| The
Process of Science: The Hypothesis |
| In Module 2 - Lab Exercise you made a hypothesis about the possible outcome of your experiment. Here you will learn about how hypothesis-driven research is conducted and how it has increased our understanding of plant-pathogen interactions |
What is an hypothesis
Hypothesis testing - an example from Pseudomonas syringae
Additional Resources
After spending so much time in science classes memorizing and taking tests, its easy to forget that science is not just a body of accumulated information, but also a process by which new discoveries are made. This process is often referred to as the SCIENTIFIC METHOD. The basic stages of the SCIENTIFIC METHOD are:
- Make observations
- Develop an explanation or HYPOTHESIS that explains the observations
- Design and perform experiments that test the HYPOTHESIS
- Interpret the results to determine if the HYPOTHESIS is supported by the experiments
As you can see, the concept of the hypothesis is a critical part of the scientific method. But what exactly is a hypothesis? You will find many different definitions, but most emphasize two essential aspects:
- An hypothesis provides an explanation for a set of observations
(and usually, the simpler the explanation the better)
- An hypothesis is testable
| Hypothesis testing - an example using Pseudomonas syringae |
HYPOTHESIS
EFFECTOR proteins are required for P. syringae pv tomato DC3000
to cause disease on Arabidopsis |
| What is the variable that we want to test? |
EFFECTORS |
| So what difference will we compare? |
Bacterial strains with and without EFFECTORS |
| What will be kept the same? |
Everything else:
- Environmental conditions
- Arabidopsis used for evaluating disease symptoms
- Timing of inculations and observations of results
- growth stage and dilution of Pseudomonas syringae
- strain of Pseudomonas syringae
|
But wait - where do we get a strain of Pseudomonas syringae pv tomato DC3000 without EFFECTORS?
Ideally, we would like to have a culture of Pto DC3000 with all the EFFECTOR genes removed.
But as often happens, the ideal experimental material is not available either because it is too expensive or not practical
We must rely on an indirect test
As you learned in Module 1 - Lab, EFFECTOR proteins rely on the TYPE III SECRETION SYSTEM for movement into the plant cell. If a component of the TYPE III SECRETION SYSTEM is mutagenized such that the secretion system is no longer functional, the effector proteins will stay inside the bacterial cell where they are unable to interact with the plant
The indirect test requires some additional controls:
We must verify that the secretion mutant is indeed not secreting any effectors:
One possible approach:
Fuse selected effector genes to a "reporter" whose secretion can be easily tested
We must verify that secretion system itself is not a virulence factor:
One possible approach:
Clone the functional secretion apparatus into a Pseudomonas species that doesn’t make effectors and test whether it induces any disease symptoms independent of the presence of effectors
Interpretation of results
Possible outcome #1:
Plants inoculated with the secretion system mutant show no disease symptoms when compared to those inoculated with unmutagenized Pto DC3000
Interpretation - Results of experimental test support the stated hypothesis that effector proteins are required for P. syringae pv tomato DC3000 to cause disease on Arabidopsis
Possible outcome #2:
Plants inoculated with secretion system mutant show disease symptoms similar to those on plants inoculated with unmutagenized Pto DC3000
Interpretation - Results of experimental test support the NULL HYPOTHESIS that effector proteins are NOT required for P. syringae pv tomato DC3000 to cause disease on Arabidopsis
Information on the scientific method and philosophy of science at the PhilosophyPages website
General background on the scientific method as well as an illustration of hypothesis development using the example of dinosaur extinction all at the DinoBuzz website
