Beanbag Genetics Research Articles

Haldane and Mayr: a response to Rao and Nanjundiah.

The discussion with Rao and Nanjundiah about the history of interactions between J. B. S. Haldane and Ernst Mayr is further extended in this note. The nature of the dispute about beanbag genetics is explicated as consisting of two separate issues, one about the role of mathematical analysis in evolutionary biology, and the other about the value of single-locus genic models.

Review of "Haldane, Mayr, and Beanbag Genetics" by Krishna Dronamraju

Review of "Haldane, Mayr, and Beanbag Genetics" by Krishna Dronamraju

The fuel of evolution

Volume 365 of the Philosophical Transactions of the Royal Society B includes a collection of 15 papers written to honour Brian Charlesworth on the occasion of his 65th birthday, which are presented under the general heading of ‘The population genetics of mutations: good, bad and indifferent’ (here referred to as GBI) edited by Loewe and Hill (2010). At first sight, this title might suggest just a simplistic way to classify mutations, as it seems obvious today that their effects on fitness follow a continuous distribution ranging from lethal to highly advantageous, albeit the mere existence of quasi-neutral ‘indifferent’ genetic variation was hotly debated a few decades ago. However, in spite of historical attacks on ‘bean-bag genetics’, the essence of the evolutionary process can be described in terms of the fate of these three different types of mutations in populations subjected to the forces of natural selection and genetic drift. The issue, beginning with a comprehensive introduction (Loewe and Hill, 2010), addresses topics such as the magnitude of spontaneous mutation rates (Kondrashov and Kondrashov), the distribution of mutational effects on fitness (Keightley and Eyre-Walker, Orr, Trindade et al.), the specific selective forces affecting different types of mutations (Lee and Langley, McVean, Sharp et al.), the consequences of mutation for the genetic architecture of quantitative traits (Crow, Mackay), and the evolutionary role of mutation in broader biological phenomena such as recombination (Barton), adaptation (Sniegowski and Gerrish, Stephan), aging (Hughes) and speciation (McDermott and Noor).

Estimating linkage disequilibria

Estimating linkage disequilibria

Mutations and Brian Charlesworth

![Graphic][1] In this issue of Philosophical Transactions of the Royal Society B , we have two distinct objectives. The first is to honour Brian Charlesworth for his contributions to science as he reaches his 65th birthday on 29 April 2010. The second is to focus on the population genetics of

Complex Diseases, Complex Genes

In his “Defense of Beanbag Genetics,” J.B.S. Haldane1 responded to critics who challenged a marginal (ie, one-locus-at-a-time) approach to studying population genetics. Such “beanbag genetics” had been accused of being too simplistic and ignoring the contributions of multiple loci in different (and ever-changing) environmental contexts. Haldane conceded this point of principle (“beanbag genetics do not explain the physiologic interaction of genes and the interaction of genotype and environment”) but went on to argue that despite its simplifications, the marginal approach had proven itself in practice and led to important insights.1 The arrival of massive amounts of data from genome-wide association studies (GWAS) has turned up the heat on a similar debate in the field of genetic epidemiology. On the one hand, the admittedly simple approach of averaging over genetic and environmental backgrounds and testing each marker in a GWAS for association with the studied trait marginally has proven quite successful,2,3 despite early concerns that by ignoring the underlying complexity this naive approach would fail.4,5 On the other hand, the loci discovered to date do not come close to explaining the observed heritability for most studied traits.6 “Pathway analyses” acknowledge complexity by considering multiple loci simultaneously and relating them to known functional annotations. In principle, pathway analyses could lead to new discoveries missed by the simple marginal analyses.7–11 Moreover, successful identification of associated pathways can clarify disease pathogenesis; indeed, for some phenotypes, multiple loci identified through GWAS have been linked to common pathways.12–15 However, in practice, multilocus pathway analyses present a number of challenges, some of which should be very familiar to epidemiologists.16,17 The paper by Breitling et al18 in this issue discusses the issue of overfitting when there is a large number of potential predictor variables. Other issues may be less familiar—the consequences of the peculiarities of genomic data and how it is annotated. Here we discuss 3 loosely defined approaches to “pathway analysis” and touch on potential pitfalls for each.

A Defense of Beanbag Genetics*

The Mendelian was apt to compare the genetic contents of a population to a bag full of colored beans. Mutation was the exchange of one kind of bean for another. This conceptualization has been referred to as ‘‘beanbag genetics’’. Work in population and developmental genetics has shown, however, that the thinking of beanbag genetics is in many ways quite misleading. To consider genes as independent units is meaningless from the physiological as well as the evolutionary viewpoint.

Commentary: Haldane and beanbag genetics

Commentary: Haldane and beanbag genetics

Commentary: Growth of beanbag genetics

Commentary: Growth of beanbag genetics

Commentary: On Haldane's ‘defense of beanbag genetics’

It is now almost 45 years since Haldane’s ‘Defense of beanbag genetics’ appeared, and the time is ripe for an evaluation of that defence, particularly in the light of developments over the last two decades. This deliberately provocative review is divided into four parts: first, a discussion of why Haldane felt that a defence was necessary; second, a review of what his defence actually was; third, suggestions as to what his defence should have been; and fourth, a discussion of what changes might be made to the defence had it been written now and not in 1964.

Commentary: The objection is sustained: a defence of the defense of beanbag genetics

Darwin couched his theory of evolution by means of natural selection in verbal arguments. According to this theory, if the variation observed between individuals was heritable, and if it contributed differentially to the survivorship and reproductive success of individuals, the process of natural selection would ensure greater representation of individuals bearing favourable traits chosen from the existing variation in subsequent generations. This concept is powerful, whether verbally or mathematically articulated. Ernst Mayr was Darwin's champion in the 20th century, defending Darwin and Darwinism vigorouslthroughout his long and industrious career that spanned 80 years.However, as outlined in Borges, even among the Darwinists, the 1950s was a time of conflict between experimental biologists and naturalist-systematists such as Mayr on one hand and theoreticians on the other. The so-called evolutionary synthesis of the 1930s and 1940s that amalgamated Darwin's theory with genetics was largely attributed to the theoretical work of Ronald.

Ornithology, evolution, and philosophy: the life and science of Ernst Mayr, 1904-2005

The young naturalist in Germany. Childhood and youth. The family. Birdwatching. The duck with a red bill. University student in Greifswald and Berlin. Friendships at school and university.- The budding scientist. PhD thesis and examination. The influence of teachers. Erwin Stresemann - teacher and friend. Assistant curator at the Museum of Natural History in Berlin. Expeditions to New Guinea and the Solomon Islands.- Ornithologist in New York. The New York years (1931 - 1953). Emigration to the United States and life in New York City. Curator of ornithology at the American Museum of Natural History. Ornithologist and zoogeographer. Birds of Oceania. Birds of Australia, the Malay Archipelago, and SE Asia. Descriptions of new species and subspecies of birds. Zoogeography.- Biological species and speciation - Mayr's first synthesis. A modern unified theory of evolution. Community architect.- Life in New York during World War II. New York City and Tenafly, New Jersey. Cold Spring Harbor (1943 - 1952). Citizenship.- Professor of Zoology at Harvard University. The Harvard years (1953 - 2005). Teaching and PhD students. Director of the Museum of Comparative Zoology. Evolutionary biology - Mayr's second synthesis. Overviews of evolutionary biology. Integrated gene complexes versus beanbag genetics. Animal Species and Evolution. Behavior and evolution. Particular topics of evolutionary biology.-Ernst Mayr - The man. Personality and general views. Health. The farm near Wilton, New Hampshire. Residence in Cambridge, Massachusetts. Advisor to the National Academy of Sciences and the NSF. National and international recognition.- Systematics and classification. Diversity. Classification. Zoological nomenclature.- History and philosophy of biology - Mayr's third synthesis. History of biology. Philosophy of biology.-

Perils of “industrial gene” and “beanbag genetics”

Perils of “industrial gene” and “beanbag genetics”

The Beanbag Genetics Controversy: Towards a synthesis of opposing views of natural selection

The beanbag genetics controversy can be traced from the dispute between Fisher and Wright, through Mayr's influential promotion of the issue, to the contemporary units of selection debate. It centers on the claim that genic models of natural selection break down in the face of epistatic interactions among genes during phenotypic development. This claim is explored from both a conceptual and a quantitative point of view, and is shown to be defective on both counts.

Haldane, Marxism, and the Conduct of Research

Previous articleNext article No AccessCommentaryHaldane, Marxism, and the Conduct of ResearchArthur M. ShapiroArthur M. Shapiro Search for more articles by this author PDFPDF PLUS Add to favoritesDownload CitationTrack CitationsPermissionsReprints Share onFacebookTwitterLinkedInRedditEmail SectionsMoreDetailsFiguresReferencesCited by The Quarterly Review of Biology Volume 68, Number 1Mar., 1993 Published in association with Stony Brook University Article DOIhttps://doi.org/10.1086/417912 Views: 3Total views on this site Citations: 3Citations are reported from Crossref Copyright 1993 The University of ChicagoPDF download Crossref reports the following articles citing this article:Sahotra Sarkar Lederberg on bacterial recombination, Haldane, and cold war genetics: an interview, History and Philosophy of the Life Sciences 36, no.22 (Sep 2014): 280–288.https://doi.org/10.1007/s40656-014-0029-7Simon Gouz Bibliographie, (Jun 2012): 627–653.https://doi.org/10.3917/edmat.gouz.2012.01.0627R. M Borges Commentary: The objection is sustained: a defence of the defense of beanbag genetics, International Journal of Epidemiology 37, no.33 (Jun 2008): 451–454.https://doi.org/10.1093/ije/dyn050

Between beanbag genetics and natural selection

The encounter between the Darwinian theory of evolution and Mendelism could be resolved only when reductionist tools could be applied to the analysis of complex systems. The instrumental reductionist interpretation of the hereditary basis of continuously varying traits provided mathematical tools which eventually allowed the construction of the ‘Modern Synthesis’ of the theory of evolution. When genotypic as well as environmental variance allow the isolation of parts of the system, it is possible to apply Mendelian reductionism, that is , to treat the phenotypic trait as if ti causally determined by discrete “genes for” the trait. howeverm such a “beanbag genetics” approach obscures the system's eye-view. The concept of heritability, defined as the proportion of the total phenotypic variance due to (additive) hereditary variation, asserts that genetic elements have discrete effects; but by relating to the genotypic variance, it avoids the trap of reffering to “genes for” characters. Variation in relative reproductive success is the phenotypic “trait” of significance for Darwinian evolution, and fitness is its genotypic component. Most traits that contribute to reproductive success are due to the effects of many loci that causally contribute to the adaptive value of those traits. by establishing a causal relationship between the heritability of traits and reproductive success the apparent tautology of the definition of fitness through reproductive success is avoided, without the need to turn to simplistic and misleading concepts, such as the “genes for” the traits.

Suicide, beanbag genetics, and pleiotropy

Suicide, beanbag genetics, and pleiotropy

A DEFENSE OF BEANBAG GENETICS.

The Mendelian was apt to compare the genetic contents of a population to a bag full of colored beans. Mutation was the exchange of one kind of bean for another. This conceptualization has been referred to as ‘‘beanbag genetics’’. Work in population and developmental genetics has shown, however, that the thinking of beanbag genetics is in many ways quite misleading. To consider genes as independent units is meaningless from the physiological as well as the evolutionary viewpoint.