Biological Concepts Research Articles

Interpreting protein abundance in Saccharomyces cerevisiae through relational learning.

Proteomic profiles reflect the functional readout of the physiological state of an organism. An increased understanding of what controls and defines protein abundances is of high scientific interest. Saccharomyces cerevisiae is a well-studied model organism, and there is a large amount of structured knowledge on yeast systems biology in databases such as the Saccharomyces Genome Database, and highly curated genome-scale metabolic models like Yeast8. These datasets, the result of decades of experiments, are abundant in information, and adhere to semantically meaningful ontologies. By representing this knowledge in an expressive Datalog database we generated data descriptors using relational learning that, when combined with supervised machine learning, enables us to predict protein abundances in an explainable manner. We learnt predictive relationships between protein abundances, function and phenotype; such as α-amino acid accumulations and deviations in chronological lifespan. We further demonstrate the power of this methodology on the proteins His4 and Ilv2, connecting qualitative biological concepts to quantified abundances. All data and processing scripts are available at the following Github repository: https://github.com/DanielBrunnsaker/ProtPredict.

Neutrophils in Physiology and Pathology.

Infections, cardiovascular disease, and cancer are major causes of disease and death worldwide. Neutrophils are inescapably associated with each of these health concerns, by either protecting from, instigating, or aggravating their impact on the host. However, each of these disorders has a very different etiology, and understanding how neutrophils contribute to each of them requires understanding the intricacies of this immune cell type, including their immune and nonimmune contributions to physiology and pathology. Here, we review some of these intricacies, from basic concepts in neutrophil biology, such as their production and acquisition of functional diversity, to the variety of mechanisms by which they contribute to preventing or aggravating infections, cardiovascular events, and cancer. We also review poorly explored aspects of how neutrophils promote health by favoring tissue repair and discuss how discoveries about their basic biology inform the development of new therapeutic strategies.

Evaluating the current state of evolution acceptance instruments: a research coordination network meeting report

AbstractHundreds of studies have explored student evolution acceptance because evolution is a core concept of biology that many undergraduate biology students struggle to accept. However, this construct of “evolution acceptance” has been defined and measured in various ways, which has led to inconsistencies across studies and difficulties in comparing results from different studies. Many studies and essays have offered evaluations and perspectives of evolution acceptance instruments, but publications with a focus on consensus building across research teams is still needed. Further, little attention has been paid to how evolution acceptance instruments may be interpreted differently by students with varied religious backgrounds. Funded by a Research Coordination Network in Undergraduate Biology Education grant from the National Science Foundation, we gathered 16 experts from different disciplinary and religious backgrounds to review current evolution acceptance instruments and create a guide to the strengths and weaknesses of these instruments, including appropriate contexts for using these instruments and their potential weaknesses with different religious populations. Finally, in an attempt to move the field forward, we articulated a consensus definition of evolution acceptance that can be used to guide future instrument development.

Deciphering climate resilience in Indian cattle breeds by selection signature analyses.

The signature of selection is a crucial concept in evolutionary biology that refers to the pattern of genetic variation which arises in a population due to natural selection. In the context of climate adaptation, the signature of selection can reveal the genetic basis of adaptive traits that enable organisms to survive and thrive in changing environmental conditions. Breeds living in diverse agroecological zones exhibit genetic "footprints" within their genomes that mirror the influence of climate-induced selective pressures, subsequently impacting phenotypic variance. It is assumed that the genomes of animals residing in these regions have been altered through selection for various climatic adaptations. These regions are known as signatures of selection and can be identified using various summary statistics. We examined genotypic data from eight different cattle breeds (Gir, Hariana, Kankrej, Nelore, Ongole, Red Sindhi, Sahiwal, and Tharparkar) that are adapted to diverse regional climates. To identify selection signature regions in thisinvestigation, we used four intra-population statistics: Tajima's D, CLR, iHS, and ROH. In this study, we utilized Bovine 50K chip data and four genome scan techniques to assess the genetic regions of positive selection for high-temperature adaptation. We have also performed a genome-wide investigation of genetic diversity, inbreeding, and effective population size in our target dataset. We identified potential regions for selection that are likely to be caused by adverse climatic conditions. We observed many adaptation genes in several potential selection signature areas. These include genes like HSPB2, HSPB3, HSP20, HSP90AB1, HSF4, HSPA1B, CLPB, GAP43, MITF, and MCHR1 which have been reported in the cattle populations that live in varied climatic regions. The findings demonstrated that genes involved in disease resistance and thermotolerance were subjected to intense selection. The findings have implications for marker-assisted breeding, understanding the genetic landscape of climate-induced adaptation, putting breeding andconservation programs into action.

Clinical and biological concept of application of surgical navigation template using flapeless technique

Introduction. Currently, the direction of minimally invasive surgical interventions in surgical dentistry is relevant to reduce the time of postoperative rehabilitation. Detachment of the mucoperiosteal flap during dental implantation leads, depending on the extent of the defect, to a hematoma, which increases the risk of complications (suture dehiscence, wound infection). Because of this, treatment tactics have been developed that allow dental implantation to be performed using surgical navigation templates using a flapless technique. However, despite the obvious effectiveness and efficiency of the method, there are few experimental studies to substantiate the flapless technique of dental implantation.Purpose: clinical substantiation of the effectiveness of the use of flapless navigation techniques for dental implantation Materials and methods: the clinical study included 40 patients with secondary partial edentia. The patients were divided into two groups: the main and control groups. A life history was collected, as well as a history of the development of the present disease. The patients underwent dental implantation surgery in the area of the lateral groups of teeth. In the main group, dental implantation was carried out using a navigation template with a complete protocol and the use of a “flapless” technique; in the control group, dental implantation was carried out with a full-thickness incision and detachment of the mucoperiosteal flap. The evaluation criteria were clinical parameters of healing in the early postoperative period, the height of the soft tissues around the dental implant in the late postoperative period (CBCT, probing), as well as the presence of complications (mucositis, peri-implantitis). The data was entered into a table for further statistical analysis.Results. In the control group, the average height of the formed gingival cuff was 1,55±0,43 mm, 95% CI (1,34–1,75), with primary healing the average height was 1,64±0,44 mm, 95% CI (1,31–1,98), with secondary healing the average height is 1,46±0,43 mm, 95% CI (1,17–1,75). In the main group, the average height of the formed gingival cuff was 2,42±0,45 mm, 95% CI (2,21–2,62), with primary healing the average height was 2,40±0,45 mm, 95% CI (2,17–2,63), with secondary healing mean height 2,50±0,53 mm, 95% CI (1,19–3,81). In the control group, the average loss of marginal bone tissue was 1,27±0,47 mm, 95% CI (1,05–1,49), with primary healing the average loss was 0,96±0,29 mm, 95% CI (0,73–1,18), with secondary healing the average loss is 1,53±0,44 mm, 95% CI (1,23–1,82). In the main group, the average loss of marginal bone tissue was 0,50±0,31 mm, 95% CI (0,35–0,65), with primary healing the average loss was 0,48±0,33 mm, 95% CI (0,31–0,65), with secondary healing the average loss is 0,63±0,12 mm, 95% CI (0,35–0,92). Comparison of the main and control groups in terms of the height of the formed gingival cuff showed a statistically significant difference (p<0,001). This indicator differs significantly between groups with primary (p=0,0004) and secondary wound tension (p=0,004). In the early period, in the control group of 20 patients, 8 (40%) had mucositis, 2 (10%) had peri-implantitis, in the main group 3 (15%) had mucositis. In the late period, in the control group, 7 (35%) had mucositis, 1 (5%) had peri-implantitis, in the main group, 2 (10%) had mucositis. A comparison of the main and control groups in terms of the presence of pain, as well as the presence of complications in the early and late periods, showed a significant difference. In the control group, 60% of patients felt pain, and in the main group, 15% (p=0,009). The presence of complications in the early period was observed in 50% in the control group and in 15% in the main group (p=0,042). In the late period, the proportion of complications decreased and amounted to 40% in the control group and 10% in the main group (p = 0,03). The groups differ in the proportion of primary and secondary healing, so in the main group 85% of patients had primary healing, and in the control group patients with secondary healing of 55% predominated (p = 0.02). Comparison of the study and control groups in terms of loss of marginal bone tissue showed a statistically significant difference (p<0,001).Conclusion. The use of a flapless navigation technique can reduce the likelihood of complications in the early and late postoperative periods, while predictably controlling the height of the gingival cuff.

On the sensitivity of computed partial charges toward basis set and (exchange-)correlation treatment.

Partial charges are a central concept in general chemistry and chemical biology, yet dozens of different computational definitions exist. In prior work [Cho et al., ChemPhysChem 21, 688-696 (2020)], we showed that these can be reduced to at most three 'principal components of ionicity'. The present study addressed the dependence of computed partial charges on 1-particle basis set and (for WFT methods) -particle correlation treatment or (for DFT methods) exchange-correlation functional, for several representative partial charge definitions such as QTAIM, Hirshfeld, Hirshfeld-I, HLY (electrostatic), NPA, and GAPT. Our findings show that semi-empirical double hybrids can closely approach the CCSD(T) 'gold standard' for this property. In fact, owing to an error compensation in MP2, CCSD partial charges are further away from CCSD(T) than is MP2. The nonlocal correlation is important, especially when there is a substantial amount of nonlocal exchange. Employing range separation proves to be "mostly" not advantageous, while global hybrids perform optimally for 20%-30% Hartree-Fock exchange across all charge types. Basis set convergence analysis shows that an augmented triple-zeta heavy-aug-cc-pV(T+d)Z basis set or a partially augmented jun-cc-pV(T+d)Z basis set is sufficient for Hirshfeld, Hirshfeld-I, HLY, and GAPT charges. In contrast, QTAIM and NPA display slower basis set convergence. It is noteworthy that for both NPA and QTAIM, HF exhibits markedly slower basis set convergence than the correlation components of MP2 and CCSD. Triples corrections in CCSD(T), denoted as CCSD(T)-CCSD, exhibit even faster basis set convergence.

Gene drives, mosquitoes, and ecosystems: an interdisciplinary approach to emerging ethical concerns

Gene drives are genetic elements that in sexually reproducing organisms spread faster than those transmitted through a Mendelian fashion. Since gene drives can be engineered to modify different aspects of physiology and reproduction, they have been proposed as a new and revolutionary tool to control vector-borne diseases, particularly those transmitted by the genera Anopheles and Aedes (Culicidae), such as malaria, Dengue and Zika virus. This approach may impact on human health by lowering the transmission of such devastating diseases. However, the release of genetically modified mosquitos (or other species) into the environment raises a series of questions related to the still incipient technology and our present understanding of the complex structure and dynamics of terrestrial and aquatic ecosystems. Moreover, there are ethical concerns about human interventions in natural ecosystems that may eventually impact our way of living or the ecosystems themselves. This work is an interdisciplinary approach that analyzes from a biological, philosophical, and theological perspective the potential ecological impacts on natural environments of the release of genetically modified species, focusing on gene drive-modified mosquitos. It includes theological approach from a Catholic point of view (although it could be easily shared by other Christians) because we hold that world religions give valuable insights even though not everyone may share their groundings. We conclude that the focal problem is the relationship between humans and nature, and the release of genetically modified species may change this relationship unpredictably. However, given the complex interactions in ecosystems, new approaches such as Earth Stewardship principles could provide new and more widely accepted answers involving biological, philosophical, and theological concepts that will help engaging all relevant actors to make a better world.

Pairing a bioinformatics-focused course-based undergraduate research experience with specifications grading in an introductory biology classroom.

Introducing bioinformatics-focused concepts and skills in a biology classroom is difficult, especially in introductory biology classrooms. Course-based Undergraduate Research Experiences (CUREs) facilitate this process, introducing genomics and bioinformatics through authentic research experiences, but the many learning objectives needed in scientific research and communication, foundational biology concepts, and bioinformatics-focused concepts and skills can make the process challenging. Here, the pairing of specifications grading with a bioinformatics-focused CURE developed by the Genomics Education Partnership is described. The study examines how the course structure with specifications grading facilitated scaffolding of writing assignments, group work, and metacognitive activities; and describes the synergies between CUREs and specifications grading. CUREs require mastery of related concepts and skills for working through the research process, utilize common research practices of revision and iteration, and encourage a growth mindset to learning-all of which are heavily incentivized in assessment practices focused on specifications grading.

Perbedaan Penguasaan Konsep Biologi Siswa SMA Jurusan IPS Berbasis Gender dengan Menggunakan Model Project Based Learning

Mastery of concepts in a field of science includes a combination of mastery of knowledge of the field of science being studied and dimensions of cognitive processes, including factual, conceptual and procedural knowledge. The importance of students' mastery of concepts related to the field of biology means that teachers must continue to train students to master biological concepts well. In general, social studies students have good knowledge in the field of social studies, but not necessarily good knowledge in the field of science, especially biology. The aim of this research is to reveal gender-based mastery of biology concepts of students majoring in social studies at SMA Negeri 7 Mataram using a project based learning model. The research method used quasi correlational involving 126 students, consisting of 45 male students and 81 female students. Data analysis used an independent sample t test at a significance level of 5%. The research results show that there is no significant difference between male and female students' mastery of concepts using the project based learning model. The average mastery of concepts for male students is 56.296, and the average mastery of concepts for female students is 57.510. The significance value (Sig. 2 tailed) is 0.618 > 0.05. The implication of this research is that the project based learning model does not provide a significant difference in students' mastery of concepts based on gender, or the project based learning model can be said to have the same effect in increasing students' mastery of biology concepts, both for male and female students.

Effectiveness of Offline Video-Based Biology Instructional Materials on Students’ Performance in Secondary Schools

This study investigated the effectiveness of offline video-based instructional materials in enhancing students’ academic performance in biology lessons in selected secondary schools in Dar es Salaam. The study used holistic multiple case study and quasi-experimental research designs to collect both qualitative and quantitative data using structured questionnaires, interviews and tests. A total of 2 teachers from school A and school B (i.e. one from each school) and 168 students (i.e. 84 from each school) were purposively selected to participate in the study. Analysis by SPSS and data reduction techniques have revealed that offline video-based instructional materials are effective in enhancing students’ academic performance in biology in the experimental groups from both schools (P=0.0001) and made students quite positive about learning biology (89.3%) - 97.6%,). As perceived by students, the enhanced academic performance is the result of improved classroom interactions due to the materials. Specifically, the use of offline video-based instructional materials improved interactions between students and biology teachers, amongst students through group activities and between students and the learning resources. Furthermore, the materials enhanced students’ interest in biology (94.0%), and understanding of concepts (92.9%) and made them retain more biology concepts (94.1%). Based on the findings, appropriate recommendations for policy, action and future research are suggested.

Representation Learning of Biological Concepts: A Systematic Review

Objective: Representation learning in the context of biological concepts involves acquiring their numerical representations through various sources of biological information, such as sequences, interactions, and literature. This study has conducted a comprehensive systematic review by analyzing both quantitative and qualitative data to provide an overview of this field. Methods: Our systematic review involved searching for articles on the representation learning of biological concepts in PubMed and EMBASE databases. Among the 507 articles published between 2015 and 2022, we carefully screened and selected 65 papers for inclusion. We then developed a structured workflow that involved identifying relevant biological concepts and data types, reviewing various representation learning techniques, and evaluating downstream applications for assessing the quality of the learned representations. Results: The primary focus of this review was on the development of numerical representations for gene/DNA/RNA entities. We have found Word2Vec to be the most commonly used method for biological representation learning. Moreover, several studies are increasingly utilizing state-of-the-art large language models to learn numerical representations of biological concepts. We also observed that representations learned from specific sources were typically used for single downstream applications that were relevant to the source. Conclusion: Existing methods for biological representation learning are primarily focused on learning representations from a single data type, with the output being fed into predictive models for downstream applications. Although there have been some studies that have explored the use of multiple data types to improve the performance of learned representations, such research is still relatively scarce. In this systematic review, we have provided a summary of the data types, models, and downstream applications used in this task.

An Analysis of the Concept of Water in Secondary School Biology Textbooks

As a result of human beings' activities to dominate nature and transform it for their own benefit as they continue to advance in science and technology, environmental problems such as climate change have become the biggest threat faced by the biosphere in the current century. One of the biggest problems of humanity today is the scarcity of water resources. It is important to reveal the meanings attributed to the concept of water in biology textbooks in order to identify and eliminate the deficiencies or gaps between the concepts related to the subject. The main purpose of this study is to analyze how the concept of water is presented in secondary school biology textbooks. In line with this purpose, answers to the following questions were sought: What biological concepts is water associated with in biology textbooks and how often is it used? Under which categories can the concept of water be classified in biology textbooks? In the study, document analysis was conducted on four biology textbooks published by the Ministry of National Education to be taught in high schools in the 2023-2024 academic year. A qualitative methodology based on inductive logic was used to analyze the data. How water is emphasized in biology textbooks was discussed, and categories were developed to conceptualize explanations about water. These categories were: water as a substance in the structure of organisms, water as a habitat for organisms, water as a substance involved in chemical reactions, water as a human health factor, water as an essential requirement for organisms, water as an environmental problem factor and water as a scarcity factor. According to the results of the textbook content analysis, it was seen that the relationships between water and health concepts in the category of water as a human health factor were well structured. In the study, it was seen that the concept of water was presented in accordance with the target achievements in line with the secondary school biology course curriculum and that the key concepts were given literally. However, it was revealed that the concept of water in textbooks should be structured according to the principles of the systems thinking approach.

Spectrum of Treg and self-reactive T cells: single cell perspectives from old friend HTLV-1.

Despite extensive regulatory T cell (Treg) research, fundamental questions on in vivo dynamics remain to be answered. The current study aims to dissect several interwoven concepts in Treg biology, highlighting the 'self-reactivity' of Treg and their counterparts, namely naturally-arising memory-phenotype T-cells, as a key mechanism to be exploited by a human retroviral infection. We propose the novel key concept, Periodic T cell receptor (TCR)-signalled T-cells, capturing self-reactivity in a quantifiable manner using the Nr4a3-Timer-of-cell-kinetics-and-activity (Tocky) technology. Periodic and brief TCR signals in self-reactive T-cells contrast with acute TCR signals during inflammation. Thus, we propose a new two-axis model for T-cell activation by the two types of TCR signals or antigen recognition, elucidating how Foxp3 expression and acute TCR signals actively regulate Periodic TCR-signalled T-cells. Next, we highlight an underappreciated branch of immunological research on Human T-cell Leukemia Virus type 1 (HTLV-1) that precedes Treg studies, illuminating the missing link between the viral infection, CD25, and Foxp3. Based on evidence by single-cell analysis, we show how the viral infection exploits the regulatory mechanisms for T-cell activation and suggests a potential role of periodic TCR signalling in infection and malignant transformation. In conclusion, the new perspectives and models in this study provide a working framework for investigating Treg within the self-reactive T-cell spectrum, expected to advance understanding of HTLV-1 infection, cancer, and immunotherapy strategies for these conditions.

Chemical synthetic approaches to mimic the TRAIL: promising cancer therapeutics.

Apoptosis is programmed cell death that eliminates undesired cells to maintain homeostasis in metazoan. Aberration of this process may lead to cancer genesis. The tumor necrosis factor related apoptosis inducing ligand (TRAIL) induces apoptosis in cancer cells after ligation with death receptors (DR4/DR5) while sparing most normal cells. Therefore, strategies to induce apoptosis in cancer cells by mimicking the TRAIL emerge as a promising therapeutic tool. Hence, approaches are taken to develop TRAIL/DR-based cancer therapeutics. The recombinant soluble TRAIL (rhTRAIL) and death receptor agonistic antibodies were produced and tested pre-clinically and clinically. Pre-clinical and clinical trial data demonstrate that these therapeutics are safe and relatively well tolerated. But some of these therapeutics failed to exert adequate efficacy in clinical settings. Besides these biotechnologically derived therapeutics, a few chemically synthesized therapeutics are reported. Some of these therapeutics exert considerable efficacy in vitro and in vivo. In this review, we will discuss chemically synthesized TRAIL/DR-based therapeutics, their chemical and biological behaviour, design concepts and strategies that may contribute to further improvement of TRAIL/DR-based therapeutics.

Enhancing Learning in Biology for Engineers: A Problem Based Case Study

Abstract— Problem-Based Learning (PBL) is acknowledged as an effective pedagogical approach that facilitates a deeper understanding of concepts, surpassing a 90% comprehension rate. Renowned as a dynamic and student-centered activity, PBL fosters out-of-the-box thinking, thereby supporting the enhancement of students' skills and creativity. This paper specifically delves into the application of problem-based learning in the context of the third-year undergraduate Biology for Engineers course. PBL activities tailored for the Biology for Engineers curriculum are meticulously crafted to provide students with a progressive and comprehensive grasp of biological concepts, coupled with their practical applications in the realm of engineering. By adopting a creative, applied, and design thinking approach, PBL enables students to traverse the intricacies of the biology course effectively. In the Biology for Engineers course, PBL activities are strategically designed to facilitate a step-by-step acquisition of in-depth knowledge and a nuanced understanding of the real-life applications of biology in engineering contexts.This deliberate approach not only augments students' experiential learning of biology but also nurtures their creativity. Significantly, the PBL methodology empowers students by instilling a sense of ownership over the course, thereby contributing to their overall academic and professional development. Keywords—Learning, Course, Problem based Learning, Activity, Biology.

The Effect of Lasers on the Healing of Periapical Lesion: A Systematic Review.

Introduction: Endodontic treatment of teeth with periapical lesions presents more clinical difficulty. Various lasers in several methods are used in endodontics, and most of them are utilized as an adjunctive protocol in order to reduce the bacterial load of the root canal system. Improved disinfection plays a crucial role in enhanced and accelerated healing of periapical lesions. This review aims to summarize studies assessing the effect of lasers on periapical lesion healing. Methods: PubMed/MEDLINE, Scopus, Embase, and Web of Science (ISI) online databases were searched, with no publication year or status restriction, for relevant articles on April 2023. Clinical studies evaluating the effect of laser application on the periapical lesion of patients using radiographic assessment were considered eligible for inclusion. Results: Eight studies were included after carefully screening the obtained articles, first by their title and abstract and then by their full texts. Diode (4), Er, Cr: YSGG (3), and Nd: YAG (1) lasers were used with output powers that varied from 0.75 to 2 watts. Photodynamic therapy was employed in two studies, and in other studies, the root canal system was directly irradiated. Irradiation of the root canal system was adjunctive to standard preparation in all studies. The healing of the teeth treated with lasers was not inferior to those conventionally treated. In all of the included studies, laser application outperformed the standard cleaning and shaping protocol; however, this improved or faster healing was not statistically significant in most studies. Conclusion: Lasers might expedite and improve the healing process of periapical lesions. Since lasers enhance the quality of cleaning of the root canal system, it is hard to point out the exact mechanism of it. Further investigations are needed to realize the effectiveness of this treatment modality and to discover the underlying biological concepts.

단백질 발현 양상 기반 생물 특성 이해를 위한 과학영재 대상 분자생물학 실험 프로그램 개발

Proteins are essential biomolecules that govern cellular activities and play a crucial role in understanding the characteristics of living organisms. A proper understanding of proteins is essential for comprehending the life sciences at the molecular level. In this study, our objective is to provide an experimental educational program for science-gifted middle school students to grasp the concepts of protein-based molecular biology. The experiments we have designed aim to analyze proteins from various organisms, helping students gain insights into their characteristics. To achieve this, we extract proteins from Escherichia coli, yeast, and human plasma/blood cells, and then separate total proteins by size using protein electrophoresis after adjusting their concentrations. Subsequently, we qualitatively determine the quantity and size of proteins through protein staining/de-staining processes. This is followed by discussions and comprehension of the major proteins in relation to biological characteristics. The entire experiment takes approximately 6 hours, allowing participants to learn diverse and universally applicable molecular experimental techniques related to protein analysis. To assess the effectiveness of this program, we conducted both a pre-test and post-test with nine participants who completed the experimental module, and we also gathered additional program feedback. The results of the experimental module showed high satisfaction among the participants, who did not encounter significant difficulties in understanding the experimental content. Furthermore, there was a slight increase in interest and career aspirations in molecular biology, and knowledge of intracellular protein roles and related molecular biology significantly improved. Therefore, This experimental program is expected to facilitate students in comprehending molecular biological concepts based on proteins and establishing a foundation for conducting molecular biology-related research, and ultimately to assist in making their informed career choices in the life sciences.

학습자 주체성 교육에서 교사의 위치와 역할

The purpose of this study is to provide critical analysis on C. Leadbeater’s model of student agency, which serves as the theoretical foundation for the Education 2030 project proposed by OECD, from a philosophical perspective of mind. Within this study, it would be argued that Leadbeater’s model exhibits two key characteristics. Firstly, it appears to align with the prevailing contemporary belief that individualism and rationalism are fundamental to achieving a good life. Secondly, this model can be seen as closely tied to the notion that biological concept of development, particularly maturation, can be employed to elucidate the principles governing the growth of student agency. From the vantage point of this study, such ideas concerning the development of mind seem to carry a substantial risk of misconstruing the role of teachers within the context of student agency education.

Identification of Student Misconceptions on Photosynthesis Material using Three Tier Test Instrument

Many misconceptions occur to students due to their low analytical skills. Misconceptions can occur in some courses that have abstract concepts. These concepts are difficult to understand and are interrelated with each other, so they require in-depth analysis. Analysis and in-depth understanding of biological concepts are needed in plant physiology courses. The research that has been conducted is a descriptive study with purpose to analyze and describe the level of understanding of student concepts on photosynthesis material. The subjects of this study were 30 biology education students at Padang State University (UNP) who took plant physiology classes in the 2022/2023 academic year. Students who have a good understanding of the concept are 10.87%, complete misconceptions are 23, 24%, false positive misconceptions are 22.54% and false negative misconceptions are 21.75%. These findings are expected to be used as a reference for lecturers teaching plant physiology courses to maximize concept understanding in learning.

Running Mice and Successful Theories: The Limitations of a Classical Analogy

AbstractBas van Fraassen’s Darwinian explanation for the success of science has sparked four decades of discussion, with scientific realists and antirealists alike using biologically inspired reasoning to support their points of view. Based on critical engagement with van Fraassen’s proposal itself and later contributions by Stathis Psillos and K. Brad Wray, we claim that central arguments on both sides of this controversy suffer from an insufficient understanding of Darwinism and its underlying biological concepts. Adding the necessary biological background turns out to subvert the argumentative force of viewing the success of scientific theories as analogous to the behaviour of biotic entities. In conclusion, we sketch more productive ways of viewing the relationship between biology and scientific realism.