Related papers: An evolutionary approach to Function
One of the basic questions of phylogenomics is how gene function evolves, whether among species or inside gene families. In this chapter, we provide a brief overview of the problems associated with defining gene function in a manner which…
Embryology has long played a foundational role in shaping our scientific understanding of animal evolution. In recent decades, growing evidence has also highlighted its role in cancer. Despite the indisputable similarities between embryonic…
In this article, we investigate our early attempts at building an ontology describing rehabilitation therapies following brain injury. These therapies are wide-ranging, involving interventions of many different kinds. As a result, these…
The Gene Ontology aims to define the universe of functions known for gene products, at the molecular, cellular and organism levels. While the ontology is designed to cover all aspects of biology in a "species independent manner", the fact…
In this article we analyse the notion of knowledge role. First of all, we present how the relationship between problem solving methods and domain models is tackled in different approaches. We concentrate on how they cope with this issue in…
This paper is placed at the intersection-point between the study of theoretical computational models aimed at capturing the essence of genetic regulatory networks and the field of Artificial Embryology (or Computational Development). A…
Ontological representations of qualities, dispositions, and roles have been refined over the past decade, clarifying subtle distinctions in life science research. After articulating a widely-used characterization of these entities within…
The functional interpretation is a systematic, syntactic method for transforming certain non-constructive proofs into constructive proofs with explicit bounds. We illustrate the interpretation by working through a concrete, fairly simple…
Philosophers frequently struggle with the relation of metaphysics to the everyday world, with its practical value, and with its relation to empirical science. This paper distinguishes several different models of the relation between…
Reproducibility has been consistently identified as an important component of scientific research. Although there is a general consensus on the importance of reproducibility along with the other commonly used 'R' terminology (i.e.,…
Fracture functions and their evolution equations are reviewed. Some phenomenological applications are briefly discussed.
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…
Categorization is a fundamental function of minds, with wide ranging implications for the rest of the cognitive system. In humans, categories are shared and communicated between minds, thus requiring explanations at the population level. In…
The present study is aimed at analysing the benefits of an ontological approach in Functional Structural Plant Modelling. The ontological approach has been used at two levels, to refine the conceptual modelling approach, and to define the…
Orthology is a central concept in evolutionary and comparative genomics, used to relate corresponding genes in different species. In particular, orthologs are needed to infer species trees. In this chapter, we introduce the fundamental…
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.…
The paper explores the nature of risk, providing a characterization using the categories of the Basic Formal Ontology (BFO). It argues that the category Risk is a subclass of BFO:Role, contrasting it with a similar view classifying Risk as…
Establishing the emergence of evolutionary behavior as a defining characteristic of 'life' is a major step in the Artificial life (ALife) studies. We present here an abstract formal framework for this aim based upon the notion of high-level…
In this article we focus on evolving information systems. First a delimitation of the concept of evolution is provided, resulting in a first attempt to a general theory for such evolutions. The theory makes a distinction between the…
The question in the title is ambiguous. At least the understanding of words essentially different and function theory should be clarified. We discuss approaches to do that. We also present a new framework for analytic function theories…