Principles Of Heredity Research Articles

Bayesian Analysis of Two-Level Fractional Factorial Experiments with Non-Normal Responses

An intractable issue on screening experiments is to identify significant effects and to select the best model when the number of factors is large, especially for fractional factorial experiments with non-normal responses. In such cases, a three-stage Bayesian approach based on generalized linear models (GLMs) is proposed to identify which effects should be included in the target model where the principles of effect sparsity, hierarchy, and heredity are successfully considered. Three simulation experiments with non-normal responses which follow Poisson, binomial, and gamma distributions are presented to illustrate the performance of the proposed approach.

The Comparison of Morphological and Molecular Characters Inheritance in Family Groups of Rat Snakes of Elaphe Genus (Serpentes: Colubridae)

The estimating of interspecific hybrids in nature is frequently difficult. Incomplete knowledge of pedigrees in natural populations limits the investigation of hybrids. Snakes breeding in captivity provide a model system for dissolving such evolutionary problem. In present investigation were studied principles of heredity of morphological and molecular characters in rat snakes ( Elaphe genus, Colubridae family). We found that in interspecific hybrids of rat snakes the number of subcaudal scales has the average meaning between the values in parental individuals. Coloration is inherited independently of the pattern of snakes. There are at least four independent characters: background coloration, type of pattern, frequency of elements in color pattern, color of bands or spots. Molecular RAPD-DNA–markers have paternal inheritance. There is inheritance of the complex of paternal RAPD fragments that could show the possibility of linkage between these specific markers. This study found the opportunity to determine the hybrid origin of rat snakes in natural populations with application of the complex analysis of morphological characters which are mostly similar with maternal species, and molecular characters which comes from the paternal species.

Comparison of Model Selection Method Using Data from Classical Designed Experiment

Model selection procedures play important role in many researches especially quantitative research. . In several area of sciences, the analysis and model selection of experiments are often used and often contains two fundamental goals associated with the experimental response of interest which are to determine the best model. The way to address these goals is to implement a model selection procedure. Then, the objectives of this research are to determine whether or not the final models selected are in agreement or differ substantially across the three approaches to model selection: using Akaike’s Information Criterion, using a p-value criterion, and using a stepwise procedure.. Generally, results from these three models are usually compare to each other. All selected models are based on the heredity principle to design the possible model for each design. The actual data from literature, consisting of the 2x3 and 32 and 3x4 factorial designs are used to determine the final model. The results show that the P-Value WH and Stepwise methods give the highest percentage of matched model.

Teaching Principles of Heredity to High School Students with Moderate and Severe Disabilities

This investigation focused on the systematic instruction of a science skill from the core content standards in accordance with the Kentucky Alternate Assessment for students with moderate and severe disabilities (MSD). Specifically, this study examined the effectiveness of using a constant time delay procedure with multiple exemplars in teaching the principles of heredity (i.e., transmission of genetic information) to high school students with MSD. In addition, the study assessed whether or not students with MSD could draw conclusions based on meaningful related nontargeted information presented in the consequence of instructional trials during the science lesson and generalize both the target and nontargeted information to novel exemplars. The results of the multiple probe design replicated across five students with MSD show that the procedures were effective.

Should “Heredity” and “Inheritance” Be Biological Terms? William Bateson's Change of Mind as a Historical and Philosophical Problem

In 1894, William Bateson objected to the terms “heredity” and “inheritance” in biology, on grounds of contamination with misleading notions from the everyday world. Yet after the rediscovery of Mendel's work in the spring of 1900, Bateson promoted that work as disclosing the “principles of heredity.” For historians of science, Bateson's change of mind provides a new angle on these terms at a crucial moment in their history. For philosophers of science, the case can serve as a reminder of the potential of Putnam's hypothesis of a division of linguistic labor for analyzing the semantic lives of scientific kind terms.

A Bayesian Analysis of Unreplicated Two-Level Factorials Using Effects Sparsity, Hierarchy, and Heredity

ABSTRACT This article proposes a Bayesian procedure to calculate posterior probabilities of active effects for unreplicated two-level factorials. The results from a literature survey are used to specify individual prior probabilities for the activity of effects and the posterior probabilities are then calculated in a three-step procedure where the principles of effects sparsity, hierarchy, and heredity are successively considered. We illustrate our approach by reanalyzing experiments found in the literature.

Genotype-Phenotype Correlation in Wilson Disease

Genotype-Phenotype Correlation in Wilson Disease

How different is Africa? A comment on Masanjala and Papageorgiou

Masanjala and Papageorgiou (Rough and lonely road to prosperity: a reexamination of the sources of growth in Africa using Bayesian model averaging, Journal of Applied Econometrics 2008; 23(5):671-682) use Bayesian model averaging to evaluate the existence of parameter heterogeneity between African and non-African countries in the framework of cross-country growth regressions. We show that their results are not robust to the use of a prior over the model space that respects the strong heredity principle put forward by Chipman for models including interaction terms.

Lawrence B. Slobodkin (1928–2009): Integrating Theory, Models, and Experiments in Ecology

Lawrence B. Slobodkin (1928–2009): Integrating Theory, Models, and Experiments in Ecology

Structured variable selection and estimation

In linear regression problems with related predictors, it is desirable to do variable selection and estimation by maintaining the hierarchical or structural relationships among predictors. In this paper we propose non-negative garrote methods that can naturally incorporate such relationships defined through effect heredity principles or marginality principles. We show that the methods are very easy to compute and enjoy nice theoretical properties. We also show that the methods can be easily extended to deal with more general regression problems such as generalized linear models. Simulations and real examples are used to illustrate the merits of the proposed methods.

From Eugenics to Lysenkoism: The Evolution of Stanisław Skowron

This article describes the relationship between Polish geneticist Stanisław Skowron's views on eugenics during the interwar period, his experiences in Nazi concentration camps during World War II, and his response to Trofim D. Lysenko's ban on genetic research in Soviet-allied states after 1948. Skowron was educated at the Jagiellonian University in Krakow and received funding from the Rockefeller Foundation to study in the United States, Italy, Denmark, and Great Britain from 1924 to 1926. His exposure to research being conducted outside of Poland made him an important figure in Polish genetics. During this time Skowron also began to believe that an understanding of biological principles of heredity could play an important role in improving Polish society and became a supporter of eugenics. In 1939 he was arrested along with other faculty members at the Jagiellonian and sent to Sachsenhausen and Dachau. In 1947 he published the first book updating Polish biologists on recent developments in genetics; however, after learning of the outcome of the 1948 session of the Lenin All-Union Academy of Agricultural Sciences in Moscow, Skowron emerged as on of the most vocal advocates for Michurinism. I argue that Skowron's conversion to Lysenkoism was motivated by more than fear or opportunism, and is better understood as the product of his need to rationalize his own support for a theory he could not possibly have believed was correct.

Mendel's Search for True-Breeding Hybrids

It has been widely believed that Gregor Mendel’s experiments with peas (genus Pisum) were designed to discover the basic principles of heredity (genetics). Those more familiar with the history of genetics know that his work with peas sought to explain the laws governing the origin and development of hybrids (Hartl and Orel 1992, p. 245; Monaghan and Corcos 1985, p. 49–50; Stern and Sherwood 1966, p. 2). His subsequent work with hawkweeds (genus Hieracium) was an attempt to find an explanation for the apparent constancy of some hybrid forms in this and other species (Orel 1984, p. 63). One of his main motives was to see if hybrids between different varieties of a species or between different species could breed true, that is, hybrids produce only more hybrids. In those days, the difference between varieties and species was not always well defined. True-breeding hybrids behaved like new species. Mendel published 2 botanical papers in German: his Pisum paper was published in 1866, the one on Hieracium was published in 1870. Both of these papers and his letters to his friend and advisor Carl Nageli have been translated into English in Stern and Sherwood (1966). In the text of the present paper, numbers following Mendel’s name refer to pages in the Stern and Sherwood book. A complete English translation of Mendel’s 1866 paper by William Bateson can be found on the internet (see Mendelweb). The concept of reproductive isolation as a hallmark of a biological species did not become popular until well into the 20th century (Mayr 1982, p. 270–275). Mendel found that his intervarietal pea hybrids were phenotypically identical but did not breed true when self fertilized, segregating pure breeding parental types (homozygotes) as well as hybrids (heterozygotes) in the now familiar ratio 1:2:1. [N.B. Modern terms are used here and elsewhere in this paper instead of Mendel’s terms that have become passe.] Mendel was aware that Charles Darwin’s book On the Origin of Species was published in 1859 before he began his pea experiments in 1862. Darwin did not really shed much light on how new species originate by natural selection. And the role of hybridization in that process was begging for experimental insights, especially for how an ancestral species can split into 2 or more daughter species that coexist in time (horizontal evolution or speciation, cladogenesis). After Mendel found some principles of hybrid behavior in his pea varieties, he hoped to find the same regularities operative in other plant species. In his famous 1866 paper (published in The Proceedings of the Brunn Natural Science Society), Mendel also reported his interspecific hybridizations with another species of plant (beans, genus Phaseolus). He hybridized bean species differing in plant height and shape of ripe pods and found that they followed the same laws of development as Pisum. The colors of both flowers and unripe pods, however, seemed to be more complex. Crosses between plants with white flowers and plants with crimson blossoms produced hybrids with flowers less intensely crimson than the parental variety. The progeny of hybrids had flowers varying from crimson to pale violet and white. The unripe seed pods also had various shades of coloring from dark green to yellow. Because white flowered plants seemed to appear in about 1/16 of the progeny of hybrids (F2), Mendel proposed that there were 2 color elements (genes) A1 and A2 that together in homozygotes contributed to crimson color. Plants with the recessive alleles a1 and a2, when homozygous together, produced white flowers. Other gene combinations contributed to the range of colors between crimson and violet. Mendel seems to be the first to conceive of multiple factors for a single character.

Structured variable selection in support vector machines

When applying the support vector machine (SVM) to high-dimensional classification problems, we often impose a sparse structure in the SVM to eliminate the influences of the irrelevant predictors. The lasso and other variable selection techniques have been successfully used in the SVM to perform automatic variable selection. In some problems, there is a natural hierarchical structure among the variables. Thus, in order to have an interpretable SVM classifier, it is important to respect the heredity principle when enforcing the sparsity in the SVM. Many variable selection methods, however, do not respect the heredity principle. In this paper we enforce both sparsity and the heredity principle in the SVM by using the so-called structured variable selection (SVS) framework originally proposed in [20]. We minimize the empirical hinge loss under a set of linear inequality constraints and a lasso-type penalty. The solution always obeys the desired heredity principle and enjoys sparsity. The new SVM classifier can be efficiently fitted, because the optimization problem is a linear program. Another contribution of this work is to present a nonparametric extension of the SVS framework, and we propose nonparametric heredity SVMs. Simulated and real data are used to illustrate the merits of the proposed method.

An Efficient Variable Selection Approach for Analyzing Designed Experiments

The analysis of experiments in which numerous potential variables are examined is driven by the principles of effect sparsity, effect hierarchy, and effect heredity. We propose an efficient variable selection strategy to specifically address the unique challenges faced by such analysis. The proposed methods are natural extensions of the LARS general-purpose variable selection algorithm. They can be computed very rapidly and can find sparse models that better satisfy the goals of experiments. Simulations and real examples are used to illustrate the wide applicability of the proposed methods.

Ethical Issues in Genetics Related to Hearing Loss

Ethical Issues in Genetics Related to Hearing Loss

GenRel—a computer model for prediction of mining equipment failures based on genetic algorithms (GAs)

This paper discusses ongoing research to formulate, develop and test a reliability assessment model (GenRel) based on genetic algorithms (GAs). GAs are powerful and broadly applicable stochastic search techniques based on the principles of natural selection, heredity and genetics. The reason for selecting GAs is the fact that the reliability of mining equipment changes over time due to its dependence upon several covariates/factors (e.g. equipment age, operating environment, number and quality of repairs). These factors combine to create a complex impact on a piece of equipment's reliability function. This impact encapsulates and inherits to some degree the individual characteristics of the factors as they evolve over time. 1 BestFit, Palisade Decision Tools (http://www.palisade.com/html/bestfit.asp) Theoretical probability distributions are commonly used to fit equipment failure data. GenRel uses the exponential probability distribution as its engine to generate predictive patterns based upon historical failure data. Overall, this paper suggests a methodology for applying GAs for reliability assessment of mining equipment. An example is given to demonstrate the effectiveness of using GAs in reliability studies. The research discussed in this paper was carried out by the Laurentian University Mining Automation Laboratory (LUMAL).

Horticulture, Horticultural Science, and 100 Years of ASHS

subject to change. The process is cumulative and science is alive only when it grows. When any society claims to know the complete truth such that further question is heresy, science dies. Horticultural knowledge accumulation has always been in a state of tension between the mundane empiricism of the gardening arts discovered by generations of growers in contrast to information generated by scientists, often academics, sometimes indifferent to the uses of their discoveries and often obsessed by the irrelevant. In the 1900s, horticultural science was considered an oxymoron. One hundred years later, we are a Society that rejects this taunt and have demonstrated that horticultural science is a truly humanistic plant science, concerned with all information relevant to the interaction of humans and the plants that serve them. Our goal is the betterment of humankind. Throughout this paper, we will discuss a number of significant advancements in science that have been made by horticulturists or by plant scientists using horticultural plants and later applied to agriculture and other fields. For example, Gregor Mendel s groundbreaking discovery of the principles of heredity in a monastery garden led to what might be considered the most important scientific revolution in modern times: the flow of genetic information from generation to generation. Photoperiodic effects on plant growth, first reported by W.W. Garner and H.A. Allard on a number of horticultural crops in 1920, set the stage for understanding the relationship between crop production, light, and temperature. Fieldlevel photosynthetic rates were first measured by A.J. Heinicke and N.F. Childers in the 1930s using an apple-tree model. These concepts were later applied to many agricultural and ecological situations to evaluate carbon dioxide fixation and photosynthetic rates. L.R. Jones and J.C. Walker developed the concept of genetic control of plant disease resistance in their work with cabbage, leading to widespread efforts to use breeding techniques to obtain host plant resistance. H.A. Jones and A.F. Clarke discovered the cytoplasmic-genic system of hybrid seed production in onion, which revolutionized in F1 hybrid crop development. Particleacceleration technology, in which DNA is blasted into plant tissue in order to produce transgenic plant cells, was invented by the horticulturist John Sanford in 1987. Few scientificfields have captured the imagination as has horticulture, perhaps because of its centrality to the development of human culture. Biblical and other religious texts are filled with horticultural metaphors, such as the placement of Adam and Eve in the Garden of Eden near the Tree of Knowledge, the olive branch as a symbol for peace, and Noah s cultivation of a vineyard as his first act after the flood. We speak of a renaissance in events as a flowering and the end of innocence as a deflowering. The education of our youth involves, appropriately, a garden of children, or kindergarten. We cultivate relationships and speak of our hard work bearing fruit, certain people as late bloomers, or others as wall flowers, or worse, gone-to-seed. Moving to a different location marks us as transplants, but staying put means we are putting down roots. Many of our best thinkers have communicated complex concepts with such horticultural metaphors. Charles Darwin used the branching tree in describing the process of evolution in nature. In his vision, the branches represent phylogenetic patterns of lineage, and the dropped branches and twigs represent extinction. This tree metaphor for what Darwin called descent with modification has completely permeated biological science and popular culture. Horticulture and its practices are woven into our consciousness and have become part of the fabric of our language and thought.

Children’s understanding of inherited resemblance: The case of two parents

Four-, 6-, and 10-year-old children were tested in a forced-choice procedure about their beliefs on the inheritance of physical characteristics. They were presented with pictures of two biological parents, and then asked to select the most likely descendant out of three alternatives: a father look-alike, a mother look-alike, and an alternative representing the combined influence of both parents. In several question pairs, additional information was given about the parent–child relationship that was clearly irrelevant to the principles of heredity to examine the extent to which domain confusions were likely to occur. The majority of the 10-year-olds consistently preferred the alternative in which the combined influence of both parents was shown and domain confusions hardly ever occurred. Four- and 6-year-olds, in contrast, were still influenced by information from alien domains, although even their reasoning about inheritance seemed to be theory-like. Overall, the results suggest that with age, children develop a more restricted and better-defined conception of the principles of heredity, in which the combined influence of both parents is acknowledged.

William Bateson: a biologist ahead of his time.

William Bateson coined the term genetics and, more than anybody else, championed the principles of heredity discovered by Gregor Mendel. Nevertheless, his reputation is soured by the positions he took about the discontinuities in inheritance that might precede formation of a new species and by his reluctance to accept, in its full-blooded form, the view of chromosomes as the controllers of individual development. Growing evidence suggests that both of these positions have been vindicated. New species are now thought to arise as the result of genetic interactions, chromosomal rearrangements, or both, that render hybrids less viable or sterile. Chromosomes are the sites of genes but genes move between chromosomes much more readily than had been previously believed and chromosomes are not causal in individual development. Development, like speciation, requires an understanding of the interactions between genes and the interplay between the individual and its environment.

Genetic algorithms for reliability assessment of mining equipment

Discusses an ongoing research work which attempts to formulate, develop and test mining equipment reliability assessment models based on genetic algorithms. Genetic algorithms are powerful and broadly applicable stochastic search techniques based on the principles of natural selection, heredity and genetics. The reason for selecting genetic algorithms is the fact that the reliability of mining equipment changes over time due to its dependence upon several covariates/factors (e.g. equipment age, the operating environment, number and quality of repairs). These factors combine to create a complex impact on an equipment’s reliability function. Gives an example of the application of genetic algorithms to capture the impact of these factors on time between failures of a piece of mining equipment.