Modularity and emergence: biology's challenge in understanding life

Assessing complexity and dynamics in epidemics: geographical barriers and facilitators of foot-and-mouth disease dissemination

Introduction

Physical and non-physical processes that occur in nature may influence biological processes, such as dissemination of infectious diseases. However, such processes may be hard to detect when they are complex systems. Because complexity is a dynamic and non-linear interaction among numerous elements and structural levels in which specific effects are not necessarily linked to any one specific element, cause-effect connections are rarely or poorly observed.

Methods

To test this hypothesis, the complex and dynamic properties of geo-biological data were explored with high-resolution epidemiological data collected in the 2001 Uruguayan foot-and-mouth disease (FMD) epizootic that mainly affected cattle. County-level data on cases, farm density, road density, river density, and the ratio of road (or river) length/county perimeter were analyzed with an open-ended procedure that identified geographical clustering in the first 11 epidemic weeks. Two questions were asked: (i) do geo-referenced epidemiologic data display complex properties? and (ii) can such properties facilitate or prevent disease dissemination?

Results

Emergent patterns were detected when complex data structures were analyzed, which were not observed when variables were assessed individually. Complex properties-including data circularity-were demonstrated. The emergent patterns helped identify 11 counties as 'disseminators' or 'facilitators' (F) and 264 counties as 'barriers' (B) of epidemic spread. In the early epidemic phase, F and B counties differed in terms of road density and FMD case density. Focusing on non-biological, geographical data, a second analysis indicated that complex relationships may identify B-like counties even before epidemics occur.

Discussion

Geographical barriers and/or promoters of disease dispersal may precede the introduction of emerging pathogens. If corroborated, the analysis of geo-referenced complexity may support anticipatory epidemiological policies.

Understanding photosynthesis in a spatial-temporal multiscale: The need for a systemic view

In October 2020, at the peak of the COVID-19 pandemic, a group of young Brazilian photosynthesis researchers organized the 1st Brazilian Symposium on Photosynthesis. The event was free and online, with the presence of important guest speakers from all over the world, who discussed their recent works on topics related to the future and perspectives of photosynthesis research. Summarizing the expectations of this symposium we highlighted the importance of adopting a systemic perspective for a better understanding of photosynthesis as a complex and dynamic process. Plants are modular and self-regulating presenting metabolic redundancy and functional degeneration. Among the various biological processes, photosynthesis plays a crucial role in promoting the direct conversion of light energy into carbon skeletons for support growth and productivity. In the past decades, significant advances have been made in photosynthesis at the biophysical, biochemical, and molecular levels. However, this myriad of knowledge has been insufficient to answer crucial questions, such as: how can we understand and eventually increase photosynthetic efficiency and yield in crops subjected to adverse environment related to climate-changing? We believe that a crucial limitation to the whole comprehension of photosynthesis is associated with a vastly widespread classic reductionist view. Moreover, this perspective is commonly accompanied by non-integrative, simplistic, and descriptive approaches to investigate a complex and dynamic process as photosynthesis. Herein, we propose the use of new approaches, mostly based on the Systems Theory, which certainly comes closer to the real world, such as the complex systems that the plants represent.

A systemic approach to the quantification of the phenotypic plasticity of plant physiological traits: the multivariate plasticity index

The phenotype of an individual emerges from the interaction of its genotype with the environment in which it is located. Phenotypic plasticity (PP) is the ability of a specific genotype to present multiple phenotypes in response to the environment. Past and current methods for quantification of PP present limitations, mainly in what constitutes a systemic analysis of multiple traits. This research proposes an integrative index for quantifying and evaluating PP. The multivariate plasticity index (MVPi) was calculated based on the Euclidian distance between scores of a canonical variate analysis. It was evaluated for leaf physiological traits in two cases using Brazilian Cerrado species and sugarcane varieties, grown under diverse environmental conditions. The MVPi was sensitive to plant behaviour from simple to complex genotype-environment interactions and was able to inform coarse and fine changes in PP. It was correlated to biomass allocation, showing agreement between plant organizational levels. The new method proved to be elucidative of plant metabolic changes, mainly by explaining PP as an integrated process and emergent property. We recommend the MVPi method as a tool for analysis of phenotypic plasticity in the context of a systemic evaluation of plant phenotypic traits.

Plant "electrome" can be pushed toward a self-organized critical state by external cues: Evidences from a study with soybean seedlings subject to different environmental conditions

In the present study, we have investigated how the low-voltage electrical signals of soybean seedlings change their temporal dynamic under different environmental conditions (cold, low light, and low osmotic potential). We have used electrophytografic technique (EPG) with sub-dermal electrodes inserted in 15-days-old seedlings located between root and shoot, accounting for a significant part of the individual seedlings. Herein, to work on a specific framework to settle this type of the study, we are adopting the term "electrome" as a reference to the totality of electrical activity measured. Taking into account the non-linear dynamic of the plants electrophysiology, we have hypothesized that the stimuli, as applied in a constant way, could push the system to a critical state, exhibiting spikes without a characteristic size, indicating self-organized criticality (SOC). The results from the power spectral density analysis (PSD), showed that the interval of the large majority of the β exponents were between 1.5 and 3, indicating that the time series, regardless environmental conditions, showed long-range temporal correlation (long memory for β≠0 and β≠2). The analyses from the histograms of the runs showed different patterns of distributions concerning the experimental conditions. However, the runs exhibiting typical spikes, mostly under low light and osmotic stress, showed power law distribution with exponent μ ≅ 2, which is an indicative for SOC. Overall, our results have confirmed that the temporal dynamic of the electrical signaling shows a complex non-linear behavior with long-range persistence. Moreover, the hypothesis that plant electrome can exhibit a self-organized critical state evoked by environmental cues, dissipating energy by bursts of electrical spikes without a characteristic size, was reinforced. Finally, new perspectives for research and additional hypothesis were presented.

Biostimulants in Plant Science: A Global Perspective

This review presents a comprehensive and systematic study of the field of plant biostimulants and considers the fundamental and innovative principles underlying this technology. The elucidation of the biological basis of biostimulant function is a prerequisite for the development of science-based biostimulant industry and sound regulations governing these compounds. The task of defining the biological basis of biostimulants as a class of compounds, however, is made more complex by the diverse sources of biostimulants present in the market, which include bacteria, fungi, seaweeds, higher plants, animals and humate-containing raw materials, and the wide diversity of industrial processes utilized in their preparation. To distinguish biostimulants from the existing legislative product categories we propose the following definition of a biostimulant as "a formulated product of biological origin that improves plant productivity as a consequence of the novel or emergent properties of the complex of constituents, and not as a sole consequence of the presence of known essential plant nutrients, plant growth regulators, or plant protective compounds." The definition provided here is important as it emphasizes the principle that biological function can be positively modulated through application of molecules, or mixtures of molecules, for which an explicit mode of action has not been defined. Given the difficulty in determining a "mode of action" for a biostimulant, and recognizing the need for the market in biostimulants to attain legitimacy, we suggest that the focus of biostimulant research and validation should be upon proof of efficacy and safety and the determination of a broad mechanism of action, without a requirement for the determination of a specific mode of action. While there is a clear commercial imperative to rationalize biostimulants as a discrete class of products, there is also a compelling biological case for the science-based development of, and experimentation with biostimulants in the expectation that this may lead to the identification of novel biological molecules and phenomenon, pathways and processes, that would not have been discovered if the category of biostimulants did not exist, or was not considered legitimate.

Biostimulants in Plant Science: A Global Perspective

This review presents a comprehensive and systematic study of the field of plant biostimulants and considers the fundamental and innovative principles underlying this technology. The elucidation of the biological basis of biostimulant function is a prerequisite for the development of science-based biostimulant industry and sound regulations governing these compounds. The task of defining the biological basis of biostimulants as a class of compounds, however, is made more complex by the diverse sources of biostimulants present in the market, which include bacteria, fungi, seaweeds, higher plants, animals and humate-containing raw materials, and the wide diversity of industrial processes utilized in their preparation. To distinguish biostimulants from the existing legislative product categories we propose the following definition of a biostimulant as "a formulated product of biological origin that improves plant productivity as a consequence of the novel or emergent properties of the complex of constituents, and not as a sole consequence of the presence of known essential plant nutrients, plant growth regulators, or plant protective compounds." The definition provided here is important as it emphasizes the principle that biological function can be positively modulated through application of molecules, or mixtures of molecules, for which an explicit mode of action has not been defined. Given the difficulty in determining a "mode of action" for a biostimulant, and recognizing the need for the market in biostimulants to attain legitimacy, we suggest that the focus of biostimulant research and validation should be upon proof of efficacy and safety and the determination of a broad mechanism of action, without a requirement for the determination of a specific mode of action. While there is a clear commercial imperative to rationalize biostimulants as a discrete class of products, there is also a compelling biological case for the science-based development of, and experimentation with biostimulants in the expectation that this may lead to the identification of novel biological molecules and phenomenon, pathways and processes, that would not have been discovered if the category of biostimulants did not exist, or was not considered legitimate.

Morphogeometric Approaches to Non-vascular Plants

Morphometric analysis of organisms has undergone a dramatic renaissance in recent years, embracing a range of novel computational and imaging techniques to provide new approaches to phenotypic characterization. These innovations have often developed piece-meal, and may reflect the taxonomic specializations and biases of their creators. In this review, we aim to provide a brief introduction to applications and applicability of modern morphometrics to non-vascular land plants, an often overlooked but evolutionarily and ecologically important group. The scale and physiology of bryophytes (mosses, liverworts, and hornworts) differ in important and informative ways from more "traditional" model plants, and their inclusion has the potential to powerfully broaden perspectives in plant morphology. In particular we highlight three areas where the "bryophytic perspective" shows considerable inter-disciplinary potential: (i) bryophytes as models for intra-specific and inter-specific phenotypic variation, (ii) bryophyte growth-forms as areas for innovation in architectural modularity, and (iii) bryophytes as models of ecophysiological integration between organs, individuals, and stands. We suggest that advances should come from two-way dialog: the translation and adoption of techniques recently developed for vascular plants (and other organisms) to bryophytes and the use of bryophytes as model systems for the innovation of new techniques and paradigms in morphogeometric approaches.

Why is it so difficult to identify a single indicator of water stress in plants? A proposal for a multivariate analysis to assess emergent properties

Because of the complexity of plant responses to water deficit, researchers have attempted to identify simplified models to understand critical aspects of the problem by searching for single indicators that would enable evaluations of the effects of environmental changes on the entire plant. However, this reductionist approach, which is often used in plant sciences, makes it difficult to distinguish systemic emergent behaviours. Currently, a new class of models and epistemology have called attention to the fundamental properties of complex systems. These properties, termed 'emergent', are observed at a large scale of the system (top hierarchical level) but cannot be observed or inferred from smaller scales of observation in the same system. We propose that multivariate statistical analysis can provide a suitable tool to quantify global responses to water deficit, allowing a specific and partially quantitative assessment of emergent properties. Based on an experimental study, our results showed that the classical approach of the individual analysis of different data sets might provide different interpretations for the observed effects of water deficit. These results support the hypothesis that a cross-scale multivariate analysis is an appropriate method to establish models for systemic understanding of the interactions between plants and their changing environment.