Lab 15 : Experimental Design

For the last lab of the semester in Bio 1, I want you to design, perform and report an experiment in the biological sciences. Your proposal and design will be counted as homework and submitted separately. Your Lab Report will summarize the materials and methods you used and the analysis of your data with conclusions. It will be the last lab due. Ideally, I would receive your hardcopy report by Friday, Dec. 12. This web page is designed to be the one-stop spot for directions for this lab. It is likely a dynamic document, so make sure you are working from a current version. Check the date and time stamp if you are working from a printed document. See the main calendar for due dates.

There are three separate parts for this assignment. The entire assignment is worth 32 points. It breaks down like this:
Before we discuss each of those in turn, let's look at the big picture.

I want each of you to figure out a project that you can get excited about. If two or more of you want to do the same thing, that will be fine. Everyone will end up working with other people that are using the same technique or organisms, but you will each do a project and will report on your project in the final lab report. That is, this is an individual assignment, eventhough you might end up working in groups.

In this class we have conducted various lab experiments, cultured various life forms and studied various processes. I am asking you to design an experiment that will use materials and methods from our labs. Since what we can do is limited both in terms of time and equipment, I've developed some ideas that I hope will inspire your creativity to investigate something about living systems. I have organized these ideas around "methods" because that is the way I have to think about them and that is the way we have to get ready for them. We will also be working in methodoligical groups so that we can coordinate equipment and organisms.


Method / Techniques
 Possible Explorations
 Chromatography
  • Drosophila eye pigments - chemical expression of genes
  • Identifying natural sugars  (glucose, fructose and sucrose)
  • Separating Natural Pigments
Electrophoresis - See note in paragraph below this table
  • Protein separation - analysis of fish proteins, extended phylogenetics
 Spectrophotometry
  • Effects of pH on photosynthesis
  • Effects of salinity on photosynthesis
  • Absorbtion spectrum of oxygenated and deoxygenated hemoglobin
  • Absorbtion spectrum of fruit juices
 Microscopy
  • Exploring Natural Water Supplies
  • Exploring Mycorrhizae
  • The Structure of Moss Gametophytes
 Microbiology
  • Bacteria in the Environment
  • Motility in Halobacterium
  • Chemical attraction/avoidance in Halobacterium
  • Effect of environmental pH in Halobacterium
  • Chemical attraction/avoidance in Sordaria
  • Effects of environmental pH in Sordaria
  • Culturing Slime Molds
 Biochemistry
  • Effects of pH on yeast metabolism
  • Wild Juices as pH Indicators
 Physiology/Behavior in Drosophila
  • Choice in Drosophilia
    • light/dark
    • sweet/sour
    • warm/cold
    • chocolate/vanilla

I understand that deciding what you want and what you can do might be a challenge. Here is a guideline that might help. Basically, with a few exceptions, you can always choose to do a lab that is very similar to one of the labs we have done, but by changing the parameters or condtions, it is a different lab. There are some restrictions in time. For example, although the Drosophila life cycle is only 10 - 14 days, I don't think we have enough time to do any crossing labs. We do have the flies, and so we can conduct other investigations if flies are your thing. Another restriction is concerned with the electrophoresis labs, to make a long story short, I am having difficulty obtaining all the necessary reagents and gels for our protein labs. If I succeed, and if there are materials left over, then a protein separation lab can be performed. If I don't, those possiblities become remote. If you are particularly interested in electrophoresis, I would suggest also picking a "second place" in case the reagents and gels are not available.


Developing a Plan - Homework 8

Please email me at bio1@bluetang.org if you have questions about an idea. You will basically have the equipment and organisms that we have used this year to construct your own investigation. There are some restrictions, as indicated in the paragraph above this one. I will need to work with each of you individually to make sure that we can round up the equipment/organism you want to use. Also, the timing of when the actual lab work is done might be arranged outside of our normal class time. I am thinking that Mondays and Fridays will be good times to do some of these labs (as fits your schedule). This way, the confusion in the lab will be kept to a minimum. If you can only do it Wednesday afternoon, then we can still do that.

As incicated above, this project will involve two homework assignments and a lab report. Homework 8 describes what you would like to do (in general) and why you want to do it. This homework will be easy to write up once you have an idea. The assignment is really about you thinking about the project and getting back to me promptly on your thoughts. You should develop a theme statement about your lab--similar to the brief theme statements we have been developing on the lab reports. In Homework 9 I'll ask you to detail your proposal in terms of materials and methods. So this is not to be included in Homework 8. Please include a short background (a few sentences) of the general idea behind the project, give the theme statement, and then proceed to describe what you want to do. Finally, include a few statements about why you chose this project.


Materials and Methods - Homework 9


This section should present the materials and methods you are using in lab 15. If you are doing something modified from the book, you can just refer to the correct pages in your reference to the lab book. There is no need to copy anything from the book onto your paper. However, all modifications, or if you are not doing anything related to the book, should be detailed in this presentation.


Lab 15 - The Lab Report

This should be a regular lab report. It should have a theme (which you should have submitted in Homework 8) and a materials and methods section (perhaps modified from Homework 9). In other words, I want you to present a complete, regular lab report but this should be updated (if necessary) from the related homeworks and reflect what you actually did. Since the homework assignments were written before you did the lab, you might need to change, add, or otherwise modify those portions. If you do need to, this is the place to report what you actually did.

Now, as far as the analysis and conclusion section of this lab, I am expecting different things depending on your lab. Here is the guide to this part:

1) For the Drosophila people: Since you did experiments that gathered numeric data (as opposed to observations), I expect a chi-squared analysis of your data. In all cases, your null hypotheisis (the one that you will test with chi-squared) is that the flies have no preference with whatever choice you wanted them to make. I noticed that some of you had a third category -- one of "no choice" or "staying in the middle" -- if your data is good enough, you can include that as a "preference" in your chi-squared analysis. Then, applying your data, you can make statements as to whether you can accept of must reject the null hypothesis. Also, be sure to describe you exact apparatus-set up in the materials and methods in enough detail that someone (else) could repeat your experiment.

2) For other experimental, but not necessarily numeric experiments: the metabolism of yeast, the chemical tests of food items, culturing body bacteria, the effect of pH on photosynthesis, the effect of oxygenation/deoxygenation of hemoglobin on the hemoglobin absorbtion spectrum, the spectrum of acidic/basic blueberry juice:  these should have one (or more) null hypotheses stated, and either accepted or rejected. It is best to state these before actually doing the lab. For example, we might  state "pH has no effect on yeast metabolism" -- and then, presumably, reject the hypothesis and then go on to state the observed effect.

3) For the purely descriptive labs : the chromatography of Drosophila eye pigments, the moss lab group, extracting DNA from peas, the absorbtion spectra of fruit juices, the electrophoresis of supermarket meat: these labs involve doing something and observing the results in a purely qualitative fashion. This is a branch of science, descriptive science, as opposed to experimental science, that is fundamental to all experimental science but is usually overlooked in "scientific method" discussions. So, for these labs-- a close, detailed description of what was done and what was observed is crucial. I will be expecting a more detailed description of the process and the observations than perhaps I would expect for the other, numeric or data-yielding labs.

If you have specific questions about how to write up your lab, please email me!


November 13, 1:30 p.m.
Updated: December 5, 9:30 a.m.