Related papers: A framework for philosophical biology
The last decades saw dramatic progress in brain research. These advances were often buttressed by probing single variables to make circumscribed discoveries, typically through null hypothesis significance testing. New ways for generating…
Rapid advances in computing technology over the past few decades have spurred two extraordinary phenomena in science: large-scale and high-throughput data collection coupled with the creation and implementation of complex statistical…
There has been a recent resurgence in the area of explainable artificial intelligence as researchers and practitioners seek to make their algorithms more understandable. Much of this research is focused on explicitly explaining decisions or…
This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
Bayesian probability theory is used as a framework to develop a formalism for the scientific method based on principles of inductive reasoning. The formalism allows for precise definitions of the key concepts in theories of physics and also…
This short text summarizes the work in biology proposed in our book, Perspectives on Organisms, where we analyse the unity proper to organisms by looking at it from different viewpoints. We discuss the theoretical roles of biological time,…
By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to…
Increasingly sophisticated experiments, coupled with large-scale computational models, have the potential to systematically test biological hypotheses to drive our understanding of multicellular systems. In this short review, we explore key…
The grand challenges in biology today are being shaped by powerful high-throughput technologies that have revealed the genomes of many organisms, global expression patterns of genes and detailed information about variation within…
The growing adoption of foundation models calls for a paradigm shift from Data Science to Model Science. Unlike data-centric approaches, Model Science places the trained model at the core of analysis, aiming to interact, verify, explain,…
We argue for a convergence of crystallography, materials science and biology, that will come about through asking materials questions about biology and biological questions about materials, illuminated by considerations of information. The…
All aspects of our society, including the life sciences, need a mechanism for people working within them to represent the concepts they employ to carry out their research. For the information systems being designed and developed to support…
We advocates here the use of (mathematical) logic for systems biology, as a unified framework well suited for both modeling the dynamic behaviour of biological systems, expressing properties of them, and verifying these properties. The…
The emergence of life from inanimate matter presents a thermodynamic challenge: the Second Law of Thermodynamics dictates a global trend towards disorder, yet life constitutes localized pockets of profound organization. This paper presents…
The search for meaningful structure in biological data has relied on cutting-edge advances in computational technology and data science methods. However, challenges arise as we push the limits of scale and complexity in biological problems.…
This paper introduces Reflective Empiricism, an extension of empirical science that incorporates subjective perception and consciousness processes as equally valid sources of knowledge. It views reality as an interplay of subjective…
Living systems exhibit a range of fundamental characteristics: they are active, self-referential, self-modifying systems. This paper explores how these characteristics create challenges for conventional scientific approaches and why they…
With the completion of human genome mapping, the focus of scientists seeking to explain the biological complexity of living systems is shifting from analyzing the individual components (such as a particular gene or biochemical reaction) to…
This paper explores the idea that information is an essential and distinctive feature of living systems. Unlike non-living systems, living systems actively acquire, process, and use information about their environments to respond to…
We show that the sheer existence of a quantum computational speedup logically implies the mutually exclusive or of well-defined causal loops. In each of them, it is as if the problem-solver knew in advance one of the possible halves of the…