Paper submitted to the World Conference on Educational Media, Hypermedia and Telecommunications (ED-MEDIA 99), June 19-24, 1999, Seattle, WA.

The Virtual Cell: An Interactive, Virtual Environment for Cell Biology

Alan R White1 Phillip E. McClean2 and Brian M. Slator3
Departments of Botany/Biology1, Plant Science2, and Computer Science3
North Dakota State University, Fargo, ND 58105

ABSTRACT

The Virtual Cell is an interactive, 3-dimensional visualization of a bio-environment. It has been prototyped using the Virtual Reality Modeling Language (VRML), and is to be available via the Internet. To the student, the Virtual Cell looks like an enormous navigable space populated with 3D organelles. In this environment, experimental goals in the form of question-based assignments promote deductive reasoning and problem-solving in an authentic visualized context. The NDSU WorldWide Web Instructional Committee (WWWIC) is engaged in developing a range of irtual environments for education. These projects span a range of disciplines, from Earth Science to Anthropology, and from Business to Biology. However, all of these projects share a strategy, a set of assumptions, an approach to assessment, and an emerging tool set, which allows each to leverage from the insights and advances of the others.

Introduction

The Virtual Cell is being developed by the NDSU World Wide Web Instructional Committee (WWWIC), a multi-disciplinary group of faculty engaged in the development of virtual/visual worlds for science education (NDSU's WWWIC). Other WWWIC projects include The Geology Explorer, The Visual Computer Program and ProgrammingLand MOO. Each of these projects share a common objective: to teach scientific problem-solving skills (deductive reasoning, experimental design, hypothesis formation) through immersion in learn-by-doing virtual environments. These projects are designed to support discovery-based learning in a self-paced, role-based, and goal-oriented framework. They are also learner oriented, immersive, and exploratory in nature. Each project aims toward highly interactive, highly graphical systems employing software tutors to guide and remediate in the event of student failure. In addition, each project individually pursues the objective of teaching discipline-specific science content through the achievement of authentic problem-solving goals, but using uniquely different approaches. The projects are designed to employ consistent elements across disciplines and, as a consequence, foster the sharing of development plans and development tools. More information about WWWIC is available at http://www.ndsu.nodak.edu/wwwic/.

Learning by Doing

The goal of post-secondary science education is to train future scientists. One problem with science education is the standard lecture/laboratory format. In lecture the professor speaks, and the student passively listens. In the worst case, lectures are no better for learning than television: a totally passive, non-interactive experience. Meanwhile, laboratories are intended to afford students with an interactive, experimental experience, but in reality these are usually rigidly structured by the laboratory outline where the intended outcome is known and the procedure is inflexible. These are not experimental experiences. If laboratories were to be truly experimental, question- and hypothesis-driven experiences, then students would need access to modern laboratory equipment and instrumentation, a vast array of expensive laboratory reagents, and a wealth of instructor time that the university cannot possibly afford. Active learning can be expensive, yet the value of active versus passive learning has become increasingly clear (Reid, 1994).

Science students need an interactive, exploration-based learning experience that teaches basic principles. Hypertext, CD-ROM presentations, and world wide web pages can make a contribution to active learning. The learner has control over many aspects of the presentation by deciding which pages to visit and in what order. However, these are non-experimental approaches that mimic a book. Browsing through hypertext is still a two-dimensional, non-interactive, and largely passive activity. An active learning alternative is the virtual environment or world where learners can experience their education in a "learning-by-doing" way. Student visitors are invited to participate in a self-paced exploration of the environment, where they can make observations, manipulate the interactive objects, and design and perform experiments. We are developing such a virtual world, The Virtual Cell, that enables exploratory, hypothesis-driven, and experimental science learning.

The Virtual Cell

The Virtual Cell is a virtual, multi-user space where students "fly" around and practice being cell biologists in a role-based, goal-oriented environment. Working individually, or with others, students learn fundamental concepts of cell biology and strategies for deductive problem solving through their experiences in the exploratory environment. This pedagogical approach gives students an authentic experience that includes elements of practical, experimental design and decision making, while introducing them to discipline content. By practical applications of the scientific method, students learn how to think, act, and react as cell biologists (Slator and Chaput, 1996).

The Virtual Cell is a 3D environment in which the student can learn about the structure and function of a cell. The Virtual Cell is populated with subcellular components: nucleus, endoplasmic reticulum, Golgi apparatus, mitochondria, chloroplast and vacuoles. Each structure is rendered as a 3D object using the Virtual Reality Modeling Language (VRML), a computer language for specifying three- dimensional worlds that can be displayed and, most importantly, interacted with via the Internet. The Virtual Cell development project can be visited at http://www.ndsu.nodak.edu/instruct/mcclean/vc/.

The Virtual Cell Experience: The Laboratory

The Virtual Cell consists of a VRML-based laboratory and a cell. In the laboratory, the learner receives a specific assignment (learners are always assigned motivating goals in our learning-by-doing environments), performs simple experiments, and learns the basic physical and chemical features of the cell and its components. The virtual laboratory procedures require a voyage into a VRML cell (see below), where experimental science meets virtual reality. The learner is supplied with a toolbox of measuring devices that assay various cellular processes. These tools include an O2 meter, CO2 meter, pH meter, sugar assay, protein assay, various stains and enzyme assays. As the students progress, they revisit the laboratory, bring cellular samples back for experimentation, and subsequently receive more assignments.

The Cell

Student understanding of the concepts related to the structure and function of the cell is an essential feature of the pedagogy of modern biology. Learning the physical components of the cell, how these components interact, and how these interactions are regulated has largely replaced the traditional organismal approach to teaching biology. The cell, though, is a complex, multidimensional environment where time and space are critical factors that determine when and where cellular events occur. It is very difficult to capture this multi-dimensionality in the 2-D space of the printed page, chalk board, or web page.

The virtual cell contains 3D representations of all the components and organelles of a cell (nucleus, mitochondria, chloroplasts, etc). The user "flies" among these organelles and uses virtual instruments to conduct experiments. All navigation is learner directed; there is no predetermined exploratory path. This feature empowers the student to direct their own learning. The student is also able to travel into linked VRML worlds that represent the interior of each of the cellular organelles. Further experimentation inside each organelle allows the student to learn about their specific functions (Wu, 1998).

For example, the learner may confront the nucleus and perform several simple experiments. The nucleus is not consuming or generating O2 or CO2, it has a positive Fulgen stain reaction and it demonstrates a negative luciferase enzyme reaction. The learner must put these results into a context. They would have to learn from a lecture, a textbook or a tutoring agent that a positive Fulgen stain means DNA is present and a negative luciferase reaction means ATP is absent. In the cell, this general information is contained in the 3D representation and offered via touch sensitive points. Putting this and information from additional experiments together, the learner should deduce that the object is the nucleus and that DNA is contained there. Additional pertinent data about the nucleus and other cellular organelles can be collected in the same manner.

More advanced levels of the Virtual Cell include the introduction of cellular perturbations and the investigation of the functions of various cellular structures or processes. In the second level, a simulation will change the cell by either introducing a mutation or adding an inhibitor that disrupts a cellular process. An alarm will sound, some cellular process will malfunction, and the learner will be given the goal of diagnosing the problem. Using the same tools as in the previous level, the learner will navigate through the cell, make observations, and perform measurements and experiments. The learner will attempt to identify the affected area, the perturbed process, and the nature of the mutation or inhibitor that is causing the problem. As a result, the user will learn details of cellular processes and functions and become familiar with the importance of various mutations and inhibitors for cell biology experimentation.

In the third level of the Virtual Cell, the learner will be given a set of goals to investigate a specific cellular structure or process. The learner will have at their disposal the tools from the first level and the mutations and inhibitors from the second level. Using these in various combinations, the student will form hypotheses, design experiments, and employ the toolbox items to perform these experiments. For example, the learner might be given the goal of determining how a membrane vesicle buds off from one compartment and is specifically targeted to fuse with another compartment. Using the tools from previous levels and their experience with designing and performing experiments, the learner could determine that proteins from two compartments recognize each other, bind in a specific fashion, and promote the fusion of a vesicle to a target compartment.

Simulations

The implementation of the Virtual Cell depends on coordinating three technologies: 1) VRML visualization, 2) a text-based MOO server (Curtis, 1992), and 3) Java client and simulation software. Students will use a standard WWW browser to launch a Java applet, which will provide a connection to an object-oriented, multi-user domain (a MOO; see below) where cellular processes are simulated and multi-user viewpoints are synchronized. The Java applet also launches an interface to the VRML representation of the Virtual Cell, allowing the student to explore and experiment within the 3D representation. To the student, the Virtual Cell will look like an enormous navigable space where deductive reasoning and problem-solving in a visualized context are necessary for completion of assigned experimental goals.

Multiuser Aspects

The object-oriented multi-user domain (MOO) simulation on which the cell is established allows students to interact directly with one another within the cell, providing advice to one another or even working together to achieve particular goals. Because the MOO is internet-based, students from separate and distant locations can simultaneously interact with the cell and with one another. Unintrusive but proactive software agents act as tutors, monitoring students' actions and "visiting" the students as the need arises. Tutor agents provide advice on equipment choices, navigation, and scientific conclusions. Tutors neither mandate or insist on student actions nor do they block or prevent student actions.

Summary

The Virtual Cell is an attempt by science educators to develop educational tools and methods that deliver the principles but also teach important content information in a meaningful way to biology students. Virtual classrooms and virtual laboratories help solve many of the problems faced in secondary and post-secondary education: distance learning becomes a reality, learner diversity is accommodated (both in terms of learning styles and life styles), and in many cases the curriculum becomes more active, more role-based, more self-paced, and more "learn by doing" than "learn by listening."

References

  1. Curtis, Pavel (1992). Mudding: Social Phenomena in Text-Based Virtual Realities. Proceedings of the conference on Directions and Implications of Advanced Computing (sponsored by Computer Professionals for Social Responsibility)

  2. Reid , T Alex (1994) Perspectives on computers in education: the promise, the pain, the prospect. Active Learning. 1(1), Dec. CTI Support Service. Oxford, UK

  3. Slator, Brian M. and Harold "Cliff" Chaput (1996) Learning by Learning Roles: a virtual role-playing environment for tutoring. Proceedings of the Third International Conference on Intelligent Tutoring Systems (ITS'96). Montreal: Springer-Verlag, June 12-14, pp. 668-676. (Lecture Notes in Computer Science, edited by C. Frasson, G. Gauthier, A. Lesgold)

  4. Wu, Yihe (1998) Simulation of the Biological Process of Steroid Hormones with VRML. M.S. Thesis. North Dakota State University, Fargo, ND

Development of the Virtual Cell is funded by the National Science Foundation under grants DUE-9752548. For further information on virtual worlds software development at North Dakota State University, visit the NDSU WWWIC web site. The authors acknowledge the large team of dedicated undergraduate and graduate students in the computer and biological sciences who have made this project so successful.  © 1998 World Wide Web Instructional Committee.