What are SPLATs? They are explained here.
The principles of classification
- The study of classification is called taxonomy, but there are
many ways of dividing up an existing group of living things, depending
on the assumptions made.
- Living things can be sub-divided according to similarities,
but the end result will depend on which similarities are studied and
taken into account.
- John Ray published a study of Cambridge plants in 1660,
setting a new standard for descriptive work in botany that would
influence his successors.
- Around 1700, while working at the Jardin des Plantes,
Joseph Pitton de Tournefort developed the idea of a genus that Linnaeus
would later seize on with delight.
- In 1753 Linnaeus published his Species Plantarum, which
marked the beginning of what we now see as the standard modern binomial
(genus and species) plant names.
- In 1758 Carl von Linné ( Linnaeus ) published the tenth
edition of his Systema Naturae. Modern binomial zoological names for
animals began at this point.
- In 1766 Buffon suggested that each Linnaean genus stemmed
from a single ancestor. This was part of Buffon's theory that all
evolution was degeneration.
- Linnaeus did not like the Comte de Buffon and his ideas at
all, and took advantage of this, as the chief namer of things, to call a
stinky weed Buffonia.
- The common five kingdom classification of living organisms
is Monera, Protista, Fungi, Plantae and Animalia. In this system, the
Archaea lie in the Monera.
- The highest level of classification is generally taken as
the kingdom, and in that system, the level below the kingdom is a
phylum.
- A species is defined as a group of organisms that share a
common gene pool and breed together, or could do so, if they were in the
same place at the same time.
- Another definition of a species regards them as a group of
organisms which share in a common gene pool. This leaves isolated
populations as a problem.
- Every species is named according to the rules of binomial
nomenclature, with a unique genus name and a species name that is unique
within that genus.
- The sub-divisions of living things are assumed to reflect
their history in evolution fairly closely, but there will always be some
argument around the edges of this.
- All sorts of data may be used in arriving at a
classification system, including genomics, biochemistry and structure,
and these may lead to conflicting results.
- In a few cases, convergent evolution may produce similar
organisms and trick scientists into grouping unrelated organisms
together, based on similar appearance.
- In a few cases, the effects of adaptive radiation may lead
to rapid change and trick scientists into separating related organisms
because they look different.
- One way to avoid confusion caused by misleading appearances
is to use genomic evidence, but horizontal gene transfer can interfere
with this form of evidence.
- One popular form but somewhat radical form of taxonomy is
called the cladistic method, another popular form of taxonomy is called
the phenetic method.
- Some groups are suspected of being polyphyletic: the bats,
for example, are composed of two groups, and some scientists think these
evolved separately.
- Having a group called 'invertebrate' shows us an unnatural
division of living things, as about all they have in common is the lack
of a backbone or notochord.
- Mammals are often grouped by their dental formula, the
numbers of incisors, canines, premolars and molars in their jaws. This
usually matches other evidence.
- In 1842, Johannes Müller rediscovered and confirmed something that Aristotle knew: that dogfish young can have a placenta-like attachment to the mother.
The history of evolutionary ideas
- T. H. Huxley was 'Darwin's bulldog', a scientist who
single-mindedly defended Darwin's notion that evolution was driven by
the process called natural selection.
- When Darwin proposed in 1859 that evolution was due to
natural selection, he was not the first to try to explain evolution, or
the first to propose that cause.
- In 1667 Nicolaus Steno recognized the homology of the
mammalian ovary with that of the egg-laying animals, thus making a major
advance in comparative anatomy.
- In 1753 Buffon wrote about the donkey, which he treated as a
degenerate horse, but this still implied the operation of a form of
evolution from earlier forms.
- In 1801 Jean-Baptiste de Lamarck elaborated his theory of
evolution based on inheritance of changes to organs acquired by
continued use and loss through disuse.
- In 1802, William Paley published his Natural Theology, an
'argument by design' for the existence of God, and boosted interest in
taxonomy and natural history.
- Two centuries later, the intellectually bankrupt 'argument
by design' is still being peddled, disguised as an 'all-new'
'intelligent design hypothesis'.
- In 1838, Charles Darwin read what Thomas Malthus had to say
about populations. This argument would be a key component in his later
reasoning about evolution.
- In 1844, Charles Darwin wrote out his first sketch of the
theory of evolution by natural selection. The main points were there,
but it lacked detailed evidence.
- In 1844, when Darwin wrote a first draft of what would
later become his world-changing 'On the Origin of species', he set it to
one side nervously.
- In 1844, Robert Chambers published his anonymous 'Vestiges
of the Natural History of Creation'. It may have encouraged Darwin to
delay publishing his ideas.
- After the anonymous publication of the 'Vestiges', there
was a lot of controversy about the identity of the author, and also
about the book itself.
- In 1857, Charles Darwin wrote a long letter to Asa Gray,
setting out his arguments for believing that evolution was driven by the
effects of natural selection.
- In 1858, spurred by Alfred Russel Wallace, Charles Darwin
wrote and presented a short paper on his evolutionary theories, and also
a letter from Wallace.
- Many of Darwin's colleagues went to great lengths to
establish that Darwin had thought of natural selection first, and had
discussed it with them.
- In 1859, Charles Darwin finally published the first edition
of 'On the Origin of species', a work that would go through a number of
revisions in his lifetime.
- Adam Sedgwick, Darwin's old geology teacher at Cambridge,
never accepted the latter's theory of evolution, remaining one of the
notion's stronger opponents.
- While Charles Darwin championed the idea of evolution
driven by natural selection, but often showed signs of him accepting the
inheritance of acquired traits.
- Where Charles Darwin differed from those who went before
him: he had the insight to see that natural selection could drive
evolution, and he had the evidence.
- Both Darwin and Wallace were prepared to recognise the role
of natural selection because they had both collected large numbers of
specimens in many places.
- In 1976, Richard Dawkins published The Selfish Gene, which
had as its thesis that genes which acted in a way to favour their
survival would be selected.
- In 1972, Stephen Jay Gould and Niles Eldredge proposed the notion that punctuated equilibrium may be seen in evolution, with quiet periods and active periods.
The principles of biogeography
- Around 400, St Augustine considered the distribution of the animals
after Noah's flood, and suggested that either men or angels must have
transported them.
- Science cannot sustain the view that there ever was a flood
like Noah's, and so does not consider this distribution puzzle as a
real problem.
- In 1860, Alfred Russel Wallace described the boundary
between the Australian and Oriental faunal regions, now usually called
the Wallace line or Wallace's line.
- The Wallace's line follows a deep-water channel which runs
between Kalimantan and Sulawesi, and between Bali and Lombok, dividing
Indonesia into two zones.
- In 1859, Asa Gray suggested the north American and Eurasian
floras had once been homogeneous, then separated by Pleistocene
glaciation and by later evolution.
- Lydekker's line and Wallace's line are examples of
biogeographic boundaries that mark the limits of ancient zones of
evolution and the spread of various taxa.
- Evidence for evolution is found in biogeography, where
related types of land animals such as Old and New World monkeys are
found on related land masses.
- Biogeography also reveals lots of useful information about the way the planet's tectonic plates have moved around in the past, carrying life forms with them.
The principles of the origins and history of life
- One theory of the origins of life with no evidence is panspermia. It
is an interesting idea, but unsupported by any fossil or other evidence
so far.
- Panspermia is based on the belief that our planet was
somehow seeded with primitive life forms that were floating around in
space, and managed to reach here.
- The main argument in favour of panspermia is that life
seems to have appeared on Earth very soon after the earliest date at
which it was possible for it.
- Around 1630, Jan Baptista van Helmont offered a recipe for
making mice by spontaneous generation by leaving wheat and an old shirt,
soaked in sweat for 21 days.
- In 1651 William Harvey published his Exercitationes de
Generatione Animalium with the aphorism "ex ovo omnia", (all come from
eggs), on the title page.
- The 1748 experiments of Buffon with John Needham seemed to
show that micro-organisms could spring up spontaneously in jars of
sterilized meat broth and gravy.
- In 1862, Louis Pasteur conclusively disproved that
spontaneous generation of living organisms ever happens with a series of
carefully controlled experiments.
- The history of life can be deduced from the evidence, which
includes many other observations other than the fossil evidence, though
that gives us a clear story.
- Before they could move onto the land, animals needed to
have a way of breathing air, because gills do not work out of water,
thanks to surface tension effects.
- Surface tension makes external gills almost useless in land
animals, because the individual 'fibres' will become matted together.
Lungs are needed instead.
- Serial endosymbiosis theory says the various parts of
eucaryotic cells were once separate organisms which came together to
form a more effective combination.
- In 1971, Lynn Margulis proposed an endosymbiont theory,
otherwise known as serial endosymbiosis theory, to explain the origins
of eucaryotic organelles.
- In 1977, researchers discovered chemosynthetically based
communities located submarine thermal springs on the Galápagos Rift.
Many others have since been found.
- Temperature affects many animals, although some living
things are extremophiles and flourish in extremely high temperatures in
volcanic and thermal springs.
- Life began early in the Precambrian era, probably at least
3800 million years ago: most of the rocks of that time have been lost or
altered since then.
- Urey and Miller sparked a mixture of gases: ammonia,
methane and steam, similar to what they thought might have been the
atmosphere on the early Earth.
- Urey and Miller wanted to see if complex organic molecules
can form, free of any living influence. The electrical sparks produced a
complicated organic 'soup'.
- We suspect now that methane was absent from the original
atmosphere, and that carbon was present as CO2. This means that the
experiment probably proves nothing.
- Life forms changed very fast after the Cambrian explosion,
for reasons which are still not completely clear, but probably relating
to increased competition.
- One plausible explanation for the Cambrian explosion is
that the evolution of vision forced animals to develop better ways of
avoiding or resisting predators.
- Life evolved in the water, then came on to land: first
plants, then the amphibians, or maybe the insects: the fossil evidence
will probably never tell us which.
- Before they could grow to any height on the land, plants needed to have conductive tissues to carry water up to their tops, and special structural tissues.
The evidence for evolution
Human evolution
Genetics and evolution
- Charles Darwin could see that natural selection was the cause of
evolution, but explaining properly had to wait for the discovery of the
science of genetics.
- Charles Darwin believed that the variation needed for
natural selection to work came from what he called 'sports', equivalent
to what we now call mutations.
- The basic principle of evolution is that natural selection
acts when changed conditions operate on chance mutations either existing
or arising in a population.
- From this viewpoint, evolution by natural selection is all
about the changes in gene frequencies in a population after some
condition or conditions change.
- Charles Darwin found one major problem with his theory of
evolution by natural selection because he believed inheritance operated
by blending parental forms.
- In blending inheritance, if you pollinate a red flowered
with pollen from a white flowered plant, the seeds will develop into
plants with pink flowers.
- Blending inheritance is quite rare in nature, and Gregor
Mendel knew this soon after Charles Darwin first published his theories
on natural selection.
- Because nobody took any notice of Gregor Mendel's work for
many years, blending inheritance remained a problem for those who
adopted Charles Darwin's ideas.
- With blending inheritance assumed, people thought from this
that any new mutation would be immediately 'swamped' by the normal
genes in the same population.
- In 1929, R. A. Fisher published his book 'The Genetical
Theory of natural selection', which made an explicit link between
Darwinian evolution and genetics.
- In 1931, Sewall Wright linked selection pressure, mutation
rates, inbreeding, and isolation, and proposed genetic drift, which he
developed the next year.
- In 1932, Sewall Wright outlined genetic drift, an effect
caused by the chance loss of alleles in small populations, without
selection being involved.
- In 1939, Julian Huxley introduced the concept of the cline
in evolutionary variation, a regular variation in gene frequencies with
changes in the habitat.
- Today, genetics is an important part of evolution, because it allows us to apply information from genomics when we want to measure how species are related.
Animal behaviour
About populations
Interdependence
Biodiversity
Climate change
About extremophiles
- Organisms living in salty conditions generally need some form of
active transport to get rid of the salt they take in with their food and
drink.
- Halophytes are a specialist group of plants, able to handle
extremely salty conditions because they have special salt-resistant
adaptations to help them.
- An estuary provides special problems for animals and
plants, in large part because of the wide variations in salinity and
what this does to water balance.
- Extreme environments which carry extremophiles include both
the Arctic and the Antarctic, hot springs, and mid-ocean vents which
are both hot and toxic.
- Unusual life forms can be found in some very improbable
places: high up in the atmosphere, deep in rocks and ice, in hot, cold,
wet and dry places.
- There are limits to what animals can survive: as a bare
minimum, they need certain levels of moisture or fluid, enough oxygen
and sufficient food.
- Biologists hope that the oceans beneath the icy surface of
Jupiter's moon, Europa, may also be extreme environments that carry some
form of life.
- Even in extremophiles, there are limits to the extremes of climate, starvation, drought, heat and general environment animals can survive in the longer term.
Ecology
The principles of the environment
- For a variety of reasons, there are limits to how small or large an
animal can be in a particular environment. These involve both physics
and chemistry.
- Bergmann's rule says animals and subspecies in colder
climates are larger than those found in hotter climates. Large size
makes it easier to conserve heat.
- Gravity affects all land animals and most aquatic animals:
there are limits to how light or heavy an animal can be: animals living
in water can be heavier.
- Atmospheric pressure and air density affect many flying
animals: at altitude, less oxygen is available for breathing, and less
air is available to push against.
- Surface tension affects many animals in unexpected ways:
land animals need lungs, not gills, small animals can 'walk' across the
surface of calm water.
- Mammals and birds are homoiothermic: they maintain their
temperature by homeostasis and insulation. Those animals which do not
are called poikilothermic.
- There are limits to what conditions animals can survive:
they need certain levels of moisture, oxygen, temperature and food as a
minimum for survival.
- The turbidity of water may be measured with a Secchi disc, which is lowered until it just disappears, and then raised until it just appears, and averaging them.
The principles of conservation and pollution
- Pollution is the release of products not worth recycling, so the
extent of any pollution can be reduced by making producers pay the cost
of dumping it.
- Many halogenated compounds are persistent in nature, in
part because they are often soluble in fats, and so may be readily
concentrated up the food chain.
- The polychlorinated biphenyls are persistent pollutants:
the major problem with some persistent pollutants is bioaccumulation up
the food chain.
- Treatment of sewage before it goes into rivers and lakes
reduces eutrophication, and the better the treatment, the less
eutrophication there will be.
- Large amounts of organic material increase the biological
oxygen demand, whether the material comes from eutrophication, sewage,
or dumping of waste.
- Atmospheric changes spread widely, even crossing the
equator into the other hemisphere. Nobody owns the air, nobody has the
right to pollute it.
- Some substances are biodegradable, which means levels in
the environment slowly fall, though sometimes the products are still a
problem in the environment.
- Eutrophication happens when water has too many nutrients,
so plants grow faster than they can be eaten: when these die and rot,
they may take all the oxygen.
- Salination is a problem with soils all over the world. In
large part, it is caused by rising groundwater, itself caused by
land-clearing that removes trees.
- An ozone hole results from ozone depletion caused by gases
released elsewhere in the world: the main one is over the South Pole
each southern summer.
- Ozone levels in the upper atmosphere are measured with a
Dobson spectrophotometer, and these show that ozone levels are dropping,
mainly over the Poles.
- Land (and soil) is a limited resource, all over the world,
it is being degraded, so clearing is needed to get more, leading to a
massive loss of habitat.
- Laterization is a common problem with soils. This involves
the leaching of some of the more soluble soil components to leave iron
and aluminium oxides.
- There is a limit to the sustainable yield from any
ecosystem, sustainability here assuming that conditions will be fully
preserved, so the system is unchanged.
- Many forms of so-called sustainable harvest do not take
into account long-term damage done to soil, biodiversity, and nearby
waterways, so are not sustainable.
- Aquaculture is a highly productive way of farming, but it
brings many problems, mainly because it is intensive, and so produces
large amounts of waste.
- Pests and feral species can be prevented from entering a
new area by maintaining a suitable quarantine system to keep them and
their seeds out.
- Pests and feral species which have arrived in an area can
be prevented from breeding by use of the sterile male technique to limit
any breeding that happens.
- Conservation of endangered species means maintaining their
genetic diversity, but it also means maintaining biodiversity in
habitats of many kinds.
- The world has many endangered species: some of them are probably more vital to our survival than others, but it is very hard to say which are which.
The principles of cell division
- All cells reproduce by growing to a larger size, and then dividing
to form two daughter cells, which then begin to grow, so that they are
also can divide.
- Normal cells have the diploid number of chromosomes,
although there are some exceptions found in reproductive systems, where
gametes are normally haploid.
- In 1875, Eduard Strasburger accurately described the
processes of mitotic cell division. It was given the name mitosis by
Walther Flemming in 1882.
- In 1885, Walther Flemming reported seeing sister chromatids
passing to opposite poles of the cell during mitosis, drawing attention
to their importance.
- Processes which occur in the nucleus include meiosis and
mitosis: nucleic acid is copied in these processes, so each new cell
carries the full set of genes.
- In meiosis, pairs of homologous chromosomes line up and
crossing-over happens at the chiasma, where portions of the two
chromosomes are exchanged.
- The result of meiosis is an independent assortment of genes
through recombination. After meiosis, gametes have the haploid number
of chromosomes.
- Most mistakes in the copying of genes, the plans for a cell
in the nucleus, are harmful to the cell that carries them, but very
rarely, they are useful.
- When cells divide to make new cells, they must copy all of
the parts in the cell to make sure that each daughter cell is fully
equipped, or else they will die.
The principles of genetics
- 1828 Karl Ernst von Baer published his The Embryology of Animals which strongly opposed preformationism, showing that mammals also have 'eggs', or ova.
- In 1866, Gregor Mendel published his experiments on the
crossbreeding of pea plants. These revealed that inheritance was not
blending, as had been assumed.
- The basic principles of genetics were first set out in
Mendel's laws, although they have since been found to be more
complicated in some cases.
- Genes may occur in multiple forms called alleles. Some
alleles may mask (be dominant over) other alleles which are called
recessive because they 'recede'.
- Homozygous individuals generally breed true when crossed
with another similar-appearing homozygous individual, unless there are
two mutations at the same time.
- Heterozygous individuals may not 'breed true' if crossed
with another heterozygote, as heterozygotes produce gametes with
different genes for a single trait.
- In some cases, alleles may show incomplete dominance, with
intermediate heterozygotes, rather than the classic Mendelian
dominant/recessive pattern.
- Gregor Mendel showed that the genes do not blend to an
average, but that the original character, in its original form, can
return in a later generation.
- While Darwin was still puzzling about blending inheritance,
Mendel had provided the answer and published it, but sadly, nobody
noticed, for almost forty years.
- Independent assortment of genes, as described by Mendel,
may be restricted by linkage effects where two genes are nearby on the
same chromosome.
- In 1902, William Bateson coined the terms F1, F2,
allelomorphism, homozygote, and heterozygote for use in the discussion
of genetics experiments.
- In 1905, William Bateson and Reginald Crundall Punnett
reported the discovery of two new genetic principles of interest:
linkage and gene interaction.
- In 1905, Edmund Wilson and Nellie Stevens independently
described the behaviour of sex chromosomes, showing that XX determines
female, XY determines male.
- In 1905, Lucien Claude Cuénot discovered the first lethal
allele, the yellow coat colour allele in mice, showing that genes could
play a role in selection.
- In 1906, C. W. Woodworth and William Ernest Castle
introduced the fruitfly Drosophila melanogaster as new experimental
material for genetic studies.
- In 1908, G. H. Hardy and Wilhelm Weinberg independently
proposed the Hardy-Weinberg Law, that gene frequencies remain constant
in the absence of selection.
- In 1909, F. A. Janssens suggested that the chiasmata
between chromosomes could be taken as evidence for the phenomenon of
crossing over among linked genes.
- In 1909, Castle and Phillips showed that an ovary from a
black guinea pig, transplanted into a white one, still gave black
offspring if mated to a black male.
- In 1909, Wilhelm Johannsen showed that natural selection
demands a source of genetic variability and introduced the terms
'genotype' and 'phenotype'.
- In 1910, Thomas Hunt Morgan proposed a theory of sex-linked
inheritance for the first mutation discovered in the fruit fly,
Drosophila, white eye.
- The identification of white-eye in Drosophila melanogaster
as a sex-linked gene was followed by the gene theory, including the
principle of linkage.
- In 1911, Thomas Hunt Morgan first proposed that the
Mendelian factors, otherwise the genes, were in fact arranged in a line
on chromosomes in some way.
- In 1913, Alfred Sturtevant used crossing-over frequencies
to get relative distances for a map of genes on the chromosome, using
sex-linked genes in Drosophila.
- Plants often hybridize outside their species: plant hybrids
can be created that cross species 'barriers', and even different genera
may be hybridized.
- Plants are often polyploid, especially cultivated
varieties, although it also happens naturally in some groups.
Tetraploids can often reproduce successfully.
- In animals, triploid individuals rarely survive. Triploid
plants can survive, though some of them do not breed very well, due to
problems at meiosis.
- In animals, trisomic individuals, with one extra
chromosome, can sometimes survive, and this may be related to the number
of genes on the extra chromosome.
- In 1927, Karpchenko got a tetraploid cabbage-radish hybrid,
thus creating the new genus, Raphanobrassica, with a full gene
complement from each parent.
- In 1937, Albert Francis Blakeslee and Oswald Avery used
colchicine to produce artificial polyploidy in plant cells, making a new
tool for experimental genetics.
- In 1941, George Beadle and Edward Tatum irradiated fungus,
Neurospora crassa, and based on the results, they then proposed the one
gene one enzyme hypothesis.
- Beadle and Tatum's irradiated Neurospora allowed them to
establish conclusively that the gene produces its effect by regulating
particular enzymes.
- In 1946, Joshua Lederberg and Edward Lawrie Tatum studied
the process of conjugation in Escherichia coli, where bacteria
interchanged genetic material.
- In 1947, Barbara McClintock published her hypothesis of
transposable elements (her 'jumping genes') to explain curious colour
variations in corn.
- In 1952, William Hayes demonstrated a variety of forms of
conjugation in bacteria, a method by which bacteria can exchange genetic
information.
- Genes differ in their effect according to the parent they come from in some cases. This is called 'imprinting', and is not yet fully understood and explained.
The principles of chromosomes
- Most people who have stopped to think about it has always known that
animals and plants inherit their appearance and nature from their
parent organisms.
- A complication for early scientists was the belief in
spontaneous generation, which assumed that parents were not needed to
provide inherited information.
- In 1831, botanist Robert Brown announced the discovery that
each living cell contains a nucleus. Others had seen nuclei, but now
they were seen as universal.
- Once people realised that we are made of cells, and that
cells reproduced by dividing, it became fairly obvious there must be
something inheritable in the cell.
- In 1879, Walther Flemming discovered a thread-like material
in the nucleus of cells. These threads were later named the
chromosomes, because they took stains.
- In 1883, Edouard van Beneden announced the principles of
genetic continuity of chromosomes and reported the occurrence of what we
would now call meiosis.
- In 1888 Theodor Boveri verified August Weismann's
predictions of chromosome reduction (which we call meiosis today) by
direct observation in the worm Ascaris.
- In 1900, Walter Sutton observed homologous pairs in the
chromosomes of a grasshopper, and he reported in 1902 that they separate
to opposite ends in meiosis.
- In 1903, Walter Sutton and Theodor Boveri independently
confirmed that the chromosomes behave in a way that matched what was
known of Mendelian inheritance.
- By the careful study of genetics, Sutton and Boveri were
able to recognise that the only thing in the cell behaving like Mendel's
genes was the chromosomes.
- Alfred Sturtevant worked in the Columbia 'fly room' and
actually constructed the first genetic map of a chromosome in 1913,
using linkage data.
- In 1927, H. J. Muller used X-rays to cause artificial gene
mutations in Drosophila, showing that the mutation rate was 1500 times
higher when X-rays were used.
- It was not enough to know that the chromosomes carry the
genes in some way, because chromosomes are made up of both protein and
nucleic acids.
- In 1956, Joe-Hin Tjio and Johan Albert Levan revised
Walther Flemming's 1898 estimate of the human chromosome count from 24
pairs to 23 pairs.
- In 1973, Bruce Ames published details of the 'Ames Test' to
identify DNA-damaging chemicals. The test has since become a widely
used to screen for carcinogens.
- All living things are made up of small units called cells.
Each cell usually contains a nucleus with coded information that the
cell uses to operate.
- Genes were first located as existing on the chromosome by
the Sutton-Boveri theory which has stood the tests of time. The genetic
code is further proof.
- The gender in animals is usually determined by the sex
chromosomes, although different groups such as birds and insects do this
differently from mammals.
- In mammals, normal males have an X-chromosome and a
Y-chromosome, females have two X chromosomes. A sperm cell carries an X
or a Y, an ovum carries an X only.
- The 'plans' for a living thing are found in chemical
strings in the nucleus of the cell, and mistakes sometimes get made when
these plans are copied.
- Each gene in the nucleus codes for a single unique protein.
Most proteins work as enzymes that catalyse the conversion of one
biochemical into another.
- A biochemical pathway involves a large number of conversions, each managed by an enzyme. If any enzyme is changed, the end product may never be produced.
The principles of nucleic acids
- There are two different nucleic acids found in the living world, DNA
and RNA, each of them used as the genetic material in some types of
organism.
- The bases in DNA, in sets of three, code for amino acids in
a protein, and this code is common to all forms of life, suggesting it
evolved very early.
- When DNA is copied, the replication is semi-conservative,
with one strand of the original DNA gaining a new second strand to make
two new double strands.
- In most organisms, DNA is used as the genetic material. It
is transcribed to RNA and then this becomes the pattern for a protein,
following the genetic code.
- Ribonucleic acid (RNA) occurs in our cells in a number of
forms: it can be found in eukaryotic cells as messenger RNA, ribosomal
RNA and transfer RNA.
- A given triplet of bases in DNA always codes for the same
amino acid. Other triplets can code for the same amino acid. Some
triplets have other functions.
- The order of the bases in a strand of DNA can be determined
in a variety of ways, usually after PCR has been used to increase the
amount of DNA available.
- The base sequences of DNA can be determined, but modern DNA
sequencing would be impossible without the DNA microarray, YACs and
BACs, and bioinformatics.
- In 1869, Johann Friedrich Miescher had proposed that all
cells' nuclei must have a specific chemistry. This substance came to be
known as nucleic acid.
- In 1871, Miescher isolated a substance which he called
nuclein from the nuclei of white blood cells that was soluble in alkalis
but not in acids.
- In 1876, Oskar Hertwig and Hermann Fol showed that
fertilized eggs have both male and female nuclei, that is the nuclei of
both parents make a contribution.
- In 1884, Eduard Strasburger suggested, based on studies of
fertilization, that the nucleus of the cell must be the carrier of the
genetic material.
- In 1928, Frederick Griffith discovered that some unknown
'transforming principle' had changed the harmless R strain of
Diplococcus to the virulent S strain.
- In his 1945 book, 'What Is Life?', Erwin Schrödinger
proposed that the genetic material, when discovered, would turn out to
be some sort of aperiodic crystal.
- Schrödinger's gentle little probes and cryptic questions
like "Why are atoms so small?" set the scene for the new generation of
molecular biologists.
- About the time Erwin Schrödinger decided that the gene had
to be an aperiodic crystal, Oswald Avery's team had found what the
aperiodic crystal must be made of.
- In 1944, Oswald Avery, Colin MacLeod and Maclyn McCarty
reported an experiment that arose out of Griffith's 1928 work, and
pointed to DNA as the key material.
- Avery, MacLeod and McCarty used two enzymes, one to break
down DNA, and one to break down protein: transformation only happened
when the DNA was left intact.
- The answer basically is that you can't build something as
complex as us out of just a few components. So atoms have to be small,
from our point of view.
- The other half of Schrödinger's question is "Why are we so
much larger than the atoms that we are made of?", and that is probably
the more interesting question.
- In 1950, Erwin Chargaff discovered a one-to-one ratio of
adenine to thymine and guanine to cytosine in DNA samples from a variety
of organisms.
- The key to understanding DNA structure lies in Chargaff's
rules from 1948 about the linkages between adenine and thymine and
between cytosine and guanine.
- Chargaff first showed that the number of guanine units
equals the number of cytosine units and the number of adenine units
equals the number of thymine units.
- In 1951, Lederberg and Zinder showed that bacteria can
exchange genes indirectly by transduction, when a virus carries genes
into the next cell it infects.
- In 1952, Rosalind Franklin used X-ray diffraction to study
the structure of DNA and suggested that its sugar-phosphate backbone was
on its outside.
- In 1952, Alfred Hershey and Martha Chase used
bacteriophages in their 'blender experiments' to establish with
certainty that DNA was the genetic material.
- Hershey and Chase used protein that was labelled with
sulfur 35 and DNA labelled with phosphorus 32 for their final proof that
DNA carried the information.
- In 1954, George Gamow proposed that the genetic code must
be made of triplets of nucleotides, based on the argument that 2 was not
enough, 4 would be too much.
- In 1956, Arthur Kornberg discovered DNA polymerase, and
used this enzyme to show that DNA is always constructed in a single
direction, the 5' to 3' direction.
- In 1957, Francis Crick and George Gamow worked out the
'central dogma' of genetics, explaining how they considered that DNA
must function to make protein.
- Crick and Gamow proposed their 'sequence hypothesis', which
said in effect that the DNA sequence specifies the amino acid sequence
in a protein.
- In 1958, Matthew Meselson and Franklin Stahl demonstrated
semiconservative replication in DNA using 15N and ultracentrifugation in
a density gradient.
- In 1959, François Jacob and Jacques Monod proposed the role
of RNA in transmitting information to the sites of protein synthesis,
the repressor-operon model.
- They also suggested that genetic information flows only in
one direction, from DNA to messenger RNA to protein, the central concept
of the central dogma.
- In 1961, Marshall Nirenberg built a strand of RNA, composed
entirely of uracil, and determines that the codon, the genetic code for
phenylalanine was UUU.
- In 1965, small supernumerary chromosomes called plasmids,
were seen to carry genetic material between bacteria, including genes
for antibiotic resistance.
- In 1966, Marshall Nirenberg and H. Gobind Khorana led teams
that cracked the genetic code, finding what base combinations code for
which amino acids.
- In 1968, Fred Sanger used radioactive phosphorus as a
tracer to decipher a 120 base long RNA sequence, using a complicated
piece of chromatography.
- In 1970, Howard Temin and David Baltimore independently
discovered reverse transcriptase enzymes that produce DNA from RNA,
going against the usual pattern.
- In 1973, Annie Chang and Stanley Cohen show that
recombinant DNA molecules can be maintained and replicated in E. coli:
the first recombinant DNA organism.
- In 1974, Manfred Eigen and Manfred Sumper showed that
mixtures of nucleotide monomers and RNA-replicase gives RNA molecules
which replicate, mutate, and evolve.
- In 1977, Fred Sanger and his team sequenced the entire
phage X174 virus, base by base, all 5386 bases of it, in a single
circular strand of DNA.
- In 1983, the complete 48,502 base pair sequence of the
linear double-stranded DNA of a virus, the temperate E. coli
bacteriophage lambda, was published.
- In 1985, Kary B. Mullis published a paper describing the
polymerase chain reaction (PCR), the most sensitive assay for DNA which
has yet been devised.
- In 1989, Alec Jeffreys coined the term 'DNA fingerprinting'
and was the first to use DNA polymorphisms in paternity, immigration,
and murder cases.
- In 1990, Mary Claire King reported the discovery of the
gene linked to breast cancer in families with a high degree of incidence
before age 45.
- In 1990, Michael Fromm reported the stable transformation
of corn using a high-speed gene gun to introduce new and desirable genes
into the nucleus.
- In 1997, Dolly the sheep was the first higher mammal cloned
from a single adult cell when a prepared nucleus from an adult cell was
added to an enucleated ovum.
- In 1997, The first-ever completed genome was published in Nature, the genome of the yeast, Saccharomyces cerevisiae. It was published as a separate supplement.
About genomics
- A gene from one organism will often work in another organism,
because most genes are widely conserved in evolution. Old genes can be
recognized in new genomes.
- A portion of DNA can be sequenced when it is turned into a
bacterial artificial chromosome, but these then need to be combined to
get the complete sequence.
- A portion of DNA can be sequenced when it is turned into a
yeast artificial chromosome, but these then need to be combined to get
the complete sequence.
- The base sequences of DNA need genetic maps to refer to.
The genes involved are usually identified and linked to a role from
similar genes in other species.
- The base sequences of DNA offer valuable information to
students of evolution, but will be even more important to medical
science, identifying new drug targets.
- Similar-looking species may be distinguished by DNA
fingerprinting, which can reveal differences in species which have
converged on a common external form.
- The information gathered in genomics work can be applied
through bioinformatics, which is a new science that involves processing
raw data to information.
- Genetic manipulation may lead in the future to the
production of safe vaccines being included in plants that humans can eat
to gain immunity to a disease.
- The Human Genome Project was set up to sequence all of the
human genome, and to identify the functions of the various genes as they
were identified.
- The hunt for single nucleotide polymorphisms is opening up many new ways of studying genomics, because it sheds light on the ways genes work.
The principles of cloning
- Clones are organisms which have identical genes, so identical twins
are clones and vegetative reproduction produces clones. Scientists can
clone some organisms.
- We eat food from clones all the time: almost all sugar cane
is produced from cuttings, which means that sugar cane is cloned, and
our sugar comes from clones.
- Cloning humans is regarded by most scientists as both
unethical and also dangerous to the new clone, due to errors that will
occur in at least some early cases.
- Cloning a mammal means taking a prepared nucleus from a
cell and placing it in an ovum which has had the nucleus removed to let
the new nucleus to take control.
- The normal nucleus in a new zygote has very few genes
operating, while committed cells, anywhere in the body, normally have
quite a few active genes.
- The preparation of a nucleus for cloning usually involves depriving the cell of nutrients, so that the nucleus largely shuts down, switching genes off.
The principles of reproduction
- Sexual reproduction begins with a diploid zygote forming when nuclei
from two haploid gametes fuse, but that only sets the scene for more
complex development.
- Sexual reproduction provides for a more efficient mixing of
genes in the offspring that result, giving them an advantage in terms
of natural selection.
- Sexual reproduction requires a reduction division or
meiosis to reduce the number of chromosomes before the gametes fuse and
restore the total.
- The male part of a flower is the stamen, which contains the
anthers that actually produce pollen grains. The ovary is located at
the centre of most flowers.
- Asexual reproduction results in almost identical 'daughter'
offspring being produced: this form is assumed to lead to slower
evolutionary changes.
- Asexual reproduction provides quick and easy reproduction,
especially in cases where it may be hard for one individual to find a
mate or breeding partner.
- Many grasses and rosette plants spread by sending out
runners into any vacant space and by trying to overgrow other plants, or
to beat them to bare space.
- Higher plants reproduce in many ways, using seeds,
cuttings, runners, and grafts, though some of these methods may be of
more use than others.
- Self-pollination is a form of sexual reproduction, even
though there is only one 'parent'. Most plants have mechanisms to favour
'outside' pollen.
- In many animals, the sex of offspring is determined by the
presence or absence of a sex chromosome, but there are several
variations on the basic plan.
- Pollen fertilizes a flowering plant when a pollen tube
grows down, carrying a haploid nucleus to a point where that nucleus can
fuse with one in the ovum.
- Pregnancy in human beings can be prevented or avoided by
using different types of barriers to keep sperm cells away from ova,
such as diaphragms and condoms.
- Pregnancy can be prevented by stopping women from ovulating
(that is, producing ova). This is the way the more common forms of 'The
Pill' operate.
- Pregnancy can be prevented by stopping men producing sperm
cells, typically by means of a vasectomy, which prevents sperm cells
entering the semen.
- Pregnancy in humans can be ended by abortion which may be
caused either by natural conditions (spontaneous abortion), or
mechanical or chemical interference.
- Pregnancy can be prevented by stopping or disrupting
implantation of a fertilized ovum (some forms of 'Pill', including the
'morning-after' Pill).
- The health of a fetus may be checked by amniocentesis,
which uses a needle to sample cells of the fetus that have been sloughed
off into the amniotic fluid.
- In 1974, the first test-tube babies were conceived in vitro, after which they were implanted artificially, developed normally, and were born normally.
Development and embryology
- Multi-celled organisms begin as one cell that develops into a fetus
which becomes a whole individual, under the control of genes that are
switched on and off.
- Animals grow and develop from a single cell, under the
control of genes that are switched on and off under the influence of
interactions between the cells.
- Plants grow and develop from seeds which contain a small
food store that provides the material for the initial growth, to the
point where leaves form.
- Most animals develop further after birth, having been born
with some parts of them less developed than others. The undeveloped
parts vary between species.
- The development of a whole organism from a single cell is
controlled by the genes found in every cell, but which are not
necessarily active unless switched on.
- Most multi-celled plants and animals have tissues, and all
advanced organisms are made up of different tissues, in which different
genes are active.
- Plants use a variety of hormones as signals from one part
of the plant to another. Gibberellin is an example of an important plant
growth hormone.
- Tissues form organs, and they are most easily studied in
thin sections. How tissues form is a fascinating aspect of biology,
still not fully understood
- Specific genes are switched on in cells of a certain kind:
in most cells, most of the genes do not operate at any given time. Many
of them do not ever operate.
- Aging is a natural process. The telomeres on the
chromosomes shorten as an organism gets older, and this seems to mark
the age of cells in some readable way.
- The Eutheria, the placental mammals, go through a period of
gestation after conception, when they are nurtured internally as their
tissues develop.
- An insect larva becomes a pupa which becomes an imago,
showing development and redevelopment over several stages, with tissues
being resorbed and reconstructed.
- Gigantism and dwarfism occur when hormonal balances are
uncontrolled in the developing body, so that the cells of the body
receive confusing signals.
- Apoptosis helps to shape developing organisms This is a
form of controlled cell suicide which serves to shape the individual,
removing excess material.
- Development often involves recapitulation of some of the
stages that were present in their distant ancestors. This leaves the way
open for neoteny.
- Stem cells are unspecialized cells that can give rise to
other types of cell. Some stem cells are more versatile than others, as
the cells are less committed.
- The most versatile stem cells are embryonic stem cells, which are better referred to as totipotent stem cells, a less emotive and more accurate name.
About systems
- All animals, from the smallest to the largest, have systems, that
carry out important tasks and relying on control which is based on
sensing and feedback.
- Plants also have a variety of systems that use sensing and
feedback to control functions such as photosynthesis and respiration
within the plant.
- When bacteria form themselves into a plaque or biofilm,
this tissue-like structure develops a form of control system, which is
called quorum sensing.
- Mammals and birds are called homoiothermic: they maintain
their temperature by homeostasis and insulation, generating heat or
cooling themselves as necessary.
- Animals which do not maintain their temperature are called poikilothermic. These animals need an external source of heat such as sunlight, in order to warm up.
The principles of control systems
- Homeostasis is a characteristic found in systems that survive: the
obvious example is mammalian temperature, but many other things are also
finely balanced.
- Effective control in living things relies on feedback
systems, where a shortage of an item triggers its production, and an
excess stops production in some way.
- Animals have a variety of control systems: nerves carry
fast messages, hormones are slow and wide-reaching, pheromones carry
signals between individuals.
- There are two kinds of signalling methods within animals
like us: target-specific messages are sent by nerves and slower general
messages are sent by hormones.
- Many hormone systems are driven by secretions from the
pituitary gland, and if indirect influences are included, most hormone
systems are pituitary-driven.
- An important male hormone is testosterone and an important
female hormone is estrogen, but other hormone is present in small
amounts in the other sex.
- The key hormone in blood sugar balance is insulin, which is
produced as and when it is needed, in cells in the pancreas called the
islets of Langerhans.
- Gonadotrophin is the name given to a group of proteins:
human chorionic gonadotrophin is produced by the placenta and in the
urine, is a pregnancy indicator.
- Around 170, Galen discovered how nerves operate when he cut
into the laryngeal nerve of a pig, after which it continued to
struggle, but stopped squealing.
- Nerves communicate at a synapse, where chemicals like
glycine and acetylcholine carry a signal from one nerve to another,
being destroyed soon afterwards.
- The operation of the nervous impulse can be described as
electrical signals, but the operation of the nervous system involves
changes in membranes.
Digestion and excretion
- Teeth are used to slice and crush food, increasing its surface area
that can be exposed to enzymes that help food break down to molecules
that can be absorbed.
- Fluoride in water toughens tooth enamel by causing chemical
changes in the enamel to a chemical form that is more resistant to the
acids of dental plaque.
- Animals have similar internal anatomy of the abdomen, with a
few simple variations that relate to the diets of herbivores,
carnivores and omnivores.
- Parts of the alimentary canal nearest to openings may be
investigated using an endoscope, a tube with light and camera, inserted
through the mouth or anus.
- The upper alimentary canal is made up of the stomach,
duodenum and ileum, the lower alimentary canal is made up of the small
intestine, caecum and anus.
- Food is moved along the alimentary canal by waves of
peristalsis, where a series of contractions around the tube push
partly-digested food on its way.
- In1825, William Beaumont began his study of the digestion
of Alexis St Martin, who had a gunshot wound which left him with a
permanent opening to the stomach.
- In 1836, Theodor Schwann isolated the first animal enzyme
when he discovered pepsin, a digestive enzyme, from extracts taken from
the stomach lining.
- Absorption transfers dissolved food from the alimentary
canal to the circulatory system: it is carried passively until it
reaches a place where it is needed.
- Certain points along the alimentary canal are controlled by
sphincter muscles, rings of muscle that surround the canal and block
unwanted returns.
- Elimination of faeces gets rid of the left-overs, the
bacteria, the fibres and the undigested food, after most of the water
has been reabsorbed.
- The kidney takes dissolved wastes from the blood and
disposes of them in urine, which is normally sterile, unless there is a
kidney infection.
- Urine is highly sterile, but makes a good culture medium
for many bacteria, which make chemical changes in the urine, producing
ammonia and later, nitrates.
- Urine production in humans is controlled by the action of
antidiuretic hormone (ADH) which controls the amount of urine sent to
the bladder for storage.
- Because bacteria turn the urea in urine to ammonia and then
into nitrates, urine has been a common industrial chemical with many
uses, since ancient times.
- Some animals in dry environments rely mainly on metabolic water for their water supplies, water that is produced by respiration of carbohydrates and lipids.
Circulation and blood
- Our body is made up of a number of systems which get matter and
energy to where it is needed. When these systems do not work properly,
we become ill.
- Blood is the main circulatory fluid in large animals, and
is essential for their survival, as diffusion only works over small
distances in animal tissue.
- Blood is pumped around our bodies by the heart. It is
pumped to the lungs to get oxygen and lose carbon dioxide, and to the
rest of the body to exchange gases.
- The heart operates as a two-stage pump, with a
thinner-walled atrium filling a muscular ventricle which then forces the
blood around the body.
- Oxygen and carbon dioxide are carried around in the blood
by haemoglobin, a complex chemical to which the oxygen and carbon
dioxide molecules can attach.
- Blood carries food molecules to where they are needed. It
also carries waste material away from the cells of our body, to where
they can be disposed of.
- The blood circulation carries oxygen around the body from
the lungs, carries carbon dioxide away from cells back to the lungs, and
food to cells.
- Around 170, Galen speculated that blood might get from one
side of the heart to the other through very fine pores, too small to be
seen with the naked eye.
- By 1574, the anatomist Fabricius had observed and described
the valves that may be found in veins, and saw that they would stop
blood from pooling in the feet.
- In 1628, William Harvey published his detailed description
of the circulation of the blood around the body, but he could only infer
that capillaries exist.
- In 1666 Richard Lower demonstrated the transfusion of blood
between two dogs, and the experiment appeared to be successful, given
that the dogs did not die.
- In 1667 Jean-Baptiste Denys transfused lamb's blood into a
15-year-old boy who was apparently unharmed, or at the worst, did not
die as a result of the transfusion.
- Around 1680, Marcello Malpighi saw capillary blood vessels
for the first time, establishing the missing link in our picture of the
body's blood circulation.
- In 1689, Anton van Leeuwenhoek began his studies of
capillary vessels in frogs' feet, bats' wings, rabbits' ears, and eels'
tails, all under the microscope.
- Human blood contains a variety of distinctive proteins that
'type' it. Each human belongs to a specific blood group, based on those
proteins in the blood.
- In 1910, Epstein and Ottenberg discovered that human blood
groups (A, B, O) were inherited on Mendelian principles, leading to
later paternity testing.
- In 1927, Karl Landsteiner discovered the M and N blood
groups. In 1940, Landsteiner and Alexander Wiener both discovered the Rh
blood factor.
- The heart and the veins have valves to force blood to flow
in one direction only: out along the arteries under pressure, back
through the veins.
- Arteries lead to arterioles and then to capillaries which
trickle blood into venules which feed into veins, which carry the blood
passively back to the heart.
- The arteries are elastic, which means they are able to
absorb the shock of the pressure wave as blood is pumped from the heart
with great force.
- The pulmonary system carries blood to the lungs where
concentration differences mean the haemoglobin loses carbon dioxide and
picks up oxygen.
- Hardening of the arteries means that rather than being
absorbed by the arteries, pressure surges are carried on to finer blood
vessels and damage them.
- An artery usually carries oxygenated blood, unless it is
the artery that carries blood to the lungs. The pulmonary vein carries
oxygenated blood.
- Arterial blockages may be cleared by angioplasty, a
procedure similar to blowing up a small balloon inside the artery, which
clears the blockage.
- Normal body movements compress veins, especially in the
legs, and each compression pushes blood along, with the valves directing
the flow one way.
- Very small animals like flatworms do not need a circulatory
system: simple diffusion from the nearest surface is enough to provide
oxygen to all their tissues.
- Large plants need water transport systems to move sugars, minerals and water from the leaves and roots to other parts of the organism where they are needed.
Gaseous exchange
- Oxygen is needed inside most organisms' cells to extract energy from
most forms of food, although oxygen gas is harmful and poisonous to
anaerobic organisms.
- Plants do not need circulatory systems to carry oxygen
because they have air spaces between their cells, and gases are able to
diffuse through those gaps.
- Animals need oxygen. Animals use all of lungs on land,
gills in water, and diffusion systems in small animals to acquire oxygen
from their environment.
- A fish can get oxygen from water through its gills, which
work to provide a large surface area for contact with the water to allow
oxygen to diffuse in.
- Small animals absorb oxygen by diffusion through the skin,
while larger animals use breathing systems to carry oxygen in: lungs and
gills and in insects, tubes.
- Our lungs fill with air when the diaphragm falls, or the ribs move up and out: as the space expands, air can move in, as it contracts, air is forced out again.
The principles of respiration
- The word 'respiration' is used in two conflicting senses: to mean
the breathing in of air, but also a controlled biochemical process of
'burning' fuel.
- Respiration is the process living things use to release
chemical energy as they break down complex molecules in a series of
controlled steps.
- In 1780 Antoine Lavoisier and Pierre-Simon de Laplace
published their memoir on heat, in which they concluded that respiration
is a form of combustion.
- Aerobic respiration involves the Krebs cycle, a series of
carefully managed biochemical steps with standard products at each step,
all controlled by enzymes.
- Respiration can be both aerobic respiration, where oxygen
is brought into the reactions and anaerobic respiration, where oxygen is
not involved.
- Of the two, aerobic respiration is more efficient than
anaerobic respiration, because it produces more ATP from a given amount
of starting material.
- While both aerobic and anaerobic respiration produce
adenosine triphosphate as the energy product, the two processes generate
different end products.
- Animals breathe in oxygen and breathe out carbon dioxide
and that is a by-product of aerobic respiration. Water is also produced
and absorbed.
- Respiration is controlled by enzymes which are protein
catalysts produced under the control of genes: if these fail to operate
correctly, the organism dies.
- Respiration has standard forms in all living things, with
only minor differences, because the controlling enzymes have been
conserved throughout evolution.
- Most of the energy generated by both aerobic and anaerobic
respiration is used to convert adenosine diphosphate (ADP) to adenosine
triphosphate (ATP).
- Animals use force to move and to live, and muscles are used
to provide the forces needed to catch, swallow and digest food, to
breathe and maintain blood flow.
- Muscles require energy from respiration, and that means they require a good blood supply: exercise ensures the development of blood supply to muscles.
Support and movement
- When the first plants moved from the water to the land, they needed
to be able to reach higher than plants around them so as to get the most
light.
- This meant that the plants had two mean needs: they needed
conductive tissue to carry water to the higher parts, and they needed
stiffening to have not bend.
- Many animals and plants have stiffening material or organs
that give them a framework on which to move. In animals, this gives the
muscles something to work on.
- Animals may have an exoskeleton or endoskeleton to provide a
degree of protection, but also to make fast movement easier, as it
gives something to pull against.
- Sharks and rays have cartilage and no bone in their
skeletons. This provides a flexible skeleton, but offers less protection
than one made of bone.
- Wood and bone are both two-phase materials, combining a
material which is strong under compression with fibres which is strong
under tension.
- The plants came to use the conductive tissue as
high-tensile fibres to provide much of the tensile strength: secondary
thickening dealt with the compression.
- Bone is a two-phase material, made of mineral material
(calcium phosphate) for compressional strength and collagen fibres to
provide tensile strength.
- Bone is a dynamic material, with small parts of its
structure continually removed and replaced, in part as a response to
charges generated within the bone.
- The pelvis is a critical part of the human skeleton, because it lets us walk upright, and its size limits the maximum possible size of a newborn baby's head.
Immune responses
- In ancient Greece, Thucydides reported that people who had already
experienced the plague were then immune to it, and able safely to nurse
other victims.
- In complex organisms such as mammals, evolution has
favoured an extremely intricate immune system that will attack any cells
recognized as 'non-self'.
- In complex organisms, there are many ways for cells to
identify 'self' and 'non-self', based on the shapes and charges of
surface markers on the cell membrane.
- Our immune system protects us from materials and organisms
recognized by the body as 'foreign', things not known to be a normal
part of the body.
- Antibodies are part of the immune system, and they
generally act by binding to an antigen, changing it so that it can no
longer operate as normal.
- The presence of particular antibodies in your blood
indicates that you have had a previous exposure to particular antigens,
typically organisms or toxins.
- Immunity can be acquired: immunization with a vaccine
stimulates the immune system by providing it with a harmless model of
molecules that need to be attacked.
- In 1890 Emil Adolf von Behring discovered antibodies and
antitoxins, and used this novel principle to develop tetanus and
diphtheria vaccines.
- A vaccine prepared from weakened or heat-killed disease
organisms gives people immunity by preparing the immune system to attack
the real thing when it arrives.
- A vaccine made from parts of the exterior of disease
organisms can give people immunity without infecting them, by preparing
the immune system to attack them.
- Vaccines against typhoid and cholera were developed in
1896, and they bubonic plague vaccine was available in 1897. All of
these used inactivated bacteria.
- The Lübeck disaster is a rare example of how vaccination
can go wrong: it happened when full-strength TB bacteria were inoculated
instead of weakened ones.
- As a general rule, there is a small but measurable risk
associated with every inoculation. There is a greater risk associated
with NOT being inoculated.
- Interferons are naturally occurring proteins that are a
part of the immune system, operating in a variety of ways to regulate
the immune system.
- Around 1020, the Arabic scientist Avicenna described
diabetes and that the urine of diabetics tastes sweet, after seeing ants
attracted to a diabetic's urine.
- Occasionally the immune response goes out of control, and
attacks part of the host organism by mistake, in what is called an
autoimmune reaction.
- Our immune system can cause autoimmune disease when it
'makes a mistake': Type I diabetes is an autoimmune disease, probably
caused by a bacterium.
- Juvenile (type I) diabetes is triggered when an autoimmune
response attacks key cells in the pancreas, and destroys them by mistake
for an infective agent.
- There appears to be a standard pattern for autoimmune
diseases, where early exposure to an organism triggers a later mistaken
attack on part of the body.
- Blood and tissue can be typed, according to the antigens
found in a particular blood sample, allowing a closer match for blood
and organ donations.
- Tissue typing is required before transplantation: organ
donations, have a better chance of success when the donor and recipient
have similar immune markers.
- The immune response can be modified or muted by drugs known
as immunosuppressants, but the same effect is also caused by HIV, the
human immunodeficiency virus.
- Immunosuppressive drugs may be needed for a transplant of
an organ from a donor to succeed, even when the match between donor and
recipient tissues is good.
- In the future, xenografting of organs may be possible,
using organs from animals which have been specially prepared to have no
immune markers.
- One source of xenografts may be pigs, but pig xenografts
may carry viruses called porcine endoretroviruses or PERVs, which might
infect the recipients.
- All multicellular organisms, both plants and animals, have
evolved ways of defending themselves against invaders and infections by
microorganisms.
- The simple immune system of the invertebrates involves
producing soluble factors which are more harmful to invaders than they
are to the host cell.
- The more complex immune system of the vertebrates involves a
quick-acting innate system that does not adapt very well and a
slower-acting adaptive system.
- The adaptive immune system has a memory for attackers which
it has encountered before, and it is this memory that make use of when
we apply vaccines.
- The innate system in vertebrates is much more complex than
the invertebrate system, with a variety of factors secreted by different
cells in the body.
- One group of factors is made of the cytokines, a group of
different proteins that are produced and secreted by cells. Another
group is the chemokines.
- Two main types of cell are involved in the adaptive immune
system. These are the two kinds of lymphocytes and the antigen
presenting cells or APCs.
- B lymphocytes are formed in the bone marrow and travel from
there directly to the lymph nodes, while T lymphocytes reach lymph
nodes by way of the thymus.
- In 1957, Macfarlane Burnet proposed his clonal selection
theory of B lymphocytes, suggesting that each B cell has antibody
receptors to a unique antigen.
- Macfarlane Burnet's theory was ridiculed at the time, but
it now lies at the very centre of our understanding of immunology and
the immune system.
- When an antigen matching the specificity of a B cell
appears, more copies of that lymphocyte are produced, resulting in
strong antibody production.
- A small number of people persist in arguing that vaccination is dangerous. Nothing is ever free of risk, it is far more dangerous to refuse to be vaccinated.
The principles of the senses
- All living things have some sort of sensing ability, whether they
are plant or animal, and this is reflected in their responses to changes
in the environment.
- Plants demonstrate a variety of senses: a potato in a shoe
box fitted with baffles demonstrates phototropism, sensing where light
is coming from.
- Plants can sense the pull of gravity: radish seeds
sprouting in water agar will grow downwards, and if rotated, will change
the direction of growth.
- Sundews wrap their leaves around their 'prey', responding
to the breakdown of prey proteins under the attack proteolytic enzymes
in the sticky 'dew'.
- Sunflowers turn their flowers around to face the sun as its
position in the sky changes during the day, indicating that they sense
the Sun's direction somehow.
- Trigger plant flowers strike pollinating insects on the
head or back when they land on the flower, either dusting them with
pollen, or taking pollen from them.
- The leaves of Mimosa pudica close up when they are touched,
and Cassia species close their leaves as the sun sets, indicating some
equivalent of animal senses.
- A number of insectivorous plants are able to detect an
insect landing on them, either using an analogue of touch or of taste as
the insect is digested.
- Most animals have a sense of smell, which has the advantage
of working in the dark. Smell works by a lock and key method on sensors
in a small part of the nose.
- We can map taste zones on the tongue, which is able to
detect salt, sweet, sour and bitter tastes on different parts, showing
these have specific receptors.
- Our sense of taste is partly smell, because while the
tongue can sense sweet, sour, salt and bitter, the nose can make much
finer discriminations.
- Taste cells are replaced at high frequency. As cancer drugs
attack fast-dividing cells, many cancer drugs can have a marked effect
on the sense of taste.
- Humans hear sound within the audio frequency range, as high
as 20 kilohertz, with the upper limit dropping with age, starting to
drop after age 20.
- The ear captures and magnifies vibrations through the bones
of the ear, and the vibrations are converted to nerve impulses that we
then interpret.
- Deafness has a number of causes, such as nerve damage,
blockage of the ear and damage to the amplifying mechanism in the ear.
Some of these can be circumvented.
- Human hearing is selective, as shown by the cocktail party
effect, where, by concentration, one person may be heard over the
turmoil of a busy room.
- The pressure in our middle ear is kept steady by the
Eustachian tube, which links the middle ear to the outside world.
Yawning opens the Eustachian tube.
- All animals have a sense of touch: the touch sense is
different from pain sense, and is only triggered by a more intense
stimulus like a sharp blow.
- Hairs and whiskers can be very sensitive to touch, and this
can be shown by just touching a single hair on somebody's arm or even
on their head.
- Some parts of our skin are more sensitive: this can be
demonstrated with a blindfold test to see where two close pressure
points can be detected as separate.
- Circadian rhythms, our daily cycle of metabolic patterns,
depends on detecting light and dark, so bright sunlight can help to
reduce the effects of jet lag.
- The Earth has a magnetic field which experiences polar
reversals at times, when the north and south poles change places over a
period of a few hundred years.
- Many animals have a magnetic sense which they use in
navigation: this sense must be pliable enough to cope with polar
reversals, so that some of them survive.
- Many living things can detect light, usually by some
chemical effect that the light causes, with the altered chemical then
being detected in some way.
- The human eye detects light when rhodopsin, a complex
chemical in the retina, is bleached by a focused image, produced by the
lens, falling on the retina.
- There are different eye structures in different groups,
indicating that the eye has evolved several times. The evidence of
homeobox genes suggests otherwise.
- Most animals can either detect light or see, in the strict
sense of forming an image on a receptive surface, so the image can be
recognized and responded to.
- Effective vision needs a lens to focus light, a receptive
surface on which the image is focused, nerves to detect the image, and a
brain to analyse the image.
- There is a blind spot where the optic nerve attaches to the
retina, as there are no sensors on this part of the retina. What one
eye misses, the other eye sees.
- Visual perception is a brain process where a set of nervous
impulses, starting in the retina and travelling along the optic nerve,
are interpreted by the brain.
- We may be said to 'see' something when the brain interprets
signals from the retina via the optic nerve, and recognizes them as
something familiar.
- Camouflage is used by predators and prey, to get food or to
avoid being food. One form of camouflage uses disruptive coloration so
shapes are harder to see.
- The main parts of the vertebrate eye include the cornea,
the vitreous humour, the lens, the aqueous humour, the retina and the
optic nerve, and a covering.
- Visual signalling is used by animals in mate selection, and
this has led to many of the weird and colourful extremes seen in the
animal world.
- There are three kinds of colour receptors in the cone cells
of the retina, detecting the three 'primary colours', and effectively
defining the primary colours.
- The cone cells of the retina differ from the rods by having
different visual photopigments so that they can respond preferentially
to certain wavelengths.
- The fovea is the most sensitive part of the retina in the
human eye: this is the central portion of the retina where colour vision
is located as well.
- The people we call 'colour' blind can in fact see most
colours. They have problems telling certain colours apart that others
see as different.
- In 1794, John Dalton was the first to describe colour
blindness. It was easy for him to observe this phenomenon, since he was
in fact extremely blind-blind.
- Dalton believed the fluid in his eyes must be blue, and
arranged for one of his eyes to be dissected, after his death, to test
this. He turned out to be wrong.
- Most visual illusions are a result of conflicting signals
reaching the brain, which is then required to make the best sense of
them that it can.
- Some animals can detect electric fields: electric fish live
in muddy water and platypuses hunt with their eyes shut, using sense
organs on the 'bill'.
- In 1940, Donald Griffin and Robert Galambos announced their discovery that insectivorous bats rely on sonar echolocation to navigate and find prey.
The principles of microscopy
- In 1610, Johann Kepler developed the basic modern arrangement for
the compound microscope, which Leeuwenhoek would put into practice, at
the end of the century.
- In 1658 Jan Swammerdam saw red blood cells under a
microscope, described red corpuscles, lymphatic valves, and changes in
the shape of muscles in contraction.
- 1665 Robert Hooke published his Micrographia, making
microscopy popular, identifies cells, and also proposed that artificial
silk may be made by extruding gum.
- In 1674 Anton van Leeuwenhoek invented the compound
microscope, and then went on to discover and describe various Protozoa,
bacteria, and rotifers.
- In 1722, Daniel Defoe made a casual reference to theories
that plague was caused by microbes, too small to be seen without the aid
of a lens or microscope.
- In 1830, Joseph Jackson Lister, the father of the more
famous Joseph Lister, showed how compound lenses can correct for
chromatic and spherical aberration.
- Medical practitioners may not need a microscope today, but
microscopes were essential to medical researchers in the past as they
sought the causes of diseases.
- Only a microscope would let researchers to examine the
shape of bacteria, and to see which stains were absorbed by the cell
wall of a suspicious bacterium.
- Only a microscope would let researchers to examine fine
detail like a number of hairs on a mosquito's leg, and so identify a
species that was a disease vector.
- Microscopes were also important to geologists, because it
is easy to identify minerals in thin sections of rock with polarized
light, filters, and a microscope.
- There is a limit to how much a microscope can magnify,
which depends on the wavelength of the light used, and the size of the
object being looked at.
- Because electrons behave in some ways like light, it is possible to make a microscope which uses electron beams instead of light to see very fine detail.
The principles of cells and tissues
- The cell is the basis of all living things, but cells are made up of
smaller parts with different functions. Only a cell can make another
cell.
- In 1663, Robert Hooke was able to see and describe plant
cells, seen in a thin slice of cork, examined under the microscope, and
he estimated their size.
- Hooke's estimate: in one inch, "near eleven hundred of them
. . . in a Cubick Inch, above twelve hundred Millions, or 1 259 712
000, a thing most incredible".
- René Joachim Henri Dutrochet was probably the first to
offer us the theory that all living things are composed of cells, rather
than Schleiden or Schwann.
- In 1858, Rudolf Virchow ruled out spontaneous generation,
saying that all cells arise from pre-existing cells, saying it in Latin:
"Omnis cellula e cellula".
- In 1860, Louis Pasteur stated his view that all living
things come from living things, which he expressed in Latin, saying:
"Omne vivum e vivo".
- All the procaryotes have regions within them which are
locally different, but they have no membrane-bound organelles inside the
outer membrane.
- The life forms we call procaryotes may also be considered
as acellular, in that they contain a whole organism in a single
container, rather than unicellular.
- Saying that a cell is filled with cytoplasm is about as
useful as saying a television set is filled with teleplasm: neither
statement contains any information.
- A cell membrane is a complex structure that interacts with
the cells' contents and surroundings to play a major part in the
operation of the cell.
- The cell membrane is more than a bag: it is an important
part of the cell which plays a major role in deciding what is, and is
not, allowed into the cell.
- Cells may take up material by active transport, where parts
of the membrane select particular molecules and carry them into (or out
of) the cell.
- Cells may take up material by pinocytosis, where the cell
membrane puckers in, surrounds a particle or some fluid, seals it off,
and then releases it inside.
- All of the organisms we call eucaryotes have membrane-bound
organelles, including the nucleus, lysosomes, endoplasmic reticulum,
Golgi bodies and mitochondria.
- Serial endosymbiosis theory says the parts of eucaryotic
cells were once separate simple organisms which linked together to form a
complex organism.
- In 1914, Warren H. Lewis and his wife, Margaret Lewis, used
bright field microscopy to be the first to describe mitochondria and
mitochondrial shape changes.
- The role of the mitochondria is to generate energy in the
cell, so the mitochondria are the centres where respiration is used to
generate ATP from ADP.
- The nucleus of a eucaryotic cell is visible under the light
microscope, especially when it is treated with a DNA-specific dye that
stains the chromosomes.
- In 1956, Henry Borsook and Paul Charles Zamecnik
established that the ribosomes of the endoplasmic reticulum were the
site of protein synthesis.
- The role of the ribosomes is to make protein as specified in accordance with the universal genetic code by the sequence of bases on a strand of messenger RNA.
Medicine and health
- Many illnesses are caused by small living things, too small to see,
that get into wounds and our digestive systems, which is why boiling
water is a good rule.
- The small life forms that sometimes make us ill are not all
harmful, especially when they are in the right place, not the wrong
place. Some of them are useful.
- The small things that cause disease can be grouped by their
appearance, their habits and in other ways as viruses, bacteria, Fungi,
Protozoa and parasites.
- Some sorts of illness are caused by things we eat, or by
things we have failed to eat and need. We need to eat a balanced diet of
different food types.
- When a disease spreads widely, this is called an epidemic,
but if it spreads across the world (as HIV has done), it is usually
called a pandemic.
- A disease spread by an animal is called a zoonosis:
examples include tuberculosis, formerly spread by cattle, avian (bird)
forms of influenza, and maybe SARS.
- We get diseases from the bites of invertebrates like flies,
mosquitoes and ticks, because the biter carries and spreads a virus,
bacterium or protozoan.
- To identify the cause of a disease, we study a large number
of people, half with, and half without the disease, and see what else
distinguishes the two groups.
- Scientists use a range of standard methods to identify the
cause of a disease, using maps, statistics, and a knowledge of how
diseases spread in populations.
- Epidemiology involves finding causes of disease and also
vectors. In modern times it has come to rely heavily on genomic methods
to identify causes of disease.
- Most of our understanding of disease relies on the germ
theory, which says that diseases are commonly caused by microbes of
different sorts invading us.
- The microbes that cause disease can be classed as protists
(protozoans), viruses, bacteria and some Fungi. No Archaea are known to
cause disease.
- Some diseases are dietary deficiency diseases, as a result
of the diet lacking some essential vitamin or mineral, or because the
needed item cannot be retained.
- Some diseases are not inherited as such, but it is possible
to have a genetic predisposition, to inherit an increased vulnerability
to a given disease.
- The term 'drug' has two distinct meanings, one relating to
drugs of addiction, the other relating to drugs used to treat illnesses.
All drugs can do harm.
- Aging and degenerative diseases include Alzheimer disease,
Parkinsonism, arthritis, macular degeneration, and cancers caused by
self-repair failures.
- Disease can be caused by dust such as silica or asbestos in
the lung, chemicals in the environment (including food) and pollution
in various forms.
- Many conditions once called environmental diseases are actually set off by microbes, including ulcers and heart disease, both formerly blamed on stress.
The principles of bacterial diseases
- In some systems, the prokaryotic Monera make up one of the five main
groups of living things, including the bacteria, the cyanobacteria and
the Archaea.
- Bacteria are usually small cells that live and reproduce
independently or in small colonies, and which have no separate
membrane-bound organelles or nucleus.
- Bacteria can usually only be seen with a microscope,
although at least one bacterium, Thiomargarita namibiensis, is large
enough to be seen with the naked eye.
- Bacteria can be distinguished by staining properties, which
show up when stains are used that are either taken up by chemicals in
the cell wall, or not.
- In 1884, Christian Joachim Gram invented his Gram stain
which could be used for the classification of bacteria, because it only
stained one type of cell wall.
- One common stain used on bacteria is the Gram stain, used
to divide bacteria in Gram positive (which take on a violet colour) and
Gram negative bacteria.
- The cell wall of a Gram negative bacterium is high in lipid
content and low in peptidoglycans, the portion that the Gram stain
normally attaches to.
- Some bacteria form biofilms, layers of bacteria and complex
molecules, often with other species involved, which behave like tissues
in higher animals.
- Bacteria form plaques of biofilm, complex interdependent
communities of bacteria that interact and form layers similar to tissues
in higher animals.
- Some bacteria may be cultured in a Petri dish on a culture
medium, but there are many more, perhaps as much as 96%, which cannot be
cultured.
- Most of the bacteria that cannot be cultured in a pure
culture are those involved in biofilms, and which require other bacteria
to be present before they grow.
- Bubonic plague is a bacterial disease. The rats carry
bacteria, fleas get them when they bite rats, and transfer them to
humans when they bite the humans.
- In 1843, Oliver Wendell Holmes observed the contagiousness
of septicaemia, and suggested that medical staff should wash their hands
to prevent its spread.
- Ignaz Semmelweis could not explain why his innovative
method designed to prevent childbed fever worked, though there could be
no doubt that it did in fact work.
- Semmelweis required those working under him to wash their
hands in strong chemicals (chlorinated lime) before touching patients,
and the fever rates plummeted.
- Semmelweis died of the same fever he had done so much to
fight, just a few years before the tide turned when Pasteur and Lister
showed that his ideas worked.
- In 1854, John Snow showed that whatever caused cholera, it
could be found in the unboiled water from one well in London's Soho,
coming close to a germ theory.
- Hermann von Helmholtz anticipated Louis Pasteur by
indicating that both fermentation and rotting were biological effects,
but he did not follow this up.
- In 1863, Pasteur showed that a micro-organism causes the
souring of wine into vinegar, and as a response, invented pasteurization
to kill the micro-organisms.
- Bacteria can be killed in an autoclave if they are exposed
for long enough to the combination of heat and steam, mainly because key
proteins are denatured.
- The bacteria that attack humans can generally be cultured,
because the culture media that are used for this imitate the human body
in many ways.
- In 1882, Robert Koch described his method for isolating
bacteria in pure culture by plating them on solid media, first gelatin,
then agar later.
- In 1876, Robert Koch cultured anthrax bacilli and showed
that anthrax is caused by a specific organism, and in the same year,
also stated Koch's postulates.
- Robert Koch developed a set of four postulates, essential
conditions that had to be met before an organism could be named as the
cause of a particular disease.
- Koch's first postulate: The organism should always be found
present in an animal with the disease, and should never be found in one
not suffering the disease.
- Koch's second postulate: The organism must be cultured in a
pure culture, containing only that one organism, away from the animal
body, so it can be isolated.
- Koch's third postulate: When such a culture of the purified
organism is inoculated into a susceptible organism, characteristic
disease symptoms should appear.
- Koch's fourth postulate: The organisms reisolated and
cultured from the experimental animals should be seen to be the same
organism that was cultured earlier.
- Even in old age, Florence Nightingale dismissed the
'germ-fetish'. She was one of the most reputable opponents of
antisepsis, even as she promoted cleanliness.
- In 1909, Charles Jules Henri Nicolle showed in a series of
monkey trials in Tunis that the bacillus of typhus fever was transmitted
by the body louse.
- In 1910, Paul Ehrlich and Sachahiro Hata introduced the so-called magic bullet salvarsan to selectively kill the organism responsible for syphilis.
The principles of viral diseases
- Because viruses are too small to be filtered out of a solution, and
too small to see, 19th centuries scientists called them by the Latin
name for poison: virus.
- A virus is typically between 20 and 300 nanometres across, a
protein coat surrounding nucleic acid. It needs to get into a cell to
reproduce itself.
- Viruses are small packets of genetic material in a protein
coat. They can only reproduce inside a living cell, which they destroy
in the process.
- A virus can be called life because it can reproduce and
mutate, or non-life because it needs to invade a cell to be able to
reproduce. Take your choice.
- Because viruses can only reproduce inside a living cell,
they are often classed as non-living, but on the other hand, they
contain genetic material.
- Some viruses specialize in attacking bacteria. These are
known as bacteriophages, and some bacteriophages have been used to treat
bacterial infections.
- In 1915, Frederick Twort suggested that bacteriophages (as
we now know them) were viruses which attack bacteria - these were later
referred to as 'phages'.
- In 1917, Felix Hubert D'Herelle, independently of Frederick
Twort, also discovered the same effect, and it was he who called it a
bacteriophage.
- In 1945, Max Delbrück and Salvador Luria organized the
first phage course at Cold Spring Harbor Laboratory which would be
taught for 26 consecutive years.
- In 1953, André Lwoff, working with bacteriophage lambda,
found that phage viruses are capable of inserting their genome into the
host genome.
- In 1955, Seymour Benzer began fine-structure genetic
mapping a phage, a process that would take five years. He concluded that
a gene has many mutable sites.
- In 1981, the first reports of AIDS began to surface.
Symptoms had been noted earlier, especially an increase in Kaposi's
Sarcoma, but now AIDS was a condition.
- AIDS is caused by HIV, the human immunodeficiency virus.
There are some people who argue that there are other causes, but the
medical evidence points at HIV.
- HIV can be passed from mother to child, and in the absence
of any of the alleged 'lifestyle causes' can develop into AIDS, and kill
the child.
- AIDS and HIV do not kill people: the virus takes away the
normal immune response, leaving people open to attack by diseases that
would usually be controlled.
- AIDS is caused by HIV, but in a very real sense, AIDS can
be said to be caused by poverty, because poor people are more likely to
be infected by HIV.
- The Durban declaration of 2000 was drafted to counter a set
of mischievous and ill-informed claims from 'AIDS sceptics' that HIV
was unrelated to AIDS.
- In 1898, Martinus Beijerinck used filtering trials to show
that tobacco mosaic disease is caused by something smaller than a
bacteria and called it a virus.
- In 1910, Peyton Rous showed that viruses play a role in
some cancers when he discovered the Rous Sarcoma Virus. He gained a
Nobel Prize for this in 1966.
- In 1937, Sir Frederick Charles Bawden discovered that the
tobacco mosaic virus contains RNA, the first virus found to contain RNA
as the genetic material.
- In 1935, Wendell Meredith Stanley was the first researcher
to purify and crystallize a virus, the tobacco mosaic virus, for which
he gained a 1946 Nobel Prize.
- In 1955, Fraenkel-Conrat and Williams separated tobacco
mosaic virus (TMV) nucleic acid from its protein coat and found that
both were necessary for infection.
- In 1960 Heinz Fraenkel-Conrat announced the complete
sequencing of the 158 amino acids which make up the protein coat of the
tobacco mosaic virus.
- Smallpox is a viral disease, and like many viral diseases,
it can be prevented with a suitable vaccine that prepares the immune
system to attack the virus.
- In 1717 Lady Mary Wortley Montagu had two of her children
variolated against smallpox. The practice continued until Edward Jenner
developed vaccination.
- In 1776, George Washington had his troops inoculated
against smallpox, using the pre-vaccination treatment called
variolation, which was common in his time.
- Variolation was a procedure that usually gave people a mild
dose of smallpox, but occasionally, it killed. In any case, it was a
lesser risk than doing nothing.
- In 1796, Edward Jenner was ethical when he attempted to
apply the standard inoculation with smallpox (variolation) on a boy who
had previously been vaccinated.
- The point of was that variolation usually caused a mild
form of smallpox, but was known to give immunity. Jenner's vaccination
offered risk-free immunity.
- In 1977, there were no cases of smallpox known, anywhere in
the world, as it had, by then, been wiped out in the wild. Laboratory
stocks still exist.
- An arbovirus is a virus spread by blood-sucking arthropods:
it is short for 'arthropod-borne virus'. A number of serious human
diseases are from arboviruses.
- Rabies is a viral disease spread by animals. It attacks the nervous system producing the classic symptoms of 'madness' associated with the disease.
The principles of cancer
- Cancer is the result of uncontrolled growth by the cells in a
particular tissue, forming a tumour that takes away resources from the
rest of the body.
- It is probably a mistake to look for a single cause for all
cancers, because cancers themselves are different, and so probably have
many different causes.
- Cancers all have one thing in common: some control that
would normally stop cells from multiplying forever has broken down, so a
tumour is able to grow.
- Chemicals which cause mutations often cause cancers as
well, because these chemicals cause mutations in the protective genes
that trigger apoptosis.
- Chemicals which cause mutations often cause cancers as
well. Cancers are usually prevented until a protective gene breaks down
when it is damaged or mutated.
- Cancers are often caused by a mutation in one of the
protective genes that normally trigger a faulty cell to self-destruct
for the benefit of the organism.
- Our immune system does not protect us against cancer,
although the normal operations of apoptosis behave in many ways as a
form of immune defence.
- Even though the immune system as such does not usually
attack cancers, our immune systems can be artificially sensitized to
attack some cancers.
- Some cancers spread by metastasis, a process which involves
cancerous cells spreading through the body and establishing secondary
cancers at new sites.
- In 1775 Sir Percival Potts noted that cancers of the nasal
cavity and scrotum are common in chimney sweeps, that environmental
factors can cause cancer.
- Some chemicals released in the environment such as exhaust
gases and even apparently harmless material like sawdust, may cause cell
damage and lead to cancers.
- People can inherit a greater probability of getting some
cancers, including skin cancers (more common in Celts) and some of the
colonic cancers.
- Many cancers are associated with aneuploidy, variations in
the chromosome number, but it is uncertain whether this is a cause or an
effect of cancer.
The principles of genetic disease and gene therapy
- In 1908, Archibald Garrod proposed that some human diseases were due
to 'inborn errors of metabolism' that result from the lack of a
specific enzyme.
- Some genetic diseases are caused by the genes we inherit,
including haemophilia, phenylketonuria, thalassemia, Huntington's
chorea, and some forms of cancer.
- Diseases can be caused by mutated genes: including are
haemophilia, cystic fibrosis and phenylketonuria. Other genes increase
the probability of disease.
- Disease can be caused by genes that leave people
predisposed to get some conditions such as cancers, or diabetes. Many of
these are not well understood.
- Radiation effects, including ultraviolet radiation from the
sun, can cause disease, generally because the radiation causes
mutations, chemical changes in DNA.
- The theory of eugenics is that some genes are always better
than others, and that 'worse' genes should be eliminated. This is
foolish and lacking in science.
- A form of transmission called sex linkage happens when
genes are carried on the sex chromosome. Such conditions are often more
common in one sex than the other.
- Because the genes for colour vision are carried on the
X-chromosome, colour blindness is found more often in male humans than
in females, who act as carriers.
- Anomalous deuteranopes, the people we call 'colour' blind,
lack one of the three kinds of cone cell in the retina, usually the ones
that detect red light.
- The peculiar pattern of sex-linked inheritance of human
blindness-blindness was first reported to The Royal Society of London by
the Reverend Michael Lort in 1779.
- The inheritance laws for sex-linked traits like
blindness-blindness were fully formulated in 1820 by Christian Friedrich
Nasse, using haemophilia as his example.
- Haemophilia and colour blindness are two well-known
conditions showing sex linkage in their patterns of inheritance, and
there are other rarer examples.
- In 1983, James Gusella used blood samples collected by
Nancy Wexler and her co-workers in Venezuela to locate the Huntington's
chorea gene on chromosome 4.
- Genetic manipulation may lead to future effective gene
therapies, although it is still less than perfect as a solution, and so
only used now in extreme cases.
- In 1959, LeJeune, Gautier and Turpin found an extra
chromosome in the nuclei of cells from children with Down syndrome,
later identified as chromosome 21.
- Recent attempts at gene therapy have only been used on desperately ill patients, in several cases, patients have died from unexpected complications.
The principles of protozoal diseases
- The eukaryotic Protista make up one of the five main groups of
living things. It is a mixed group, mainly unicellular, but some are
colonial.
- Some diseases are caused by parasites, including malaria,
cryptosporidiosis, and a variety of diseases caused by worms and flukes
which live in our bodies.
- Many serious diseases are caused by protists (or
protozoans), including amoebic dysentery, African sleeping sickness,
malaria, leishmaniasis and Giardia.
- Protozoa are single-celled like bacteria, but they have membrane-bound organelles inside their cells, suggesting a very different line of evolution and descent.
The principles of prionic diseases
- Proteins are made of folded chains of amino acids: prions are
misfolded proteins, causing a variety of 'prionic' diseases which attack
the brain.
- In technical language, prion diseases are a family of rare
progressive neurodegenerative disorders affecting both humans and
animals.
- That means the prion diseases begin slowly and get worse over time, attacking the nervous system of the animal they attack.
- Known prionic diseases include kuru, Creutzfeldt-Jakob
disease (and vCJD) in humans, scrapie in sheep, CWD in deer and BSE or
'mad cow disease' in cattle.
- Scrapie was the first disease known, and for a very long
time, scientists believed that the disease could not cross what they
called 'the species barrier'.
- Scientists now believe that BSE was caused when ground-up
nerve tissue from diseased sheep was fed to cattle as a food supplement.
- Scientists strongly suspect that vCJD (variant
Creutzfeldt-Jakob disease) in humans was caused by eating cows suffering
from BSE.
- Other human prion diseases are: GSS
(Gerstmann-Straussler-Scheinker syndrome); FFI (Fatal familial Insomnia)
and Alpers Syndrome.
- Prions can pass on their misfolding to other proteins, causing prionic diseases to spread. The only answer is to destroy all carcases of diseased animals.
Nutrition and food
- Animals use food for the replacement of worn-out parts of their
bodies, turning over tissues like blood at a high rate, other tissues
more slowly.
- A sufficient diet for any animal must provide enough
energy, must include enough protein of the right sort and enough of each
vitamin that an animal needs.
- Animals need food as a source of energy, and as a source of
raw material for building tissues and cells and the repair of damaged
tissues and cells.
- The anatomy of an animal reflects what it eats, especially
in the teeth and claws, and in those parts of the body used to reach or
catch up with food.
- The vitamin needs of different species of animal vary,
depending on which of the needed vitamins they can make for themselves
from their normal diet.
- The teeth of an animal give a good clue as to what it eats:
carnivores have large canines and shearing teeth to cut raw meat and no
grinders.
- The teeth of an animal give a good clue as to what it eats:
herbivores have large grinding teeth to make a pulp of tough vegetation
and no shearing teeth.
- The teeth of an animal may be misleading about what it
eats: male gorillas have large canine teeth, which they use in threat
displays to other males.
- Human starvation is a major killer of our fellow humans,
both directly through starvation, and by weakening people so they cannot
fight off disease.
- Deficiencies in the diet can cause diseases such as
pellagra, scurvy, rickets, goitre and beriberi, all of which may be
cured by a better diet.
- In 1657, James Cook (not the navigator) published the case
notes on scurvy of John Hall, William Shakespeare's son-in-law, leading
to some later confusion.
- In 1753 James Lind published his Treatise on Scurvy,
establishing that lemon juice cured scurvy, though it would be a long
while before it was fully accepted.
- In 1906, Frederick Hopkins suggested the existence of what
we now call vitamins and that a lack of these essential compounds caused
scurvy and rickets.
- In 1921, Sir Edward Mellanby discovered vitamin D and
showed that its absence causes rickets in dogs kept indoors, while
cod-liver oil cured it.
- In 1914, Goldberger had noted that only orphanage children
between 6 and 12 years old got the disease, but no orphanage staff, and
no younger or older children.
- It turned out later that those under six were given plenty
of milk, and those over twelve were given more meat. Everything pointed
to some dietary deficiency.
- In 1915, Joseph Goldberger showed pellagra was a vitamin
deficiency disease, after he noted an age distribution that was later
related to diet in an orphanage.
- Some diseases are caused by environmental factors,
including toxins in foods that may be produced by microbes, and
carcinogens in food, air and water.
- There are various methods of food preservation, which make
it impossible for microbes to live in or on the food, or place a barrier
between microbes and food.
- Food preservation can be done by boiling to sterilize,
followed by sealing to keep germs out, by adding strong solutions of
salt or sugar, or by freezing.
- Some animals rely mainly on metabolic water for their water, this being water that is formed during the respiration of lipids and carbohydrates.
Drugs and medicines
- Herbal drugs rely on effects that have evolved over long periods,
but they have uncertain strength, while medical versions of those drugs
are more predictable.
- Herbal drugs rely on chemical effects that evolved over
long periods to be biologically active in some way, and just happen to
also affect some other condition.
- The study of past use of plant medicines is ethnobotany. It
involves identifying those plants which experimentation has identified
as effective against disease.
- In 1785 William Withering published 'An Account of the
Foxglove and Some of Its Medical Uses', introducing the traditional herb
digitalis as a medical drug.
- In 1809 Benjamin Silliman and a partner opened the first
two soda water fountains in New York City, promoting the drink as a
remedy against yellow fever.
- In 1941, Selman Abraham Waksman coined the term
'antibiotic' to describe compounds produced by microorganisms which are
able to kill bacteria.
- Antibiotics have evolved naturally to combat other life
forms, mostly in the soil, on the moist skin of frogs, or in other
places where competition is intense.
- Antibiotics are selective poisons that kill some sorts of
bacteria which lack resistance, but it should not be assumed that they
do not harm us as well.
- Many frogs secrete antibiotics on their skin, an important
adaptation in an animal that lives mostly in damp places. Some frogs
also secrete toxins.
- Many living things living in damp and moist conditions
produce antibiotics, chemicals that limit the growth of bacteria on the
organism producing them.
- Antibiotics are effective against some bacteria. They are
selective poisons that kill bacteria: they are more poisonous to
bacteria than to our cells.
- Many bacteria are resistant to some antibiotics, and given
time and enough exposure, especially in small doses, can develop
resistance to any known antibiotic.
- The development and spread of antibiotic resistance is
favoured by uncontrolled use of antibiotics in medicine and agriculture
and by horizontal gene transfer.
- Virus diseases cannot be treated with antibiotics, but a great deal of waste of antibiotics goes on when they are prescribed for viral illnesses.
About plants
- Plants all have cellulose cell walls, higher plants form specialized
tissues like aerenchyme and conductive tissues, and plant cells contain
plastids.
- Plants get their energy by respiration of chemical stores,
generally in the form of carbohydrates, to convert adenosine diphosphate
to adenosine triphosphate.
- The minerals that plants need are absorbed by passive
uptake as water which contains dissolved salts is drawn in from the soil
by the root hairs.
- Plants have limitations and needs, such as water, light and
minerals, and they compete with other plants for these, both by growing
upwards, and chemically.
- Algae are very simple plants with common features in the
ways they reproduce (always in water), and their comparative lack of
specialized tissues.
- The green algae are a subset of the algae, linked loosely
by the chemistry of their photosynthetic pigments and their habits, the
ways they grow.
- Many of the lower plants such as mosses and ferns exhibit
alternation of generations, with haploid and diploid forms, each giving
rise to the other.
- Mosses and other bryophytes make a natural grouping because
they have a number of traits (lack of conductive tissue, method of
reproduction) in common.
- Ferns make a natural grouping, because they have similar
features such as conductive tissue, and the life cycles seen in their
reproductive methods.
- Gymnosperms (the pines and their relatives) make a natural
grouping, because they grow in similar ways, are anatomically similar,
and reproduce the same way.
- Higher plants have vascular tissue systems with phloem and
xylem, which allows them to rise up off the ground, and get more energy
from the Sun.
- Higher plants have complex leaf tissue systems, with an
epidermis with stomates, and an inner area, rich in chloroplasts and air
gaps to allow air access.
- Higher plants have root tissue systems which are able to
gather in the water and minerals that the plant needs. Some roots have
symbionts attached.
- Higher plants have growth areas within them: cambium and
meristem in particular, where new cells are formed and differentiated
into the needed tissues.
- Wood is a two-phase material, with lignin for rigidity and
cellulose fibres for tensile strength, which plants need to get higher
than other plants.
- Some plants are annual, growing through a complete cycle
once a year (or more often in some cases), some are perennial, lasting
for many years, like trees.
- Flowering plants or angiosperms may be divided into
dicotyledons and monocotyledons, which have other traits such as the
forms of leaves and roots in common.
- Angiosperms have different ways of getting pollen to travel
from one plant to another, relying on wind, birds, insects, and even
small mammals in some cases.
- Angiosperms have a variety of ways to spread their seeds to
new areas, using wind, the digestive systems of animals, hooks and
adhesives among other things.
- Angiosperms often hybridize outside their species though
usually within their genus, but sometimes further afield, if tetraploid
individuals occur.
- Higher plants have a range of tissue systems, with
different types of cell in different parts, performing different
functions to maintain the plant.
- At times of stress, the leaves of angiosperms drop off at
the abscission layer, a point where the plant seals itself off to
prevent undue water loss.
- Dying leaves are yellow because, before a leaf is dropped
from a plant, most of the available nutrients are taken back into the
plant, to be used again.
- Many angiosperms produce alkaloid poisons in their leaves
to defend them against herbivores, and the herbivores need to evolve
ways to deal with this.
- Angiosperms can also exchange genetic material outside
species barriers when microbes carry genes into plants, a process called
horizontal gene transfer.
- Angiosperms sometimes produce adventitious roots from
branches, providing new sources of water and support for large trees,
once the roots are established.
- Roots are used by plants to obtain water and minerals,
generally from the soil, but roots also keep plants upright against the
forces of gravity and wind.
- Plants can sense the down direction, and roots grow
downwards, although once in the soil, the secondary roots of many plants
will also grow towards water.
- Pollen fertilizes a flowering plant when a pollen tube
grows down the style, so one of the nuclei can travel down the tube and
fuse with a nucleus in the ovum.
- In the laboratory, plant hybrids can be created that cross
species barriers, but the same process also happens in nature, and in
agriculture.
- Many plants have spines or hairs on their leaves and stems
to discourage herbivores from grazing on them, depriving the plant of
water, energy and minerals.
- Over time, plants have evolved to produce chemicals that attract useful animals such as pollinators, while also making chemicals that repel potential predators.
The principles of photosynthesis
- Plants are producer organisms, but they need both oxygen for
respiration and carbon dioxide for photosynthesis in order to operate as
a living organism.
- Most photosynthesis happens in leaves, but it can also take
place in cladodes and phyllodes, which are modified and flattened stems
and petioles.
- All of the photosynthetic parts of plants (leaves, cladodes
and phyllodes) contain chloroplasts, small organelles where
photosynthesis actually takes place.
- Photosynthetic parts need stomates or pores to let gases in
and out: the opening of the stomates is controlled by the guard cells
on either side of the stomate.
- Photosynthesis in plants would not take place without the
chlorophyll that is contained in the chloroplasts, which is used to
produce energetic electrons.
- According to serial endosymbiosis theory, chloroplasts were
once independent organisms which then found welcoming shelter inside
other primitive organisms.
- Plants appear to be green because chlorophyll does not
extract the energy from green light, and this wavelength is reflected
away from the leaf.
- In any conditions, there will always be a limiting factor
on productivity in plants, some item which is in short supply and so
limits photosynthesis.
- Plants use at least two different photosynthetic pathways,
known as C3 and C4. C4 plants are more efficient than C3 plants in
photosynthesis.
- The difference between C3 and C4 plants lies in just a few
key enzymes, but it leads to curious effects which may be detected long
after the plant has died.
- The uptake of the stable isotopes of carbon, carbon-12 and
carbon-13, varies between C3 (less carbon-13) and C4 plants, which have
more carbon-13.
- An examination of the stable carbon isotopes in animal material reveals whether the animals ate C3 or C4 plants, and so may indicate past climate details.
About fungi
- Fungi are a mixed group of living things, linked by features of
their cells. Most fungi are multicelled, and many of their cells contain
more than one nucleus.
- Fungi are found in most environments, but are particularly
important in places like forest floors, where they consume litter and
many microarthropods eat them.
- Most fungi reproduce by spores, though some fungi reproduce
by growing extensions of their hyphae into new areas, once a spore has
established a new growth.
- Fungi play an essential role by breaking down and recycling
dead material, so that the nutrients contained in the dead material can
be used again.
- Because they live in highly competitive environments, many
fungi produce antibiotics and other poisons that are able to harm
predators or bacteria.
- Fungi have caused poisoning by ergotism in the past, when
the ergot fungus has attacked a rye crop. Other fungi can make nut crops
poisonous.
- Fungi cause a number of unpleasant or dangerous diseases in
humans like tinea (athlete's foot), thrush, aspergillosis,
histoplasmosis, ergotism and ringworm.
- The Basidiomycetes (mushrooms, toadstools and similar
forms) make a natural grouping within the Fungi, linked by a number of
characteristics.
- Yeasts can be observed in the process of respiration, and
may be shown to use a remarkably similar set of genes and biochemicals
found in other organisms.
- A fungus can sometimes be found associated with one of the
algae in a lichen: this is often regarded as a symbiosis, but is more
like helotism.
- Fungi form mycorrhiza on many plants, symbiotic threads that grow out from the roots, and play the same role as root hairs, taking up water and minerals.
About fish
- Fish make a natural group of animals, because they have similar
methods of reproduction and breathing, and structures such as gills,
fins and scales.
- Like the reptiles and the amphibians, the fish are
poikilothermic or cold-blooded, and this can bring special problems for
fish in polar waters.
- Fish are found in both fresh and salt waters all over the
world, though some fish can survive out of water for a short while,
enough to move from pool to pool.
- Some of the early fish developed their fins into something
not unlike legs, and moved onto the shore, giving rise to the earliest
four-legged amphibians.
- Bony fish show a wide variety of adaptations in their
structures and behaviour. Some fish also show a limited ability to learn
from their experiences.
- Bony fish are generally able to adjust their buoyancy, in
much the same way that submarines do by adding or removing gases from a
swim bladder.
- Sharks and rays have cartilage for their skeletons and no
bone, and they have a number of other common characteristics, like the
lack of a swim bladder.
- Sharks have heterocercal tails which produce lift as they
swim. This, with the angling of their pectoral fins, keeps the negative
buoyancy sharks from sinking.
- Some sharks reproduce in unexpected ways, some of them
nurturing eggs within their body and actually producing live young,
while others lay eggs.
- Fish rely on a variety of senses, including sound (vibration detection), smell (taste), sight, and electric senses which are effective in muddy water.
About amphibians
- Amphibians make a natural grouping of animals, almost all other than
the axolotls having a juvenile aquatic stage and an adult terrestrial
stage.
- Modern amphibians are the descendants of the first
vertebrates to move out of the water onto the land. Most of them have
evolved a great deal since that time.
- The development of an egg into a tadpole and the
metamorphosis of a tadpole to an adult may be observed with ease, making
them ideal laboratory animals.
- Frogs and toads fit the terrestrial vertebrate body
pattern, having an endoskeleton with four pentadactyl limbs, and a brain
located in the skull.
- Many of the amphibians have well-developed powers of
regeneration, and they may even be able to regenerate lost limbs. Other
vertebrates lack this ability.
- Many amphibians around the world are endangered species,
but the reason is still a matter for debate. It may be caused by
pesticides, Fungi, or something else.
- Amphibians undergo a form of metamorphosis as they develop
from tadpole to adult, a change in body form that is far greater than
that of any other vertebrate.
- The amphibians, which have external fertilization, gave rise at some point to the early reptiles, which had internal fertilization.
About reptiles
- Reptiles make a natural group, because they all have scales and
similar internal anatomy. They vary in their methods of reproduction,
and are divided by this.
- Lizards mostly have legs, though some have lost them.
Snakes have no legs, but evolved from reptiles with legs, as can be seen
in the fossil record.
- Snakes are a natural part of the environment, and play a
part in maintaining normal natural balances. They should be preserved,
like all the other parts.
- Most people who are bitten by a snake are bitten while
trying to catch or kill a snake that could just as easily have been left
alone. There is a lesson here.
- Tuatarans are primitive reptiles which only managed to
survive in a few isolated parts of New Zealand, where they were able to
avoid predators and competitors.
- Turtles and tortoises are reptiles that have shells.
Turtles need to come ashore to lay their eggs, which leaves them and
their young at risk from predators.
- Dinosaurs are one of the groups of extinct reptiles, and
based on their skeletons, they may be further divided into lizard-hipped
and bird-hipped forms.
- Extinct reptiles can be reconstructed from fossil evidence,
but reconstructions are often coloured by people's assumptions about
how the animals behaved.
- Dinosaurs lived for a long time, a long time ago, and
probably died out (as dinosaurs) as a result of an asteroid strike that
changed the climate.
- Dinosaurs are usually referred to as having died out, but
there is a lot of evidence to suggest that the birds are just modern
warm-blooded dinosaurs.
- There are some scientists who would happily treat the birds
as part of the reptiles group, while others would include the
monotremes as reptiles.
- There are many theories about how the dinosaurs died, and
we will probably never know what really happened, but the asteroid
theory looks good.
- There were other ancient reptiles around at the time of the
dinosaurs that were not dinosaurs, and some of them survive today, like
crocodilians and tuatarans.
- The first people to make the ancient reptiles well known
were Caspar Wistar, Mary Anning and Gideon Mantell. Richard Owen also
helped.
- Even now, we only have a very partial picture of the dinosaurs, because the fossil record is far from complete, but every year, new founds are made.
About birds
- Birds make a natural group of animals, all having feathers and scaly
legs, all being warm-blooded and egg-laying. On the ground, they move
on two legs.
- Aside from their physical similarities, birds have many
similar behaviours: most of them make nests for their eggs, care for
their young, and tend to flock together.
- Birds of a species all nest in the same way, because
nest-building behaviour is driven by instinct, although the materials
used for the nest may vary.
- Birds select a mate with care, and most birds provide
detailed support for their young, except for cuckoos, hatching the eggs
and feeding the young birds.
- Cuckoo behaviour is a trade-off that works for the cuckoos,
which can spend more of their energy in producing extra eggs, rather
than feeding their young.
- If enough birds began to behave like cuckoos, the strategy
would no longer pay off, and the birds would either need to change their
behaviour or go extinct.
- As a general rule, species which are under threat of
extinction have no way of perceiving the threat, so it is improbable
that they will change their behaviour.
- Birds are adapted in many ways for how they live: they are
able to live in all of the environments where humans can live, and a few
where humans cannot.
- Wild birds can be identified in a variety of ways: from
traces and tracks, by their calls, their plumage and beaks, their size,
location, and the way they fly.
- All birds show behaviour, and birds of the same species
show similar behaviour, but most birds are also able to learn new
behavioural patterns.
- Flightless birds have evolved from flying birds, which was a
change that allowed them to grow larger or to function better in the
absence of predators.
- Flight feathers can be recognized even in a fossil, because
the feathers are asymmetrical, with the narrower edge to the front
(leading edge) of the wing.
- Fossils of Archaeopteryx have feathers on their wings which are narrower on the leading edge (front side), showing that Archaeopteryx could fly.
About mammals
- Mammals make a natural group which subdivides into three, based on their methods of reproduction: the monotremes, the marsupials and the placentals.
- All mammals are warm-blooded, they all have at least a few modified hairs, and they generally care for their young. They are usually classified by their teeth.
- For each mammal, it is possible to write a dental formula, describing the numbers of each of the different types of teeth in each jaw.
- Teeth last long after an animal dies. While teeth are useful in identifying the groups that extinct mammals belong to, there are a few inconsistencies.
- According to the dental formula of a koala, it is some sort of fat possum. The molecular evidence, on the other hand, suggests that it is an arboreal wombat.
- All of the mammals other than monotremes are viviparous, bearing their young alive. Monotremes are the only furry and warm-blooded egg-layers.
- Monotremes have many reptilian features, including egg-laying, their gait as they walk, their egg-laying, and their body temperature, which is more variable.
- Marsupials have common features: most of the females (but not all) have pouches in which the young are carried, and the reproductive systems are distinctive.
- Placental mammals have their young develop within the uterus, getting nourishment from a placenta, which is fetal tissue in contact with the mother's tissues.
About invertebrates
- Having a group called 'invertebrate' shows us an unnatural division
of living things, as about all they have in common is the lack of a
backbone or notochord.
- In most cases, invertebrates are quite small, though there
are exceptions to this rule like the giant squid, one of the largest
organisms found on the planet.
- Because the invertebrates are not a natural grouping in any
sense, there are very few general comments or principles that can be
stated about them.
- Within the unnatural grouping that we call the
invertebrates, there are many subgroups which are useful and make a
great deal of sense for scientific work.
- Earthworms and their relatives make a natural group of living things: they burrow in the soil, feed at the surface, have senses and are easy to culture.
About molluscs
- The molluscs, the snails and their relatives make a natural group,
based on their body plan and general anatomy and their mode of
reproduction.
- Snails live in water and on land, and even in the most
unlikely places, including a number of deserts. Some snails are very
efficient at conserving water.
- Some snails eat plants, grinding tissue with a radula,
while others are carnivorous. Tropical cone shells are dangerously
venomous, hunting and catching prey.
- Normal shelled snails can be found with both right-handed
(normal thread) and left-handed (reverse or gas thread) shells. Most
species have just one form.
- Snails can be cultivated fairly easily, and are worth
careful observation for their methods of eating and locomotion, as seen
when they move across glass.
- Slugs are shell-less snails with a somewhat different body
plan, but they also possess asymmetrical arrangements left over from
when they had shells.
- Octopuses are highly intelligent, and can be trained to
perform a variety of complex tricks. They will also solve problems
involving travelling through mazes.
- Some octopuses lay out items on the sandy sea floor in a
pattern that probably assist them in finding the way back to their
shelter when danger threatens.
- Some octopuses, particularly the blue-ringed octopus, carry a powerful toxin that can kill humans. This is tetrodotoxin, which they probably get from microbes.
About arthropods
- Arthropods with more than eight legs form several easily
distinguished groups, the main ones being the crustaceans, the
millipedes and the centipedes.
- Millipedes make a natural group: they are vegetarians, and
they have two pairs of legs to each segment. Because of their diet, they
are easy to culture.
- Centipedes make a natural group of venomous carnivores,
with one pair of legs on each segment, unlike millipedes, which have two
pairs of legs per segment.
- Spiders, scorpions and ticks make a natural grouping, based
on their number of legs, but in other ways, they are quite distinct in
their behaviour and anatomy.
- Spiders hunt in a variety of ways: orb weavers use a normal
'spider web', but others cast a net over their prey, while others chase
their prey down in the open.
- Orb weaver spiders can be kept and observed, so long as
they are placed on a frame standing in and over water, where they can
make a web, but not escape.
- Some species of spiders, and some strains within species,
can be social, grouping together. This is a useful characteristic when
spiders arrive in a new place.
- Australian huntsmen spiders arrived in New Zealand in the
recent past, and while they are rarely social in Australia, they are
commonly social in New Zealand.
- Crustaceans make a natural group that is easy to study:
slaters or woodlice can be cultured, and freshwater crustaceans can
easily be kept in tanks.
- Charles Darwin used a careful analysis of their anatomy to
show that barnacles are not shellfish but arthropods: their tentacles
are highly modified legs.
- Insects make a natural grouping, because they all have six
legs, and either have four wings, or can be shown to have evolved from
four-winged ancestors.
- The changes in insects are called metamorphosis: starting
as an egg, an insect larva becomes a pupa which becomes the adult form,
called an imago.
- In social insects, it is common for all members of a colony
to have exactly the same genes, and for one individual to lay all the
eggs on behalf of all of them.
- In social insects, having identical genomes is important,
because the actions of the sterile workers still go to improve the
survival of their genome.
- The beetles or Coleoptera are a very diverse group of
insects, but all of them have elytra, which are modified wings,
protecting their flight wings.
- Flies have four wings, but fly with just two, the other two
(the halteres) being reduced to a very small size and used for balance
in flight.
- The role of the halteres in balance may be demonstrated by
removing the halteres from an adult fly, which will then be unable to
fly in the normal way.
- Fruit flies can be cultured in the laboratory, and they
were commonly used in genetics experiments, because they go through
generations very rapidly.
- Mosquitoes are a natural division of the flies, based on
their reproduction and feeding patterns, where males feed on plants,
females on animals.
- Mosquitoes have three clear stages of development, with the
egg, the larva and the pupa in water: mosquito development may be
observed in captivity.
- The Hymenoptera (ants, wasps and bees) make a natural
grouping: almost all of the Hymenoptera form group nests that have a
complex social structure.
- Termites, otherwise called the Isoptera, have a complex
social structure, featuring a variety of specialized forms or castes
within the nest.
- Butterflies and moths are a natural grouping, but the
butterflies and moths cannot be divided naturally on any differences, as
the division is not a natural one.
- Butterflies and moths show a variety of adaptations to
their environments and predators, including the development of 'fright
eye' patterns on their wings.
- Caterpillars have specific food preferences, and females
will normally lay eggs on food plants suitable for the caterpillars, for
obvious evolutionary reasons.
- The Lepidoptera, the moths and butterflies, are varied in
their size and form, they differ greatly in their food choices, and some
migrate over long distances.
- Case moths always use local dead plants for their covering,
and this can be demonstrated in the laboratory. Some case moths never
develop wings.
- Some caterpillars and moths are protected by the toxins
they eat, and in some cases, they can even pass this protection on to
the next generation.
- Moths pollinate some white, heavily-perfumed flowers at night, and it seems that the flowers have developed these traits specifically to attract the moths.
The principles of biotechnology
- Biotechnology uses living forms, mainly simple cells like
bacteria to make products that could come from other sources, but does
it faster and more cheaply.
- Much of biotechnology involves producing enzymes. Enzymes
are useful because they are substrate-specific and generally have no
side-effects on the end-users.
- A major product of modern biotechnology is
biopharmaceuticals, although this may change as the technology becomes
more mature and more products are possible.
- Organisms living under extreme conditions are known as
extremophile organisms: they typically live either in very hot or very
toxic conditions, or both.
- Extremophiles are interesting sources of new enzymes,
because they need such things to survive: Taq-polymerase, used in PCR,
was obtained from an extremophile
- Environmental technology often involves bioremediation,
using either existing extremophiles or modified organisms to make
dangerous substances safe.
- In 1973, Stanley Norman Cohen and Herbert Wayne Boyer
demonstrated that restriction enzymes could be used to transfer genes
from one species to another.
- The information gathered in genomics work can be applied
through bioinformatics, a new science that links modern biological
knowledge and computing.
- We know very little about the microbes that share our
planet, because most of them remain hidden at this stage, unless they
infect us, our crops or our animals.
- Most of the world's bacteria do not infect or harm us or
the organisms we are most concerned about, and cannot be grown for study
in pure cultures.
- Many bacteria in the world are known only in complex
ecosystems called biofilms, where they live with other species of
bacteria in a cooperative system.
- In 1980, The U. S. Supreme Court ruled in the Chakrabarty
case that genetically altered life forms could be patented and so obtain
legal protection.
- Where companies had previously relied on trade secrets, the
Chakrabarty case meant genetic engineering methods could now be used
with more confidence.
- In 1988, Leder and Stewart received a US patent for the
Harvard mouse, genetically altered to be susceptible to cancer. A
European patent was refused in 1989.
- In 1994 British and American research institutions agreed not to patent human gene sequences, closing down some of the growing ethical fury over gene patents.
The technology of agriculture
- Humans have been practising agriculture for about 10,000 years after
agriculture was independently invented in at least Mesopotamia, America
and New Guinea.
- For all that we know, there may have been other independent
inventions of agriculture in other societies, but so far, we have no
evidence of this.
- The development of agriculture allowed humans to settle in
one place and so have better shelter, and also own more possessions than
they could carry around.
- Farmers were generally able to produce more food than they
and their families needed, and this opened the way to some people being
able to specialize.
- Some parts of the farming cycle left farmers with nothing
to do but watch their crops grow. This gave them time to think, to
observe, and perhaps even tinker.
- Farmers were able to observe the same basic situation, year
by year, with slight differences that allowed them to observe cause and
effect at close hand.
- One of the key changes that allowed agriculture was the
development of systems of irrigation, but these required more organized
societies to maintain them.
- The aqueduct was an early means of transporting water with
no energy cost, using gravity to carry the water, although inverted
siphons were also used at times.
- The aqueduct could work by gravity when builders could
survey a suitable route, build supports and construct a waterproof
channel to carry water without leaks.
- The qanat of ancient Persia was an early means of
transporting water with no energy cost, relying on a tunnel going
upwards, beneath the water table in hills.
- Irrigation, combined with agriculture, delivered regular
food surpluses allowing some people to specialize in making things that
they could sell or barter.
- Irrigation and agriculture together led to a society in
which some people could become full-time soldiers and rulers, while
others could become scholars.
- In 1630, Johann Glauber suggested the use of saltpeter,
sodium nitrate, as a fertilizer, implying a recognition of the need for
nitrogen when growing plants.
- In 1645 Sir Richard Weston described crop rotation as he
saw it in Flanders: the first reference in English to the habit of using
different crops in one field.
- Around 1701, Jethro Tull invented the seed drill, allowing
farmers to sow seed more efficiently and more economically, increasing
the efficiency of large farms.
- Most crops are grown as monoculture crops, making massive
outbreaks of pests easier, but offering large economies of scale. Sprays
make the risk less.
- Most sprays kill more than just the pests they are aimed
at. Many of the pesticides are accumulated to dangerous levels, either
in the soil or the food chain.
- Many organohalogens are used as pesticides in farming, and
the use of these pesticides in agriculture is driven by a consumer
demand for blemish-free food.
- Overgrazing can be a problem in some situations, trading
off long-term viability of a farm for short-term gain by a farmer.
Economic pressures may favour this.
- In many cases, the energy output from a farm in the form of food is less than the energy input in terms of materials like fertilizer and pesticides, and fuel.
There are other SPLATS to be found, but you will need to go back to the main SPLATS page to find the links.
© The author of this work is Peter Macinnis, who asserts his sole right to the product as it is packaged here, recognising that many of the ideas are common. You are free to use this as a model to do your own version. Copies of this whole file or site may be made and stored or printed for personal or educational use. You can contact me at macinnis44@gmail.com, but only if you add my first name to the front of that email address — this is a low-tech way of making it harder to harvest the e-mail address I actually read.
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