Coregulation mapping based on individual phenotypic variation in response to virus infection

Background

Biology is moving fast toward the virtuous circle of other disciplines: from data to quantitative modeling and back to data. Models are usually developed by mathematicians, physicists, and computer scientists to translate qualitative or semi-quantitative biological knowledge into a quantitative approach. To eliminate semantic confusion between biology and other disciplines, it is necessary to have a list of the most important and frequently used concepts coherently defined.

Results

We propose a novel paradigm for generating new concepts for an ontology, starting from model rather than developing a database. We apply that approach to generate concepts for cell and molecule interaction starting from an agent based model. This effort provides a solid infrastructure that is useful to overcome the semantic ambiguities that arise between biologists and mathematicians, physicists, and computer scientists, when they interact in a multidisciplinary field.

Conclusions

This effort represents the first attempt at linking molecule ontology with cell ontology, in IMGT-ONTOLOGY, the well established ontology in immunogenetics and immunoinformatics, and a paradigm for life science biology. With the increasing use of models in biology and medicine, the need to link different levels, from molecules to cells to tissues and organs, is increasingly important.     

历久弥新：进化中的代谢工程

20世纪90年代,Bailey及Stephanopoulos等提出了经典代谢工程的理念,旨在利用DNA重组技术对代谢网络进行改造,以达到细胞性能改善,目标产物增加的目的。自代谢工程诞生以来的30年,生命科学蓬勃发展,基因组学、系统生物学、合成生物学等新学科不断涌现,为代谢工程的发展注入了新的内涵与活力。经典代谢工程研究已进入到前所未有的系统代谢工程阶段。组学技术、基因组代谢模型、元件组装、回路设计、动态控制、基因组编辑等合成生物学工具与策略的应用,大大提升了复杂代谢的设计与合成能力;机器学习的介入以及进化工程与代谢工程的结合,为系统代谢工程的未来开辟了新的方向。文中对过去30年代谢工程的发展趋势作了梳理,介绍了代谢工程在发展中不断创新的理论与方法及其应用。     

Emancipation Through Interaction – How Eugenics and Statistics Converged and Diverged

The paper discusses the scope and influence of eugenics in defining the scientific programme of statistics and the impact of the evolution of biology on social scientists. It argues that eugenics was instrumental in providing a bridge between sciences, and therefore created both the impulse and the institutions necessary for the birth of modern statistics in its applications first to biology and then to the social sciences. Looking at the question from the point of view of the history of statistics and the social sciences, and mostly concentrating on evidence from the British debates, the paper discusses how these disciplines became emancipated from eugenics precisely because of the inspiration of biology. It also relates how social scientists were fascinated and perplexed by the innovations taking place in statistical theory and practice.     

Interface Biology of Implants

Implants are widely used in various clinical disciplines to replace or stabilize organs. The challenge for the future is to apply implant materials to specifically control the biology of the surrounding tissue for repair and regeneration. This field of research is highly interdisciplinary and combines scientists from technical and life sciences disciplines. To successfully apply materials for regenerative processes in the body, the understanding of the mechanisms at the interface between cells or tissues and the artificial material is of critical importance. The research focuses on stem cells, design of material surfaces, and mechanisms of cell adhesion. For the third time around 200 scientists met in Rostock, Germany for the international symposium “Interface Biology of Implants.” The aim of the symposium is to promote the interdisciplinary dialogue between the scientists from the different disciplines to develop smart implants for medical use. In addition, researchers from basic sciences, notably cell biology presented new findings concerning mechanisms of cell adhesion to stimulate research in the applied field of implant technology.Key words: interface, implant, stem cells, adhesion, mechanics, surface, biomaterialMedical implants play a growing role in routine clinical practice. In addition to replace or stabilize injured tissue permanently or transiently, the application of implant materials to stimulate the regeneration of tissue is becoming a challenge in the field of regenerative medicine. The use of implant materials is based on the idea that biomaterials function not only as mechanical support for cells and tissue but also provide a matrix to induce signal transduction in the cells that control complex molecular mechanisms responsible for proliferation und differentiation. In this context, the interface between artificial materials and living cells or tissue is an exciting field of great scientific interest and constitutes one of the most dynamic and expanding field in science and technology. Progress in this field is mainly driven by the fundamental importance for clinical applications. The research is characterized by a multidisciplinary collaboration between physics, engineers, biologists and clinicians.In May 2009, for the third time after 2003 and 2006 around 200 scientists met in Rostock-Warnemünde for the symposium “Interface Biology of Implants” to discuss biointerface processes at a fundamental level. The main goals of this symposium are to simulate the interdisciplinary dialogue between scientists of the different disciplines and to introduce current knowledge of basic research in cell biology and material science into the applied field of implant technology. The programme was organized in invited presentations of 20 internationally renowned scientists and complemented by short talks of mostly young scientists selected from the submitted abstracts. In addition, 80 posters presented latest results in this multidisciplinary field.The symposium was opened with a keynote lecture presented by Hartmut Hildebrand (Lille). He gave an overview about the 7,000 years old history of application of implant materials. Rare photographs were shown which demonstrated that in these early times prostheses mainly made from metallic materials were used to restore teeth, extremities and the skull of the human body. These old documents stressed the historical relevance of medical application of implant materials.The symposium on two days was composed of four sessions covering the interdisciplinary research in the field. The session “Stem cells and biomaterials” discussed the biological response and signalling mechanism of stem cells in the interaction with a material surface. The session “Bioactivation of implant surfaces” focussed on the tailoring of surfaces to control the cell physiology. To stimulate the field by recent data in basic cell biology, talks were presented in the third session, dealing with molecular mechanisms involved in cell adhesion. A special session dealt with the role and mechanism of controlling cells by mechanics.     

Interface Biology of Implants

Implants are widely used in various clinical disciplines to replace or stabilize organs. The challenge for the future is to apply implant materials to specifically control the biology of the surrounding tissue for repair and regeneration. This field of research is highly interdisciplinary and combines scientists from technical and life sciences disciplines. To successfully apply materials for regenerative processes in the body, the understanding of the mechanisms at the interface between cells or tissues and the artificial material is of critical importance. The research focuses on stem cells, design of material surfaces, and mechanisms of cell adhesion. For the third time around 200 scientists met in Rostock, Germany for the international symposium “Interface Biology of Implants”. The aim of the symposium is to promote the interdisciplinary dialogue between the scientists from the different disciplines to develop smart implants for medical use. In addition, researchers from basic sciences, notably cell biology presented new findings concerning mechanisms of cell adhesion to stimulate research in the applied field of implant technology.     

Trends in computational biology: a summary based on a RECOMB plenary lecture, 1999.

Computational biology, a term coined from analogy to the role of computing in the physical sciences, is now coming into its own as a major element of contemporary biological and biomedical research. Information science and computational science provide essential tools for next generation biological science efforts, from focusing the direction of experimental studies to providing knowledge and insight that can not otherwise be obtained. Going beyond the revolution in biology reflected in the successes of the genome project and driven by the power of molecular biology techniques, computational approaches will provide an underpinning for the integration of broad disciplines for development of a quantitative systems approach to understanding the mechanisms in the life of the cell.     

Interrelationship Between Fractal Ornament and Multilevel Selection Theory

Interdisciplinarity is one of the features of modern science, defined as blurring the boundaries of disciplines and overcoming their limitations or excessive specialization by borrowing methods from one discipline into another, integrating different theoretical assumptions, and using the same concepts and terms. Often, theoretical knowledge of one discipline and technological advances of another are combined within an interdisciplinary science, and new branches or disciplines may also emerge. Biosemiotics, a field that arose at the crossroads of biology, semiotics, linguistics, and philosophy, enables scientists to borrow theoretical assumptions from semiotics and extend them to different biological theories. The latter applies especially to extended synthesis, wherein culture is viewed as one of the factors influencing evolution. In the present research, the semiotic system of Ukrainian folk ornament is analyzed through the theory of fractals, key features of which are recursion and self-similarity. As a result, an assumption is made about the fractal structure of culture and social life on a conceptual level. What follows is a discussion of how this assumption can contribute to the multilevel selection theory, one of the foundations of extended synthesis, which employs the concept of self-similarity at all levels of the biological hierarchy.     

Lysenko Affair and Polish Botany

This article describes the slight impact of Lysenkoism upon Polish botany. I begin with an account of the development of plant genetics in Poland, as well as the attitude of scientists and the Polish intelligentsia toward Marxist philosophy prior to the World War II. Next I provide a short history of the introduction and demise of Lysenkoism in Polish science, with a focus on events in botany, in context with key events in Polish science from 1939 to 1958. The article outlines the little effects of Lysenkoism upon botanists and their research, as well as how botanists for the most part rejected what was often termed the “new biology.” My paper shows that though Lysenko’s theories received political support, and were actively promoted by a small circle of scientists and Communist party activists, they were never accepted by most botanists. Once the political climate in Poland altered after the events of 1956, Lysenko’s theories were immediately abandoned.     

The Professionalization of Science Studies: Cutting Some Slack

During the past hundred years or so, those scholars studying science have isolated themselves as much as possible from scientists as well as from workers in other disciplines who study science. The result of this effort is history of science, philosophy of science and sociology of science as separate disciplines. I argue in this paper that now is the time for these disciplinary boundaries to be lowered or at least made more permeable so that a unified discipline of Science Studies might emerge. I discuss representative problems that stand in the way of such an integration. These problems may seem so formidable in the abstract that no one in their right mind would waste their time trying to bring about a unified field of Science Studies. However, those of us who limit ourselves to the study of the biological sciences have already formed a society in which workers from all disciplines can share their expertise -- the International Society for the History, Philosophy and Social Studies of Science.     

Science and policy: valuing framing, language and listening

This paper considers the context for science contributing to policy development and explores some critical issues that should inform science advocacy and influence with policy makers. The paper argues that the key challenges are at least as much in educating conservation scientists and science communicators about society and policy making as they are in educating society and policy makers about science. The importance of developing processes to ensure that scientists and science communicators invest in the development of relationships based on respect and understanding of their audience in both communities and amongst policy makers provides a critical first step. The objectives of the Global Strategy for Plant Conservation acknowledge the importance of developing the capacities and public engagement necessary to implement the Strategy, including knowledge transfer and community capacity building. However, the development of targets to equip institutions and plant conservation professionals to explicitly address the barriers to influencing policy development through knowledge transfer and integration require further consideration.     

Beyond Paradise—Meeting the Challenges in Tropical Biology in the 21st Century

Tropical ecosystems support a diversity of species and ecological processes that are unparalleled anywhere else on Earth. Despite their tremendous social and scientific importance, tropical ecosystems are rapidly disappearing. To usher tropical ecosystems and the human communities dependent upon them through the environmental transformations of the 21st century, tropical biologists must provide critical knowledge in three areas: 1) the structure and function of tropical ecosystems; 2) the nature and magnitude of anthropogenic effects on tropical ecosystems; and 3) the socio‐economic drivers of these anthropogenic effects. To develop effective strategies for conservation, restoration, and sustainable management of tropical ecosystems, scientific perspectives must be integrated with social necessities. A new set of principles built on a framework for pursuing relevant tropical biological research will facilitate interdisciplinary approaches, integrate biological knowledge with the social sciences, and link science with policy. We propose four broad recommendations for immediate action in tropical biology and conservation that are fundamental to all biological and social disciplines in the tropics: 1) assemble and disseminate information on life's diversity in the tropics; 2) enhance tropical field stations and build a worldwide network to link them with tropical field biologists at their field sites; 3) bring the field of tropical biology to the tropics by strengthening institutions in tropical countries through novel partnerships between tropical and temperate zone institutions and scientists; and 4) create concrete mechanisms to increase interactions between tropical biologists, social scientists, and policy makers.     

Towards disciplinary disintegration in biology

Interdisciplinary integration has fundamental limitations. This is not sufficiently realized in science and in philosophy. Concerning scientific theories there are many examples of pseudo-integration which should be unmasked by elementary philosophical analysis. For example, allegedly over-arching theories of stress which are meant to unite biology and psychology, upon analysis, turn out to represent terminological rather than substantive unity. They should be replaced by more specific, local theories. Theories of animal orientation, likewise, have been formulated in unduly general terms. A natural history approach is more suitable for the study of animal orientation. The tendency to formulate overgeneral theories is also present in evolutionary biology. Philosophy of biology can only deal with these matters if it takes a normative turn. Undue emphasis on interdisciplinary integration is a modern variant of the old unity of science ideal. The replacement of the ideal by a better one is an important challenge for the philosophy of science.     

Interdisciplinary integration in biology? An overview

Philosophical theories about reduction and integration in science are at variance with what is happenign in science. A realistic approach to science show that possibilities for reduction and integration are limited. The classical ideal of a unified science has since long been rejected in philosophy. But the current emphasis on interdisciplinary integration in philosophy and in science shows that it survives in a different guise. It is necessary to redress the balance, specifically in biology. Methodological analysis shows that many of the grand interdisciplinary theories involving biology actually represent pseudo-integration covered up by inappropriate, overgeneral concepts. Integrationism is not bad, but it must be kept within reasonable bounds. If the present analysis is appropriate, there will have to be fundamental changes in research strategy both in science and in the philosophy of science.     

An integrated,modular approach to data science education in microbiology

We live in an increasingly data-driven world, where high-throughput sequencing and mass spectrometry platforms are transforming biology into an information science. This has shifted major challenges in biological research from data generation and processing to interpretation and knowledge translation. However, postsecondary training in bioinformatics, or more generally data science for life scientists, lags behind current demand. In particular, development of accessible, undergraduate data science curricula has the potential to improve research and learning outcomes as well as better prepare students in the life sciences to thrive in public and private sector careers. Here, we describe the Experiential Data science for Undergraduate Cross-Disciplinary Education (EDUCE) initiative, which aims to progressively build data science competency across several years of integrated practice. Through EDUCE, students complete data science modules integrated into required and elective courses augmented with coordinated cocurricular activities. The EDUCE initiative draws on a community of practice consisting of teaching assistants (TAs), postdocs, instructors, and research faculty from multiple disciplines to overcome several reported barriers to data science for life scientists, including instructor capacity, student prior knowledge, and relevance to discipline-specific problems. Preliminary survey results indicate that even a single module improves student self-reported interest and/or experience in bioinformatics and computer science. Thus, EDUCE provides a flexible and extensible active learning framework for integration of data science curriculum into undergraduate courses and programs across the life sciences.     

On Disciplinary Fragmentation and Scientific Progress

Why are some scientific disciplines, such as sociology and psychology, more fragmented into conflicting schools of thought than other fields, such as physics and biology? Furthermore, why does high fragmentation tend to coincide with limited scientific progress? We analyzed a formal model where scientists seek to identify the correct answer to a research question. Each scientist is influenced by three forces: (i) signals received from the correct answer to the question; (ii) peer influence; and (iii) noise. We observed the emergence of different macroscopic patterns of collective exploration, and studied how the three forces affect the degree to which disciplines fall apart into divergent fragments, or so-called “schools of thought”. We conducted two simulation experiments where we tested (A) whether the three forces foster or hamper progress, and (B) whether disciplinary fragmentation causally affects scientific progress and vice versa. We found that fragmentation critically limits scientific progress. Strikingly, there is no effect in the opposite causal direction. What is more, our results shows that at the heart of the mechanisms driving scientific progress we find (i) social interactions, and (ii) peer disagreement. In fact, fragmentation is increased and progress limited if the simulated scientists are open to influence only by peers with very similar views, or when within-school diversity is lost. Finally, disciplines where the scientists received strong signals from the correct answer were less fragmented and experienced faster progress. We discuss model’s implications for the design of social institutions fostering interdisciplinarity and participation in science.     

对我国分子生态学研究近期发展战略的一些思考

分子生态学是多学科交叉的整合性研究领域, 是运用进化生物学理论解决宏观生物学问题的科学。经过半个多世纪的发展, 本学科已日趋成熟, 它不仅已经广泛渗透到宏观生物学的众多学科领域, 而且已经成为连接和融合很多不同学科的桥梁, 是目前最具活力的研究领域之一。其研究的范畴, 从最基础的理论和方法技术, 到格局和模式的发现和描述, 到对过程和机制的深入探讨, 再到付诸于实践的行动和规划指导等各个层次。分子生态学的兴起给宏观生物学带来了若干飞跃性的变化, 使宏观生物学由传统的以观察、测量和推理为主的描述性研究转变为以从生物和种群的遗传构成的变化和历史演化背景上检验、证明科学假设及揭示机制和规律为主的机制性/解释性研究, 因而使得对具有普遍意义的科学规律、生态和进化过程及机制的探索成为可能。分子生态学已经进入组学研究时代, 这使得阐明复杂生态过程、生物地理过程和适应性演化过程的机制性研究由原来难以企及的梦想变成完全可以实现的探求; 它也带来了全新的挑战, 其中最有深远影响的将是对分子生态学研究至关重要的进化生物学基础理论方面的突破, 例如遗传变异理论、种群分化理论、表观遗传因素的作用, 乃至进化生物学的基本知识构架等等。这些方面的进展必将使宏观生物学迎来一场空前的革命, 并对生态学的所有分支学科产生重大影响, 甚至催生诸如生态表观组学这样的新分支学科。对于中国科学家来说, 分子生态学组学时代的开启, 更是一个千载难逢的机遇, 为提出和建立生命科学的新方法、新假说、新思想和新理论提供了莫大的探索空间——此前我们对宏观生物学方法、理论和思想的发展贡献很小。然而, 限制组学时代重大突破的关键因素是理论、概念、理念、实验方法或分析方法方面的创新和突破, 这正是我国分子生态学研究最薄弱的环节。我国教育部门应尽快调整生命科学本科生培养的理念和方法, 以培养具备突出创新潜力的年轻一代后备人才; 同时, 科研项目资助部门和研究人员不仅应清醒地认识本学科领域的发展态势, 更要及时调整思路, 树立新的项目管理理念和治学 理念。     

What history tells us

The history of science was long considered to be something peripheral to science itself. By supplying interesting stories and gossip, it seemed, at best, to provide material for enlivening lectures. In general, it was deemed a suitable activity for retired scientists. This view has been revised considerably in the past years and indeed, today seems hopelessly out of date. History and philosophy of science are increasingly held to be an essential component of the education of scientists. By becoming acquainted with these areas, practicing scientists — and in particular biologists — can better appreciate the significance of the models and theories that underpin their research, especially with the accelerating succession of one idea by the next. The present series, of which the article that follows is the first, aims to give historical glimpses that bear on contemporary biology. The hope is that these glimpses will be both a source of inspiration and of help in resisting useless fashions.     

生态学的科学概念及其演变与当代生态学学科体系之商榷

生态学既是生物学的分支学科,也是环境科学、地球系统科学的重要组成部分,其研究成果可直接服务于植物、动物、微生物的生物多样性保护、生物资源利用及生物产业管理等应用领域.生态系统概念将经典生态学或者基础生态学研究扩展到了生态系统生态学或者生态系统科学的新阶段,奠定了大尺度及全球生态环境科学研究的理论基础,促进了生物学、地理...     

Taking the Relational Turn: Biosemiotics and Some New Trends in Biology

A cluster of similar trends emerging in separate fields of science and philosophy points to new opportunities to apply biosemiotic ideas as tools for conceptual integration in theoretical biology. I characterize these developments as the outcome of a “relational turn” in these disciplines. They signal a shift of attention away from objects and things and towards relational structures and processes. Increasingly sophisticated research technologies of molecular biology have generated an enormous quantity of experimental data, sparking a need for relational approaches that could help to find recurrent patterns in the mass of data. Earlier conceptions of relational biology and cybernetics, once deemed too abstract and speculative, are now resurrected and applied by means of new computational and simulation tools. I think this receptivity should be extended to incorporate nets of semiotic relations as heuristic guides for discerning global patterns of interactions in living systems. In this article I review aspects of systems biology and new directions in evolutionary theory, focusing on the role of circular and downward causation in relational structures and dynamical networks. I also indicate promising avenues of integration of some ideas of biosemiotics with those emerging from these new currents in biology. Relational developments in biology bear a telling similarity to a parallel relational turn presently manifest in the philosophy of science, rooted in the philosophy of physics and mathematics and in different varieties of structural and informational realism. The recognition of the relational nature of reality within these disciplines entails a tacit repudiation of nominalistic biases in science that have hindered the reception of semitiotic conceptions in biology. In previous investigations I explored connections between two kinds of relational structures: the networks of self-referential circular loops that appear pervasively in living systems, and the triadic relational structures that Peircean semiotics places at the basis of all semiotic transactions. Current relational views in the sciences seem oblivious to the difference between dyadic and triadic relations. Incorporating this essential distinction from biosemiotics into other fields could be a first step in seizing the opportunities opened by the relational turn for a renewal of biology and of natural philosophy in general, across disciplinary boundaries.     

The winemaker's bug: From ancient wisdom to opening new vistas with frontier yeast science

The past three decades have seen a global wine glut. So far, well-intended but wasteful and expensive market-intervention has failed to drag the wine industry out of a chronic annual oversupply of roughly 15%. Can yeast research succeed where these approaches have failed by providing a means of improving wine quality, thereby making wine more appealing to consumers? To molecular biologists Saccharomyces cerevisiae is as intriguing as it is tractable. A simple unicellular eukaryote, it is an ideal model organism, enabling scientists to shed new light on some of the biggest scientific challenges such as the biology of cancer and aging. It is amenable to almost any modification that modern biology can throw at a cell, making it an ideal host for genetic manipulation, whether by the application of traditional or modern genetic techniques. To the winemaker, this yeast is integral to crafting wonderful, complex wines from simple, sugar-rich grape juice. Thus any improvements that we can make to wine, yeast fermentation performance or the sensory properties it imparts to wine will benefit winemakers and consumers. With this in mind, the application of frontier technologies, particularly the burgeoning fields of systems and synthetic biology, have much to offer in their pursuit of "novel" yeast strains to produce high quality wine. This paper discusses the nexus between yeast research and winemaking. It also addresses how winemakers and scientists face up to the challenges of consumer perceptions and opinions regarding the intervention of science and technology; the greater this intervention, the stronger the criticism that wine is no longer "natural." How can wine researchers respond to the growing number of wine commentators and consumers who feel that scientific endeavors favor wine quantity over quality and "technical sophistication, fermentation reliability and product consistency" over "artisanal variation"? This paper seeks to present yeast research in a new light and a new context, and it raises important questions about the direction of yeast research, its contribution to science and the future of winemaking.