生物进化研究的回顾与展望

生物进化是自然科学的永恒之迷。随着历史的发展和科学的进步,生物进化思想从早期的萌芽,到自然选择学说、新达尔文主义,从现代综合理论,到分子进化的中性学说。再到新灾变论和点断平衡论等。当前,由于生物学各分支学科的飞速发展．它们就各自的研究对象在宏观和微观上不断地拓展和深入,并在不同的层次上形成了广泛的交叉、渗透和融合,现代的进化生物学研究从宏观的表型到微观的分子,从群体遗传改变的微进化到成种事件以及地史上生物类群谱系演化的宏进化,从直接的化石证据到基于形态性状、分子证据和环境变迁的综合推理,从基于遗传基础的比较基因组学到演化机理的进化发育生物学等。可以预见,在新的世纪里,在哲学和具体方法论(如系统论、控制论和信息论)的指导下,在生命科学、其他自然科学乃至社会科学工作者的通力合作下,综合遗传、发育和进化等研究领域的各种理论成果,生物进化理论即将出现也一定会出现的一个新的大综合和新的大统一。     

保护生物学概要

保护生物学的形成是对生物危机的反应和生物科学迅速发展的结果。它是应用科学解决由于人类活动干扰或其它因素引起的物种、群落和生态系统出现的问题的新学科。其”目的是提供保护生物多样性的原理和工具“,其基础科学和应用科学的综合性交叉学科。系统学、生态学、生物地理学和种群生态学的原理和方法是保护生物学重要的理论和实践基础。     

Synthesizing insight: artificial life as thought experimentation in biology

What is artificial life? Much has been said about this interesting collection of efforts to artificially simulate and synthesize lifelike behavior and processes, yet we are far from having a robust philosophical understanding of just what Alifers are doing and why it ought to interest philosophers of science, and philosophers of biology in particular. In this paper, I first provide three introductory examples from the particular subset of artificial life I focus on, known as ‘soft Alife’ (s-Alife), and follow up with a more in-depth review of the Avida program, which serves as my case study of s-Alife. Next, I review three well-known accounts of thought experiments, and then offer my own synthesized account, to make the argument that s-Alife functions as thought experimentation in biology. I draw a comparison between the methodology of the thought-experimental world that yields real-world results, and the s-Alife research that informs our understanding of natural life. I conclude that the insights provided by s-Alife research have the potential to fundamentally alter our understanding of the nature of organic life and thus deserve the attention of both philosophers and natural scientists.     

Synthetic biology, inspired by synthetic chemistry

The topic synthetic biology appears still as an 'empty basket to be filled'. However, there is already plenty of claims and visions, as well as convincing research strategies about the theme of synthetic biology. First of all, synthetic biology seems to be about the engineering of biology - about bottom-up and top-down approaches, compromising complexity versus stability of artificial architectures, relevant in biology. Synthetic biology accounts for heterogeneous approaches towards minimal and even artificial life, the engineering of biochemical pathways on the organismic level, the modelling of molecular processes and finally, the combination of synthetic with nature-derived materials and architectural concepts, such as a cellular membrane. Still, synthetic biology is a discipline, which embraces interdisciplinary attempts in order to have a profound, scientific base to enable the re-design of nature and to compose architectures and processes with man-made matter. We like to give an overview about the developments in the field of synthetic biology, regarding polymer-based analogs of cellular membranes and what questions can be answered by applying synthetic polymer science towards the smallest unit in life, namely a cell.     

Emotional intimacy with nature and life & intellectual interest in life of pre-service biology teachers for environmental education

We investigated emotional intimacy with nature and life, and intellectual interest in life among South Korean pre-service teachers (N = 114) training in biology education, analysing the differences between these two constructs as well as their relationship to environmental behaviour and sensitivity. In addition, differences in the respondents’ experiences of nature, concerns about environmental problems and willingness to perform environmental education were explored. Four groups of pre-service biology teachers, categorised by the two investigated personal variables, showed different responses for the environment-related characteristics and other variables. Our results suggest that biology teachers should have higher emotional and intellectual interest in nature and life, and a balance between emotional intimacy with nature and life, and intellectual interest in life is needed to prepare them.     

Undergraduate structural biology education: A shift from users to developers of computation and simulation tools

The use of theory and simulation in undergraduate education in biochemistry, molecular biology, and structural biology is now common, but the skills students need and the curriculum instructors have to train their students are evolving. The global pandemic and the immediate switch to remote instruction forced instructors to reconsider how they can use computation to teach concepts previously approached with other instructional methods. In this review, we survey some of the curricula, materials, and resources for instructors who want to include theory, simulation, and computation in the undergraduate curriculum. There has been a notable progression from teaching students to use discipline-specific computational tools to developing interactive computational tools that promote active learning to having students write code themselves, such that they view computation as another tool for solving problems. We are moving toward a future where computational skills, including programming, data analysis, visualization, and simulation, will no longer be considered an optional bonus for students but a required skill for the 21st century STEM (Science, Technology, Engineering, and Mathematics) workforce; therefore, all physical and life science students should learn to program in the undergraduate curriculum.     

Make biology relevant again! Pre-service teachers’ views on the relevance of biology education

ABSTRACT

Biology education should be relevant to young students so that they can become interested in biology and understand biological topics in their everyday and vocational lives. We conducted interviews and collected mind maps to examine Finnish pre-service biology teachers’ (N = 16) views on the relevance of biology education. Furthermore, we analysed Finnish secondary school biology curricula, which were compared with the pre-service teachers’ answers. We classified the views on relevance into nine main categories using grounded theory as the methodological frame of reference. Pre-service teachers emphasised the relevance of biology to the student’s own life, whereas scientific practices and the nature of science were expressed in secondary school curricula more often. Novice pre-service teachers put more value on general knowledge, while more experienced pre-service teachers were more likely to mention sustainable futures and societal aspects in their reasoning. Based on the results, we identified two stages in the development of the views. This study suggests that pedagogical studies, teaching experience and teacher training have an impact on the pre-service teachers’ views about the relevance of biology education. Moreover, we could find differences between curricula and pre-service teachers’ views, especially regarding scientific practices and the role of the nature of science in biology education.     

Exploring the Relationships among Epistemological Beliefs, Nature of Science, and Conceptual Change in the Learning of Evolutionary Theory

We explored the relationship between epistemological beliefs and nature of science in a college biology course. One hundred thirty-three college students participated in the research. Exploratory factor analysis with 29 Nature of Science (NOS) items yielded three aspects of NOS: empirical, tentative, and sociocultural nature of scientific knowledge. Pearson r correlations suggested that students who have immature epistemological beliefs are more likely to also have immature beliefs of nature of science. In addition, students’ epistemological beliefs significantly correlate with their conceptual change but their beliefs about nature of science did not. The research is significant in that it provides empirical evidence explaining the relationship between students’ epistemological beliefs and nature of science as well as the relationships between epistemological beliefs and conceptual change in evolution theory.     

Acceptance of Evolution Increases with Student Academic Level: A Comparison Between a Secular and a Religious College

Acceptance of evolution among the general public, high schools, teachers, and scientists has been documented in the USA; little is known about college students’ views on evolution; this population is relevant since it transits from a high-school/parent-protective environment to an independent role in societal decisions. Here we compare perspectives about evolution, creationism, and intelligent design (ID) between a secular (S) and a religious (R) college in the Northeastern USA. Interinstitutional comparisons showed that 64% (mean S + R) biology majors vs. 42/62% (S/R) nonmajors supported the exclusive teaching of evolution in science classes; 24/29% (S/R) biology majors vs. 26/38% (S/R) nonmajors perceived ID as both alternative to evolution and/or scientific theory about the origin of life; 76% (mean S + R) biology majors and nonmajors accepted evolutionary explanations about the origin of life; 86% (mean S + R) biology majors vs. 79% (mean S + R) nonmajors preferred science courses where human evolution is discussed; 76% (mean S+R) biology majors vs. 79% (mean S + R) nonmajors welcomed questions about evolution in exams and/or thought that such questions should always be in exams; and 66% (mean S + R) biology majors vs. 46% (mean S + R) nonmajors admitted they accept evolution openly and/or privately. Intrainstitutional comparisons showed that overall acceptance of evolution among biologists (S or R) increased gradually from the freshman to the senior year, due to exposure to upper-division courses with evolutionary content. College curricular/pedagogical reform should fortify evolution literacy at all education levels, particularly among nonbiologists.     

An exploratory study of student teachers’ conceptions of teaching life science outdoors

Abstract

The purpose of this exploratory qualitative study was to investigate elementary student teachers’ conceptions of teaching life science outdoors. The study involved 99 student teachers who were enrolled in an elementary science methods course at a large public university in the United States of America. The study utilised drawings, and narratives to investigate the nature of these teachers’ conceptions. Data analysis revealed that three conceptions of teaching life science were common among the participants: (1) teaching life science is predominantly conceptualised as being situated in the schoolyard, (2) teaching life science outdoors is teacher-directed, and (3) teaching life science outdoors is disconnected from in-class science instruction. Implications include the need for (1) teacher education programmes to provide reflective supports that explicate student teachers’ conceptualisation of teaching life science and thus exposing prior frameworks; and (2) teacher educators to examine student teachers’ prior frameworks for teaching life science outdoors and provide knowledgeable theory and practice platforms that will serve as frameworks for student teachers to adopt, connect and routinize outdoor life science teaching with in-school teaching of life science.     

The Nature of Folk-Botanical Life Forms

Original work by Brent Berlin, Eugene Hunn, Cecil Brown, and other ethnoscientists has produced significant findings pertaining to claims of universality for folk-biological ranks, in general, and folk-botanical life forms, in particular. These findings implicitly call into question conventional wisdom in the history of biology, which tends to consider life forms as the outworn vestiges of scholastic tradition or as merely socially practical ways of carving up the living world. Unfortunately, however, ethnobiologists continue to rely on faulty analytical schema for assessing the nature of life forms which philosophers and historians of biology have developed in their ignorance of the popular conceptual foundations of folk taxonomy. The error is compounded by the adoption into ethnosystematics of the most empiricistically reductionist, and logically confused, interpretation of such schema that derives from the neo-Adansonian, or pheneticist, school of modern system-atics. This interpretation confounds (1) meaning and reference, (2) the semantics of cognitively distinct object domains, and (3) the conceptual differences between common sense and science. These points are challenged, and it is concluded that life forms, though anthropocentrically biased, are no more "artificial" or "special-purpose" than higher-order scientific taxa. Finally, the problem of so-called "unaffiliated" and "ambiguous" generics is addressed and a new analysis offered.     

Mechanism and vitalism. A history of the controversy

This is an attempt to interpret the history of mechanism vs. vitalism in relation to the changing framework of culture and to show the interrelation between both these views and experimental science. After the scientific revolution of the seventeenth century, causal mechanism of classical physics provided the framework for the study of nature. The teleological and holistic properties of life, however, which are incompatible with this theory yielded — as a result both of internal developments within biology and of a general reaction against dogmatic rationalism — to a vitalistic interpretation of life which ascribed a mysterious force to living organisms. It will be shown that both mechanism and vitalism are related to the experimental climate of the time in which they were popular. The controversy has now lost its raison d'être as a result of the development of the theory of systems and of a better understanding of the chemistry and evolution of life.     

合成生物学伦理、法律与社会问题探讨

合成生物学是以基因组学、系统生物学知识和分子生物学技术为基础,综合了科学与工程的一门新兴交叉学科。它使生命科学和生物技术研发进入了以人工设计、合成自然界中原本不曾出现的人造生命体系,以及对这些人工体系进行体内、体外优化,或利用这些人造生命体系研究自然生命规律为目标的新时代。然而,合成生物学研究在迅速发展、表现出巨大潜力和应用前景的同时,也引发了社会各界对相关社会、伦理、安全,以及知识产权等问题的重视与讨论。就世界各国针对合成生命对传统意义上生命概念的挑战、合成生物学产品存在的潜在风险危害、合成生物学研究的风险评估与监管等问题进行回顾综述和相关探讨。     

Darwin's artificial selection as an experiment

Darwin used artificial selection (ASN) extensively and variedly in his theorizing. Darwin used ASN as an analogy to natural selection; he compared artificial to natural varieties, hereditary variation in nature to that in the breeding farm; and he also compared the overall effectiveness of the two processes. Most historians and philosophers of biology have argued that ASN worked as an analogical field in Darwin's theorizing. I will argue rather that this provides a limited and somewhat muddled view of Darwinian science. I say "limited" because I will show that Darwin also used ASN as a complex experimental field. And I say "muddled" because, if we concentrate on the analogical role exclusively, we conceive Darwinian science as rather disconnected from contemporary conceptions of "good science". I will argue that ASN should be conceived as a multifaceted experiment. As a traditional experiment, ASN established the efficacy of Darwin's preferred cause: natural selection. As a non-traditional experiment, ASN disclosed the nature of a crucial element in Darwin's evolutionary mechanics: the nature of hereditary variation. Finally, I will argue that the experiment conception should help us make sense of Darwin's comments regarding the "monstrous" nature of domestic breeds traditionally considered to be problematic.     

Sex, Death, and Evolution in Proto- and Metazoa, 1876–1913

In the period 1875–1920, a debate about the generality and applicability of evolutionary theory to all organisms was motivated by work on unicellular ciliates like Paramecium because of their peculiar nuclear dualism and life cycles. The French cytologist Emile Maupas and the German zoologist August Weismann argued in the 1880s about the evolutionary origins and functions of sex (which in the ciliates is not linked to reproduction), and death (which appeared to be the inevitable fate of lineages denied sexual conjugation), an argument rooted in the question of whether the ciliates and their processes where homologous to other cellular organisms. In the beginning of the twentieth century, this question of homology came to be less important as the ciliates were used by the British protozoologist Clifford Dobell and the American zoologist Herbert Spencer Jennings to study evolutionary processes in general rather than problems of development and cytology. For them, homology mattered less than analogy. This story illustrates two partially distinct problems in evolutionary biology: first, the question of whether all living things have common features and origins; and second, whether their history and current nature can be described by identical mechanisms. Where Maupas (contra Weismann) made the ciliates qualitatively the same as all other organisms in order to create a cohesive evolutionary theory for biology, Jennings and Dobell made them qualitatively different in order to achieve the same end. This revised version was published online in July 2006 with corrections to the Cover Date.     

Synthetic Biology and the Moral Significance of Artificial Life: A Reply to Douglas,Powell and Savulescu

I discuss the moral significance of artificial life within synthetic biology via a discussion of Douglas, Powell and Savulescu's paper 'Is the creation of artificial life morally significant’. I argue that the definitions of 'artificial life’ and of 'moral significance’ are too narrow. Douglas, Powell and Savulescu's definition of artificial life does not capture all core projects of synthetic biology or the ethical concerns that have been voiced, and their definition of moral significance fails to take into account the possibility that creating artificial life is conditionally acceptable. Finally, I show how several important objections to synthetic biology are plausibly understood as arguing that creating artificial life in a wide sense is only conditionally acceptable.     

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.     

The rise of a microparadigm in oncology

Summary The study of the history of ideas is usually devoted to big problems and to concluded debates. We have attempted to analyze a current theory whose fate and explanatory power is still not determined. The term microparadigm is used to define a currently and widely accepted theory limited in time and in the field of application, compared to the greater problems usually investigated by historians of science. Among the characteristics defining a microparadigm we found: 1) the status of an accepted theory with creative scientific power; 2) the presence of anomalies and unproven inferences; 3) a limited field of application; 4) the peculiarity of interaction with non-scientific ideas. In this context, we discuss the rise of the current microparadigm concerning the pathogenesis and biology of lymphoid neoplasms. We show that the current view of the neoplastic lymphoid cells as populations frozen at a particular differentiative stage has been creative for the last 10 years, thus allowing the generation of a large body of data that would not have been collected within the previous view of the leukemic cell as completely anarchic. This paradigm, although containing some anomalies, has survived the impact of molecular biology in hematology and is still creative. We think that microparadigms are widely distributed in everyday science and that an analysis of them is as useful for active scientist as is the study of macroparadigms, which by themselves cannot be representative of everyday science. Finally, the study of microparadigms while they are still operative can be useful to evidence the weakness of the theory and to suggest where new data should be sought.     

Popper, falsifiability, and evolutionary biology

First, a brief history is provided of Popper's views on the status of evolutionary biology as a science. The views of some prominent biologists are then canvassed on the matter of falsifiability and its relation to evolutionary biology. Following that, I argue that Popper's programme of falsifiability does indeed exclude evolutionary biology from within the circumference of genuine science, that Popper's programme is fundamentally incoherent, and that the correction of this incoherence results in a greatly expanded and much more realistic concept of what is empirical, resulting in the inclusion of evolutionary biology. Finally, this expanded concept of empirical is applied to two particular problems in evolutionary biology — viz., the species problem and the debate over the theory of punctuated equilibria — and it is argued that both of them are still mainly metaphysical.