Righteous modeling: the competence of classical population genetics

In a recent article, ??Wayward Modeling: Population Genetics and Natural Selection,?? Bruce Glymour claims that population genetics is burdened by serious predictive and explanatory inadequacies and that the theory itself is to blame. Because Glymour overlooks a variety of formal modeling techniques in population genetics, his arguments do not quite undermine a major scientific theory. However, his arguments are extremely valuable as they provide definitive proof that those who would deploy classical population genetics over natural systems must do so with careful attention to interactions between individual population members and environmental causes. Glymour??s arguments have deep implications for causation in classical population genetics.     

Speaking out about the social implications of science: the uneven legacy of H. J. Muller

H. J. Muller (1890-1967) was unusual as a scientist because he spoke out on numerous occasions about the uses and abuses of genetics in society. In this article, I follow Muller's efforts to do so and the consequences that they had on his career, his productivity as a research scientist, and his reputation. The shifting sites of Muller's work--which ranged from Columbia University to Texas, from Berlin to Moscow and Leningrad, from Madrid to Edinburgh, and from Amherst to Indiana University--made his activism unusual. Muller paid a price for his activism, and his reputation today is still marred by what most historians would consider risky judgments and reversals of position about genetics and society. My analysis is not a defense but rather an evaluation of the circumstances that led him to these positions and an analysis of the consequences of challenging society when scientists believe their science is being ignored or abused.     

Oswald T. Avery: Nbel Lureate or noble luminary?

In 1944, Oswald T. Avery and his associates reported that DNA was the chemical substance acting to genetically transform species of pneumococcal bacteria. Many believe that Avery warranted the Nobel Prize for this discovery. Avery's work is evaluated here in light of the Nobel archives, which have made public the names of those who nominated Avery for this award and the basis for each of the nominations. Based on the archival record, it seems that key biological chemists "were not convinced by Avery's claim that DNA was the basis of heredity, that no geneticists nominated Avery, and that most nominators overlooked Avery's work on DNA in favor of his work on the immunogenicity of the bacterial capsule. Three critical scientific factors that adversely affected acceptance of Avery's work were the possibility of protein contamination of DNA, the role of DNA transformation limited to a few species of bacteria, and the possibility that DNA was acting as a chemical mutagen on the true genetic substance. In addition, Avery's own idiosyncratic behavior may have unintentionally confounded acceptance of his groundbreaking discovery.     

Thirty‐five years of spatial autocorrelation analysis in population genetics: an essay in honour of Robert Sokal (1926–2012)

We could not start this review, literally from the beginning, without expressing our sadness over the passing of Professor Robert R. Sokal. We are sure, nevertheless, that the importance of his scientific achievements will ensure he is long remembered. In this modest tribute to Professor Sokal, we highlight his contributions to the field of population genetics and spatial statistical methods. Specifically, we discuss how two papers, co‐authored with Professor N. L. Oden and published in the pages of the Biological Journal of the Linnean Society in 1978, revolutionized the field of analytical population genetics. In these papers, Sokal and Oden created an elegant framework for inferring evolutionary processes (e.g. isolation‐by‐distance, demic diffusion, selection gradients, genetic drift) from the spatial autocorrelation analysis of genetic variation patterns. We also highlight the pivotal importance of Sokal's work to the development of emerging fields (e.g. landscape and conservation genetics). We hope this virtual issue containing the papers that Professor Sokal published in BJLS, and later, related papers by other researchers, will help to remember his work and maintain his legacy of spatial analysis in genetics, ecology, and evolutionary biology. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ??, ??–??.     

R.A. Fisher's contributions to genetical statistics

R. A. Fisher (1890-1962) was a professor of genetics, and many of his statistical innovations found expression in the development of methodology in statistical genetics. However, whereas his contributions in mathematical statistics are easily identified, in population genetics he shares his preeminence with Sewall Wright (1889-1988) and J. B. S. Haldane (1892-1965). This paper traces some of Fisher's major contributions to the foundations of statistical genetics, and his interactions with Wright and with Haldane which contributed to the development of the subject. With modern technology, both statistical methodology and genetic data are changing. Nonetheless much of Fisher's work remains relevant, and may even serve as a foundation for future research in the statistical analysis of DNA data. For Fisher's work reflects his view of the role of statistics in scientific inference, expressed in 1949: There is no wide or urgent demand for people who will define methods of proof in set theory in the name of improving mathematical statistics. There is a widespread and urgent demand for mathematicians who understand that branch of mathematics known as theoretical statistics, but who are capable also of recognising situations in the real world to which such mathematics is applicable. In recognising features of the real world to which his models and analyses should be applicable, Fisher laid a lasting foundation for statistical inference in genetic analyses.     

Genetic screening and genetic counseling: knowledge, attitudes, and practices in two groups of family planning professionals.

67 obstetrical and gynecological physicians and 102 professional staff members of family planning clinics (FPCs) in the Pittsburgh, Pennsylvania, area returned questionnaires relating to knowledge of basic genetic principles and attitudes towards genetic screening and genetic counseling. The best understood genetic risk was Down's syndrome in children born to mothers over 40 years of age. Nearly 90% of physicians and 85% of FPC staff knew this but only 12% of physicians and 30% of FPC staff knew it is caused by chromosomal aberration. Next best understood defect is sickle cell anemia. In overall knowledge the physicians had a mean score of 4.45 of 7 genetic questions, FPC staff, 3.32. However, FPC workers who had received in-service genetic training scored 4.42 (p less than .001). Knowledge of the 2 genetic clinics in the area and acceptance of the principles of genetic screening were associated with the individual's acceptance of sterilization as a method of birth control and acceptance of abortion if the fetus had significant risk of being born deformed. Both of these associations were at the significant level for both physicians and FPC workers. Both physicians and FPC workers who have themselves had genetic counseling or who have family members who have had such counseling show higher acceptance levels. An association was also found between acceptance and genetic educational background. About 92% of respondents who had read articles or textbooks pertaining to genetics during the preceding year approved of including genetic information as part of maternal and child health projects compared with 82% of those who had not (p less than .02). Among the physicians 36% felt it should be required, 34% voluntary, and 30% did not know; for FPC workers, 59, 27, and 14%, respectively. Protestants and Jews tended to favor required premarital screening while Catholics tended to oppose it (p less than .007). It is disconcerting that over 50% of the physicians did not know the recurrence risk of PKU and over 20% did not know the gene is the basic unit of inheritance. While it is true that over 1/2 completed basic professional education more than 20 years ago when genetics was not part of the medical school curriculums this basic knowledge needs to have been acquired during continuing medical education. In this study more than 1/3 of the FPC staff indicated they had been asked to provide genetic counseling or had referred clients. This points up the importance of such workers in a comprehensive genetic counseling service.     

James F. Crow and the art of teaching and mentoring

To honor James F. Crow on the occasion of his 95th birthday, GENETICS has commissioned a series of Perspectives and Reviews. For GENETICS to publish the honorifics is fitting, as from their birth Crow and GENETICS have been paired. Crow was scheduled to be born in January 1916, the same month that the first issue of GENETICS was scheduled to appear, and in the many years that Crow has made major contributions to the conceptual foundations of modern genetics, GENETICS has chronicled his and other major advances in the field. The commissioned Perspectives and Reviews summarize and celebrate Professor Crow's contributions as a research scientist, administrator, colleague, community supporter, international leader, teacher, and mentor. In science, Professor Crow was the international leader of his generation in the application of genetics to populations of organisms and in uncovering the role of genetics in health and disease. In education, he was a superb undergraduate teacher whose inspiration changed the career paths of many students. His teaching skills are legendary, his lectures urbane and witty, rigorous and clear. He was also an extraordinary mentor to numerous graduate students and postdoctoral fellows, many of whom went on to establish successful careers of their own. In public service, Professor Crow served in key administrative positions at the University of Wisconsin, participated as a member of numerous national and international committees, and served as president of both the Genetics Society of America and the American Society for Human Genetics. This Perspective examines Professor Crow as teacher and mentor through the eyes and experiences of one student who was enrolled in his genetics course as an undergraduate and who later studied with him as a graduate student.     

A fungal perspective on human inborn errors of metabolism: alkaptonuria and beyond

Crucial for the establishment and development of biochemical genetics as a self-standing discipline was Beadle and Tatum's choice of Neurospora crassa as experimental organism some 60 years ago. Although Garrod's insights on biochemical genetics and his astonishingly modern concepts of biochemical individuality and susceptibility to disease had been ignored by their contemporaries, Beadle acknowledged on several occasions how close Garrod had come to the "one-gene-one-enzyme" hypothesis. In an unexpected turn of events, several genes involved in human inborn errors of metabolism, including the gene for Garrod's favorite disease, alkaptonuria, have been characterized by exploitation of the experimental advantages of another mold, Aspergillus nidulans, which shares with N. crassa the experimental advantages that prompted pioneers of biochemical genetics to use them: rapid growth, facile genetic manipulation, and an environment (the composition of the growth medium) that can be manipulated à la carte.     

Mendel's experiments: A reinterpretation

Conclusion My conclusion is that Mendel deliberately, though without any real falsification, tried to suggest to his audience and readers an unlikely and substantially wrong reconstruction of the first and most important phase of his research. In my book I offer many reasons for this strange and surprising behavior,⁵³ but the main argument rests on the fact of linkage. Mendelian genetics cannot account for linkage because it was based on the idea of applying probability theory to the problem of species evolution. Central to the theory is the law of probability according to which the chance occurrence of a combination of independent events is the product of their separate probabilities. This is the common basis of Mendel's first and second laws, but this is why Mendel's second law on independent assortment is enunciated in too general a way. From Morgan's work we now know that characters may not always be independent if their genes are located very close one to the other on the same chromosome. And this was also the basis of Mendel's personal drama: he surely observed the effects of linkage, but he had no theoretical tools with which to explain it. So he presented his results in a logical structure consistent with the central idea of his theory. Had he described the real course of his experiments he would have had to admit that his law worked for only a few of the hundreds of Pisum characters — and it would thus have been considered more of an exception than a rule. This is why he insisted on the necessity of testing the law on other plants, and this is why in his second letter to Carl Nägeli he admits that the publication of his data was untimely and dangerous.⁵⁴.We can argue that already in 1866 Mendel was less confident that his so-called second law had the same general validity as the first — and that later he lost his confidence altogether. Contemporary testimony indicates that in the end he became as skeptical as all his contemporaries as to the scientific relevance of his theory.⁵⁵ But he was wrong. His research is in no way the fruit of methodological mistakes or forgery, and it remains a landmark in the history of science. He was only the victim of a strange destiny in which the use of probability theory was responsible, at the same time, for the strength and for the weakness of his theory. We must still consider him the father and founder of genetics.     

Mathematics and biology: a Kantian view on the history of pattern formation theory

Driesch's statement, made around 1900, that the physics and chemistry of his day were unable to explain self-regulation during embryogenesis was correct and could be extended until the year 1972. The emergence of theories of self-organisation required progress in several areas including chemistry, physics, computing and cybernetics. Two parallel lines of development can be distinguished which both culminated in the early 1970s. Firstly, physicochemical theories of self-organisation arose from theoretical (Lotka 1910-1920) and experimental work (Bray 1920; Belousov 1951) on chemical oscillations. However, this research area gained broader acceptance only after thermodynamics was extended to systems far from equilibrium (1922-1967) and the mechanism of the prime example for a chemical oscillator, the Belousov-Zhabotinski reaction, was deciphered in the early 1970s. Secondly, biological theories of self-organisation were rooted in the intellectual environment of artificial intelligence and cybernetics. Turing wrote his The chemical basis of morphogenesis (1952) after working on the construction of one of the first electronic computers. Likewise, Gierer and Meinhardt's theory of local activation and lateral inhibition (1972) was influenced by ideas from cybernetics. The Gierer-Meinhardt theory provided an explanation for the first time of both spontaneous formation of spatial order and of self-regulation that proved to be extremely successful in elucidating a wide range of patterning processes. With the advent of developmental genetics in the 1980s, detailed molecular and functional data became available for complex developmental processes, allowing a new generation of data-driven theoretical approaches. Three examples of such approaches will be discussed. The successes and limitations of mathematical pattern formation theory throughout its history suggest a picture of the organism, which has structural similarity to views of the organic world held by the philosopher Immanuel Kant at the end of the eighteenth century.     

Nikolaĭ Vladimirovich Timofeev-Resovskiĭ (1900-1981). (Essay on his life and works)

The article contains a brief review of the basic works (1925-1981) written by Nikolay V. Timofeeff-Ressovsky--one of the famous geneticist of the elapsing century, the founder of radiobiology and radiation genetics, biocenology and radioecology, a prominent evolutionary biologist. In genetics, his name is associated with the development of fundamental problems of population genetics, phenogenetics, gene interaction and investigations of the role of environmental and genetic factors in expression of different characters. Timofeeff-Ressovsky classical works on mutagenesis process and especially, radiation mutagenesis, promoted penetration of methods and approaches applied in molecular physics and chemistry, into genetic analysis, and accelerated forming of the modern molecular genetics. A special place in the development of population genetics is occupied by the hypothesis of microevolutionary process developed by Nikolay V. Timofeeff-Ressovsky along with other famous biologists in the end of the 30-ies. This hypothesis connected Darwin's evolutionary theory with rapidly developing concepts of genetics. In the last years of his life, Timofeeff-Ressovsky was especially interested in a global problem which was called by him "The Biosphere and Humanity". Here was especially strikingly shown the broadness of his approach to the analysis of the biosphere phenomena in the best traditions of the Russian natural science. In the course of time, the wealth of Nikolay V. Timofeeff-Ressovsky's scientific heritage not only remains valuable, but also takes on more profundity and value.     

Early 20th-century research at the interfaces of genetics, development, and evolution: reflections on progress and dead ends

Three early 20th-century attempts at unifying separate areas of biology, in particular development, genetics, physiology, and evolution, are compared in regard to their success and fruitfulness for further research: Jacques Loeb's reductionist project of unifying approaches by physico-chemical explanations; Richard Goldschmidt's anti-reductionist attempts to unify by integration; and Sewall Wright's combination of reductionist research and vision of hierarchical genetic systems. Loeb's program, demanding that all aspects of biology, including evolution, be studied by the methods of the experimental sciences, proved highly successful and indispensible for higher level investigations, even though evolutionary change and properties of biological systems up to now cannot be fully explained on the molecular level alone. Goldschmidt has been appraised as pioneer of physiological and developmental genetics and of a new evolutionary synthesis which transcended neo-Darwinism. However, this study concludes that his anti-reductionist attempts to integrate genetics, development and evolution have to be regarded as failures or dead ends. His grand speculations were based on the one hand on concepts and experimental systems that were too vague in order to stimulate further research, and on the other on experiments which in their core parts turned out not to be reproducible. In contrast, Sewall Wright, apart from being one of the architects of the neo-Darwinian synthesis of the 1930s, opened up new paths of testable quantitative developmental genetic investigations. He placed his research within a framework of logical reasoning, which resulted in the farsighted speculation that examinations of biological systems should be related to the regulation of hierarchical genetic subsystems, possibly providing a mechanism for development and evolution. I argue that his suggestion of basing the study of systems on clearly defined properties of the components has proved superior to Goldschmidt's approach of studying systems as a whole, and that attempts to integrate different fields at a too early stage may prove futile or worse.     

Mendel, the empiricist

In contemporary texts in biology and genetics, Mendel is frequently portrayed as a theorist who was the father of classical genetics. According to some authors, he created his theory of inheritance to explain the results of his experimental hybridizations of peas. Others have proposed that he designed and carried out his experiments to demonstrate the correctness of a theory of inheritance he had already developed. We disagree strongly with these views of Mendel. Instead, we have come to regard him as an empirical investigator trying to discover the empirical natural laws describing the formation of hybrid peas and the development of their offspring over several generations. We have supported our view with an analysis of portions of Mendel's paper and his letters to Carl N ageli.     

Ernst Rüdin: Hitler’s Racial Hygiene Mastermind

Ernst Rüdin (1874–1952) was the founder of psychiatric genetics and was also a founder of the German racial hygiene movement. Throughout his long career he played a major role in promoting eugenic ideas and policies in Germany, including helping formulate the 1933 Nazi eugenic sterilization law and other governmental policies directed against the alleged carriers of genetic defects. In the 1940s Rüdin supported the killing of children and mental patients under a Nazi program euphemistically called “Euthanasia.” The authors document these crimes and discuss their implications, and also present translations of two publications Rüdin co-authored in 1938 showing his strong support for Hitler and his policies. The authors also document what they see as revisionist historical accounts by leading psychiatric genetic authors. They outline three categories of contemporary psychiatric genetic accounts of Rüdin and his work: (A) those who write about German psychiatric genetics in the Nazi period, but either fail to mention Rüdin at all, or cast him in a favorable light; (B) those who acknowledge that Rüdin helped promote eugenic sterilization and/or may have worked with the Nazis, but generally paint a positive picture of Rüdin’s research and fail to mention his participation in the “euthanasia” killing program; and (C) those who have written that Rüdin committed and supported unspeakable atrocities. The authors conclude by calling on the leaders of psychiatric genetics to produce a detailed and complete account of their field’s history, including all of the documented crimes committed by Rüdin and his associates.     

Timeline: Hermann Joseph Muller, evolutionist

This essay is dedicated to the proposition that Hermann Joseph Muller, widely regarded as the greatest geneticist of the first half-century of the subject, was also one of the greatest evolutionists of this period. His Nobel Prize-winning work, which showed that radiation increases the mutation rate, is in every genetics textbook, and his prescient ideas have influenced almost every aspect of the discipline. Here I emphasize his less well-known contribution to the neo-Darwinian theory of evolution.     

Walter Garstang: a retrospective

Although, Walter Garstang died over 60 years ago, his work is still cited—sometimes praised, but sometimes belittled. On the negative side, he often appropriated ideas of others without attribution, ignored earlier studies conflicting with his theories, and clung to notions like inheritance of acquired characters, progressive evolution, and saltation after many of his contemporaries were advancing toward the modern synthesis. Moreover, his evolutionary scenarios—especially his derivation of vertebrates from a sessile ascidian—have not been well supported by recent work in developmental genetics and molecular phylogenetics. On the positive side, Garstang firmly established several points of view that remain useful in the age of evolutionary development (evo-devo). He popularized the valid idea that adaptive changes in larvae combined with shifts in developmental timing (heterochrony) could radically change adult morphology and provide an escape from overspecialization. Moreover, his re-statement of the biogenetic law is now widely accepted: namely, that recapitulation results when characters at one stage of development are required for the correct formation of other characters at subsequent stages (his stepping stone model). In other words, ontogeny creates phylogeny because some developmental features are constraints, favoring particular evolutionary outcomes while excluding others. This viewpoint is a useful basis for advancing concepts of homology and for comparing the phylogeny of ontogenies across a series of animals to ascertain the timing and the nature of the underlying ontogenetic changes.     

George Beadle: from genes to proteins

George W. Beadle's life spanned much of the period during which genetics changed from an abstract to a molecular science. Beadle himself catalysed the transition from classical to molecular genetics when, together with Edward Tatum, he discovered that each gene is linked to the production of a protein. This article traces his life from a modest farm to the centre of biology and a principal role in the development of the scientific enterprise.     

Richard Goldschmidt: hopeful monsters and other 'heresies'

Richard Goldschmidt is remembered today as one of the most controversial biologists of the twentieth century. Although his work on sex determination and physiological genetics earned him accolades from his peers, his rejection of the classical gene and his unpopular theories about evolution significantly damaged his scientific reputation. This article reviews Goldschmidt's life and work, with an emphasis on his controversial views.