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Aristotle is often named as the first zoologist or biologist because of his writings on animals. Although Aristotle's major intention in these books was to illustrate his ideas of how knowledge and understanding might advance, at least one modern biologist (C. Darwin) has recognized Aristotle's depth and breadth as being of surviving merit. Of greater surprise is the ongoing attention that his works continue to receive, including publications in contemporary scientific journals. This review identifies 38 peer-reviewed papers on various topics from Aristotle's biological writings that have been published during the last 50 years. These papers are described according to content (genetics, population biology, anatomy, brain, movement), specific creatures (fish, scorpions, elephants, insects, birds), publication outlet, distribution over the fifty year period surveyed, and visible trends in the topics studied. It is concluded that, in the highly-competitive field of peer-reviewed scientific publication and citation, Aristotle's biology continues to excite the interest of scientists and remains salient to modern science itself. [ABSTRACT FROM AUTHOR]

Since the early 1990s, ecologists and evolutionary biologists have aggregated primary research using meta‐analytic methods to understand ecological and evolutionary phenomena. Meta‐analyses can resolve long‐standing disputes, dispel spurious claims, and generate new research questions. At their worst, however, meta‐analysis publications are wolves in sheep's clothing: subjective with biased conclusions, hidden under coats of objective authority. Conclusions can be rendered unreliable by inappropriate statistical methods, problems with the methods used to select primary research, or problems within the primary research itself. Because of these risks, meta‐analyses are increasingly conducted as part of systematic reviews, which use structured, transparent, and reproducible methods to collate and summarise evidence. For readers to determine whether the conclusions from a systematic review or meta‐analysis should be trusted – and to be able to build upon the review – authors need to report what they did, why they did it, and what they found. Complete, transparent, and reproducible reporting is measured by 'reporting quality'. To assess perceptions and standards of reporting quality of systematic reviews and meta‐analyses published in ecology and evolutionary biology, we surveyed 208 researchers with relevant experience (as authors, reviewers, or editors), and conducted detailed evaluations of 102 systematic review and meta‐analysis papers published between 2010 and 2019. Reporting quality was far below optimal and approximately normally distributed. Measured reporting quality was lower than what the community perceived, particularly for the systematic review methods required to measure trustworthiness. The minority of assessed papers that referenced a guideline (~16%) showed substantially higher reporting quality than average, and surveyed researchers showed interest in using a reporting guideline to improve reporting quality. The leading guideline for improving reporting quality of systematic reviews is the Preferred Reporting Items for Systematic reviews and Meta‐Analyses (PRISMA) statement. Here we unveil an extension of PRISMA to serve the meta‐analysis community in ecology and evolutionary biology: PRISMA‐EcoEvo (version 1.0). PRISMA‐EcoEvo is a checklist of 27 main items that, when applicable, should be reported in systematic review and meta‐analysis publications summarising primary research in ecology and evolutionary biology. In this explanation and elaboration document, we provide guidance for authors, reviewers, and editors, with explanations for each item on the checklist, including supplementary examples from published papers. Authors can consult this PRISMA‐EcoEvo guideline both in the planning and writing stages of a systematic review and meta‐analysis, to increase reporting quality of submitted manuscripts. Reviewers and editors can use the checklist to assess reporting quality in the manuscripts they review. Overall, PRISMA‐EcoEvo is a resource for the ecology and evolutionary biology community to facilitate transparent and comprehensively reported systematic reviews and meta‐analyses. [ABSTRACT FROM AUTHOR]

Effective bioinspiration requires dialogue between designers and biologists, and this dialogue must be rooted in a shared scientific understanding of living systems. To support learning from "nature's overarching design lessons" the Biomimicry Institute has produced ten "Unifying Patterns of Nature". These patterns have been developed to engage with those interested in finding biologically inspired solutions to human challenges. Yet, although well-intentioned and appealing, they are likely to dishearten biologists. The aim of this paper is to identify why and propose alternative principles based on evolutionary theory. [ABSTRACT FROM AUTHOR]

Among biologists and philosophers, there is an ongoing debate over the Modern Synthesis and the Extended Evolutionary Synthesis. Some argue that our current evolutionary biology is in need of (at least) some substantial revision or nontrivial extension, while others maintain that the Modern Synthesis remains the foundational framework for evolutionary biology. It has been widely debated whether the Extended Evolutionary Synthesis provides a more promising framework than the Modern Synthesis. The nature and methodological implications of the Extended Evolutionary Synthesis were also examined. This paper offers an integrated historical and philosophical examination of the debate over the Extended Evolutionary Synthesis. It reviews the development of evolutionary biology of the twentieth century. It argues that there are substantial conceptual and theoretical differences between the Modern Synthesis and the Extended Evolutionary Synthesis, but they are not incommensurable paradigms in the Kuhnian sense. It also argues for a functional approach to the debate over these two frameworks of evolutionary theory. [ABSTRACT FROM AUTHOR]

In recent years, the explanatory term "scaffold" has been gaining prominence in evolutionary biology. This notion has a long history in other areas, in particular, developmental psychology. In this paper, we connect these two traditions and identify a specific type of explanatory strategy shared between them, namely scaffolding explanations. We offer a new definition of "scaffold" anchored in the explanatory practices of evolutionary biologists and developmental psychologists that has yet to be clearly articulated. We conclude by offering a systematic overview of the various dimensions of scaffolding explanations that further suggests both their usefulness and range of application. [ABSTRACT FROM AUTHOR]

Neovascularization, the formation of new blood vessels, has received much research attention due to its implications for physiological processes and diseases. Most studies using traditional in vitro and in vivo platforms find challenges in recapitulating key cellular and mechanical cues of the neovascularization processes. Microfluidic in vitro models have been presented as an alternative to these limitations due to their capacity to leverage microscale physics to control cell organization and integrate biochemical and mechanical cues, such as shear stress, cell–cell interactions, or nutrient gradients, making them an ideal option for recapitulating organ physiology. Much has been written about the use of microfluidics in vascular biology models from an engineering perspective. However, a review introducing the different models, components and progress for new potential adopters of these technologies was absent in the literature. Therefore, this paper aims to approach the use of microfluidic technologies in vascular biology from a perspective of biological hallmarks to be studied and written for a wide audience ranging from clinicians to engineers. Here we review applications of microfluidics in vascular biology research, starting with design considerations and fabrication techniques. After that, we review the state of the art in recapitulating angiogenesis and vasculogenesis, according to the hallmarks recapitulated and complexity of the models. Finally, we discuss emerging research areas in neovascularization, such as drug discovery, and potential future directions. [ABSTRACT FROM AUTHOR]

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The article discusses the trends in submissions and publications for the Annals of Applied Biology journal. While there was a steady increase in submissions until 2021, there was a reduction in submissions in 2022 and 2023. However, the number of published papers remained consistent. The journal encourages researchers to consider submitting their work to Annals of Applied Biology and highlights the various types of publications they accept. The article also acknowledges the support of the Association of Applied Biologists and Wiley in promoting and publishing the journal. Special issues linked to AAB-organized events are also announced, and new editors are welcomed to the board. The article concludes by inviting readers to follow the journal on social media and providing links to the journal's website and the AAB website. [Extracted from the article]

The paper describes a class that introduces Aristotle's Poetics from the perspective of his scientific, especially biological, treatises: a systematic analysis of what emotions a tragedy is supposed to elicit and how they are resolved by the audience (homoeopathy). Students read 11 ancient and modern plays and view one film, observing whether his theory of the Tragic explains our responses. The final project includes the writing of a tragic story (not a drama) evincing the students' own understanding of the Tragic based on the readings. [ABSTRACT FROM AUTHOR]

The organization of the living world covers a vast range of spatiotemporal scales, from molecules to the biosphere, seconds to centuries. Biologists working within specialized subdisciplines tend to focus on different ranges of scales. Therefore, developing frameworks that enable testing questions and predictions of scaling requires sufficient understanding of complex processes across biological subdisciplines and spatiotemporal scales. Frameworks that enable scaling across subdisciplines would ideally allow us to test hypotheses about the degree to which explicit integration across spatiotemporal scales is needed for predicting the outcome of biological processes. For instance, how does genomic variation within populations allow us to explain community structure? How do the dynamics of cellular metabolism translate to our understanding of whole-ecosystem metabolism? Do patterns and processes operate seamlessly across biological scales, or are there fundamental laws of biological scaling that limit our ability to make predictions from one scale to another? Similarly, can sub-organismal structures and processes be sufficiently understood in isolation of potential feedbacks from the population, community, or ecosystem levels? And can we infer the sub-organismal processes from data on the population, community, or ecosystem scale? Concerted efforts to develop more cross-disciplinary frameworks will open doors to a more fully integrated field of biology. In this paper, we discuss how we might integrate across scales, specifically by (1) identifying scales and boundaries, (2) determining analogous units and processes across scales, (3) developing frameworks to unite multiple scales, and (4) extending frameworks to new empirical systems. [ABSTRACT FROM AUTHOR]

Selection of the appropriate species and strain of laboratory animals are among the scientist's major concerns. Tarabul's gerbil (Gerbillus tarabuli) is a small, seasonally breeding, desert rodent native to Africa. Despite its unique biological features, which make it an ideal model candidate for biomedical research, only a few reports have used it in research. Hence, the present review aims to provide more data about this species, covering all aspects of its biology, such as taxonomy, morphology, anatomy, ecology, wildlife biology, molecular biology, physiology, neurobiology, genetics, reproduction, development, evolutionary biology, and conservation biology, and covers current progress in exploration of G. tarabuli, discussing its valuable characteristics, which are widely useful for research in various fields. This review paper is destined for biologists, scientists, mammologists, zoologists, academics, and students. [ABSTRACT FROM AUTHOR]

Ervin Bauer (1890–1938) was the first to build a general molecular-based biological theory. He defined the basic principles of theoretical biology from a thermodynamic perspective, focusing on the capacity of biological systems to produce and support the state of sustainable non-equilibrium. His central work "Theoretical Biology" (1935) was written long before modern advances in molecular biology, genetics, and information theory. Ervin Bauer and his wife Stefánia were executed in Stalin's Great Terror. This paper presents a brief introduction to Ervin Bauer's life and includes his short biography. [ABSTRACT FROM AUTHOR]

Ervin Bauer was the only biologist who recognized that the best way to develop theoretical biology on an equal footing with theoretical physics was to follow the method that has ensured the great successes of modern theoretical physics: the general method of science. Following this method, he succeeded to find the universal principle of biology. From this principle he managed to derive all the basic equations of biology, that of metabolism, reproduction, growth, responsiveness and successfully explained all the fundamental phenomena of life. In this paper, I introduce Bauer's theoretical biology and discuss whether he understood it within the framework of the modern physical worldview, or in a broader framework. I point out that the theoretical biology of Ervin Bauer is the first to go beyond the physical worldview, to establish a deeper, biological worldview, and thus to represent a major advance in our understanding of the nature of life, with a significance even greater than that of the Copernican turn. Clarifying the difference between the living and the non-living, it is important to consider the difference between machines and living organisms. It is well known that machines are the manifestations of a dual control; globally, their behavior is controlled by their given structure, while locally, their behavior is governed by the physical laws. Based on Bauer's theoretical biology, it is pointed out that living organisms manifest a three-level causality; the 'additional', biological level corresponds to the autonomous, time-dependent control of their structures. [ABSTRACT FROM AUTHOR]

The increase in molecular data and the use of computer technologies in biology have led to the emergence of professional biocurators, who populate biological databases and knowledgebases with high-quality information. Although crucial to life science knowledge production, biocuration is, to a large extent, invisible labour that takes place behind the scenes of data-centric life science. The field suffers from a lack of recognition and status that has been linked to a language of service and a scientific system that is not equipped to recognise and reward new types of scientific practices. However, as the majority of biocurators are highly educated female biologists, biocuration is also reproducing the problematic pattern of women leaving the scientific tenure track in favour of less prestigious positions. Instead of viewing the issue as just another example of 'the leaky pipeline,' the gendering of biocuration could be seen as an interplay of gendered structures in science, organisations and society which makes a career in biocuration attractive for female scientists while at the same time positioning the activity as non-scientific low-status work. By illuminating some of the ways gender works in the processes which render certain kinds of technoscientific work invisible, biocuration serves as an example of how existing social structures influence the emerging data-centric science. [ABSTRACT FROM AUTHOR]

The potential for basic research to uncover the inner workings of regenerative processes and produce meaningful medical therapies has inspired scientists, clinicians, and patients for hundreds of years. Decades of studies using a handful of highly regenerative model organisms have significantly advanced our knowledge of key cell types and molecular pathways involved in regeneration. However, many questions remain about how regenerative processes unfold in regeneration-competent species, how they are curtailed in non-regenerative organisms, and how they might be induced (or restored) in humans. Recent technological advances in genomics, molecular biology, computer science, bioengineering, and stem cell research hold promise to collectively provide new experimental evidence for how different organisms accomplish the process of regeneration. In theory, this new evidence should inform the design of new clinical approaches for regenerative medicine. A deeper understanding of how tissues and organs regenerate will also undoubtedly impact many adjacent scientific fields. To best apply and adapt these new technologies in ways that break long-standing barriers and answer critical questions about regeneration, we must combine the deep knowledge of developmental and evolutionary biologists with the hard-earned expertise of scientists in mechanistic and technical fields. To this end, this perspective is based on conversations from a workshop we organized at the Banbury Center, during which a diverse cross-section of the regeneration research community and experts in various technologies discussed enduring questions in regenerative biology. Here, we share the questions this group identified as significant and unanswered, i.e., known unknowns. We also describe the obstacles limiting our progress in answering these questions and how expanding the number and diversity of organisms used in regeneration research is essential for deepening our understanding of regenerative capacity. Finally, we propose that investigating these problems collaboratively across a diverse network of researchers has the potential to advance our field and produce unexpected insights into important questions in related areas of biology and medicine. This Perspective highlights the fundamental questions in the regeneration process from start to finish and how they might be addressed to facilitate cross-species studies. [ABSTRACT FROM AUTHOR]

Definition: The term "bioinspiration" defines a creative approach based on the observation of biological principles and transfer to design. Biomimicry is the recent approach, which describes a large field of scientific and technical activities dealing with an interdisciplinary cooperation between biology and other fields with the goal of solving practical problems addressing innovation or sustainable development. Architecture has been influenced by many aspects of natural and social sciences, among these, biology is currently blending into design activities. Bioinspiration has evolved and shifted architectural practices towards numerous innovative approaches through different bioarchitectural movements from the past until the present. However, there is a blur of biomimicry within bioinspiration in architecture between the direct copy of mere natural forms and the true understanding of biological principles, which is the pivot of sustainable development. The main challenge remains in the gap between the profound knowledge of biology, its related scientific fields and the creative process of architectural design, including cross-disciplinary collaboration between architects and biologists. This entry presents main bioarchitectural movements and how it leads to today's biomimicry. It proposes to define biomimicry methodologies and how this approach applies to architectural design contexts through the study of existing case studies. The opportunities, challenges and the future outlook of the field will also be discussed. [ABSTRACT FROM AUTHOR]

Understanding how and why phenotypic traits covary is a major interest in evolutionary biology. Biologists have long sought to characterize the extent of morphological integration in organisms, but comparing levels of integration for a set of traits across taxa has been hampered by the lack of a reliable summary measure and testing procedure. Here, we propose a standardized effect size for this purpose, calculated from the relative eigenvalue variance, Vrel$V_{rel}$. First, we evaluate several eigenvalue dispersion indices under various conditions, and show that only Vrel$V_{rel}$ remains stable across samples size and the number of variables. We then demonstrate that Vrel$V_{rel}$ accurately characterizes input patterns of covariation, so long as redundant dimensions are excluded from the calculations. However, we also show that the variance of the sampling distribution of Vrel$V_{rel}$ depends on input levels of trait covariation, making Vrel$V_{rel}$ unsuitable for direct comparisons. As a solution, we propose transforming Vrel$V_{rel}$ to a standardized effect size (Z‐score) for representing the magnitude of integration for a set of traits. We also propose a two‐sample test for comparing the strength of integration between taxa, and show that this test displays appropriate statistical properties. We provide software for implementing the procedure, and an empirical example illustrates its use. [ABSTRACT FROM AUTHOR]

Now characterised by high-throughput sequencing methods that enable the study of microbes without lab culture, the human "microbiome" (the microbial flora of the body) is said to have revolutionary implications for biology and medicine. According to many experts, we must now understand ourselves as "holobionts" like lichen or coral, multispecies superorganisms that consist of animal and symbiotic microbes in combination, because normal physiological function depends on them. Here I explore the 1960s research of biologist René Dubos, a forerunner figure mentioned in some historical accounts of the microbiome, and argue that he arrived at the superorganism concept 40 years before the Human Microbiome Project. This raises the question of why his contribution was not hailed as revolutionary at the time and why Dubos is not remembered for it. [ABSTRACT FROM AUTHOR]

Millions of people across the world have been exposed to the wildlife documentaries of David Attenborough and Bernhard Grzimek, who have thus greatly influenced the public's views on nature and biodiversity. We investigated the way organisms' biology is portrayed in these documentaries, quantifying different types of animal interactions shown. We evaluated 1498 (Attenborough) and 391 (Grzimek) interactions within- and between-species from documentaries covering a wide range of environments and animal taxa, first aired between 1956 and 2019. We tested whether the relative frequencies of different interactions were influenced by temporal trends as well as by the presenters and their production teams who likely reflect the given Zeitgeist in the UK compared to the European mainland. For our categorisation of animal interactions, we contrasted interspecific versus intraspecific interactions and antagonistic versus cooperative behaviour. While Grzimek's documentaries put a stronger emphasis on cooperation and Attenborough's on antagonistic behaviour, the trends were not statistically significant. Furthermore, these patterns show no significant change over time, contrasting with the changing view among biologists that cooperation is more predominant than considered in the traditional understanding of nature as 'red in tooth and claw'. [ABSTRACT FROM AUTHOR]

Field biology is an area of research that involves working directly with living organisms in situ through a practice known as "fieldwork." Conducting fieldwork often requires complex logistical planning within multiregional or multinational teams, interacting with local communities at field sites, and collaborative research led by one or a few of the core team members. However, existing power imbalances stemming from geopolitical history, discrimination, and professional position, among other factors, perpetuate inequities when conducting these research endeavors. After reflecting on our own research programs, we propose four general principles to guide equitable, inclusive, ethical, and safe practices in field biology: be collaborative, be respectful, be legal, and be safe. Although many biologists already structure their field programs around these principles or similar values, executing equitable research practices can prove challenging and requires careful consideration, especially by those in positions with relatively greater privilege. Based on experiences and input from a diverse group of global collaborators, we provide suggestions for action-oriented approaches to make field biology more equitable, with particular attention to how those with greater privilege can contribute. While we acknowledge that not all suggestions will be applicable to every institution or program, we hope that they will generate discussions and provide a baseline for training in proactive, equitable fieldwork practices. [ABSTRACT FROM AUTHOR]

Synthetic biologists engineered the first genetic toggle switch and clock at the turn of the 21st century. Since the development of these first gene circuits, methods for circuit design and construction have improved dramatically, narrowing the gap between concept and proof-of-principle implementation. Engineered genetic constructs have started to leave the lab for the real world where they are being used in applications, including medicine, biosensing, and industrial chemical production. The field of synthetic gene circuits has also grown from focusing on single, isolated circuits to designing complex systems that operate across multiple populations in carefully engineered consortia. In addition, design methods have progressively moved toward including detailed models of the interactions between the host genome and the synthetic gene circuits that it contains in order to better predict circuit dynamics. This article will review some of the most recent advances in gene circuit design and implementation, with a focus on synthetic gene circuits being applied to address real-world problems. [ABSTRACT FROM AUTHOR]

Summary: Historically, understanding of the human mast cell (MC) compartment has lagged behind the appreciation of other cell lineages. MCs exist in vascularised tissues but do not under normal circumstances circulate in blood, and there has been no pharmacological agent identified that totally and selectively inhibits human MC function. There are no substantiated accounts of an apparently healthy individual who is severely lacking in MCs. Thus, some of the approaches employed to understand the function of a specific immune cell are not available to the MC biologist. The disease categories that have provided the greatest insight into MC biology have been monoclonal and IgE‐mediated MC disorders. This has led to the categorisation of MC diseases as intrinsic or extrinsic to the MC compartment and to the recognition of the role of mediators in MC activation disorders. Mastocytosis as a clonal disorder not only impacts the MC compartment through changes intrinsic to the MC, but also by the effects of episodes of significant release of MC mediators. The availability of newer therapeutic approaches developed to treat monoclonal MC disorders offer insights into how to more selectively approach management of MC centric diseases. [ABSTRACT FROM AUTHOR]

Even though complexity is a concept that is ubiquitously used by biologists and philosophers of biology, it is rarely made precise. I argue that a clarification of the concept is neither trivial nor unachievable, and I propose a unifying framework based on the technical notion of "effective complexity" that allows me to do justice to conflicting intuitions about biological complexity, while taking into account several distinctions in the usage of the concept that are often overlooked. In particular, I propose a distinction between two kinds of complexity, "mechanical" and "emergent", which can be understood as different ways of relating the effective complexity of mechanisms and of behaviors in biological explanations. I illustrate the adequacy of this framework by discussing different attempts to understand intracellular organization in terms of pathways and networks. My framework provides a different way of thinking about recent philosophical debates, for example, on the difference between mechanistic and topological explanations and about the concept of emergence. Moreover, it can contribute to a proper assessment of metascientific arguments that invoke biological complexity. [ABSTRACT FROM AUTHOR]

During the last few decades, biologists have made remarkable progress in understanding the fundamental processes that shape life. But despite the unprecedented level of knowledge now available, large gaps still remain in our understanding of the complex interplay of eco-evolutionary mechanisms across scales of life. Rapidly changing environments on Earth provide a pressing need to understand the potential implications of eco-evolutionary dynamics, which can be achieved by improving existing eco-evolutionary models and fostering convergence among the sub-fields of biology. We propose a new, data-driven approach that harnesses our knowledge of the functioning of biological systems to expand current conceptual frameworks and develop corresponding models that can more accurately represent and predict future eco-evolutionary outcomes. We suggest a roadmap toward achieving this goal. This long-term vision will move biology in a direction that can wield these predictive models for scientific applications that benefit humanity and increase the resilience of natural biological systems. We identify short, medium, and long-term key objectives to connect our current state of knowledge to this long-term vision, iteratively progressing across three stages: (1) utilizing knowledge of biological systems to better inform eco-evolutionary models, (2) generating models with more accurate predictions, and (3) applying predictive models to benefit the biosphere. Within each stage, we outline avenues of investigation and scientific applications related to the timescales over which evolution occurs, the parameter space of eco-evolutionary processes, and the dynamic interactions between these mechanisms. The ability to accurately model, monitor, and anticipate eco-evolutionary changes would be transformational to humanity's interaction with the global environment, providing novel tools to benefit human health, protect the natural world, and manage our planet's biosphere. [ABSTRACT FROM AUTHOR]

Identifying individual animals is crucial for many biological investigations. In response to some of the limitations of current identification methods, new automated computer vision approaches have emerged with strong performance. Here, we review current advances of computer vision identification techniques to provide both computer scientists and biologists with an overview of the available tools and discuss their applications. We conclude by offering recommendations for starting an animal identification project, illustrate current limitations, and propose how they might be addressed in the future. [ABSTRACT FROM AUTHOR]