Gopal P. Sarma

Unit testing, model validation, and biological simulation

The growth of the software industry has gone hand in hand with the development of tools and cultural practices for ensuring the reliability of complex pieces of software. These tools and practices are now acknowledged to be essential to the management of modern software. As computational models and methods have become increasingly common in the biological sciences, it is important to examine how these practices can accelerate biological software development and improve research quality. In this article, we give a focused case study of our experience with the practices of unit testing and test-driven development in OpenWorm, an open-science project aimed at modeling Caenorhabditis elegans. We identify and discuss the challenges of incorporating test-driven development into a heterogeneous, data-driven project, as well as the role of model validation tests, a category of tests unique to software which expresses scientific models.

The Art of Memory and the Growth of the Scientific Method

I argue that European schools of thought on memory and memorization were critical in enabling growth of the scientific method. After giving a historical overview of the development of the memory arts from ancient Greece through 17th century Europe, I describe how the Baconian viewpoint on the scientific method was fundamentally part of a culture and a broader dialogue that conceived of memorization as a foundational methodology for structuring knowledge and for developing symbolic means for representing scientific concepts. The principal figures of this intense and rapidly evolving intellectual milieu included some of the leading thinkers traditionally associated with the scientific revolution; among others, Francis Bacon, Renes Descartes, and Gottfried Leibniz. I close by examining the acceleration of mathematical thought in light of the art of memory and its role in 17th century philosophy, and in particular, Leibnizs project to develop a universal calculus.

OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans

The adoption of powerful software tools and computational methods from the software industry by the scientific research community has resulted in a renewed interest in integrative, large-scale biological simulations. These typically involve the development of computational platforms to combine diverse, process-specific models into a coherent whole. The OpenWorm Foundation is an independent research organization working towards an integrative simulation of the nematode Caenorhabditis elegans, with the aim of providing a powerful new tool to understand how the organisms behaviour arises from its fundamental biology. In this perspective, we give an overview of the history and philosophy of OpenWorm, descriptions of the constituent sub-projects and corresponding open-science management practices, and discuss current achievements of the project and future directions. This article is part of a discussion meeting issue ‘Connectome to behaviour: modelling C. elegans at cellular resolution’.

Should We Train Scientific Generalists

I examine the topic of training scientific generalists. To focus the discussion, I propose the creation of a new graduate program, analogous in structure to existing MD/PhD programs, aimed at training a critical mass of scientific researchers with substantial intellectual breadth. In addition to completing the normal requirements for a PhD, students would undergo an intense, several year training period designed to expose them to the core vocabulary of multiple subjects at the graduate level. After providing some historical and philosophical context for this proposal, I outline how such a program could be implemented with little institutional overhead by existing research universities. Finally, I discuss alternative possibilities for training generalists by taking advantage of contemporary developments in online learning and open science.

AI Safety and Reproducibility: Establishing Robust Foundations for the Neuropsychology of Human Values

We propose the creation of a systematic effort to identify and replicate key findings in neuropsychology and allied fields related to understanding human values. Our aim is to ensure that research underpinning the value alignment problem of artificial intelligence has been sufficiently validated to play a role in the design of AI systems.

AI Safety and Reproducibility: Establishing Robust Foundations for the Neuroscience of Human Values

We propose the creation of a systematic effort to identify and replicate key findings in neuroscience and allied fields related to understanding human values. Our aim is to ensure that research underpinning the value alignment problem of artificial intelligence has been sufficiently validated to play a role in the design

Scientific Data Science and the Case for Open Access

“Open access” has become a central theme of journal reform in academic publishing. In this article, I examine the consequences of an important technological loophole in which publishers can claim to be adhering to the principles of open access by releasing articles in proprietary or “locked” formats that cannot be processed by automated tools, whereby even simple copy and pasting of text is disabled. These restrictions will prevent the development of an important infrastructural element of a modern research enterprise, namely, scientific data science, or the use of data analytic techniques to conduct meta-analyses and investigations into the scientific corpus. I give a brief history of the open access movement, discuss novel journalistic practices, and an overview of data-driven investigation of the scientific corpus. I argue that particularly in an era where the veracity of many research studies has been called into question, scientific data science should be one of the key motivations for open access publishing. The enormous benefits of unrestricted access to the research literature should prompt scholars from all disciplines to reject publishing models whereby articles are released in proprietary formats or are otherwise restricted from being processed by automated tools as part of a data science pipeline.