Scientific Transparency Research Articles

Development of a generic crop model template in the cropping system model APSIM

The Agricultural Production Systems sIMulator, APSIM, is a cropping system modelling environment that simulates the dynamics of soil–plant-management interactions within a single crop or a cropping system. Adaptation of previously developed crop models has resulted in multiple crop modules in APSIM, which have low scientific transparency and code efficiency. A generic crop model template (GCROP) has been developed to capture unifying physiological principles across crops (plant types) and to provide modular and efficient code for crop modelling. It comprises a standard crop interface to the APSIM engine, a generic crop model structure, a crop process library, and well-structured crop parameter files. The process library contains the major science underpinning the crop models and incorporates generic routines based on physiological principles for growth and development processes that are common across crops. It allows APSIM to simulate different crops using the same set of computer code. The generic model structure and parameter files provide an easy way to test, modify, exchange and compare modelling approaches at process level without necessitating changes in the code. The standard interface generalises the model inputs and outputs, and utilises a standard protocol to communicate with other APSIM modules through the APSIM engine. The crop template serves as a convenient means to test new insights and compare approaches to component modelling, while maintaining a focus on predictive capability. This paper describes and discusses the scientific basis, the design, implementation and future development of the crop template in APSIM. On this basis, we argue that the combination of good software engineering with sound crop science can enhance the rate of advance in crop modelling.

Science journals and conflict of interests: a new deal

Following the Public Library of Science initiative [see Trends Biochem. Sci. (2001) 26, pp 14, 354 and 414], a new wave of controversy and debate is swirling around medical and scientific journals. The editors of some of the most authoritative medical journals, including the New England Journal of Medicine, the Lancet, the Annals of Internal Medicine and the Journal of the American Medical Association, have decided to set a new policy designed to prevent the censorship of research reports by pharmaceutical companies (The Wahington Post, August 5, 2001). The move stems from increasing concern that drug companies exercise too much control over the results of the research they fund, sometimes even blocking publication of unfavourable studies. Under the new policy, journal editors will thus question papers if they suspect that the researchers involved, usually from academic institutions, are not guaranteed scientific independence. However, the issue of potential conflict of interests goes well beyond medical research. ‘This is a pervasive problem in medical research and it's now creeping into basic science’, said Richard Horton, editor of the Lancet (Financial Times, August 23, 2001]. Nature's editor Philip Campbell agrees with this view and aims to implement a ‘Declaration of financial interests’ [Nature (2001) 412, 751], an explicit invitation for Nature authors to disclose competing interests. A summary of this information, or a note of abstinence should authors decline the invitation, will be published alongside the author's paper. So, with the mood obviously set within the scientific community, we can only speculate as to the origins of the next announcement promoting scientific independence and transparency. AR

Who did what? Authorship and contribution in 2001.

Numerous examples of irresponsible authorship are associated with the rise in the number of authors per article and with the documented rise in authorship disputes. Multiple co-investigators have become the norm, and a result is that old concepts of authorship-which, when there was but one author, automatically linked credit with accountability-have eroded. The answer, in the tradition of scientific transparency, is for authors to decide together their individual contributions and disclose these to their readers. This disclosure is now required by many major general medical journals and has been adopted by the International Committee of Medical Journal Editors as the standard.

Health economic models: a question of balance--summary of an open discussion on the pharmacoeconomic evaluation of non-steroidal anti-inflammatory drugs.

Pharmacoeconomics and pharmacoeconomic models are increasingly being used to guide health care decisions. In designing and using these models, an appropriate balance must be struck between scientific rigour and model transparency. It is therefore important to consider carefully how the various model components, such as model perspective, internal and external validity, and choice of comparators and outcomes, should be integrated into the model. These factors are discussed in relation to the pharmacoeconomic evaluation of non-steroidal anti-inflammatory drugs.

Towards internationally acceptable standards for food additives and contaminants based on the use of risk analysis

Internationally acceptable norms need to incorporate sound science and consistent risk management principles in an open and transparent manner, as set out in the Agreement on the Application of Sanitary and Phytosanitary Measures (the SPS Agreement). The process of risk analysis provides a procedure to reach these goals. The interaction between risk assessors and risk managers is considered vital to this procedure. This paper reports the outcome of a meeting of risk assessors and risk managers on specific aspects of risk analysis and its application to international standard setting for food additives and contaminants. Case studies on aflatoxins and aspartame were used to identify the key steps of the interaction process which ensure scientific justification for risk management decisions. A series of recommendations were proposed in order to enhance the scientific transparency in these critical phases of the standard setting procedure.

The need for scientific knowledge, transparency and verification in the promotion of environmental conventions

This paper discusses the link between science and policymaking the need for the greatest degree of transparency in decision-making and verification of effective implementation of international agreement. These are considered to be priorities from a political viewpoint. The discussion is given against the background of the author as an EC Commissioner with special responsibility for Transport, Environment and Nuclear Safety from 1985 to 1989, and the initiator of the EC Freedom of Environmental Information Directive.