A case study in explanatory power: John Snow's conclusions about the pathology and transmission of cholera

In the mid-1800s, there was much debate about the origin or ‘exciting cause’ of cholera. Despite much confusion surrounding the disease, the so-called miasma theory emerged as the prevalent account about cholera’s cause. Going against this mainstream view, the British physician John Snow inferred several things about cholera’s origin and pathology that no one else inferred. Without observing the vibrio cholerae, however,—data unavailable to Snow and his colleagues—, there was no way of settling the question of what exactly was causing cholera and how, or if, it was passed on. The question then arises as to how Snow arrived at conclusions so systematically different from those of his opponents. In this paper, I want to look at Snow’s reasoning in some detail, and show that there were certain principles, explanatory power in particular, that were epistemologically important to Snow in their own right. I will show that Snow himself takes explanatory power to be an epistemic property, and makes explicit links between explanatory power and confirmation. Systematically juxtaposing Snow’s claims and his opponents’, I will show that Snow was right to tout the explanatory power of his theory, and that his conclusions about the epistemic superiority of his theory over that of the miasmatists’ were justified.     

Bringing Web 2.0 to bioinformatics

Enabling deft data integration from numerous, voluminous andheterogeneous data sources is a major bioinformatic challenge.Several approaches have been proposed to address this challenge,including data warehousing and federated databasing. Yet despitethe rise of these approaches, integration of data from multiplesources remains problematic and toilsome. These two approachesfollow a user-to-computer communication model for data exchange,and do not facilitate a broader concept of data sharing or collaborationamong users. In this report, we discuss the potential of Web2.0 technologies to transcend this model and enhance bioinformaticsresearch. We propose a Web 2.0-based Scientific Social Community(SSC) model for the implementation of these technologies. Byestablishing a social, collective and collaborative platformfor data creation, sharing and integration, we promote a webservices-based pipeline featuring web services for computer-to-computerdata exchange as users add value. This pipeline aims to simplifydata integration and creation, to realize automatic analysis,and to facilitate reuse and sharing of data. SSC can fostercollaboration and harness collective intelligence to createand discover new knowledge. In addition to its research potential,we also describe its potential role as an e-learning platformin education. We discuss lessons from information technology,predict the next generation of Web (Web 3.0), and describe itspotential impact on the future of bioinformatics studies.      

An appraisal of seed enumeration and videographic techniques for determining seed removal rates by birds

We examined the efficacy of seed enumeration and videographic techniques for determining seed removal by birds from indigenous (Chrysanthemoides monilifera and Olea europaea subsp africana) and alien (Lantana camara and Solanum mauritianum) shrubs at different study sites in the Cape Floristic Region. The seed enumeration technique involved counting the numbers of fruits and associated seeds removed monthly by birds, excluding those naturally abscised, from the shrub canopy. The videographic technique involved visual counts from images of the numbers of fruits and associated seeds consumed by birds over specific time intervals captured by a digital camcorder. Daily seed removal rates by all birds, irrespective of species, measured by both techniques were similar with no significant interactions evident between measuring techniques, site and shrub species. Both techniques displayed higher seed removal from tiny‐seeded S. mauritianum than other shrub species; this was also evident among individual bird species. However, the seed enumeration technique was unable to discriminate between foraging organisms, contamination of traps by wind‐blown fruits abscised from neighbouring branches and fruit theft from the canopy and the traps. In contrast, the videographic technique provided permanent visual and time‐lapse records for individual foraging bird species allowing greater measurement precision and interpretation of fruit removal behaviour by birds. We recommend use of the videographic technique over the seed enumeration technique for studying vertebrates’ seed removal in a detailed manner.     

项目驱动的实验教学新模式的构建与实践——以微生物学实验为例

由于生源质量和学习目标的多元化,以教师为主导、验证性实验为主要内容的微生物学实验教学模式已无法满足学生的个性化学习需求,为此我们以微型科研项目为载体,在提供一定数字资源的基础上,采用加强线上自学、课内和课外实验相结合的手段进行微生物学实验技能和科研素质的训练,结果显示该模式有效地提高了实验教学的效果、学生的自主学习能力、发现问题和解决问题的能力。     

The synthetic theory of evolution: general problems and the German contribution to the synthesis

Summary A metatheoretical and historiographical re-analysis of the Evolutionary Synthesis (the process) and the Synthetic Theory (the result) leads to the following conclusion: The Synthetic Theory is not a reductionistic, but rather a structuralistic theory with a limited range of relevant hierarchical levels. Historically the Synthesis was not a sudden event but a rational long-term project carried out between 1930 and 1950 by a large number of biologists in several countries. In the second part of our paper the contributions of several German biologists to the Synthesis are analyzed.     

Distributed Shared Arrays: Portable Shared-Memory Programming Interface for Multiple Computer Systems

This paper describes the design and implementation of a parallel programming environment called Distributed Shared Array (DSA), which provides a shared global array abstract across different machines connected by a network. In DSA, users can define and use global arrays that can be accessed uniformly from any machines in the network. Explicit management of array area allocation, replication, and migration is achieved by explicit calls for array manipulation: defining array regions, reading and writing array regions, synchronization, and control of replication and migration. The DSA is integrated with Grid (Globus) services. This paper also describes the use of our model for gene cluster analysis, multiple alignment and molecular dynamics simulation. In these applications, global arrays are used for storing the distance matrix, alignment matrix and atom coordinates, respectively. Large array areas, which cannot be stored in the memory of individual machines, are made available by the DSA. Scalable performance of DSA was obtained compared to that of conventional parallel programs written in MPI.