The role of active movement in fungal ecology and community assembly

Movement ecology aims to provide common terminology and an integrative framework of movement research across all groups of organisms. Yet such work has focused on unitary organisms so far, and thus the important group of filamentous fungi has not been considered in this context. With the exception of spore dispersal, movement in filamentous fungi has not been integrated into the movement ecology field. At the same time, the field of fungal ecology has been advancing research on topics like informed growth, mycelial translocations, or fungal highways using its own terminology and frameworks, overlooking the theoretical developments within movement ecology. We provide a conceptual and terminological framework for interdisciplinary collaboration between these two disciplines, and show how both can benefit from closer links: We show how placing the knowledge from fungal biology and ecology into the framework of movement ecology can inspire both theoretical and empirical developments, eventually leading towards a better understanding of fungal ecology and community assembly. Conversely, by a greater focus on movement specificities of filamentous fungi, movement ecology stands to benefit from the challenge to evolve its concepts and terminology towards even greater universality. We show how our concept can be applied for other modular organisms (such as clonal plants and slime molds), and how this can lead towards comparative studies with the relationship between organismal movement and ecosystems in the focus

A Unifying Theory of Biological Function

A new theory that naturalizes biological function is explained and compared with earlier etiological and causal role theories. Etiological theories explain functions from how they are caused over their evolutionary history. Causal role theories analyze how functional mechanisms serve the current capacities of their containing system. The new proposal unifies the key notions of both kinds of theories, but goes beyond them by explaining how functions in an organism can exist as factors with autonomous causal efficacy. The goal-directedness and normativity of functions exist in this strict sense as well. The theory depends on an internal physiological or neural process that mimics an organism’s fitness, and modulates the organism’s variability accordingly. The structure of the internal process can be subdivided into subprocesses that monitor specific functions in an organism. The theory matches well with each intuition on a previously published list of intuited ideas about biological functions, including intuitions that have posed difficulties for other theories

Livelisystems: a conceptual framework integrating social, ecosystem, development and evolutionary theory

Human activity poses multiple environmental challenges for ecosystems that have intrinsic value and also support that activity. Our ability to address these challenges is constrained, inter alia, by weaknesses in cross disciplinary understandings of interactive processes of change in socio-ecological systems. This paper draws on complementary insights from social and biological sciences to propose a ‘livelisystems’ framework of multi-scale, dynamic change across social and biological systems. This describes how material, informational and relational assets, asset services and asset pathways interact in systems with embedded and emergent properties undergoing a variety of structural transformations. Related characteristics of ‘higher’ (notably human) livelisystems and change processes are identified as the greater relative importance of (a) informational, relational and extrinsic (as opposed to material and intrinsic) assets, (b) teleological (as opposed to natural) selection, and (c) innovational (as opposed to mutational) change. The framework provides valuable insights into social and environmental challenges posed by global and local change, globalization, poverty, modernization, and growth in the anthropocene. Its potential for improving inter-disciplinary and multi-scale understanding is discussed, notably by examination of human adaptation to bio-diversity and eco-system service change following the spread of Lantana camera in the Western Ghats, India

A conceptual model for unifying variability in space and time: Rationale, validation, and illustrative applications

With the increasing demand for customized systems and rapidly evolving technology, software engineering faces many challenges. A particular challenge is the development and maintenance of systems that are highly variable both in space (concurrent variations of the system at one point in time) and time (sequential variations of the system, due to its evolution). Recent research aims to address this challenge by managing variability in space and time simultaneously. However, this research originates from two different areas, software product line engineering and software configuration management, resulting in non-uniform terminologies and a varying understanding of concepts. These problems hamper the communication and understanding of involved concepts, as well as the development of techniques that unify variability in space and time. To tackle these problems, we performed an iterative, expert-driven analysis of existing tools from both research areas to derive a conceptual model that integrates and unifies concepts of both dimensions of variability. In this article, we first explain the construction process and present the resulting conceptual model. We validate the model and discuss its coverage and granularity with respect to established concepts of variability in space and time. Furthermore, we perform a formal concept analysis to discuss the commonalities and differences among the tools we considered. Finally, we show illustrative applications to explain how the conceptual model can be used in practice to derive conforming tools. The conceptual model unifies concepts and relations used in software product line engineering and software configuration management, provides a unified terminology and common ground for researchers and developers for comparing their works, clarifies communication, and prevents redundant developments

Towards Automatic Parsing of Structured Visual Content through the Use of Synthetic Data

Structured Visual Content (SVC) such as graphs, flow charts, or the like are used by authors to illustrate various concepts. While such depictions allow the average reader to better understand the contents, images containing SVCs are typically not machine-readable. This, in turn, not only hinders automated knowledge aggregation, but also the perception of displayed in-formation for visually impaired people. In this work, we propose a synthetic dataset, containing SVCs in the form of images as well as ground truths. We show the usage of this dataset by an application that automatically extracts a graph representation from an SVC image. This is done by training a model via common supervised learning methods. As there currently exist no large-scale public datasets for the detailed analysis of SVC, we propose the Synthetic SVC (SSVC) dataset comprising 12,000 images with respective bounding box annotations and detailed graph representations. Our dataset enables the development of strong models for the interpretation of SVCs while skipping the time-consuming dense data annotation. We evaluate our model on both synthetic and manually annotated data and show the transferability of synthetic to real via various metrics, given the presented application. Here, we evaluate that this proof of concept is possible to some extend and lay down a solid baseline for this task. We discuss the limitations of our approach for further improvements. Our utilized metrics can be used as a tool for future comparisons in this domain. To enable further research on this task, the dataset is publicly available at https://bit.ly/3jN1pJ

Marriages of Mathematics and Physics: A Challenge for Biology

The human attempts to access, measure and organize physical phenomena have led to a manifold construction of mathematical and physical spaces. We will survey the evolution of geometries from Euclid to the Algebraic Geometry of the 20th century. The role of Persian/Arabic Algebra in this transition and its Western symbolic development is emphasized. In this relation, we will also discuss changes in the ontological attitudes toward mathematics and its applications. Historically, the encounter of geometric and algebraic perspectives enriched the mathematical practices and their foundations. Yet, the collapse of Euclidean certitudes, of over 2300 years, and the crisis in the mathematical analysis of the 19th century, led to the exclusion of “geometric judgments” from the foundations of Mathematics. After the success and the limits of the logico-formal analysis, it is necessary to broaden our foundational tools and re-examine the interactions with natural sciences. In particular, the way the geometric and algebraic approaches organize knowledge is analyzed as a cross-disciplinary and cross-cultural issue and will be examined in Mathematical Physics and Biology. We finally discuss how the current notions of mathematical (phase) “space” should be revisited for the purposes of life sciences

Microbial carbon use efficiency: accounting for population, community, and ecosystem-scale controls over the fate of metabolized organic matter

Microbial carbon use efficiency (CUE) is a critical regulator of soil organic matter dynamics and terrestrial carbon fluxes, with strong implications for soil biogeochemistry models. While ecologists increasingly appreciate the importance of CUE, its core concepts remain ambiguous: terminology is inconsistent and confusing, methods capture variable temporal and spatial scales, and the significance of many fundamental drivers remains inconclusive. Here we outline the processes underlying microbial efficiency and propose a conceptual framework that structures the definition of CUE according to increasingly broad temporal and spatial drivers where (1) CUEP reflects population-scale carbon use efficiency of microbes governed by species-specific metabolic and thermodynamic constraints, (2) CUEC defines community-scale microbial efficiency as gross biomass production per unit substrate taken up over short time scales, largely excluding recycling of microbial necromass and exudates, and (3) CUEE reflects the ecosystem-scale efficiency of net microbial biomass production (growth) per unit substrate taken up as iterative breakdown and recycling of microbial products occurs. CUEE integrates all internal and extracellular constraints on CUE and hence embodies an ecosystem perspective that fully captures all drivers of microbial biomass synthesis and decay. These three definitions are distinct yet complementary, capturing the capacity for carbon storage in microbial biomass across different ecological scales. By unifying the existing concepts and terminology underlying microbial efficiency, our framework enhances data interpretation and theoretical advances