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Computers in the teaching of undergraduate biochemistry
BIOCHEMICAL EDUCATION
October 1979 vol 7 no 4
83
P CUNNINGHAM COMPUTERS IN THE TEACHING OF U N D E R G R A D U A T E BIOCHEMISTRY
Interest in the use of computers as an aid to undergraduate teaching in the Biological Sciences arose out of the activities of projects such as Computers in the Undergraduate Science Curriculum (CUSC) sponsored by the National Development Programme in Computer Assisted Learning (NDPCAL). In January 1978, a project was initiated at Queen Elizabeth College (QEC), under the auspices of the Boards of Studies in Biochemistry and Computer Science of London University, to assess and develop the use of computers in undergraduate Biochemistry teaching. An officer with experience in both Computing and Biochemistry was appointed to liaise with the academic staff and to take part in undergraduate course teaching to ensure m a x i m u m student contact. At the start of the project, it was decided that any material to be developed should fulfil the following criteria: (1) No specialized knowledge of computing was to be assumed. (2) The topic to be covered was to be of central interest within Biochemistry, so that Institutions other than QEC would find the material of value. (3) The material was to augment traditional teaching methods, the computer being used to generate learning opportunities provided by no other educational medium. Although all of the students involved in the project had some p r o g r a m m i n g knowledge, the exclusive aim was to teach Biochemistry, and not to encourage the students to get involved in the workings of the computer program they were using. Hence it was imperative, when designing the material, to bear in mind the user's perspective, that is, the output from the computer has to be easily interpretable by the user. Any decision made by the user has to be based on information already available either from the program or a set of written (or verbal) guidelines. It is important to stress that the program c a n n o t always be regarded as complete in itself, although some programs can be used for self tuition. This is especially true during development of the program, as changes in the dialogue are often required in the light of experience after early student trials. One obvious biochemical topic which readily lends itself to computation is kinetics. Although many students are able to recite fundamental equations in, for example, enzyme kinetics, it is the experience of this author that they have very little appreciation of either the assumptions behind the (model) equations or the terms employed. The requisite equations can be incorporated into a program and the user allowed to alter the parameters by responding to a suitable dialogue, the results are printed, either as a graph or a table and the user encouraged to interpret the output. Very often students require prompting to see the relevant features of the output and to generate hypotheses to account for those features. A test can then be performed to see whether the model behaves in a m a n n e r consistent with the hypothesis. Perhaps it is this feature which makes the computer attractive, allowing rapid, systematic investigations of model systems. To be successful, both the dialogue within the program and any additional student notes must be carefully thought out to ensure that the user can fully utilize the underlying logic within the program. The arrangement of the session itself is an important factor to be considered if the students are to realize the full potential of any material presented in this manner. The n u m b e r of students and available terminals often dictates the arrangement of the classes. The optimum n u m b e r of students appears to be two per terminal, so that there is an opportunity for student-student interaction as well as student-computer interaction. If there are more students per terminal there is a tendency for the less able student to become isolated and not participate in any decision making process during the session; a single student per terminal unless highly motivated, often being unable to interpret fully the information provided by the
Department of Biochemistry Queen Elizabeth College U n i v e r s i t y of L o n d o n C a m p d e n Hill, L o n d o n W 8 7 A H , U K program. T h u s by a combination of rapid calculating and carefully designed program dialogue, the interaction between students and the computer can promote a degree of awareness of biochemical concepts that traditional teaching methods (lecture, seminar, tutorial) are often unable to achieve. Perhaps some examples could be used to illustrate this point. A simple program in equilibrium kinetics (RATES) allows the user to set initial concentrations and rate constants of a simplified metabolic pathway (four molecular species interacting with first order unimolecular kinetics). After the parameters have been set, either from default values or student selection, a table of component concentration against time is generated by the program. Although most of the students claimed to understand the phenomenon, at least in the closed system, very few were able to adequately explain the behaviour of the system. After three or four experimental runs with arbitrary parameter values they were able to articulate a pattern of behaviour which could be tested systematically to verify their educated guesses. From this they were able to clari~ their understanding of rates of reaction, rate constants and the differential equations they had all been previously presented in lectures. With the same package, the students were then able to observe and subsequently explain the change in behaviour of the model pathway when it was modified to allow a continuous flow of metabolite through the system. Another package includes models of allostcric enzyme behaviour (SIGMA) and permits the user to experiment with the various constants proposed in each model. The program prints velocitysubstratc tables together with some additional information such as the fraction of the protein in a particular conformation and the students are asked to explain how the model works. Such an openended task required the constant involvement of a tutor to help the students to interpret the results and articulate their interpretations at the molecular level. Although the d e m a n d s on the teacher were high, the role played by the computer was essential in maintaining an a b u n d a n t supply of relevant data for analysis. Other packages were used which required little or no teacher involvement during the session. One program (ENZHIB), which allowed the user to select from a variety of enzyme-inhibitor reaction schemes, was successfully used to reinforce the classical forms of enzyme-inhibitor interactions. The program generated velocity-substrate plots in response to the user defining the relevant rate constants and concentrations. As well as mathematically correct data being generated, simulated experimental data with varying levels of random error were produced so that the effects of such errors in a n u m b e r of diagnostic plots could be observed and assessed by the students. Simulation of experiments is another area where the computer can play an important role in augmenting traditional teaching methods. Biochemistry undergraduates are all taught the principles of protein sequencing; however, due to shortage of time, money and laboratory space, a rigorous testing of their understanding of those principles is prevented. PROSEQ is a program developed to allow the user to sequence a random (but reproducible) linear polypeptide of 75-100 residues. By mimicking current laboratory techniques, the program ensures that in order to sequence the polypeptidc, the students have to have grasped the concepts behind the experimental procedures, and realized the utility and limitations of the techniques available to them. Such a package requires little tutor interaction beyond introducing the format of the program output and provides an ideal follow-up to a series of lectures on this topic. These programs have been used at first, second and third year levels, and are currently being transcribed for use on small standalone computers such as the 'PET'. Individuals interested in any of the programs described should contact the author for full information.
October 1979 vol 7 no 4
83
P CUNNINGHAM COMPUTERS IN THE TEACHING OF U N D E R G R A D U A T E BIOCHEMISTRY
Interest in the use of computers as an aid to undergraduate teaching in the Biological Sciences arose out of the activities of projects such as Computers in the Undergraduate Science Curriculum (CUSC) sponsored by the National Development Programme in Computer Assisted Learning (NDPCAL). In January 1978, a project was initiated at Queen Elizabeth College (QEC), under the auspices of the Boards of Studies in Biochemistry and Computer Science of London University, to assess and develop the use of computers in undergraduate Biochemistry teaching. An officer with experience in both Computing and Biochemistry was appointed to liaise with the academic staff and to take part in undergraduate course teaching to ensure m a x i m u m student contact. At the start of the project, it was decided that any material to be developed should fulfil the following criteria: (1) No specialized knowledge of computing was to be assumed. (2) The topic to be covered was to be of central interest within Biochemistry, so that Institutions other than QEC would find the material of value. (3) The material was to augment traditional teaching methods, the computer being used to generate learning opportunities provided by no other educational medium. Although all of the students involved in the project had some p r o g r a m m i n g knowledge, the exclusive aim was to teach Biochemistry, and not to encourage the students to get involved in the workings of the computer program they were using. Hence it was imperative, when designing the material, to bear in mind the user's perspective, that is, the output from the computer has to be easily interpretable by the user. Any decision made by the user has to be based on information already available either from the program or a set of written (or verbal) guidelines. It is important to stress that the program c a n n o t always be regarded as complete in itself, although some programs can be used for self tuition. This is especially true during development of the program, as changes in the dialogue are often required in the light of experience after early student trials. One obvious biochemical topic which readily lends itself to computation is kinetics. Although many students are able to recite fundamental equations in, for example, enzyme kinetics, it is the experience of this author that they have very little appreciation of either the assumptions behind the (model) equations or the terms employed. The requisite equations can be incorporated into a program and the user allowed to alter the parameters by responding to a suitable dialogue, the results are printed, either as a graph or a table and the user encouraged to interpret the output. Very often students require prompting to see the relevant features of the output and to generate hypotheses to account for those features. A test can then be performed to see whether the model behaves in a m a n n e r consistent with the hypothesis. Perhaps it is this feature which makes the computer attractive, allowing rapid, systematic investigations of model systems. To be successful, both the dialogue within the program and any additional student notes must be carefully thought out to ensure that the user can fully utilize the underlying logic within the program. The arrangement of the session itself is an important factor to be considered if the students are to realize the full potential of any material presented in this manner. The n u m b e r of students and available terminals often dictates the arrangement of the classes. The optimum n u m b e r of students appears to be two per terminal, so that there is an opportunity for student-student interaction as well as student-computer interaction. If there are more students per terminal there is a tendency for the less able student to become isolated and not participate in any decision making process during the session; a single student per terminal unless highly motivated, often being unable to interpret fully the information provided by the
Department of Biochemistry Queen Elizabeth College U n i v e r s i t y of L o n d o n C a m p d e n Hill, L o n d o n W 8 7 A H , U K program. T h u s by a combination of rapid calculating and carefully designed program dialogue, the interaction between students and the computer can promote a degree of awareness of biochemical concepts that traditional teaching methods (lecture, seminar, tutorial) are often unable to achieve. Perhaps some examples could be used to illustrate this point. A simple program in equilibrium kinetics (RATES) allows the user to set initial concentrations and rate constants of a simplified metabolic pathway (four molecular species interacting with first order unimolecular kinetics). After the parameters have been set, either from default values or student selection, a table of component concentration against time is generated by the program. Although most of the students claimed to understand the phenomenon, at least in the closed system, very few were able to adequately explain the behaviour of the system. After three or four experimental runs with arbitrary parameter values they were able to articulate a pattern of behaviour which could be tested systematically to verify their educated guesses. From this they were able to clari~ their understanding of rates of reaction, rate constants and the differential equations they had all been previously presented in lectures. With the same package, the students were then able to observe and subsequently explain the change in behaviour of the model pathway when it was modified to allow a continuous flow of metabolite through the system. Another package includes models of allostcric enzyme behaviour (SIGMA) and permits the user to experiment with the various constants proposed in each model. The program prints velocitysubstratc tables together with some additional information such as the fraction of the protein in a particular conformation and the students are asked to explain how the model works. Such an openended task required the constant involvement of a tutor to help the students to interpret the results and articulate their interpretations at the molecular level. Although the d e m a n d s on the teacher were high, the role played by the computer was essential in maintaining an a b u n d a n t supply of relevant data for analysis. Other packages were used which required little or no teacher involvement during the session. One program (ENZHIB), which allowed the user to select from a variety of enzyme-inhibitor reaction schemes, was successfully used to reinforce the classical forms of enzyme-inhibitor interactions. The program generated velocity-substrate plots in response to the user defining the relevant rate constants and concentrations. As well as mathematically correct data being generated, simulated experimental data with varying levels of random error were produced so that the effects of such errors in a n u m b e r of diagnostic plots could be observed and assessed by the students. Simulation of experiments is another area where the computer can play an important role in augmenting traditional teaching methods. Biochemistry undergraduates are all taught the principles of protein sequencing; however, due to shortage of time, money and laboratory space, a rigorous testing of their understanding of those principles is prevented. PROSEQ is a program developed to allow the user to sequence a random (but reproducible) linear polypeptide of 75-100 residues. By mimicking current laboratory techniques, the program ensures that in order to sequence the polypeptidc, the students have to have grasped the concepts behind the experimental procedures, and realized the utility and limitations of the techniques available to them. Such a package requires little tutor interaction beyond introducing the format of the program output and provides an ideal follow-up to a series of lectures on this topic. These programs have been used at first, second and third year levels, and are currently being transcribed for use on small standalone computers such as the 'PET'. Individuals interested in any of the programs described should contact the author for full information.