Introductory Scenarios

"Hooks" and Problems To Introduce Topics

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For many topics, it is impractical to develop a full-blown inquiry.  It is preferable to "hook" the students with a problem, or scenario that grabs their attention, or leads them into the type of thought process that they need to internalize the information.  The following is a list--far too brief--of scenarios and problems that can be used successfully at the beginning of class.


We are always looking for more examples of inquiry- and problem-based learning that can be shared.  If you have something you find helpful, and would  like to share it, send it to us and we will incorporate it into these pages, or the pages of more extensive inquiry- and problem-based lesson plans.


Currently Available:


Molecules -- a focus on function in one important area


Cells -- a focus on fundamental functions

Fungi on rotting logs

Bacteria on a leaf, bacteria in a hydra, and a hamburger in a human

Bacteria, yeast, sponges, and people

Understanding Plants

Using nutrition as a hook

Enzyme Specificity

Digestion of different meals


Modeling Inheritance

Genotype and Phenotype

Genetics of the white locus

Genetics of morphology

Molecular Genetics -- gene expression, etc.


Evidence that protein sequence matters

The role of mRNA

The genetic code

Protein folding: from translation to function


Population Biology

The decline in the world's commercial fish stocks


Crop breeding

Random mutation and directional evolution

Genetic drift

The evolutionary ladder?

Evolving in order to survive

Antibiotic Resistance

Routine use of antibiotics in animal feed






Water molecules (pdf)--the structure of water molecules gives them important properties upon which so much of biology, chemistry, and cooking depend.  We often spend little time on this topic, but it proves to be essential to understanding cell membranes and protein folding.  But, the interactions of water molecules, and the non-interactions of hydrocarbon molecules, are hard to visualize.  It can be hard to understand why these molecules have the properties they do, and without knowing why, students often have little recourse but rote memorization.  Why not give our students the basic knowledge?  Here, we compare oxygen and carbon atoms, and ask how each would bond with hydrogen atoms.  Once bonded, where are the electrons and protons in the molecules?  Might there be a "plus" side and "minus" side to water molecules?  This +/- difference makes water molecules polar, and makes them behave like little magnets, and align with one another.  Hydrocarbons don't do this, and are, in effect, squeezed out of solution by water molecules. Interestingly, a great way to get this across is to discuss mayonnaise.  Oil and water don't mix, but adding lecithin acts like magic to enable the formation of mayonnaise.  Once students have grasped this, it is surprisingly easy to discuss protein folding! (There are animations of several of these concepts here.)

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Cells are fundamental learning-bottleneck for many students.  Even as seniors in college, some students still use cell interchangeably with molecule.  Some have a vague notion that they have cells "inside them" somewhere...maybe ten of them.  Clearly, these students have missed several basic principles in both chemistry and biology.  There is little data to indicate precisely where this learning-bottleneck is.  The following are several different approaches aimed at several different aspects of basic cell biology.


Rotting Logs (pdf) -- a walk through a forest shows that there are many fallen trees.  The older the fallen log, the more it has decayed.  Decay occurs as microorganisms (bacteria and fungi) release digestive juices (enzymes) to break the wood into small enough pieces that they can absorb them (i.e. the molecules of which the wood is built.)  The microorganisms absorb these small molecules to use as food.  Here, we offer photographs of a woodland in southern Indiana, showing fallen trees of various ages, fungi that are consuming them, and some photomicrographs of several different fungal species.  Apparently, very tiny organisms can consume very large trees.  We pose the question: how can organisms so small eat logs that are so big?  This question requires that students think of cells as functioning, living things, and to consider what individual cells must be able to do to eat.  Focusing on function before looking inside and naming the parts gives students a context into which to put the details as they learn them later.  The "Bacteria on a Leaf" problem extends this question to a human context.

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Bacteria on a Leaf, Bacteria in a Hydra, and a Hamburger in a Human (pdf) -- We can ask the same question over and over with cells: what must the individual cells be able to do for the organism to survive.  Bacteria on a leaf, as with fungi on a rotting log, must be able to secrete digestive enzymes to convert the leaf material into small enough pieces that the bacterial cells can absorb them.  Bacteria are single-celled organisms; secretion of digestive enzymes and absorption of food molecules are enough for them to live.  For multicellular organisms, more functions are required.  Hydra are simple, with digestive cells and at least two other cell types: tentacles and "holdfast" cells that hold the animal onto its substrate.  The digestive cells must do exactly what bacterial cells do, but they must also be able to pass some of the food molecules to the other cells of the organism.  Humans are much the same: digestive cells in the digestive system release enzymes and absorb small molecules, then pass some of these molecules on to other cells via the distribution system we call the bloodstream.  The other cells need not release digestive enzymes to break down their food, but they still must absorb small molecules to "eat."  That is why, in short, we have a digestive system at all.  To some extent, this problem focuses on the function of the digestive system, but it also asks students to think of cells as individual living units that function pretty much the same way in all species.

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Bacteria, yeast, sponges, and people (pdf)-- This is a slightly different view of the problem raised in the Bacteria on a Leaf scenario.   Each of us is a collection of individual cells that cooperate with one another.  The properties of individual cells dictate a tremendous part of our physiology.  At the same time, increasing complexity of the species calls for increasing numbers of cellular capabilities. For example, bacteria can get by on releasing digestive enzymes and absorbing the food molecules produced by digesting larger macromolecules.  Yeast must do the same, but must also be able to mate--which requires that cells of one mating type can recognize cells of the other mating type, and that the two cell types can grow toward each other and fuse.  Sponges are a little more complex, and have half-a-dozen different cell types. As with hydra in the "Bacteria on a Leaf" problem, digestive cells must pass food on to other cells.  The different cell types cooperate with each other to create the sponge.  Humans and other mammals carry this cell-cell cooperation to a greater extreme, but the individual, fundamental, living units are still cells.  Their basic properties are pretty much the same as those of yeast or bacteria.

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Understanding  Plants using Nutrition as a Hook


Different types of  foods have different amounts of the basic nutrients that humans need.  Why?  Each type of food does something in the plant or animal from which we take it.  Seeds (pdf) have a particular function, and are faced with particular difficulties in their earliest days of germination.  To make it through these difficulties, they are properly prepared.  The embryo is planted (either by humans or by environmental conditions) underground, where there is no light.  In addition, embryos have no leaves.  How can a plant embryo build roots and the shoot, and build the first leaves without being able to use photosynthesis?  The main mass of the seed is stored food, which the embryo digests and uses.  When we steal plants' seeds and eat them, we take advantage of this basic fact of plant biology.  Other types of foods (doc) also have functions that dictate their nutritional qualities--potatoes, onions, and carrots are over-winter storage organs that must store food for the plant to grow its first leaves in the spring.  Leaves (spinach, lettuce) carry out photosynthesis, but store very little of the glucose they make.  They send it to the growing shoots, roots, seeds, and over-winter storage organs.  Stems (celery) are little more than transport tubes, or straws.  In our experience, looking at plants through the lens of food, and why different plant parts provide much, or little nutritional benefit, helps students understand plants themselves.  As an accompanying resource, this simple animation helps illustrate what plants actually do with the glucose that they produce by photosynthesis.

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Enzymes, digestion, and why cellular chemistry works the way it does


Enzyme/Substrate Specificity: Enzymes bind their substrates because their shapes are appropriate to do so.  The "lock and key" analogy captures this, but in a way that is apparently difficult to translate into a good visual image of a real enzyme.  Here, we provide chemical structures and match their shapes with complementary pockets in enzymes, for several carbohydrates that can have different effects on people who do, or do not, produce the corresponding digestive enzymes.  The outcomes are different in a variety of scenarios involving consuming different meals. (pdf)  We hope that by linking the concept of enzymes to human digestion and to phenomena that students understand, the concepts will be more memorable.  Note that it helps to understand how cells work, and why there is a digestive system in the first place; the scenarios of rotting logs and bacteria on a leaf are designed to help with these fundamentals.

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We traditionally focus on dominance and recessiveness, ratios of F2 progeny, etc.  This is conceptual, confusing, and overshadows some of the other fundamentals.  This is unfortunate, especially since very few alleles of very few genes actually show strict dominance relationships.  But, all are inherited.


Modeling Inheritance: Here, we offer a means of modeling the inheritance, over many generations, of a particular allele that leads to the unusual trait of blue skin in humans.  Modeling the blue people  (doc) illustrates inheritance, as well as the inherent uncertainty of meiotic segregation (but not the mechanism of meiosis).  It also helps make the link between genotype and phenotype, since homozygotes, who have little NADH diaphorase activity, have blue skin, while heterozygotes, who have more (but not enough) enzyme activity have blue lips and fingernails, and are blue at birth.

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Genotype and Phenotype: Maybe it's just the big words, but students always have trouble linking genotype and phenotype.  They can memorize that A means dominant and a means recessive, and they learn the symbology rather than the biology.  They tend to be mystified when confronted with, for example, the genetics of the white locus, for which there are hundreds of alleles so we can't use upper- and lower-case letters to represent them.  By examining the genetics and the biochemistry together, for some non-traditional crosses, it is easy to build a better understanding of how genes cause traits, what it means for an allele to be "dominant" or "recessive," and what is actually represented in a Punnett square.


But, pigments are different from morphology.  When we move on to the unit on Evolution, we tend to focus on morphological traits like giraffe necks, and not on pigments in fly eyes.  To understand evolution, and to understand genetics itself, students need an introduction to the genetics of morphology.  This is augmented by an all-too-brief discussion, How do genes influence phenotypes?

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Molecular Genetics


The process of gene expression is very difficult to internalize.  One way to get at it is to give our students analogies.  Usually, we give the analogy, and then describe the actual process.  We tend to overlook the fact that it took us several iterations of instruction before we figured it out.  Our students are likely to require several iterations as well.  One important thing to tell our students is that biologists don't think of gene expression as a "series of steps" in a list.  Rather, they visualize the process happening.  They play a "mental movie" of the process.


Analogies:  One thing that may be missing is an understanding of the overall logic.  The analogy of a widget factory (pdf) is a common one, but the version presented here does not tell students who does what.  Rather, it asks them what processes are necessary to make this work?  An alternate version is to cast the problem in the setting of a restaurant (pdf).  Unfortunately, analogies are usually inadequate to resolve the difficulties students have figuring out how gene expression works.  Often, in using these analogies and moving to the second step (re-think the necessary processes in terms of cellular machinery and molecules), students simply write out the steps that they remember from memorizing the book.

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It may help to turn this around completely, and work (a) from the data and (b) historically and (c) take it one step at a time. 


Evidence that protein sequence matters: Different Proteins are Different -- What happens when you cook an egg?  It forms a gel; the individual protein molecules unfold, stick together, and form a tangled web.  Yet, when you cook milk, this doesn't happen.  Milk protein must be different from egg protein.  If you add lemon juice to cooking milk, however, you get a remarkable transformation as the protein molecules unfold, stick together, and form a tangled web (which is essentially how cheese is made, particularly paneer). Why do these two proteins behave so differently upon cooking?  They contain the same amino acids...the only thing that can differ is the sequence of amino acids.  But, how can students understand why the sequence makes a difference? They must know something (not too much) about protein folding, and something (not too much) about the basis of hydrophobic/hydrophilic interactions, which depend upon water molecules.

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The role of mRNA: When given the structures of DNA, RNA, and protein, and when told there is an RNA intermediate, students tend to say "huh?"  There is no logical reason for mRNA; why not build protein by reading DNA directly?  Students want to know why things are like they are--but all science can provide is descriptions of how things work.  Rather than tell our students how gene expression works, all at once, why not let them discover that there is an RNA intermediate?  DNA to [???] to Protein (pdf) suggests one way to do so.  Once we know there must be something between gene activation and synthesis of the protein, then we can try to figure out what it is and how it works.

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The genetic code:  If we know there is some kind of RNA intermediate, how does it work?  Again, it can help to start with actual data, but without the terminology or all of the details.  That is, what kinds of experiments did Marshall Nierenberg's lab actually carry out to figure out the genetic code? (pdf)  If we go through a few of these, we might enable our students to figure out for themselves the basic rules of protein synthesis.  Then, when we come back and look at the details of how it works, they have some basic information upon which to hang the details.  Once we have the basic picture and have begun to examine the details, then it might be possible to interpret and understand animations of transcription and translation.

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Protein Folding--from translation to function: Protein folding turns out to be an essential next step--one that we often overlook.  Often, textbooks focus on the types of folds that proteins typically have--alpha helix, beta sheet, etc.  Unfortunately, these words can be memorized without really understanding what protein folding really is.  The process of protein folding can be presented quite simply as (1) first, the rough folding of the polypeptide chain into a globule, in which the hydrophobic amino acids are in the center, and hydrophilic amino acids on the outside, then (2) second, the sorting out of the globule, in which charged amino acids form positive/negative charge-interactions.  As this sorting out proceeds, the alpha helix and beta sheet are formed.  A good way to illustrate this is through physical models.  [Note: working with models is not an inquiry activity.  However, it does present students with information, simplified though it may be, and it requires that they explain how this information explains protein folding.]  By modeling protein folding, it is possible to illustrate how mutations alter protein function, and thus illustrate the basis of genetic dominance.

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Mutations:  Unfortunately, mutations are difficult to fathom.  The typical genetics unit discusses the inheritance patterns of different alleles, but doesn't necessarily indicate where the alleles came from, or how different alleles cause changes in the phenotype.  We suspect that this results from not  really understanding how a change in DNA sequence can (or may not) change a protein's function.  What do mutations do to a gene (pdf) is a set of examples that require that students think clearly about what happens--first, during translation, and next, during protein folding.  For this to be successful, however, it is necessary to have some sense of the role that protein folding plays in gene expression (above) and the creation of phenotype from genotype.

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Population Biology


I am a molecular geneticist, so my understanding of population biology is limited.  However, it makes sense in the context of the looming (and serious) problem  of overfishing.  Some 70% of the world's commercial fisheries are in decline, which, if no action is taken, will lead to extinction of the species we depend upon for life.  The Red Fish/Blue Fish (doc) scenario provides an inroad into this important topic.

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There are far too many misconceptions surrounding evolution.  The scenarios listed here attempt to overcome some of them.  For example, the common notion is that individuals change somehow "in order to evolve."  This is not the case, of course.  Rather, each individual lives its life normally.  If its genotype happens to be successful, then it has more offspring, and that genotype becomes more common.  There are several ways to get at this, in different contexts.

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Crop breeding provides a good inroad to the principles of evolution, and can be discussed without using "the E word," which sometimes conjures up misconceptions that interfere with learning.  How did Europeans turn hot peppers into bell peppers (pdf) after Columbus brought back pepper seeds to Europe?  The rules are those of basic evolution: genetic variation, selection from among the variants for those with traits that are most advantageous in the particular environment, and continued mutation.  There are numerous such examples, historically documented, and therefore certainly true. 

Selective breeding of dogs provides another interesting example, since different groups of humans selected different morphologies and behaviors from the same basic wolf stock. 

Similarly, the diversification of cabbages, Brussels sprouts, broccoli, kale, and cauliflower from a wild seaside plant shows also shows the effects of different populations, with different mutations, experiencing different selection pressures--and becoming different.

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Random mutation and directional evolution: One of the difficult concepts of evolution is that random mutation can give rise to directional evolution.  Examples from realistic natural populations provide some insights--for example, directional selection for leaf morphology (pdf) from the same starting genetic diversity.  Unfortunately, this seems "so obvious" that the basic information often fails to replace the initial conceptions.  It can be more instructive, sometimes, to provide a simulation of natural selection (doc).  This one seems trivial in many respects, but is based on some of the basic rules of real life: each generation gives rise to the next generation; almost all individuals can have offspring, but some can be out-competed by others; individuals best suited to the environment have the most offspring, and outcompete the others most effectively; mutations occur wholly at random; the changes in the character of the population occur at the level of the distribution of genotypes in the population, and not changes of individuals.  What's fun is using the same set of randomly-determined mutations for two different environments, yet discovering that the outcomes are different.  The environments gave direction to evolution.

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Genetic Drift:  Not all evolution is a result of natural selection. Genetic drift can have as great an impact, or greater.  A good example is illustrated by Mark Miller's Great Chile Poster (the links change often, but a quick browser search will bring it up).  Why are there so many different types of chiles?  In short, different villages save their seeds from year to year, essentially creating separate populations.  As mutations occur at random, different populations become different.  To demonstrate the mechanism, a very simple genetic drift simulation (doc) works well.

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The Evolutionary Ladder?:  Does evolution necessarily require a "progression toward perfection"?  There is a general misconception that this is so.  However, as Gould describes so well in Full House, if evolution started at "zero," it had nowhere to go but up.  Evolutionary mechanisms can easily lead to loss of complexity (cf. blind cave animals), or to no change at all if the environment is stable.  Another red fish/blue fish scenario (pdf) gets at this--from the viewpoint of the optimum temperature for enzyme activity, in an effort to link gene expression and biochemistry to organismal phenotypes.  If one takes the time, one can also go further, and help illustrate the difference between adaptation and acclimation.

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Evolving In Order to Survive:  Yet another misconception that must be addressed is the idea that "species mutate or evolve in order to survive."  Sagan and Druyan's Shadows of Forgotten Ancestors, an excellent source of information, is the origin of this scenario for the origin of the human instinct, fear of the dark (doc).  Our ancestors did not sit around the fire saying "we'd better mutate so that, 100,000 years from now, our descendents living in Phoenix will be afraid of the dark."  Instead, those who were afraid lived until morning, and passed on their genes.  Those who ventured out were eaten by night-hunting predators--the "monsters under the bed."

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Antibiotic Resistance


Antibiotic resistance represents the intersection of two distinct issues: evolution and the politics of food.  A serious misconception is that "if I eat antibiotics too much, I become resistant, and they don't work in me any more."  A second misconception is that none of the diseases that affect animals are relevant to humans.  A good look at the meat industry is worthwhile.  The ChixFix (pdf) scenario envisions the routine use of antibiotic in chicken feed, and compares it to a geneticist's analysis of the origin of antibiotic resistance in the laboratory--then uses the information to consider impending legislation to ban routine use of antibiotics in animal feed.  With the rise of multi-drug-resistance plasmids, and pathogenic strains such as E. coli H7:O157, this becomes a serious issue.


The use of antibiotics in animal feed is more serious than the ChixFix scenario indicates, however.  The typical "concentrated feeding operation," in which cows are raised on a steady diet of corn, produces rapid weight-gain and lower cost to consumers.  But it does so at the expense of disrupting the ecology of the cow's rumen, necessitating the use of antibiotics to cure disease (specifically, life-threatening "bloat".)  This is a difficult political issue, inasmuch as banning routine use of antibiotics on livestock will force increased prices by itself, an effect that would be compounded by decreased supply.  These are not trivial problems--and require political, environmental, and ultimately cultural changes in the United States.  They also require an understanding of evolutionary mechanisms among politicians, Agribusiness, and the general public.

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