Idealized, Inaccurate but Successful: A Pragmatic Approach to Evaluating Models in Theoretical Ecology

Ecologists attempt to understand the diversity of life with mathematical models. Often, mathematical models contain simplifying idealizations designed to cope with the blooming, buzzing confusion of the natural world. This strategy frequently issues in models whose predictions are inaccurate. Critics of theoretical ecology argue that only predictively accurate models are successful and contribute to the applied work of conservation biologists. Hence, they think that much of the mathematical work of ecologists is poor science. Against this view, I argue that model building is successful even when models are predictively inaccurate for at least three reasons: models allow scientists to explore the possible behaviors of ecological systems; models give scientists simplified means by which they can investigate more complex systems by determining how the more complex system deviates from the simpler model; and models give scientists conceptual frameworks through which they can conduct experiments and fieldwork. Critics often mistake the purposes of model building, and once we recognize this, we can see their complaints are unjustified. Even though models in ecology are not always accurate in their assumptions and predictions, they still contribute to successful science.     

RNA Granule Protein 140 (RNG140), a Paralog of RNG105 Localized to Distinct RNA Granules in Neuronal Dendrites in the Adult Vertebrate Brain

RNA granules mediate the transport and local translation of their mRNA cargoes, which regulate cellular processes such as stress response and neuronal synaptic plasticity. RNA granules contain specific RNA-binding proteins, including RNA granule protein 105 (RNG105), which is likely to participate in the transport and translation of mRNAs. In the present report, an RNG105 paralog, RNG140 is described. A homolog of RNG105/RNG140 is found in insects, echinoderms, and urochordates, whereas vertebrates have both of the two genes. RNG140 and RNG105 are similar in that both bind to mRNAs and inhibit translation in vitro, induce the formation of RNA granules, are most highly expressed in the brain, and are localized to dendritic RNA granules, part of which are accumulated at postsynapses. However, they differ in several characteristics; RNG105 is highly expressed in embryonic brains, whereas RNG140 is highly expressed in adult brains. Furthermore, the granules where RNG105 or RNG140 is localized are distinct RNA granules in both cultured cells and neuronal dendrites. Thus, RNG140 is an RNA-binding protein that shows different expression and localization patterns from RNG105. Knockdown experiments in cultured neurons also are performed, which demonstrate that suppression of RNG140 or RNG105 reduces dendrite length and spine density. Knockdown effects of RNG140 were not rescued by RNG105, and vise versa, suggesting distinct roles of RNG105 and RNG140. These results suggest that RNG140 has roles in the maintenance of the dendritic structure in the adult vertebrate brain through localizing to a kind of RNA granules that are distinct from RNG105-containing granules.     

From basepairs to birdsongs: phylogenetic data in the age of genomics

Given the quantity of molecular data now available, including complete genomes for some organisms, one can ask whether there is a need for any data beyond complete genomic sequences for phylogenetic analysis. One reason to look beyond the genome is that not all character information is encoded in organismal genomes. We propose a hierarchy of characters that ranges from biologically transmitted but nongenomically encoded characters, such as bird songs, to characters that are genomically encoded. All of these characters can retain historical information and are potentially useful for phylogenetic analysis. In addition, a number of phenotypic levels that are expressions of the genome can be identified. The question whether it is worth including any of these levels if all of the underlying sequence data have been collected arises, since issues of redundancy occur. Utilization of phenotypic levels that are ultimately based on sequences may facilitate reconstructing homologies that are not evident from sequence data alone. We propose the use of simultaneous analysis of sequence data and as many levels of phenotypic characters as possible to take advantage of homology information that may be more easily recovered from the latter. A method that eliminates redundancy to the degree that it can be detected is proposed.     

铈代替铅电镜酶组织化学显示培养脊神经节神经元TMP活性

目的探讨铈法显示脊神经节神经元初代培养细胞的TMP(三偏磷酸酶)活性。方法应用电镜酶组化技术,以铈作为捕捉剂代替常规以铅作为捕捉剂来检测观察脊神经节初代培养的神经元内溶酶体的TMP活性。结果脊神经节神经元初代培养细胞内存在TMP阳性的溶酶体,其TMP阳性反应颗粒较常规以铅作为捕捉剂来显示溶酶体不仅孵育液充分溶解呈清亮透明,电镜下反应产物颗粒也微细均匀,而且避免了反应产物的扩散及非特异性沉淀。结论以铈作为捕捉剂来检测溶酶体的TMP活性用于电镜下观察,其方法稳定、易行,是一种能很好显示溶酶体标记酶的电镜酶组化技术方法。     

Tipping points in tropical tree cover: linking theory to data

It has recently been found that the frequency distribution of remotely sensed tree cover in the tropics has three distinct modes, which seem to correspond to forest, savanna, and treeless states. This pattern has been suggested to imply that these states represent alternative attractors, and that the response of these systems to climate change would be characterized by critical transitions and hysteresis. Here, we show how this inference is contingent upon mechanisms at play. We present a simple dynamical model that can generate three alternative tree cover states (forest, savanna, and a treeless state), based on known mechanisms, and use this model to simulate patterns of tree cover under different scenarios. We use these synthetic data to show that the hysteresis inferred from remotely sensed tree cover patterns will be inflated by spatial heterogeneity of environmental conditions. On the other hand, we show that the hysteresis inferred from satellite data may actually underestimate real hysteresis in response to climate change if there exists a positive feedback between regional tree cover and precipitation. Our results also indicate that such positive feedback between vegetation and climate should cause direct shifts between forest and a treeless state (rather than through an intermediate savanna state) to become more likely. Finally, we show how directionality of historical change in conditions may bias the observed relationship between tree cover and environmental conditions.     

His Own Synthesis: Corn, Edgar Anderson, and Evolutionary Theory in the 1940s

Tracing the contributions of Edgar Anderson (1897--1969) of the Missouri Botanical Garden to the important discussions in evolutionary biology in the 1940s, this paper argues that Anderson turned to corn research rather than play a more prominent role in what is now known as the Evolutionary Synthesis. His biosystematic studies of Iris and Tradescantia in the 1930s reflected such Synthesis concerns as the species question and population thinking. He shared the 1941 Jesup Lectures with Ernst Mayr. But rather than preparing his lectures as a potentially key text in the Synthesis, Anderson began researching Zea mays -- its taxonomy, its origin, and its agronomic role. In this study, Anderson drew on the disciplines of taxonomy, morphology, genetics, geography, anthropology, archaeology, and agronomy among others in his own creative synthesis. Though his maize research in the 1940s represented the most sustained work of his career, Anderson was also drawn in many directions during his professional life. For example, he enjoyed teaching, working with amateurs, and popular writing. This revised version was published online in July 2006 with corrections to the Cover Date.     

A Personal Reflection on the Replicon Theory: From R1 Plasmid to Replication Timing Regulation in Human Cells

Fifty years after the Replicon Theory was originally presented, detailed mechanistic insight into prokaryotic replicons has been obtained and rapid progress is being made to elucidate the more complex regulatory mechanisms of replicon regulation in eukaryotic cells. Here, I present my personal perspectives on how studies of model replicons have contributed to our understanding of the basic mechanisms of DNA replication as well as the evolution of replication regulation in human cells. I will also discuss how replication regulation contributes to the stable maintenance of the genome and how disruption of replication regulation leads to human diseases.     

From cancer big data to treatment: Artificial intelligence in cancer research

In recent years, developing the idea of “cancer big data” has emerged as a result of the significant expansion of various fields such as clinical research, genomics, proteomics and public health records. Advances in omics technologies are making a significant contribution to cancer big data in biomedicine and disease diagnosis. The increasingly availability of extensive cancer big data has set the stage for the development of multimodal artificial intelligence (AI) frameworks. These frameworks aim to analyze high-dimensional multi-omics data, extracting meaningful information that is challenging to obtain manually. Although interpretability and data quality remain critical challenges, these methods hold great promise for advancing our understanding of cancer biology and improving patient care and clinical outcomes. Here, we provide an overview of cancer big data and explore the applications of both traditional machine learning and deep learning approaches in cancer genomic and proteomic studies. We briefly discuss the challenges and potential of AI techniques in the integrated analysis of omics data, as well as the future direction of personalized treatment options in cancer.     

Disease in the History of Modern Latin America: From Malaria to AIDS and From Popular Medicine to Medical Populism: Doctors, Healers, and the Public Power in Costa Rica 1800–1940

Disease in the History of Modern Latin America: From Malaria to AIDS . Diego Armus, ed. Durham, NC: Duke University Press, 2003. 326 pp.
From Popular Medicine to Medical Populism: Doctors, Healers, and the Public Power in Costa Rica 1800–1940 . Steven Palmer. Durham, NC: Duke University Press, 2003. 329 pp.     

From Reductionism to Reintegration: Solving society’s most pressing problems requires building bridges between data types across the life sciences

Decades of reductionist approaches in biology have achieved spectacular progress, but the proliferation of subdisciplines, each with its own technical and social practices regarding data, impedes the growth of the multidisciplinary and interdisciplinary approaches now needed to address pressing societal challenges. Data integration is key to a reintegrated biology able to address global issues such as climate change, biodiversity loss, and sustainable ecosystem management. We identify major challenges to data integration and present a vision for a “Data as a Service”-oriented architecture to promote reuse of data for discovery. The proposed architecture includes standards development, new tools and services, and strategies for career-development and sustainability.

Data integration is key to the reintegration of biology and the pursuit of global issues such as climate change, biodiversity loss, and sustainable ecosystem management. This Essay defines the primary challenges in data integration and presents a vision for a "Data as a Service" (DaaS) oriented architecture that enables frictionless data reuse, hypothesis testing, and discovery.     

From mouth to anus: Functional and structural relevance of enteric neurons in the Drosophila melanogaster gut

The intestinal tract is the main organ involved in host nutritional homeostasis. Intestinal function in both vertebrates and invertebrates is partly controlled by enteric neurons that innervate the gut. Though anatomical and functional aspects of enteric neurons are relatively less characterized in Drosophila than in large insects, analyses of the role of the enteric neurons in flies have remarkably progressed in the last few years. In this review, we first provide a summary of the structure and function of the Drosophila intestine. We then discuss recent studies of the structure and function of enteric neurons in Drosophila melanogaster.     

From heroes to vulnerable victims: labelling Christian Turks as genuine refugees in the 1970s

Abstract

In 1975, the first Christian Turks applied for asylum in the Netherlands. They were at first denied, and only in the early 1980s did they finally begin to win refugee status from the Dutch government. In the meantime, they faced years of uncertainty. Campaigns of lobbyists in the years between 1977 and 1983 contributed to end their waiting. Their campaigns caused a drastic change of the image of the ‘deserving refugee’ in the Netherlands. This article explores the arguments that lobbyists used to influence decision-makers. It shows how and why the public and political image of the ‘deserving refugee’ had to change in order to successfully claim refugee status.     

Implementation of hypocalcaemia prevention programmes in commercial dairy herds: From theory to practice

Hypocalcaemia prevention programmes have been widely studied in experimental settings, but their feasibility has not been assessed under field conditions. The main objective of this study was to evaluate, in the context of small dairy farms in western France, whether and how dairy farmers implement prevention programmes and manage the feeding of dry cows to prevent hypocalcaemia. Seventy-nine commercial Holstein dairy farms in Brittany (France) were enrolled in a qualitative study in 2019. We conducted in-person interviews with the farmers to 1) understand the rationale behind the type and seasonality of prevention programmes they implemented and 2) assess how closely they followed common recommendations when implementing them. Most farmers (80 %) used at least one prevention programme, especially supplying a mineral mix formulated to meet the needs of dry cows in late gestation (53 %), acidifying the diet in late gestation (37 %), and supplying calcium at calving (oral or injectable form, 37 %). The use of programmes depended on whether the diet composition varied throughout the year. Among farmers who provided an acidified diet, 25 % did not supply a specific mineral mix to dry cows to ensure an adequate amount of P, Ca, and Mg, which could decrease the effectiveness of the acidification programme. A lack of reliability in feeding practices, such as not weighing feed or not delivering feed frequently enough, was identified for 61 % of contributing farms. Management practices could result in supplying an unsuitable amount of P, Ca, or Mg immediately before calving; for example, inappropriate batching practices around calving were identified for 22 % (cows) to 32 % (heifers) of farms. In addition, nearly all contributing farmers had no processes in place to monitor the effectiveness of the programmes implemented. Reasons for this overall lack of compliance should be explored.     

Stability and synchrony across ecological hierarchies in heterogeneous metacommunities: linking theory to data

Understanding stability across ecological hierarchies is critical for landscape management in a changing world. Recent studies showed that synchrony among lower‐level components is key to scaling temporal stability across two hierarchical levels, whether spatial or organizational. But an extended framework that integrates both spatial scale and organizational level simultaneously is required to clarify the sources of ecosystem stability at large scales. However, such an extension is far from trivial when taking into account the spatial heterogeneities in real‐world ecosystems. In this paper, we develop a partitioning framework that bridges variability and synchrony measures across spatial scales and organizational levels in heterogeneous metacommunities. In this framework, metacommunity variability is expressed as the product of local‐scale population variability and two synchrony indices that capture the temporal coherence across species and space, respectively. We develop an R function ‘var.partition’ and apply it to five types of desert plant communities to illustrate our framework and test how diversity shapes synchrony and variability at different hierarchical levels. As the observation scale increased from local populations to metacommunities, the temporal variability of plant productivity was reduced mainly by factors that decreased species synchrony. Species synchrony decreased from local to regional scales, and spatial synchrony decreased from species to community levels. Local and regional species diversity were key factors that reduced species synchrony at the two scales. Moreover, beta diversity contributed to decreasing spatial synchrony among communities. We conclude that our new framework offers a valuable toolbox for future empirical studies to disentangle the mechanisms and pathways by which ecological factors influence stability at large scales.     

From theory to practice in pattern-oriented modelling: identifying and using empirical patterns in predictive models

To robustly predict the effects of disturbance and ecosystem changes on species, it is necessary to produce structurally realistic models with high predictive power and flexibility. To ensure that these models reflect the natural conditions necessary for reliable prediction, models must be informed and tested using relevant empirical observations. Pattern-oriented modelling (POM) offers a systematic framework for employing empirical patterns throughout the modelling process and has been coupled with complex systems modelling, such as in agent-based models (ABMs). However, while the production of ABMs has been rising rapidly, the explicit use of POM has not increased. Challenges with identifying patterns and an absence of specific guidelines on how to implement empirical observations may limit the accessibility of POM and lead to the production of models which lack a systematic consideration of reality. This review serves to provide guidance on how to identify and apply patterns following a POM approach in ABMs (POM-ABMs), specifically addressing: where in the ecological hierarchy can we find patterns; what kinds of patterns are useful; how should simulations and observations be compared; and when in the modelling cycle are patterns used? The guidance and examples provided herein are intended to encourage the application of POM and inspire efficient identification and implementation of patterns for both new and experienced modellers alike. Additionally, by generalising patterns found especially useful for POM-ABM development, these guidelines provide practical help for the identification of data gaps and guide the collection of observations useful for the development and verification of predictive models. Improving the accessibility and explicitness of POM could facilitate the production of robust and structurally realistic models in the ecological community, contributing to the advancement of predictive ecology at large.     

Major changes in trophic dynamics in large, deep sub-alpine Lake Maggiore from 1940s to 2002: a high resolution comparative palaeo-neolimnological study

1. We describe the changes in trophic dynamics in Lake Maggiore from c. 1943 to 2002 using subfossil cladoceran data from a high resolution sediment record, long‐term contemporary data series and historical information. During this period the lake went through a eutrophication phase until 1980 followed by oligotrophication. 2. During the eutrophication period a major increase occurred in the abundance of Chydorus sphaericus, the proportion of planktonic cladocerans and total abundance of cladocerans in the sediment. Since 1980 the abundance declined again and subfossil Eubosmina mucro length and contemporary Daphnia body length increased, most probably as a result of higher abundance of invertebrate predators. 3. Changes in the fish stock composition caused by the introduction of exotic fish during the pre‐eutrophication period and a complete ban on fishing because of Dichloro‐diphenil‐ethanes (DDTs) pollution of the lake (during oligotrophication) could also be detected in the community assemblage and size structure of the sediment zooplankton. 4. We found good correspondence between trophic changes inferred from cladoceran subfossils (community composition, size and predation pressure) and contemporary data, suggesting that sediment samples can be used to infer past development in trophic dynamics, including predation by fish and pelagic invertebrates in lakes with scarce neolimnological data. 5. Furthermore, by combining palaeolimnological cladoceran data rarely obtained from contemporary samples (e.g. benthic and plant‐associated cladocerans, mucro length of bosminids) with contemporary data of organisms poorly represented in the sediment record (e.g. remains of Bythotrephes and fishes) a more complete understanding of changes in trophic dynamics was obtained. 6. The detection in the sediments of meteorological events whose effects on zooplankton had been recorded in the long‐term studies also provided evidence that eutrophication tends to override climate signals. 7. We conclude that a combined palaeo‐neolimnological approach can be a powerful tool for elucidating past changes in the trophic dynamics of lakes and the interaction with climate induced changes, not least when high resolution sediment records are available.