the Scientific Method and the Scientist
"Equipped
with his five senses,
man
explores the Universe around him
and calls the adventure Science."A
Edwin P. Hubble
astronomer - 1948
The Scientific Method is the orderly process
of asking
and answering questions about
the Natural World
through repeated and
unbiased observations and
experimental tests...
 next
A |
Gk: Bios
=
life
Logy = study
of
the term biology was coined by Gottfried
R. Treviranus in 1802.
Biology is one of the Natural
Sciences which also include...
Physics
is the study of atomic
particles of matter that interact
by a set of rules (gravity, electromagnetism, strong
& weak nuclear
forces) that may be distilled into predictive formulas,
Golden ages = 16th (Galileo), 17th
(Newton), and 20th (Einstein) centuries.
Chemistry is a
more complicated application of
physics
& its rules
to a few molecules interacting in a test tube.
Golden ages = 18th (Priestley O2),
19th (Dalton), 20th (polymers) centuries.
Biology,
then is an even more complicated application of chemistry rules,
in a special test tube (a cell),
which may run via predictive formulas?
but, as we'll learn, Biology's
rules are messy and they're infinite...
the
multitude of molecular interactions
are almost impossible to predict.
Golden genomic age - 20th (Watson
& Crick) and 21st (Doudna & Charpentier)
centuries.
|
Biology is an activity carried out by thousands of researchers all contributing to a general picture of Life and the Nature that evolved on our plant, Earth, and is commonly described as the... Study of Life and the Living Condition. Biology recognizes the CELL as the basic unit of life and attempts to describe the properties of the cell as the living condition, including its origins, growth, reproduction, structure, heredity, and evolution. |
|
Biology attempts to understand HOW INANIMATE
MOLECULES built a highly ordered
and
complex interactive system that
exhibits EMERGENT PROPERTIES,
which we characterize as cells being ALIVE.
Biology has established that
all life shares a
CARBON BASED CHEMISTRY, depends
upon WATER,
and is capable of SELF-REPLICATION,
which defines a rich set of
characteristics we refer to as the ‘LIVING CONDITION’.
|
 |
| Neils Bohr (NP in Physics for Atomic Theory 1922) "We may look at a living organism either as a living organism or as a jumble of molecules". The aim of modern biology... is to interpret the properties of living within the structure of their molecules. |
|
Textbooks explore biology, with a little
detail, by looking at the the rich storehouse of discoveries
made by all the [rockstars]
biologists who have come before us, such as...
Do you recognize any of these "famous"
biologists?
To explain the Biology of Living Things is too difficult
for one to do in one's own generation time.
It's
for one to do a small bit, with certainty, now, and
leave the rest for those who come after us.
(paraphrased
from Issac Newton - 1643-1727)
The Scientific
Method is not trusting blindly in our
past knowledge (your textbook)... or not having
absolute faith in the accumulated
knowledge of our forefathers. Science is a Human endeavor
beset by social and cultural
influences, irrationality and even fraud, but in the
end science does
establish, with clarity, who is
right and who is wrong.
In science "I made a mistake"
is often the best strategy to the truth and
how the world functions.
(paraphrased
from Carlo Rovelli - Reality is
Not What it Seems. (2017)
For now, we will
begin our small bit by reviewing how they used the SCIENTIFC METHOD.
the Scientific Method...
a Video Descriptionview@home-10 min
Scientific
Theories often have only 2 components:
1. one
component describes PATTERNs OBSERVED in the natural
world
2. other component identifies a
PROCESS or
MECHANISM responsible for the pattern
To solve a scientific
observation/problem a scientist must first
Recognize and State the
problem?
a graphic of the steps involved in the Scientific Method*
SCIENTIFIC METHOD*read this .....is
a PROCESS for
investigating
Nature;
it's the methodology
by which scientists,
collectively & over time, attempt to construct
an accurate,
reliable, consistent, & non-biased representation of observed natural world.
is a process for investigating the
things (patterns)
we observe around us...
is
a means for describing... the
mechanisms (laws/rules)
that govern our physical
world...
is a careful
observation & measurement of
patterns
of living things &
their processes...
it employs rigorous methodology
and
it devises
experiments to validate a clearly stated
hypothesis...
"Science is what scientists do, and
there are
as many
scientific methods as there
are
individual scientists. The
scientific method is what working scientists
do."
Cartoon
Quote by...
Percy Bridgman, "On
scientific method," in Reflections
of a Physicist,
New York:
Philosophical Library, 1955
next
SCIENTIFIC METHOD... often involves a number of COMMON PRACTICES:
1. Observations... an accurate description of a
phenomenon or group of phenomena.
i.e., a
gathering of the data... either directly
or
from previous studies...
an observation:
Bil
150 students sitting in the top of a lecture hall,
often fall asleep?
Begin
to ask Questions:
about how's
& why's (mechanism) of things you
observed.
What is the process or mechanism responsible for
them falling asleep?
In
the scientific method questions must be framed in measurable terms.
Begin to look for ways
to Ask a Testable Question:
others may have asked
& even answered the same type of question...
do literature searches:
textbooks, journal & internet
articles...
reading other people's findings may lead to more
interesting questions,
and help define or modify your
testable question better.
POSE
a MEASUARABLE QUESTION:
It is known that warm air
rises so, pose a testable
question...
"Does sitting in
warmer air at top of lecture hall
promote student sleep"?
¥
next
-
2. Postulating the Question... i.e., Formulating an explanation (testable hypothesis) of the
observations & the posing of a critical and experimentally testable question is hard -
If students fall asleep in class... Does warm air at top of auditorium promote sleep?
Develop possible explanations: - Formulating
a
Hypothesis*... an explanation, based upon
observations and,
assumptions, that leads to a formal testable prediction -
is a proposed explanation for our observation, which is experimentally testable...
our observation: compare numbers asleep vs. awake in hot & cold temperatures...
fiddle with the air conditioning &/or thermostat in the room...
hot... cold...hot...cold, hot...cold etc.... -
One
must state the testable hypothesis as precisely
as possible and must list
list the expected predictions that the hypothesis might make...
"warmer air at top of lecture hall promotes sleep"
often involves critical analysis & critical thinking - and there may also be alternative hypotheses -
- ... sitting in the top or back of the classroom keeps a student
-
... out of reach of instructor
& its quiet & cozy...
... or maybe "it's a boring lecture that promotes sleep". -
¥ next
-
3. Experimental Testing and Predictions...
a hypothesis is making a prediction to be experimentally tested.
- "Lowering the
temperature at the top
of the
auditorium can prevent their
sleeping"
-
Designing an
experiment to test a Hypothesis is a big
part of Scientific Method:
Experiments requires experience, creativity, and sense of what is practical.
√ read methods published by others - modify them to your purpose,
√ brainstorm with others - different perspectives are helpful,
√ you may be limited by equipment availability, costs, and time.
Let's look at a BUSINESS ANALOGY that is similar to hypothesis testing?* -
► Experiments are best designed to FALSIFY, not to prove a hypothesis.
When an experiment works, it does NOT prove the hypothesis,
more likely it just does not falsify the hypothesis being tested.
-
There is
often
no proof in science, only
'disproof' :
the scientific method is all about disproving what was once believed
to be truth & reality, but evidence may be collected in support of a hypothesis.
When scientists publish their data, they never say "results prove..."
but rather "results suggest..." or "results provide support for..."
DESIGNING the Experiment is a hallmark of the scientific
method...
the
design of an experiment should be to... FALSIFY the HYPOTHESIS
and
experimental methods need to meet certain
CRITERIA including:
- being
unbiased...
- defining the variables...
factors that are liable to vary or change
during experimentation:
Example Experiment:
plant hormone auxin*
(used in the stem elongation experiment below)...
dependent
variables: the variable being modified by
treatment
such as - cell, stem
or root length
in mm, etc.., number of parts, etc...,
must be measurable & observable units;
independent
variable: only one variable being manipulated, which
may change...
height, weight, age, sex, amount of hormone,
etc..., often it is time.
controlled
variables: all
other factors kept constant and not allowed to
change,
all experiments must have a control... standard
for comparison (a
challenge)
Variables plant growth
hormone
auxin
in the plant stem growth experiment:
dependent variable:
cell, stem, or root length
(growth).
independent
variable:
growth over time at one auxin concentration
¥ next
and
controlled variables:
temp, humidity, day length, amount of fertilizer.
a big part of experimental design is
materials & methods
(the procedures
used)
based on previous published works, colleagial
suggestions, intuition, etc...
our auxin hypothesis...
if auxin is added to DWARF PLANTS, we predict
stem lengths will increase?
our
experimental design will analyze effect of auxin
on dwarf plants: Controls*
1. auxin controls: negative control:
dwarf plants NOT given auxin
positive control:
normal
plants NOT given auxin
2. determining the proper
auxin concentration levels:
should not be too low
(no effect detected) nor too
high (toxic);
should be within physiological
range [10-6
to 10-10M] of cells
3. must be
recordable:
quantitatively
measureable, such as stem
length (mm)
4. must
be replicable... redone several
times, to be statistically
valid
experiments ought to show
consistent results
again
and again, from test to test.
¥ next
to help make predictions
about an outcome, experiments may involve
making a MODEL...
a picture
is worth a 1,000 words... a drawing
can be a model of how a structure might
work.
The purpose
of a Model (a kind of
analogy or mental image) is to give one a
conceptual
likeness of how something functions...
water waves is a
model image to emulate light waves.
Protocols to
help model a hypothesis:
Hypothetico-Deductive Model... which
involves the formulation of the hypothesis,
conceivably falsifiable by a test of observable
data, and from experiments one
may deduce a general answer to the
hypothesis... .
often involves...
Deductive
Reasoning... (from general case to the
specific)
IF...THEN deductive logic
IF all birds have feathered wings, and a
robin is a bird,
THEN robins have
feathered wings.
- in daily
life*
Inductive Reasoning... (from a specific case to a general
principle)
it
is the ability to deduce intuitive/creative
principles...
objects fall to ground when
dropped...
thus,
a
force
[gravity] must act on the object...
"sparrows are birds...
birds have wings... thus birds can fly"
¥next
Additional aspects of the
Scientific Method include...
Scientific
Method is cumulative...
- no endeavor of humankind rivals
Science in its incremental
processes
toward a more complete understanding of the
observable world.
"The beauty of science is
that all important discoveries are made
by building on the discoveries of others". JC
Venter...A Life Decoded, 2007
Scientific
Method must repeatable...
- everything that
science "knows" - even long established
theories -
are subject to
reexamination as new information is
collected.
"all
scientific knowledge is tentative, and open
to challenge"
Scientic Method shows adaptability...
-
not all experiments are
clear cut, scientific results must fit into known
facts.
- something is purposefully changed by the
researcher in the environment
- random assignment of multiple study groups is
often employed.
► Now
let's recall our auxin experiment hypothesis and its predictions:
negative control:
dwarf plants treated with water
= remain short
(dwarf)
positive control:
normal plants treated with water =
remain normal height
test treatment:
dwarf plants treated
with auxin
= grow taller
(normal)
so let's do the
experiment and collect some data...
¥ next
The Collection &
Interpretation of Experimental Data...
Data collection
often draws upon previously known knowledge...
and scientists
fit the new knowledge into framework of what they
already know...
Observations
and Measurements must always use the same criteria (Standardization)...
in our Auxin experiments: plant height always measured
from pot rim to
shoot tip*
Variability in data from
experiment to experiment must be estimated via ...
statistical
analyses:
some common statistical methodologies include ...
t-test
-
compares the means of two groups
ANOVA
-
compares means of three (3) or more groups
chi square - compares how
closely the observed or measured data
is to the expected results (ex: genetic
crosses)
linear regression
- a single independent variable (time) is
used to
predict a
value of a dependent variable (mm)
What
are some of the ways that biologists
present their collected
data?*
¥
next
Organizing Data... raw data is often expressed in tables and figures.
tables: often used to emphasize numbers themselves, rather than a trend
figures: graphs show
trends;
pictures, photos, diagrams are
visuals;
line graphs - show
effect of independent
variable on X-axis - (time)
the dependent (measured)
variable on
Y-axis - (length)
bar graphs - compare
sets of data that may be discontinuous
i.e., maybe different groups
the
best way to display your data often depends on what
you want to show
Examples*: aim is to show when
maximum growth rate is reached after several
weeks
sometimes data may be misleading:
Will chocolate
lead to a Nobel Prize*?
another urban legend:
younger scientist make the great
discoveries ?
Homework
Assignment
¥
next
It's may seem easy in the
Hypotheical-Deductive model to make an initial hypothesis...
but it's hard
to make an effective CORRELATION
between CAUSE and EFFECT.
Drawing a
conclusion...
if experimental outcomes match your
predictions,
then your hypothesis
is not falsified, but is supported,
if
not, then your hypothesis is negated.
Do your results agree
with findings of others?
if not, do
you know why not ???
a different species or strain of organism,
different model of instrumentation,
different methods, seasonal variation in reagents,
etc???
Experimental Results are a TOOL:
Scientists usually assume that no theory is 100%
correct.
so experiments provide a sense of direction
for doing more experiments.
do NOT let predictions
affect your objectivity.
do NOT make results fit
your predictions (personal bias).
you may modify your hypothesis to better fit the
observed results...
modifications of a hypothesis help scientists gain
assurance
that their explanations may eventually be valid.
Negative results are often more important than
positive ones.
¥ next
-
Affirmed data may let one formulate or substantiate a THEORY... -
... a set of rules & mechanisms governing what was observed.
a THEORY is... a hypothesis that has stood the experimental test of time.
Theory of GRAVITY is always subject to testing & refutation as new ideas emerge;
If experiments always support a hypothesis, it is regarded as a THEORY or LAW
of nature, but if it doesn't we must scrap that theory...
-
Scientists are constantly double-checking their own ideas and, even if they don't, other
scientists will do so. The goal is to get at the truth. Indeed, a good scientist should
never hold firmly to their ideas and should be open to changing their viewpoint as more
data comes in. Slowly. but surely, scientific ideas are refined by this process, getting
closer and closer to the TRUTH.
In scientific disciplines, the words "hypothesis", "theory", & "law" may have different
connotations in relation to acceptance or knowledge about a group of phenomena.
A scientific theory or law represents a hypothesis, or a group of related hypotheses,
which have been confirmed through repeated experimental tests over a long period of
time and the results are considered to have general significance. -
"Nothing in Science reaches the level of Theory without a vast pool of facts
and tested hypotheses behind it"... james rollins 'Black Order' (2006)
The great Theories of Biology may be compared, as creative
achievements, with the great works of art or literature.
-
next
-
the Scientific
Method has limitations...
- the scientific method can not deal with hypotheses
- that are NOT EXPERIMENTALLY TESTABLE...
-
How many of you believe there is life elsewhere in the Universe?*
A show of hands, please!
"IRONIC
SCIENCE"... (non-testable
hypotheses, that appear scientifically based)
previous
example: Is there
life elsewhere in the Universe?
Human do not have the technology to answer that
question yet.
The
vast size of the observable universe (93 billion LY
in diameter) with up to
2
trillion galaxies (many larger than the Milky Way)
precludes human observation.
Some other examples of Ironic Science:
Nuclear winter* or
a meteor*
that causes
dinosaurs mass extinctions? ice ages?, etc.
Can scientists do
any experimentation to test these hypotheses???
Mount
St. Helens image & impact*
+ MODIS Earth-on-fire*
Amazonian deforestation,
are they part of Global Climate Change ? ...
These are systems that
involve great Complexity
and make it
difficult to predict exactly
what is going to happen at any given
time, in the present or the future.
Chaos
theory deals with the behavior of nonlinear dynamical
systems that are characterized
by sensitivity to
initial conditions. Examples include the atmosphere,
the solar system,
plate
tectonics, turbulent
fluids, economies, and many biological systems, as
population
growth.
next
ADDITIONAL THINGS TO CONSIDERATION about the
SCIENTIFIC METHOD:
Technology & Advances in
Instrumentation...
plays
a role as important as any hypothesis or concept.
Scientific
instruments extend our
senses for observation of the natural world.
Developments in instrumentation have greatly advanced
cellular biology analyses...
examples: 1)
microscopy from mm to nm (light to
electron microscopy),
2) rapid through-put DNA sequencing machines,
3) tagging
of molecules within cells stains vs. fluorescent markers.
►
"Although concepts
and ideas
occupy
a central place in the grand sweep of our
under standing
of the nature of the world around us, it is a
mistake to imagine that they play a greater
role than
tools
and techniques in achieving
scientific progress".
Few scientific
revolutions are concept driven.
Human Genome Project,
J.M. Thomas,1994
► "Progress in science often
depends upon new
techniques, new discoveries, and new
ideas,
probably in that order."
Shimomura, Chalfie, Tsien win
2008 Nobel Prize for GFP
► "Advances in
Science are enabled by technology advances that allows
us to see what we have
not been able to see before."
Lloyd Watts, Computational
Intelligence: The Experts Speak. IEEE
Press, 2003.
What about ERROR
in scientific experiments happens... it
may have have several sources...
1. No instrument measurements are
absolutely precise.
Accuracy
is limited by the smallest division
an instrument can measure.
There's also intrinsic
error in instruments --> RANDOM
ERROR... or
unpredictable
variations in
measurement*
signals (background noise). The precision
of a measuring instrument and accuracy may be
improved by making multiple
measurements of the same thing with the same
instrument an expressing the variation.
Knowing the Limits of
Resolution of an
instrument is critical to accuracy.
2.
There is NON-RANDOM or systemic error, due to factors which may
bias
the results.
No
experiment, can be perfectly precise...
A. Human error:
failure to follow
procedures, failure to use the equipment properly,
failure to prepare solution correctly,
measurements made by 2 researchers,
simple arithmetic errors, etc...
B. Fudging data:
Another
common mistake is to rule out or ignore
data
which do not support
the
hypothesis... Humans have psychological
tendency to find "something
wrong",
with
data, which does not support their
hypotheses. see:
Bungles, Lies, & Fraud
¥
next
ERROR cont.
C. a scientist's
personal BIAS can effect the outcome of an
experiment...
most fundamental error is to mistake
the hypothesis for an explanation of a
phenomenon,
without performing experimental tests. Sometimes "common
sense"
and "logic" can tempt us into believing
that no test is needed.
...teacher can intimidate
student in front to keep awake
Bias is Unavoidable*read@home
....humans have implicit
biases, yet we often ignore them.
Bias may be overcome... via
open communication among members of the scientific
community because experimental tests are
repeated by different scientists...
using different
types of experimental setups... again and again.
Sharing
your results... the "PUBLISH
or PERISH" Rule
1. in a paper in a referred (peer-reviewed) journal publication +
Open
Access
2. at a poster
session at a scientific meeting
3. via seminars at scientific
meetings or symposiums
-
-
Over a period spanning a
variety of experimental tests
(usually many
years),
a consensus develops in scientific community, as to which experimental results
have stood the test of time and become ----> THEORY. -
the word THEORY...
to scientist the word THEORY means ESTABLISHED FACT or TRUTH,
but, to lay person (nonprofessional) the word THEORY may mean...
a speculation, a guess, an unknown, or a lack of knowledge.
- Scientific Insanity: doing the same experiment over & over,
-
but expecting a different
result each time
If Science is what scientists do, then What Makes a good Scientist?
 |
<--Paradigm back to Bb Scientific Societies* | |
| copyright c2023, Charles Mallery, Department of Biology, U. of Miami. | ||
|
|
||
SKIP ALL THE MATERIAL
BELOW...
previous material no longer relevant
next
Some THOUGHTS and QUOTATIONS...
on what the Scientific Method
is...
& who is a Scientist...
The scientific method was initiated by the Greek philosophers [2600 years ago].
Thales (590 bc) is considered the founder of the scientific method...
The prime question asked was.. "what differentiates living from non-living".
"Science is what scientists do, and there are as many scientific methods as there
are individual scientists. The scientific method is what working scientists do."
Cartoon Quote by... Percy Bridgman, "On scientific method," in Reflections of a Physicist,
New York: Philosophical Library, 1955 Cartoon
What
experimental results from hypothesis testing tell
us...
a Hypothesis is
always open to further testing (i.e., not
proven correct)...
but, a Hypothesis can
be falsified (proven wrong) or refuted,.
Experimental
testing can support the hypothesis as a likely explanation,
not by proving it is correct, but rather by
finding that it is NOT FALSE.
There is
often
no proof in science, only
'disproof':
but evidence may be collected
in support of a
hypothesis...
When scientists publish their data, they never say "results prove..."
but rather "results
suggest..."
or
"results
provide support for..."