Teaching Bioinformatics in Concert

Can biology students without programming skills solve problems that require computational solutions? They can if they learn to cooperate effectively with computer science students. The goal of the in-concert teaching approach is to introduce biology students to computational thinking by engaging them in collaborative projects structured around the software development process. Our approach emphasizes development of interdisciplinary communication and collaboration skills for both life science and computer science students.     

Teaching tree thinking in an upper level organismal biology course: testing the effectiveness of a multifaceted curriculum

The ability to interpret and reason from Tree of Life diagrams is a key component of twenty-first century science literacy. This article reports on the authors’ continued development of a multifaceted research-based curriculum – including an instructional booklet, lectures, laboratories and a field activity – to teach such tree thinking to biology students. Results are presented from a study involving biology students enrolled in an upper level organismal biology class. All students received the multi-week tree-thinking curriculum, and learning was assessed by comparing pretest and posttest scores on the novel tree-thinking assessment instrument developed by the authors. Quantitatively, the authors found large gains in tree-thinking abilities due to their instruction. The results also provided qualitative evidence that the authors succeeded in their more general goal of helping students to appreciate the interconnectedness of Earth’s biodiversity through the utility of phylogenetic trees.     

Characterization of pathogenic human MSH2 missense mutations using yeast as a model system: a laboratory course in molecular biology

This work describes the project for an advanced undergraduate laboratory course in cell and molecular biology. One objective of the course is to teach students a variety of cellular and molecular techniques while conducting original research. A second objective is to provide instruction in science writing and data presentation by requiring comprehensive laboratory reports modeled on the primary literature. The project for the course focuses on a gene, MSH2, implicated in the most common form of inherited colorectal cancer. Msh2 is important for maintaining the fidelity of genetic material where it functions as an important component of the DNA mismatch repair machinery. The goal of the project has two parts. The first part is to create mapped missense mutation listed in the human databases in the cognate yeast MSH2 gene and to assay for defects in DNA mismatch repair. The second part of the course is directed towards understanding in what way are the variant proteins defective for mismatch repair. Protein levels are analyzed to determine if the missense alleles display decreased expression. Furthermore, the students establish whether the Msh2p variants are properly localized to the nucleus using indirect immunofluorescence and whether the altered proteins have lost their ability to interact with other subunits of the MMR complex by creating recombinant DNA molecules and employing the yeast 2-hybrid assay.     

Teaching biology students to think divergently

A group of first-year biology students (N = 16) at a tertiary institution was instructed in techniques designed to increase their divergent thinking skills and thus their ability to generate ideas about issues in biology. A comparison was made between the performance of this group and a control group (N = 15) who had not received any training. The experimental group obtained significantly higher scores than the controls on post-test measures of divergent thinking for both general and biological topics. These differences in the biology measures were maintained in a delayed post-test. Results were interpreted as supporting the need for, and effectiveness of, simple techniques designed to improve thinking skills, specifically in biology.     

《动物生物学》教学对生命科学发展和人才培养的作用

动物生物学是揭示动物生命活动规律的科学。作为生命科学专业本科学生最早接触到的主干课程之一,动物生物学的教学对于学生了解生物学的基本概念和基础知识、构建生命科学的知识体系和思维方式、培养和巩固专业兴趣十分重要。系统回顾和总结了动物生物学研究对生命学科发展的贡献,阐明了动物生物学教学对生命科学人才培养与学科建设的作用,引起广大的生物学教学工作者和管理者对动物生物学教学的重视,促进传统重要基础课程的建设与发展。     

The Quantitative Methods Boot Camp: Teaching Quantitative Thinking and Computing Skills to Graduate Students in the Life Sciences

The past decade has seen a rapid increase in the ability of biologists to collect large amounts of data. It is therefore vital that research biologists acquire the necessary skills during their training to visualize, analyze, and interpret such data. To begin to meet this need, we have developed a “boot camp” in quantitative methods for biology graduate students at Harvard Medical School. The goal of this short, intensive course is to enable students to use computational tools to visualize and analyze data, to strengthen their computational thinking skills, and to simulate and thus extend their intuition about the behavior of complex biological systems. The boot camp teaches basic programming using biological examples from statistics, image processing, and data analysis. This integrative approach to teaching programming and quantitative reasoning motivates students’ engagement by demonstrating the relevance of these skills to their work in life science laboratories. Students also have the opportunity to analyze their own data or explore a topic of interest in more detail. The class is taught with a mixture of short lectures, Socratic discussion, and in-class exercises. Students spend approximately 40% of their class time working through both short and long problems. A high instructor-to-student ratio allows students to get assistance or additional challenges when needed, thus enhancing the experience for students at all levels of mastery. Data collected from end-of-course surveys from the last five offerings of the course (between 2012 and 2014) show that students report high learning gains and feel that the course prepares them for solving quantitative and computational problems they will encounter in their research. We outline our course here which, together with the course materials freely available online under a Creative Commons License, should help to facilitate similar efforts by others.This is part of the PLOS Computational Biology Education collection.     

Opening Remarks: Thinking and Deciding

SYNOPSIS. Apart from providing students with the fundamentalconcepts and some of the data supporting these concepts, anintroductory university course in biology should suggest waysof thinking about important human problems that relate to biology.Most of these problems such as abortion, genetic engineering,right to life, environmental pollution, and overuse of naturalresources, have no single solution that will be accepted byall people. Science cannot specify what the solution shouldbe—that must be a human choice. However, the data andprocedures of science can be invaluable in helping human beingsmake informed choices and, once a choice has been made, makemore probable the achieving of the desired goal.     

Evolution and nature of science instruction

In this article, I provide an analysis of my work (1985–present) with non-major biology students and science teacher candidates in developing strategies for teaching and enhancing learning with respect to evolutionary science. This first-person account describes changes in evolution instruction over the course of a career based on personal experiences, research-informed practices, and a critical collaboration with colleague Mike U. Smith. I assert four insights concerning the influence and efficacy of teaching nature of science (NOS) prior to the introduction of evolution within college courses for science non-majors and science teacher candidates. These insights are: (a) teach explicit NOS principles first; (b) integrate evolution as a theme throughout a course in introductory biology (but after NOS principles have been introduced); (c) use active learning pedagogies; and (d) use non-threatening alternative assessments to enhance student learning and acceptance of evolutionary science. Together, these insights establish a pedagogy that I (and my colleagues) have found to be efficacious for supporting novice students as they engage in the study of evolutionary science.     

Using a course-long theme for inquiry-based laboratories in a comparative physiology course

I developed an inquiry-based laboratory model that uses a central theme throughout the semester to develop in undergraduate biology majors the skills required for conducting science while introducing them to modern and classical physiological techniques. The physiology laboratory uses a goal-oriented approach, with students working cooperatively in small groups to answer basic biological questions. The student teams work to develop skills associated with experimental design, data analysis, written and oral communication, science literacy, and critical thinking. The laboratory curriculum is a research-based model that offers the advantage of students asking open-ended questions by use of a variety of techniques. For the students and instructor alike, this presents an exciting and challenging approach for learning physiology and basic biological principles. Another advantage of this laboratory model is that it is flexible and adaptable; the central theme can be any that the instructor chooses, and the goals and techniques developed are based on student and instructor needs and interests. Students who have completed this model at Loyola College in Maryland have become equipped with the skills essential for any area of the biological sciences and, most importantly, showed elevated excitement and commitment to learning.     

Butterflies & wild bees: biology teachers’ PCK development through citizen science*

Citizen science is a rapidly growing emerging field in science and it is gaining importance in education. Therefore, this study was conducted to document the pedagogical content knowledge (PCK) of biology teachers who participated in a citizen science project involving observation of wild bees and identification of butterflies. In this paper, knowledge about how these biological methods can be taught to students is presented. After two years in the project, four teachers were interviewed and their PCK was captured in the form of content representations (CoRes) and Pedagogical and Professional-Experience Repertoires (PaP-eRs). These results can help future citizen science projects to link their activities to the school curriculum. But not only success can be reported: although one of the project team’s aims was to make the Nature of Science accessible to the teachers and students in the course of the project, the teachers did not take this aspect into account. This paper discusses the possible reasons and proposes various strategies for improving citizen science in the context of school biology learning.     

以前沿进展启迪创新思维——“微生物生物学”课程特色专题讲座

"微生物生物学"课程作为理科基地学生的必修课程,对学生夯实专业基础理论知识、开拓科研视野具有积极而重要的作用。如何平衡基础与前沿、理论与实践、教学与科研之间的关系,对课程的内容、形式等都提出了更高的要求。为了丰富和增加学生对微生物学的理解和认识,为生物学理科基地学生明确研究方向提供信息。微生物生物学课程每学期安排8学时专题讲座,其内容不仅与本系教师的科研工作紧密相关,而且还邀请各领域校外专家,讲座内容丰富,涵盖了课程大纲中的主要内容。为学生们深刻明确学习目的、激发科研兴趣、启迪创新性思维搭建了一个平台。通过面对面的交流互动,同学们不仅可获得更多课外知识,了解当今微生物学领域的研究热点,还可从讲座专家那里获得更多切实的科研体会。     

Teaching cell biology in the large-enrollment classroom: methods to promote analytical thinking and assessment of their effectiveness

A large-enrollment, undergraduate cellular biology lecture course is described whose primary goal is to help students acquire skill in the interpretation of experimental data. The premise is that this kind of analytical reasoning is not intuitive for most people and, in the absence of hands-on laboratory experience, will not readily develop unless instructional methods and examinations specifically designed to foster it are employed. Promoting scientific thinking forces changes in the roles of both teacher and student. We describe didactic strategies that include directed practice of data analysis in a workshop format, active learning through verbal and written communication, visualization of abstractions diagrammatically, and the use of ancillary small-group mentoring sessions with faculty. The implications for a teacher in reducing the breadth and depth of coverage, becoming coach instead of lecturer, and helping students to diagnose cognitive weaknesses are discussed. In order to determine the efficacy of these strategies, we have carefully monitored student performance and have demonstrated a large gain in a pre- and posttest comparison of scores on identical problems, improved test scores on several successive midterm examinations when the statistical analysis accounts for the relative difficulty of the problems, and higher scores in comparison to students in a control course whose objective was information transfer, not acquisition of reasoning skills. A novel analytical index (student mobility profile) is described that demonstrates that this improvement was not random, but a systematic outcome of the teaching/learning strategies employed. An assessment of attitudes showed that, in spite of finding it difficult, students endorse this approach to learning, but also favor curricular changes that would introduce an analytical emphasis earlier in their training.     

A first attempt to bring computational biology into advanced high school biology classrooms

Computer science has become ubiquitous in many areas of biological research, yet most high school and even college students are unaware of this. As a result, many college biology majors graduate without adequate computational skills for contemporary fields of biology. The absence of a computational element in secondary school biology classrooms is of growing concern to the computational biology community and biology teachers who would like to acquaint their students with updated approaches in the discipline. We present a first attempt to correct this absence by introducing a computational biology element to teach genetic evolution into advanced biology classes in two local high schools. Our primary goal was to show students how computation is used in biology and why a basic understanding of computation is necessary for research in many fields of biology. This curriculum is intended to be taught by a computational biologist who has worked with a high school advanced biology teacher to adapt the unit for his/her classroom, but a motivated high school teacher comfortable with mathematics and computing may be able to teach this alone. In this paper, we present our curriculum, which takes into consideration the constraints of the required curriculum, and discuss our experiences teaching it. We describe the successes and challenges we encountered while bringing this unit to high school students, discuss how we addressed these challenges, and make suggestions for future versions of this curriculum.We believe that our curriculum can be a valuable seed for further development of computational activities aimed at high school biology students. Further, our experiences may be of value to others teaching computational biology at this level. Our curriculum can be obtained at http://ecsite.cs.colorado.edu/?page_id=149#biology or by contacting the authors.     

基于哲学思维的“分子生物学”教法改革初探

针对“分子生物学”教学中出现的问题,通过分析“分子生物学”中哲学思想及其认知特点,文章进行了基于哲学思维的“分子生物学”教学方法改革初步探讨。期望通过引入哲学思维,培养学生的哲学思想,开拓学生的创新思维,提升他们的认知水平,增强自然科学学生的人文素养,进一步提升“分子生物学”的教学效果。     

The effect of dance over depression

Dance and movement therapy are consisted of music, easy exercises and sensorial stimulus and provide drugless treatment for the depression on low rates. In this study, it has been aimed to examine the effect of dance over the depression. A total of 120 healthy male and female conservatory students ranged from 20 and 24 ages volunteered to participate in this study. They were divided randomly into 1 of 2 groups: dance training group (DTG; N = 60) and control group (CG; N = 60). A dance training program was applied to the subjects three days a week (Tuesday, Thursday, and Saturday) during 12 weeks. The subjects in the control group did not participate in the training and participated only in the pre and post test measurements. Beck Depression Scale was used for the pre and post test measurements of subjects. 12 weeks of dance training has been found to be effective on the depression levels of the subjects participating in the research as the training group (p < 0.05). The depression level of males and females before training has meaningfully decreased after 12 weeks of dance training (p < 0.05). When the depression levels of the subjects participated in research as the control group were separately evaluated for males and females, no meaningful change has been found in the depression levels during 12 weeks (p > 0.05). In conclusion, it has been seen that dance affects the depression levels of university students positively and decreases their depression levels.     

Botanical literacy: What and how should students learn about plants?

Botanists benefit from a scientifically literate society and an interested and botanically literate student population, and we have opportunities to promote literacy in our classes. Unfortunately, scientific illiteracy exists, in part, because students are technologically advanced but lack intellectual curiosity and rigor. Botanical illiteracy results from several interacting factors, including a lack of interest in plants and infrequent exposure to plant science before students reach college. If scientific or botanical literacy is a goal, we must understand what literacy means and how we can help students reach that goal. A model of biological literacy recognizes four levels; students enter courses at the lowest level possessing misconceptions about concepts; however, misconceptions can be used to our advantage, especially by using concept inventories. Inquiry-based instruction is advocated for all science courses, and learning theory supports inquiry. Seven principles of learning inform recommendations about how botanists should teach, including using themes and "thinking botanically" to illustrate all biological concepts. Overall, consideration of the botanical content taught is less critical than the methods used to teach that content. If botanists emphasize thinking and process skills with an understanding of concepts, we will prepare scientifically literate students and citizens and benefit from our efforts.     

An investigative laboratory course in human physiology using computer technology and collaborative writing

Active investigative student-directed experiences in laboratory science are being encouraged by national science organizations. A growing body of evidence from classroom assessment supports their effectiveness. This study describes four years of implementation and assessment of an investigative laboratory course in human physiology for 65 second-year students in sports medicine and biology at a small private comprehensive college. The course builds on skills and abilities first introduced in an introductory investigations course and introduces additional higher-level skills and more complex human experimental models. In four multiweek experimental modules, involving neuromuscular, reflex, and cardiovascular physiology, by use of computerized hardware/software with a variety of transducers, students carry out self-designed experiments with human subjects and perform data collection and analysis, collaborative writing, and peer editing. In assessments, including standard course evaluations and the Salgains Web-based evaluation, student responses to this approach are enthusiastic, and gains in their skills and abilities are evident in their comments and in improved performance.     

Elementary education majors experience hands-on learning in introductory biology

Faculty members from the University of South Dakota attended the Curriculum Reform Institute offered by the University of Wisconsin at Oshkosh, WI, during the summer of 2002 to design a course sequence for elementary education majors that better meets their needs for both content and pedagogy based on the science education standards. The special section of introductory biology that resulted from this workshop is designed to use laboratories and activities that either help students learn major concepts in the life sciences or model how to teach these concepts to their future K-8 students. This study describes how the active, hands-on learning opportunity for preservice teachers with its emphasis on both content and performance-based assessment was implemented in an introductory biology course for elementary education majors during the spring of 2004. During the initial offering of this course, student perceptions about what helped them to learn in the special section was compared with their nonscience major peers in the large lecture-intensive class that they would have taken. Each group of students completed early and late web-based surveys to assess their perceptions about learning during the courses. After the completion of the course, students in the special section appreciated how the relevance of science and conducting their own scientific experimentation helped them learn, enjoyed working and studying in small groups, valued diverse class time with very little lecture, were more confident in their abilities in science, and were more interested in discussing science with others. This course format is recommended for science classes for preservice teachers.     

Enhancing Elementary Students’ Experiences Learning about Circuits Using an Exploration–Explanation Instructional Sequence

Using an exploration–explanation sequence of science instruction helps teachers unveil students’ prior knowledge about circuits and engage them in minds-on science learning. In these lessons, fourth grade students make predictions and test their ideas about circuits in series through hands-on investigations. The teacher helps students make connections between their hands-on experiences collecting data and new terms. This lesson shows how teachers can incorporate formative assessments such as checkpoints, self tests, and exit slips into the explanation phase of instruction so students can evaluate and self-monitor their understanding of circuits in series. These activities meet the National Science Education Standards for active, student-center learning environments that cultivate the critical thinking skills necessary to learn science.     

Teaching evolution: challenging religious preconceptions

Teaching college students about the nature of science should not be a controversial exercise. College students are expected to distinguish between astronomy and astrology, chemistry and alchemy, evolution and creationism. In practice, however, the conflict between creationism and the nature of science may create controversy in the classroom, even walkouts, when the subject of evolution is raised. The authors have grappled with the meaning of such behaviors. They surveyed 538 students in a public, liberal arts college. Pre/post course surveys were analyzed to track changes in student responses to questions that were either consistent or inconsistent with the Theory of Evolution after a semester of instruction in a college biology or zoology course in which evolution was taught. Many students who were initially undecided about issues regarding evolution had shifted in their viewpoints by the end of the course. It was found that more education about the evidence for and the mechanics of evolutionary processes did not necessarily move students toward a scientific viewpoint. The authors also discovered a "wedge" effect among students who were undecided about questions pertaining to human ancestry at the beginning of the course. About half of these students shifted to a scientific viewpoint at the end of the course; the other half shifted toward agreement with statements consistent with creationism.