Related papers: A framework for philosophical biology
The objective of this short report is to reconsider the subject of bioinformatics as just being a tool of experimental biological science. To do that, we introduce three examples to show how bioinformatics could be considered as an…
A vast array of transformative technologies developed over the past decade has enabled measurement and perturbation at ever increasing scale, yet our understanding of many systems remains limited by experimental capacity. Overcoming this…
The physiological tradition of biological research analyzes biological systems using reduced descriptions much as an engineer uses a 'black box' description of an amplifier. Simple models have been used by physiologists for a very long…
Provided that there is no theoretical frame for complex engineered systems (CES) as yet, this paper claims that bio-inspired engineering can help provide such a frame. Within CES bio-inspired systems play a key role. The disclosure from…
Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms.…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…
The mathematical models used to capture features of complex, biological systems are typically non-linear, meaning that there are no generally valid simple relationships between their outputs and the data that might be used to validate them.…
The rapidly increasing interest in the quantum properties of living matter stimulates a discussion of the fundamental properties of life as well as quantum mechanics. In this discussion often concepts are used that originate in philosophy…
Causality is a fundamental part of the scientific endeavour to understand the world. Unfortunately, causality is still taboo in much of psychology and social science. Motivated by a growing number of recommendations for the importance of…
We are facing a real challenge when coping with the continuous acceleration of scientific production and the increasingly changing nature of science. In this article, we extend the classical framework of co-word analysis to the study of…
Ecosystems are commonly conceptualized as networks of interacting species. However, partitioning natural diversity of organisms into discrete units is notoriously problematic, and mounting experimental evidence raises the intriguing…
The pursuit of creating artificial intelligence (AI) mirrors our longstanding fascination with understanding our own intelligence. From the myths of Talos to Aristotelian logic and Heron's inventions, we have sought to replicate the marvels…
A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine…
Reproducibility is a fundamental requirement of the scientific process since it enables outcomes to be replicated and verified. Computational scientific experiments can benefit from improved reproducibility for many reasons, including…
Theoretical physicists have been fascinated by the phenomena of life for more than a century. As we engage with more realistic descriptions of living systems, however, things get complicated. After reviewing different reactions to this…
Since the turn of the millennium, computational modelling of biological systems has evolved remarkably and sees matured use spanning basic and clinical research. While the topic of the peri-millennial debate about the virtues and…
``The purpose of life is to obtain knowledge, use it to live with as much satisfaction as possible, and pass it on with improvements and modifications to the next generation.'' This may sound philosophical, and the interpretation of words…
A modeling formalism is proposed for the description and study of living and life-like systems. It provides an abstract conceptual model framework for real life and evolution of biological organisms. It is proposed, that this model…
A substantial school in the philosophy of science identifies Bayesian inference with inductive inference and even rationality as such, and seems to be strengthened by the rise and practical success of Bayesian statistics. We argue that the…