Integrating 3D Molecular Visualizations in Elementary, High School

Chapter 11

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Making the Unseen Seen: Integrating 3D Molecular Visualizations in Elementary, High School, and Higher Education Miri Barak* Department of Education in Science and Technology, Technion- Israel Institute of Technology, Haifa 32000, Israel *E-mail: [email protected]

This chapter describes three studies that attempted to change the predominant traditional lecture-based instruction by integrating 3D visualizations into chemistry courses. The three studies had one similar objective: to examine the effect of 3D web-based molecular visualizations on students’ learning outcomes, centering on five cognitive abilities. The studies were conducted among elementary, high school, and university students. Data were collected by applying quantitative methods within a pre- and post-experimental design. The findings in all three studies suggested that in order to enhance the construction of scientifically correct mental models, students should be engaged in the construction and manipulation of 3D visualizations. Passive observations of 2D molecular drawings in textbooks or even teachers’ demonstrations of 3D molecular visualizations are not sufficient for enhancing higher levels of cognitive abilities. Among the many advantages of using advanced technologies in chemical education, web-based visualizations are significantly important for helping students to "see the unseen", thus improving their chemical understanding.

Introduction In the past two decades, an increasing number of educators are abandoning teacher-centered, lecture-based modes of instruction, moving towards more learner-centered models (1). This shift is in response to the ongoing criticism about © 2013 American Chemical Society In Pedagogic Roles of Animations and Simulations in Chemistry Courses; Suits, J., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 2013.


the domination of lecture-based teaching that induces shallow understandings of the learning material (2, 3). Motivated by a desire to change the predominant lecture-based teaching mode, and building on the constructivism learning theory, educators encourage the development of active learning environments. In active learning environments, students are involved in more than listening passively. Emphasis is placed less on transmitting information and more on developing students’ cognitive and operative skills (4). Active learning environments enable learners to create their own mental framework and formulate their own conceptual models (5). In chemical education, the use of 3D molecular visualizations can promote active learning by encouraging students to solve problems, provide explanations, manipulate 3D visualizations, and construct computerized models. Integrating active learning strategies as part of the formal learning sessions can advance students’ learning as well as address the need for a pedagogical change (6). This chapter includes a literature review on internal and external visualizations and the use of three dimensional (3D) visualization in chemical education. It provides an overall view of three chemistry courses in elementary, high school, and higher education. It then describes three related studies that examined the integration of web-based 3D molecular visualizations and their effect of students’ learning outcomes. Finally, the summary and discussion section provides some new insights regarding the use of visualizations for chemical education.

Internal and External Visualizations and Chemical Education Visualization is conceptualized as a basic form of cognition and it plays a central role in our imagery, abstraction, and creativity abilities. Visualization exists internally, as a mental image in our mind. But it also exists externally, as a 3D physical model, a 2D drawing on paper, or an image on a computer screen. Internal and external visualizations are mutually reliant, depending on the level of abstraction and the individual’s imagery/spatial ability. Those who have low imagery ability use external visualizations in order to better understand complex and abstract ideas. Those who have high imagery ability do not need external visualizations for understanding complex phenomena; however, they can present visual models in order to convey their knowledge and ideas to others (7). External visualizations may augment internal visualizations by providing additional information or insights. It can present a more complex process than can be internally visualized within a persons’ limited capacity of visual-spatial working memory (7). In recent years, advances in technology have improved the ability to create external visualizations. Developments in multimedia capabilities (graphics, audio, and video) made it possible to produce powerful visualizations of abstract scientific phenomena and processes (8–10). According to Mayer’s dual coding theory on learning and multimedia (11), there are two separate channels for processing information: visual-pictorial and auditory-verbal, both mutually important for enhancing meaningful and deep learning. Indeed, studies indicated that by providing well-designed external visualizations, such as colorful, 3D 274 In Pedagogic Roles of Animations and Simulations in Chemistry Courses; Suits, J., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 2013.


molecular representations, students can construct internal visual representations and thus enhance their learning outcomes (8, 12). Williamson and Abraham (12) found that students who used external visualizations in the form of molecular animations, improved their conceptual understanding of the particulate nature of chemical reactions, compared to those who studied chemistry in a traditional way. Similarly, Barak and Dori (8) found that the use of external visualizations enhanced students’ conceptual understanding and modeling skills. External visualizations such as physical or computerized models, animations, and/or interactive simulations can be integrated into the teaching and learning processes for describing, explaining, and discussing scientific phenomena. They can illustrate complex phenomena on a macroscopic level or by "zooming in" into the microscopic level. In the chemistry discipline, 3D computerized representations are well-integrated into research and teaching. In general, there are three types of computerized representations of molecules: those that present animations of chemical processes and/or reaction pathways; those that allow the manipulation of molecular models - rotating, changing representation modes, measuring lengths of bonds, etc.; and those that facilitate the modification of molecular models and the construction of new models. These visualization tools transfer abstract ideas into concrete ones, thus help teachers explain complex phenomena and help students understand chemical concepts and processes (8, 13). The use of computerized molecular representations has been studied since the 1990’s by many chemical education researchers. In 1995, Williamson and Abraham (12) reported that animations enhance students’ understanding of chemical concepts and promote their ability to construct dynamic mental models of chemical processes. Lipkowitz and colleagues (14) used visual representations for teaching the topic of mineralogy and as a bridge between the disciplines of geology and chemistry. Kantardjieff and colleagues (15) introduced 3D visualizations while using Silicon Graphics workstations, engaging students in exploration activities. Later on, at the beginning of the new millennium, Sanger and colleagues (16) used computer visualizations to help students understand chemical processes. They found that students who used computer visualizations were less likely to quote memorized mathematical relationships and more likely to understand abstract concepts and phenomena. Fleming and his colleagues (17) developed an animation package that animated reaction pathways. They presented a new teaching approach for constructing an understanding of molecular orbital interactions. In 2001, Donovan and Nakhleh (18) indicated that the web-based representations used in their general chemistry course were instrumental in visualizing and understanding chemistry. These results were in line with the findings of Dori and colleagues (19), indicating that the use of web-based molecular 3D visualizations positively effected students’ achievements, provided the students are actively engaged in constructing the computerized models. In summary, studies indicated that 3D visualizations enhances students’ spatial abilities (13), learning achievements (18, 19), conceptual understanding (8, 12), and motivation to learn science (20). Since chemistry learning involves the understanding of abstract phenomena, 3D visualizations are applied in order to disclose the "unseen". Indeed, 275 In Pedagogic Roles of Animations and Simulations in Chemistry Courses; Suits, J., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 2013.


visualizations enable the creation of mental representations of complex concepts and it can substitute for cognitive processes, such as: abstraction, imagination, or creativity, that some students lack. However, ill-designed and oversimplified visualizations may cause misunderstandings among students. In addition, they may harm the learning process by preventing the use of ones’ own imagination, and thus, hinder the creation of mental models (21). If the visualizations are ill-designed and too much or too little information is displayed, they may prevent learners from performing effortful cognitive processes required for a deeper understanding (21). Choosing well-designed 3D visualizations and incorporating them as an integral part of the learning process is significant for effective and meaningful learning. Following this line of thought, this chapter describes three studies that integrated web-based 3D molecular visualizations into chemistry learning while examining students’ learning outcomes.

Three Studies: An Overall View This chapter describes three studies with one similar objective: to examine the effect of web-based 3D molecular visualizations on students’ learning outcomes. Each study was conducted among a different research population: elementary, high school, and university students. The first study describes the integration of 3D animations into elementary school science curriculum, examining students’ chemical understanding, explanation skills, and motivation to learn science. The second study describes the integration of 3D molecular visualizations of proteins’ structure and function into the curriculum of high school chemistry courses. It examined whether, and to what extent, learning via visualizations of biomolecules effect students’ chemical understanding. The third study describes the use of visualization software for the construction of dynamic molecular models. This study examined university students’ conceptual understanding and their ability to transfer across the four levels of chemical understanding: macroscopic, microscopic, symbol, and process (19). In all three studies, the experimental groups used 3D visualizations as part of their learning process. They were engaged in assignments that could only be answered after they truly understood the scientific concepts and phenomena presented in the 3D molecular visualizations. Conversely, the control groups were taught in a traditional way, by using textbooks with static 2D pictures of molecular models. As described above, the three studies were similar; but, there were two main differences: the participants’ age (elementary, high school, and university) and the applied visualization software. Based on the constructivism theory, all experimental students were actively engaged in the learning process; however, their ability to manipulate the computerized molecular models depended on the software’s capabilities. The elementary students were mostly engaged in observing funny and entertaining animated movies created by BrainPop (http://www.brainpop.com). Most animated movies included a "zoom in" effect (from macro to micro), allowing the young students to "see" the structure and behavior of molecules in various situations. The high school students used the Side-by-Side Images 276 In Pedagogic Roles of Animations and Simulations in Chemistry Courses; Suits, J., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 2013.


of Amino Acids’ website, developed by Carnegie Mellon University (https://www.bio.cmu.edu/courses/03231/BBlocks/AAVFrameset.htm), allowing them to compare 3D structures of amino acids and peptides. They rotated the molecular models and changed their representation modes from ball and stick to space-fill or sticks. They measured the length of the bonds (in Å units) and indicated the polarity of each side chain. The university students used MDL ISIS Draw (http://mdl-isis-draw.software.informer.com) for drawing structural formulas, and ViewerLite 5.0 (http://viewerlite.software.informer.com/5.0) for viewing the 3D computerized models. They did all the activities that the high school students did, with the addition of constructing the molecular models on their own. In all three studies, data were collected by applying the quantitative method, within a pre- and post-experimental design (22), using the general linear model (GLM) for statistical analysis. Analysis of Covariance (ANCOVA) was used to compare post-questionnaire scores while holding the pre-questionnaire scores "constant" for a validated comparison.

Study 1: Integrating Animations into Elementary School Science Education The first study was conducted in the context of reforms in elementary school science education in Israel. The study examined a program that integrated web-based animated movies, created by BrainPop (http://www.brainpop.com), into the curriculum of grade four and five students. Each animated movie is 3-to-5 minutes long, providing explanations about scientific concepts in an entertaining and dynamic way. Each movie includes animated characters who lead students through educational activities, while providing curriculum-based contents that are aligned with the national science education standards. The teachers’ section contains lesson plans, laboratory experiments, and ideas for using BrainPop animations in the classroom. Study 1 Research Questions and Participants In order to examine the effect of web-based 3D molecular visualizations on elementary school students’ learning outcomes, the following research question was raised: Whether and to what extent the use of visualizations effect students’: conceptual understanding, explanation skills, and motivation to learn science? The research participants were divided into two groups: experimental and control, according to the preferences of the science teachers. The experimental group included 926 students from five elementary schools, composed of 435 fourth graders and 491 fifth graders. The control group included 409 students from two elementary schools, composed of 206 fourth graders and 203 fifth graders. Among the 14 science teachers that participated in the study, nine taught the experimental students and five taught the control students. Among them, there were two teachers who taught in both experimental and control schools. In such large scale studies, the distribution of good and poor teachers among both research groups is similar. 277 In Pedagogic Roles of Animations and Simulations in Chemistry Courses; Suits, J., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 2013.


The experimental schools integrated the animated movies at least once a week, about one animation for each topic. The teachers demonstrated the animated movies to their students in the classroom and encouraged them to work on their own or in pairs in computer clusters. The students watched the animations while answering questions or carrying out learning assignments. The animations comprise of animated characters who lead the students through educational activities, including 3D visualizations of particle movement and structure. The topics in "Matter and Chemistry" include: atomic model, body chemistry, chemical bonds, state of matter, compounds and mixtures, and more. Differing from the experimental group students, the control group students studied the science courses in a traditional way – using textbooks with still-pictures and exercise sheets. Gender distribution was close to even, almost 13% declared that they participate in extracurricular activities in science education, and only about 10% declared that their parents’ occupation relates to science (medical doctors, scientists, engineers etc.). Pearson Chi-Square test indicated no statistically significant differences between the research groups in respect to gender distribution, class distribution, parents’ occupation, and extracurricular activities.

Study 1 Pre- and Post-Questionnaires The pre- and post-questionnaires administered in this study consisted of four parts. The first part indicated the students’ demographic details, such as: class, gender, parents’ occupation, and extracurricular activities. The second part examined students’ conceptual understanding. It included eight multiple-choice questions, based on national science standards and topics, such as: natural materials and substances, energy preservation, living organism, etc. The third part examined students’ explanation skills. It included four true/false questions with a requirement to write an explanation for each choice. The fourth part examined students’ motivation to learn science. It included 20 items on a 1-to-5 Likert-type scale, divided into four categories: Self-efficacy, Interest and enjoyment, Connection to daily living, and Importance to the student. This part was adapted from Glynn and Koballa (23), modified to fit elementary school students, and has been published in Barak, Ashkar, and Dori (20). The pre- and post-questionnaires were similar in their construct, but with different contents for the 4th and 5th grade students, according to the themes taught in each cohort. Each of the 4th and 5th grade questionnaires had two versions with the same questions displayed in a different order. The students who received version A as their pre-questionnaire, were given version B as their postquestionnaire, and vice versa. The questionnaires were validated by four experts in science education and three elementary school teachers, reaching 100% consent. The reliability, determined by internal consistency, Alpha Cronbach was 0.88 for the motivation section. The questionnaires were administered to the students at the beginning and the end of the academic year.

278 In Pedagogic Roles of Animations and Simulations in Chemistry Courses; Suits, J., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 2013.

Study 1 Findings The findings section includes two parts. The first part presents students’ understanding of scientific concepts and their explanation ability. The second part presents students’ motivation to learn science.


Students’ Understanding of Scientific Concepts and Their Explanation Ability ANCOVA test indicated that the difference in students’ gained conceptual understanding can only be explained by their participation in the BrainPop animated movies program (F(1, 1332)=127.50, p

Integrating 3D Molecular Visualizations in Elementary, High School

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