At the Biological Modeling and Simulation Frontier

We provide a rationale for and describe examples of synthetic modeling and simulation (M&S) of biological systems. We explain how synthetic methods are distinct from familiar inductive methods. Synthetic M&S is a means to better understand the mechanisms that generate normal and disease-related phenomena observed in research, and how compounds of interest interact with them to alter phenomena. An objective is to build better, working hypotheses of plausible mechanisms. A synthetic model is an extant hypothesis: execution produces an observable mechanism and phenomena. Mobile objects representing compounds carry information enabling components to distinguish between them and react accordingly when different compounds are studied simultaneously. We argue that the familiar inductive approaches contribute to the general inefficiencies being experienced by pharmaceutical R&D, and that use of synthetic approaches accelerates and improves R&D decision-making and thus the drug development process. A reason is that synthetic models encourage and facilitate abductive scientific reasoning, a primary means of knowledge creation and creative cognition. When synthetic models are executed, we observe different aspects of knowledge in action from different perspectives. These models can be tuned to reflect differences in experimental conditions and individuals, making translational research more concrete while moving us closer to personalized medicine

"It's for a good cause, isn't it?" - Exploring views of South African TB research participants on sample storage and re-use

<p>Abstract</p> <p>Background</p> <p>The banking of biological samples raises a number of ethical issues in relation to the storage, export and re-use of samples. Whilst there is a growing body of literature exploring participant perspectives in North America and Europe, hardly any studies have been reported in Africa. This is problematic in particular in light of the growing amount of research taking place in Africa, and with the rise of biobanking practices also on the African continent. In order to investigate the perspectives of African research participants, we conducted a study with research participants in a TB study in the Western Cape, South Africa.</p> <p>Methods</p> <p>Semi-structured interviews were conducted using an interview guide which drew on the most prominent themes expressed in current literature on sample storage, re-use and exportation. Interviews were conducted in Afrikaans and subsequently translated into English by the same interviewer. Interviews were transcribed verbatim and analysed qualitatively.</p> <p>Results</p> <p>The results of our study indicate that the majority of participants were supportive of giving one-time consent to the storage and re-use of their samples. The concept of research being for a “good cause” was a central prerequisite. Additionally, a significant minority requested that they be re-contacted if a future use was not stipulated on the original consent. There was also considerable variation in how participants understood the concept of a ‘good cause’, with participants describing three distinct categories of research, of which two were generally thought to constitute ‘good cause’ research. Research that was for-profit was considered to fall outside the spectrum of ‘good cause’ research. Participants displayed confidence in the abilities of the researchers to make future decisions regarding sample use, but seemed unaware of the role of ethics committees in either this process or more generally.</p> <p>Conclusions</p> <p>Participants expressed a wide and complex range of views about issues of sample storage and re-use, and they showed a great deal of trust in researchers. Participants’ willingness to have their samples stored and re-used is consistent with findings from existing studies. However, in contrast to existing literature, participants were generally not in favour of for-profit research. Further research needs to be done to explore these ideas in other communities, both in South Africa and other countries.</p