The scientific method

Aristotle (384 – 322 BCE) was a Greek philosopher and the first
person to study biology in a systematic manner. He investigated
biological patterns but mistakenly proposed life “spontaneously
generated” from non-living matter.
“So with animals, some spring from parent animals
according to their kind, whilst others grow spontaneously
and not from kindred stock; and of these instances of
spontaneous generation some come from putrefying
earth or vegetable matter, as is the case with a number of
insects, while others are spontaneously generated in the
inside of animals out of the secretions of their several
organs.“
—Aristotle,
History of Animals, Book V, Part 1

This idea was held into the 17th century when the scientific method
and experiments were used to disprove spontaneous generation.
 The scientific method starts with a question: Theory
who, what, when, where, why, or how Highest level
of certainty
• From observations a hypothesis is proposed and
tested by collection of empirical evidence, followed
by peer-review, replication, and finally acceptance. Accepted
• A theory is the result of applying the scientific method
repeatedly! Corroborated
• Real science is evidence-based and iterative, if a Unquestionably
theory is unsupported the scientific community
re-thinks the theory. This is how science advances. Testing
Repeated

Experiment and/or Corroborated

collect data

Question and/or Not corroborated

Observations Hypothesis
by the evidence
 1) Ask a question
• A new dairy farm
recently began operating
next to a creek near your
home.
• You are concerned that
cows will pollute the
water and have a
negative impact on fish
and amphibians.
• You decide to do some You wonder…will this farm
background research on affect water quality?
the topic.
 2) Conduct a literature review
▪ Clean water is important to fish and amphibians

▪ Manure contains lots of nutrients that promote the growth of

algae and degrade water quality; low levels of oxygen in the
water

▪ Cows break down creek banks and eat riparian vegetation

▪ Stream bugs (macroinvertebrates) are good indicators of

water quality (BIBI) and are easy to collect and identify

▪ We should expect better water quality upstream of the dairy

and poorer water quality downstream of the dairy

▪ We need a hypothesis!
 Hypotheses (pl.) are…
Explanations of processes or phenomena made after the
problem has been stated and a literature review has been
conducted
• A hypothesis is:
– A tentative guess, a good hunch – mildly asserted to
guide the investigation (a working hypothesis), or
– accepted as highly probable based on prior
knowledge (an educated guess), or
– represents the expected relationship between the
variables, and
– is always in the form of a statement.
Why do we need a Null and Alternative hypothesis?
The NULL hypothesis says there is no statistical difference between two
variables. So a NULL and ALTERNATIVE hypotheses provide two
mutually exclusive statements. We test the NULL hypothesis for
significance and reject or fail to reject. We do not prove the
ALTERNATIVE. We use sample data to test the NULL hypothesis.

The Null Hypothesis (H0) (AKA the nullifiable hypothesis)

States a population parameter (mean, standard deviation) is equal to
a hypothesized value or a claim that is based on previous analyses or
specialized knowledge.

The Alternative Hypothesis (H1) or (HA)

States that a population parameter is different than the hypothesized
value in the null hypothesis. The alternative hypothesis is what you
might believe to be true or hope to prove true. What we conclude
when we reject H0.
 Example:
State the Null and Alternative hypotheses?
People believe the world is flat.
Null hypothesis
H0: The world is flat

Alternative hypothesis
H1: The world is not flat (two
sided, maybe its round or some
other shape)
H2: The world is round (one
sided)
3) Develop a Null and Alternative hypothesis

There will be MORE stream macroinvertebrates

that indicate poor water quality downstream of
the dairy than upstream of the dairy.

• Null hypothesis • Alternative hypothesis

H0: Water quality will be H1: Water quality will be

the same upstream and degraded downstream of
downstream of the dairy. the dairy.
 4) Make observations or gather evidence
• Scientific investigations begin with
observations of nature (noticing,
collecting, describing in detail,
recording information in a careful,
accurate, and organized manner)
*Spontaneous generation started as
observations of maggots emerging from
rotting flesh, fleas appearing from dust,
and tapeworms excreted by animals
• “garbage in, garbage out”

Stream survey: you sample the

macroinvertebrates both upstream and
downstream of the dairy pasture. You
collect in a given area per unit time, count
them and identify to species.
 Types of variables
• Hypotheses are tested by noting or changing the
independent variable (IV).
• When a variable isn’t completely independent it’s an
explanatory variable. An explanatory variable is often
affected by other variables (i.e., water temperature and
dissolved oxygen).
• The response (the measurement we care about) is
called the dependent variable (DV) or response.
• Some variables may be constant such as time, space,
temperature, or other factors.
5) Test the results by statistical analysis
• In our stream survey what is the IV (what was changed)?
– Change in land use from natural to agricultural.
• What is the DV (response)?
– Abundance/species of macroinvertebrates collected
• What is held constant?
– Time and space; sampled on one day, one stream (this
can be subjective)
• We could collect additional explanatory variables such as
water temperature, pH etc. (these factors are related).
• We segregate our data by location; upstream or downstream
• We use statistical techniques to determine if the
macroinvertebrate populations are different
 Types of data
All experiments involve data
• Descriptive data are qualitative
• binomial (yes/no, sex)
• nominal (species)
• ordinal (ordered, S, M, L)
• Numerical data are quantitative
• continuous (length, weight)
• discreet (counts)
• Spatial (geographic coordinates in 2
or 3 dimensions (lat, lon, elevation)
• Temporal (time)
 Review types of data
In 1864 Louis Pasteur declared that “life only comes from life,”
based on his famous swan-neck flask experiment.

What is the IV? The flask neck What type of data is the IV? Binomial (P/A)
What is the DV? Bacterial growth What type of data is the DV? Binomial (P/A),
What was controlled? Volume, time, type of culture media, nominal (type),
temperature, light, etc. ordinal (L,M,S)
Scientific method in action
Italian physician Francisco Redi conducted an experiment to
test Aristotle’s theory of spontaneous generation.
What was his H0?
• One flask containing raw meat was left open to the air. As
nothing new was being introduced this represented the
control group.
• Two additional flasks were set out and covered, one with
an airtight lid and one with gauze.
• These were the experimental groups exposed to the
independent variable (different covers).
• The response was the presence or absence of maggots on
the meat after a given amount of time.
• Only the unsealed flask grew maggots. Redi’s
conclusion supported his hypothesis -- maggots
do not spontaneously generate but grow from
tiny eggs laid by flies.
– Conclusions always indicate whether the original
hypothesis is supported or rejected.
– Does this prove that the flies observed were the ones
which produced the maggots?
6) Experiment is complete, publish the
results
• Other scientists review and critique the
experimental design, data collection, analysis,
and quality and novelty of the experiment
– This is the peer review!
• Accepted or Rejected
• Accepted manuscript become
part of current scientific
understanding.
• Hypotheses should not be confused with
theories, which are large, broad explanations
composed of many hypotheses and experimental
results.
– A theory would not be rejected by a single
experiment, but a hypothesis could be
– For example, the germ theory states that some
diseases are the result of microorganisms in the body
– But a hypothesis that all disease is caused by
microbes would be rejected
• A scientific law is a description of an observed
phenomenon.
– Laws do not explain the phenomenon, simply state it.
 Scientific thinking is…
…empirical: based on experience and observations that are
rational, testable, and repeatable, and…

…self correcting: in the process of using the scientific method,

incorrect ideas are discarded in favor of more accurate
explanation