Resolving spatial and temporal patterns of coral bleaching risk using image analysis: an active learning experience to improve climate change literacy in college students

Recent studies indicate poor understanding of the causes and consequences of climate change among college students. In an effort to improve climate change literacy, we have developed an authentic research experience for upper level undergraduate students focused on resolving spatial and temporal patterns of coral reef bleaching, an ecologically and economically important consequence of climate warming. In the research, students use a public archive of maps generated by the United States National Oceanographic and Atmospheric Association (NOAA) that use coloration to depict ocean areas experiencing above-average surface temperatures and where corals are at an increased risk of bleaching. Students are required to quantify the total area of coloration on individual maps using open-source image analysis software called Image J. By quantifying coloration (ie bleaching risk) over a large number of maps in a chronological sequence, students can test hypotheses regarding the relationship between ongoing climate warming and coral bleaching risk. Students are required to summarise their findings in a scientific journal-style report that incorporates graphical representations and statistical tests of their coral bleaching risk data. The research activity is cost-effective, repeatable, requires little specialised knowledge and addresses common programmatic learning outcomes that target scientific communication, quantitative reasoning and sustainability.     

Producing scientific posters,using online scientific resources,improves applied scientific skills in undergraduates

ABSTRACT

To succeed, undergraduate science students need to both acquire knowledge, and learn to apply it effectively. Here a novel 1^st year undergraduate module (incorporating blended learning, applied bioinformatic skills and scientific posters) is described and its effectiveness evaluated (quantitatively and qualitatively). The aims were to engage students and teach applied skills through a process-oriented guided-inquiry learning (POGIL) based project, utilising common online tools. Given a nucleotide entry and utilising the National Centre for Biotechnology Information (NCBI) platform students had to identify a specific human syndrome. Students then retrieved and summarised key scientific data, presenting it as a scientific poster. The module effectiveness was demonstrated by the students ability to acquire knowledge (content) and apply it (process), by finding and extracting data from online databases. Assessment included evaluation of the students ability to analyse, visualise and explain acquired data as a scientific poster. Module evaluation used qualitative students surveys and quantitative assessment (pre- and post- module, multiple-choice quiz, assessing content or process specific knowledge). The module led to a significant increase in students applied, process specific, knowledge and enhanced their learning experience. This module demonstrates a successful method for incorporating applied learning into an undergraduate module, developing multiple applied professional skills.     

Students’ investigations of torque

Students come to class with little understanding about torque, angular velocity, and angular acceleration despite the fact that these physical science concepts are frequently observed. For example, torque occurs when car and bicycle tires rotate, the movement of fishing pole when hooking a fish, and when a person uses a hammer to drive in a nail. Interestingly, students also have a plethora of misunderstandings about scientific inquiry. For example, many students believe that all scientific investigations contain an experiment, and that they are all consist of very specific steps comprising the scientific method. In this week long lesson, 9–12 grade students engage in scientific and engineering practices to examine factors that affect the amount of angular acceleration of a catapult arm. Students also reflect on their own understandings of scientific inquiry within the context of the lesson and address misconceptions they might have. Throughout the activities of this lesson, students to engage in discourse, critical thinking, problem solving, reflection, and modification of ideas to design a catapult that will effectively launch a projectile.     

Data archiving in ecology and evolution: best practices

Many ecology and evolution journals have recently adopted policies requiring that data from their papers be publicly archived. I present suggestions on how data generators, data re-users, and journals can maximize the fairness and scientific value of data archiving. Data should be archived with enough clarity and supporting information that they can be accurately interpreted by others. Re-users should respect their intellectual debt to the originators of data through citation both of the paper and of the data package. In addition, journals should consider requiring that all data for published papers be archived, just as DNA sequences must be deposited in GenBank. Data are another valuable part of the legacy of a scientific career and archiving them can lead to new scientific insights. Archiving also increases opportunities for credit to be given to the scientists who originally collected the data.     

Pedometer and Human Energy Balance Applications for Science Instruction

Teachers can use pedometers to facilitate inquiry learning and show students the need for mathematics in scientific investigation. The authors conducted activities with secondary students that investigated intake and expenditure components of the energy balance algorithm, which led to inquiries about pedometers and related data. By investigating the accuracy of pedometers and variables that may impact reported step counts, students can better understand experimental design and statistical concepts. Students can also examine other data (distance walked, kilocalories expended) using multifunction pedometers and apply the concepts of correlation and regression. This topic fits well with thematic learning and responds to concerns about excess energy intake and insufficient physical activity in the U.S. population.     

Selective use of the primary literature transforms the classroom into a virtual laboratory

CREATE (consider, read, elucidate hypotheses, analyze and interpret the data, and think of the next experiment) is a new method for teaching science and the nature of science through primary literature. CREATE uses a unique combination of novel pedagogical tools to guide undergraduates through analysis of journal articles, highlighting the evolution of scientific ideas by focusing on a module of four articles from the same laboratory. Students become fluent in the universal language of data analysis as they decipher the figures, interpret the findings, and propose and defend further experiments to test their own hypotheses about the system under study. At the end of the course students gain insight into the individual experiences of article authors by reading authors' responses to an e-mail questionnaire generated by CREATE students. Assessment data indicate that CREATE students gain in ability to read and critically analyze scientific data, as well as in their understanding of, and interest in, research and researchers. The CREATE approach demystifies the process of reading a scientific article and at the same time humanizes scientists. The positive response of students to this method suggests that it could make a significant contribution to retaining undergraduates as science majors.     

We're Going on a Fossil Hunt!

Scientists understand that scientific ideas are subject to change and improvement. Fourth- through eighth- graders develop this understanding about the nature of science as they gather and examine fossil evidence from the Paleozoic era, record their findings, and read and write about science for authentic purposes as scientists do. Students recognize the tentative nature of science and experience differences in interpretation of evidence. Students also learn that scientists use writing and sketching as tools of inquiry.     

医院全成本核算数据集成化管理的探讨

面对目前医院全成核算系统存在的各种弊端及困难,通过依托内部运行机制及现有的各项数据资源进行合理整合,无缝地将不同系统间的数据,按照统一的接口规则、标准的调控规范,采用科学的方法进行融合,实现全成本核算数据的高度集成化管理。利用科学的方法路线与技术路线详细分析并阐述了数据集成化的构建内容、集成化的管理作用,并对集成化管理的战略影响进行了必要的展望。     

基因芯片数据分析过程:从原始数据到生物学意义

基因芯片实验要得到可靠的生物学结论,必须基于优化的实验设计和科学的数据分析。讨论了与基因芯片数据分析方法相关的实验设计方面的几个问题,简述了差异表达分析、聚类分析及功能富集分析等分析方法及其进展,并介绍了部分软件及应用。     

基于本体论的植物遗传资源数据整合研究

随着现代生物学的发展,全球范围内建立了大量的生物学数据共享中心,同时,在生物学发展的带动下,植物遗传资源数据变得更为复杂、异构化和海量。本文在分析国内外几大著名的数据整合共享中心的基础上,简要介绍了本体论的概念及其在生物学领域中的研究现状,提出了基于生物本体论将植物遗传数据、数据挖掘工具、科技文献和科技交流进行整合的设想,并对数据整合需要考虑的几个问题进行了讨论。     

Anticipation of Personal Genomics Data Enhances Interest and Learning Environment in Genomics and Molecular Biology Undergraduate Courses

An important discussion at colleges is centered on determining more effective models for teaching undergraduates. As personalized genomics has become more common, we hypothesized it could be a valuable tool to make science education more hands on, personal, and engaging for college undergraduates. We hypothesized that providing students with personal genome testing kits would enhance the learning experience of students in two undergraduate courses at Brigham Young University: Advanced Molecular Biology and Genomics. These courses have an emphasis on personal genomics the last two weeks of the semester. Students taking these courses were given the option to receive personal genomics kits in 2014, whereas in 2015 they were not. Students sent their personal genomics samples in on their own and received the data after the course ended. We surveyed students in these courses before and after the two-week emphasis on personal genomics to collect data on whether anticipation of obtaining their own personal genomic data impacted undergraduate student learning. We also tested to see if specific personal genomic assignments improved the learning experience by analyzing the data from the undergraduate students who completed both the pre- and post-course surveys. Anticipation of personal genomic data significantly enhanced student interest and the learning environment based on the time students spent researching personal genomic material and their self-reported attitudes compared to those who did not anticipate getting their own data. Personal genomics homework assignments significantly enhanced the undergraduate student interest and learning based on the same criteria and a personal genomics quiz. We found that for the undergraduate students in both molecular biology and genomics courses, incorporation of personal genomic testing can be an effective educational tool in undergraduate science education.     

Data exploration in phylogenetic inference: scientific, heuristic, or neither

The methods of data exploration have become the centerpiece of phylogenetic inference, but without the scientific importance of those methods having been identified. We examine in some detail the procedures and justifications of Wheeler's sensitivity analysis and relative rate comparison (saturation analysis). In addition, we review methods designed to explore evidential decisiveness, clade stability, transformation series additivity, methodological concordance, sensitivity to prior probabilities (Bayesian analysis), skewness, computer‐intensive tests, long‐branch attraction, model assumptions (likelihood ratio test), sensitivity to amount of data, polymorphism, clade concordance index, character compatibility, partitioned analysis, spectral analysis, relative apparent synapomorphy analysis, and congruence with a “known” phylogeny. In our review, we consider a method to be scientific if it performs empirical tests, i.e., if it applies empirical data that could potentially refute the hypothesis of interest. Methods that do not perform tests, and therefore are not scientific, may nonetheless be heuristic in the scientific enterprise if they point to more weakly or ambiguously corroborated hypotheses, such propositions being more easily refuted than those that have been more severely tested and are more strongly corroborated. Based on common usage, data exploration in phylogenetics is accomplished by any method that performs sensitivity or quality analysis. Sensitivity analysis evaluates the responsiveness of results to variation or errors in parameter values and assumptions. Sensitivity analysis is generally interpreted as providing a measure of support, where conclusions that are insensitive (robust, stable) to perturbations are judged to be accurate, probable, or reliable. As an alternative to that verificationist concept, we define support objectively as the degree to which critical evidence refutes competing hypotheses. As such, degree of support is secondary to the scientific optimality criterion of maximizing explanatory power. Quality analyses purport to distinguish good, reliable, accurate data from bad, misleading, erroneous data, thereby assessing the ability of data to indicate the true phylogeny. Only the quality analysis of character compatibility can be judged scientific—and a weak test at that compared to character congruence. Methods judged to be heuristic include Bremer support, long‐branch extraction, and safe taxonomic reduction, and we underscore the great heuristic potential of a posteriori analysis of patterns of transformations on the total‐evidence cladogram. However, of the more than 20 kinds of data exploration methods evaluated, the vast majority is neither scientific nor heuristic. Given so little demonstrated cognitive worth, we conclude that undue emphasis has been placed on data exploration in phylogenetic inference, and we urge phylogeneticists to consider more carefully the relevance of the methods that they employ. [T]he cult of impressive technicalities or the cult of precision may get the better of us, and interfere with our search for clarity, simplicity, and truth [Popper, 1983, p. 60. Empirical papers chosen for publication are judged to be of interest to a broad systematics audience because they represent exemplary case studies involving some important contemporary issue or issues. These may be unusually thorough explorations of data, applications of new methodology, illustrations of fundamental principles, and/or investigations of interesting evolutionary questions. [Systematic Biology: Instructions for authors, 2002; italics added]     

The Dawn of Open Access to Phylogenetic Data

The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that require increasing levels of expertise and computational investment. Moreover, the resulting phylogenetic data provide an explicit historical perspective that critically informs research in a vast and growing number of scientific disciplines. One such use is the study of changes in rates of lineage diversification (speciation – extinction) through time. As part of a meta-analysis in this area, we sought to collect phylogenetic data (comprising nucleotide sequence alignment and tree files) from 217 studies published in 46 journals over a 13-year period. We document our attempts to procure those data (from online archives and by direct request to corresponding authors), and report results of analyses (using Bayesian logistic regression) to assess the impact of various factors on the success of our efforts. Overall, complete phylogenetic data for of these studies are effectively lost to science. Our study indicates that phylogenetic data are more likely to be deposited in online archives and/or shared upon request when: (1) the publishing journal has a strong data-sharing policy; (2) the publishing journal has a higher impact factor, and; (3) the data are requested from faculty rather than students. Importantly, our survey spans recent policy initiatives and infrastructural changes; our analyses indicate that the positive impact of these community initiatives has been both dramatic and immediate. Although the results of our study indicate that the situation is dire, our findings also reveal tremendous recent progress in the sharing and preservation of phylogenetic data.     

现代生物医学研究中医学研究生“大数据”利用能力的培养

科研能力的水平是我国研究生教育质量的重要指标。现代生物医学研究中呈现的"大数据"特点给研究生科研能力培养提出了新的要求。本文在分析"大数据"基本特点和总结医学科研思维模式在"大数据"影响下发生的转变的基础上,对提高医学研究生获取和利用"大数据"信息的能力提出一些具体建议,希望能够推动医学研究生科研能力的培养。     

The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types

The Genome Sequence Archive (GSA) is a data repository for archiving raw sequence data, which provides data storage and sharing services for worldwide scientific communities. Considering explosive data growth with diverse data types, here we present the GSA family by expanding into a set of resources for raw data archive with different purposes, namely, GSA (https://ngdc.cncb.ac.cn/gsa/), GSA for Human (GSA-Human, https://ngdc.cncb.ac.cn/gsa-human/), and Open Archive for Miscellaneous Data (OMIX, https://ngdc.cncb.ac.cn/omix/). Compared with the 2017 version, GSA has been significantly updated in data model, online functionalities, and web interfaces. GSA-Human, as a new partner of GSA, is a data repository specialized in human genetics-related data with controlled access and security. OMIX, as a critical complement to the two resources mentioned above, is an open archive for miscellaneous data. Together, all these resources form a family of resources dedicated to archiving explosive data with diverse types, accepting data submissions from all over the world, and providing free open access to all publicly available data in support of worldwide research activities.     

Making Sense of Scientific Biographies: Scientific achievement,nature of science,and storylines in college students’ essays

In this article, the educative value of scientific biographies will be explored, especially for non-science major college students. During the ‘Scientist’s life and thought’ course, 66 college students read nine scientific biographies including five biologists, covering the canonical scientific achievements in Western scientific history. Students’ essays were initially analysed in terms of four dimensions of scientific achievement: personal traits and talent, socio-cultural environment, scientific inquiry and debate, and historical significance. Further analysis focused on noticeable aspects in the nature of science (NOS). Based on the analyses, the idea of a story grid was devised in order to identify major storylines that show students various ways of making sense of scientific biographies. The analysis shows the aspects in which biographies are instrumental for students to identify and engage critically with issues related to the NOS. The article concludes with some implications for designing history of science courses for non-science major college students.     

Isolation and characterization of Saccharomyces cerevisiae mutants defective in chromosome transmission in an undergraduate genetics research course

An upper-level genetics research course was developed to expose undergraduates to investigative science. Students are immersed in a research project with the ultimate goal of identifying proteins important for chromosome transmission in mitosis. After mutagenizing yeast Saccharomyces cerevisiae cells, students implement a genetic screen that allows for visual detection of mutants with an increased loss of an ADE2-marked yeast artificial chromosome (YAC). Students then genetically characterize the mutants and begin efforts to identify the defective genes in these mutants. While engaged in this research project, students practice a variety of technical skills in both classical and molecular genetics. Furthermore, students learn to collaborate and gain experience in sharing scientific findings with others in the form of written papers, poster presentations, and oral presentations. Previous students indicated that, relative to a traditional laboratory course, this research course improved their understanding of scientific concepts and technical skills and helped them make connections between concepts. Moreover, this course allowed students to experience scientific inquiry and was influential for students as they considered future endeavors.     

Yeast for Mathematicians: A Ferment of Discovery and Model Competition to Describe Data

In addition to the memorization, algorithmic skills and vocabulary which are the default focus in many mathematics classrooms, professional mathematicians are expected to creatively apply known techniques, construct new mathematical approaches and communicate with and about mathematics. We propose that students can learn these professional, higher-level skills through Laboratory Experiences in Mathematical Biology which put students in the role of mathematics researcher creating mathematics to describe and understand biological data. Here we introduce a laboratory experience centered on yeast (Saccharomyces cerevisiae) growing in a small capped flask with a jar to collect carbon dioxide created during yeast growth and respiration. The lab requires no specialized equipment and can easily be run in the context of a college math class. Students collect data and develop mathematical models to explain the data. To help place instructors in the role of mentor/collaborator (as opposed to jury/judge), we facilitate the lab using model competition judged via Bayesian Information Criterion. This article includes details about the class activity conducted, student examples and pedagogical strategies for success.