In This Lesson:
Unit 0
Nature of Science
and Scientific
Method
(Lesson 1 of 1)
Today is Tuesday,
st
September (!) 1 , 2015
Pre-Class:
Take out your homework. We’re going to be
discussing your scientific method definitions
in lab groups soon.
Note: The syllabus receipt can go in the
Turn-In Box on the computer cart. Show me
your calculator and lab notebook and I’ll
check you off.
Today’s Agenda
• The real meaning behind the scientific
method.
• A horse that could count.
• Evolution Pre-Test.
• Where is this in my book?
– Page 16 and following…
By the end of this lesson…
• You should be able to orient yourself in
scientific history.
• You should be able to describe the scientific
method from a “purpose” standpoint (not
memorization of the steps).
Evolution Pre-Test
• Before we start, let’s just get this pre-test out
of the way.
• Remember, though it doesn’t directly count
for your grade, it’s important that you try your
best.
• The feedback is very real.
Evolution Pre-Test
• Username:
– [firstnamelastname]832
• Password:
– Gleicher[house/apt #]
Important
Buttons
Change
Question
How to
Save for
Later
In the beginning…
• Okay, let’s be honest here: Science is young.
• Think about your other classes – languages
have been around for a long time, math dates
back quite a ways, and history is quite literally
ancient.
• Science? Yeah, it started in earnest with the
ancient Greeks, but it’s been through a lot,
and it shows its youth every once in a while.
• Here’s what I mean…
Middle Ages:
Geocentrism vs. Heliocentrism
• Geocentrism: The Earth
is the center of the solar
system. Don’t mind that
Galileo guy with “proof”
otherwise.
• Heliocentrism: The Sun is
the center of the solar
system.
http://en.wikipedia.org/wiki/File:Justus_Sustermans_-_Portrait_of_Galileo_Galilei,_1636.jpg
Renaissance:
Spontaneous Generation
• Maggots come from rotting meat, rats come from leaky
roofs, mice come from sweaty underwear.
• Even Jan van Helmont, the guy who coined the word
“gas,” had it wrong:
– “If you press a piece of underwear soiled with sweat
together with some wheat in an open mouth jar, after about
21 days the odor changes and they ferment, coming out of
the underwear and penetrating through the husks of wheat
into mice. But what is more remarkable is that mice of both
sexes emerge, and these mice successfully reproduce with
mice born naturally from parents...But what is even more
remarkable is that the mice which come out of the wheat are
not small mice, not even miniature adults or aborted mice,
but adult mice emerge!”
• Jan van Helmont (not being very science-y)
1891: Clever Hans
• A horse that can perform basic arithmetic:
Today:
• Jenny McCarthy citing a discredited paper to
claim that vaccines lead to autism.
• A sizable chunk of the population denying
climate change in the face of real data.
• Evolution deniers.
• And the icing on the cake of willful ignorance:
Learn with Shiloh.
So…now what?
• In the words of Dr. George Mehler, “YOU are the
vanguard of the enlightenment.”
• In other words, it’s up to you folks out there to
take a discerning and objective look at the world.
– Don’t believe all you’re told, don’t believe all you see,
and demand proof at all times.
• This is hard to do. Don’t believe me?
– Observation Test
– Stroop Test
The Scientific Method
• We now get to the scientific method.
• How do you remember it?
• Here’s how I like to present it:
– Identify problem
– Form hypothesis
– Design/perform experiment
– Gather/analyze data
– Draw conclusion
• Don’t memorize it. Ever.
The Scientific Method
• What does it mean?
– Head to your lab tables (I’ll show you where you
sit in a second) and discuss your homework. Try
to get a real conversation going.
The Scientific Method
• The scientific method is the way to avoid
things like counting horses and
celebrities/politicians posing as scientists.
• You need to feel it, not memorize it.
• To help you do that, here are a few
experiments. Figure out the flaws, if any.
Experiment #1: The Pepsi Challenge
• This was a marketing technique
(and use of the scientific
method) by Pepsi.
• In the test, a “test taker” is
given two blank cups, one of
which contains Pepsi, one Coca
Cola. He/she doesn’t know
which is which.
• The “test taker” tries a sip or
two of each and decides which
he/she likes better. Most
people seem to take Pepsi.
• Is this a valid experiment?
http://www.stephendenny.com/wp-content/uploads/2010/03/pepsi-challenge.jpg
Experiment #1: The Pepsi Challenge
• Turns out, not quite.
• True, people really do pick
Pepsi more, but:
– It’s not a double-blind
study.
• The experimenter knows
which is which.
– It’s not a full drink.
• People prefer Pepsi in small
quantities because it’s
sweeter, but for a whole
drink Coke is chosen.
http://www.stephendenny.com/wp-content/uploads/2010/03/pepsi-challenge.jpg
Experiment #2: UPenn’s Myopia Study
• In the late 1990s, the
University of
Pennsylvania Medical
Center finds that children
who often sleep with the
lights on tend to develop
myopia later in life.
• Buy it?
Experiment #2: UPenn’s Myopia Study
• Penn forgot to look at one
really important thing:
– The kids’ parents.
• Oddly, parents with myopia
tend to leave the lights on
for their kids more than
other parents.
– That, however, doesn’t
cause myopia. It’s genetic.
• Conclusion: Kids with
myopia come from parents
with myopia.
Experiment #3: Chantix™
• Chantix™ is a prescription
medication for quitting
smoking.
– Because apparently telling
people on the package that it’s
going to kill them isn’t enough.
• An independent, double-blind
study (more on that in a
second) found that 11.9% of
people on Chantix™ were not
smoking after 24 weeks on the
prescription.
• Good results or no?
http://spinfuel.com/vaping-news/wp-content/uploads/2014/06/chantix.jpg
Experiment #3: Chantix™
• Turns out…you can’t be sure if
that’s good or not.
• You need to know the rate of
success on a placebo.
• If I inform you that in this same
study, 11.9% on Chantix™
stopped after 24 weeks but
2.3% stopped on a placebo, is it
good now?
– Actually, we’re still not sure.
That’s something we’ll look at
later this year.
http://spinfuel.com/vaping-news/wp-content/uploads/2014/06/chantix.jpg
Lessons
• Experiment #1 – Pepsi Challenge:
– Double Blind Study – make sure both the participant and the
researcher interacting with the participant don’t know which
treatment group (variable/control) the participant is in,
otherwise you might introduce experimental bias.
• Experiment #2 – UPenn Myopia:
– Correlation Does Not Equal Causality – just because two
things appear to have a relationship (sleeping with lights on
and myopia) doesn’t mean they’re actually connected.
• Experiment #3 – Chantix™:
– Analyze Your Data – Don’t make conclusions without data,
and make sure you’re comparing to a control or baseline.
Bias
• Always watch out for experimental bias in
your data. Here are two examples:
– You do a study on rats and pick the first 20 you
can catch.
• Your data will be skewed toward slow rats.
– You conduct a survey via text message.
• Your participants have to be wealthy/tech-savvy
enough to have cell phones.
Features of a Good Experiment
• High sample size (n)
– In other words, they tested a lot of subjects.
• Has a control group and variable groups
– An un-modified sample and a sample being tested.
• Only one variable tested at a time
– Sources of error are minimized.
– Side note: A second variable that is tested at the same
time as the “main” one is called a confounding variable or
a confound.
• Can be repeated by others
– Procedure is clear.
Example Experiment
• Hypothesis:
– Spiders given caffeine build asymmetrical webs.
• Experiment:
– Gather 100 spiders of same species.
• High sample size, no additional variables.
– Give 50 spiders caffeine and water, give other 50 plain
water.
• Control group (plain water) and variable group (caffeine and
water).
– Record procedure clearly.
• Repeatability.
Controls and Constants
• By the way, don’t forget that controls are
different from constants.
– Constants are things kept the same in an
experiment. Sometimes constants are referred to
as “controlled variables.”
• Example: All spiders used in the experiment were the
same species.
– Controls are the test subjects treated “normally.”
• Example: Spiders not given any kind of “treatment” like
caffeine.
Spiders on Drugs
• Scientists actually did this test.
– NASA scientists!
• Here’s what they found:
– Normal spiderweb
Spiders on Drugs
• Caffeine:
• Mescaline/peyote:
Spiders on Drugs
• Marijuana:
• Benzedrine/Speed:
Spiders on Drugs
• Sleeping Pills:
And finally…
• LSD:
More on Controls
• There is a distinction between positive
controls and negative controls:
– Negative controls are what you’re most familiar
with – just don’t do anything to the negative
control group.
– Positive controls are ways to check that what
you’re doing works.
• Here’s an example…
Zebra Finches
• Zebra finches are birds with bright
orange/red beaks.
• In my experiment, I used nail polish to
(harmlessly) paint birds’ beaks to see if
the increased redness made them more
aggressive/dominant.
• Negative control birds were not painted
and gave us a baseline.
• Positive control birds were painted and
measured to ensure that we actually
were making their beaks redder.
– We need to confirm that the nail polish
has an effect.
Other Quick Vocabulary Reminders
• Placebo – Something designed to look like a
“treatment” but that doesn’t actually do anything.
– Also called a sugar pill.
– TED: Eric Mead – The Magic of the Placebo
• Independent Variable – What the researcher
changes to create the control and variable groups.
– Think something like “Chantix or placebo.”
• Dependent Variable – What the researcher measures
to carry out the experiment.
– Think something like “quitting rate of smokers.”
Graphing Tips
• Write these down. Make them big and bold (and
maybe even right in the front of your notebook).
– Dependent variables are graphed on the Y-axis,
independent variables go on the X-axis.
– Also, bar graphs are good for categories (when there is
no continuous “gradient” for the independent variable).
• The effects of two different drugs on a disease would be good
for a bar graph. The drugs aren’t connected to each other.
– Line graphs are good for continuous variables.
• Anything changing over time goes into a line graph.
• Typically this will be time or temperature. KNOW THAT!
Other Quick Vocabulary Reminders
• Hypothesis – An informed “guess” as to the
relationship between variables.
• Must be testable.
– More on this in a few slides.
• Theory – A hypothesis that has been accepted
essentially as fact. A wealth of data and experiments
support it as accurate. Often quite complex.
– If someone says, “Well, I don’t know, it’s just a theory,”
s/he probably doesn’t know what “theory” means.
• Law – A relatively simple phenomenon that occurs
invariably with certain conditions.
– Theories are complex and speak to many situations; laws
are simple and speak to specific situations.
Other Quick Vocabulary Reminders
• Sample size
– How many subjects were tested.
– Generally, if you give 50 smokers Chantix and 50
smokers a placebo, your sample size is 50, not 100.
– Sample size is given by n (n=50 for the above
example).
• Significance
– If you say a conclusion is “significant,” you better have
statistics to back it up.
– If you have not actually done a mathematical analysis
of your data, do not use the word significant. At all.
“Significant” is Significant
• To put it another way:
– Two baseball players each get one at bat.
– The first (Player 1) hits a home run.
– The second (Player 2) strikes out.
• Is Player 1 significantly better?
• No.
– One at bat each (n=1) is simply not enough to
determine a statistical significance.
– We would need a lot more, along with some statistical
tests (more in the next unit) to make that claim.
• Does Player 1 appear to be better?
• Sure. But don’t say Player 1 is significantly better.
About Hypotheses
• It’s natural for students to say things like, “My
hypothesis was correct.”
– Don’t. And I better not see that phrase in your lab
reports.
• In science, we either accept a hypothesis or
reject it. They’re neither right nor wrong.
• Additionally, there’s something called the null
hypothesis. Let’s see what that means.
The Null Hypothesis
• Suppose you think that sugar in coffee will
make the coffee sweet.
– That’s a deduction, by the way.
• The null hypothesis, then, is that sugar has no
effect on coffee.
– The null hypothesis is always “no relationship.”
• Key: When you reject your own hypothesis,
you are accepting the null hypothesis.
One last thing…
• By some definitions, there are actually three
scientific methods.
• The most familiar to you is the one we just
talked about – the classical method.
– Developed in part by that Galileo dude.
• There are also:
– Observational Method (Discovery)
– Synthesis Method
Other Scientific Methods
• Observational:
– Sometimes you just
need to discover
something.
• Synthesis
– Using the alreadypublished work of
other scientists.
– Watson and Crick
didn’t experiment!
Isaac Newton:
• “If I have seen further it is by standing on the
shoulders of giants.”
• (referencing the synthesis method, in part)
The Relationship is Circular
Classical
(Experiments)
Publish the
Results
Observations
Publish the
Results
Publish the
Results
Synthesis
Closure: Labeling the Experiment
• A biologist thinks that exercising is good for mice.
• He takes 20 two-week-old mice and gives them all identical cages
and identical diets, and he keeps them in the same room.
• 10 mice also receive an exercise wheel. The other 10 receive an
exercise wheel that does not spin.
• He records their life spans and compares.
–
–
–
–
–
–
–
–
What is the hypothesis?
What is the sample size?
What are the constants?
What is the control (or control group)?
What is the variable (or variable group)?
What’s the independent variable?
What’s the dependent variable?
Could anything have been done better?
Closure: Answers
• Hypothesis
– Mice that exercise live longer.
• Sample Size
– 10 (20 total mice, but in two groups of 10).
• Constants
– Same age, same room, same cage, same exercise wheels.
• Control
– Mice with a non-spinny wheel.
• Variable/Treatment Group
– Mice with a spinny wheel.
• Independent Variable
– Exercise or no exercise.
• Dependent Variable
– Life span.
• Improvements
– Same litter of mice, bigger sample size.
Closure: Bad Science?
• Bad Science:
– TED: Ben Goldacre – Battling Bad Science
• Publication Bias:
– TED: Ben Goldacre – What Doctors Do Not Know
About the Drugs They Prescribe
• Science Denial:
– TED: Michael Specter – The Danger of Science
Denial
Closure: Abstract Reading
• The “abstract” of a scientific paper is usually a
short summary of all of the procedures and
findings of the researchers.
• Take a look at this one and let’s see what we
can interpret:
No effects of gluten in patients with self-reported non-celiac
gluten sensitivity after dietary reduction of fermentable, poorly
absorbed, short-chain carbohydrates.
• Abstract
• BACKGROUND & AIMS:
• Patients with non-celiac gluten sensitivity (NCGS) do
not have celiac disease but their symptoms improve
when they are placed on gluten-free diets. We
investigated the specific effects of gluten after
dietary reduction of fermentable, poorly absorbed,
short-chain carbohydrates (fermentable, oligo-, di-,
monosaccharides, and polyols [FODMAPs]) in
subjects believed to have NCGS.
No effects of gluten in patients with self-reported non-celiac
gluten sensitivity after dietary reduction of fermentable, poorly
absorbed, short-chain carbohydrates.
• METHODS:
• We performed a double-blind cross-over trial of 37 subjects
(aged 24-61 y, 6 men) with NCGS and irritable bowel
syndrome (based on Rome III criteria), but not celiac disease.
Participants were randomly assigned to groups given a 2week diet of reduced FODMAPs, and were then placed on
high-gluten (16 g gluten/d), low-gluten (2 g gluten/d and 14 g
whey protein/d), or control (16 g whey protein/d) diets for 1
week, followed by a washout period of at least 2 weeks. We
assessed serum and fecal markers of intestinal
inflammation/injury and immune activation, and indices of
fatigue. Twenty-two participants then crossed over to groups
given gluten (16 g/d), whey (16 g/d), or control (no additional
protein) diets for 3 days. Symptoms were evaluated by visual
analogue scales.
No effects of gluten in patients with self-reported non-celiac
gluten sensitivity after dietary reduction of fermentable, poorly
absorbed, short-chain carbohydrates.
• RESULTS:
• In all participants, gastrointestinal symptoms consistently and
significantly improved during reduced FODMAP intake, but
significantly worsened to a similar degree when their diets
included gluten or whey protein. Gluten-specific effects were
observed in only 8% of participants. There were no dietspecific changes in any biomarker. During the 3-day
rechallenge, participants' symptoms increased by similar
levels among groups. Gluten-specific gastrointestinal effects
were not reproduced. An order effect was observed.
• CONCLUSIONS:
• In a placebo-controlled, cross-over rechallenge study, we
found no evidence of specific or dose-dependent effects of
gluten in patients with NCGS placed diets low in FODMAPs.
Citation
• Biesiekierski, J. R., Peters, S. L., Newnham, E. D.,
Rosella, O., Muir, J. G., & Gibson, P. R. (2013). No
effects of gluten in patients with self-reported nonceliac gluten sensitivity after dietary reduction of
fermentable, poorly absorbed, short-chain
carbohydrates. Gastroenterology, 145(2), 320-328.