The major and the first research-centered biology course for "Biology in Practice"

Sarah C. R. Elgin, Washington University in St Louis, Shan Hays, Western Colorado University, Vida Mingo, Columbia College (SC), Christopher Shaffer, Washington University in St Louis, Jason Williams, Cold Spring Harbor Laboratory

Overview

We envision a progression for implementation of the core concepts and courses described, adapted to the circumstances / resources and current curriculum of a given institution. We advocate for adoption of the freshman research lab (Bio 101) as a first step, with subsequent development of the upper level program that builds on the freshman experience, scaffolding from one year to the next. Organization of upper level research experiences can be through the laboratories of existing courses, adapted to include research, or through development of multi-year project courses with vertical integration that allows senior students to mentor sophomores/juniors.Back to overview »

Design Philosophy

Who is our audience (institutional context)

We are developing our work with the following institutional characteristics in mind:

  • A campus of 5K-10K undergraduates (e.g. a large state college; four-year curriculum). A plan that works in this setting can most likely be readily adapted to smaller schools. Community colleges (2-year curriculum) generally aim to articulate with state colleges, so they will need to be able to use the strategies discussed here.
  • Primarily undergraduate institutions (may have some MA students, but not a research university). R1 universities have many more resources and mechanisms for engaging students in research; nonetheless, their students would benefit from the freshman course described here.
  • Freshman biology major entry class that has 3 hrs per week large lecture, 3 hrs per week lab (~ 24 students per lab section).
  • A group of biology faculty (may be in a "Natural Sciences" department); majority have PhD.
  • Students are often focused on job-readiness, while others plan to pursue graduate school or professional credentials; school may offer articulations/workforce certifications.

Our goal is to encourage us all to provide research-based biology education for a broad and diverse population of students across the country.

How will this degree program/certificate address the fundamental values and anchors:

  • Fundamental values/anchors for foundational knowledge: how this program will address them, starting in the freshman year course and building through the the rest of the program:
    • Exposure to the breadth of biology: Lectures will provide examples of questions of interest that students might pursue and then address protocols, techniques, and trouble-shooting, based on "need to know" for the lab investigation, with the aim of familiarizing students with the "tools of the trade." For example, field work--> organismal collection and investigation --> molecular characterization (bar coding).
    • Thinking about how to ask questions: broad possibilities --> measurable variables, incremental knowledge, testable questions.
    • Acquiring background information to build on prior investigations.
    • Keeping a good lab notebook, recording data, and establishing measures of error.
    • Acknowledging the interdisciplinary nature of habitats, organisms, cells, and molecules. For example, the chemistry of a pond (pH, salinity etc.), the corresponding physiology of pond inhabitants, including cell types and diversity, and and the nature of intermolecular interactions between molecules in these organisms' cells.
    • Quantitative reasoning in analysis of data (visualization and statistics).
    • Writing (including illustrating and supporting) final results and conclusions.
  • Fundamental values/anchors for meta knowledge and how this program will address them:
    • Peer instruction is a valuable component that rounds out the learning experience and improves communication skills. It will be integral to most courses in this major.
    • Background reading both of popular materials (e.g. Scientific American) and the scientific literature can introduce students to the thinking of other scientists.
    • Problem solving and critical thinking are an inherent part of a scientific investigation.
    • Science communication is a valued part of instruction. Students need to explain their design, their actions, and their results using their own words.
    • A final presentation, either oral or written, for a general or scientific audience, will be an integral part of every course.
  • Fundamental values/anchors for humanistic knowledge and how this program will address them:
    • Students learn best when they can shape their own questions. While overarching research aims will frequently be defined by the faculty, we aim to help students place their scientific work in the context of their interests and their understanding of science and its place in society.
    • Student questions often relate to problems relevant to their community and society as a whole. We aim to help them place their scientific work in cultural and global context.
    • Research projects often depend on teamwork, either to provide sufficient hands or to provide the breadth of expertise needed, so a team-based approach will be used frequently, as designed by the faculty.
  • Practical considerations 
    • Peer instruction helps makes this program sustainable.
    • Use of computational methods is a low-cost on-ramp to research experience.

Courses and Sequencing

Entry: the freshman year research lab

 

  1. Bio 101: Research-Integrated Introduction to Biology.  This course provides foundational knowledge on biology research principles and applied practices (somewhat guided inquiry with defined tools and workflow - there are lots of choice as to subject matter).  An example is the freshman lab at James Madison University developed by Ray Enke, in which students survey an ecological system, identify an organism of interest, and investigate that organism, culminating in bar-code identification, thus familiarizing themselves with ecology, organismal biology, and molecular genetics.   Here we develop this option as a full course with lecture plus lab (8/hr per week) in the fall semester, with a follow-on research lab (3-4 hr/wk) that can be used in conjunction with different lecture options  (Option A).  Other examples include SEA-PHAGES, developed by Graham Hatfull, involving microbiology and genomics (Option B; Hanauer et al. 2019  https://www.pnas.org/content/114/51/13531).  See Indorf et al, CBE—Life Sciences Education - 18:ar38, 1–15, Fall 2019 for many examples of freshman CUREs.

Option A:  Catalog Course Description                                                

The goals of this course are to introduce you to the breadth of biology and to introduce you to research in this discipline.  We begin with some ecology field work in Forest Park, progress to characterization of your chosen organism (a plant, fungus, or insect), and end by using DNA sequencing (bar-coding) to identify and characterize that organism.  Lectures will provide the background needed to look at life from population/ecology, whole organism, and cell/molecular perspectives. The course introduces principles of experimental design, the tools we will use, and the societal context for the investigations we will undertake.  Options to join a team or design your own research project.  MW or TuTh, 1pm – 5 pm (2 hr lecture/6 hr lab per week),  plus occasional optional guest lectures and discussions (live-streamed and recorded).   Letter grade; no audits. Open to all students, whether prospective science majors or not.  Freshmen or first-semester transfer students only.  No prerequisites.

Students who take Bio 101 in the fall are encouraged to enroll in Bio 102 in the spring.  Bio 102 encompasses the application of biology research principles through student-driven projects.  Projects emerge from Bio 101 activities; students may continue and expand existing projects or develop new ones, using primarily the same tools, but incorporating additional approaches as negotiated with the lab instructor.  One 3-hr lab period per week plus occasional optional guest lectures and discussions (live-streamed and recorded).   Letter grade; no audits. Prerequisite: Bio 101.  May be substituted for the lab section of Bio XXX.

 Option B: Catalog Course Description for Phage Hunters (local adaptation):           

This year-long course on phage gives students a broad overview of biology including genetics, evolution, biochemistry, cell biology, and ecology, with a focus on cellular structures and mechanisms of biological macromolecular processes.   Considerations for human health are woven in throughout the year. The laboratory component will meet 4 hours per week and engages students in a national research program to discover novel viruses from the environment, study their genomic makeup, and undertake detailed investigations into the function and properties of specific genes. The lab will introduce students to both experimental methodologies as well as diverse computational methods of analysis, giving students insights into the ways in which biological molecules combine and function to create living systems. Lecture MWF noon-1, Lab TTh 1-3.  Letter grade; no audits.  Open to all students, whether prospective science majors or not. No prerequisites.

Bio 205 Introductory Science Research Skills

A one-semester course to provide transfer students, or advanced students who wish to switch into the Biology major, the opportunity to develop the skills continuing students developed in the freshman-level lab courses. Course description similar to Bio 101.  Prerequisite: sophomore-level standing

Upper level research courses:       

 Bio 201, 301, 401: Advanced Research Lab

There are many ways that research experiences can be integrated into the upper level curriculum.  We illustrate some of these here.  In all cases the course will be given for a letter grade, ensuring full faculty credit.  Participation in a prescribed number of upper level lab courses (or equivalent individual mentored lab experiences) will be a required part of the major.   In all cases it is highly desirable that the investigation have significance beyond the classroom, either to the scientific community or to the local community, and that it result ultimately in publication - a paper in the scientific literature (likely reporting several years work), a report to a community body, or a series of microPublications, which can be smaller units (e.g., annotation of one gene in a newly sequenced species).

Option A:  All upper-level courses that currently use a lab along with lecture introduce a research component into that lab, creating a CURE (Course-based Undergraduate Research Experience).  The research project will, in many cases, take up all available lab time, at 3 hr/wk, but might be concentrated into the last half of the semester.  Alternatively, the format could be switched to 2 hr lecture and 6 hr lab/wk.  The lab topic should reflect the research interests of the faculty member teaching the course.

Option B:  Upper level research lab courses are split away from the lecture courses.  Lecture classes pay attention to the research process through discussion of ground-breaking experiments in the field, reflection on the original literature, etc.  Lab courses meet 6-8 hr/wk, creating opportunities for more in-depth work using wet bench, field resources, online data resources, or some combination of these.

For both options above, the degree of student choice in experimental design will vary with the topic, and may be limited by the equipment available.  To the degree possible, the overall project will be designed so that each student (or team) has ownership of their piece.  For example, a biochemistry lab centered on protein purification and characterization might examine the same enzyme isolated from different sources; determine the enzyme activity under a variety of conditions; or look at the impact of specific mutations that the students have designed.  A lab in neurobiology that depends on fairly sophisticated equipment (e.g. intracellular recording) might coach students through an initial experiment and then invite them to design an experiment changing one or two variables, defending their choice and predicting outcomes.   A lab in vertebrate anatomy might investigate variation in structural parameters or be coupled with physiology to investigate structure-function relationships.  Significant investigations in genomics and ecology can be done entirely online, using data already available.

Option C:  Upper level research lab courses are distinct from the rest of the curriculum, are "vertically integrated," and are organized around the research interests of each faculty member with relevance to a current scientific question or a community need (e.g. citizen science; SENCER- National Center for Science & Civic Engagement, http://sencer.net).   A team of students is engaged with the faculty mentor guiding each project and students are encouraged to be a member of that team for three years.  Thus, seniors can guide the initial efforts of sophomores, creating a learning continuum that supports the faculty efforts and provides the more experienced students with opportunities to improve their skills in communications, team management, etc; course credit increases with the experience level of the student.  This approach has been particularly successful in engineering, bio tech and other entrepreneurial settings (see https://www.vip.gatech.edu).

Option D:  This course is intended to engage sophomore/junior/senior students in research. Students will be exposed to many of the practical aspects of original research*.  Working in a collaborative research team with a faculty mentor, students will develop a mock grant proposal that will include hypothesis generation, experimental design, data analysis, and visualization***. Students are expected to integrate primary literature as they build their mock grant proposal**.  They will go through a peer review process with other research students to enhance their written and oral science communication skills**. Bench research will begin fall semester and continue into the spring with options for subsequent year participation.  At the end of the research experience, students will give an oral presentation (poster or talk) in a research symposium for undergraduates in the Spring. This will be similar in many ways to the experience of a first-year graduate/pre-professional student*.

The selection of a topic will include a partnership between students and the research mentor based on faculty expertise. Students are encouraged to include areas of research that are impactful to their community (local, regional or national/global). Examples include cultural, ethical, and/or social questions in public health, such as diabetes in Native Americans and cystic fibrosis in individuals of Irish descent; understanding the molecular mechanisms of Anopheles mosquito's infection in malaria; other genomics explorations; and questions in organismal biology. The course will require students to incorporate foundational, humanistic and meta-knowledge integration into the research experience.

Prerequisite: Bio 101 and 102/(103) OR Corequisite: Bio 205

References:  * from=Lance Barton- Cancer Biology- Austin College (syllabus); **=Vida Mingo's Genetics course; ***Course Source- Mock Grant

 

Other Requirements 

  1. Requirement: Statistics and Experimental Design
  2. Requirement: A computer programming course - visualization of data (e.g. introduction to R, Python, etc.)
  3. Requirement: Ethical, Legal, and Social Issues in Research (This might be paired with Bio 102.)
  4. Requirement: Scientific Communication (Writing, Oral Presentation, and Department Symposium). (Alternatively, this could be integrated into one or more of the research courses or provided as an option in any of several research courses.  In any event, the experience must include multiple opportunities to critique the writing of peers on the same assignment, receive critiques from peers and faculty, and rewrite once or twice for final submission.
  5. The Department will set its own requirements for the number and type of upper level Biology courses to be taken for the major.  These should be organized such that the student has exposure to all of the five core areas described in "Vision and Change."  (Faculty can identify which of the V&C themes are covered in their course.)
  6. The Department will set its own requirements for courses in chemistry, physics, and math.
  7. The institution will set its own requirements for general education.  (Note that a general freshman writing course will not satisfy the spirit of the Scientific Communication course above, but some combination of writing practice in the English Department and in the biology courses may well do so.)

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