N.K. Kol'tsov's theory of synthetic biology

The state of theoretical biology in the twentieth century is characterized, as well as the appearance and development of N.K. Kol'tsov's scientific program, his original methodology of interdisciplinary synthesis, and, based on it, the concept of theoretical biology.     

The strategy concept and John Maynard Smith’s influence on theoretical biology

Here we argue that the concept of strategies, as it was introduced into biology by John Maynard Smith, is a prime illustration of the four dimensions of theoretical biology in the post-genomic era. These four dimensions are: data analysis and management, mathematical and computational model building and simulation, concept formation and analysis, and theory integration. We argue that all four dimensions of theoretical biology are crucial to future interactions between theoretical and empirical biologists as well as with philosophers of biology.     

免疫学技术在细胞生物学教学中的应用

免疫学技术在细胞生物学理论与实验课程中具有重要的应用价值,两者的有机结合能使细胞生物学课程教学更丰富形象,有利于教学质量的提高。目前,免疫学技术普遍只停留于细胞生物学理论课本知识教授中,在对学生开展的细胞实验操作课程中应用较少。如能将免疫荧光标记、流式细胞术等相关技术引入到实验教程中,不仅能使细胞实验结果更形象生动,更能拓宽学生知识领域与实验技能,有利于其综合能力的培养。     

M.M. Kamshilov's Informational–Biogeochemical Concept of Life

The broad interdisciplinary synthesis based on theoretical biology and biospheric ecology attempted by M.M. Kamshilov, a disciple of A.S. Serebrovsky, I.I. Schmalhausen, and V.I. Vernadsky, and his original informational–biogeochemical concept of life were described.     

Parts and Theories in Compositional Biology

I analyze the importance of parts in the style of biological theorizing that I call compositional biology. I do this by investigating various aspects, including partitioning frames and explanatory accounts, of the theoretical perspectives that fall under and are guided by compositional biology. I ground this general examination in a comparative analysis of three different disciplines with their associated compositional theoretical perspectives: comparative morphology, functional morphology, and developmental biology. I glean data for this analysis from canonical textbooks and defend the use of such texts for the philosophy of science. I end with a discussion of the importance of recognizing formal and compositional biology as two genuinely different ways of doing biology – the differences arising more from their distinct methodologies than from scientific discipline included or natural domain studied. Ultimately, developing a translation manual between the two styles would be desirable as they currently are, at times, in conflict.     

Mixing ecology and epidemiology.

Mixing matrices can be used to describe subgroup interactions in mathematical models which have heterogeneity in population structure. A discussion is presented of two different approaches to the formulation of such mixing matrices. The relation between the two different methods is discussed, using examples based upon models of the transmission dynamics of HIV. There follows a discussion of the application of the mixing matrix approach to other areas in population biology, and a complementary overview of recent advances in theoretical ecology that may have applications in theoretical epidemiology.     

Theoretical models of wound healing: past successes and future challenges

The complex biology of wound healing is an area in which theoretical modelling has already made a significant impact. In this review article, the authors describe the key features of wound healing biology, divided into four components: epidermal wound healing, remodelling of the dermal extracellular matrix, wound contraction, and angiogenesis. Within each of these categories, previous modelling work is described, and the authors identify what they regard as the main challenges for future theoretical work.     

Methodology of biological thought in works of V. N. Beklemisheva (1890-1862)

During his work in Perm University (1918-1932) Vladimir Nikolaevich Beklemishev created theoretical and methodological foundations for the concepts of constructive morphology and structure of the living cover of the Earth. His conclusions about topical problems of general biology are still valuable for biological thinking.     

Conditions for a theoretical biology: is biology truly an autonomous science?

In a line of a previous paper, the conditions for a theoretical biology were discussed and it was pointed out that the primary condition is that biology is an autonomous science. This statement is connected to the problem of reductionism. A discussion of the autonomy of biology shows that reductionism cannot be maintained, although particularly in physiology often physics and mathematics are used. Development, organization and evolution of biological systems are typical areas of autonomous biological researches and of autonomous theoretical developments. A sort of reduction to history seems today a nonsensical attempt to reduce the area of free theoretical biological activity.     

基于前沿热点案例的合成生物学教学模式的探索与实践北大核心CSCD

作为一门理论性与应用性都很强的课程,“合成生物学”对生物工程领域创新性人才培养发挥着至关重要的作用。为此,华中农业大学开设了“合成生物学”课程。首先,以“重基础知识、抓创新实践、追前沿进展”为理念,通过组建高水平的“合成生物学”教学团队,并不断调整优化课程内容,形成了新颖合理的课程体系。其次,在教学过程中,及时将高水平学术期刊及时事热点新闻报道中有关合成生物学的案例引入课堂教学中,丰富了教学内容,提高了学生的学习兴趣。再次,以前沿热点案例为切入点,通过以“学”为中心的授课模式,引导学生深入探讨,提高了学生的思辨思维与创新能力。本课程取得了很好的教学效果,并有效促进了创新型人才培养,在此与同行交流,以期能为“合成生物学”及相关课程的教学改革提供一些新的启发与思考。     

Homology in comparative, molecular, and evolutionary developmental biology: the radiation of a concept

The present paper analyzes the use and understanding of the homology concept across different biological disciplines. It is argued that in its history, the homology concept underwent a sort of adaptive radiation. Once it migrated from comparative anatomy into new biological fields, the homology concept changed in accordance with the theoretical aims and interests of these disciplines. The paper gives a case study of the theoretical role that homology plays in comparative and evolutionary biology, in molecular biology, and in evolutionary developmental biology. It is shown that the concept or variant of homology preferred by a particular biological field is used to bring about items of biological knowledge that are characteristic for this field. A particular branch of biology uses its homology concept to pursue its specific theoretical goals.     

Enzymes and theoretical biology: sketch of an informational perspective of the cell.

In the theoretical scenarios of biology, new insights can be gained by the introduction of information-processing and artificial intelligence concepts, helping to organize the explanation of the many intra- and inter-cellular phenomena that molecular biology is accumulating. Enzymes contain some of the immediate clues; the whole informational processing of prokaryotic cells is another central subject of search. Additionally, prolonging the informational perspective of the cell, a significant parallel can be drawn between informational processes in biological, social and artificial intelligence systems. A more tangible definition of biological complexity and biological intelligence emerges.     

A theoretical framework for defining some concepts in evolution.

We present a theoretical framework for biological evolution with the intention of giving precise mathematical definitions of some concepts in evolutionary biology such as fitness, evolutionary pressure, specialization and natural selection. In this framework, such concepts are identified with well-known mathematical terms within the theory of dynamical systems. We also discuss some more general implications in evolution; for instance, the fact that our model naturally exhibits a frequency spectrum of the type 1/f for low frequencies of evolutionary events.     

Timing matters

Cells are entities in space and time. Systems biology strives to understand their composition, structural organization as well as dynamic behavior under different conditions. Here, measures for dynamic properties such as characteristic times, time hierarchy and time-dependent response are reviewed. Using a number of examples from yeast and micro-organism systems biology, the importance of considering the timing in experimental and theoretical research is discussed.     

The Galton-Watson branching process as a quantitative tool in parasitology.

Stochastic growth processes abound in the biology of parasitism, and one mathematical tool that is particularly well suited for describing such phenomena is the Galton-Watson branching process. Introduced more than a century ago to settle a debate over the rate of disappearance of surnames in the British peerage, branching processes are applied today in fields as diverse as quantum physics and theoretical computer science. In this article, Dale Taneyhill, Alison Dunn and Melanie Hatcher provide a simple introduction to branching processes, and demonstrate their uses in quantitative parasitology.     

Lipid,lipoprotein, and apolipoprotein models: past,present, and future

Mones Berman's untimely death on 12 August 1982 put an end to his work in the development of theoretical biology. Arguments are examined, and it is concluded that a formal theory of lipoprotein metabolism flourished and expanded under the guidance of Dr. Berman. Not many scientists in the field of biology spend a major portion of their energies on theoretical work xxx was outstanding because of his early decision to follow the theoretical path.     

Lysenko's contributions to biology and his tragedies.

Trofim Denisovich Lysenko's life and work have been much analyzed and discussed in the world's literature. It is well known that Lysenko is notorious and has been regarded as a charlatan. Less well known is that he once made greater contributions to Biology and has been misunderstood in some aspects. In this paper, Lysenko s contributions to plant physiology, genetics, agro-biology and evolutionary biology are briefly reviewed. His tragedies and mistakes, such as mixing science and politics, denying the existence of genes, failing to build up suitable scientific collectives for the metabolism-biochemical studies of heredity, as well as his theoretical one-sidedness, are also discussed, thus reconsidering the case of Lysenko from a comprehensive and objective viewpoint.     

The mathematical biophysics of Nicolas Rashevsky

N. Rashevsky (1899-1972) was one of the pioneers in the application of mathematics to biology. With the slogan: mathematical biophysics : biology :: mathematical physics ; physics, he proposed the creation of a quantitative theoretical biology. Here, we will give a brief biography, and consider Rashevsky's contributions to mathematical biology including neural nets and relational biology. We conclude that Rashevsky was an important figure in the introduction of quantitative models and methods into biology.     

Disentangling the complexities of vertebrate sex allocation: a role for squamate reptiles?

Sex allocation is an important field in evolutionary biology, both historically and currently. However, while sex allocation theory has successfully predicted sex ratio bias in some taxa, most notably parasitic wasps, vertebrates are notorious for their poor fit to theoretical models. We argue that this arises from the use of very complex model systems to test relatively simple theoretical models. We further argue that squamate reptiles – lizards and snakes – have unduly been neglected in sex allocation studies and in fact may conform more readily to the underlying assumptions of existing theoretical models than many other vertebrates. We provide a five-point argument in favor of the use of squamates as model systems in sex allocation based on their diversity in sex determining mechanisms, life history biology, and ease of experimental manipulations.