质疑、创新与合理性——纪念《植物学通报》创刊主编曹宗巽先生诞辰100周年

为纪念《植物学通报》创刊主编曹宗巽先生诞辰100周年, 该文回顾了作者与曹先生结识的机缘和承接其未竟的黄瓜(Cucumis sativus)单性花发育调控机制研究衣钵的过程, 以及从实验结果到传统解释的逻辑困境, 通过追溯曹先生当年带回国内的有关植物性别研究早期专著而找到问题源头的柳暗花明的经历。同时分享了由于这段独特而宝贵的研究经历而引发的对什么是科学研究这个基本问题的思考, 希望对有志于探索未知自然的年轻人有所裨益。     

Statistical Confusion Among Graduate Students: Sickness or Symptom?

Abstract: Statistics is one of the most important yet difficult subjects for many ecology and wildlife graduate students to learn. Insufficient knowledge about how to conduct quality science and the ongoing debate about the relative value of competing statistical ideologies contribute to uncertainties among graduate students regarding which statistical tests are most appropriate. Herein, we argue that increased education of the available statistical tests alone is unlikely to ameliorate the problem. Instead, we suggest that statistical uncertainties among graduate students are a secondary symptom of a larger problem. We believe the root cause lies in the lack of education on how to conduct science as an integrated process from hypothesis creation through statistical analysis. We argue that if students are taught to think about how each step of the process will affect all other steps, many statistical uncertainties will be avoided.     

生态学假说试验验证的原假说困境

试验方法是生态学假说的主要验证方法之一,但也存在由原假说引发的质疑.Quinn和Dunham(1983)通过对Platt(1964)的假说-演绎模型进行分析,主张生态学不可能存在可以严格被试验验证的原假说.Fisher的证伪主义与Neyman-Pearson(N-P)的非判决性使得统计学原假说不能被严格验证;而生态过程中存在的不同于经典物理学的原假说H₀(α=1,β=0)与不同的备假说H₁′(α′=1,β′=0)的情况,使得生态学原假说也很难得到严格的实验验证.通过降低P值、谨慎选择原假说、对非原假说采取非中心化和双侧验证可分别缓解上述的原假说困境.但统计学的原假说显著性验证(NHST)不应等同于生态学假说中有关因果关系的逻辑证明方法.因此,现有大量基于NHST的生态学假说的方法研究和试验验证的结果与结论都不是绝对的逻辑可靠的.     

The Green Design Apprenticeship

In order to convey the results of our industrial ecology research to broader audiences, the Green Design Institute research group at Carnegie Mellon University offers the Green Design Apprenticeship for local high school students. The Green Design Apprenticeship introduces participants to industrial ecology concepts and how they intersect with engineering. The content of the program has evolved to include the topics of life cycle assessment, energy and water resources, transportation, and the built environment. The program has resulted in exposing a new generation of scholars to industrial ecology and has also benefited the research of graduate students involved with the program. The process of developing the instructional materials for younger, novice students based on complex industrial ecology research was a challenging task requiring thoughtful and iterative planning. Through the development and delivery of the program, we have experienced awareness of where our own research fits into the larger industrial ecology scope, have improved our communication of complex industrial ecology concepts into simple terms, and have gained valuable insight for engaging students in our teaching.     

The teacher writing toolkit: enhancing undergraduate teaching of scientific writing in the biological sciences

ABSTRACT

Teaching scientific writing in biology classes is challenging for both teachers and students. This article offers and reviews several useful ‘toolkit’ items that instructors of science writing can use to improve college student success. The tools in this kit are both conceptual and practical, and include: 1) Understanding the role of student metacognition, cognitive instruction, and strategic teaching, 2) Recognition of different student writing levels, 3) Applying the writing process, 4) Demonstrational classroom revision and editing, 5) Student-teacher sentence editing, 6) Student peer editing and guided student editing, 7) Student copy-editing, 8) Reflective writing, 9) Addressing plagiarism, paraphrasing, and proper in-text citations and referencing, and 10) Using external, on campus and online resources. Additionally, we discuss the new challenges of teaching scientific writing online versus face-to-face. The discussions, approaches, and exercises presented in this paper empower teachers in assisting students in their development of a personal writing style, while simultaneously building student confidence. The tools we present augment our previous presentation of the student writing toolkit, and can improve and enhance the teaching of scientific writing to undergraduate students.     

Stimulating the Need to Know…

Nations, James D. Tropical Rainforest: Endangered Environment . New York: Franklin Watts, 1988. 143 pp. $12.90 hardcover. Reviewed by Jorge Zamacona Evenes.

Sharp, D.W.A., ed. The Penguin Dictionary of Chemistry , 2d ed. New York: Penguin, 1990. 434 pp. $9.95 paperback. Reviewed by Wayne Hanley.

Hale, W.G., and J.P. Margham. The HarperCollins Dictionary of Biology. New York: Harper Collins, 1991. 569 pp. $12.95 paperback; $25.00 hardcover. Reviewed by Wayne Hanley.

Sparks, John, and Tony Soper. Penguins. New York: Fact On File, 1987. 246 pp. $1995 hardcover. Reviewed by Wayne Hanley.

Mountfort, Guy. Rare Birds of the World . A Collins/ICBP Handbook. New York: Penguin (The Stephen Greene Press), 1988. 256 pp. $2995 hardcover. Reviewed by John W. McLure.

Woodcock, Martin. Collins Handguide to the Birds of the Indian Subcontinent . New York: Penguin (The Stephen Greene Press), 1989. 176 pp. $11.95 paperback. Reviewed by James Scheib.

Harris, Michael. The Collins Field Guide to the Birds of Galapagos . New York: Penguin (The Stephen Greene Press), 1989. 160 pp. $1995 hardcover. Reviewed by Jim Fuller.

Brudenell-Bruce, P. G. C. The Collins Guide to the Birds of New Providence and the Babama Islands. New York: Penguin (The Stephen Greene Press), 1989. 142 pp. $14.95 paperback. Reviewed by Carol A. Thompson.     

The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments

As much of the focus of genetics and molecular biology has shifted toward the systems level, it has become increasingly important to accurately extract biologically relevant signal from thousands of related measurements. The common property among these high-dimensional biological studies is that the measured features have a rich and largely unknown underlying structure. One example of much recent interest is identifying differentially expressed genes in comparative microarray experiments. We propose a new approach aimed at optimally performing many hypothesis tests in a high-dimensional study. This approach estimates the optimal discovery procedure (ODP), which has recently been introduced and theoretically shown to optimally perform multiple significance tests. Whereas existing procedures essentially use data from only one feature at a time, the ODP approach uses the relevant information from the entire data set when testing each feature. In particular, we propose a generally applicable estimate of the ODP for identifying differentially expressed genes in microarray experiments. This microarray method consistently shows favorable performance over five highly used existing methods. For example, in testing for differential expression between two breast cancer tumor types, the ODP provides increases from 72% to 185% in the number of genes called significant at a false discovery rate of 3%. Our proposed microarray method is freely available to academic users in the open-source, point-and-click EDGE software package.