Teachers Guide Overview BioLogica is multilevel courseware for genetics. All the levels are linked so that changes in one level are reflected in all the other levels. The BioLogica activities guide learners through a sequence of challenges and monitor their progress, offering them helpful hints as they work. Selected data can be collected from the student s work on the puzzles. Levels and Views Levels are the organizational areas of the biological organism. Views are the pages in the software that represent the levels as well as tools used in genetics. Level: Phenotype View Cell Level: Meiosis View Level: Gene/Allele View Molecular Level: DNA View Organism: Phenotype View The first view the students see is the Organism View in which they are asked to write their observations of the different dragons. Vocabulary is introduced: traits, genotypes and phenotype. 1
When they click on one of the dragons, the Chromosome: Gene/Allele View allows them to manipulate the alleles and observe the changes in phenotype. Each of these is a pull down menu. As the alleles are changed, these changes in the genotype are reflected by changes in the phenotype. 2
Cell: Meiosis View This view allows students to run meiosis, choose gametes with particular alleles, fertilize and produce an offspring with that phenotype. The chromosomes are randomly assorted during meiosis, but only one offspring may be produced at a time. Magnifying Glass Click to see a close-up view of the chromosomes and their allele labels. Germ Cell about to start Meiosis Stop Button Click to Start Meiosis Drag this Slider to the end to speed up gamete formation. 3
In order to follow the chromosomes and their attendant genes, a large meiosis window is available by clicking on the magnifying glass in the corner of the meiosis window. The student can follow the course of meiosis and choose the gamete containing the alleles they need to produce a baby with particular traits. Note that the allele labels are visible. Magnifying Glass. Click to return to the Meiosis View. Molecular Vie The Replay Button returns the gamete to its original condition. Click to go directly to the gametes. Click to see a slow motion version of meiosis 4
Molecular View: DNA Genes are made up of DNA. By changing the bases in the DNA, the students change the alleles. These changes are reflected in changes in the phenotype of the organism. Once again, the rules of inheritance may be investigated.. DNA Molecule made up of bases. Click on the Apply button to put the mutated allele into the organism s genome. Click on the Revert button to undo changes to the DNA molecule. 5
Pedigree View: This view could be called the family tree view. Since large numbers of offspring may be produced in each generation by crossing 2 individuals, students are able to follow the path of inheritance and start learning about the statistics involved in genetics. Traits may be followed through several generations. Use the Chromosome Tool to observe the chromosomes of a selected organism. Use the Snip Tool to remove organisms or generations. Use the Cross Tool by clicking on 2 parent organisms The Cursor is used to select one or more organisms. 6
Variation and Selection The watchwords of evolution are diversity, or variation, and selection. In nature, sources of variation include: Random segregation of chromosomes in meiosis Random fertilization of gametes Crossing over between homologous chromosomes Mate selection Mutations BioLogica models these processes through: Direct manipulation of the DNA at the molecular level Gamete selection for fertilization in meiosis Crossover during meiosis. The beauty of modeling is that the results of these manipulations manifest themselves immediately in the organism. This reinforces the principle that genotype determines phenotype. The random pairings of chromosomes are mentioned in the text of several activities. You may want to reinforce this by drawing attention to the random pairings of chromosomes during meiosis. Crossing over is an important mechanism of variation. When it is available (very soon!) it will be implemented either manually or be allowed to occur automatically. Another example of random variation is in the Pedigree view in which multiple offspring from the same parents can be created and displayed. Using BioLogica Suggested Sequence of Activities Since the activities increase in complexity from the first to the last, we strongly recommend that learners complete the first six activities (Introduction, Rules, Meiosis, Inheritance, Monohybrid and Mutations) more or less in sequence as they provide necessary experience with BioLogica s representation of key genetics concepts as well as how to use the BioLogica interface. Subsequent activities extend the learner s experience with the multiple levels in BioLogica as well as his/her critical thinking skills. Horns Dilemma, Scales and Plates are puzzles designed to challenge and test the learner s understanding of genetics using techniques that real geneticists use. Invisible Dragons is a game that tests the learner s ability to devise strategies for reasoning backwards towards the solution. GenScope is not a scripted activity. It is the BioLogica implementation of a different program, GenScope, which is a general purpose tool. Teachers may use it to work out their own scripts or worksheets. It has no specific pedagogical goal or instruction protocol. 7
Resources Activity notes and Hints sometimes refer students to the Practice Sessions, to be found on the menu bar, if they seem to be having difficulties with the activity. Which Practice Session to use is sometimes a mystery to the students. Here is a brief description of each of the four sessions: Geno-Pheno allows the student to change alleles and watch the effect on the phenotype of the organism. Meiosis allows the student to inspect the chromosomes in the gametes, select gametes for fertilization, and examine the resulting offspring. Crossing-over will be implemented soon. Pedigree allows the student to breed male and female organisms and to observe the distribution of traits in successive generations. Mutations allows the student to alter the DNA molecule, which sometimes results in new alleles (and traits.) There is also a glossary, which can be accessed from the menu bar. And there are other species besides dragons that the students can investigate, namely peas and hamsters. These species appear automatically in some of the activities (Dihybrid and Sex-Linkage). Punnett squares are made available in certain activities to help the students model alleles distributions and probabilities. The BioLogica software also has the ability to track the activities of the student. The important mouse clicks, ones which show that the student understands (or doesn t) the principles behind the puzzles, are recorded as well as the answers to questions. All of this information is collected and is available to you, the teacher. It is collected on the server and may be downloaded and used for diagnostic purposes, grading, and as feedback to the student. Description of BioLogica Activities Please Note: Since BioLogica development continues even as we type, these description may not entirely match those of the version of BioLogica that you download. A brief description of each of the BioLogica Activities follows. Introduction What do dragons look like and why? 8
Introduction guides the user through BioLogica s representations of chromosomes, genes, and alleles, and stresses the connection between genotype and phenotype. As learners use pull down menus in the Chromosome View to change allele combinations, the Organism View allows them to see changes in the dragons. The activity includes two challenge puzzles in which students try to make one dragon look like another by manipulating its genes. Become familiar with the interface by using pull down menus in the Chromosome View to make changes in the appearance of the organism in the Organism View. Enable the user to link representations in BioLogica with genetics, chromosomes, genes, alleles. Genotype determines phenotype. Definition of traits, genotype, phenotype, chromosomes, genes and alleles. Views Rules How do Genes Affect Appearance? The Rules activity is divided into three sub-activities that can be selected and run independently using the menu. Traits deals with the four autosomal traits of dragons the presence or absence of horns and wings, the number of legs and the shape of the tail. Firebreathing introduces a sex-linked trait. Color is another sex-linked trait, but this one is polygenic and pleiotropic. One of the color alleles is a recessive lethal. Explore the effects of changing alleles and allele combinations on phenotype. Learn the concepts of dominant and recessive genes, incomplete dominance, and sex-linkage, as well as homozygous and heterozygous gene combinations. 9
Key Concepts Genotype determines phenotype Particular allele combinations produce particular traits. Dominance/recessive/incomplete dominance/sex-linkage inheritance Views Meiosis: Why Don t Members of a Family Look More Alike? Meiosis is also divided into 3 sub-activities. Introduction to Meiosis focuses on learning the interface and how the representations model meiosis and fertilization. Students are introduced to the concept of the random distribution of the alleles. They can manipulate meiosis or gamete formation, inspect the alleles in each gamete in an enlarged window, and choose particular gametes for fertilization. Meiosis Shuffles and Deals presents a dynamic model of meiosis linked to the diagrams showing the phases of meiosis as found in textbooks. Designer Dragons challenges students to create specific offspring by examining chromosomes in the gametes of each parent and selecting those that will produce the desired phenotype in the offspring. Understand monohybrid inheritance, especially the equal contribution of genes from each parent. Understand random shuffling of genes into the gametes. Select gametes with specific alleles for fertilization in order to produce a particular phenotype. Meiosis Fertilization Random chromosomal segregation Selection of gametes with specific alleles Meiosis 10
Inheritance: What Determines What the Offspring Look Like? Inheritance utilizes the Pedigree or family tree view. It allows students to follow the inheritance of traits through many generations of offspring. The student has no control over the process, which serves to emphasize the randomness of allele distribution in nature. By contrast, the Meiosis activity directed the student to select the particular gametes needed to produce a particular baby dragon. It is through the Inheritance activity that we finally introduce the students to the important role that random assortment and probability play in genetics. The Monohybrid activity builds on this theme and is a useful follow-on to this activity. Show the effect of randomness on the distribution of traits through successive generations. Take a look at Probability. Monohybrid inheritance Probability Pedigree Monohybrid: Do Traits Really Skip Generations? The Monohybrid Activity introduces Punnett squares which help students understand the combinatorics of gene distribution. This device combines the lessons from the Meiosis and Inheritance activities: that each parent contributes 1/2 the chromosomes, and therefore 1/2 the genes, that each baby inherits in a random fashion. How these genes are expressed depends on rules that the student has already discovered, so that s/he is able to make predictions about what fraction of the offspring are likely to have a particular trait. Examine the effect of random selection on the distribution of traits. Explore the use of Punnett squares in order to understand the combinatorics of gene distribution. 11
Practice making predictions using information from Punnett squares. Monohybrid inheritance Punnett squares Probability and Predictions Meiosis Pedigree Mutations What Happens When You Change the DNA? Mutations introduces students to the DNA of particular alleles and challenges them to modify the DNA of a dragon and observe the consequences. The interface for introducing mutations is much like that of a word processor one clicks to position the cursor, then hits Backspace to erase base pairs to the left, and types A, G, C, or T to insert bases in a sequence. Become familiar with the Molecular Level of BioLogica DNA view. See how changes in the DNA result in changes in the genotype of the individual. Generalize the notion of rules to include more than two alleles,. DNA Mutation Inheritance How Are Mutations Inherited? Mutation Inheritance expands on the previous activity s exploration of how mutations are inherited. It also gives the students more practice in using Punnett squares to determine the probability of inheriting a mutated trait. 12
Become aware that mutated genes follow similar rules to non-mutated genes. Practice using Punnett squares and solving probability problems. DNA changes as a basis for mutations Modes of inheritance Probability DNA Horns Dilemma Can Two Horned Parents Have a Hornless Baby? Description : Horns Dilemma challenges the student to use the knowledge gained in previous activities to solve a puzzle. BioLogica asks students to produce a hornless (homozygous recessive) dragon from two parents with horns. Initially, one of the parents is homozygous for horns and the student must change it to heterozygous to achieve the goal. Solve a problem using multilevel thinking and maintaining confidence in the computer model Exercise effect-to-cause and cause-to-effect reasoning. Inheritance of recessive traits. Each offspring inherits 1/2 of its genes from each of its parents. Meiosis s Dihybrid Cross Look at Two Traits at Once Dihybrid Cross explores the inheritance patterns of two traits at a time and the differences that occur when the traits are on the same or different chromosomes. 13
Recognize the patterns associated with the genes being on the same or different chromosomes Understand probable outcomes involved in the inheritance of two separate traits. Mendel s law of Independent Assortment Probability of a particular set of traits occurring can be determined. Pedigree Meiosis Sex-Linkage - What Difference Does it Make if a Gene is on the X Chromosome? The sex-linkage activity reintroduces principles of the inheritance of the X and Y chromosomes. Students use the fire-breathing gene to model how the sex chromosomes are inherited. Students begin to recognize patterns as tools of genetics specifically and Biology generally. Understand how sex-linked genes are inherited. Understand the difference between autosomal and sex-linked inheritance. Sex-linked inheritance Pattern recognition Pedigree Meiosis Scales Dragon Found with Mystery Trait 14
This activity, Scales, asks students to use their knowledge of genetics to investigate an autosomal trait scaly skin the gene for which has been hidden. They answer four questions using inductive reasoning: Are scales inherited? Is the gene dominant or recessive? Is the trait sex-linked or autosomal? Which chromosomes are the genes on? Learn the strategies for investigating a new trait. Practice using statistics to determine inheritance patterns. How to infer mode of inheritance from statistics Inheritance patterns Pedigree Plates: Another Mystery Trait Although Plates is similar to the Scales activity, this trait is sex-linked and incompletely dominant. Students must determine the location and the inheritance pattern of this new trait by approximating the reasoning processes of professional geneticists. Learning Goals Practice using indirect reasoning to answer the questions. Using inductive reasoning to solve a problem. Pedigree 15
Invisible Dragons The Invisible Dragons activity, presented as a game, poses a difficult problem for the students to solve using all the techniques they have learned throughout this series of activities. They must figure out the genetic makeup of two invisible dragons by making crosses, looking at the chromosomes, and even making back crosses. As players, they start out with $20,000 in the bank. Each procedure they use costs money, as does each wrong answer. Players make money by answering questions correctly. Develop strategies for determining parents genome Key Concept: Developing Strategies Cross the 2 invisible dragons (male and female), then cross two dragons with dominant traits. If a recessive trait shows up in the next generation, then each of the parents must be heterozygous. Do a backcross cross a recessive offspring with either parent. If the dominant trait appears, then that parent must have the dominant allele. Check the F1 generation for an incompletely dominant trait apparent if there are three traits appearing in the F1 generation. Check the F1 generation for sex-linked traits. You can usually tell what the father s sex-linked genes are this way. Pedigree GenScope This is an open-ended interface to all the BioLogica functionality. It is essentially a BioLogica implementation of GenScope that runs on both the Mac and the PC. It may be used to test ideas for scripts and worksheets by the teacher. Students are welcome to use it also they might find it fun to explore genetics in an openended environment. 16
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