Tag: experimental design

Improving the aim of fungi

by gwilson on Oct.01, 2015, under A Day in the Life..., Projects

dung_cannonIn BIMS, we believe a student “gets it” more quickly when the topics covered in lab are intertwined and connected – not when they follow the disjointed and unrelated approach seen at most colleges and universities.  For that reason, we are teaching our Gen Bio I lab through student participation in four major projects.  We believe we can give students a good look at the various topics central a first semester freshman biology course through Winogradsky columns (their “pets”), experiments with the fungus Pilobolus, photosynthesis with alginate balls containing the alga Chlorella, and fermentation experiments using the yeast Saccharomyces.

Pilobolus is a fungus that grows on the dung of herbivorous animals.  It is sometimes called the “shotgun fungus” or “dung cannon” because of its means for dispersing spores.  Its life cycle includes production of spores that shoot out from the fungal colony to land on nearby grasses.  When a herbivore eats those grasses, the fungus germinates and grows in the animal waste where it produces more spores to shoot out and start the cycle over again.  The key to success for the fungus is a light-sensitive structure that helps aim the spores away from surrounding dung toward an open area where new grass can be found.

The question our students have been asked to determine is whether it is possible to improve the accuracy of the fungus by natural selection.  Cultures are grown in a closed container with a hole provided for light to pass through.  Our students are placing sterile coverslips over the holes to catch any spores that are accurately shot at the light.  Those inaccurate spores hit and stick to the other parts of the container.  So each group will create one of these chambers and after two weeks will take photos of the inside of the chamber to document where spores hit (the scatter pattern).  Then, the cover slips are removed and used to inoculate new plates of media.  The experiment is repeated with new chambers to see if spore accuracy is improved by using spores that were accurate the first time.  If the spores hitting the coverslip give rise to fungal colonies with more accurate spores, the scatter pattern for the second test should be much smaller and more concentrated than before.

What are we learning?  Phototropism, some mycology, cell biology, cultivation techniques, experimental design, data analysis, and much more.  Will this work?  We’ll let you know in a few weeks!

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Our Guiding Principles – Part 5

by gwilson on Jul.31, 2012, under Program

malaney presentation 2I have a friend who as a graduate student invested five years into a research project in immunology.  She walked into a meeting with her dissertation committee one summer thinking it was the last briefing on her work before defending for her doctorate, and left the room with a non-thesis masters.  Something in her project had gone terribly wrong in the eyes of the committee and five years of work and promise ended up worthless in the end for an unsuspecting graduate student.  She was a determined student and started over in another program and in about four more years received her doctorate.  What a horror story!

Our fifth guiding principle is “choose projects with a high probability of success“.  We do not believe in placing students in situations where the outcome of their capstone work could leave them with nothing to show for the semester.  There are two ways we do this.  First, we do not allow students to enter into research where the results are a huge gamble – “win big or go home” is not our idea of sound research…at least not with a student’s first self-designed project conducted in their last year of college as a requirement for graduation.  For this reason, we seldom allow students to start with a blank piece of paper for their design.  Student-conceived project ideas tend to be too grandiose and risk-laden to be practical under our timeline.  Remember our other guiding principles:  ”Keep it simple, keep it short!”, and “Just because we can, doesn’t mean we should!”  So, we talk with the student and try to steer them into projects where the basic infrastructure and literature base and track record for results are clearly established on our campus.  Then we talk about what is known in the literature and what is not known, allowing the student to carve out a short, simple project that is meaningful (has unknown outcomes and thus represents real research).  So, you might say the project is student chosen from within departmental imposed parameters.

The second way we help students build a project with a high probability of success is through careful attention to experimental design.  We pride ourselves on helping students design projects that maximize results while minimizing work and time.  We want students to complete their planned experiments, conduct follow-up experiments, and produce their research paper or poster quickly.  That can only happen in this way.  So, we make sure that the first experiment (the initial planned work by the student) provides data that is unique and useful whatever the outcome. Experiments that either work or don’t work are not considered (the suggestion from that is either success or failure is the only result possible).  Instead, experiments are designed with the follow-up experiment in mind – if it turns out this way, we’ll do this…but if it turns out that way, we’ll do that.  By taking this approach, we teach students the importance of not just designing an experiment, but planning a project.

In the coming months, take a look at our webpage where the results of student capstone projects will be posted.  It is called “The Lab Report”. (

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Our Guiding Principles – Part 3

by gwilson on Jul.24, 2012, under Program

dsc02-150x150Our third guiding  principle for BIMS research projects is “Keep it Meaningful“.  There are plenty of ways to approach involving students in the enterprise of research.  One approach is to do quasi-research, projects that are original to the student but for which the outcome is known.  Repeating the work of others as a way to teach students the mechanics of designing, conducting, analyzing, and reporting a research study is a standard process used in teaching.  I’d bet everyone reading this has been in a lab at one time or another where the goal was to do an “experiment”, record the results and analyze them against the known outcome for that work.  That is a legitimate means for teaching skills, but we don’t believe that is an exposure to research.  An exercise of skills rather than an experiment to learn new knowledge.   There are plenty of courses at our school and others that take this approach.  We choose not to make this the sum total of their learning experience.

A second common approach to exposing students to research is to engage them as individual workers with their own modest component of an on-going project.  Dr. Jones is working on characterizing an enzyme’s sensitivity to chemical and environmental changes, and Student Johnny is given the task of testing divalent cations in the process.  Unlike the first approach above, this is truly research that reveals new knowledge.  However, it is science as an “assembly line” process.  Researchers in this type of compartmentalized research serve as workers doing their portion of a project with little knowledge of anything beyond their small part.  In reality, BIG science is done that way; each scientist and lab pitches in their findings to give a more complete portrait of the problem and its answers.  As with the exercise approach above, we do involve our students in projects like this in some courses (or in portions of courses).  However, we also want our students to see more than the toenail of the elephant.

We choose instead to involve our students, at some point in their BIMS experience, in designing, conducting, analyzing, and reporting on a project of their own creation.  Not an exercise repeating work previously done.  Not as a cog in a machine.  A compartmentalized project of short duration with unique and unknown outcomes.  Typically, this is their capstone project, designed in collaboration with BIMS faculty.  The benefits are huge.  Planning an experiment requires consideration of all variables rather than a pertinent subset.  It requires scheduling and preparation, background research on prior work done in the field, discipline in conducting work, discovery and repair of flaws in design, the deep thought needed to analyze and explain findings, the exacting nature of scientific writing.  Where the other approaches teach skills and how to work in an active research setting, this approach gives students the added skills of leadership and project management.  Ideal projects lead students to integrate learning from a variety of courses as they complete their work.

We believe “keeping it meaningful” means students will see the more global view of how research is designed and conducted so that no matter their future, they have the skills to face the unknown around them with confidence in their approach and toolbox for success.

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