Вы находитесь на странице: 1из 40

Lecture 1

Introduction to Molecular Biology


&
Experimental Designs
Molecular Biology?
• Deals with the nature of biological phenomena
at the molecular level through the study of DNA and
RNA, proteins, and other macromolecules involved
in genetic information and cell. (Kernerman Webster)
• The study of biological phenomena at the molecular
level (Collins dictionary)
Who were the pioneers?
o Charles Darwin (1809-1882) (The origin of species)
o Antony van Leeuwenhoek (1632-1723); Robert
Hooke (1635-1703); Theodor Schwann (1810-1882);
Matthias Schleiden (1804-1881) (Cell theory)

Darwin
What happened next?
• Followed by influx of research on genetic
materials in cells
• Discovery of DNA, composition of genes,
relationship between genes and proteins, gene
cloning
• Ian Wilmut and his colleagues cloned Dolly from
adult cell (1997)
• Completion of the human Genome Project (April
2003)
• The “Omics” era
Key areas in Molecular Biology

• Recombinant DNA Technology


• Gene Expression and Regulation
• Structure and function of biological
macromolecules
• Genomics, proteomics, bioinformatics
Some applications of MB
• Agriculture (GM crops, improved traits crops)
• Medicine (Gene therapy)
• Food industry
• Industrial (enzyme production)
• Forensic science
• And many more…..
Part 2:
Experimental Design
Basics of Experimental Design
• Common sense

• Biological insight

• Careful planning
Why do we need to design experiments?
• To minimize:
• random variation
– inter-sample variation,
– within-treatment variation (noise)

• To account for:
• confounding factors
– Confounding variables
– Variables that affect the relationship (the data you
are collecting) between independent variable and
dependent variable (False correlation)
– As a result, you may ended up analysing the
results/ data incorrectly.
– Eg. third variables
Stages in Experimental Design

1. Preliminaries
2. Structure
3. Measurements
4. Final checks
1. Preliminary : Define hypothesis
Experiments should be focused:

Question

Hypothesis

Prediction
2. Structure:
How to test the hypothesis?
• Correlational study
• Use of naturally occurring variation
• No (as little as possible) investigator interaction

• Manipulative study
• Studying the effects of artificial manipulation
• The investigator does something to the subject of
study in order to find out the effects this
manipulation has on a particular process or system
a. Correlational study
• Advantages:
• Easier
• Saves time and effort
• Does not cause any unintended harm to the
subject
• Biologically relevant variation

• Disadvantages:
• It is affected by third variables
• It is affected by reverse causation
b. Manipulative study
• Advantages:
• Not affected by third variables
• Not affected by reverse causation

• Disadvantages:
• Difficult
• Longer & involves more work
• May cause unintentional harm to the subject of study
• The manipulation may not be biologically relevant
Third variables and reverse causation?

Example:
Study on the relationship
between Fetal Development and
Gum Disease
E.g. of third variables and reverse causation

Situation 1
Gum disease (Variable A) in pregnant
mothers causes abnormal fetal
development (Variable B) .
The abnormal fetal development leads to
lower birth weights. Perhaps the mother’s
immune system is using too much energy to
fight off the disease — energy that then is
not available to the developing fetus.
E.g. of third variables and reverse causation

Situation 2
Abnormal fetal development (Variable B)
causes gum disease in pregnant mothers
(Variable A) Perhaps the abnormal
development is sapping the mother’s
strength, thereby leaving her more
vulnerable to various diseases.
Situation 3
A third variable (Variable C) causes the
development of maternal gum disease
(Variable A) and abnormal fetal
development (Variable B) .
Perhaps impoverished pregnant women
(poverty being an unmeasured third
variable) are less likely to have adequate
health care, which leaves both the women
and their developing fetuses more
vulnerable to disease.
Deciding on the appropriate
approach
The decision depends on the research
questions
• Field vs. Laboratory
• in vivo vs. in vitro
How to control random variation
or noise?
• Replication
• Measurements on a number of independent
experimental subjects that have been subjected to
the same manipulations

• Randomization
• Random samples from a large population of
individuals
• Beware of haphazard sampling
Watch out for pseudoreplication!
• If the samples (or experimental subjects) are not
independent,
• Experiment is being pseudoreplicated; not replicated

• Examples:
• Multiple measurements on the same individual as if they
were independent measurements
• Measurements taken from genetically related individuals
are not independent
Controls
• A control is:
• A reference against which the results of an experiment can
be compared
• Negative control
• The control group is not subjected to any manipulation or
treatment
• Positive control
• The control group is manipulated in the same way as the
treatment group

An experiment is considered flawed if it has


no control!
All experiments require a control!
3. Taking measurements
• Calibration
• Possible errors:
• Inaccuracy and imprecision
• Intra-observer variability
• inconsistency in a observer
• Inter-observer variability
• inconsistency in between more than one observer
• Observer effects
Recording data
• Don’t try to take too many measurements or too much data at
once

• Be careful of using shorthand codes

• Keep experimental data in more than one copy

• Keep a detailed record of the experimental protocol

• Keep an up-to-date record of the experiments in a field


journal or lab book

• Do not overwork

Can you read this?


Sampling schemes
• Random sampling (most commonly used)

• Sequential sampling

• Stratified sampling

• Systematic sampling
Sampling schemes
1. Random sampling (most commonly used)
• Subject chosen by a method involving an unpredictable
component.
• Sampling error: random variation in the results.

Why?: The sample usually is not a representative of the


population from which it was drawn.
• However, in the case of random samples, mathematical theory is
available to assess the sampling error.
• Thus, estimates obtained from random samples can be
accompanied by measures of the uncertainty associated with the
estimate. Eg: Standard error
Sampling schemes
2. Sequential sampling
• The researcher picks a single or a group of subjects in a given time
interval, conducts his study, analyzes the results then picks another
group of subjects if needed and so on.
• Provides limitless option when it comes to sample size and
sampling schedule.
• Enables the researcher to fine-tune his research methods and
results analysis.
• It is not expensive, not time consuming and not workforce
extensive
• Drawback: This sampling method is hardly representative of the
entire population. Its only hope of approaching representativeness
is when the researcher chose to use a very large sample size
significant enough to represent a big fraction of the entire
population.
Jan 2014 May 2014 Oct 2014
Collect data, analysis Collect data, analysis Collect data, analysis

Conclusion
Sampling schemes
3. Stratified sampling
• Is a method of sampling from a population.
• Stratification: the process of dividing members of the
population into homogeneous subgroups before sampling.
Every element in the population must be assigned to only
one stratum. The strata should also be collectively
exhaustive: no population element can be excluded.
• Proportionate allocation uses a sampling fraction in each of
the strata that is proportional to that of the total population.
For instance, if the population consists of 60% in the male
stratum and 40% in the female stratum, then the relative size
of the two samples (three males, two females) should reflect
this proportion.
• Drawback: It is not useful when there are no similar
subgroups.
http://www.formyschoolstuff.com/school/math/glossary/s.htm
Sampling schemes
4. Systematic sampling
• Is a random sampling technique which is frequently chosen by
researchers for its simplicity and its periodic quality.
• In systematic random sampling, the researcher first randomly
picks the first item or subject from the population. Then, the
researcher will select each “n”'th subject from the list.
• For example, the researcher has a population total of 100
individuals and need 12 subjects. He first picks his starting
number, 5. Then the researcher picks his interval, 8. The members
of his sample will be individuals 5, 13, 21, 29, 37, 45, 53, 61, 69,
77, 85, 97.
• Starts from No.2
• Take sample from every third person
Supporting materials:
https://www.youtube.com/watch?v=SMGRe824kak
Preliminaries
Structure
Measurements
Final Checks
Self study:
1. Experimental Design in Science: Definition and Method
(Youtube: https://www.youtube.com/watch?v=7q8acfBx5to)
2. Understanding Research Design:
(Youtube: https://www.youtube.com/watch?v=kJ01TMt0XJk)
3. The Scientific Method:
(Youtube: https://www.youtube.com/watch?v=tUP8rFWzVt4)

References:
1. Graeme D. Ruxton and Nick Colegrave (2003) Experimental Design for
the Life Sciences. Oxford University Press, Oxford, UK.
2. Alan G. Clewer and David H. Scarisbrick. (2001) Practical Statistics and
Experimental Design for Plant and Crop Science. John Wiley & Sons Ltd.
3. Gerry P. Quinn, Michael J. Keough (2002) Experimental Design and Data
Analysis for Biologists. Cambridge University Press, Cambridge, UK.
4. bio.hubu.edu.cn/doc/fenzi2.ppt
Take away key points
• How to design your own experiment?
• Experimental design
1. Preliminaries: Question, Hypothesis,
Prediction
2. Structure: Correlational study,
Manipulative study
3. Taking measurements: Random sampling,
Sequential sampling, Stratified sampling,
Systematic sampling
4. Final checks

Вам также может понравиться