Multiple Explanations in Darwinian Evolutionary Theory

Variational evolutionary theory as advocated by Darwin is not a single theory, but a bundle of related but independent theories, namely: (a) variational evolution; (b) gradualism rather than large leaps; (c) processes of phyletic evolution and of speciation; (d) causes for the formation of varying individuals in populations and for the action of selective agents; and (e) all organisms evolved from a common ancestor. The first four are nomological-deductive explanations and the fifth is historical-narrative. Therefore evolutionary theory must be divided into nomological and historical theories which are both testable against objective empirical observations. To be scientific, historical evolutionary theories must be based on well corroborated nomological theories, both evolutionary and functional. Nomological and general historical evolutionary theories are well tested and must be considered as strongly corroborated scientific theories. Opponents of evolutionary theory are concerned only with historical evolutionary theories, having little interest in nomological theory. Yet given a well corroborated nomological evolutionary theory, historical evolutionary theories follow automatically. If understood correctly, both forms of evolutionary theories stand on their own as corroborated scientific theories and should not be labeled as facts.     

Arguments against non-programmed aging theories

Until recently, non-programmed theories of biological aging were popular because of the widespread perception that the evolution process could not support the development and retention of programmed aging in mammals. However, newer evolutionary mechanics theories including group selection, kin selection, and evolvability theory support mammal programmed aging, and multiple programmed aging theories have been published based on the new mechanics. Some proponents of non-programmed aging still contend that their non-programmed theories are superior despite the new mechanics concepts. However, as summarized here, programmed theories provide a vastly better fit to empirical evidence and do not suffer from multiple implausible assumptions that are required by non-programmed theories. This issue is important because programmed theories suggest very different mechanisms for the aging process and therefore different mechanisms behind highly age-related diseases and conditions such as cancer, heart disease, and stroke.     

Evidence for Evolution Versus Evidence for Intelligent Design: Parallel Confusions

The popular defense of intelligent design/creationism (ID) theories, as well as theories in evolutionary biology, especially from the perspective that both are worthy of scientific consideration, is that empirical evidence has been presented that supports both. Both schools of thought have had a tendency to rely on the same class of evidence, namely, the observations of organisms that are in need of being explained by those theories. The result is conflation of the evidence that prompts one to infer hypotheses applying ID or evolutionary theories with the evidence that would be required to critically test those theories. Evidence is discussed in the contexts of inferring theories/hypotheses, suggesting what would be possible tests, and actual testing. These three classes of inference being abduction, deduction, and induction, respectively. Identifying these different inferential processes in evolutionary biology and ID allow for showing that the evidence to which theories and hypotheses provide understanding cannot be the same evidence supporting those theories and hypotheses. This clarification provides a strong criterion for showing the inability of an ID theory to be of utility in the ongoing process of acquiring causal understanding, that is the hallmark of science.     

Incommensurability and theory comparison in experimental biology

Incommensurability of scientific theories, as conceived by Thomas Kuhnand Paul Feyerabend, is thought to be a major or even insurmountable obstacletothe empirical comparison of these theories. I examine this problem in light ofaconcrete case from the history of experimental biology, namely the oxidativephosphorylation controversy in biochemistry (ca. 1961-1977). After a briefhistorical exposition, I show that the two main competing theories which werethe subject of the ox-phos controversy instantiate some of the characteristicfeatures of incommensurable theories, namely translation failure,non-corresponding predictions, and different claims about what kinds ofentitiesexist in the world. By examining how the controversy was eventually resolved, Ithen show that at least this pair of incommensurable theories couldneverthelessbe empirically compared.     

Dielectric self-energy in Poisson-Boltzmann and Poisson-Nernst-Planck models of ion channels

We demonstrated previously that the two continuum theories widely used in modeling biological ion channels give unreliable results when the radius of the conduit is less than two Debye lengths. The reason for this failure is the neglect of surface charges on the protein wall induced by permeating ions. Here we attempt to improve the accuracy of the Poisson-Boltzmann and Poisson-Nernst-Planck theories, when applied to channel-like environments, by including a specific dielectric self-energy term to overcome spurious shielding effects inherent in these theories. By comparing results with Brownian dynamics simulations, we show that the inclusion of an additional term in the equations yields significant qualitative improvements. The modified theories perform well in very wide and very narrow channels, but are less successful at intermediate sizes. The situation is worse in multi-ion channels because of the inability of the continuum theories to handle the ion-to-ion interactions correctly. Thus, further work is required if these continuum theories are to be reliably salvaged for quantitative studies of biological ion channels in all situations.     

Toward a conceptual framework for biology

Science progresses faster when researchers operate within an explicit framework of concepts and theories, but currently biology has no explicit, overarching conceptual framework and few general theories. The single general theory currently recognized is that of evolution, which was put forth by Charles Darwin 150 years ago. Recently, Scheiner and Willig (2008) explicated a similarly general theory of ecology. In this paper, using the theory of evolution as an exemplar, I discuss the nature of theory in biology and put forth an overarching theory, as well as new general theories for cells, organisms, and genetics. Along with the theories of evolution and ecology, these constitute a general conceptual framework for the biological sciences. This framework reveals linkages among the various parts of biology, makes explicit the assumptions behind more narrow theories and models, and provides new insights into the structures of biological theories. This framework can also be used as a teaching tool, moving the teaching of biology beyond the transference of a vast compendium of facts. My hope is that this essay will lead to a vigorous discussion and debate across all of biology about the nature and structure of its theories.     

The complexity of living bodies and the structure of biological theories

It has been suggested that biological theories differ from physical theories because the subject matter of biology differs from the subject matter of physics especially in the fact that living bodies are more complex than nonliving bodies. It is shown that the interactional complexity of living bodies can only be expressed by invoking biological theories. The claim that living bodies are complex is, therefore, ultimately a claim about the nature of scientific theories rather than a claim about the nature of the subject matter of biology resting upon a presystematic judgement.     

About emergent properties and complexity in biological theories.

Our aim is to present some ideas about the notion of scientific theory which includes the biological theories. We examine relationships among theories and examples of theoretical situations. In this context we propose definitions of emergent property and complexity. These definitions are exemplified by the development of some biological theories.     

Is information a proper observable for biological organization?

In the last century, jointly with the advent of computers, mathematical theories of information were developed. Shortly thereafter, during the ascent of molecular biology, the concept of information was rapidly transferred into biology at large. Several philosophers and biologists have argued against adopting this concept based on epistemological and ontological arguments, and also, because it encouraged genetic determinism. While the theories of elaboration and transmission of information are valid mathematical theories, their own logic and implicit causal structure make them inimical to biology, and because of it, their applications have and are hindering the development of a sound theory of organisms. Our analysis concentrates on the development of information theories in mathematics and on the differences between these theories regarding the relationship among complexity, information and entropy.     

Acta Botanica Boreali-Occidentalia Sinca

Acta Botanica Boreali-Occidentalia Sinca is amied at publishing innovative achievements in botanical researches,introducing current trends and innovative theories in botany at home and abroad and discussing the theories and practices of botanical resources and conservancy in order to enhance the development of basic theories and applied innovative techniques in botany and serving economic construction in China.     

The Evolutionary Structure of Scientific Theories

David Hull's (1988c) model of science as a selection process suffers from a two-fold inability: (a) to ascertain when a lineage of theories has been established; i.e., when theories are descendants of older theories or are novelties, and what counts as a distinct lineage; and (b) to specify what the scientific analogue is of genotype and phenotype. This paper seeks to clarify these issues and to propose an abstract model of theories analogous to particulate genetic structure, in order to reconstruct relationships of descent and identity.     

Some comments on “Reduction”

Summary Something is wrong with current discussions about theory reduction. The question of whether higher level theories are reducible to lower level theories cannot be posed in a sensible way if methodological principles that are needed to evaluate scientific theories are disregarded. If this is recognized, the problem looses much of its alleged importance.     

Acta Botanica Boreali-Occidentalia Sinica

Acta Botanica Boreali-Occidentalia Sinica is amied at publishing innovative achievements in botanical researches,introducing current trends and innovative theories in botary at home and abroad and discussing the theories and practices of botanical resources and conservancy in order to enhance the development of basic theories and applied innovative techniques in botany and serving economic construction in China.     

Microbiology of the phyllosphere: a playground for testing ecological concepts

Many concepts and theories in ecology are highly debated, because it is often difficult to design decisive tests with sufficient replicates. Examples include biodiversity theories, succession concepts, invasion theories, coexistence theories, and concepts of life history strategies. Microbiological tests of ecological concepts are rapidly accumulating, but have yet to tap into their full potential to complement traditional macroecological theories. Taking the example of microbial communities on leaf surfaces (i.e. the phyllosphere), we show that most explorations of ecological concepts in this field of microbiology focus on autecology and population ecology, while community ecology remains understudied. Notable exceptions are first tests of the island biogeography theory and of biodiversity theories. Here, the phyllosphere provides the unique opportunity to set up replicated experiments, potentially moving fields such as biogeography, macroecology, and landscape ecology beyond theoretical and observational evidence. Future approaches should take advantage of the great range of spatial scales offered by the leaf surface by iteratively linking laboratory experiments with spatial simulation models.     

Hippocampus and memory. Can we have our place and fear it too?

Theories of hippocampal function are often split into cognitive map theories and relational/episodic memory theories. In this issue of Neuron, show that hippocampal cells respond to the combination of spatial location and conditioned stimuli in a nonspatial fear conditioning task, suggesting a potential bridge between the competing theories of hippocampal function.     

Acta Botanica Boreali-Occidentalia Sinica

Acta Botanica Boreali-Occidentalia Sinica is amied at publishing innovative achievements in botanical researches,introducing current trends and innovative theories in botany at home and abroad and discussing the theories and practices of botanical resources and conservancy in order to enhance the development of basic theories and applied innovative techniques in botany and serving economic construction in China.     

Acta Botanica Boreali-Occidentalia Sinica

Acta Botanica Boreali-Occidentalia Sinica is amied at publishing innovative achievements in botanical researches,introducing current trends and innovative theories in botany at home and abroad and discussing the theories and practices of botanical resources and conservancy in order to enhance the development of basic theories and applied innovative techniques in botany and serving economic construction in China.     

A pluralist approach to sex and recombination

One of the greatest challenges for evolutionary biology is explaining the widespread occurrence of sexual reproduction and the associated process of genetic recombination. A large number of theories have been developed that provide a sufficient short-term advantage for sex to offset its two-fold cost. These theories can be broadly classified into environmental (or ecological) and mutation-based models. Traditionally, the different theories have been viewed as competing, and empirical work has attempted to distinguish between them. Here we highlight the advantages that may be gained from considering that multiple mechanisms (environmental and mutational) may be at work, and that interactions between the theories may be very important.     

南亚热带退化生态系统恢复和重建的生态学理论和应用

退化生态系统的恢复与重建是一项十分复杂的系统工程,其功能和动态过程涉及物质、能量、空间、时间和多样性等基本的生态变量。在南亚热带的气候生态因子中,既有光、温、水充裕的有利一面,也有秋旱、台风和暴雨等不利的因素,但总的来说,影响退化生态系统恢复的主导生态因子是土壤因子,如土壤肥力和土壤水份。极度退化的生态系统的恢复与重建,第一步就是控制水土流失,提高土壤肥力和土壤理化结构,这还需要工程措施和生物措施相结合．退化生态系统的植被的恢复与重建,最有效和最省力的是顺从生态系统的演替发展规律来进行,生态系统演替理论是指导退化生态系统重建的重要的理论基础．退化生态系统恢复与重建的优化结构的构建,依赖于对空间、生物、能量生态学原理的理解。种群密度制约、种群空间分布格局、边缘效应、生态位分化、食物链、生物多样性等原理均对生态系统结构的构建有指导意义．而生态系统的群体发展,则受物质定律的影响．