A signaling pathway transmits information from an upstream system to downstream systems, ideally unidirectionally. A key bottleneck to unidirectional transmission is retroactivity, which is the additional reaction flux that affects a system once its species interact with those of downstream systems. This raises the question of whether signaling pathways have developed specialized architectures ...

What is normally described as bias? A possible definition comprises attempts to distort or mislead to achieve a certain perspective, i.e. subjective descriptions intended to mislead. If designers were able to exclude bias from informing systems, then this would maximize their effectiveness. This implicit conjecture appears to underpin much of the research in our field. However, in our efforts t...

Modularity is a property by which the behavior of a system does not change upon interconnection. It is crucial for understanding the behavior of a complex system from the behavior of the composing subsystems. Whether modularity holds in biology is an intriguing and largely debated question. In this paper, we discuss this question taking a control systems theory view and focusing on signaling sy...

Many reverse-engineering techniques in systems biology rely upon data on steady-state (or dynamic) perturbations – obtained from siRNA, gene knockdown or overexpression, kinase and phosphatase inhibitors, or other interventions – in order to understand the interactions between different ‘modules’ in a network. This paper first reviews one popular such technique, introduced by the author and col...

This article employs quantitative and qualitative approaches to examine images of neurobiology published in a science news database, sampled across two-year interval. Upon comparing the headlines, author argues that identifiable digital effects — such as blobs bright colour, sparks light, superimposed lines correlate with articles reporting on new observations neuronal action. A semiotic analys...

We do not have an adequate theory of consciousness. Both dualism and materialism are mistaken because they deny consciousness is part of the physical world. False claims include (i) behaviorism, (ii) computationalism, (iii) epiphenomenalism, (iv) the readiness potential, (v) subjectivity, and (vi) materialism. Ontological subjectivity does not preclude epistemic objectivity. Observer relative p...

Landscape character assessment (LCA) methods have been used in the past few decades to analyze, classify, and map landscape types, using objective subjective approaches, with aid of both quantitative qualitative data. This paper addresses critically evaluates compromises ways which contemporary LCA methodologies employ (or profess they employ) versus data analytical tools, their conceptualizati...