jan14 scimethod helicobac

Biol 1306

1

2

Dextromethorphan

3

Dextromethorphan

4

Juice cleanse - Detox

• Thoughts on juice cleanses?

• What does “detox” mean?

• How do juice cleanses work (in the body)?

• How does the body react during a juice

cleanse?

5

BluePrint Cleanse

• BluePrintCleanse will gently rid your body of impurities, regain an

alkaline balance and normalize digestion and metabolism. Too

often, a cleanse stirs up detox symptoms that are far too intense for

the “average” person. BPC is designed for people that would like to

give their insides a rest while simultaneously going on about their

daily lives. One needn’t gamble with extremes to feel the benefits of

a cleanse.

• $65 per day

6

Hain Celestial

• Hain Celestial

– $5.7 billion market cap

– Whole Foods’ biggest supplier

• Hain Celestial bought BluePrintJuice

– For $25 million in Jan 2013

– Currently, BluePrint products bring in over

$40 million in annual revenue

7

1.4 What Is Science?

• Science is the systematic inquiry – through

observation and experiment – into the

origins, structure, and behavior of living

and nonliving environments

1.4 What Is Science?

• Science is based on the principle that all

events have natural causes

– The belief that all events can be traced to

natural causes that we can comprehend

(natural causality)

1.4 What Is Science?

• The scientific method is an important tool of

scientific inquiry

– The scientific method consists of six interrelated

elements

• Observation

• Question

• Hypothesis

• Prediction

• Experiment

• Conclusion

1.4 What Is Science?

• The six steps of scientific inquiry

1. Observation of a specific phenomenon

2. The observation, in turn, leads to a question

3. The question leads to formulation of a

hypothesis, based on previous

observations, which is offered as an answer

to the question

1.4 What Is Science?

• The six steps of scientific inquiry (continued)

4. The hypothesis leads to a prediction, which is

the expected outcome of testing if the hypothesis is

correct

5. The prediction is tested by carefully designed

additional observations or carefully controlled

manipulations called experiments

6. The experiments produce results that either support

or refute the hypothesis, allowing the development

of a conclusion

1.4 What Is Science?

• Biologists test hypotheses using controlled

experiments

– Two types of situations are established

• A baseline or control situation in which all possible

variables are held at a constant

• An experimental situation in which one factor, variable,

is manipulated to test the hypothesis to determine

that this variable is the cause of an observation

– Science is useless unless communicated

1.4 What Is Science?

• Scientific theories have been thoroughly tested

– A scientific theory is a general and reliable

explanation of important natural phenomena that has

been developed through extensive and reproducible

observations and experiments

15

Ulcers

A Case Study in the

Scientific Method

Ulcers

16

17

CQ1: What do you think causes

ulcers?

A: Stress.

B: Excessive stomach acids.

C: Bacteria.

D: A bad diet and alcohol use.

E: Being overweight.

18

What Causes Ulcers?

Design an experiment to test if the “excess

acid hypothesis” is true.

In your small groups, design the

experiment. Remember, be specific about

how you would treat your groups and what

you would measure!

19

CQ2: Which is a good way to test the

“excess acid hypothesis”?

A: Examine ulcer patients of a range of ages and measure their stomach acid levels.

B: Have volunteers drink alcohol and measure their stomach acid levels.

C: Lower stomach acid levels of some volunteers (using drugs/antacids), and measure numbers of ulcers in all volunteers.

D: Examine patients of a range of ages and measure the number of ulcers in each person.

E: Put volunteers through a stress test and then measure their stomach acid levels.

20

CQ3: What step in the scientific

method does this test represent?

A: Making observations.

B: Developing a hypothesis.

C: Determining predictions.

D: Testing a hypothesis.

E: Assessing support for a hypothesis.

21

A Possible Study Design

• Doctors divide patients into two groups:

• After 3 months, the number of ulcers per patient is assessed.

• Predict what the results would look like if the excess acid theory was supported.

Group 1 received antacids and

were instructed to take them

3x/day

Group 2 received sugar pills

and were instructed to take

them 3x/day

22

Group 1 Group 2

Treatment Group

# U

lcers

/ pa

tien

t

Draw this graph: Predict what the results would

look like if the “excess acid theory” was supported

by the results of this study:

23

CQ4: Which graph most closely matches

the results you predicted?

Group 1 Group 2

Treatment Group

Group 1 Group 2

Treatment Group

Group 1 Group 2

Treatment Group

Group 1 Group 2

Treatment Group

# U

lcers

/ patient

# U

lcers

/ patient

# U

lcers

/ patient

# U

lcers

/ patient

A

C D

B

24

• Unfortunately, this type of controlled experiment was NOT conducted.

• BUT, patients who took antacids had decreased ulcer symptoms.

• If the patients stopped taking the antacids their ulcers returned.

Image by: Midnightcomm

25

Dr. J. Robin Warren: (pathologist)

Examines stomach

biopsies of patients

with various stomach

ailments.

26

CQ5: The slides that Dr. Warren examined had

smudges that were not clearly visible under low

power, so he attached a high-power lens to his

microscope. What do you think he was able to

see then?

A: Many cells at once.

B: Only one cell at a

time.

C: Organelles within the

cells.

D: Bacteria.

E: Viruses .

LOW

POWER

27

Dr. Warren thought he saw:

• Helicobacter pylori (a new species of bacteria)

• But no one else believed him!

The black squiggly spots on the slide

are bacteria that Dr. Warren observed

In his biopsy slides.

28

CQ6: Dr. Warren’s colleagues did not believe

there were bacteria in the stomach. Why do you

think other pathologists did not believe bacteria

were in the stomach biopsies?

A: Bacteria are never found inside the human body.

B: The pH of the stomach is too acidic for any bacteria to survive.

D: Ulcers and stomach cancer are caused by age, stress and diet – bacteria have nothing to do with the problems the patients came to the hospital for.

29

So, Dr. Warren:

• Used a special stain

that highlights

bacteria on his

slides.

• This convinced his

colleagues that the

bacteria were there.

30

Talk to your neighbor

• Dr. Warren thinks H. pylori causes

ulcers.

• What is another hypothesis to explain

why Dr. Warren was finding bacteria on

his slides? (there are at least three

alternative hypotheses...)

31

Alternative explanations

(hypotheses):

1. The biopsy specimens were contaminated AFTER samples were taken from the patients.

2. The bacteria live in the stomach, but do no damage.

3. The bacteria are an opportunistic species that arrives AFTER ulcers have already weakened the stomach’s defenses.

32

Dr. Barry J. Marshall Joins Dr.

Warren’s Research

• Hypothesis: Bacteria CAUSE stomach ulcers.

• If you were working with Drs. Warren & Marshall to design a study to determine whether the bacteria caused ulcers, how would you do it?

33

Their First Survey Study: • 100 stomach ulcer patients surveyed

(biopsy taken).

• 100% had H. pylori present.

34

CQ7: The doctors treated ulcer patients

with antibiotics to see if the disease

stopped. What is missing from their study?

A: An experimental treatment.

B: A control group.

C: An independent variable.

D: A dependent variable.

E: A hypothesis.

35

Important Aspects of

Experimental Design

• Testable hypothesis, i.e., a way to measure a

response and a way to divide groups up into:

• Control and Treatment Groups

– Control is group that does not get the

hypothesized treatment.

– Treatment is group that does get the

hypothesized treatment.

36

The Importance of Controls

Why do we need controls? Explain to

your neighbor …

37

If they set up their antibiotic study with a treatment

group receiving antibiotics and a control group

receiving a placebo (no antibiotics), what results

would you expect if the original “excess acid

hypothesis” was supported?

Control Experimental

Num

ber

of ulc

ers

aft

er

2 m

onth

s

38

CQ8: What results would you expect if the old

“excess acid hypothesis” were supported? N

um

ber

of ulc

ers

aft

er

2 m

onth

s

Num

ber

of ulc

ers

aft

er

2 m

onth

s

Num

ber

of ulc

ers

aft

er

2 m

onth

s

Nu

mb

er

of ulc

ers

aft

er

2 m

onth

s

Con Exptl

Con Exptl Con Exptl

Con Exptl

A B

C D

39

What results would you expect if Drs.

Warren and Marshall’s “bacteria cause

ulcers” hypothesis is supported?

Control Experimental

Num

ber

of ulc

ers

aft

er

2 m

onth

s

40

CQ9: What results would you expect if the “bacteria

cause ulcers hypothesis” were supported? N

um

ber

of ulc

ers

aft

er

2 m

onth

s

Num

ber

of ulc

ers

aft

er

2 m

onth

s

Num

ber

of ulc

ers

aft

er

2 m

onth

s

Nu

mb

er

of ulc

ers

aft

er

2 m

onth

s

Con Exptl

Con Exptl Con Exptl

Con Exptl

A B

A D

C

41

Actual Results of Warren &

Marshall’s Study

• When treated with antibiotics, 80% of patients were permanently cured of their ulcers.

• To further demonstrate the cause and effect relationship, Dr. Marshall (who did NOT suffer from ulcers), swallowed a flask of H. pylori from the lab. – Within a week he was suffering from symptoms of

gastritis and had H. pylori populations in his stomach!

– He cured himself with an antibiotic treatment.

42

CQ11: If you were shown the results of the

Warren & Marshall antibiotic study, you

would conclude:

A: The excess acid hypothesis is supported and is the best explanation for the causation of ulcers.

B: The bacteria cause ulcers hypothesis is supported and is the best explanation for the causation of ulcers.

C: The excess acid hypothesis has not been overturned, but bacteria might have something to do with ulcers.

D: This study supports the bacteria cause ulcers hypothesis, but I need more evidence.

43

EPILOGUE

44

Medical doctors worldwide were

NOT easily convinced

• Drs. Warren and Marshall had trouble getting their results published in scientific journals and presenting results at scientific meetings.

• It took over 15 years and many more studies from researchers all over the world, before the “bacteria cause ulcers” hypothesis was accepted by the medical community.

45

Drs. Warren & Marshall win the 2005

Nobel Prize in Medicine & Physiology

The Nobel Prize committee recognized

Warren & Marshall’s work changed peptic

ulcers from one of the world’s most

common chronic, debilitating diseases to

one easily cured with a simple drug

regimen.

Opened new avenues of research -

microbial causes of other chronic

inflammatory diseases.

Also increased understanding of links

between chronic infection, inflammation,

and cancer.