submodules of the genome and Interactome networks related to cell cycling and cell growth. Contrary to the commonly held view of `standard’ Darwinist models of evolution, the evolution of organisms and species occurs through coupled multi-molecular transformations induced not only by the environment but actually realized through internal re-organizations of genome and interactome networks. The biological, evolutionary processes involve certain epigenetic transformations that are responsible for phenotypic expression of the genome and Interactome transformations initiated at the quantum-molecular level. It can thus be said that only quantum genetics can provide correct explanations of evolutionary processes that are initiated at the quantum—multi-molecular levels and propagate to the higher levels of organismal and species evolution. Biological evolution should be therefore regarded as a multi-scale process which is initiated by underlying quantum (coupled) multi-molecular transformations of the genomic and interactomic networks, followed by specific phenotypic transformations at the level of organism and the variable biogroupoids associated with the evolution of species which are essential to the survival of the species. The theoretical framework introduced in this article also paves the way to a Quantitative Biology approach to biological evolution at the quantum-molecular, as well as at the organismal and species levels. This is quite a substantial modification of the `established’ modern Darwinist, and also of several so-called `molecular evolution’ theories.

Complexity, Emergent Systems and Complex Biological Systems: Complex Systems Theory and Biodynamics. [Edited book by I.C. Baianu, with listed contributors (2011)]

2011-12-16T00:04:45Z

An overview is presented of System dynamics, the study of the behaviour of complex systems, Dynamical system in mathematics Dynamic programming in computer science and control theory, Complex systems biology, Neurodynamics and Psychodynamics.

Natural Variation and Neuromechanical Systems

2009-11-14T11:34:42Z

Natural variation plays an important but subtle and often ignored role in neuromechanical systems. This is especially important when designing for living or hybrid systems which involve a biological or self-assembling component. Accounting for natural variation can be accomplished by taking a population phenomics approach to modeling and analyzing such systems. I will advocate the position that noise in neuromechanical systems is partially represented by natural variation inherent in user physiology. Furthermore, this noise can be augmentative in systems that couple physiological systems with technology. There are several tools and approaches that can be borrowed from computational biology to characterize the populations of users as they interact with the technology. In addition to transplanted approaches, the potential of natural variation can be understood as having a range of effects on both the individual's physiology and function of the living/hybrid system over time. Finally, accounting for natural variation can be put to good use in human-machine system design, as three prescriptions for exploiting variation in design are proposed.

The phenomenon of biological evolution: 19th century misconception

2009-09-07T10:17:27Z

Scientists still think that biological evolution is driven by the process named natural selection. Perhaps this 19th century notion was indeed a revolutionary idea at the time when it has been introduced. However, now it seems that natural selection hypothesis most probably is wrong. It does not explain, above all, why biological organization arise in the course of evolution. I show, on a rather abstract level of consideration, that exists another explanation why this intriguing phenomenon - life evolution - take place. Here it is argued that biological organization is solely a product of self-replication.

Evolution of ethnocentrism on undirected and directed Barabási-Albert networks

2009-05-30T15:39:57Z

Using Monte Carlo simulations, we study the evolution of contigent cooperation and ethnocentrism in the one-move game. Interactions and reproduction among computational agents are simulated on undirected and directed Barabási- Albert (BA) networks. We first replicate the Hammond-Axelrod model of in-group favoritism on a square lattice and then generalize this model on undirected and directed BA networks for both asexual and sexual reproduction cases. Our simulations demonstrate that irrespective of the mode of reproduction, ethnocentric strategy becomes common even though cooperation is individually costly and mechanisms such as reciprocity or conformity are absent. Moreover, our results indicate that the spread of favoritism toward similar others highly depends on the network topology and the associated heterogeneity of the studied population.

How Close a Bataknese One Another?: Study of Indonesian Batak’s Family Tree

2008-01-23T16:17:55Z

The paper conjectures some alternative acquisitions of mathematical models to see the Batak family tree that could enrich our understanding of the anthropological study of Bataknese people. We discuss some aspects of Bataknese Clan-group in Batak traditional social life. Since the family tree is drawn according to the genealogical patterns of degrees relative to the first Batak in northern Sumatera, the paper discusses interesting features of Malthusian growth rate. The latter discussions is about the relatedness of a clan-group of Bataknese one another as reflected in the family tree by observing the topology of the web. The conjectures for future development is also drawn.

ROLE OF FETAL THIGH CIRCUMFERENCE IN ESTIMATION OF BIRTH WEIGHT BY ULTRASOUND

2006-09-08Z

OBJECTIVE: To evaluate the accuracy and usefulness of predicting birth weight by measuring fetal thigh circumference by ultrasound. METHODS: In 110 pregnant women, fetuses without structural or chromosomal anomalies were studied prospectively and cross-sectionally. Thigh circumference (TC) was determined at the mid level of the thigh. Biparietal diameter (BPD), Head circumference (HC), Abdominal circumference (AC), and Femur length (FL) were measured using standard techniques. Fetal weights were estimated within a week prior to delivery. Statistical analysis of various ultrasound birth weight formulae in different weight categories was done and compared with each other and also with clinical methods. RESULTS: Estimated fetal birth weight using TC correlated well with actual birth weights in all categories and was superior to clinical and birth weight formulae using BPD, HC, AC and FL measurements. CONCLUSIONS: There was a good correlation between ultrasound measurement and actual postnatal measurements of thigh circumference (r2=0.89, p<0.01). Thigh circumference measurement was simple and there was better accuracy when it was combined along with BPD, HC, AC and FL measurements.

EPIDEMIOLOGY THROUGH CELLULAR AUTOMATA

2004-03-17Z

This paper performs the utilization of cellular automata computational analysis as the dynamic model of spatial epidemiology. Here, explored elementary aspects of cellular automata and its application in analyzing contagious disease, in this case avian influenza disease in Indonesia. Computational model is built and map-based simulation is performed using several simplified data of such transportation through sea in Indonesia, and its accordance with poultries in Indonesia, with initial condition of notified avian influenza infected area in Indonesia. The initial places are Pekalongan, West Java, East Java, and several regions in Sumatera. The result of simulation is showing the spreading-rate of influenza and in simple way and describing possible preventive action through isolation of infected areas as a major step of preventing pandemic.

An Anthropological Perspective on Magistrate Jelderks’ Kennewick Man Decision

2004-07-30Z

The “Kennewick Man” controversy is an extremely important case in the history of American anthropology. As anthropologists with backgrounds in American Indian studies and American archaeology, we have a particular interest in this case. In this paper we present our perspective on the Kennewick Man case as anthropologists with expertise in archaeology, Pacific Northwest precontact history, Plateau ethnology, and cultural resource law. In general we find that the August 30, 2000, decision of Magistrate John Jelderks of the United States District Court for the district of Oregon to be incorrect and without anthropological foundation. Based on an analysis of the evidence reviewed by the Department of the Interior and Magistrate Jelderks we conclude that the Department of the Interior made a reasonable decision in determining that a preponderance of the evidence supports repatriation of the Kennewick Man to the defendants.

American Indian Demographic History and Cultural Affiliation: A Discussion on Certain Limitations of the Use of mtDNA and Y chromosome Data

2004-07-30Z

Mitochondrial DNA (mtDNA) and Y chromosome studies have been used increasingly over the last 20 years by anthropological geneticists and others to reconstruct the peopling of the Americas as well as to infer American Indian cultural affiliation and demographic histories. While the promise of this method is great, there are several problems inherent in some of its current uses. These limitations are discussed concerning the following six currently accepted methods: interpretation of coalescent times as times of origin; 2) the current uses of haplogroups; 3) sample sizes; 4) use of language groups to define population groups; 5) use of contemporary American Indian reservations to infer prehistoric tribal history; and 6) a combination of these to determine American Indian population history, historic migrations, and demographic history. This paper concludes that caution must be exercised in claiming too much for the method. Instead, it is recommend that it be used in conjunction with other established sources of data such as oral history, ethnography, linguistics, and archaeology when attempting to reconstruct American Indian cultural history or in determining the cultural affiliation of groups.

Male-induced estrus synchronization in the female Siberian hamster (Phodopus sungorus sungorus)

2013-05-04T23:22:04Z

Olfactory cues play an integral role in the organization of events that mediate reproductive success. In a variety of species, priming pheromones, in particular, are important for ensuring reproductive fitness. To date, very little research has focused on how male-emitted priming pheromones, such as those that regulate the onset of puberty and estrus synchronization in females, affect the reproductive physiology of the female Siberian hamster (Phodopus sungorus sungorus). This lack of research may be due to the physiology of the Phodopus genus; vaginal cytology cannot be used as a reliable indicator of estrus or ovulation. Using a jugular cannulation technique to determine estrous stage by blood analysis of prolactin and luteinizing hormone, we sought to determine if male priming pheromones affect estrous cyclicity in the female Siberian hamster and, if so, whether the production of these priming pheromones is androgen dependent. Our results showed that females exposed to bedding from mature, intact males showed a significantly higher incidence of proestrus 3 days later than did females exposed to the bedding of mature, gonadectomized males. Therefore, we found that not only do male Siberian hamsters emit chemical signals that induce estrus synchronization, but also that this ability is likely to be androgen dependent.

Co-Evolution of Language-Size and the Critical Period

1998-03-24Z

Species evolve, very slowly, through selection of genes which give rise to phenotypes well adapted to their environments. The cultures, including the languages, of human communities evolve, much faster, maintaining at least a minimum level of adaptedness to the external, non- cultural environment. In the phylogenetic evolution of species, the transmission of information across generations is via copying of molecules, and innovation is by mutation and sexual recombination. In cultural evolution, the transmission of information across generations is by learning, and innovation is by sporadic invention or borrowing from other cultures. This much is the foundational bedrock of evolutionary theory. But things get more complicated; there can be gene-culture co-evolution. Prior to the rise of culture, the physical environment is the only force shaping biological evolution from outside the organism, and cultures themselves are clearly constrained by the evolved biological characteristics of their members. But cultures become part of the external environment, and influence the course of biological evolution. For example, altruistic cultures with developed medical knowledge reduce the cost to the individual of carrying genes disposing to certain pathologies (such as diabetes); and such genes become more widespread in the populations maintaining such cultures. Assortative mating can affect biological evolution, and particular cultures may influence the factors which are sorted for in mating. (For a careful discussion of the effects of cultural evolution on natural selection, see Cavalli-Sforza and Bodmer, 1971:774- 804). This paper examines mechanisms involved in the co-evolution of a biological trait, the critical period for language acquisition, and a property of human cultures, the size of their languages. A gene/culture interaction will be shown that can be described as a kind of symbiosis, but perhaps more aptly as an `arms race'. In this introduction, we will sketch the basic mechanics of the interaction in very broad terms; the rest of the paper will explain and justify the details. The implications of our model for second language acquisition are given toward the end of the paper.

Evolving cooperation in the non-iterated prisoner's dilemma: The importance of spatial organization

1998-06-15Z

Most work on evolving cooperation in the Prisoner's Dilemma treats the non-iterated game as an undesirable simple case that should be risen above. It has been taken as a given that populations evolving to play the non-iterated game will always converge on defection. This paper questions this assumption, and demonstrates that organizing a population spatially dramatically changes the nature of the game and allows cooperation to emerge.

Innateness and Canalization

1998-06-18Z

Cognitive scientists often employ the notion of innateness without defining it. The issue is, how is innateness defined in biology? Some critics contend that innateness is not a legitimate concept in biology. In this paper I will argue that it is. However, neither the concept of high heritability nor the concept of flat norm of reaction (two popular accounts in the biology literature) define innateness. An adequate account is found in developmental biology. I propose that innateness is best defined in terms of C. H. Waddington's concept of canalization.

Meme and Variations: A Computational Model of Cultural Evolution

1999-01-22Z

This paper describes a computational model of how ideas, or memes, evolve through the processes of variation, selection, and replication. Every iteration, each neural-network based agent in an artificial society has the opportunity to acquire a new meme, either through 1) INNOVATION, by mutating a previously-learned meme, or 2) IMITATION, by copying a meme performed by a neighbor. Imitation, mental simulation, and using past experience to bias mutation all increase the rate at which fitter memes evolve. Memes at epistatic loci converged more slowly than memes at over- or underdominant loci. The higher the ratio of innovation to imitation, the greater the meme diversity, and the higher the fitness of the fittest meme. Optimization is fastest for the society as a whole with an innovation to imitation ratio of 2:1, but diversity is comprimized.

Approach to a model of the aging phenomenon

2001-06-26Z

Numerous physiological theories of aging have been proposed; most of them approach the problem in an essentially local manner, stressing the role of a particular factor intervening at a certain level and the resulting pathological consequences. But they do not allow for a combination of the different phenomena observed in the aging process. This paper proposes a more unified and global approach to this process. It is presented in the frame of a mathematical model for complex systems with a hierarchy of internal regulation centers (CR), developed by the authors in preceding papers; the dynamics of such a system depends on a dialectics between these CRs due to their different complexity level and different timescales. Aging for an organism is described as a consequence of this dialectics, that progressively triggers a "cascade of de/resynchronizations" between the CRs, resulting from the reduction in stability of complex components (increase in turnover or acceleration of degradation) and the increase in transmission delays for functioning and repair. This temporal imbalance comes from the interplay between external stochastic disturbances and more or less predetermined sub-systems with limited capacities for repair.

Is the monkeys' world scientifically impenetrable?

1998-09-29Z

Cheney & Seyfarth (C&S) argue for a hybrid approach which 'place (empiricistic findings) tentatively within the framework of a more mentalistic approach'(p.9). The book is an important contribution to clarify the value and limits of the intentional approach in interpreting monkey behaviour, particularly C&S's excellent field work with vervets. But, unintentionally, it also demonstrates that cognitive science is more a perspective than a scientific discipline. In order to illustrate this, I shall consider the following topics: evolution of intelligence, concept formation, philosophy of science

Organismic Supercategories: I. Proposals for a General Unified Theory of Systems- Classical, Quantum, and Complex Biological Systems.

2004-10-06Z

The representation of physical and complex biological systems in terms of organismic supercategories was introduced in 1968 by Baianu and Marinescu in the attached paper which was published in the Bulletin of Mathematical Biophysics, edited by Nicolas Rashevsky. The different approaches to relational biology, developed by Rashevsky, Rosen and by Baianu et al.(1968,1969,1973,1974,1987,2004)were later discussed. The present paper is an attempt to outline an abstract unitary theory of systems. In the introduction some of the previous abstract representations of systems are discussed. Also a possible connection of abstract representations of systems with a general theory of measure is proposed. Then follow some necessary definitions and authors' proposals for an axiomatic theory of systems. Finally some concrete examples are analyzed in the light of the proposed theory. An abstract representation of biological systems from the standpoint of the theory of supercategories is presented. The relevance of such representations forG-relational biologies is suggested. In section A the basic concepts of our representation, that is class, system, supercategory and measure are introduced. Section B is concerned with the mathematical representation starting with some axioms and principles which are natural extensions of the current abstract representations in biology. Likewise, some extensions of the principle of adequate design are introduced in section C. Two theorems which present the connection between categories and supercategories are proved. Two other theorems concerning the dynamical behavior of biological and biophysical systems are derived on the basis of the previous considerations. Section D is devoted to a general study of oscillatory behavior in enzymic systems, some general quantitative relations being derived from our representation. Finally, the relevance of these results for a quantum theoretic approach to biology is discussed. http://www.springerlink.com/content/141l35843506596h/