Search

The scientific community is often asked to predict the future state of the environment and, to do so, the structure (biodiversity) and the functions (ecosystem functioning) of the investigated systems must be described and understood. In his "handful of feathers" metaphor, Charles Darwin explained the difference between simple and predictable systems, obeying definite laws, and complex (and unpredictable) systems, featured by innumerable components and interactions among them. In order not to waste efforts in impossible enterprises, it is crucial to ascertain if accurate predictions are possible in a given domain, and to what extent they might be reliable. Since ecology and evolution (together forming "natural history") deal with complex historical systems that are extremely sensitive to initial conditions and to contingencies or 'black swans', it is inherently impossible to accurately predict their future states. Notwithstanding this impossibility, policy makers are asking the community of ecological and evolutionary biologists to predict the future. The struggle for funding induces many supposed naturalists to do so, also because other types of scientists (from engineers to modellers) are keen to sell predictions (usually in form of solutions) to policy makers that are willing to pay for them. This paper is a plea for bio-ecological realism. The "mission" of ecologists and evolutionary biologists (natural historians) is not to predict the future state of inherently unpredictable systems, but to convince policy makers that we must live with uncertainties. Natural history, however, can provide knowledge-based wisdom to face the uncertainties about the future. Natural historians produce scenarios that are of great help in figuring out how to manage our relationship with the rest of nature. [ABSTRACT FROM AUTHOR]

• I briefly summarize Michael Savageau's "Biochemical Systems Analysis" papers, published in volumes 25 and 26 of the journal. • These papers kickstarted Biochemical Systems Theory, which originated many of the core concepts and tools of Systems Biology. • I identify the most relevant developments in Biochemical Systems Theory since 1969. Michael Savageau's Biochemical Systems Analysis I, II, III papers, published in volumes 25 and 26 of the journal, kickstarted a research programme that originated many of the core concepts and tools of Systems Biology. This article briefly summarizes these papers and discusses the most relevant developments in Biochemical Systems Theory since their publication. [ABSTRACT FROM AUTHOR]

Holothuria scabra is one of the most intensively studied holothuroids, or sea cucumbers (Echinodermata: Holothuroidea), having been discussed in the literature since the early 19th century. The species is important for several reasons: (1) it is widely distributed and historically abundant in several shallow soft-bottom habitats throughout the Indo-Pacific, (2) it has a high commercial value on the Asian markets, where it is mainly sold as a dried product (beche-de-mer) and (3) it is the only tropical holothuroid species that can currently be mass-produced in hatcheries. Over 20 years have elapsed since the last comprehensive review on H. scabra published in 2001. Research on H. scabra has continued to accumulate, fuelled by intense commercial exploitation, and further declines in wild stocks over the entire distribution range. This review compiles data from over 950 publications pertaining to the biology, ecology, physiology, biochemical composition, aquaculture, fishery, processing and trade of H. scabra, presenting the most complete synthesis to date, including scientific papers and material published by local institutions and/or in foreign languages. The main goal of this project was to summarize and critically discuss the abundant literature on this species, making it more readily accessible to all stakeholders aiming to conduct fundamental and applied research on H. scabra, or wishing to develop aquaculture, stock enhancement and management programs across its geographic range. [ABSTRACT FROM AUTHOR]

• I briefly describe the Boolean modeling approach to investigate gene regulatory networks (GRNs). • I discuss the foundational contributions by the three seminal manuscripts more than 15 years ago. • Finally, the applications of the Boolean modeling approach to the large-scale omics data is discussed. Boolean modeling is a mathematical modeling framework used for defining and studying gene-regulatory networks (GRNs). It serves as a means to develop mechanistic models, offering insights into the trajectories and dynamic properties of GRNs. In this review, I delve into seminal papers published in the Journal of Theoretical Biology that have spearheaded this field. Additionally, I explore the application of these modeling methods in the current era of data-intensive science. [ABSTRACT FROM AUTHOR]

• Overview of the discovery and preliminary characterisation of CXCL17. • Discussion of contradictory reports regarding the chemotactic activity of CXCL17. • Discussion of contradictory reports regarding the proteolytic processing of CXCL17. • Discussion of contradictory reports regarding the adoption of a chemokine fold by CXCL17. • Concluding remarks. Chemotactic cytokines (chemokines) are a group of around 40 small proteins which share a similar protein fold and are well known for their ability to direct the migration of leukocytes to a variety of tissue locations. CXCL17 was the last member of the chemokine family to be assigned and was admitted to the family based on theoretical modelling of the CXCL17 structure and chemotactic activity for monocytes and dendritic cells. Of Interest, CXCL17 expression appears to be restricted to mucosal tissues such as the tongue, stomach and lung, suggestive of specific roles at these locations. A putative CXCL17 receptor, GPR35 was reportedly identified and mice deficient in CXCL17 were generated and characterised. More recently, however, some apparent contradictions regarding aspects of CXCL17 biology have been raised by ourselves and others. Notably, GPR35 appears to be a receptor for the serotonin metabolite 5-hydroxyindoleacetic acid rather than for CXCL17 and modelling of CXCL17 using a variety of platforms fails to identify a chemokine-like fold. In this article, we summarize the discovery of CXCL17 and discuss key papers describing the subsequent characterisation of this protein. Ultimately, we pose the question, 'What defines a chemokine?' (185 words) [ABSTRACT FROM AUTHOR]

• I briefly summarize two classic papers by W. D. Hamilton, published in Volume 7 of the journal (in 1964). • In this work Hamilton introduced 'inclusive fitness' and I explain why the concept was transformative. • I identify three key developments in inclusive-fitness theory since 1964, and I suggest there is scope to develop the theory further. [ABSTRACT FROM AUTHOR]

This commentary describes a highly-cited paper by John Gutteridge and myself that appeared in Arch. Biochem. Biophys. It is dedicated to the memory of John Gutteridge, my frequent co-author and a lifelong friend, who sadly passed away on July 5, 2021. [ABSTRACT FROM AUTHOR]

This commentary describes a highly-cited paper by John Gutteridge and myself that appeared in Arch. Biochem. Biophys. It is dedicated to the memory of John Gutteridge, my frequent co-author and a lifelong friend, who sadly passed away on July 5, 2021. [ABSTRACT FROM AUTHOR]