basic science partnership (bsp)

Course reading Text: GLASS, J. D. (2007): Experimental

Design for Biologists. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

Supplement reading: CERF, O. et al. (2009) : Tests for determining in-use concentrations of antibiotics and disinfectants are based on entirely different concepts: “Resistance” has different meanings. International Journal of Food Microbiology 136, 247–254.

Syllabus 4 discussions/ lectures

Individual talks from different labs

Last session of course your presentations from your lab projects

Independent Project/Presentation Each student should create a 15 minute

PowerPoint presentation on the current lab project

Explain: 1.basic biology behind the mechanisms being

researched 2.include techniques as a methods section Your results section (optional)

Outline for our course: Session 1

Book chapters 1-9 Session 2

Book chapter 10, plus additional paper Session 3

Book chapters 11-14 Session 4

15-19 Quiz

This time ... Since you did not have the book so far I will cover the

first chapters today and you should read them up until next time.

Additional literature: Supplement reading: CERF, O. et al. (2009) : Tests for

determining in-use concentrations of antibiotics and disinfectants are based on entirely different concepts: “Resistance” has different meanings. International Journal of Food Microbiology 136, 247–254.

CHAPTER 1-9Key words:

Hypothesis

Problem/Question framework

System establishment

Model building

Philosophy of Science by Sir Karl Raimund Popper

Why do we set up hypothesis in science today? Karl Popper:

Born in Vienna, Austria worked in London, UK Schools:

Analytic Critical Rationalism Fallibilism Evolutionary epistemology Liberalism

Source: http://www.nndb.com/people/164/000087900/

Philosophy of Science by Sir Karl Raimund Popper How did Popper developed his ideas about

science and philosophy?

Source: http://www.nndb.com/people/164/000087900/

Philosophy of Science Sir Karl Raimund Popper

Physical world

Subjective personal perceptions

Objective abstract products of the human mind

Source: http://www.knowledgejump.com/knowledge/popper.html

Who was Popper? He attended the local Realgymnasium Went to the University of Vienna in 1918 In 1919 Popper joined the left-wing politics,

the Association of Socialist School Students, Soon abandoned it entirely because of the doctrinaire character.

Karl R. Popper (1902-1994) He discovered the psychoanalytic theories of

Freud and Adler, and listened entranced to a lecture which Einstein gave in Vienna on relativity theory.

The dominance of the critical spirit in Einstein, and its total absence in Marx, Freud and Adler, struck Popper as being of fundamental importance.

Karl R. Popper (1902-1994) For Popper the critical spirit in Einstein

theory had crucial and testable implications which, if false, would have falsified the theory itself.

The total absence of critical spirit in Marx, Freud and Adler, couched in their theories in terms which made them amenable only to confirmation.

Karl R. Popper (1902-1994) The dominant philosophical group in Vienna

at the time was the Vienna circle, the circle of ‘scientifically-minded’ intellectuals.

The principal objective of the members of the Circle was to unify the sciences, which carried with it, in their view, the need to eliminate metaphysics.

Karl R. Popper (1902-1994) Popper became increasingly critical of the

main tenets of logical positivism. He articulated his own view of science, and

his criticisms of the positivists, in his first work, published under the title Logik der Forschung in 1934.

Karl R. Popper (1902-1994) The book attracted more attention than

Popper had anticipated. Popper was invited to lecture in England in

1935. The growth of Nazism in Germany and

Austria compelled him, like many other intellectuals who shared his Jewish origins, to leave his native country.

Karl R. Popper (1902-1994) After a teaching position in New Zealand in

1937 he finally moved to England in 1946 to teach at the London School of Economics, and became professor of logic and scientific method at the University of London in 1949.

His ideas finally became so prominent that biological science almost always starts with formulating a hypothesis.

What is a hypothesis? Definition:

A research hypothesis is the statement created by a researcher when they speculate upon the outcome of a research or experiment.

Why do we need hypothesis in science?

Every true experimental design must have this statement at the core of its structure, as the ultimate aim of any experiment.

Hypothesis Usually the hypothesis is the result of a

process of inductive reasoning where observations lead to the formation of a theory. Scientists then use a large battery of deductive methods to arrive at a hypothesis that is testable, falsifiable and realistic.

Hypothesis If a research hypothesis, stands the test of

time, it eventually becomes a theory, such as Einstein’s General Relativity.

Even then, as with Newton’s Laws, it can still be falsified or adapted.

Hypothesis The precursor to a hypothesis is a research

problem, usually framed as a question.

The research hypothesis is a paring down of the problem into something testable and falsifiable.

What is Critical Rationalism?

Popper rejected the term of classical empiricism, and of the classical observationalist-inductivist account of science that had grown out of it.

What is Critical Rationalism? Scientific ideas can only be tested

indirectly because scientific theories are abstract and human knowledge generally, is irreducibly conjectural or hypothetical, and is generated by the creative imagination of humans.

What is Critical Rationalism? No number of positive outcomes at the

level of experimental testing can confirm a scientific theory, but a single counterexample is logically decisive: it shows the theory, from which the implication is derived, to be false.

Hence falisfication

What does it mean a hypothesis is falsifiable?

The term "falsifiable" does not mean something is false; rather, that if it is false, then this can be shown by observation or experiment.

Popper's account of the logical asymmetry between verification and falsifiability lies at the heart of his philosophy of science.

What does it mean a hypothesis is falsifiable? Falsifiability, as defined by the philosopher, Karl

Popper, defines the inherent testability of any scientific hypothesis.

Science and philosophy have always worked together to try to uncover truths about the world and the universe around us. Both are a necessary element for the advancement of knowledge and the development of human society.

When is a hypothesis not practicable? Human Genome Project Why did scientists not set out a hypothesis

such as: “There are ten genes in the genome involved

in insulin production”

Source: http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml

Difference between critical rationalist and question/answer framework Critical Rationalist : Here the scientist uses

prior knowledge to frame a hypothesis and formulate a conclusion about the unknown.

Question/answer methodology:

The scientist uses prior knowledge upon which to ask a question about the unkown.

CHAPTER 4

Comparing the different approaches

Decide on an experimental project

Make a hypothesis Subject the hypothesis to

falsification Get a result Determine whether the

result holds true in repeating

Decide on an experimental project

Ask a question Get an answer Ask the question again

and observe its accuracy

Critical Rationalism Question/answer mode

A system of sequential queries Why don’t you set up a

hypothesis to walk to Harvard Medical School when you are at Boylston Street ?

A system of sequential queries You could formulate a

hypothesis:

“Walking on Boylston towards Brookline will take me to LHRRB in the Longwood area.”

A system of sequential queries You could formulate a

hypothesis:

“Walking on Boylston towards Brookline will take me to LHRRB in the Longwood area.”

This hypothesis can than be subjected to falsification.

Why don’t we do that?

What is the inductive space? The background information that is already

existing about a specific question prior to the study

Example in Chapter 6: Why can the question be:

“What is the function of MuRF1?” given we know MuRF1 is a protein.

Types of questions The open- ended question

“What color is the sky?” Define the scope of the problem

The close- ended question “The sky is red” Two analyses:

Red, not- red

Discrete questions Not all open- ended questions are all

encompassing

Project A Project B

Which genes are implicated in glucose metabolism

What is the function of gene X?

What is the role of gene X in glycose metabolism ?

Discrete questions

Project A Project B

Which genes are implicated in glucose metabolism

What is the function of gene X?

What is the role of gene X in glycose metabolism ?

?

Discrete question afterprojetc study

Inductive reasoning Initial observation lead to the discovery of a

certain pattern. This allows a tentative prediction to be made

which leads to a general theory about how things work.

Inductive reasoning Charles Darwin for example observed the

variety of Darwin finches on the Galapagos islands and based on that build his theories.

Inductive reasoning After some thought and reasoning, he saw

that these populations were geographically isolated from each other and that the variation between the sub-species varied over distance.

Inductive reasoning He therefore proposed that the finches all

shared a common ancestor, and evolved and adapted, by natural selection, to exploit vacant ecological niches. This resulted in evolutionary divergence and the creation of new species, the basis of his ‘Origin of Species’.

Inductive reasoning This was an example inductive reasoning, as

he started with a specific piece of information and expanded it to a broad hypothesis. Science then used deductive reasoning to generate testable hypotheses and test his ideas.

Inductive reasoning In the lab nowadays you do not have to travel

to the Galapagos islands in order to expand your inductive space.

You would rather

consult a computer

and do a web search

Deductive reasoning Deductive reasoning is what most scientists

recognize as the standard scientific method, where a researcher starts with a wider theory.

The researcher generates a testable hypothesis and designs an experiment to observe the results, and prove or disprove the theory.

Deductive reasoning Deductive reasoning, starts with a general

principle and deduces that it applies to a specific case.

Inductive reasoning is used to try to discover a new piece of information while deductive reasoning is used to try to prove it.

Deductive reasoning Example J. J. Thompson’s Cathode Ray-Experiment

was an excellent example of this process, where he had ideas about how electrons behaved and generated theories about their nature.

Therefore, Thompson generated hypotheses, designed experiments and tried to find conclusive answers to add credence and weight to his initial theory.

J. J. Thompson’s Cathode Ray-ExperimentDeductive reasoning

He found that by applying a magnetic field across the tube, there was no activity recorded by the electrometers and so the charge had been bent away by the magnet. This proved that the negative charge and the ray were inseparable and intertwined.

http://www.experiment-resources.com/cathode-ray.html#ixzz0pFB6EBah

J. J. Thompson’s Cathode Ray-ExperimentDeductive reasoning

Out of this deduction Television was developed

Thompson receiver the Nobel prize in Physics in 1906.

http://www.experiment-resources.com/cathode-ray.html

CHAPTER 6

How experimental conclusions are used to represent reality

How experimental conclusions are used to represent reality

How to build a model

What is the function of MuRF1?

What are the functions of proteins?

What category does MuRF1 proteins fall into?

Transcription factors

Phosphatases

Proteases

AcetylasesTranscription factors

Known versus unknown

Model building How does the scientist access the inductive

space in the example of MuRF1 function? The scientist uses bioinformatic tools such as

BLAST or FASTA to find out that MuRF1 belongs to a protein family referred to as

E3 ubiquitin ligases.

Model building Now the scientist has to perform an

experiment to see whether MuRF1 is an E3 ubiquitin ligase.

If the experiment is repeated and the result still indicates MuRF1 is a E3 ubiquitin ligase then the model can be stated as followinf: MuRF1 functions as an E3 ubiquitin ligase

Model buildingMuRF1 functions as an E3 ubiquitin ligase The question: What is the function of MuRF1? Is the framework question that can now be

further specified.

Refining the inductive space

What are the functions of proteins?

What is the function of E3 ubiquitin ligases?

MDM2

Skp2

CHAPTER 7Establishing a System for Experimantation

The value of positive, negative and sensitive controls in experimental designs

Need to validate your system What does it mean to validate a system? Explain the metaphor of the car.

Control serves as reference point Validating controls

The use of controls

The use of controls What is a negative control?

What is a negative control good for? To appreciate the number of times that the positive

readout was achieved compared to the negative readout

The use of controls What is a positive control? What is a positive control good for?

To ensure that the subject being surveyed can be detected

So the scientist is sure that this specific subject yields a result

The positive control Tell me what happens to the scientist

validating null cells as a negative control to detect M –cadherin

But he/she skips the necessity of a positive control…

Source: http://www.microvet.arizona.edu/courses/mic419/ToolBox/elisa3.jpg

The positive control What does this mean now? The scientist proofed that there is no antibody

recognition by the M-cadherin. Then he/she performed the experiment and

discovers that there is no M-cadherin detection.

Why?

The positive control Does it mean there is no M-cadherin

expressed by the cells? If the scientist now includes a positive control

he discovers a strong signal.

The use of controls What is a sensitivity control?

What is a sensitivity control good for? To ensure that the subject being surveyed can be

detected

CHAPTER 8 and 9Discussion Points

Designing the experiment Definitions Time courses Experimental repetition

Designing the experiment Definitions: What different colors does the

sky have? Time courses: How often do you have to

measure the sky color during the course of a day?

Experimental repetition: How often do you have to repeat an experiment in order to predict the future?

Designing the experiment Representative conditions: When would you measure the color of the

sky? An experiment has to be designed to be

studied under representative conditions.

Analyzing the data and interpreting the experiment

1/1/07 1/2/07 1/3/07 1/4/07 1/5/07 1/6/07 1/7/07

6:05 a.m. black black black black black black black


6:15 a.m. black black black black black black gray


6:25 a.m. black black black black black gray gray

6:30 a.m. black black black black gray gray red

6:35 a.m. black black black gray gray red blue

Why repeat an experiment ?1/1/07 1/2/07 1/3/07 1/4/07 1/5/07 1/6/07 1/7/07





6:25 a.m. black black black black black gray gray

6:30 a.m. black black black black gray gray red

6:35 a.m. black black black gray gray red blue

The choice of experimental controls

1) Record data over a specific range of light wavelenghts

2) Position the instrument in a particular direction

3) Decide upon which time period you record 4) Regular and particular intervals during

time period 5) Repeat the time course a number of times

Reading material for next time Session 2 Book chapter 10

Supplement reading: CERF, O. et al. (2009) : Tests for determining in-use concentrations of antibiotics and disinfectants are based on entirely different concepts: “Resistance” has different meanings. International Journal of Food Microbiology 136, 247–254.

Any more questions?

CHAPTER 10Determining EcoRI´s restriction site

Additional reading: CERF, O. et al. (2009) :

Tests for determining in-use concentrations of antibiotics

and disinfectants are based on entirely different concepts: “Resistance” has different meanings.

International Journal of Food Microbiology 136, 247–254.

Chapter 10 Designing the experimental project

-A biological example-

Example of experimental design: Determining EcoRI´s restriction site

Source: http://www.djblabcare.co.uk/djb/data/image/14/0/Hettich_EBA20_Portable_Centrifuge.jpeg

Designing the experimental project-cutting DNA into pieces-

How does a restriction enzyme work?

http://employees.csbsju.edu/hjakubowski/classes/SrSemMedEthics/Human%20Genome%20Project/DNA1.html

Designing the experimental project-Inserting a DNA sample into a plasmid-

Source: http://www.bio.davidson.edu/Courses/Molbio/MolStudents/spring2003/Keogh/plasmids.html

Restriction enzymes There are three different types of restriction

enzymes.

Restriction enzymes Type I Recognise specific sequences·but then

track along DNA (~1000-5000 bases) before cutting one of the strands and releasing a number of nucleotides (~75) where the cut is made. A second molecule of the endonuclease is required to cut the 2nd strand of the DNA e.g. EcoK.

Require Mg2+, ATP and SAM (S-adenosyl methionine) cofactors for function.

Restriction enzymes Type II Recognise a specific target sequence

in DNA, and then break the DNA (both strands), within or close to, the recognition site e.g. EcoRI

Usually require Mg2+

Restriction enzymes Type III Intermediate properties between

type I and type II. Break both DNA strands at a defined distance from a recognition site e.g. HgaI

Require Mg2+ and ATP

The restriction enzymes cut site:

At what sequence does EcoR1 cut DNA?

The process of ligation

Sticky ends are also known as cohesive ends.

What is a plasmid? Independently replicating extra- chromosomal

structures in bacteria.

Designing the experimental project-A biological example-

Can other cells get our modified DNA plasmids too?

Two classes of plasmids:

Conjugative Non-conjugative

Conjugative plasmidsHorizonal gene transfer: The tra genes encode some of

the proteins required for the manufacture of a pilus - macromolecular tube that joins one cell to another and allows the transfer of plasmids

The ORI site: What is an origin of replication (ORI)?

Source: http://homepages.strath.ac.uk/~dfs99109/BB211/Plasmidnotes.html

Designing the experimental project-A biological example- Still, do we know now if the cell “swallowed” the

DNA junk or not?

Plasmids are maintained in cells due to selective pressure - the ability to confer an advantageous phenotype

What can plasmids do? Phenotypes that can confer advantage to a host cell

include Antibiotic resistance, Antibiotic production Sugar fermentation for energy Degradation of aromatic compounds for energy Heavy metal resistance Toxin production

Designing the experimental project-A biological example- Why can’t we pour our

bacterial culture in the trash? Why not it is just bacteria? Bacterial resistance to

antibiotics.

DNA uptake into bacterial cells Natural

Transformation Conjugation Transduction

Artificial Electroporation Bacteriophages Lac operon, blue/ white selection Chemical through substances such as CaCl2

Examples of Horizontal gene transfer

So how does the modified DNA come into a cell?

Source: http://biogetopics.wordpress.com/2008/11/27/bacterial-resistance/

Artificial techniques for DNA uptake Electroporation Bacteriophages Lac operon, blue/ white selection

How does DNA uptake happen in the lab?

This process is called Electroporation.

Designing the experimental project-Ampicillin resistance-

Origin of replication

How can we grow the plasmids in culture?

Source: http://picsdigger.com/keyword/ti%20plasmid/

DNA uptake by phages Phage infection

Lytic cycle Lysogenic cycle

Source: http://textbookofbacteriology.net/phage.html


The Lambda phage

Electron microscopy imageSource: http://www.bio.davidson.edu/Courses/Molbio/MolStudents/spring2003/Keogh/plasmids.html


The mechanism of infection:

AdsorptionIrreversible attachmentSheath contractionNucleic acid injection

Source: http://www.nsf.gov/od/lpa/news/02/pr0207images.htm

The lactose metabolism of E. coli Another method of plasmid uptake screening

in bacteria.

Designing the experimental project-A biological example- Prokaryotes such as the bacterium E. Coli,

have an efficient mechanism for metabolizing lactose. Three proteins that are important in lactose metabolism are all encoded in a single expressible unit odf DNA, called the lac operon.

Designing the experimental project-A biological example- The bacterium does not waste energy

expressing these proteins if lactose is not present in the growth medium. It only makes these proteins when lactose is available to be metabolized.

Designing the experimental project-A biological example- http://www.sumanasinc.com/webcontent/

animations/content/lacoperon.html

Designing the experimental project Start the engine,

please!

Designing the experimental project-Explaining the lac operon- Can we see the gene

when looking through a a microscope?

Selecting for those plasmids which have the gene of interest integrated.

Designing the experimental project

-The blue/white screening-

However bacterial colonies in general, are white, and so a bacterial colony with no vector at all will also appear white. These are usually suppressed by the presence of an antibiotic in the growth medium. A resistance gene on the vector allows successfully transformed bacteria to survive despite the presence of the antibiotic.

Designing the experimental project Blue/ white

selection

Source: www.absoluteastronomy.com/.../Blue_white_screen

Designing the experimental project-The blue/white screeing-

The hydrolysis of colourless X-gal by the β-galactosidase causes the characteristic blue colour in the colonies; it shows that the colonies contain vector without insert. White colonies indicate insertion of foreign DNA and loss of the cells' ability to hydrolyse the marker.

-The blue/white screening- Easy to pick the blue colonies from an agar

plate.

Summary of a cloning experiment

Cut Paste Insert Grow Purify

CHAPTER 10 Discussion PointBacterial resistance to antibiotics

Bacterial resistance to antibiotics Antibiotics and disinfectants

Supplement reading: CERF, O. et al. (2009) :Tests for determining in-use concentrations of antibioticsand disinfectants are based on entirely different concepts: “Resistance” has different meanings.International Journal of Food Microbiology 136, 247–254.

Designing the experimental project-A biological example- Why are antibiotics not the magic bullet and

universal use is restricted and limited?

Reading material for next time Session 3 Book chapters 11 until 14

Any questions?

CHAPTER 11 Experimental repetition: The Process of Acquiring Data to Model Future Outcomes

Categories of Experimental repeats Is it sufficient if the scientist measures the

color of the sky only once? Multiple measurements at a single time point Single measurements over the course of many

days Many measurments of the sky color during the

course of the whole day Multiple measurements at different time points

Questions What does it mean to verify a model? Why is it important to find a representative of

the general case? What´s wrong if I take one rat and analyse the

mRNA expression and compare it with another rat?

Biological example

Control High-fat diet 12 hours

Rat one Rat two

Does this rat represent the General case?

So how many rats shall we take?

CHAPTER 12 The negative control

Discussion points

The negative control Definition: A setting where the experimental

subject is not perturbed by the variable under study.

“Unperturbed by X”

The negative control- The caffeine/blood pressure example Control for relevant

variables Measure “X” and tell

from “not-X” Want to measure only

“X and only X” is varied

Caffeine or something else in the Coffee?

Does caffeinated coffee affect blood pressure, and if so, is the caffeine responsible? In this questions there are two variables

Factor X

Coffee (with all its ingredients)

Caffeine

Study design

Establish six groups each 50 people Determine the subjects` starting blood

pressure. Take initial blood and urine samples. Get only people with a blood pressure range

between 140/90 and 90/60. Match study subjects by gender

Study design

Body mass index should be ranging between 19 and 40.

Match groups for average BMI, age, normal diet

Exclude people with anxiety disorders or hypertension.

Group settings

Group Treatment

A

B

C

D

E

F

No treatment

Water

Decaffeinated coffee

Caffeinated water

Caffeinated coffee

Caffeinated cola

Group controls

Group Treatment

A

B

C

D

E

F

No treatment: Unperturbed by any change

Water: Unperturbed by additional ingredients in coffee

Decaffeinated coffee: Unperturbed by coffee

Caffeinated water: Unperturbed by coffee

Caffeinated coffee: The actual test case

Caffeinated cola: Assumption control

The negative control

Group A

Group B


Caffeinated coffee

Why is it not enough to have only two groupscaffeinated and Decaffeinated coffee?


Group A

Group B


Caffeinated coffee

10% increase in blood pressure


The negative control- study design


Caffeinated coffee



Caffeinated water 10% increase in blood pressure

The negative control- study design


Caffeinated coffee




Water 5% increase in blood pressure

Why is it necessary to have the just water control?

The negative control-study design


Caffeinated coffee





Caffeinated cola

Nothing 0% increase in blood pressure




Caffeinated coffee





Caffeinated cola

Nothing 0% increase in blood pressure


Intrasystem/intersystem control Difference between

The intrasystem negative control A negative control provides a point of contrast to

ensure unbiased measurement measures “not-X”

The intersystem negative control “unperturbed by X” control X is the system being

applied Ensuring the system is not in itself perturbing the

outcome

CHAPTER 13 The requirement for the positive control

Discussion Points

The positive control Is the system capable of detecting the

experimental readout? A demonstration that a measuring system is

operational positive control

The positive control

Treatment % Increase in blood pressure

Water 10

Caffeinated water 10

The positive control

Treatment % Increase in blood pressure

Water 10

Caffeinated water 10

Hypertensive drug 30

The positive controlTreatment % Increase in blood pressure

Water 10

Caffeinated water

10

Hypertensive drug 30

Caffeinated water; caffeine equivalent Of one cup of coffee

Caffeinated water; caffeine equivalent Of two cups of coffee

Caffeinated water; caffeine equivalent Of three cups of coffee

Caffeinated water; caffeine equivalent Of four cups of coffee

12

15

20

The experimental design

A

B

C

D

E

F

Group Treatment

No treatment

Water

Noncaffeinated coffee

Caffeinated water

Caffeinated colaCaffeinated cola

Caffeinated coffee

Why can the “caffeinated cola” group not be a positive control?

The positive control Remember: The question to address was: Does caffeinated coffee affect blood pressure

and if so, is the caffeine responsible? A positive control has to be capable of

detecting the readout What is the readout in our case?

The experimental design

A

B

C

D

E

F

Group Treatment

No treatment

Water

Noncaffeinated coffee

Caffeinated water

Caffeinated coffee

Caffeinated cola

More positive controls… Is this positive control enough? What other benefits from an additional

positive control does the author point out?

CHAPTER 14 Method and Reagent Control

Discussion Points

Method and reagents controls Is a single

methodology or reagent causing an effect?

Or is there some unseen additional mechanism that is missed?

Method and reagents controls The method applied might yield different results

individual scientists use uniform approaches. Is a cell biologist using the same methods as a

pharmacologist?

Method and reagents controls Is a lawyer supposed to know how to measure

blood pressure? What was the point the author illustrated in

this chapter?

Method and reagents controls The reagents (e.g.: small molecules, genetic

constructs, antibodies, detection tools...)

Method and reagents controls The methodology control

Method 1

Method 2

A second mechanism that controlsfor the first method used

A ‘NON-Method 1 control”

Reading material for next time BSP Session 4 Chapters: 15-19

Any more questions?

CHAPTER 15 Subject controls

Discussion Points

Finding a responsive subject The study subject has to representative the

“typical” case? What is the typical case?

Do these boys represent a typical case?

Can we take all people for a weight loss study?

Subject control What example does the author give?

Is it suitable to choose only highly motivated people for a study on a weight loss drug?

Does it matter if a cancer drug can only help people with a certain gene mutation? As long as it helps someone.

Why control for a particular subject type?

Randomizing study subjects After a screening process Patients do not know which group they are in The scientist is not able to pick study subjects

and assign them to a specific group

Double blinded studies Why do scientists use

double blinded trials?

What is the difference between single and double blinded?

Matching subject controls in some studies Animal experiment No chance of an placebo effect in animals

Matching study subjects Great variation in the

experimental output

Matching study subjects

Do all mice have the same strenght?

Matching study subjects In order to yield results the scientist will

distribute individual animals into certain groups.

Alternatively one has to expand the group size manyfold, which can be problematic.

Why can it be problematic?

Variables and genetic “Model systems” Clonal strains of animals were producted over

the last century that scientists use today. There are many identical inbreed mice strains,

fruit flies, worms, zebra fish frogs and even single-celled brewer´s yeast as genetic model systems available nowadays.

Variables and genetic “Model systems” Can we compare a fruit

fly to humans?

Variables and genetic “Model systems” Many findings in animals will eventually be

found to hold in humans too. But what if our gene of interest is under the

influence of another gene and alters its function?

We are missing effects induced by particular genetic variations.

Who was Gregor Mendel? Gregor Johann

Mendel (1822 - 1884) was a member of an Augustinian order in Brunn, Austria.

http://kentsimmons.uwinnipeg.ca/cm1504/mendel.htm

How can we study gene functions? One way to study the function of a gene is to

delete its function in the genome. This is called knock out. The mice are said to

be genetically null for this particular gene.

How to make a know- out mouse

F1

1:2:1

Parents

How to make a know- out mouse

F1

+/ko +/ko

Only about 25% of the progeny in F2 will be homozygoze for the knock out.This has to be phenotypically determined.

ko/ko

heterozygot

Variables and genetic “Model systems”

What if all humans would be the same?

Could we then conduct genetic studies in humans?

The genetic background of genes

Changing the genetic background-Congenic inbred strains-

Heterozygous and homozygous subject controls It makes a difference

which genetic background your experimental animal has?

The use of cell cultures Why do we use cell

cultures in biological experiments?

CHAPTER 16Discussion Points

Assumption control

Good efficacy of drug X In early stage cancer

patientsEnd stage cancer patients

Does our drug help patients in the advanced cancer stage too?

Assumption control



Shall we simply increase the does of the drug? Why not?

Assumption control



How can we assume that late stage cancer patients respond in the same way as early stage patients?

Assumption control



The assumption control would be a group of subjectswith end- stage cancer.

Because... ?

Assumption control



The early stage cancer group does not represent the end stage cancer group

CHAPTER 17Experimentalist Controls

Discussion Points

What is the “objective truth”? Accessible from different angles Intersubjective Independent

Intersubjectivity What if only one scientist observes something

and others can not confirm this finding is the scientist then wrong?

Intersubjectivity If you find one million people that believe

there are kangaroos in Austria does this testify your observation to be true?

Intersubjectivity Intersubjectivity relies on “Objectivity” Objectivity does not require any “believe” or

any “help” from the person observing.

Establishing Objectivity

Different evaluators Why don’t just all scientist do some research

by themselves? Wouldn’t this accelerate the scientific

progress? More scientists can work on more questions

and more things could be discovered in a shorter period of time.

Why not?

Different evaluators The principal investigator will interpret the

data to prevent bias the PI will check with different evaluators

Different evaluators The structure of a science labs

The principal investigator

Postdoctoral fellowsGraduate students

Research assistant

PhD studentsOther laboratories

Computers

Different evaluators More than one scientist Research is done in

groups Remember method and

reagents control Discussing results in

groups is important

CHAPTER 18A Description of Biological Empiricism

Discussion Points

What is Empiricism? It is a theory of knowledge that asserts that

knowledge arises from sense experience. Empiricism is one of several competing views

that predominate in the study of human knowledge, known as epistemology.

What is Empiricism? Empiricism emphasizes the role of experience

and evidence, especially sensory perception, in the formation of ideas, while discounting the notion of innate ideas.

Finding causal links in biological systems

Factor C Factor B

Factor A

Specific phenotype

Assigning causality and assessing the requirements for necessity and sufficiency

A B A can be either necessary (=required) for B

or Sufficient to result in B

Finding causal links in biological systems A causes B

Eating fatty food(A)

Heart disease (B)

Finding causal links in biological systems However, heart diseases may only develop in

people with high cholesterol levels.


Heart disease

+High cholesterol levels

Finding causal links in biological systems So, does it mean eating fatty food causes

heart disease?


Heart disease

+High cholesterol levels

Finding causal links in biological systems Aren’t there people suffering a heart attack

without eating fatty food too?

Finding causal links in biological systems Therefore eating fatty foods may neither be

necessary nor sufficient to result in heart attacks in individuals with high cholesterol levels.

Finding causal links in biological systems Yet, the consumption of fatty food may

demonstrably cause heart attacks in those with high cholesterol levels.

Thus, a causal link may exist only in a particular context.

Determining causal links in biology Gene A and Gene B have to be simultaneously

deleted in order to observe a change in the ear phenotype.

Gene A

Gene B

Determining causal links in biology Statement one: Neither Gene A nor Gene B is required or

sufficient for the phenotype.

Gene A

Gene B

Determining causal links in biology Statement two: In the absence of one gene both Gene A and

Gene B are necessary and sufficient for the ear phenotype.

Nonuniversal truth Lots of biological experiments are gigantic

and thus only a small nonreproducible result might be yielded.

Nonuniversal truth Critics will point out that the future case

might be different.

Remember the elephants metaphor!

So does this mean empiricism is flawed?

Thank you for your participation

basic science partnership (bsp)

Documents

karl popper

vienna circle

sir karl raimund popperhow

sir karl raimund popperwhy

different concepts

different meanings

book chapters

different labs