Michael R. Dietrich

MicroRNAs and metazoan macroevolution: insights into canalization, complexity, and the Cambrian explosion

One of the most interesting challenges facing paleobiologists is explaining the Cambrian explosion, the dramatic appearance of most metazoan animal phyla in the Early Cambrian, and the subsequent stability of these body plans over the ensuing 530 million years. We propose that because phenotypic variation decreases through geologic time, because microRNAs (miRNAs) increase genic precision, by turning an imprecise number of mRNA transcripts into a more precise number of protein molecules, and because miRNAs are continuously being added to metazoan genomes through geologic time, miRNAs might be instrumental in the canalization of development. Further, miRNAs ultimately allow for natural selection to elaborate morphological complexity, because by reducing gene expression variability, miRNAs increase heritability, allowing selection to change characters more effectively. Hence, miRNAs might play an important role in shaping metazoan macroevolution, and might be part of the solution to the Cambrian conundrum.

Paradox and Persuasion: Negotiating the Place of Molecular Evolution within Evolutionary Biology

Les chercheurs en biologie moleculaire ont impose leurs recherches au sein de la biologie et ont du se distinguer des travaux effectues en biologie des organismes

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 Goldschmidts life and work, with an emphasis on his controversial views.

Integration without Unification: An Argument for Pluralism in the Biological Sciences

In this article, we consider the tension between unification and pluralism in biological theory. We begin with a consideration of historical efforts to establish a unified understanding of evolution in the neo‐Darwinian synthesis. The fragmentation of the evolutionary synthesis by molecular evolution suggests the limitations of the general unificationist ideal for biology but not necessarily for integrating explanations. In the second half of this article, we defend a specific variety of pluralism that allows for the integration required for explanations of complex phenomena without unification on a large scale.

Monte Carlo experiments and the defense of diffusion models in molecular population genetics

In the 1960s molecular population geneticists used Monte Carlo experiments to evaluate particular diffusion equation models. In this paper I examine the nature of this comparative evaluation and argue for three claims: first, Monte Carlo experiments are genuine experiments: second, Monte Carlo experiments can provide an important meansfor evaluating the adequacy of highly idealized theoretical models; and, third, the evaluation of the computational adequacy of a diffusion model with Monte Carlo experiments is significantlydifferent from the evaluation of the emperical adequacy of the same diffusion model.

Explaining the “Pulse of Protoplasm”: The search for molecular mechanisms of protoplasmic streaming

Explanations for protoplasmic streaming began with appeals to contraction in the eighteenth century and ended with appeals to contraction in the twentieth. During the intervening years, biologists proposed a diverse array of mechanisms for streaming motions. This paper focuses on the re-emergence of contraction among the molecular mechanisms proposed for protoplasmic streaming during the twentieth century. The revival of contraction is a result of a broader transition from colloidal chemistry to a macromolecular approach to the chemistry of proteins, the recognition of the phenomena of shuttle streaming and the pulse of protoplasm, and the influential analogy between protoplasmic streaming and muscle contraction.

Publication Trends in Model Organism Research

In 1990, the National Institutes of Health (NIH) gave some organisms special status as designated model organisms. This article documents publication trends for these NIH-designated model organisms over the past 40 years. We find that being designated a model organism by the NIH does not guarantee an increasing publication trend. An analysis of model and nonmodel organisms included in GENETICS since 1960 does reveal a sharp decline in the number of publications using nonmodel organisms yet no decline in the overall species diversity. We suggest that organisms with successful publication records tend to share critical characteristics, such as being well developed as standardized, experimental systems and being used by well-organized communities with good networks of exchange and methods of communication.

Manipulating Underdetermination in Scientific Controversy: The Case of the Molecular Clock

Where there are cases of underdetermination in scientific controversies, such as the case of the molecular clock, scientists may direct the course and terms of dispute by playing off the multidimensional framework of theory evaluation. This is because assessment strategies themselves are underdetermined. Within the framework of assessment, there are a variety of trade-offs between different strategies as well as shifting emphases as specific strategies are given more or less weight in assessment situations. When a strategy is underdetermined, scientists can change the dynamics of a controversy by making assessments using different combinations of evaluation strategies and/or weighting whatever strategies are in play in different ways. Following an underdetermination strategy does not end or resolve a scientific dispute. Consequently, manipulating underdetermination is a feature of controversy dynamics and not controversy closure.

The problem of the gene

During the early 20th century the diverse practices of genetics were unified by the concept of the gene. This classical gene was simultaneously a unit of structure, function, mutation, and recombination. Starting in the 1940s, however, the classical gene began to fragment. Today when we speak of a gene for some malady, a regulatory gene, a structural gene, or a gene frequency, it is entirely possible that we are deploying different gene concepts even though we are using the same term. The problem of the gene addresses the fragmentation of the classical gene concept by asking to what extent a comprehensive and unifying gene concept is possible or desirable. Fully comprehensive gene concepts seem untenable today, but, within different disciplinary domains, unifying, but non-comprehensive, gene concepts can be epistemically worthwhile. The problem of the gene persists, however, not because of its epistemic value, but because of its political value. Using both the arguments for newly proposed gene concepts and the historical dispute over the classical gene, I argue that the desirability of gene concepts rests in part on the political ramifications of their deployment and contestation.

The Role of Causal Processes in the Neutral and Nearly Neutral Theories

The neutral and nearly neutral theories of molecular evolution are sometimes characterized as theories about drift alone, where drift is described solely as an outcome, rather than a process. We argue, however, that both selection and drift, as causal processes, are integral parts of both theories. However, the nearly neutral theory explicitly recognizes alleles and/or molecular substitutions that, while engaging in weakly selected causal processes, exhibit outcomes thought to be characteristic of random drift. A narrow focus on outcomes obscures the significant role of weakly selected causal processes in the nearly neutral theory.