Lecture 1

1. What two features do all scientific theories have?

All scientific theories must accurately describe a large class of observations on the basis of a
model that contains only a few arbitrary assumptions. They must also make definite
predictions about the results of future observations.

2. Is it important to be able to define science? Use an example in your answer.

Yes, it is important to be able to define science. Something can only be defined as science if
it is supported by empirical evidence (data) from repeated observations. Furthermore, it is
important to have a skepticism for anything presenting itself as science, and peer review
and
discussion can help further corroborate its accuracy.

If science is not properly defined, we (the public) may mistake false information for science.
For example, in 1948, a child psychology expert named Dr. Benjamin Spock published a
childcare book that included the advice that babies should be placed on their fronts to
sleep.
This was later determined to be untrue and in fact, could pose a health risk for infants. Dr.
Spock’s advice did not have empirical evidence to support his claims, therefore, it is not
considered as science.

3. How does scientific expertise differ from opinion?

Scientific expertise can only come from the accumulation of empirical evidence from
repeated experimentation. It must also have a theoretical framework to interpret it, and a
public discussion to evaluate it. An opinion, on the other hand, can be held by anyone and
does not require anything to evaluate its accuracy.

4. Discuss an example of a recent case where ignoring scientific evidence by “experts”

has led to children dying.
In 2017 (this year), a 10 year old child diagnosed with a malignant liver tumor was advised
to
undergo chemotherapy by an oncologist in Australia. As the child’s parents had thus far
been
treating the child with natural therapies (ie. fruit, vegetables, herbs and the application of
mud/clay to her body), they did not want to treat her with chemotherapy which they
believed
would kill her.

Ignoring the oncologist’s advice, the parents brought her to a General Practitioner (GP) in a
clinic to evaluate the tumor. The parents were facing a court hearing that could have passed
a
motion to treat the child with chemotherapy regardless of whether the parents gave their
consent or not. After reviewing a CT scan and an ultrasound, the GP informed the parents
that the tumor had shrunk, leading the parents to believe that their natural therapies were
working. The GP also provided a fitness to fly certificate, allowing the child to fly with her
parents to South America in an attempt to skip the court hearing.
Unfortunately, the child’s health rapidly deteriorated and she died two months later. By
ignoring scientific expertise by an oncologist (cancer expert), and listening to the advice of a
GP who is not specialized in cancer care, the child died.

Lecture 2
1. Using a diagram, explain the key steps in the scientific method. What additional step
does Peter Doherty include?
Ask a question  do background research  construct a hypothesis  test your hypothesis
with experimentation  analyze your data and draw a conclusion  report your results

After analyzing the data from the experiment, the hypothesis may be revised. If this occurs,
experimentation must be conducted again to confirm the hypothesis.

Peter Doherty’s additional step was publish – ie. publish the results of the experiment in a
journal.

2. What are the three central components of scientific thinking?

Empiricism, rationalism and skepticism. Empiricism refers to the collection of objective data
that can be verified by replication of results (these results must be similar within an margin
of
error).

Rationalism refers to logic and using natural explanations that makes sense. Occam’s razor
should be used – ie. the simplest explanation is probably the right one

Skepticism refers to questioning the accuracy of the results obtained from the experiment.
This can be conducted via an open discussion, or peer review. Peer review also works to
filter
out unnecessary components of a research publication, and improves quality.

3. What is the role of inductive and deductive reasoning in the scientific method?
Deductive reasoning refers to deducing a conclusion from 2 premises (observations). In this
type, a hypothesis must be developed first. Inductive reason refers to making an
observation
first, then reasoning from that. Here, observations must be mate and data must be
collected,
then an explanation can be induced. Once the results are modelled from an induced
explanation, they can be used in deductive reasoning to arrive to a deduced conclusion –
however, this conclusion must be tested.

4. Compare the public and scientific meaning of hypothesis and theory.

The scientific meaning of a hypothesis is an idea or explanation that must be tested through
experimentation, while a theory is a well-substantiated explanation of a
phenomenon/aspect
of the natural world.

The public meaning of a hypothesis is similar to the scientific meaning of a theory, in that it
refers to a conclusive explanation for a certain aspect of the world. The public meaning of a
theory is a guess.

The main difference between the public and scientific meanings of hypothesis and theory is
that the public meaning does not include the requirement of verification of what the
hypothesis/theory encompasses, whereas the scientific meaning does.

5. How does a skeptical scientist differ from a cynic or a denialist?

A skeptical scientist questions the legitimacy of any conclusions/results, whereas a cynic or
denialist may deny/disbelieve in theories/conclusions/results due to the promotion of their
own agenda. They may also subscribe to logical fallacies (such as red herrrings,
misrepresentation of information, jumping to conclusions, etc), cherry pick data to support
their own conclusions instead of objectively analyzing all the data available, buy into
conspiracy theories with little evidence, or have impossible expectations for what the data
should be.

Lecture 4
1. List the different types of audiences that scientists have to communicate with, and
why.
- Communicate with other scientists: this can be done via a peer review, or through an open
discussion with other scientists. Peer reviews act as a filter and improve the quality of
research as another scientist’s opinion can help identify any errors the first scientist may
have
missed while writing their research paper. Peer reviewers can also provide suggestions to
improve the quality of research. An open discussion can help a scientist gain a better and
clearer view of his research, and build on the knowledge of other professionals.
- Communicate with students: this helps students learn about science from a professional.
- Scientist to funding agency: this is important so scientists can appeal for funding for their
research.
- Scientists to government: scientists can advise governments on creating/revising their
policies to better serve the community. This can be seen in the environmental agencies,
wherein scientists who conduct research on the environment can provide the government
with empirically supported advice to pass motions that help the environment.
- Scientist to industry: scientists can advise the industry to refine and better their
procedures.
- Scientist to managers: Managers are typically the ones who make policies within a
company
happen, make and implement decisions for the company, and serve the company. Scientists
can help advise managers in terms of policies and decisions.
- Scientists to general public: scientists can help inform the general public on what is going
on in the scientific world as well as advise them.
2. What are some of the economic, democratic, cultural, political and utilitarian drivers
of science communication?
Economic – science can contribute to the national economy and individual wealth. For
example, this can be achieved through development of medicine and vaccines, GMO-foods,
stimulating milk production in cows and egg production in chickens, etc.
Democratic/Political – science can give the general public the information they require to
make educated decisions on how to vote for policies/government members, etc.
Cultural – The best science can be considered as high art.
Social – At every evolutionary stage, science underpins the development of society. For
example, in the stone, bronze, copper and iron ages, science provided the information to

utilize these elements to construct tools. In the industrial and biological sector, science
helps
refine industrial processes as well as cure diseases, provide medical treatment, etc.
Utilitarian – People owe much of their health and well-being to scientific invention (ie.
medical sector).

3. List factors affecting people’s trust in science.

- When science ignores society’s values, or fails to consult or listen to them. This can occur
when something goes wrong in research and the scientist evades responsibility. For
example,
in the case of Pfizer distribution of Trovan, a new antibiotic theorized to combat meningitis,
11 of 200 child test subjects in Nigeria died. Whether this was due to the disease or the
medication is unknown, however, Pfizer failed to provide the children involved in the drug
trial with the full information of the trial. They were therefore denied informed consent,
which is an ethical violation. However, Pfizer faced little consequence and denied that the
deaths were due to the antibiotics distributed. This is an example of how scientists can
cause
public mistrust in science by violating the ethical rights of human test subjects, and evading
responsibility for their actions.

This can also occur when scientists publish information with the intention of manipulating
the public to think in a certain way. This is also known as propaganda. Science is meant to
be
objective and unbiased; it is merely supposed to present information backed by empirical
data
and logic. When scientists publish propaganda (biased work), or are seen to be working with
a hidden agenda (for example, helping the elite and discarding the poor), public mistrust
develops.

Lastly, public mistrust in science can also arise due to fear of change, or that new scientific
revelations may result in unpredicted negative consequence. Science may also challenge
people’s ethical, moral and religious concerns.

4. What are the different levels of communication, and what is their extension to citizen
science?
- Monologue: This is when the scientist is considered the expert in the room, and delivers
knowledge to a receiver, or a group or receivers. This can be in the form of a speech or
conference, and allows scientists to convey information, and/or their research findings to
the
general public (citizens).

Dialogue: This is when scientists are in conversation, and they are all considered experts.
This allows scientists to discuss their research findings and opinions on scientific matters
with other professionals. This will help them have a better and more thorough view of their
field, and they will be able to provide citizens with more information later on.

- Debate: This is when scientists debate on a certain topic and share differing opinions.
Various opinions on a topic can be compared and contrasted to improve the quality of
science.

- Community engagement: This is when the community is involved in science. Scientists

look to citizens for their input, as well as advice on how they could proceed with their
research. In this case, the scientist is merely one partner in conversation.

Lecture 5
1. Outline what is meant by the news cycle and how social media has disrupted the
traditional cycle.
The news cycle refers to the process of how news is conveyed to the public from reporters
and/or journalists. In the 20
th
century, before the invention of the internet and social media, a
newspaper would break a story in the morning and the evening news would carry the story
and convey further reports/developments. In the 21
st
century, stories now break on Twitter
and other forms of social media such as Facebook, and are updated on these platforms as
soon as new developments take place. Only after this does the story break on traditional
media such as television and newspapers, however social media will continue to cover and
reference the store for more time.

2. Outline strategies for communicating with journalists, managers and politicians.

Journalists: If the communication is based on news, write a media release. It is also
advisable
to write a blog/youtube video and link it on social media so the story gains more traction
and
publicity. Another option is to write a letter to the editor (ie. an opinion article), or get into a
school/university publication. Lastly, media/journalists can be invited to events to cover it.

During interviews with journalists, answers should be kept short and enthusiastic, and
positives should be focused on as the media likes to sensationalize science news. Bridge
your
the journalist – this will help keep it positive. Also remember to bookend your answers so
they can cut bits off, and use examples/analogies while limiting jargon so your message can
be understood by the general public.

Managers: Advise the manager on what he needs to know so he can do a better job. For
example, this offer advice on policy refinements or adjustments.

Politicians: Advise politicians on how to refine their policies to be better in line with the
current scientific knowledge. Ex. Environmental agencies.

3. Describe the barriers to communication between managers and scientists.

Managers tend to view scientists as information brokers and disunited, as well as
infuriatingly uncertain about policy adjustments. Scientists tend to view managers as
pushing
for certainty, wanting answers to boring questions, as well as a source of resources and
influence.

4. What is the “Nana principle”? Why is this important?

The “Nana principle” is this: If it is not acceptable to Nana (ie. your grandmother), don’t post
it to social media”. This will ensure that anything posted to social media will be politically
correct and accurate, so as to maintain a reputation of professionality.

5. List 5 do’s and don’ts for communicating with politicians.

1. Do be brief and concise, don’t take up too much of their time.
Politicians are busy people and they have a lot to do. When communicating with them, be
brief and to the point so you don’t waste their time.
2. Do provide recommendations for action.
Ensure the information you give them is relevant to a particular topic and be sure to have
recommendations for action for them. This is to demonstrate the value of the information
you
provide, so that they can take it seriously.
3. Do find out who they are.
Do research on their interests, speeches and committees so you have a better
understanding of
who they are and what they stand for. You can then tailor your information to meet their
ideals and they will be more likely to hear you out. It is best to write down the important
information on a one page document

4. Do practice your speech before meeting them.

Make sure you are clear on what you plan to present.

5. Dress appropriately and be on time.

Be professional!

Lecture 6
1. What are the different types of communication that take place at conferences?
Talks, panels and posters.
2. What are three important factors in making your presentation engaging?
Passion, conviction and optimism.

3. What are the 5 sections of the 5-box talk?

4. List 4 things to check before giving a talk.

1. Know your audience (who), why they are there, and where you are (ie. a talk at a
conference and a lecture in a university will require different levels of formality) and make
sure your information is presented in a way that engages them.

2. Check that your slides are all working and all the information you need is on them.

3. Ensure you are thoroughly prepared in terms of information material.

4. Ensure you are on time and dressed appropriately.

Lecture 7
1. Describe three hallmarks that differentiate pseudoscience from science.
1. Science uses empirical data that is up to date, whereas pseudoscience uses old data, for
example, from the ancient Egyptians, if any data is used at all.

2. Science is not selective when it comes to the data used, but pseudoscience cherry picks

3. Science welcomes testing and verification, and the results are replicable over repeated
experiments. Pseudoscience does not welcome independent testings and results are
typically
not replicable.

2. List and give an example of three factors that can influence our perception.
1. Cherry picking data to draw a certain conclusion.
2. Using subjective language like “believe” to push an untrue fact.
3. Using a lot of jargon to give off the impression of reliability.

3. Compare and contrast the definitions of science, bad science and pseudoscience.
Science – follows the scientific method wherein a question is asked, background research is
performed, a hypothesis is constructed, the hypothesis is tested via repeated
experimentation,
the data is analyzed (must be similar within a margin of error), a conclusion is drawn and the
results are reported.

Bad science – Does not follow scientific method. Uses poor experimentation techniques and
thereby produces unreliable results. It also does not consider all explanations for data
results,
and tends to omit information or may be based on false assumptions/poor logic. When
reported, it may also omit important information so as to justify a wrong conclusion. The
results obtained from bad science cannot be replicated when using the scientific method.
Pseudoscience – Pseudoscience is similar to bad science in that it does not follow the
scientific method, and the results obtained cannot be replicated, but it differs in the sense
that
instead of designing an experiment to investigate a hypothesis, it looks for evidence that will
support a hypothesis. Pseudoscience is typically designed to create sensational conclusions
and can often be used as a tool for fearmongering.

4. We use the acronym FiLCHeRS to determine if something is pseudoscience. What do

the letters in the acronym stand for?
Fi- Falsifiability. This refers to the possibility of a hypothesis being proved wrong. In
science, experiments are falsifiable, and robust tests are used to evaluate it’s falsifiability.
Quantitative data is used to prove or disprove a claim, and the experiment is designed to
produce reliable results (ie. controls used, double-blind/blind experiments, replicates, etc).
Pseudoscience utilizes none of these techniques.

L – Logic. Science is logical, and arguments made are both valid and sound. Pseudoscience is
not.

C – Comprehensive. All the evidence available is analyzed in science, and the evidence
available must be exhaustive before conclusions can be drawn. Pseudoscience does not care
about having a comprehensive amount or look at evidence.

H – Honest. Science evaluates data objectively and honestly with no hidden agenda.
Pseudoscience does not.

eR – Replicable. Science produces replicable results – ie. repeated tests will produce similar
results within a margin of error. Pseudoscience does not produce replicable results.

S – Sufficiency. The evidence provided is sufficient for a conclusion to be drawn in science,

but not in pseudoscience.

Lecture 8
1. What are some of the key techniques used by illusionists to make their tricks appear
so real?

2. How does the role of the false dichotomy: utility vs validity factor into
pseudoscientific claims?
Utility refers to whether it is useful, whereas validity refers to whether it is scientifically
accurate, and whether it is supported by enough empirical evidence to reflect the claim it
represents. Pseudoscience is typically targeted towards the layman, as a scientist will be
able
to immediately identify pseudoscience. Laymen typically focus on utility – ie. whether a
certain claim will be useful to them, which is why pseudoscience holds appeal for them: it
tells them what they want to hear!

3. What makes humans continue to trust in pseudoscientific claims or products when we

have so much evidence to the contrary?
There is a public mistrust of science. This is because of several factors, but the most
important one is that science is objective and presents conclusions drawn from empirical
data. Therefore, science may not always be in line with what the public wants to hear – it ca

produce conclusions that go against someone’s religious, cultural, ethical or moral beliefs.
Science can also produce conclusions that may create a fear of unpredicted consequences in
the layman. Pseudoscience, on the other hand, does not rely on empirical data to produce
conclusions, and is typically illogical and untrue. More often than not, however,
pseudoscience makes claims that appeal to the public, ie. claims that are in line with what
the
public wants to hear. Therefore, humans continue to trust in pseudoscientific claims or
products even though there is so much evidence to the contrary.

Lecture 9
1. Modern science arose once in Western Europe – 1600. Describe how different
cultures and specific people facilitated the establishment of modern science.
In the 1600s, there were four key individuals that facilitated the establishment of modern
science. They were Sir Francis Bacon, Galileo Galilee, Rene Descartes and Sir Isaac Newton.

Sir Francis Bacon provided the structural framework from which the scientific method as we
know it today developed. He established the concept of empiricism – which means that any
scientific conclusion must be backed by data drawn from experiments. He also established
rationalism, which refers to using an inductive approach wherein conclusions are drawn
from
the results (ie. data and evidence). Thirdly, he was skeptic of Aristotle – and skepticism is
one of the foundations of science. He questioned existing paradigms and looked for
empirical
evidence to support any scientific theories/conclusions instead of just accepting everything
as
truth. He believed that scientific conclusions can only be drawn from direct observation, not
from the beliefs and writings of ancient authority figures. He also believed that for a
scientific conclusion to be deemed accurate, it must be objective, and the results must be
reproducible under multiple tests.

Galileo Galilee caused one of the biggest paradigm shifts in the scientific field by theorizing
that the Earth revolves around the Sun (the paradigm at that time was that the Sun revolves
around the Earth). He also believed in empiricism and questioning authority, two hallmarks
of a good scientist.

Rene Descartes formalized the scientific process followed by Galileo Galilee and Sir Francis
Bacon. He also rejected all ideas based on assumptions and/or emotional beliefs, and
argued

that only ideas that could be proven by or systematically deduced from direct observations
could be accepted. This is a key step in the modern scientific process. Sir Isaac Newton
discovered gravity. He believed in Occam’s razor; that the answer with the least
assumptions was most likely to be the correct one. He also argued that the same natural
effects must be assigned to the same causes, and that qualities of bodies are universal – the
first development in the definition of a scientific theory. He also contributed to the
formation of the concept of a hypothesis, by arguing that conclusions drawn from
experimental data and repeated observations should be viewed as accurate unless
otherwise corrected. Lastly, in 1660, he formed The Royal Society of London, which was the
first learned society of the times. This society allowed scientists to meet, discuss and publish
their findings, thereby sharing their expertise and improving the quality of their research.
This contributed to the development of the peer review process in modern science as well
as the concept of publishing research.

2. Who invented the numerals we use today? Why are they important to this story about
science? The early middle ages (ie. dark ages) were known as the Islamic Golden Age, as
during this time, Islamic cultures were thriving with knowledge and scientific discoveries.
The Hindu-Arabic numeric system, invented between the 1st and 4th centuries by Indian
mathematicians, was popularized during this time, and contributed to the establishment of
modern math.

3. How did Thomas Aquinas help in the development of modern science? Thomas Aquinas
was a Dominican Friar of Italy – not a scientist. However, he created the political and
religious climate which allowed science to develop in the mid 1200s. He recognized the
importance of knowledge and ordered the translation of the complete works of Aristotle
from Greek to Latin, to make it more accessible. He also integrated Greek thought into the
Church doctrine, for example, the concept of heresy and Wisdom of God. By creating an
environment where religion and science were not mutually exclusive things, and by
preserving the works of Aristotle, a great scientist of his time, he paved the way for modern
science to develop.

4. Describe the story of Archimedes. Why does Professor Peter Doherty consider him the
“first scientist”?

Archimedes was a Greek scholar who discovered the concepts of buoyancy, density,
calculating the volume of an irregular shape, and derived an accurate approximation for the
numeric value of pi. He is most well known for his “eureka” moment, where he discovered
that when an object is placed into a tub of water, the amount of water it displaces can be
used
to calculate it’s density.

Professor Peter Doherty considers him the “first scientist” as his method of discovering
science is extremely similar to the modern scientific method. He followed the procedure of
identifying a problem, using logic to propose a solution, building a model based on known
information, making a prediction, testing it with experiments, and then discussing the
results
with the public. He valued using physical evidence to argue scientific conclusions (for
example, the Earth is spherical due to shadows, falling objects, curved phases of the moon,
etc), and developed deductive reasoning, which refers to drawing conclusions from
empirical
evidence – one of the foundations of the modern scientific process. Lastly, he also
developed
the correspondence theory of truth, which refers to how true or false a statement is
depends
on whether it accurately describes the world – the foundation of the modern definition of a
theory.

3. Define empiricism, rationalism and skepticism. Using examples in the lecture, outline
the contribution of the Greeks to their development.
Empiricism refers to accumulating data that is objective and verifiable by having repeated
experiments obtain the same results within a margin of error. Aristotle contributed to the
development by empiricism by arguing that physical evidence must be used to explain
phenomena on Earth (ie. the earth is spherical because of the presence of shadows, falling
objects, curved phases of the moon, etc).

Rationalism refers to using logic and natural explanations to explain phenomena that occur
on Earth. Euclid of Alexandria first developed this concept, which is reflected in Euclidean
geometry and mathematics – all of his theories and concepts were explained by logical laws
that adhered to the laws of the Earth.

Skepticism refers to questioning the validity of current beliefs. Aristotle contributed to the
development of this concept by having public discussions and looking for empirical evidence
to support any beliefs as valid. He developed the correspondence theory of truth which

maintains that a statement can only be considered true or false after evaluating whether it
accurately describes the world or not.

Lecture 10
1. What is the motto of the Royal Society? Do you think it is an appropriate motto for a
learned society dedicated to science?
The motto of The Royal Society is Nullius in verba, which can be translated to Take
nobody’s word for it. This is an appropriate motto for a learned society dedicated to
science,
as it stresses the importance of skepticism and empiricism. Science is an evolving discipline,
wherein new evidence that is brought to light can challenge existing paradigms.
Furthermore,
no theory should be taken as truth unless it can be proven by empirical evidence – a
comprehensive amount of data and results must be obtained, and these results must be
similar
(allowing a margin of error) across repeated experimentation.

2. List the four rules of scientific thinking as formulated by Sir Isaac Newton.
1. Occam’s razor – this refers to how the theory with the least assumptions is more likely to
be the correct one.
2. The same natural effects must be assigned to the same causes.
3. Qualities of bodies are universal.
4. Propositions deduced from observation should be viewed as accurate until other
phenomena contradict them.

3. What two conclusions did Sir Francis Bacon come to about science?
1. Nature should be understood through direct observation, not by the beliefs and writings
of
ancient authority figures.
2. Observation should be objective and reproducible.

Lecture 11
1. List the 5 traps for those starting out in the scientific endeavour.
1. Ignoring/ruling out data that does not support the hypothesis.
2. Extrapolating beyond the data.
3. Mistaking the hypothesis for the explanation.
4. Thinking something is so obvious that it doesn’t need testing.
5. Confusing correlation with causation

2. Define the term “scientific revolution”.

Scientific revolution refers to a paradigm shift; when a previously accepted scientific theory
is found to be inaccurate in light of new evidence.

3. Why was Galileo’s description of the solar system so provocative?

In the 1500-1600s, the Church played a large role in the political situation of Europe. They
believed that the Sun revolved around the Earth. Galileo’s description of the solar system –
that the Earth revolved around the Sun – challenged their beliefs and confronted the
Church,
therefore, it was so provocative.

4. Discuss one of the three paradigm shifts studied. Address the following:
- What was the existing paradigm?
- What was it replaced with?
- By who? (Champions and small players)
- What role did technology play?
- How was the research communicated?
- What happened next?

The existing paradigm in the 1600s was that the Sun revolved around the Earth. This was
due
to some pre 5
th
century Ancient Greek scholars (namely Aristotle), having a geocentric view
wherein the Earth was in the centre of the universe and all other planets/heavenly bodies
revolved around it. When Saint Thomas Aquinas came into power in the 1200s, he
commanded that all of Aristotle’s texts be translated from Greek to Latin. Upon reading his
geocentric theory of the world, the Church adopted it. It is important to note that for the
Earth
to be at the center of the Earth, complex models had to be developed to describe motion,
which violates Occam’s razor.

In the 12
th
century, during the Islamic Golden Age, many Arabic scholars developed a
heliocentric model of the world, wherein the Sun was at the centre and the Earth revolved
around it. This could have been adopted from the theories of some Greek scholars who
believed in the heliocentric model.

In the early 1500s, Nicolaus Copernicus formulated and published the heliocentric
hypothesis
in Latin. However, he could not provide physical evidence for his theory as it was based on

mathematical theory, and it gained little traction. Another contributing factor to its lack of
popularity was the fact that printing was only just starting (reducing accessibility), and that
it
was published in Latin, a language that only the elite knew.

In the early 1600s, Galileo developed the telescope. With this technology, he managed to
find
physical evidence to prove the heliocentric hypothesis of Copernicus – demonstrating the
value of empiricism in science. He published his work in Italian, a more accessible language,
and the printing press had also gained more popularity at this time. However, as his theory
confronted the Church’s ideals, he was placed under house arrest. This demonstrates his
scepticism as he challenged existing ideals. This is when the paradigm shift truly began in
society.

However, Galileo believed that the Earth moved in a circular orbit. Works by Tycho Brahe
and Johannes Kepler collected massive data sets that showed that the Earth’s orbits were
elliptical. In the late 1600s/early 1700s, Sir Isaac Newton developed the concept of gravity,
which explained the heliocentric model and provided a mechanism for it. Einstein eventually
developed the Theory of Gravity, which provided a bigger picture and cemented the
heliocentric model as truth. The paradigm shift had occurred.

Lecture 12
1. Apply the principles learnt in this lecture to the experience of Barry Marshall and
Robin Warren, discussed in the previous lecture.

2. List the features of the sort of people who typically drive change in scientific theories.
They are typically young, often from outside the field, and are ignored and ridiculued by the
establishment.

Lecture 13
1. Define research misconduct. Is an ethical violation always misconduct?
Research misconduct is defined as fabrication, plagiarism, or deception in proposing,
carrying out, or reporting the results of research, and failure to declare/manage a serious
conflict of interest. Yes, an ethical violation is always misconduct.

2. Which of the three ideals of science seems to be most effective in detecting fraud.
Why do you think that?
Peer review is the most effective in detecting fraud. This is because it allows an individual’s
work to be checked by other professionals, who will eventually be able to catch any fraud
presented in a research paper. The ideal of universalism will not be able to detect fraud as it
focuses on judging quality of research fairly (ie. not taking a scientist’s personal life into
account when judging his research). The ideal of replicability and reproductability can also
detect fraud, however, there have been documented cases wherein the original researcher
who committed the fraud extended that to all his other research, therefore, the results
were
presented as replicable when they were all fraudulent. An example of a case like this is Jan
Hendrik Schon.

3. Outline the examples given in the lecture and discuss how they relate to these ideals.
Include information on who they were, where they worked, their field, and the nature of
the alleged misconduct.
(read notes)

4. What are some of the pressures that scientists (and others) are under. How would this
encourage people to behave badly? Relate these to the “traps for unaware scientists”.
Economic desperation could cause scientists to behave badly. For example, they may
change
the data to support their hypothesis to get more money.
Psychological disturbance may also encourage people to behave badly as they may not have
the mental capacity to accurately evaluate their research findings, and may involve their
own
emotions and violate ethical codes to meet their own agenda.
Institutional pressures, incentives and constraints can also influence an individual to violate
ethical codes, as they can create a stressful and/or imperfect environment.

5. What are the basic rules around keeping records in lab note books?
All data must be recorded and data files must be cross referenced in a lab note book, or
printed out and affixed to the book. Each notebook must be numbered, dated and the name
of
the scientist must be written. Each page must be signed and dated, and a signature of a
witness to attest to the credibility of the data must be present. Notes should be written in
black permanent ink to reduce the possibility of erasure. Raw data and samples must be

retained for a minimum of 5 years in the lab where the research was conducted, or until
there
is no more need for them.

Lecture 14
1. Define the deontological and utilitarian views of using animals in research.
The deontological approach is so named from the Latin term “deon”, which means duty.
This
approach judges the morality of an action based on rules – these rules refer to ethics in
terms
of using animals in research. It argues that using animals in research must be handled
ethically.
The utilitarian approach maximizes utility and believes that ends justify the means –
experiments on animals are okay if it benefits humanity.

2. When did the RSPCA become established in the UK and the USA?
The RSPCA was first established in the UK in 1824. The American version, known as the
ASPCA, was established in the UK in 1866.

3. What factors affect whether using animals in experimentation is appropriate?

There are 3 broad factors that evaluate whether using animals in experimentation is
appropriate.

The first is the NH&MRC recommendation for experimental design with animals. This can
also be referred to as the 3Rs,
Reduction – Use fewer animals to gain more information
Refinement – Use methods that alleviate/minimize potential pain or distress.
Replacement – Use methods without animals (ie. computer simulations, cell or tissue
cultures), or use “lower” animals such as the Drosophila.

The next is the 5 freedoms:

- Freedom from hunger and thirst
- Freedom from discomfort (ie. must have a good resting area, shelter, etc)
- Freedom from pain, injury or disease.
- Freedom to express normal behaviour
- Freedom from fear and distress

The last is the Animal Ethics Committee (AEC), which must approve the use of animals in
research in Monash. This committee includes a vetenarian, an animal researcher, a welfare
member, and an independent layperson. The AEC extends to all live non-human vertebrates
and live crustaceans but does not include animals such as brine shrimps and Daphnia.

4. Outline the simplest of Harry Harlow’s experiments. In what way did his study
design consider the animals’ welfare? At what stage did other researches start
becoming concerned with his experiments?
Harry Harlow studied infant dependency – whether the variable of contact comfort affected
a
baby rhesus monkey’s preference in regards to spending time with a designed “mother”. He
had two “mothers” designed – one made out of wire, and one covered in soft cloth. The
wire
mother had milk to nurse the baby monkey, whereas the cloth mother did not. The results
of
his experiment showed that the baby monkey preferred the soft, cloth mother to the wire
mother and only went to the wire mother for food.

Harlow did not consider the animals’ welfare in his study design. He isolated the infant
rhesus monkey from contact with other monkeys and living creatures, a violation of one of
the 5 freedoms– the freedom to express normal behaviour and the freedom from fear and
distress.

Lecture 15
1. List three points in the Nuremburg code and discuss how they are applied using
specific examples.
One of the points in the Nuremberg code is that all human participants must volunteer for
the
study. This means that they cannot be forced or coerced into participation. This is applied in
experiments today by providing the prospective participant with all the information about
the
study, and allowing them to make a fully informed decision (informed consent). Typically, a
contract is signed by the participant, acknowledging that they have read about and
understood
all the aspects of the study and consent to participating in it.

Another point is that the subject is allowed to opt out at any point of the study. Despite
giving
informed consent, if the participant feels like they no longer want to participate in the study
(for any reason), they must be allowed to leave the study. For example, if a drug clinical trial
that lasts for 8 weeks wants to test the effects of a newly developed drug, and a participant

wishes to discontinue the trial after 4 weeks of taking the drug due to adverse side effects,
they must be allowed to do so. The third point is that the study must be stopped if there is
a risk of injury, death or disability to the participants. Drawing on the earlier example of a
drug clinical trial, if the drug is realized to cause temporary or permanent damage (ie.
paralysis) in the participants, the trial must be stopped immediately.

2. What is required for “informed consent” in terms of experiments? How did the Nigerian
Drug trials violate this principle? For a participant to give their informed consent to be a
subject in an experiment, they must be thoroughly briefed on the process of the
experiment. All the information available must be given to them. If the participant is under
the age of 18, or disabled, consent must be given by their parents/guardian. In the Nigerian
Drug trials, Pfizer tested a new broad spectrum antibiotic called Trovan that was theorized
to combat meningitis. 200 children took part in it, however, consent was not obtained from
all of their parents/guardians, and no one was informed on what the drug was and what the
effects and side effects were.

3. Describe the experiments on obedience and authority conducted by Stanley Milgram in

the 1960s. How have these contributed to our understanding of human behaviour? What
ethical principles did they allegedly violate? The Milgram experiment on obedience and
authority was conducted on male adults ranging in age from 20-50 years old. They drew
straws to determine who was going to play the role of the “teacher” and who was going to
be the “learner”, however this was fixed and one of Milgram’s research associates was
always the learner. The “learner” would be strapped to a char with electrodes, and the
teacher would test him by naming a word and asking him to recall its partner/pair from a list
of 4 possible choices. When the learner made a mistake, the teacher was told to administer
an electric shock to him – this level of electric shock would increase every time. When the
teacher refused to administer a shock, the experimenter would order and prod the teacher
to ensure they continued. After 4 prods, if the teacher still refused, they were allowed to
abstain from giving an electric shock. It is important to note that no electric shock was
actually given and the “learner” (an associate of Milgram!) would yell in

pretend pain every time he was “shocked”. The learner was also separated from the
teacher’s
view, so the teacher could not see him.

This experiment showed that ordinary people are likely to follow orders given by an
authority
figure even to the extent of killing an innocent human being – ie. obedience to authority is
ingrained in us all from the way we are brought up.

This experiment was unethical as it violated several codes of ethics. Firstly, it deceived the
participants and did not obtain informed consent as the participants genuinely believed that
they were shocking a real person and were unaware that the learner was a confederate of
Milgram’s. The participants were also not protected from psychological harm and have been
recorded to experience visible distress. Lastly, Milgram did not give the participants an
opportunity to withdraw from the experiments (he kept ordering and prodding them to
administer the electric shock), which is a violation of a participant’s right to withdraw from
an experiment at any time.

Lecture 16
1. What effect does under-reporting of negative results have on subsequent
metaanalyses?
Under-reporting of negative results will give the view that the experiment typically yields
positive results. While this bias may not be obvious when reading one journal at a time, in a
meta-analysis (a comprehensive compilation of several journals), this bias can be
exacerbated
and the consistency, precision and magnitude of the effect can be exaggerated.

2. What effect does registering trials have on the reporting of results?

Registering trials increases the likelihood of negative results being reported.

3. Why do scientists tend to be less alarmist rather than more?

Scientists dislike catastrophic explanations as it is in opposition of Occam’s razor, which
states that the most obvious and simplest explanation is likely the correct one.

Past year exam questions (Section B)

1a) Explain how you would convert information in the article on pages 17-20 of this
booklet (used in Section A) for inclusion in a popular science magazine or a report on
the local radio news. You should discuss at least four significant changes you would
make, and the reason for each. (8 marks)

Firstly, the title of the journal article would be changed to a catchier, attention grabbing
title.
For example, instead of being titled “The content of protein and non-protein (free and
protein-bound) tryptophan in Theobroma cacao beans”, the article could be titled “What’s
in
your chocolate?”. A scientific journal article is designed to be read by other scientists or
students studying science, therefore, it must prioritize quality of information over
“catchiness”. A popular media article, on the other hand, is designed for the general public,
and must therefore have a captivating title so as to attract the layman to read it.

Secondly, the scientific jargon will be eliminated from the article. This is so that any layman
will be able to understand the article. For example, the sentence, “Trp is necessary not only
for protein synthesis but also for most biogenetic and biosynthetic pathways, being the
precursor of alkaloids, phytohormones (indoleacetic acid), NAD coenzymes, and other
important biological substances, such as serotonin and melatonin,” would be rewritten to
“Trp is used as a building block for proteins as well as in other important processes in the
human body.” Trp would have been confirmed as the abbreviation of tryptophan earlier in
the
article.

Thirdly, the word count of the article must be reduced and only the main points of the
article
must be communicated. In scientific writing for other scientists/science students, it is
important to include all the details for the methods, results, discussion etc, but when it
comes
to communicating science to the general public, the nitty-gritty is unnecessary. Therefore, I
would limit the article to a maximum of 500 words. The first 2-3 sentences would be
composed of some background information on cocoa and chocolate. One sentence would
then be allocated to briefly explaining why it is important to know the trp content of cocoa
beans. The next 3-4 sentences would describe the method used (with limited jargon) to
quantify the amount of trp in cocoa. Another 3-4 sentences would describe the results, and
the relevance of these results in today’s world. The last sentence would serve as a
conclusion.

Lastly, I would include an image to engage the readers of the popular media article.

1b) Identify three different audiences to which a scientist might need to communicate
their work. Briefly explain why it is important for scientists to be able to communicate
their work to a variety of audiences, including the ones you have identified. (7 marks)

The three different audiences to which a scientist might need to communicate their work to
are other scientists, the general public, and the government.
Science is essential to many different sectors of this world. It can be applied in an
economical
sense, to contribute to the national economy and individual wealth. For example,
biotechnology research can help produce genetically modified organisms (GMO) to increase
crop yield for farmers (ex. pest-resistant tomatoes). This contributes to both a farmer’s
revenue, as well as the country’s economic standing if they choose to export tomatoes.

In fact, science can be used as a utilitarian argument. Without science, we would not have
the
technology we have today – everything from electricity to cell-phones to the foods we eat
to
even the medicines we take – has been invented, developed, and made accessible by
science.
People owe much of their wealth and well-being to scientific invention. By communicating
science to others, we increase their accessibility to these inventions so their lives can be
bettered.

It can also be used to drive democracy. Communicating science to the general public will
give them information, which can enfranchise them. It can even be used to drive culture –
the
best science might be considered high art.

Lastly, science underpins the evolution of every stage of mankind – from the stone age, to
the
bronze age, to the iron age, to the industrial age, and finally, to the biological age. It stands
to
reason that science will continue to play an important role in the evolution of mankind.

When we communicate science to the general public, we help educate them on what is
going
on in the world around them. We also give them the chance to get involved in the process
of
discovering and developing new technologies and researching into the various sciences.

When we communicate science to the government, it is typically to give them

recommendations on how to amend their policies. For example, an environmental scientist

could conduct research on the effect of CFCs on climate change, and identify the maximum
level of CFCs that can be released into the atmosphere per year to keep the damage to the
ozone layer to a minimum. He/she can then pass this recommendation along to the
government so they can enact laws that control the amount of CFCs released into the
atmosphere by corporations.

Lastly, communicating science to other scientists benefits the original scientist more than
others. One example of this is peer-review. Peer-review acts as a filter and improves the
quality of work – a scientist who submits his research findings for peer review can receive
constructive feedback on how to improve his experimental design, etc, and thus produce
research of a higher quality.

2a) The three ideals of science are universalism, peer review and replication. Explain
what is meant by each ideal. (6 marks)

Universalism refers to how science will be judged on the quality of science, and not who did
the work, where it was done, where it was published, etc. This is to prevent the
discrimination of other scientists based on their personal life, country they come from, etc.

Peer review refers to the process of other scientists (typically 2) reviewing a research article
before it is published. It acts as a filter to improve the quality of research and allows the
original scientist(s) to gain valuable feedback from other professionals in the same field.

Replication refers to how experiments must be replicated multiple times with similar results
(within a margin of error). Only if this is possible will the research, and the science behind it,
be considered true. However, if replication is not feasible, the concept of reproducibility
comes into play wherein data sets and software must be made available to verify published
findings and conduct alternate analyses.

2b) Using specific examples from the lectures, discuss the effectiveness of each of these
ideals in protecting the integrity of science from fraud, misconduct and error. (9 marks)

The ideal of universalism can help protect the integrity of science by ensuring there is no
discrimination regarding what gets published. For example, in Feb 2002, Antonia Lasaga, a

professor at Yale University, was charged with child sex crimes. Geochimica et
Cosmochimica Acta decided to publish his article in their journal in Jan 2002, while he was
accused and standing trial. The ideal of universalism was applied in this case – science is
published based on its objective merit, and not based on the scientist’s personal life, where
the research was conducted, etc.

The ideal of peer review can weed out research articles that use fake and fraudulent data.
For
example, in the early 2000s, a German physicist (Jan Hendrik Schon) working in the Bell
labs in the USA reported having discovered exciting breakthroughs in nanotechnology. He
was publishing roughly 1 paper every 2 weeks for a total of 6 years. During peer review, a
scientist realized that two different papers contained the same diagram, even though they
were supposed to be about different experiments. A full investigation was launched and
whole data sets were found to be reused in different experiments. Some graphs were even
found to be produced with mathematical functions instead of experimental data. Of course,
Schon was fired, his PhD was revoked and his research papers were withdrawn. This serves
as an excellent example as to how peer review can protect the integrity of science from
fraud.

The ideal of replicability can identify research articles that use fraudulent and/or erroneous
data, as well as identify scientific claims that can be considered to be true. For example, in
1998, Andrew Wakefield claimed a link between the MMR vaccine and autism and IBS.
Subsequent studies reported opposing results, and therefore, Wakefield’s claims could not
be
confirmed as true. This also alerted the authorities to Wakefield’s ethical misconduct in
using
developmentally challenged children in his studies, without obtaining informed consent
from
their guardians. Therefore, replicability can protect science from fraud, misconduct and
error.

3a) Using a diagram or flow chart outline the key steps in the scientific method. (5
marks)