Related papers: A framework for philosophical biology
The discipline of `theoretical biology' has been developing from its inception several decades ago almost in parallel with the advances in biology, so much so that the latter is often considered to be almost exclusively an empirical…
Theoretical physics is the search for simple and universal mathematical descriptions of the natural world. In contrast, much of modern biology is an exploration of the complexity and diversity of life. For many, this contrast is prima facie…
The ubiquity of computation in modern scientific research inflicts new challenges for reproducibility. While most journals now require code and data be made available, the standards for organization, annotation, and validation remain lax,…
Theory and empirical science should be in constant dialogue, but often find it hard to understand one another. Here we describe a graduate-level university course we developed to improve matters. The course was designed to help…
Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems,…
Computational biology is on the verge of a paradigm shift in its research practice - from a data-based (computational) paradigm to an information-based (cognitive) paradigm. As in the other research fields, this transition is impeded by…
Philosophy of science attempts to describe all parts of the scientific process in a general way in order to facilitate the description, execution and improvements of this process. So far, all proposed philosophies have only covered existing…
One of the greatest research challenges of this century is to understand the neural basis for how behavior emerges in brain-body-environment systems. To this end, research has flourished along several directions but have predominantly…
In the last few decades or so, we witness a paradigm shift in our nature studies - from a data-processing based computational approach to an information-processing based cognitive approach. The process is restricted and often misguided by…
Biology is data-rich, and it is equally rich in concepts and hypotheses. Part of trying to understand biological processes and systems is therefore to confront our ideas and hypotheses with data using statistical methods to determine the…
The molecular biology revolution of the last seventy five years has transformed our view of living systems. Scientific explanations of biological phenomena are now synonymous with the identification of the genes, proteins, and signaling…
Biomedical research centers can empower basic discovery and novel therapeutic strategies by leveraging their large-scale datasets from experiments and patients. This data, together with new technologies to create and analyze it, has ushered…
The traditional foundation of science lies on the cornerstones of theory and experiment. Theory is used to explain experiment, which in turn guides the development of theory. Since the advent of computers and the development of…
Computational philosophy is the use of mechanized computational techniques to unearth philosophical insights that are either difficult or impossible to find using traditional philosophical methods. Computational metaphysics is computational…
We lay the groundwork for a formal framework that studies scientific theories and can serve as a unified foundation for the different theories within physics. We define a scientific theory as a set of verifiable statements, assertions that…
Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been…
Modeling and simulation are recognized as important aspects of the scientific method for more than 70 years but its adoption in biology has been slow. Debates on its representativeness, usefulness, and whether the effort spent on such…
The fields of computing and biology have begun to cross paths in new ways. In this paper a review of the current research in biological computing is presented. Fundamental concepts are introduced and these foundational elements are explored…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
Biology has taken strong steps towards becoming a computer science aiming at reprogramming nature after the realisation that nature herself has reprogrammed organisms by harnessing the power of natural selection and the digital prescriptive…