Editorial of Special Issue "Current Trends in Chemistry Towards Biology".

One of the definitions of chemical biology is that it is a scientific discipline spanning the fields of chemistry, biology, and physics; it primarily involves the application of chemical techniques, tools, analyses, and often compounds (also known as chemical probes), which are produced through synthetic chemistry, in order to study and manipulate biological systems [...].

Teaching genetics with integrative thoughts of conservation biology.

Biodiversity losses along with the exponential growth of global human population and human-provoked over-exploitation of natural resources. Genetic factors played an important role in the conservation of endangered species. Conservation genetics is a cross-field disciplinary of genetics and conservation biology. The course of conservation genetics is not available in colleges and universities, and the course of genetics does not directly reflect the content of biological conservation. We have taught genetics with integrative thoughts of conservation biology. In the form of case studies, we have integrated recent advances of research and technology in the relevant fields into the genetics classroom. As a result, we improved the undergraduates' motivation and interest in active learning, provoked the mutual promotion of "basic knowledge of genetics, awareness of ecological protection, and cultivate interdisciplinary thinking", and set up the groundwork for cultivating interdisciplinary talents who not only master solid basic knowledge, but also have the concept of ecological civilization.

Student Perspectives of Success and Failure in Biology Lecture: Multifaceted Definitions and Misalignments.

Investigating definitions of success and failure among introductory biology students is essential for understanding what underlies their self-efficacy; a student who gets a B on an exam may lose self-efficacy if they define failure as anything less than an A. Yet, whether students have the same definitions for success as they have for failure in these classes is unknown, nor how those definitions relate to course performance. To better understand student definitions for success and failure and their implications, this mixed-methods study collected survey data from students in two introductory biology courses about their definitions of success and failure and their self-reported grades. Coding of open-ended responses revealed four broad themes related to both success and failure: Performance, Content, Preparation, and Attitude. Although there were common themes in how students defined success and failure overall, individual students often (65%) described success or failure in relation to different standards. We also found some definitions of success and failure were predicted by grades. These results highlight the complexity of building self-efficacy in introductory biology and suggest the need for greater awareness and acknowledgment of the different standards students use to judge their success and failure.

Organisms have gravity: taking an organism-centered approach in experimental biology.

When you take the time to observe another organism, there is a sort of gravity that can take hold, a mixture of curiosity and connection that expands and strengthens the more you interact with that organism. Yet, in research, a connection with one's study organism can, at times, feel countercultural. Study organisms are sometimes viewed more as tools to conveniently study biological questions. Here, we explicitly highlight the importance of organism-centered research not only in scientific discovery, but also in conservation and in the communication and perception of science.

How Do Students Critically Evaluate Outdated Language That Relates to Gender in Biology?

Cisheteronormative ideologies are infused into every aspect of society, including undergraduate science. We set out to identify the extent to which students can identify cisheteronormative language in biology textbooks by posing several hypothetical textbook questions and asking students to modify them to make the language more accurate (defined as "correct; precise; using language that applies to all people"). First, we confirmed that textbooks commonly use language that conflates or confuses sex and gender. We used this information to design two sample questions that used similar language. We examined what parts of the questions students modified, and the changes they recommended. When asked to modify sample textbook questions, we found the most common terms or words that students identified as inaccurate were related to infant gender identity. The most common modifications that students made were changing gender terms to sex terms. Students' decisions in this exercise differed little across three large biology courses or by exam performance. As the science community strives to promote inclusive classrooms and embrace the complexity of human gender identities, we provide foundational information about students' ability to notice and correct inaccurate language related to sex and gender in biology.

A Road Map for Planning Course Transformation Using Learning Objectives.

The Vision and Change report called for biology educators to transform undergraduate biology education. The report recommended educators transparently state what students should know and be able to do and create assessments to measure student learning. Using backward design, learning objectives (LOs) can serve as the basis for course transformation. In this essay, we present a roadmap for planning successful course transformations synthesized from the literature. We identified three categories of critical features for successful course transformation. First, establishing a sense of urgency and offering faculty incentives to engage in this time-consuming work creates a needed climate for change. Second, departments are empowered in this process by including key stakeholders, building faculty teams to work collaboratively to identify LOs used to drive pedagogical change, develop assessment strategies, and engage in professional development efforts to support the process. Third, there must be intentional effort to manage resistance and ensure academic freedom and creativity in the classroom. General recommendations as well as areas for further research are discussed.

A CURE Lab in Introductory Biology at a Regional Comprehensive University Negatively Impacts Student Success in the Associated Lecture Course Among Students from Groups Underrepresented in Science.

Course-based undergraduate research experiences (CUREs) have been proposed as a mechanism to democratize access to the benefits of apprentice-style scientific research to a broader diversity of students, promoting inclusivity and increasing student success and retention. As we evaluate CUREs, it is essential to explore their effectiveness within the environments of regional comprehensive universities and community colleges, because they are important access points for a wide variety of students. It is also important to address the potential influence of volunteer bias, where students can opt to enroll in either the CURE or a traditional lab, on the outcomes of CUREs. We evaluated a CURE at a regional comprehensive university under conditions both with and without volunteer bias. We find that nonvolunteer students report a lower sense of discovery and relevance of the CURE compared with students who volunteered for the course. Importantly, we also find that our replacement of the traditional lab class with a CURE resulted in lower scores on exams in the associated lecture course among students who are both BIPOC and Pell eligible. We call for additional research on the effects of CUREs at nonresearch-intensive institutions and without volunteer bias, to better understand the impact of these classes.

Biology in the 21st century: Natural selection is cognitive selection.

Natural selection has a formal definition as the natural process that results in the survival and reproductive success of individuals or groups best adjusted to their environment, leading to the perpetuation of those genetic qualities best suited to that organism's environmental niche. Within conventional Neo-Darwinism, the largest source of those variations that can be selected is presumed to be secondary to random genetic mutations. As these arise, natural selection sustains adaptive traits in the context of a 'struggle for existence'. Consequently, in the 20th century, natural selection was generally portrayed as the primary evolutionary driver. The 21st century offers a comprehensive alternative to Neo-Darwinian dogma within Cognition-Based Evolution. The substantial differences between these respective evolutionary frameworks have been most recently articulated in a revision of Crick's Central Dogma, a former centerpiece of Neo-Darwinism. The argument is now advanced that the concept of natural selection should also be comprehensively reappraised. Cognitive selection is presented as a more precise term better suited to 21st century biology. Since cognition began with life's origin, natural selection represents cognitive selection.

On the relationship between scientific theory and ontology in everything flows.

In their anthology Everything Flows: Towards a Processual Philosophy of Biology, Daniel J. Nicholson and John Dupré argue that modern theories of biology imply that the fundamental structure of reality is processual at its core. In the present work, I first examine the implicit and explicit metaphysical presuppositions the editors make in order to allow for such an inference from scientific theory to ontology. After showing the difficulties of a naïve transfer of theoretical entities to fundamental ontology, I argue that the editors can nevertheless extend their claims beyond the mere articulation of different domain ontologies. This leads to the idea of a scientifically informed induction base for an ontology of processes.

Trees as a metaphor to understand relationships in biology.

The phylogenetic tree has been a core conceptual tool for evolutionary biology for nearly 200 years. This editorial explores the role of the tree as a metaphor, discussing two new PLOS Biology Essays that look to the future.

Library size confounds biology in spatial transcriptomics data.

Spatial molecular data has transformed the study of disease microenvironments, though, larger datasets pose an analytics challenge prompting the direct adoption of single-cell RNA-sequencing tools including normalization methods. Here, we demonstrate that library size is associated with tissue structure and that normalizing these effects out using commonly applied scRNA-seq normalization methods will negatively affect spatial domain identification. Spatial data should not be specifically corrected for library size prior to analysis, and algorithms designed for scRNA-seq data should be adopted with caution.

Undergraduate Biology Lecture Courses Predominantly Test Facts about Science Rather than Scientific Practices.

Scientific practices are the skills used to develop scientific knowledge and are essential for careers in science. Despite calls from education and government agencies to cultivate scientific practices, there remains little evidence of how often students are asked to apply them in undergraduate courses. We analyzed exams from biology courses at 100 institutions across the United States and found that only 7% of exam questions addressed a scientific practice and that 32% of biology exams did not test any scientific practices. The low occurrence of scientific practices on exams signals that undergraduate courses may not be integrating foundational scientific skills throughout their curriculum in the manner envisioned by recent national frameworks. Although there were few scientific practices overall, their close association with higher-order cognitive skills suggests that scientific practices represent a primary means to help students develop critical thinking skills and highlights the importance of incorporating a greater degree of scientific practices into undergraduate lecture courses and exams.

From covalent transition states in chemistry to noncovalent in biology: from ß- to Φ-value analysis of protein folding.

Solving the mechanism of a chemical reaction requires determining the structures of all the ground states on the pathway and the elusive transition states linking them. 2024 is the centenary of Brønsted's landmark paper that introduced the ß-value and structure-activity studies as the only experimental means to infer the structures of transition states. It involves making systematic small changes in the covalent structure of the reactants and analysing changes in activation and equilibrium-free energies. Protein engineering was introduced for an analogous procedure, Φ-value analysis, to analyse the noncovalent interactions in proteins central to biological chemistry. The methodology was developed first by analysing noncovalent interactions in transition states in enzyme catalysis. The mature procedure was then applied to study transition states in the pathway of protein folding - 'part (b) of the protein folding problem'. This review describes the development of Φ-value analysis of transition states and compares and contrasts the interpretation of ß- and Φ-values and their limitations. Φ-analysis afforded the first description of transition states in protein folding at the level of individual residues. It revealed the nucleation-condensation folding mechanism of protein domains with the transition state as an expanded, distorted native structure, containing little fully formed secondary structure but many weak tertiary interactions. A spectrum of transition states with various degrees of structural polarisation was then uncovered that spanned from nucleation-condensation to the framework mechanism of fully formed secondary structure. Φ-analysis revealed how movement of the expanded transition state on an energy landscape accommodates the transition from framework to nucleation-condensation mechanisms with a malleability of structure as a unifying feature of folding mechanisms. Such movement follows the rubric of analysis of classical covalent chemical mechanisms that began with Brønsted. Φ-values are used to benchmark computer simulation, and Φ and simulation combine to describe folding pathways at atomic resolution.

The emergence of theoretical biology: Two fundamental works of Ervin Bauer (1890-1938) in English translation.

Ervin Bauer (1890-1938) outlined the paradigm of theoretical biology from the perspective of biophysics and bioenergetics. His molecular-based biological theory is centered on the principle of sustainable non-equilibrium, which is continuously produced and maintained by all biological systems throughout their life. Ervin Bauer became the victim of Stalin's Great Terror. Here we present two of the fundamental works of Ervin Bauer in English translation: the paper "The definition of living beings on the basis of their thermodynamic properties, and the fundamental biological principles that follow from it" published in Naturwissenschaften (1920) and the excerpts from his magnum opus "Theoretical Biology" (1935). These works became a bibliographical rarity. A complete English translation of "Theoretical Biology" is an important task for the future.

The history of Ervin Bauer's publications on the theory of life.

Ervin Bauer (1890-1938) made historical contributions to contemporary biology, provided a new definition of life, defined the contents of theoretical biology. He worked in different countries, perturbed by deep historical events. These historical events necessarily impacted his fate and finally led to the violent loss of his life and the life of his wife. His work and with it his theory of life had a no less complicated history than the history of his personal life. Bauer's main work "Theoretical Biology" was published in 1935 in Russian. The author and his wife Stefánia became victims of the Great Purge. They were executed in 1938, all their publications were banned and most copies of "Theoretical Biology" destroyed. Ervin and Stefánia Bauer were rehabilitated in 1956 but renewed publication of Bauer's works was delayed. The first reprint edition of "Theoretical Biology" of 1967 was not in Russian, but was a translation into Hungarian, the native language of Bauer. The first Russian reprint of "Theoretical Biology", in which the original Russian chapters are followed by short English summaries, was published in Hungary in 1982. This edition was prepared by Hungarian and Russian scientists. The best-known Russian edition of "Theoretical Biology" was published in 2002 in St. Petersburg. A complete English translation of Bauer's main work "Theoretical Biology" is still outstanding.

A Concept of Complementarity Between Complexity and Redundancy can Account for Kant's Biological Teleology and Unify Mechanistic and Finalistic Biology.

Over 160 years after Darwin and 70 years after the discovery of DNA, two fundamental questions of biology remain unanswered: What differentiates the living from the nonliving? How can mechanistic and finalistic or holistic biology be unified? Niels Bohr introduced a concept of complementarity in quantum physics and based on the paradox of light as a simultaneous wave and particle, conjectured that a similar concept might exist in biology that would solve the paradox of life originating from the nonliving. Bohr proposed that two mutually exclusive-independent observations may be necessary to explain a phenomenon and provided support to Immanuel Kant's idea that the "purposive" behaviour of organisms could only be explained in teleological terms and that mechanical and teleological approaches were necessary and complementary to explain biology. We present a concept of complementarity whereby biochemical pathways or cellular channels for the flow of information are simultaneously complex and redundant and complexity and redundancy complement each other. The postulates of biological complementarity are that (1) it was an essential condition in the origin of life; (2) it provided physiological flexibility that allowed organisms to mount self-protection response and complexity to evolve in the face of deleterious mutations before the evolution of bi-parental sex; (3) it laid the foundation for the evolution of a choice of response when confronted with threat; and (4) it applies to all levels of biological organizations and, thus, can serve as a basis for the unification of mechanistic and holistic biology. It is proposed that teleology is simultaneously constitutive and heuristic: constitutive because organisms' "purposive" behaviours are adaptive and are grounded in mechanism (complexity and redundancy), and heuristic because with our finite cognition and our goal-oriented (humans alone are aware of "tomorrow") and anthropomorphic pre-disposition, teleology will remain useful as a guide to our making sense of the world, even how to ask a meaningful question.

Inflammatory breast cancer biomarkers and biology.

Inflammatory breast cancer (IBC) is a unique breast cancer with a highly virulent course and low 5- and 10-year survival rates. Even though it only accounts for 1-5% of breast cancers it is estimated to account for 10% of breast cancer deaths annually in the United States. The accuracy of diagnosis and classification of this unique cancer is a major concern within the medical community. Early molecular and biological studies incidentally included IBC samples with other conventional breast cancers and were not informative as to the unique nature of the disease. Subsequent molecular studies that focused specifically on IBC demonstrated that IBC has a unique biology different from other forms of breast cancer. Additionally, a handful of unique signature genes that are hallmarks of IBC have also been suggested. Further understanding of IBC biology can help with diagnosis and treatment of the disease. The current article reviews the history and highlights of IBC studies.

Symbiosis takes a front and center role in biology.

All animals and plants likely require interactions with microbes, often in strong, persistent symbiotic associations. While the recognition of this phenomenon has been slow in coming, it will impact most, if not all, subdisciplines of biology.

Future opportunities in solute carrier structural biology.

Solute carriers (SLCs) control the flow of small molecules and ions across biological membranes. Over the last 20 years, the pace of research in SLC biology has accelerated markedly, opening new opportunities to treat metabolic diseases, cancer and neurological disorders. Recently, new families of atypical SLCs, with roles in organelle biology, metabolite signaling and trafficking, have expanded their roles in the cell. This Perspective discusses work leading to current advances and the emerging opportunities to target and modulate SLCs to uncover new biology and treat human disease.

An Endodontology Icon Who Fostered an Appreciation for Pulpal Biology and Its Relevance to Restorative Dentistry and Periodontics: Dr. Kaare Langeland.

The impact of ground-breaking research on the dental pulp and its response to dental procedures, materials and associated diseases significantly influenced the evolution and scope of Endodontics, creating a science of Endodontology. While there were scattered studies in the early 20th century in this regard, the clarification and codification of these concepts took a major leap forward in the late 1950s due to the academic prowess and in-depth research endeavors of Dr. Kaare Langeland. The story begins during World War I in Norway.