How theories became knowledge: Morgan's chromosome theory of heredity in America and Britain

T. H. Morgan, A. H. Sturtevant, H. J. Muller and C. B. Bridges published their comprehensive treatise The Mechanism of Mendelian Heredity in 1915. By 1920 Morgan's ``Chromosome Theory of Heredity' was generally accepted by geneticists in the United States, and by British geneticists by 1925. By 1930 it had been incorporated into most general biology, botany, and zoology textbooks as established knowledge. In this paper, I examine the reasons why it was accepted as part of a series of comparative studies of theory-acceptance in the sciences. In this context it is of interest to look at the persuasiveness of confirmed novel predictions, a factor often regarded by philosophers of science as the most important way to justify a theory. Here it turns out to play a role in the decision of some geneticists to accept the theory, but is generally less important than the CTH's ability to explain Mendelian inheritance, sex-linked inheritance, non-disjunction, and the connection between linkage groups and the number of chromosome pairs; in other words, to establish a firm connection between genetics and cytology. It is remarkable that geneticists were willing to accept the CTH as applicable to all organisms at a time when it had been confirmed only for Drosophila. The construction of maps showing the location on the chromosomes of genes for specific characters was especially convincing for non-geneticists.     

显微系统化与大学生科研培训计划中科研思维的培养

显微系统化是指将各种显微镜融合并统一利用,联合操作,所用程序一体化、规范化、统一化和数字化。显微系统化通过系统化管理,在大学生科研培训计划（Student Research Training Program,SRTP）中实施。实行显微系统化,可突破显微镜本身时间和空间上的局限性,能够进一步完善科学、高效的科研培训计划模式,对从感性方面培养大学生理解科研的概念和建立科研思维的能力、提高大学生科研素养具有重要作用。     

Many-worlds interpretation of quantum theory and fundamental problems of biophysics

The main aspects connected with the many-worlds interpretation of quantum theory are discussed in the article. A possible relation of the interpretation with fundamental biological problems is emphasized. The context of the many-worlds interpretation is discussed in the frames of the so-called “wave function reduction” problem. Thus, some difficulties that arise when we try to imagine how a wave function is reduced in the many-worlds interpretation, are focused on. It is shown that explanations suggested by now as to how the “wave function reduction” happens cannot claim to be the final answer to this question, even though they are not formally contradictory.     

Human genetics of infectious diseases: a unified theory

Since the early 1950s, the dominant paradigm in the human genetics of infectious diseases postulates that rare monogenic immunodeficiencies confer vulnerability to multiple infectious diseases (one gene, multiple infections), whereas common infections are associated with the polygenic inheritance of multiple susceptibility genes (one infection, multiple genes). Recent studies, since 1996 in particular, have challenged this view. A newly recognised group of primary immunodeficiencies predisposing the individual to a principal or single type of infection is emerging. In parallel, several common infections have been shown to reflect the inheritance of one major susceptibility gene, at least in some populations. This novel causal relationship (one gene, one infection) blurs the distinction between patient-based Mendelian genetics and population-based complex genetics, and provides a unified conceptual frame for exploring the molecular genetic basis of infectious diseases in humans.     

Checks and balances: the welcomed tension between philosophy and science

There is a tension between science and philosophy, but this tension need not engender enmity or derision. Scientists and philosophers can work together, and we argue that working together is beneficial to both, even if it is sometimes uncomfortable. We offer examples of how philosophy can autonomously and effectively inform scientific practice. Science and philosophy share certain methodological concerns and practices; therefore, scientists who disregard philosophy are vulnerable to critical conceptual mistakes. If our arguments are correct, and if it can also be shown that science informs philosophy, then, while it is possible for both disciplines to operate autonomously, each should welcome the checks and balances that each provides for one another in the investigation and explanation of reality.     

The heuristics of biologic theory: the case of self-nonself discrimination

Mel Cohn has responded to our critique of the minimal model of self-nonself discrimination proposed by Langman and him. In this response to Mel Cohn, we summarize the essential differences between our points of view and highlight one criterion (of many) for preferring one theory to another in the complex field of biology: a preferred theory, rather than solving a problem, is heuristic. A good theory is one that activates a scientist to perform experiments that are novel and productive.     

The theory of organism and the culturalist foundation of biology

Summary After the disappearance of organism was diagnosed, the discussion about the role of a theory of organism in biology is characterised by a significant contradiction. On the one hand, the importance of a theory of organism is stated. Particularly developmental biology demands organism-centred approaches as a basis for conceptual integration. On the other hand, several modern biological disciplines such as genetics and molecular biology simply don’t need a theory of organism for their work. Consequently, the determination of the status of the organism and its relevance for biology at all is an unsolved problem. In order to clarify the methodological status of the organism in biology we start with the reconstruction of three important propositions. A life oriented approach and a hierarchy concept - which both are from a neo-Darwinian origin - are confronted with a structuralist approach of organism, that can be characterised as a non-Darwinist approach. Our own attempt for the solution of the organism problem applies the tools of culturalist methodology. In accordance to this pragmatic approach, the term organism is introduced as a concept of notion. A constructional morphological case study exemplifies the applicability of this concept. From the culturalist point of view a methodological foundation of biology can be achieved, that provides a consistent basis for a comprehensive integration of biological knowledge.     

Mendelian inheritance in Germany between 1900 and 1910. The case of Carl Correns (1864-1933)

Carl Correns (1864-1933) came to recognize Mendel's rules between 1894 and 1900 while trying to find out the mechanism of xenia, that is, the direct influence of the fertilizing pollen on the mother plant in maize and peas among other species. In this paper, I am concerned with the ten years of Correns' work after the annus mirabilis of 1900 until 1910, when the main outlines of the new science of genetics had been established. It is generally assumed that after 1900 Correns quickly began probing the limits of Mendelian inheritance, both as far as the explanatory force of formal transmission genetics and the generality of Mendel's laws are concerned. A careful examination of his papers however shows that he was much more interested in the scope of Mendelian inheritance than in its limits. Even his work with variegated Mirabilis plants, which historiographical folklore still presents as a result of Correns' growing interest in cytoplasmic inheritance, can be shown to have been conducted to corroborate just the opposite, namely, the validity of the nuclear paradigm. The paper will show that Correns' research results in those years (among them the Mendelian inheritance of sex in higher plants) were the outcome of a complex experimental program which involved breeding experiments with dozens of different species.     

A graph theoretic approach to the development of minimal phylogenetic trees

Summary The problem of determining the minimal phylogenetic tree is discussed in relation to graph theory. It is shown that this problem is an example of the Steiner problem in graphs which is to connect a set of points by a minimal length network where new points can be added. There is no reported method of solving realistically-sized Steiner problems in reasonable computing time. A heuristic method of approaching the phylogenetic problem is presented, together with a worked example with 7 mammalian cytochrome c sequences. It is shown in this case that the method develops a phylogenetic tree that has the smallest possible number of amino acid replacements. The potential and limitations of the method are discussed. It is stressed that objective methods must be used for comparing different trees. In particular it should be determined how close a given tree is to a mathematically determined lower bound. A theorem is proved which is used to establish a lower bound on the length of any tree and if a tree is found with a length equal to the lower bound, then no shorter tree can exist.     

The astral relaxation theory of cytokinesis revisited

Cytokinesis in animal cells is accomplished by the active constriction of the equatorial regions of a cell by an actomyosin-containing contractile ring. The mitotic apparatus specifies the position and orientation of the furrow such that the mitotic spindle is always bisected. Global cortical contractions occur in the cortex of a cell prior to cytokinesis that are independent of the presence of the mitotic apparatus. It was proposed some years ago that the asters of the mitotic apparatus could act to relax the preformed cortical tension in their vicinity. This would produce a differential in tension between the equatorial regions and the adjacent regions of the cortex so that the equatorial regions would contract, forming a cleavage furrow. It can be shown that, as it stands, this theory cannot explain cleavage. However, if cortical contractile elements are assumed to be laterally mobile in the plane of the cortex, then the astral relaxation theory can account for many of the aspects of cleavage, including the formation of the contractile ring. Similar schemes may account for the behaviour of the lamellapodia of motile cells.     

Quantitatively Evaluating Restoration Experiments: Research Design, Statistical Analysis, and Data Management Considerations

Conceptual and logistical challenges associated with the design and analysis of ecological restoration experiments are often viewed as being insurmountable, thereby limiting the potential value of restoration experiments as tests of ecological theory. Such research constraints are, however, not unique within the environmental sciences. Numerous natural and anthropogenic disturbances represent unplanned, uncontrollable events that cannot be replicated or studied using traditional experimental approaches and statistical analyses. A broad mix of appropriate research approaches (e.g., long-term studies, large-scale comparative studies, space-for-time substitution, modeling, and focused experimentation) and analytical tools (e.g., observational, spatial, and temporal statistics) are available and required to advance restoration ecology as a scientific discipline. In this article, research design and analytical options are described and assessed in relation to their applicability to restoration ecology. Significant research benefits may be derived from explicitly defining conceptual models and presuppositions, developing multiple working hypotheses, and developing and archiving high-quality data and metadata. Flexibility in research approaches and statistical analyses, high-quality databases, and new sampling approaches that support research at broader spatial and temporal scales are critical for enhancing ecological understanding and supporting further development of restoration ecology as a scientific discipline.     

Methodologies for examining problem solving success and failure

When designing research to examine the variables underlying creative thinking and problem solving success, one must not only consider (a) the demands of the task being performed, but (b) the characteristics of the individual performing the task and (c) the constraints of the skill execution environment. In the current paper we describe methodologies that allow one to effectively study creative thinking by capturing interactions among the individual, task, and problem solving situation. In doing so, we demonstrate that the relation between executive functioning and problem solving success is not always as straightforward as one might initially believe.     

Modifier theory of meiotic drive: Is Mendelian segregation stable?

The evolutionary fate of rare modifiers, based on the modifier theory of meiotic drive, is studied in this paper. It is shown that a polymorphism based on Mendelian segregation is never stable for any recombination frequencies between 0 and $\text{1}\text{2}$, and that, for tight linkage between the main locus and the modifier locus, the modifier locus tends towards heterozygosity.     

Historic and functional biology: the inadequacy of a system theory of evolution

In the first half of the 20th century neo-Kantianism in a broad sense proved itself the main conceptual and methodological background of the central European biology. As such it contributed much to the victory on the typological, idealistic-morphological and psycho-vitalistic interpretations of life. On the other hand it could not give tools to the biologists for working out a strictly darwinian evolution theory. Kant's theory of organism was conceived without evolution as a theory of the internal functionality of the organism. There was only some 'play' with the evolutionary differentiation of the species. Since then the disputes around the work of August Weismann, a synthetical evolution theory which is now behind time, arose. This theory developed from coinciding claims, elaborated by geneticists, mathematicians, and by biologists studying development, natural history and systematics. This was done under a strong influence of marxist ideas. Through the interweaving of such different approaches it was possible for this evolutionary synthesis to influence successfully the development of evolution research during more than 40 years. Philosophically speaking modern evolution theory means therefore an aversion, even a positive abolition of Kantian positions. A number of biologists however--as L. von Bertalanffy--refused to adhere to a misinterpreted Kantian methodology and oriented themselves to an approach via system theory, which obtained a place in evolution research. In fact this is a Kantian approach as well. They only repeated the Kantian dilemma of the evolution which can also be found in Lamarck and Hegel. The system theory of the functionality of the organism never reaches to the level of the evolving species, but remains always on the level of epigenetic thinking, because of its philosophical origin. This paper points out the consequences of this still current dilemma. At the same time an all-enclosing reflection on the methodological, epistemological and the important historical questions of evolutionary biology in its scientific context is recommended.     

The genetical theory of multilevel selection

The theory of multilevel selection (MLS) is beset with conceptual difficulties. Although it is widely agreed that covariance between group trait and group fitness may arise in the natural world and drive a response to ‘group selection’, ambiguity exists over the precise meaning of group trait and group fitness and as to whether group selection should be defined according to changes in frequencies of different types of individual or different types of group. Moreover, the theory of MLS has failed to properly engage with the problem of class structure, which greatly limits its empirical application to, for example, social insects whose colonies are structured into separate age, sex, caste and ploidy classes. Here, I develop a genetical theory of MLS, to address these problems. I show that taking a genetical approach facilitates a decomposition of group‐level traits – including reproductive success – into the separate contributions made by each constituent individual, even in the context of so‐called emergence. However, I uncover a novel problem with the group‐oriented approach: in many scenarios, it may not be possible to express a meaningful covariance between trait and fitness at the level of the social group, because the group's constituents belong to separate, irreconcilable classes.     

A New Paradigm for Developmental Science: Relationism and Relational-Developmental Systems

The Cartesian-Split-Mechanistic scientific paradigm that until recently functioned as the standard conceptual framework for sub-fields of developmental science (including inheritance, evolution, and organismic—pre-natal, cognitive, emotional, motivational, socio-cultural—development) has been progressively failing as a scientific research program. An alternative scientific paradigm composed of nested meta-theories with Relationism at the broadest level and Relational-Developmental-Systems as a mid-range meta-theory is offered as a more progressive conceptual framework for developmental science. Termed broadly the Relational-Developmental-Systems paradigm, this framework accounts for the findings that are anomalies for the old paradigm, accounts for the emergence of new findings, and points the way to future scientific productivity—and a more optimistic approach to evaluate-evidence-based applications aimed at promoting positive human development and social justice.     

COLONY: a program for parentage and sibship inference from multilocus genotype data

Pedigrees, depicting genealogical relationships between individuals, are important in several research areas. Molecular markers allow inference of pedigrees in wild species where relationship information is impossible to collect by observation. Marker data are analysed statistically using methods based on Mendelian inheritance rules. There are numerous computer programs available to conduct pedigree analysis, but most software is inflexible, both in terms of assumptions and data requirements. Most methods only accommodate monogamous diploid species using codominant markers without genotyping error. In addition, most commonly used methods use pairwise comparisons rather than a full-pedigree likelihood approach, which considers the likelihood of the entire pedigree structure and allows the simultaneous inference of parentage and sibship. Here, we describe colony, a computer program implementing full-pedigree likelihood methods to simultaneously infer sibship and parentage among individuals using multilocus genotype data. colony can be used for both diploid and haplodiploid species; it can use dominant and codominant markers, and can accommodate, and estimate, genotyping error at each locus. In addition, colony can carry out these inferences for both monoecious and dioecious species. The program is available as a Microsoft Windows version, which includes a graphical user interface, and a Macintosh version, which uses an R-based interface.     

Integration of a B chromosome into the A genome of a wasp

B chromosomes are genome symbionts, the presence of which in many eukaryote species is explained, in most cases, by their violation of Mendelian rules, usually based on meiotic or mitotic instability, leading to their accumulation in the germ line (drive). However, B chromosome integration into the genome as a regular member of the chromosome set should imply the loss of drive. A possible way of bypassing this difficulty is to regularize meiosis when the B chromosome is frequent in the population, in order to yield gametes with one B chromosome. In diploid organisms, this task needs to be achieved in the two sexes, but in haplodiploids the problem simplifies to only the diploid sex. We have found, to the authors' knowledge, the first evidence of a B chromosome that is regularizing its meiotic behaviour and limiting its number to one B chromosome per haploid genome, the same dosage as the standard (A) chromosomes, in the solitary wasp Trypoxylon albitarse. It suggests a possible mechanism for B chromosome integration as a regular member of the chromosome complement.     

On extending the usefulness of projectors in teaching biology

This paper reports the design of an interactive computer program in microbial genetics. The computer program is divided into three stages, background information, simulation, and data treatment. The results obtained from the simulation allow four genes to be sequenced along the bacterial chromosome. The simulation mimics experimental errors, the production of exconjugants and backmutants. The data can be analysed using options contained in the program. The simulation is of particular educational value because it allows the student to work at his own pace and to develop his ability to analyse data in relation to a complex conceptual model.