“How to do a Good Experiment”

Marc S. Mendonca, Ph.D. Since before the time of the Ancient Greeks, thousands of years ago, people have tried to find out more about the world around them, wondering how and why things work. Scientists come up with many great ideas to show how things work, but for an idea to become accepted, it has to be tested. The tool scientists use to test their theories is called the scientific method. Whether you are studying stars, caterpillars or medicines, this method remains the same. If you have an idea, or a question, you have to be able to prove it and give evidence so that other scientists can check and test your results.

Full reference: Martyn Shuttleworth (Mar 19, 2008). How to Conduct Science Experiments. Retrieved from Explorable.com: https://explorable.com/conduct-science-experiments 1) Pick a Scientific Topic

Experiments whose results cause sweeping scientific paradigm shifts are very, very rare. (Sorry) The vast majority of experiments answer small (focused), specific questions. Science is built upon the accumulation of data from countless experiments. Pick a topic or an unanswered question with a small, testable scope. Science moves really fast! Serious scientific research requires you do extensive background reading (before you plan your experiments). Deep Dive Into the Literature Have past experiments (i.e. the published literature) answered the question you want to study? If yes, then what questions have been left unanswered in your area of research interest? What is your overarching Hypothesis? (The BIG IDEA) Narrow your research focus to one testable problem at a time! Deep Dive Into the Literature How to begin? • Actively read a book(s) that surveys the entire field that can act as a jumping-off point

• Talk to people (e.g. your advisor, postdocs) who are well-versed in the field and get their suggestions for what to look at

• Use technology… Find all-around resources like Wikipedia and use those as jumping-off points

• For academic reading, focus on reading review articles which summarize findings

GO TO SEMINARS!!!!! Deep Dive Into the Literature

You should be reading ………. Deep Dive Into the Literature

You should be reading on a regular basis! Deep Dive Into the Literature

You should be reading on a regular basis!

Carefully read one paper every day!! Deep Dive Into the Literature

Read the primary literature in your area of interest

Start with papers that have high impact/citation numbers

Read “deeply” i.e. the older literature!!

Find the “original” papers in your area of interest. (these are frequently not the highly cited papers)

Read technique papers!!!! 2) Make a hypothesis Your hypothesis should be a quantitative declarative sentence and a prediction of the experimental results. Informed by the results of literature research and perhaps some preliminary data you or your lab have gathered Remember you are testing your hypothesis: (it could be wrong, either way you learn from good experiments) 2) Isolate your variable(s)

Good scientific experiments test specific, measurable parameters called variables.

In general, when you perform an experiment for a range of values for the variable you are testing (dose response)

When doing experiments try to adjust only the specific variable(s) you are testing for 3) Plan you data collection

Know what data you want to collect and when!

If you do not know the time scale cover short and long ranges of time.

Design a table to write down data, time points, etc.

(Note when things went well and when “the wheels came off” and things did not go so well) 4) Be Methodical!!

Carefully plan what reagents you are going to use and how you will use them!

Make sure reagents are vetted, fresh, and at proper temperature and pH.

Keep your experiments to a schedule! (do not assume 15 minutes or 30 minutes or 1 day will not matter) 5) Record your data and procedures

Record “all” your data and procedures immediately into your lab book. (outliers too) Repeat experiments, three to five times. Quantitate your endpoints, calculate means ± s.d. . Use appropriate statistical methods to test for significance.

If appropriate, plot your data (look for visual trends) Plot trend lines, best fit curves, etc. 6) Analyze data from each experiment, organize and state your results, develop your conclusions.

Was your hypothesis correct?

Were there observable trends in the data?

Were there any unexpected data or trends?

Do you have unanswered questions that can be the basis of future experiments?

Write up your results into a meeting abstract and build a poster or talk at a meeting.

Write up a draft of your paper. Volume 186, Number 5, November 2016 ISSN 0033–7587

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In this issue: Review by Mary Sproull and Kevin Camphausen, “State- of-the-Art Advances in Radiation Biodosimetry for Mass

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4 Tilton et al., “Identification of Differential Gene

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3 and Low Doses of Low-LET Ionizing Radiation in a 8 Reconstituted Human Skin Tissue” So…. Why is only 20% of the published biomedical literature reproducible?

Good Science for “Dummies” YOU MUST TAKE CONTROL OF YOUR EXPERIMENTS!! YOU MUST TAKE CONTROL OF YOUR EXPERIMENTS!!

A control is a set of base values against which you use to compare your experimental results/data from your experiment. Without these you have no idea whether your results are higher, lower, or “not statistically different”. YOU MUST TAKE CONTROL OF YOUR EXPERIMENTS!!

A control is a set of base values against which you use to compare your experimental results/data from your experiment. Without these you have no idea whether your results are higher, lower, or “not statistically different”.

CONTROLS, CONTROLS, CONTROLS….. Because CONTROLS ARE SO……… Because CONTROLS ARE SO………

BORING!!!!! To cut or not to cut……… To cut or not to cut……… Quiet, the tumor cells are sleeping… Quiet, the tumor cells are sleeping… Quiet, the tumor cells are sleeping… Quiet, the tumor cells are sleeping… Quiet, the tumor cells are sleeping… Quiet, the tumor cells are sleeping… Quiet, the tumor cells are sleeping…

Quiescent Cells = Stem Cells CONTROLS = SCIENTIFIC RIGOR CONTROLS = SCIENTIFIC RIGOR

VET YOUR REAGENTS

VET YOUR REAGENTS

VET YOUR REAGENTS

VET YOUR REAGENTS CONTROLS = SCIENTIFIC RIGOR

VET YOUR REAGENTS

ARE YOUR CELLS WHAT YOU THINK THEY ARE?

ARE YOUR VECTORS, PROBES, & ANTIBODIES WHAT YOU THINK THEY ARE? Deep Dive Into the Literature

Write a NIH Type Specific Aims Page on Your Research Idea