NATURE OF SCIENCE NOTES

Serendipity and scientific discoveries

1.6 the discovery of Cyclins was accidental

Serendipity: an unexpected scientific discovery made by accident

Tim Hunt conducted research into the protein synthesis in sea urchin eggs
during fertilisation he found that a certain protein was found to increase
then decrease in concentration (unlike other proteins that remained
constant)
further research found that these repeated changes in concentration
coincided with the phases of the cell cycle
newly found protein was named cyclin
proved cyclins are a key factor in the control of the cell cycle
Hunt did not set out to discover how the cell cycle was controlled
(serendipity)

D2 The role of gastric acid in digestion was established by William

Beaumont while observing the process of digestion in an open wound
caused by a gunshot

Alexis St. Martin was a Canadian fur trader who received a gunshot wound
to his side. He survived.
The wound healed so that the inside of the stomach could be seen from
the outside.
William Beaumont, the surgeon who first treated the wound, used the
opportunity to study the process of digestion continued this over an 11
year period.
He published his results in 1833.
Beaumont is credited with overturning the notion that digestive processes
within the stomach are solely physical, providing evidence through his
experiments of the chemical nature of digestion.

Assessing risks associated with scientific research

3.5 scientists assess the risks associated with GM crops or livestock

Possible risks associated with genetic modification

Fears traced back to the 1970s
Paul Berg planned an experiment where the DNA from the monkey virus
SV40 was going to be inserted into E.coli
Other scientists expressed concerns because SV40 was known to cause
cancer in mice
Therefore risks that the genetically engineered bacterium could cause
cancer in humans

Since then risks associated with genetic modification have been identified:

Fierce debates have led to bans in some countries

The risks can be assessed in two ways:

1. What is the chance of an accident?

2. How harmful would the consequence be?

6.3 Florey and chains test on the safety of penicillin would not be
compliant on current protocols on testing

Risks of using new drugs are minimised by strict protocols

These protocols include:
1. Initial test performed on animals
2. Small tests done on healthy humans
3. If these tests proved successful then the drug is used on patients
with the disease
Tested the new penicillin drugs on humans only after a very short
period of animal testing
No proper protocols or risk assessments and there easily could have
been severe side effects
Patients they used were all on the verge of death or severely ill
(another defiance of protocol)
Several were cured of their illness and the drug was supposedly
successful
Penicillin was introduced far more rapidly since it bypassed proper
protocol, and was introduced during D-Day in 1944 to treat patients
with bacterial infections

Use theories to explain natural phenomena

2.2 The theory that hydrogen bonds form between water molecules
explains the properties of water

There is strong experimental evidence for the existence of hydrogen

bonds
There is a theory that they form between water molecules
This theory explains the adhesive, thermal, solvent and cohesive
properties of water
It is these distinctive properties of water that makes water so useful to
living organisms
This theory hasnt been proven, however we can assume that a theory is
correct if there is evidence for it and it has not been falsified
It helps to predict behaviour and to explain natural phenomena

4.2 The concept of energy flow explains the limited length of food chains

In order work out how many stages there are in a food chain we can
consider the diet of a top carnivore at the end of the chain
Eg. if an osprey feeds on fish that feeds on shrimp which feeds on
phytoplankton, there are 4 stages in the food chain
There are rarely more than 4 or 5 stages in a chain
We cannot expect food chains to be limitless
We try to explain natural phenomena, such as the restricted length of food
chains, using scientific theories

In this case it is the concept of energy flow along food chain and the
energy losses that occur between trophic levels that can provide an
explanation

5.2 the theory of evolution by natural selection can explain the

development of antibiotic resistance in bacteria.
When antibiotics were introduced it was expected they would offer a permanent
method of controlling bacterial diseases.
There have been increasing problems of antibiotic resistance in pathogenic
bacteria:

After an antibiotic is introduced and used, bacteria showing resistance

appear within a few years
Resistance to the antibiotic spreads to more and more species of
pathogenic bacteria
In each species the proportions of infections that are caused by a resistant
strain increases

There been cumulative changes in the antibiotic resistance properties of

populations of bacteria. Therefore antibiotic resistance is an example of
evolution.

Using models as representation of the real world

1.3 - there are alternative models of membrane structure.

Gorter and Grendel extracted phospholipids from plasma membrane,

deduced by calculations of area occupied by the layers that membrane
contains a bilayer.
o Their model did not explain where proteins are located.
In 1930s, Davson and Danielli proposed sandwich model.
o High magnification electron micrographs of membrane in 1950s
shows two dark lines (proteins) with lighter band (phospholipids) in
between fitted the model.

1966, Fluid mosaic model was proposed by Singer and Nicolson.

o Proteins occupy variety of positions in membrane.

2.6 - Crick and Watsons elucidation of the structure of DNA using model
making

The structural organisation of the DNA molecule was correctly proposed in

1953 by James Watson and Francis Crick
Their efforts were guided by an understanding of molecular distances and
bond angles developed by Linus Pauling, and were based upon some key
experimental discoveries
As Watson and Cricks model building was based on trial and error, a
number of early models possessed faults such as the first model having a
triple helix
The final construction of a correct DNA molecule owed heavily to the X-ray
crystallography data generated by Rosalind Franklin

9.1 - mechanisms involved in water transport in the xylem can be

investigated using apparatus and materials that show similarities in
structure to plant tissues

A potometer can be used in a laboratory to simulate the movement of

water in xylem of plants
An inverted, water-filled porous pot replaces the leaf shoot
Evaporation and the cohesive/adhesive properties of water power water
movements up the fine tubes

Falsification of theories with one theory being superseded by

another
1.3 Evidence falsified the Davson-Danielli model
-

The davson-danielli model was accepted by most biologists for around 30

years but during the 1950s/60s an accumulations of evidence did not fit
the model:
1. Freeze etched electron micrographs:
Technique involves rapid freezing of cells and then fracturing them
Fracturing occurs along lines of weakness cell membranes

Globular structures scattered through images of centre of

membrane were thought to be trans-membrane proteins
2. Structure of membrane proteins:
Improvements of biochemical techniques allowed for extraction of
protein from membrane
They were found to be of varying sizes, unlike the type of structural
protein that would form continuous layers on periphery of
membrane
3. Fluorescent antibody tagging:
Red or greed fluorescent markers were attached to antibodies that
bind to membrane proteins
shows that membrane proteins are free to move within the
membrane rather than being fixed in a peripheral layer

All evidence led to revalidation of Davson-Danielli model. This is important as it

sparked the evolution of the next model

2.1 - The artificial synthesis of urea helped to falsify vitalism

Urea was discovered in 1970s and it was assumed to be a product of the

kidneys. It was widely believed that organic compounds in animals and
plants could only be made with the help of a "vital principle".

In 1828, Friedrich Wohler a German chemist synthesised urea artificially

using silver isocyanate and ammonium chloride --> the first organic
compound to be synthesised artificially and no vital principle had been
involved in the synthesis (the kidneys were not needed). This was
evidence against the theory of vitalism and helped to falsify the theory.

Biologists now accept that processes in living organisms are governed by

the same chemical and physical forces as in non- living matter. However, it

is still impossible to make complex proteins such as hemoglobin without

using ribosomes and other components of cells.

5.4plant families have been reclassified as a result of evidence from

cladistics.

The reclassification of plants on the basis of discoveries in cladistics is a

good example of an important process in science: the testing of theories
and of replacement of theories found to be false with new theories.

The classification of angiospermophytes into families based on their

morphology was begun by the French botanist Antoine Laurent de Jussieu
in Genera plantarum, published in 1789 and revised repeatedly during the
19th century.

D.1 - scurvy was thought to be specific to humans because attempts to

induce the symptoms in laboratory rats and mice were unsuccessful.

In 1907 Holst and Frolisch published research paper displaying their

success in forming an animal model of scurvy.
The caused Guinea pigs to develop scurvy by feeding them whole grains.
Cured this through dietary modification eg. Lemon juice and cabbage
Their ideas were unpopular at the times, because nutritional deficiency
was previously unheard of
Their animal model allowed for the systematic study of the factors that led
to the development of scurvy, as well as the preventive value of different
substances
The use of the Guinea pig was a lucky coincidence, was later shown to be
one of the only animals to not produce their own vitamin C a lack of
which leads to scurvy

Experimental Design
1.4accurate quantitative measurement in osmosis experiments are
essential.
In most experiments there are some doubts and uncertainties, but they can be
minimized.
The experiment then provides strong evidence for or against a hypothesis.
This checklist can be used when designing an experiment:

Results should if possible be quantitative as these give stronger evidence

than descriptive results.
Measurements should be as accurate as possible, using the most
appropriate and best quality meters or other apparatus.
Repeats are needed, because biological samples are variable.
All factors that might affect the results must be controlled, with only the
factors under investigation being allowed to vary.

2.5 - accurate quantitative measurements in enzyme experiments require

to replicates to ensure reliability

To obtain strong evidence these experiments must carefully follow these

principles:

o
o
o

Results should also be quantitative

Measurements should be accurate, which means closest to true
value
Experiment should be repeated to compare reliability of results

Developments in scientific research follow improvements in

technology
3.1 gene sequencers, essentially lasers and optical detectors, are used
for the sequencing of genes

DNA is broken up into small lengths, these are sequenced separately

without fluorescence
Coloured fluorescent markers are used to mark the DNA copies
Samples mixed together, DNA copies are separated in one lane of gel
according to the number of nucleotides
Laser scans along the lane to make the fluorescent fluoresce
Optical detector is used to detect the colours of fluorescence along the
lane. Series of peaks of fluorescence, corresponding the number of
nucleotides
Computer deduces the base sequence from the sequence of colour of
fluorescence detected

Developments in scientific research follow improvements in

techniques
3.2 autoradiography was used to establish the length of DNA molecules
in chromosomes

Autoradiography is used to measure DNA molecules.

Developments in microscopy have allowed images to be produced of
structures that were previously invisible.
1940s onwards discovered where specific substance were located in
tissues or cells.

John cairns used the technique in a different way, obtaining images of a whole
DNA molecule from E.coli. It was shown to be a chromosome, also revealed
replication forks in DNA for the first time. Then used to investigate the structure
of eukaryote chromosomes

Developments in scientific research follow improvements in

apparatus
1.2 - the invention of electron microscopes led to greater understanding of
cell structure

The use of light microscopes limited scientific research as many biological

structures are smaller than 0.2 micrometres, but light microscopes they
cannot produce clear images of structures smaller than 0.2 micrometres.
Electron microscopes, which were developed in Germany, allowed for the
production of images 200 times smaller than with light microscopes.
The electron microscope invalidated many previous ideas of structures of
eukaryotic cells. For example, the darker green areas of the chloroplast
were thought be droplets of chlorophyll, but the electron microscope

showed that the grana are actually stacks of flattened membrane sacs.
The mitochondria were shown as tiny rods or spheres without structure in
light microscopes, they are shown in the electron microscope to have
internal membrane structure.
The electron microscope also revealed previously unknown features of the
ultrastructure of cells, such as lysosomes and ribosomes.

6.6 William Harvey was hampered in his observational research into

reproduction by lack of equipment. The microscope was invented 17 years
after his death

Harvey published his research into sexual reproduction in 1651 when he

was 73 years old.
He knew had not solved the mystery of sexual reproduction because
effective microscopes were not available when he was working.
It meant that the fusion of gametes and subsequent embryo development
remained undiscovered.
Additionally, he chose to experiment on deer, because embryos in the
deer that he used remain microscopically small for a long period.
Microscopes were invented 17 years after his death, allowing the
discovery of sperm, eggs and early stage embryos.
Scientific research has often been hampered for a time by deficiencies in
apparatus.
As a result, discoveries have only been made following improvements.
This will continue into the future we can look forwards to further
understandings of the natural world as new techniques and technologies
are invented!

8.3 - sources of 14C and autoradiography enabled Calvin to elucidate the

pathways of carbon fixation

Discoveries in biology can sometimes make progresses in other biological

research possible
Martin Kamen and Samuel Ruben discovered 14C in 1945
However the half-life of the radioactive isotope is ideal in the process of
tracing pathways of photosynthesis
Melvin Campbell and his team initially supplied algae with 12CO2, however
changed to 14CO2
By taking samples of the algae at different time intervals they could see
what part of the algae contained the radioactive isotope

9.2 - Experimental methods for measuring phloem transport rates using

aphid stylets and radioactively-labelled carbon dioxide were only possibly
when radioisotopes were available
Radioactively-labelled carbon within CO2, which can be detected using film

or radiation detectors
As carbon is metabolised it will be found in different molecules within the
plant, meaning the formation and movement of radioactive molecules can
be traced
A Geiger counter is used to measure radiation levels in crops.
Measurement of phloem transport rates now became possible.

11.2 Fluorescent calcium ions have been used to study the cyclic
interactions in muscle contraction

Fluorescence is the emission of electromagnetic radiation, often visible

light, by a substance illuminated by electromagnetic radiation of a
different wavelength.
Can only be detected by a light microscope
Many experiments testing for fluorescence have been conducted.
i.e. Contraction of single muscle fibres of the acorn barnacle Balanus
Nubilus by injecting samples of aequorin (bioluminescent protein). When
muscles were stimulated, there was initially a strong bioluminescence
associated with Ca2 from the sarcoplasmic reticulum. After time, it began
to decrease after the cessation of the stimulus.
Also, researchers cut apart Nitella Axillaris cells. These cells are unique as
they have a network of actin filaments underlying their membranes.
Researchers attached fluorescence to myosin molecules in an effort to
show myosin can walk along actin filaments. In doing so, the ATP
dependence of myosin-actin interaction.

D4 The invention of the stethoscope led to improved knowledge of the

workings of the heart

Stethoscopes were invented in the 19th century by Rene Laennec

The design has been significantly modified since then.
Prior to this, practitioners would place their ears directly on the chest of
patients to listen to the heartbeat.
However in the 19th century:
o Many patients were too obese for sounds to be heard though this
method.
o Washing was not the social norm and some patients were infested
with vermin
o With female patients modesty was an issue.
These variables pressured the development of the tool.
However, there were also unintended benefits of the device:
o It became one of the first tools that allowed for the non-invasive
investigation of internal anatomy.
o Eg. Different types of heart abnormalities result in different sounding
heartbeats which can be detected through the stethoscope.

Developments in scientific research follow improvements in

computing
7.3 the use of computers has enabled scientists to make advances in
bioinformatics applications such as locating genes within genomes and
identifying conserved sequences.
Bioinformatics involves the use of computers to store and analyse the huge
amounts of data being generated by the sequencing of genomes and the
identification of gene and protein sequences.

Such information is often amassed in databases that are accessible to the

general public, for example, GenBank, the DDBJ or the nucleotide sequence
database maintained by the EMBL (the European Molecular Biology Laboratory).

A scientist studying a particular genetic disorder in humans might identify

sequence similarities that exist in people with the disorder.
They might then search for homologous sequences in other organisms via a
BLAST search and these sequences might have a common ancestral origin but
have accumulated differences over time due to random mutation.
Conserved sequences are homologous sequences are identical or nearly
identical across species.

The functions of conserved sequences are often investigated in model organisms

such as E. coli, yeast (S. cerevisiae), fruit flies (D. melanogaster),etc.
These particular organisms are often used because their entire genomes have
been sequenced.

In addition to the BLAST program, ClustalW can be used to align homologous

sequences to search for changes.
PhyloWin can be used to construct evolutionary trees based on sequence
similarities.

Developments in scientific research follow improvements in analysis

and deduction
9.3 improvements in analytical techniques allowing the detection of
trace amounts of substances has led to advances in the understanding of
plant hormones and their effect on gene expression
Genomics has improved understanding of the role of plant hormones

Improvements in analytical techniques allowed the detection of trace

amounts of substances of substances have led to advances in the
understanding of plant hormones and their effect on gene expression.
Microarrays have allowed researchers to detect gene expression as
opposed to just the phenotype.
This involves passing the contents of a cell over a section of single
stranded DNA to test which sections bond.

Looking for patterns, trends and discrepancies

1.1although most organisms conform to cell theory, there are
exceptions.

In the early stages of scientific investigations, it is necessary to look for

trends
Trends are: things that appear to be found generally rather than just in
specific cases
From these trends we make theories
These theories are ways of explaining and interpreting the natural world,
allowing us to make predictions
Sometimes we find exceptions called discrepancies
Scientists have to judge if the discrepancies are common, or serious
enough to make predictions too unreliable: if they are, then the theory is
discarded
Robert Hooke who first coined the term cell looked at many different
types of plant tissues, and discovered a trend, leading to his formation of
cell theory
There are discrepancies to the theory however:
o Giant algae: can grow to a length of 100mm, so they go against
the theory that cells are the smallest units of life they dont have
emergent properties (unicellular)
o Skeletal muscle: muscle fibres enclosed inside a membrane,
which have hundreds of nuclei inside a single cell that is 300+mm
long
More discrepancies may be found, but it is unlikely that the cell theory will
be discarded, because a majority of organisms consist of cells

2.4 most but not all organisms assemble proteins from the same amino
acids.

Most organisms make proteins using the same 20 amino acids

Amino acids are sometimes modified after polypeptide synthesis but
the initial process of linking amino acids on ribosomes with peptide
bonds usually involves the same 20 amino acids.
We can exclude the possibility that this trend is due to chance.
Hypotheses to explain this include:
o That the 20 amino acids were produced by chemical processes on
Earth before the origin on life meaning the first organisms and
therefore all organisms used them
o That the 20 amino acids are ideal for making a wide range of
proteins, so natural selection will always favour organisms that use
them and do not use other amino acids
o That all life has evolved from a single ancestral species which used
these 20 amino acids. Due to the way polypeptides are made by
ribosomes, it is difficult for any organism to change the amino acids
in use, either by removing existing ones or adding new ones
Exception: Some species have been found to use one of the three stop
codons (codons that signal the end of polypeptide synthesis) to encode an
extra non-standard amino acid.

For example, some species use UGA to code for selenocysteine and
some use UGA to code for pyrrolysine.

4.1 - plants and algae are mostly autotrophic but some are not

almost all plants & algae are autotrophic making their own complex
organic compounds using CO2 and other substances
There are some exceptions that no longer make food by photosynthesis,
and instead obtain carbon compounds from other organisms; they are,
therefore heterotrophs
Dodder, which feeds on the stems of other plants, obtains carbon
compounds from them
Epipogium aphyllum (a.k.a. Ghost Orchid) lives entirely underground
except when it flowers, and obtains carbon compounds from fungi living
on the roots of trees
Therefore, we cannot assume that a plant or alga is autotrophic, as there
are exceptions

5.1 - there are common features in the bone structure of vertebrate limbs
despite their varied use
Vertebrate limbs are used in many different ways, such as; walking,
running, jumping, flying, swimming, grasping and digging.

These varied uses require joints that articulate in different ways, different
amounts of force. Reasonable to expect them to have very different bone
structure but there are common features of bone structure that are found
in all vertebrate limbs

Reasonable explanation so far proposed in this case is evolution from a

common ancestor. As a consequence the common bone structure of
vertebrate limbs has become a classic piece of evidence for evolution.

7.2 - there is mounting evidence that the environment can trigger

heritable changes in epigenetic factors

Chemical modification of chromatin that impact gene expression also

impact the visible characteristics of an individual.
These chemical modifications are called epigenetic tags.
There is mounting evidence that chemical modifications that occur to the
hereditary material in one generation might be passed on to the next
generation both at the cellular and organism level.
Sum of epigenetic tags is the epigenome.
Cells have their own methylation pattern allows for unique set of
proteins to be produced in order for cell to function. Methylation pattern is
passed over to daughter cell in cell division- environment affects
inheritance.
Sperm and eggs develop from cells with epigenetic tags. When two
reproductive cells meet, the epigenome is erased through a process called
reprogramming
Around 1% of the epigenome is not erased and survives yielding a result
called imprinting

10.2 - Mendel used observations of the natural world to find and explain
patterns and trends. Since then, scientists have looked for discrepancies
and asked questions based on further observations to show exceptions to
the rules. For example, Morgan discovered non-mendelian ratios in his
experiments with Drosophila.

Morgan was critical of Mendels theory of inheritance and wasnt

convinced by aspects of emerging chromosomal theory of inheritance.
Thomas Hunt Morgan discovered non-Mendelian ratios in his experiments
with the fruit fly.
Morgan believed that the variation that he saw in organisms was better
explained by environmental influence.
However, his own subsequent observations of the pattern of inheritance of
white eyes led him to reconsider his perspective.
At the same time as his results reinforced aspects of Mendels conclusions,
Morgans studies identified exceptions to Mendels principle of
independent assortment.

10.3 - patterns of chromosome number in some genera can be explained

by speciation due to polyploidy.

A polyploidy organism is one that has more than two sets of homologous
chromosomes.
Polyploidy can result from hybridisation events between different species.
There are also polyploids whose chromosomes originate from the same
ancestral species. This can occur when chromosomes duplicate in
preparation for meiosis but then meiosis doesnt occur. The result is a
diploid gamete that when fused with a haploid gamete produced a fertile
offspring.
Polyploidy occurs most commonly in plants, though it does also occur in
less complex animals.
The red viscacha, a rodent from Argentina, has the highest chromosome
number of any mammal and it has been hypothesised that this is the
result if polyploidy. Its chromosome number is 102 and its cells are roughly
twice normal size.

Cooperation and collaboration between groups of scientists

6.5 - Biologists are contributing to research into memory and learning

Higher functions of the brain including memory and learning are partly
understood at present and are being researched actively
Traditionally, they have been investigated by psychologists
Techniques of molecular biology are being used to unravel the
mechanisms at work
Other branches of science (cooperation & collaboration) are also making
important contributions in these areas:
o Biophysics
o Medicine
o Pharmacology
o And computer science

The nature of science is reliant on cooperation and collaboration

between groups of scientists
Commonly, breakthroughs are often made in science when different
techniques are combined to solve a problem

5.3 scientists use the binomial system to identify a species rather than
the many different local names.

Recognisable groups of organisms are known to biologists as species

The same species can have many different local names, even within one
language
Science is an international venture, therefore even though local names
can be an element of culture, names need to be understood throughout
the world.
The binomial system was developed to allow this, credit goes to Swedish
biologist goes to Carl Linnaeus in the 18 th century.
Two part naming system
The style recognises that there are many groups of similar species

Theories are regarded as uncertain:

6.2 - William Harvey overturned theories developed by the ancient Greek
philosopher Galen on movement of blood in the body

According to Galen, blood is formed in liver and pumped to right ventricle

of the heart
Blood is passed through left ventricle where it meets air from lungs and
becomes vital spirits
William Harvey was unwilling to accept this without evidence
o Therefore he made observations to deduce that blood circulates
through pulmonary and systemic circulations. As well as existence
of capillaries, arteries and veins

Educating the public on scientific claims

D.3 Scientific studies have shown that high-density lipoprotein could be
considered good cholesterol

Lipids are transported in the blood in vesicles known as lipoproteins

Lipoproteins are composed of a hydrophilic exterior of phospholipids,
proteins and cholesterol and a core of cholesterol and fats (triglycerides).

Making careful observations:

3.3 - meiosis was discovered by microscope examination of dividing germline cells
Improved microscopes allowed for detailed images of cell structures.
Dyes stain the nucleus of the cell which aided the reveal of thread-like

structures in dividing nuclei that were named chromosomes. From this, the
process of meiosis and mitosis was discovered.
Key Observation: In a horse threadworm there are two chromosomes in
the nuclei of egg and sperm cells, whereas the fertilized egg contains four.
This indicated that the chromosome number is doubled by fertilization.

Hypothesis came from this development: that there must be a special

nuclear division in every generation that halves the chromosome number.
Nuclear divisions has already been observed during gamete development.
These divisions were identified as the method used to halve the
chromosome number and were named meiosis.
Sequence of meiosis was worked out through observation of cells taken
from the ovaries of rabbits between 0 and 28 days old. This species was
advantageous as females meiosis begins at birth and occurs slowly over
days.

7.1 - Rosalind Franklins X-ray diffraction provided crucial evidence that

DNA is a double helix

Diffraction is when an X-ray beam is directed at a material, and most of it

passes through
The remaining scattered particles make up diffraction
In a crystal, the particles are arranged in a repeating pattern so that
diffraction occurs in a regular way
The scattered rays are collected, and rotated in 3 different dimensions to
investigate the pattern of scattering
It can then be recorded using X-ray film
In 1950, Maurice Wilkins developed a method of producing arrays of DNA
molecules that were orderly enough for a diffraction pattern to be
obtained
Rosalind Franklin began in the same research department as Wilkins, and
she developed a detector that produced clear images of diffraction
patterns in DNA
From this pattern, these deductions were made:
o The cross in the centre of the pattern indicated that the molecule
was helical in shape
o The angle of the cross shape showed the pitch of the helix
o The distance between the horizontal bars showed the turns of the
helix to be 3.4nm apart
Her observations were critically important in the discovery of the double
helix structure of DNA by Watson and his buddy Crick

10.1 - careful observation and record keeping turned up anomalous data

that Mendels law of independent assortment could not account for.
Thomas Hunt Morgan developed the notion of linked genes to account for
anomalies.

Some discrepancies arose between observations and Mendels principle of

independent assortment.
William Bateson and Reginald Punnett conducted crosses with sweet peas.
One of the parent plants had long pollen (LL) and purple flowers (PP). The
other had round pollen (ll) and red flowers (pp).
Instead of the expected ratio of 9:3:3:1, there were far more of the
individuals with the parental phenotypes seen in the P generation and
much smaller numbers of the non-parental phenotypes, known as
recombinants.
Bateson and Punnett realised their results did not conform to Mendels
principle of independent assortment but did not develop a clear
explanation for the discrepancy.

Thomas Hunt Morgan observed similar discrepancies in fruit flies.

His discovery of sex linkage led him to develop a theory of gene linkage
that accounted for the higher than expected number of parental
phenotypes and the notion of crossing over to explain the presence of the
recombinants.

Evaluating claims
2.3 Health claims made about lipids need to be assessed
There are many claims regarding whether a food is beneficial or harmful to the
body. Therefore, in order to assess these claims, experiments are conducted with
the use of laboratory animals to test the effects of diet on health.
This is because:

Animals can be bred to be genetically uniform having the same age, sex,
and health condition, limiting extraneous variables.
Variables other than diet (e.g. temperature/exercise) can be controlled in
order to limit the number of extraneous variables.
Diets can be designed so that only one element of the diet varies,
therefore the effect of this element on animal health can be measured.

Although animal research can give insight into human behaviour, it cannot be
completely applied to humans due to a difference in physiological processes.

Although not completely reliable, it is beneficial as it is not possible to

conduct similar experiments with humans due to a variance in terms of
age, sex, health and genetic variations. In addition, it would be difficult to
control other variables such as exercise, and the participants dietary
intake.

Therefore, research into dietary health risks uses epidemiological studies. This
involves finding a large group of people, measuring their food intake and
assessing their health over a long period of time. Statistical procedures can then
be used to determine whether factors in the diet are associated with a particular
disease.

Making accurate, quantitative measurements:

4.3 - it is important to obtain reliable data on the concentration of carbon
dioxide and methane in the atmosphere
Carbon dioxide and methane concentrations have important effects

Carbon dioxide concentration effects photosynthesis rates and the pH of

seawater
Both gases influence global temperatures
Through their effect on the amount of heat energy in the oceans, they can
impact ocean currents, rainfall, and frequency of extreme weather

Consider the following predictions:

Carbon dioxide concentration of the atmosphere is currently higher than at
any time in the past 20 million years

 Human activities has increased carbon dioxide and methane

concentrations
Human activity will cause carbon dioxide concentrations to continue to
rise

Reliable data is essential for evaluating these hypotheses- especially over

a long period so data can be compared
Data of gas concentrations in the atmosphere are collected, and are of
immense value to scientists

Ethical implications of research

1.1 research involving stem cells is growing in importance and raises
ethical issues

In the origins of stem cell research there was research carried out that
today would be considered highly unethical for example medical
research was performed without patients informed consent.
Decisions about whether research is ethical depends upon the possible
implications and purpose of the research
Further, from where the stem cells are taken is key in discussing the
ethical implications.

11.1 Jenner tested his vaccine for smallpox on a child

Edward Jenner was an 18th century scientist

He encountered a milkmaid who had cowpox disease and therefore
thought she could not get smallpox
Jenner infected an eight yr. old boy with cowpox from which he soon
recovered, he then gave smallpox to the boy to see if he could resist it.
He was the first to use humans as test subjects in testing a vaccine.
No preliminary research at all was conducted before the testing, neither
were tests on other animals conducted.
The test subject was below the age of consent, and he infected him with
an extremely virulent, often fatal disease causing agent.
Experiments were performed before ethical guidelines around human
testing existed
Nuremberg trial in post WW2 brought about the Nuremberg Code for
ethical testing on humans, with further guidelines introduced in 1993.
Jenners experiments would not be approved in the modern age.

Assessing the ethics of scientific research

2.8 the use of invertebrates in respirometer experiments has ethical
implications

There has been intense debate about using animals in experiments

Do we consider consequences and intention?
Are there absolute principles of right and wrong?
There are certain questions that must be answered to decide whether
experiments are ethically acceptable before the carrying out before
respirometer.

Is it acceptable to remove animals from their natural habitats for

experimental use, and can they be safely returned.
Will the animals face pain or harm?
Can risk to the animals be minimised in particular can contact with
the alkali be prevented
Is using animals essential

2
3
4

Assessing claims
4.4 Assessment of the claims that human activities are producing
climate change

Climate change has been more hotly debated than almost any other area
of science.
What reasons could there be for opposition to climate change science?
o Scientists are trained to be cautious about their claims and to make
sure that they have sufficient evidence.
o They are expected to admit when there are uncertainties, which can
give the impression that evidence is weaker than it actually is.
o Global climate patterns are very complex and hard to predict, for
example, tipping points in climate patterns when sudden massive
changes occur at the moment it is estimated that this will occur
after 2 degrees of warming, however we cannot be sure until it
happens.
o Companies make huge profits from coal, oil and natural gas and it is
in their interest for fossil fuel combustion to continue. It would not
be surprising if they paid for reports to be written that minimise the
risks of climate change.
What reason do climate change scientists defend their findings so much?
o The consequences of changes in climate patters could be very
severe for humans and other species.
o Many scientists feel there is need for immediate action, even if
uncertainties remain in climate change science.

Obtain evidence for theories:

2.7 - Meselson and Stahl obtained evidence for the semi- conservative
replication of DNA

1958, Matthew Meselson and Franklin Stahl

Created a method (called caesium chloride density gradient
15

centrifugation) to separate DNA containing

14

in its bases from DNA with

The process is spinning a solution of caesium chloride in an ultracentrifuge

at nearly 45,000 revolutions per minute, for 20 hours. A gradient is
established when the denser caesium concentration at the bottom
They cultured E.Coli for fourteen generations in a medium where the
15

nitrogen source was

They then transferred the bacteria quickly to a medium in which all the
14

nitrogen was
They collected samples of DNA from the bacterial culture for several hours
They extracted the DNA and measured its density by caesium chloride
gradient centrifugation.
DNA could be detected because it created a dark band when the tubes
were illuminated with UV (as it absorbs UV light)

6.4 Epidemiological studies had contributed to our understanding of the

causes of lung cancer

Epidemiology is the study of the incidence and causes of disease.

Most epidemiological studies are observational, not experimental.
Theories about the causes of disease are proposed.
To obtain evidence for or against a theory, survey data is collected.
This allows the association between the disease and its theoretical cause
to be tested.
o Eg. To test the theory that smoking causes lung cancer, the smoking
habits of people who have developed lung cancer and people who
have not are needed.
There are very large epidemiological surveys that provide strong evidence
for a link between smoking and lung cancer (See Topic 1.6)
However a correlation between a risk factor and a disease does not prove
cause.
There are usually confounding factors which also have an effect on the
incidence.
o Eg. An association has been found by epidemiologists between
leanness and increased risk of lung cancer.
However, analysis shows that leanness does not increase the risk of lung
cancer, it more that smoking reduces appetite, so is associated with
leanness, and smoking is a risk factor to the development of lung cancer.
To compensate for confounding factors, it is necessary to collect data on
many factors, apart from the once being investigated.
This allows statistical procedures to take account of confounding factors.
o Eg. Age and sex are almost always recorded.

Paradigm Shifts
8.2 the chemiosmosis theory produced a paradigm shift in the field of
bioenergetics.

In 1969 peter Mitchell proposed a chemiosmotic theory to explain the

coupling of electron transport in the inner mitochondrial membrane for
ATP synthase.
It was a very radical and different hypothesis that was not accepted until
much later in 1978.
He was awarded a Nobel prize for chemistry in 1978
He proposed that the electrons where passed along electron carrier
proteins allowing the pumping of proteins across the membrane.

Here the hydrogen ions accumulate lowering the pH and represents a

store of potential energy.

9.4 - more than 85% of the worlds 250,000 species of flowering plants
depend on pollinators for reproduction. This knowledge has led to
protecting ecosystems rather than individual species.

In the past conservation has focused on specific species with dwindling

numbers. This however is less of the focus as new improvements in
knowledge has informed scientists of the importance and links between
species in an ecosystem. Conservation is now focused on an ecosystem as
a whole including producers and consumers.

Curiosity about particular phenomena

11.3 - Investigations were carried out to determine how desert animals
prevent water loss in their wastes.

Animals in arid environments survive with little or no water.

Physiologists noted that extremely concentrated urine is formed and no
sweat is produced.
In deserts, some flora and fauna are only visible at certain times
Animals remain cool during daytime
Respiratory moisture condenses in nasal passages
Metabolic water derived from dry seeds
Urine is concentrated by counter-current exchange in extra-long loop of
Henle
Feces dehydrated prior to egestion

Assessing risks and benefits of scientific research:

11.4 - the risks to human male fertility were not adequately assessed
before steroids related to progesterone and estrogen were released into
the environment as a result of the use of the female conceptive pill.

High levels of estrogen are present in pregnant women and inhibit FSH
release.
If pills containing estrogen are consumed development of mature follicles
are inhibited.
First contraceptive pill was introduced in 1943.
In meid-1980s there were reports of elevated levels of pill hormones in
water.
In 199s, many studies concluded that male sperm count had reduced by
50% over the past 50 years.
In 2004 in the UK, it was found that 84% of male fish were showing signs
of feminization, that is they were intersex
There is limited information that pollution of steroids related to estrogen
and progesterone is the causative agent behind reduced male fertility.
In 2012, a policy was proposed to limit the concentrations of pill hormone
in water.
Upgrading technology for wastewater treatment could eliminate most of
the pollution.
Drugs are widely used in animals so preventing animals to urinate near
river water could reduce the amount of drugs leaking into surface waters.

Scientists have a role in informing the public:

D.6 - Scientific research has led to a change in public perception of
smoking

In the early 20th century, there was belief that tobacco smoking would
improve ventilation.
Doctors even prescribed smoking of medicine for conditions such as
asthma.
During 1930s and 1940s there was rising public concern about the health
risks of smoking cigarettes.
Tobacco companies then used advertising on cigarette packets with
images of physicians and scientists to ensure that their brands were safe.
In 1964, a report showed that there was a link between smoking and
chronic bronchitis and other cancers.
The number of smokers steady declined in developed nations, with nearly
half of all adults that smoked quitting.
Health departments had used strong policy measures and convincing
scientific evidence to achieve this.

Testing the general principles that underlie the natural world

1.5 - the principle that cells only come from preexisting cells need to be
verified

Spontaneous generation is the formation of living organisms from

nonliving matter
Greek philosopher reported a plant had sprung up from soil where it was
not previously present and described this as an example of spontaneous
generation
Francesco Redi showed maggots only developed in rotting meat if flies
were allowed to come into contact with it

Apart from evidence from experiments of pasteur and others, there are other
reasons for biologists universally accepting cells only come from preexisting cells
Cell is a highly complex structure and no natural mechanism has been
suggested for producing cells from simpler subunits
No example is known of increases in the number of cells in a population,
organism or tissue without cell division occurring
Viruses are produced from simpler subunits but they do not consist of cells and
they can only be produced inside the host cells that they have infected