Related papers: A framework for philosophical biology
Citations are the cornerstone of knowledge propagation and the primary means of assessing the quality of research, as well as directing investments in science. Science is increasingly becoming "data-intensive", where large volumes of data…
At any moment in time, evolution is faced with a formidable challenge: refining the already highly optimised design of biological species, a feat accomplished through all preceding generations. In such a scenario, the impact of random…
We discuss foundational issues of quantum information biology (QIB) -- one of the most successful applications of the quantum formalism outside of physics. QIB provides a multi-scale model of information processing in bio-systems: from…
Ever since the advent of molecular biology in the 1970s, mechanical models have become the dogma in the field, where a "true" understanding of any subject is equated to a mechanistic description. This has been to the detriment of the…
Here we introduce a new design framework for synthetic biology that exploits the advantages of Bayesian model selection. We will argue that the difference between inference and design is that in the former we try to reconstruct the system…
We attempt to provide a comprehensive model of evolution of science across millennia taking into account the contributions of other intellectual traditions, cultural value system and increasing in sophistication of humans in their study of…
Independent computational reproducibility of scientific results is rapidly becoming of pivotal importance in scientific progress as computation itself plays a more and more central role in so many branches of science. Historically,…
Although reproducibility is a core tenet of the scientific method, it remains challenging to reproduce many results. Surprisingly, this also holds true for computational results in domains such as systems biology where there have been…
Diversity measurement underpins the study of biological systems, but measures used vary across disciplines. Despite their common use and broad utility, no unified framework has emerged for measuring, comparing and partitioning diversity.…
Bioinformatics has witnessed a paradigm shift with the increasing integration of artificial intelligence (AI), particularly through the adoption of foundation models (FMs). These AI techniques have rapidly advanced, addressing historical…
Every scientific endeavour consists of (at least) two components: A hypothesis on the one hand and data on the other. There is always a more or less abstract level - some theory, a set of concepts, certain relations of ideas - and a…
In computer science, we can theoretically neatly separate transmission and processing of information, hardware and software, and programs and their inputs. This is much more intricate in biology, Nevertheless, I argue that Shannon's concept…
Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative"…
Simple assumptions represent a decisive reason to prefer one theory to another in everyday scientific praxis. But this praxis has little philosophical justification, since there exist many notions of simplicity, and those that can be…
The goal of this paper is to advance an extensible theory of living systems using an approach to biomathematics and biocomputation that suitably addresses self-organized, self-referential and anticipatory systems with multi-temporal…
We compare two distinct approaches for querying data in the context of the life sciences. The first approach utilizes conventional databases to store the data and intuitive form-based interfaces to facilitate easy querying of the data.…
This paper makes a number of connections between life and various facets of genetic and evolutionary algorithms research. Specifically, it addresses the topics of adaptation, multiobjective optimization, decision making, deception, and…
The paper defends the thesis that it's possible to maintain some conceptual preconditions of overcoming of relativistic intentions in modern philosophy of science ("there are no any general foundations in philosophy of science"). We found…
While lab courses are an integral part of studying physics aiming at a huge variety of learning objectives, research has shown that typical lab courses do not reach all the desired goals. While diverse approaches by lab instructors and…
Biological science produces large amounts of data in a variety of formats, which necessitates the use of computational tools to process, integrate, analyse, and glean insights from the data. Researchers who use computational biology tools…