The Scientific Method
Research Methods
CPE 401 / 6002 / 6003
Professor Will Zimmerman CEng FIChemE
BScEng, MScEng, PhD (all ChE), PhD minor (Applied Maths)
Chair, Biochemical Dynamical Systems
Motivation
Salesman: You do research, right?
Professor: Yes.
Salesman: Then you don’t know what you are doing!
Professor (indignant): WHAT?
Salesman: If you knew what you were doing, it
wouldn’t be research, right?
(He lost that sale!!!!)
Scientific research is conducted in a realm of UNCERTAINTY.
We do not know the outcome of our tests, but we do know how
We should conduct them – according to the SCIENTIFIC METHOD
What is the Scientific Method?
 Attitude: open mindedness
 Step 1: Identify the target
 Step 2: Scholarship – gather information – make
/collect observations
 Step 3: Hypothesis formation
 Step 4: Test predictions of hypothesis with proper
experimental methods.
 Step 5: Check and interpret your results
 Step 6: Either start again at any previous step or
report your results.
Attitude: Open mindedness
 A scientist must be receptive to new ideas, but then must be skeptical
and conservative in the approach to claims made with such new ideas.
This is the fundamental duality of the scientific method: no progress
in science is made by dogmatic acceptance of canonical ideas. If
canonical ideas were capable of solving the open questions, they
would have already. However, new ideas are not “scientific laws”.
They could be fundamentally flawed (self-inconsistent) or
unverifiable (taken on faith?)
 Scientists should be critically minded, which means searching for selfinconsistencies in new ideas, agreement/disagreement with
observations, and unbiased – theories that are apparently “ridiculous”
might just reflect our own bias – apply the scientific method before
dismissing hypotheses “out of hand.” It is human nature to be
“conservative” and closed-minded and many “scientists” are biased.
Step 1: Identify the target
One of the least attractive features of modern research practice is that
research projects are frequently “externally” defined by non-scientific
(political or market forces) agendas. Even if your projects aims are
externally defined, how you get there (objectives) is usually under the
control of the investigators. The “playing field” is defined, but the
route through that field is owned by the researcher. The key attribute
of a mature researcher is “ownership” of a research agenda.
For doctorates, the central condition is that the doctoral thesis should
make original contributions to science. Therefore the target for the
research should be to pursue “unbroken ground”.
The constraint for a Master’s thesis or dissertation is the much less
restrictive “training in the methods of research.” Nevertheless, it is a
“misnomer” to say that a research project could be unoriginal (cf.
salesman’s point). With a Master’s project, the ownership may never
reside with the student. With a doctorate, it must.
Step 2: Scholarship – gather
information
A key observation is that research is not limited to scholarship. In many
cultures, the definition of a learned person is that they are a scholar.
The Anglo-American (perhaps European Enlightenment legacy) is that
research is just as much about creativity as knowledge. Identifying
the target (creative step 1) is as important as placing its context in the
hierarchy of science (what is known).
Nevertheless, step 2, which really should be done simultaneously with
step 1, is to gather information about the target. In my opinion, the
thing that separates Professors from ordinary researchers is the “vision
thing” – the ability to select targets in light of what is know
simultaneously and with relative ease. These two steps are “having a
nose” for where one might find new science.
For new researchers, the gathering information step is finding out about
the field surrounding the target, and placing it in context. Trivially,
the gathering information step could determine that the target is not
original at all.
Step 3: Hypothesis formation
This is the philosophical step and the biggest creative
element. It is a concise statement of something that
the researcher has found is unproven in the body of
scientific knowledge about the target, if it is proven,
will have profound consequences.
In general, science is distinguished from all other forms
of scholarly activity by being hypothesis driven.
(Computational) Modelling is an activity that is
automatically a hypothesis – the model is the
hypothesis.
Sensor and technology development is itself a hypothesis
– that such a sensor leads to a measurement inference
or such a technology will be effective.
Some hypothesis examples from my
own research (confidential):
 Helical turbulence. There is a pairwise mechanism for the build up large scale
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structures in helical turbulence that leads to better mixing and control over
molecular contacting patterns. Technological implication: low NOx, high
efficiency of combustors.
Colloidal electricity generation. Variation of magnetic permeability due to
inhomogeneous fluid mixtures oscillating in a magnetic field create AC
electricity in a pick up coil. Oscillatory motion of partially charged colloidal
particles in an electric field create a streaming potential that is an AC electric
field.
Oscillation of the air-liquid interface in a forming bubble can pinch of much
smaller bubbles and therefore enhance mass transfer (wastewater treatment).
Capacitance or acoustic “spectroscopy” applied to wavy air-liquid interfaces
can inform about the surface tension and viscosity of the liquid by variation of
the interface oscillation and/or the frequency of the applied field.
Microfluidic plasma generation creates more efficient formation of hydroxyl
radicals that can be used, instead of ozone, to sterilize aqueous liquids.
Step 4: Testing hypothesis through
experiment / observation.
When the hypothesis is originally formed, part of the scholarship (step 2) is to test the
hypothesis against known observations / experiments. If this is easy, we usually
lump it together with hypothesis formation (step 3). If it is difficult, we call this test
against known observations “analysis” and consider it separately, on pair with new
experiments.
If the hypothesis cannot be shown to disagree with known observations by analysis,
then the researcher must create an experimental plan to test it. Running experiments
that no one else has ever run is a trivial addition to knowledge. The originality of
the contribution to science is why the experiments should be run – what are the
predictions of the hypothesis that they test and how do they test it. The experimental
planning and testing of the hypothesis are skill sets that are fundamentally
philosophical and applications of logic. The tools, perhaps surprisingly, are
primarily statistical. Biologists are particularly good at understanding that statistics
underly the formation of hypotheses, the experimental plan (central role of
replication, error, variability and reproducibility), and the determination of the
consistency of the hypothesis predictions with the experimental results.
Step 5: Check and interpret results
This is the most frustrating part of training many researchers. It
combines:
 Critical and logical thinking
 Statistical inference and parameter estimation
 Knowledge of the subject matter – interpretation is based on
putting the results in the context of what is known about the
field already. What did you expect to find based on the
hypothesis to be tested.
Step 6: Iterate or report
 If the research programme was well crafted, the hypothesis will be
tested. If the hypothesis was an aim or objective of the research
programme, the results should be reported.
 Are scientists guilty of “cherry-picking”? Are only positive results
reported?
 Reports should be as honest and complete as possible. They should be
accurate. It is not the job of referees / examiners to correct
researchers mistakes.
 Scientific review should be open-minded and unbiased. Reviewers,
however, should put the onus of proof on the investigators – are the
hurdles reported sufficient to justify the claims. Are the activities
reported fully and accurately so that others are clear about the
hypothesis, predictions based upon it, and the tests conducted for
consistency.
Food for thought: no theory is ever proven. In fact theories are only
ever disproven or shown to be consistent with experimental
observations.
Is this really the way science is done? Or is it
just how it is presented?
An alternative approach to science is what I call a “fishing
expedition.”:
1. You think you smell where there might be fish.
2. You collect as many fish as you can.
3. After considering all the fish, you notice an interesting feature.
4. You report that fish have this interesting feature.
I call this “descriptive science” or pattern recognition.
If the research is conducted this way, it should still be reported
according to the scientific method. When this is done, a logical
and orderly mind may find “holes” in the analysis which suggest a
variations of the hypotheses and new tests which are used to
validate the hypotheses. In this light, the fishing expedition is
really part of hypothesis formation.
Essay Assignment
Write a two page essay on the application of the scientific method to any
of the following “hot” topics in current scientific discourse:
1. Evolution vs. intelligent design.
2. Electricity generation by “zero point energy”.
3. Perpetual motion machine developed in Dublin, Ireland.
4. “Cherry picking results in scientific trials”
5. The Bible Code.
6. “So what the BLEEP do we know?”
7. Quantum mechanics: Does God play dice?
8. What is consciousness? Are our brains just computing machines?
(Roger Penrose)
9.
Autism and MMR (Andrew Wakefield)
Stand rules on plagiarism (collusion and borrowing apply) – put it in your
own words and grammar, cite your sources, and argue a case based on
your opinion about how the scientific methods has been or should be
applied.
Summary
 There is only one “scientific method”. You might argue
that you are engineers or technologists, and therefore hold
yourself to a lower standard of conduct. But “estimates”
and “guesswork” are still covered in the scientific method.
 Fishing expeditions / pattern recognition / descriptive
science is just information gathering, not the scientific
method. It can be an integral part of hypothesis formation,
but it is open to the criticism that the results are biased by
“cherry-picking.”