Science Spin 58

ISSUE 58
May/June 2013
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Marine biodiversity
Fixing DNA in a fash
Big lesson from small fies
Weird and wonderful
animals
How long is Irelands coast?
The sensaTional brain
Dr Veronica Miller explains what
goes on inside our heads what
makes us smart, why we get
emotional, how memories are
stored and what happens when
things go wrong.
Available from
www.sciencespin.com
and indepedent bookshops.
Full colour hardback 25.
BRAIN
What is it and how it works
Dr Veronica Miller
THE SENSATIONAL
Y
our heart beats, fngers feel, muscles move, eyes
see, ears hear, toes tingle and tongue tastes. A
four year old wouldnt need a degree in anatomy
to tell you that. From day one we can feel our body in
action. A quick blink tells us our eyes synthesise sight.
A nibble on a chilli pepper tells us
our tongues taste. And a shock
to the system sets our hearts
thumping, showing us what
makes blood shoot about our
bodies.
But, if you ask a
four-year old what
their brain does,
theyll probably just
scratch their heads in
wonder. And perhaps
you would too.
Billions of electrical impulses
are produced every millisecond in our brains. These
actively motivate our minds, move our limbs , yet, apart
from the odd headache, you may wonder how we know
the brain is working and what exactly it does?
To understand the brain its not enough to know a few
physical details, important as they might be, because each
is in reality just part of the whole. In many ways this is
like an ancient story from India about the Three blind
men and an elephant.

In this story, a rajah was asked to settle a
dispute in his court between those
who believed life was eternal and
those who did not. In order to fnd
out how the men could come
to a frm conclusion on such
an important matter, the rajah
gathered six blind men and sent
them to the jungle to encounter an
elephant. They were told to return
to the court and describe the elephant
to him.
The frst blind man laid his hands on the elephants side
and described the elephant to the rajah as being like a wall.
The second man felt the elephants sharp tusks and told
the rajah that the elephant was more like a spear. The third
felt the elephants trunk and said that the elephant was
snake-like. The fourth felt the elephants wrinkly knees and
In
tro
d
u
cIn
g
th
e bra
In
BRAIN
7
fake; if you show people a series
of pictures showing smilers most
of us will pick out the fake from
the true smiles. With age we learn
that facial expressions can be faked
to some extent, but blushing and
shaking with nerves are less likely to
be faked. These subtle and not-so-
subtle clues about emotional states
are all registered within the brain.
Three, two, one, go
So despite the fact that our spines tingle
and hearts race with excitement, its
actually the brain that controls our emotions. Inside our
brains are pleasure pain and fear centres in our limbic
and cortical brain areas. You could rank our emotional
responses, much in the way that the James-Lange theory
does into three diferent levels.
Firstly we have the autonomic system response. The
primary autonomic areas in the brain are the brainstem
and the hypothalamus. The brainstem mediates our
heart rate, breathing sweating and eyes dilating
and is the frst area of the brain to be activated in
emotional situations. Then messages are fred from it
to the hypothalamus to trigger the release of diferent
chemicals into the bloodstream preparing us for an
emotional response. James Olds and Peter Milner
discovered this in 1954 after fnding that electrical
stimulation of the hypothalamus in
animals produced euphoric, rage
or attack behaviours.
Secondly, and up a level, we
have the limbic system consisting
of the hippocampus and
amygdala. The amygdala controls
our fear and anxiety responses, and
the hippocampus makes short term
memories, so that we know what to
do next time the emotional response
is needed. If you stop the hippocampus
and amygdala working in animals by
cutting of their blood supply, you fnd
that the animals become very docile and
lack normal emotional responses, such as fear or anger.
The third tier of emotional cake is the input to our
cortex and output generated by it to the limbic and
autonomic areas via the relay station in the thalamus to
help us make informed decisions as to how to respond to
the emotional situation. Whether to fght or take fight.
Eye sense fear and I feel afraid
Fear can be fast and slow an instantaneous fright
when somebody jumps out at you as you walk along a
darkened corridor, and a longer-lasting feeling of unease
as you walk home at night-time along a dark road. Quick
fears are processed within seconds in our bodies and are
mainly processed via the autonomic and limbic systems.
A cross section through the brain stem.
BRAIN
37
Upfront 2
Fixing DNA in a fash
Pric Keane explains how the frst few trillionths of a second is
important in protecting DNA from sunlight 10
Big discovery from little fies
Immunology owes a lot to fundamental research 13
Weird and wonderful animals
Sive Finlay introduces us to the Lowland Streaked Tenrec 15

The gene hunter
Sen Duke talked to Aoife McLysagh about her passion for science 16
Dr Hows science wows
Exploring friction 18
Fractal Ireland
Stefan Hutzler explains how to measure the length of Irelands coast 19
Mapping ancient basins
Recording how some landscape in France took shape 21

Marine diversity
There is a lot more life at sea than on land 26
Young scientists
Taking a look at diesel laundering, wood-chip fuel and gas for the lab 29
The origin of feces
All about the subject no one wants to think about 31

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Asteroid close-up
As EsAs spacecraft, Rosetta, came
within 800 km of the asteroid steins, it
captured this image showing how the
surface has been battered and pock-
marked by impacts. The asteroid is fve
km wide and the largest impact crater
is about 2 km wide and almost 300
metres deep. The central crater is 650
km wide and 80 metres deep. About 40
craters have been noted in total.
Rosetta was launched in 2004
and following a long and complex
trajectory making use of Mars and
Earths gravity, it will fnally arrive
around the comet known as 67 P/
Churyumov-Gerasimenko. It will then
remain in orbit around the comet as it
travels on towards the Sun.
In 2008 Rosetta went by Steins, and
Ted stryk, professor of philosophy and
part-time astronomer processed the
data to produce this image showing up
details in high contrast.
Open learning
A GRoup of volunteers have launched
an alternative education space in Dublin.
The organisers aim to foster self-directed
learning where everyone is free to learn
or impart their knowledge. unlike
the prevailing top-down approach
to education, this approach is largely
Arctic camels
ThE last place we would expect to see
a camel is in the Arctic, but three and a
half million year old fossil bones show
that they once inhabited that region. A
team of scientists from the university
of Manchester and the Canadian
Museum of Nature found fragments
of a tibia, the lower leg bone. The
fragments were collected from a sandy
deposit at an elevated site on Ellesmere
Island and the scientists reported that
the extremely cold conditions there
had helped preserve proteins, adding
enormously to the value of these
fossils.
Digital imaging enabled the scientists
to reassemble the 30 fragments, and it
was possible to extract a small amount
of collagen, one of the main protein
components in bone.
By comparing the collagen to
37 present-day mammal species a
close match was found with modern
Dromedary camels. A close match was
also found with another fossil camel from
the Yukon area.
Although the match was close, the
bone fragments show that the Arctic
camel was bigger than modern species.
The tibia was about 30 per cent larger
than those in living camel species.
It is thought that the camel lived in a
boreal-type forest environment during
a warmer phase. Camels may have
originated in the far north, and scientists
wonder if some of the features we see
now could have been shaped originally
in a much colder environment.
dependent on self-motivation and
sharing, open Learning Ireland also aims
to serve those who have been alienated
by negative experience in school, or
have found themselves cut of from
participation in formal education.
For more information:
http://openlearningireland.com
China links
FoLLowInG an agreement between China and Ireland to co-operate on agri-
food, nanotechnology, biomedical developments, ICT and other areas, the Irish
Government has made up to 1 million available to support suitable initiatives.
China is providing matching fnance, and the Irish funding is being channelled
through Science Foundation Ireland. university College Dublin and nuI Maynooth
are leading projects that will involve all seven Irish universities, the Royal College
of Surgeons Ireland, the Institutes of Technology in Dublin, Cork and waterford,
and Teagasc. These organisations will be collaborating with about 30 research and
higher education institutes in China.
Battery implants
InSERTInG medical devices can keep
our bodies working, but one of the risks
is that the batteries might leak, and of
course they can run out of power.
Researchers at the Polish Academy of
Sciences in warsaw have come up with
a safer and longer-lasting solution in the
form of an air-breathing bio-battery.
The concept is much the same as the
common experiment in schools in which
two electrodes inserted into a potato or
lemon can generate a current.
Instead of using a potato, the
researchers make use of naturally
occurring substances in or around the
body. According to the researchers
the zinc-oxygen biobatteries produce
more power than existing batteries,
and because there are no strong acids
or bases, there is no need for a heavy
protective housing. To generate power,
the only requirement is to insert the
electrodes into the body.
As the researchers point out, the
concept is not new, but improvements
to the cathode mean that a zinc-oxygen
battery can continue to produce 1.7 volts
for several hours. over the past few years
the research group has been developing
a cathode incorporating enzymes within
a carbon nanotube and silicate matrix.
The cathode is in a cell containing an
electrolyte which consists of a solution
containing hydrogen ions. Pores in the
silicate matrix allow oxygen in, and with
the assistance of the enzyme, reduction
takes place, and the carbon nanotubes
transport electrons to the surface.
After about one and a half weeks
the efciency goes down because the
enzyme wears out. The researchers are
now looking at how the enzyme might be
regenerated to prolong biobattery life.
Western
wilderness
oVER 11,000 hectares of north
west Mayo have been declared
a wilderness area. An agreement
was made between Coillte and the
Department of Arts, Heritage and
the Gaeltacht to return much of this
area which includes the existing
Ballycroy National Park and Nephin
mountain to a wilder state. under
this agreement Coillte is to take 4.400
ha out of commercial forestry.
More fellows
The number of postgraduates working
on food and agriculture has increased.
Under the Teagasc Walsh Fellowship
Programme 64 new postgraduates being
approved for support. This is the largest
number of approvals since the Walsh
Fellowship Programme began and it
represents a major investment of over 4
million in fostering emerging scientifc
talent.
The new postgraduates, many of
whom are conducting research for a
PhD, join the existing 140 Walsh Fellows
and will work under the supervision of
Teagasc and university staf.
Under the Walsh Fellowship
Programme Teagasc works in
collaboration with the universities and
institutes, and there are well established
links to research organisations in europe,
the US and New Zealand. Professor
Gerry Boyle, Director of Teagasc, said
that Fellows are encouraged to engage
with the best in international science and
research.
For more details:
www.teagasc.ie/research/postgrad
Magnetic bacteria
LoNG before sailors learned how to
use a compass bacteria were orientating
themselves along magnetic lines. At
the University of Huddersfeld, Amy
Mornington has been studying how some
bacteria have membrane-encapsulated
magnetosomes. These magnetosomes
contain magnetite, an iron oxide that also
occurs in a variety of animals, including
bees, pigeons and salmon.
UPFRONT
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Boys to the right
hUMANS are not the only ones to be left or right handed. Many other animals also
display a distinct preference for leading with the right or left paw or hoof. It was often
thought that a structure known as the corpus callosum in the brain is involved. This
particular structure acts as a communications bridge between the two halves of the
brain.
however, Dr Yegor Malashichev at Saint Petersburg State University has reported in
BioMed Central that marsupials without a corpus collosum, such as the sugar glider or
short-tailed oppossum also have a distinct preference in favour of the left or right and
the preference is related to gender.
With non-marsupial mammals, males are usually left-handed, and females right-
handed, yet with marsupials that walk on four limbs, males are usually right-handed,
and females left-handed.
The marsupial sugar glider, Petaurus breviceps, has no corpus callosum.
Mini-makers
oN Saturday 27th July 2013 makers will be busy in and around Trinity College
Dublin and the Science Gallery. Workshops, performances and other hands-on
events are planned as participants build their own devices. Just making things has
become highly popular as people apply a variety of skills in creating weird and
wonderful devices. To a dedicated maker there is really no such thing as junk,
but turning it into something useful or entertaining is the challenge.
Makers or groups who want to participate by exhibiting what they can do can
download a submission form from:
http://www.makerfairedublin.com/open-call-2013
More information from Shaun oBoyle at the TCD Science Gallery, 01 8964405 or
email shaun.oboyle@sciencegallery.com
While the role of magnetite in
orientating organisms is easier to
understand, Amy Morningtons aim
is to fnd out how it is produced. By
understanding how the biomineralisation
works in nature, it may become possible
to mimic the process to produce
magnetite commercially. Potential
applications including drug delivery, are
not viable at present, but discovering
how bacteria produce magnetite might
lead to a more cost-efcient process.
Killing cancer cells
WheN cancers develop the body
can react by inducing the cells to self-
destruct. however, if a gene, known as
p53, is defective, the defence mechanism
does not work, and the cancer continues
to grow.
Researchers at the Karolinska
Institutet in Sweden have found that
it is possible to restore p53 activity by
administering a substance known as
APR-246. A study was conducted on 22
patients with advanced blood or prostate
cancers, and the researchers, working
under Dr Soren Lehmann, have reported
positive results indicating that the p53
gene had become active, and in two of
ten patents that were evaluated, there
were signs of tumour regression.
These are preliminary results, and the
main aim of the study was to fnd out
how ARP-246 is tolerated by the body.
It was found that tolerance is good,
and the researchers expressed confdence
that this drug will help, especially in
combination with other treatments. Up
to half of the cancers including ovarian
cancer and most tumours are thought
to arise from a defect in the p53 gene.
however, Professor Klas Wiman, who
discovered APR-246, commented that
tumours are extremely complex, so other
factors are probably involved.
Research images
Biomedical students at NUi Galway have exhibited a number of
striking images that show of the artistic side of science. Although
produced for research, the images produced in the lab often have such
a strong visual impact that they rival conventional works of art. The
second year biomedical students had these images up on display at a
two-day exhibition in the Galway Museum. A number of NUI Galway
scientists were involved in creating these images including Drs Maura
Grealy and Eilis Dowd from Pharmacology; Dr Lynn OConnor,
Biomedical Science; Professor Peter Dockery, Alex Black and Drs Dara
Cannon and Fabio Quondamatteo from Anatomy; and Professors Noel
Lowndes, Brian McStay and Ciaran Morrison, and Dr Andrew Flaus
from Biochemistry.

This image showing a thin slice of brain tissue comes from Dr Eilis Dowd in
Pharmacology. Star shaped cells, known as astrocytes, have been treated with
a green fuorescent dye to make them show up against the background. By
studying these cells scientists are able to conduct research on neurodegenerative
diseases.
This image is made up of 25 frames in a time-lapse series showing the
progressive movement of the nucleosome in a cell during division. By observing
the details of cell division researchers can spot the diferences that might indicate
disease. This image is from the lab of Dr Andrew Flaus, Biochemistry.
Hyaline cartilage, shown here, occurs in joints and elsewhere in our body.
Images such as this provide scientists with information about structure and
function, enabling them to develop treatments for diseases such as osteoarthritis.
Image from the lab of Prof Peter Dockery, Anatomy.
Triggering psychosis
SOME people have a genetic variant that
afects the quality of an enzyme involved
in the production of kynurenic acid, a
chemical involved in nerve-to-nerve
signalling. Researchers at the Karolinska
Institutet in Sweden have found that
people with this particular genetic
diference have a high risk of developing
psychosis. Reporting their results in
Molecular Psychiatry, the researchers
noted that levels of kynurenic acid are
higher in the brains of people with
schizophrenia or bipolar disease with
psychosis.
Kynurenic acid is produced in
response to stress or infection, and in
people with the genetic variant, the levels
produced are higher. According to Martin
Schalling, Professor of Medical Genetics
at the Karolinska Institutet, up to 80
per cent of those with psychosis related
to bipolar disease have inherited the
condition. Infammation caused by stress
or infection is a key trigger in setting
of psychotic episodes. The researchers
think that readily available drugs to bring
down infammation could prove useful in
treatment.
UPFRONT
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SCIENCE SPIN Issue 58 Page xx
The Marine Institute recently
presented up to one thousand
primary school students on the
East Coast of Ireland and Cork
with the Explorers Certifcate of
Participation after completing
activities and projects set
within the Explorers Education
Programme.
The Explorers Education
Programme seeks to develop
an interest in Irelands coast and
extensive 220 million acre marine
resource, which is one of the
largest in the EU, among primary
school students.
The Programme now includes
Dublin, Wicklow and Cork and
continues to be an outstanding success
under the guidance of the Lifetime Labs,
Cork, and the Blackrock Education Centre
and the National Sea-Life Centre Bray,
commented Dr Noirin Burke, Explorers
Education Ofcer at Galway Atlantaquaria.
Working with a dedicated group of marine
educators with the common goal of
introducing students to Irelands rich marine
resources, the programme and workshops
are currently used by over 50 schools
reaching over 5000 thousand students, she
added.
On the East Coast of Ireland, Explorers
aquarium tanks with a variety of sea
life typically found in rockpools around
Ireland were installed into nine classrooms
of diferent schools for six weeks by the
National Sea-Life Centre, Bray.
Using the aquariums to bring sea
life into classrooms is an innovative
way for students to learn about
Irelands marine species and to gain
vital skills in science, literacy, maths
and geography, said Toms Briain,
coordinator of the Explorers Project
at Blackrock Education Centre.
Providing teachers with an
information workshop and weekly
visits to the schools to fnd out about
the students experiences and caring for
the aquariums provided a fantastic way
to engage with the students on marine
topics. Providing opportunities for students
to develop an interest in the marine now
will no doubt be of huge beneft to the
sustainable development of our marine
resource in the future, he noted.
At the Lifetime Lab, Cork, students
from 21 primary schools participated in
the Explorers Primary Marine Science
Workshops, engaging with marine related
experiments and activities on topics such as
the Real Map of Ireland including
Irelands marine resource and
identifying marine species found
on Irish coastlines.
Speaking about the popular
workshops that ran for two weeks,
manager of the Lifetime Lab
and organiser of the workshops
Mervyn Horgan said, Raising
awareness of marine science
in classrooms brings long term
benefts to students and to
Ireland. The Explorers Education
Programme and workshops are
an innovative way of engaging
in science education, combining
topics of sea life, science and
geography with practical
experiments and activities.
Dr Burke also thanked the Marine Institute,
noting that The support provided by
the Institute ensures that the Explorers
Education Programme continues to engage
with students on a variety of marine related
topics early in their education. In addition to
developing a richer appreciation of marine
life at a young age, the students have
gained essential skills in maths, literacy,
geography, science and art required in their
future education.
The Explorers Education programme
was developed by the Marine Institute in
collaboration with a number of key partners
including Galway Atlantaquaria, Sealife Bray
Aqauriaum, Blackrock Education Centre,
Galway Education Centre and the Lifetime
Lab, Cork and has been running for over
seven years. A wide variety of
marine based lesson plans, activities
and science experiments, including
details on the Real Map of Ireland
Irelands marine resource, can be
downloaded from www.explorers.ie.
Primary school students awarded for participating
in the Explorers Education Programme
www.explorers.ie
Celebrating the award at St Anthonys
National School, Cork
St Kevins National School, Sallynoggin, Co.
Dublin
UPFRONT
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Downside of advances
Many people who would have died
from kidney or liver failure in the past
can now survive in good health thanks
to advances in organ transplanting.
Unfortunately, however, where ethical
guidelines are lax or absent alltogether,
organs are being harvested from people
who have fallen into a poverty trap.
Monir Moniruzzaman, a medical
anthropologist at Michigan Medical State
University has drawn attention to an
appalling situation in Bangladesh. Monir,
who came originally from Bangladesh,
began investigating the extent of this
trade, and in spite of the fact that it is
technically illegal, he found that entire
families had sold organs to pay of
relatively small debts. Ironically, the
loans, which could be as small as $50,
were often given to help people set up
small businesses.
Monir, reporting his grim fndings
in Medical Anthropology Quarterly, said
that in 2005 there was one transplant
hospital in Dhaka, capital of Bangladesh.
Since then the number has increased and
will soon be ten. as Monir observed,
the people giving up their organs out
of desperation often fail to receive
payment, people are left in poor health
after botched operations, brokers forge
documentation, and medical ofcials and
doctors, who should be expected to know
better, are in on this nasty racket because
the illegal trade is so lucrative.
Rock art
RockS dont last forever, they just
take longer than most other things to
wear away. one of the big problems
with ancient rock carvings, such as
those on Irelands high crosses, is
that leaving them in the open leaves
them exposed to natural weathering.
at the same time, trekking across
the landscape to look at a polymer
replica of the real thing, now housed
under cover in a museum, is not
such an attractive option.
Ireland is far from being alone in having ancient stone carvings out in the open, and
researchers at newcastle University have drawn attention to neolithic and Bronze age
examples in northumberland. David Graham, Professor of Ecosystems Engineering
at the university said that these panels, with carved swirls and circles, are at risk. We
need to start looking at how we can preserve them now, he said, and this involves
understanding more about how these rocks deteriorate.
The researchers, working with Dr Patricia Warke from Queens University Belfast,
have been studying 18 rock panels located across northumberland. Most of the panels
are of sandstone, and the researchers were able to identify some factors that infuence
the rate of deterioration. as expected, the more exposed they are, the greater the risk,
but the level of cations in local soils is also a factor. Improving drainage around the
panels can help slow down deterioration.
a paper on the study can be accessed from:
http://www.sciencedirect.com/science/article/pii/S1296207413000666
One of the victims of this obscene and
unethical trade shows the scar left after giving
up his kidney. Often there is no aftercare,
health deteriorates, and many never even
receive the money they have been promised.
Carbon to carbon
DIaMonDS and graphene are just
diferent forms of carbon, so what
happens if attempts are made to bond
the two together. When researchers from
the national University of Singapore and
Hasselt University in Belgium coated a
diamond with graphene and raised the
temperature to see if they would bond
they came up with an unexpected result.
When the temperature went above 400c
water, trapped between the two layers,
became highly corrosive.
Professor Loh kian Ping from
Singapore commented that the
arrangement is like a pressure cooker,
but what no one had known before was
that superheated water could become
corrosive enough to etch into the
diamond.
The discovery opens up a new way
to study the behaviour of liquids at
high temperature and pressure, and it
is likely to have applications in micro-
electronics.
Research grants
RESEaRcHERS have until 14th august
to apply for Marie curie fellowship
grants. This year funding amounts to
227 million, and about 1,000 researchers
will beneft this year.
Marie curie fellows receive broad
ranging support enabling them to gain
experience in institutions abroad.
Saintly scientists
nExT March a medal will be presented to
a distinguished Irish scientist living and
working in the US. This is to be an annual
award presented to winning scientists
each 17th March as part of St Patricks
Day celebrations.
nominations will be sought from the
Irish diaspora by Science Foundation
Ireland.
www.marine.ie
Ireland's National Agency for Marine Research and Innovation
Marine Institute
Foras na Mara
Our Ocean
A Shared Resource
UPFRONT
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Losing fat
A pArticulAr type of immune cell, known as invariant
natural killer t-cell, iNKt, has been found to have a controlling
infuence on fat. An international team of researchers led by Dr
Lydia Lynch at TCD, and involving Prof Donal OShea and Prof
Cliona OFarrelly from TCD, has found that with obesity these
cells are lost, but they can be restored when weight is lost.
it was thought that these iNKt cells were uncommon in
humans, but the researchers discovered that they are plentiful in
fat, and that they have a role in regulating body weight.
the decrease in iNKt had been noted initially during studies
of patients attending St Vincents Obesity Clinic. These patients
with low levels of iNKt had a higher risk from heart attacks
and type 2 diabetes than lean individuals. However, if they had
lost weight following a surgical intervention to restrict the gut,
(bariatric surgery), iNKT increased back to normal levels.
Support for these fndings came from animal studies in which
mice were put on a high-fat diet. With weight gain, the iNKT
cells were lost, but when put back on a normal diet, weight was
lost and the iNKT cells returned.
To get more details, the same tests were carried out on diferent
strains of mice, one a normal control, and two defcient in iNKT.
Given the high-fat diet, all the mice gained weight, but the iNKt-
defcient ones grew 30 per cent fatter than the controls, and they
developed the mouse-equivalent of diabetes 2 in six weeks.
in a follow-up study, iNKt cells were harvested from the
normal mice and injected into mice that were iNKT defcient.
remarkably, the diabetes 2 in these fat mice was reversed, yet
while continuing to eat a high-fat diet they lost about ten per
cent of their weight.
Finally, the researchers administered a lipid known as alpha-
galactosylceramide, aGc, to mice with a diminished pool
of iNKT cells. This lipid is known to activate iNKT cells, and
it was found that a small dose of aGc resulted in a dramatic
improvement, reducing weight and reversing diabetes 2.
Patenting genes
ACCOrDiNg to a ruling, made by Australias Federal Court,
naturally occurring genes can be patented. in a controversial
case, Justice John Nicholas decided that the act of removing a
gene is artifcial, and therefore a patent can be applied to it. The
case arose out of a patent fled by Myriad genetics. The company
was developing a diagnostic test for cancer, and the ruling means
that Myriad genetics now holds an exclusive right on diagnostic
tests based on detection of a naturally occurring gene.
Applying results
iN FebruAry the european research Council awarded
60 grants, each worth up to 150,000, to help researchers
commercialise their results. This follows an earlier round in
September 2012 under which 33 grants were awarded.
in this round, one award went to a researcher at university
College Dublin, Professor Martin Albrecht, who is developing a
solar powered catalytic technique for splitting water to generate
energy.
Fighting infections
CHeWiNg of betal leaves is widespread in india and countries in
south east Asia and the use of this stimulant goes back thousands
of years. The plant, Piper betle, is a creeper, extensively grown in
West bengal as an economic crop.
Debmalya barh from the institute of integrative Omics
and Applied biotechnology in West bengal, with a team of
international researchers, have found that one of the compounds
in the leaves, piperdarine, acts as a powerful antibiotic against
a number of pathogens including those causing tuberculosis
and hemorrhagic diarrhoea. reporting their fndings in
Integrative Biology and Plos One, the researchers claim that
piperdarine is more powerful than common antibiotics, such as
Chloramphenicol, Penicillin and Ampicillin.
the article in Plos One is available from
http://dx.plos.org/10.1371/journal.pone.0052773
Research grants
reSeArCHerS have until 14th August to apply for Marie
Curie fellowship grants. This year funding amounts to 227
million, and about 1,000 researchers will beneft this year.
Marie Curie fellows receive broad ranging support enabling
them to gain experience in institutions abroad.
UPFRONT
www.sciencespin.com
End for Herschel
The eSAs herschel space observatory,
with its 3.5 metre wide mirror, has
run out of liquid helium coolant, so its
cameras and spectrometers are about to
close down. The space observatory was
launched in May 2009 and over three
years it has captured data across a wide
range of wavelengths, from far-infrared
to submillimetre, enabling astronomers
to probe deep into the Universe. The
observatory was positioned 1.5 million
km from earth. From this point earth
and Sun always remained in the same
position, and the telescope had a clear
uninterrupted view into deep space.
The liquid nitrogen was needed to
keep instruments chilled to near absolute
zero. At launch the observatory had a
2,300 litre supply of liquid nitrogen, but
over time this is lost, and the supply is
now almost exhausted.
eSA report that herschel has
performed better than expected, and
scientists will be working on the
accumulated data for years to come.
While no one is sure when exactly the
liquid nitrogen will run out, herschel is
likely to be parked in an orbit around
the Sun some time in May this year.
eSA herschel space observatory image of Andromeda (M31) using both PACS and
SPIRe instruments to observe at infrared wavelengths of 70 mm (blue), 100 um (green)
and 160 mm and 250 mm combined (red). The image spans approximately 1 x 3 degrees.
Andromeda is a spiral galaxy 2.5 million light years away from earth, and is thought to
include 10 to the power of 12 stars, twice as many as are in the Milky Way. In another
3.75 billion years it is possible that the Andromeda Galaxy and Milky Way will collide
and merge.
Credits: eSA/herschel/PACS & SPIRe Consortium, O. Krause, hSC, h. Linz
Seaweeds
GReen plants and reddish seaweeds
diverged from each other about 1,500
million years ago. The way in which the
red seaweeds carry out photosynthesis
has been adopted by most of the
phytoplankton, such as diatoms and
dinofagellates, so many species have
sided with this branch. Yet, as a group of
scientists led by the Station Biologique de
Roscof in Brittany, point out, compared
to green plants, not that much is known
about the red seaweeds.
The group focused on Chondrus
crispus, commonly known as Irish Moss,
or Carrageenan. This species is common
along the rocky Atlantic shores, and
boiled with milk and sugar it makes a
popular blancmange. Carrageenan is also
used widely in the food industry, and has
an ofcial E number, E407.
The group found that the genome
of red seaweeds is quite diferent from
those of green plants. The genes are more
compact, and some genes which occur in
one group do not appear in the other. It is
thought that symbiotic relationships with
protozoa enabled the red seaweeds to
acquire new genes, but it is also thought
that genes were lost. Toni Gabaldn, from
the Centre for Genomic Regulation in
Spain, said that the red seaweeds seem
to have gone trough an evolutionary
bottleneck, causing them to lose genes.
Mob rule
nOT long after the scientifcally ill-informed ruling from Europes highest court
on stem cells that created such problems for researchers, the Italian health minister,
Renato Balduzzi, has given approval for dubious stem cell treatments. There is no
evidence to show that the treatments being ofered by the Stamina Foundation for a
range of illnesses actually work, and one stem cell researcher from the University of
Milan, elena Cattaneo, has been quoted in Nature as remarking that it is alchemy.
however, when pro-Stamina protesters took to the streets of Rome, the health
minister decided that political popularity comes before evidence based science. not
alone did the dubious procedures get approval, but the publicity, backed by show-
biz personalities, is said to have boosted demand for treatment.
The decision has angered stem cell researchers because it plays into the hands of
unscrupulous operators who ofer false hopes to people desperately seeking a cure
for themselves or their children.
The decision to approve procedures that had previously been declared a danger
to public health by a prosecutor in Turin, Rafaele Guariniello, highlights the lack
of scientifcally-informed guidelines on stem cell research and treatment in Italy.
Ireland also has no clear guidelines on stem cell research.
Blast from the past
As matter began to form after the Big
Bang light was released and as the
Universe expanded the wavelengths of
this light was stretched out. Astronomers
can now detect this stretched out light
as microwave radiation. The European
space Agencys Planck space telescope
has been recording this radiation and
mapping out its distribution. Data
collected over a year and a half of
observations has now been combined
into an image that shows some of the
oldest light was created just 380,000 years
after the Big Bang.
Thesmallfuctuationscorrespondto
regions where matter began to condense
and star formation began.
scientists are excited by this charting
of ancient light because it reveals a great
deal about what the early Universe was
like. The picture that emerged from
this mapping reveals that some of our
assumptions about the early Universe
were incorrect. The distribution of
radiation turns out to be uneven rather
than much the same in all directions with
a broad band of older (colder) radiation
stretching across from one side to the
other. Earlier observations had hinted
that such asymmetry might exist, but this
more comprehensive mapping has shown
that it is a major feature, showing that the
Universe is not as uniform as previously
thought.
The Planck observations have also
made scientists revise some of their
estimate on the make up of the Universe
and its age. The age has been pushed
back by about 50 million years, making
the Universe 13.82 billion years old.
There appears to be slightly more matter
than previously thought, and less of the
mysterious dark energy that is thought
to be causing the Universe to be drawn
out at an ever accelerating rate.
Cloning success
OnE of the biggest problems with
cloning has been that the clones do
not have perfect health. Researchers
at the RIKEn Centre for Biology
in Kobe have discovered that
this problem can be solved by
eliminating genetic changes that
normally occur from generation
to generation. Until quite recently
it was thought that genes passed
on without much or any change,
but now it is known that they can,
inefect,betaggedsothattheir
expressionbecomesmodifed.
These are termed epigenetic
changes,andtheyhaveabiginfuenceon
how animals, including outselves, take
shape.
In a cloning experiment with mice
the Japanese researchers lead by Dr
Teruhiko Wakayama, used an inhibitor,
trichostatin, to prevent the epigenetic
changes occurring. The cloned mice
were not alone healthy, but they could
in turn be cloned to produce another
healthy generation of clones. After
repeating the cloning procedure
25 times, the 581 mice remained
healthy, they had a normal lifespan
of two years and they remained
fertile, giving rise to healthy
ofspring.
In contrast to this, repeated
cloning of mammals up to this had
always resulted in an accumulation
of abnormalities.
UPFRONT
www.sciencespin.com
DNA
, that stringy stuf in our
cells, contains four important
chemicals: adenine (A), thymine (T),
guanine (G) and cytosine (C). These
are the nucleobases, the molecules that
encode the information for life. They are
also willing absorbers of ultraviolet (UV)
light, and because of this sunlight can be
a major nuisance for our skin.
Absorption is the process where
energy from light (a photon) is taken in
by a molecule, causing an electron to
jump into an excited state. Excited states
are energetic and unstable, and when
they occur within a DNA nucleobase,
they can initiate the damaging chemical
reactions that result in sunburn and skin
cancer.
It has been known for many years
that UV light attacks DNA, but until just
over a decade ago the excited states of
DNA were elusive, because they were
too short-lived for any lab instrument
to record. However, with advances in
femtosecond lasers (that produce fashes
of light lasting about 10
-15
seconds), we
can now study these excited states in
great detail.
The ability to study very fast processes
in DNA is a welcome development, as
the behaviour of the excited state in
those frst few picoseconds (10
-12
seconds)
after absorption decides much of what
eventually happens to our skin cells.
Although this can sometimes result in the
adverse health efects mentioned above,
our DNA is actually quite resilent to UV
light and can even be regarded as its own
sunscreen.
This self-defence mechanism is most
vividly expressed in the behaviour of the
individual nucleobases, and represents
the frst achievement of femtosecond
laser studies of DNA. Despite having
diferent chemical structures, the
nucleobases all react similarly to the
absorption of UV light; they deactivate,
fast. Within one picosecond (10
-12

seconds) of absorption, the nucleobase
excited states have lost most of their
ability to cause damage. Computer
simulations show that this is achieved
by a process of molecular gymnastics.
The nucleobases, which are usually
fat, distort their shape and release the
excess energy through vibrations of
the chemical bonds, which persist for
about ten picoseconds after the excited
state has been swiched of. In efect,
the high energy UV light is rapidly
dispersed through a series of lower
energy processes, which can be described
simply as heat, but is more technically
known as ultrafast internal conversion.
No bonds are broken, and the very rapid
quenching of the excited state minimises
the chance of any harmful reactions
happening.
However, if the chemical structure
of a nucleobase is altered slightly, the
deactivation can slow considerably, and
the potential for chemical reactivity
increases. It appears, therefore, that the
nucleobases are optimised to survive
UV radiation. This survival feature may
partly explain why A, T, G and C became
building blocks of life. Nowadays, we
can be thankful that atmospheric oxygen
and the ozone layer removes most of the
dangerous UV rays (UVC and most UVB)
before they reach us, but this protection
may not have been present billions
of years ago when the chemistry of
primordial life was evolving. As a result,
a high tolerance for UV light was likely
to have been a prerequisite for biological
success.
The ultrafast deactivation of the
excited nucleobases is a neat example
of natural selection on the molecular
scale, but cannot completely explain
the interactions of UV with DNA. In
double-stranded DNA the nucleobases
are all joined up by a sugar/phosphate
backbone, they are base-paired with
their complement in another strand
through hydrogen bonds (A with T, G
with C), and they stack on top of other
nucleobases within their own strand.
All these features are signifcant, as
the behaviour of excited states is very
sensitive to chemical structure.
In fact, having other nucleobases
so close together is where much of
the trouble starts. When two thymine
nucleobases appear next to each other
in a sequence, UV light can cause them
to fuse together to form a dimer, which
inhibits further replication of the strand.
Although relatively common, these TT
dimers are well repaired by enzymes in
the cell that recognise and remove the
damaged sequences. By contrast, cytosine
dimers (CC) are rarer, but are much
more dangerous because they are poorly
repaired. One reason is that they rapidly
transform to uracil (the nucleobase that
replaces thymine in RNA), which is
complementary to A rather than G. If the
damaged strande is copied, CC becomes
TT, and a potentially cancerous mutation
occurs.
In general, UV damage to DNA is
concentrated at the pyrimidines (T
and C) rather than the larger purines
(A and G). This is mainly due to the
structural features of pyrimidines versus
purines, but ultrafast laser experiments
have thrown up some other intriguing
coincidences. When the sugar/phosphate
molecules are attached to T or C (but
not A or G), about 15 per cent of the UV
energy diverts through another excited
state, which retains the energy up to
100 times longer than the nucleobase
alone. These are known in spectroscopy
parlance as dark states, a rather apt
name when neither the reasons nor
consequences of their formation are
understood. It is possible that they are
involved in the formation of dimers,
although some experiments suggest that
these dimers are formed too rapidly for
dark states to matter. Alternatively, they
could be involved in the other photo-
Fixing DNA a fash
Praic Keane writes that the frst few trillionths of a second makes a
big diference in how sunlight afects our DNA
reactions that C or T undergo,
or they could even have no
role at all.
While we are still in the
dark about dark states, their
presence represents one of
the important considerations
in DNAs relationship with
UV: the amount of time the
energetic excited states remain
active. The longevity of the
excited states is also infuenced
by the other structural features
of DNA, namely base-stacking
and base-pairing. Base-
stacking and base-pairing are
bonding forces that hold the
double helix together, and
they can also be regarded as
avenues for communication
between nucleobases. This
provides the means to either
dissipate the energy of UV
light on the one hand, or to
spread the efects of damage
on the other.
Given the complexity of
DNA, the roles of base-stacking and base-
pairing are less well understood than
the fast deactivation that occurs in single
nucleobases. When the nucleobases are
stacked, the excited states get longer-
lived, although this is quite sensitive to
the type of nucleobases in each strand.
There is evidence that these excited
states result in the transfer of an electron
from one nucleobase to another. The
loss of an electron from a molecule is
termed oxidation, and the promotion of
anti-oxidants in our diet suggests that
oxidation in our DNA is something to be
avoided. Fortunately, it appears that any
electron transfer that occurs after UVB
exposure is efciently reversed within
about 100 picoseconds. Nevertheless,
these electron transfer processes could
have more subtle efects, such as making
certain parts of the DNA strand more
sensitive to damage than others.
Some debate also surrounds the
importance of base-pairing. Computer
calculations have suggested that the
base-pair provides a route to rapidly
deactivate the excited state. This has
since been challenged by experiment,
and some evidence suggests that the
base-pair does not transfer energy from
one strand to the next. This would have
implications for the integrity of DNA, as
it might prevent both strands from being
damaged, thereby leaving an intact copy
of the damaged strand.
It should also be noted that base-
pairing does not always follow the
Watson-Crick protocol where A goes
with T and G with C. Some nucleobases
can base-pair with other identical bases,
giving rise to other structures apart from
the famous double-helix. For example,
DNA rich in either C or G can form
exotic four-stranded shapes called the
i-motif and G-quadruplex, respectively.
These structures have attracted attention
in recent years due to their connection
with telomeric DNA, the sequences in
the chromosome that control cell death,
and the cell immortality associated
with cancer. Both the i- motif and
G-quadruplex form long-lived excited
states after UV excitation, more so
than in normal double-stranded DNA.
Furthermore, these structures can absorb
light at slighly longer wavelengths,
where the efectiveness of atmospheric
ozone decreases. Further study is needed
to investigate how signifcant this is
biologically, or whether damage to these
rarer structures is relatively tolerable.
Much remains to be learnt about the
very fast but very important processes
can occur in our DNA immediately after
UV exposure. Despite the perceived
and much lamented lack of sunshine
in Ireland, Irish scientists from UCD
(Dr Susan Quinn) and TCD (Prof John
Kelly) have contributed signifcantly to
this exciting area of study. This is due
to a long-running collaboration
with the Rutherford Appleton
Laboratories in the UK, which
is home to an advanced laser
set-up known as ULTRA. On
ULTRA, a UV laser is shone on a
piece of DNA to form the excited
state, and a second infrared
laser is used to examine how
the bonds are altered thereafter.
Any chemical changes that
occur after excitation, or the
movement of energy through the
molecule, can then be tracked
over very short timescales. Since
these processes are so quick, the
light from the laser pulse needs
to be very short, because it is
crucial to observe the DNA after
the UV light has switched of.
Consequently, this is one of those
areas of science that is driven as
much by technological progress
as it is by theory or experiment.
Most of the studies to date
have taken a bottom up
approach, by looking at very
short sequences, or sequences containing
only one or two types of nucleobase.
The greater challenge is to study, and
more importantly, to understand, the
complicated DNA sequences that exist
in our cells. Of course, the eventual
efects of UV light also depends on the
slower biological processes in the cell,
such as repair mechanisms, and the way
damaged sequences are replicated. This
is where the physicists and chemists step
back, and the biologists and medical
scientists take over. UV light is also
important to biology in many other ways,
besides the direct absorption by DNA.
For example, a certain amount of UVB
is necessary for the sythesis of Vitamin
D, and the impact of lower energy UVA
cannot be dismissed. UVA is not absorbed
by DNA, but it is not blocked by the
ozone layer either, so is up to 100 times
more abundant than UVB. Its indirect
efects on DNA, and consequently our
wellbeing, are a serious cause for concern
as well. In the meantime, it is probably
prudent not to push our bodies hard-
won defence mechanisms too far. Leave
the experiments for the lab, and learn to
love the shade!
Dr Paraic Keane is involved in research on
photochemistry and has an MSc in Science
Communications from DCU.
Before the fad of becoming browned of caught
on people like Claude Monets lady with a
parasol preferred to stay in the shade.
Coliste an Phiarsaigh, Glanmire, was announced as the
winning team at the fnal of the National CanSat competition
at the Lifetime Science Lab in Cork on the 16th March.
The students took on the challenge to create a CanSat a
simulation of a real satellite which fts into the volume
of a soft drinks can. The CanSat includes all the major
elements found in a satellite, such as power, sensors and a
communication system. Students from seven schools have
worked for a number of months designing, building and
testing their CanSats in the lead up to the fnal at the Lifetime
Lab in Cork.
The winning team CaPSat made up of nine students from
Coliste an Phiarsaigh, will now go onto compete at the
European CanSat fnal in The Netherlands in April, where
their CanSat will be launched to an altitude of approximately
1km by a rocket. The travelling team will be sponsored on
their journey by Cork Electronics Industry Association (CEIA),
ESERO Ireland (European Space Education Resource Ofce),
co-funded by the European Space Agency and Discover
Science & Engineering, Science Foundation Irelands (SFI)
education and outreach programme.
Ann Fitzpatrick, ESERO Ireland Manager, said The purpose of
the CanSat competition is to open up the possibilities of space
and exploration to secondary school students. In December
2012 we saw Enbio sign a 500,000 contract with the European
Space Agency to better protect satellites in space. This is just one
example of an Irish company that is thriving in the space sector,
and it highlights the space related opportunities that are available
for students and graduates. ESERO Irelands ambition, with the
assistance of the European Space Agency, is to foster the skills
that are required for this industry at an early age and the CanSat
competition provides a practical experience of a real space project
for second level students. Working in partnership with CEIA we
plan to expand the National CanSat competitions across Ireland
with support from industry and third level institutions the fnal in
Cork is a great step towards realising this goal.
Irish students to represent Ireland at the
European CanSat competition
Summer workshop for teachers
Secondary school teachers have been invited to participate in a
summer workshop organised by the European Space Agency, ESA.
The workshop will be held at ESAs centre in Noordwijk in The
Netherlands from 20th to 23rd August 2013.
During the workshops teachers will be presented with engaging
and novel ways to show the relevance of science, technology,
engineering and maths to space.
The workshop is open to teachers of STEM subjects but places
are limited. Teachers interested in participating should submit a
completed online application form by 21st May. There is no charge,
but participants must arrange their own travel to The Netherlands.
http://www.esa.int/Education/Teachers_Corner/ESA_Summer_Workshop_for_Teachers_2013
www.discover-science.ie
I
s fundamental science important? High
profle scientist Luke ONeill certainly
thinks so and at last years European
Science Open Forum (ESOF) event in
Dublin he stressed that you cannot
underestimate the importance of basic
science.
Luke, based in Trinity College Dublin,
has earned an international reputation for
his work on immunology, an important
feld because it helps us to understand
how the body can defend itself against
all kinds of diseases. Understandably this
is also the sort of research that attracts
funding because there is always a high
probability that results can be turned into
commercial products.
Immunology is one of the strengths
of Irish science, yet, as Luke observed,
this level of performance could never
have been planned in advance. All of the
current success, he said, can be tracked
back to the type of research that most
people might dismiss as having little or
no practical value. For something like
forty years Jules A Hofmann worked on
fruit fies, those little Drosophilia insects
that like to congregate around over-ripe
fruit. Hofmann, said Luke, is a real
hero to us all, and the reason for this is
that he made a fundamental discovery
that sparked of an explosion of interest
in how animals defend themselves
against invading micro-organisms.
Luke remarked that it was because of
this fundamental discovery that he
became an immunologist. My work
was inspired by Hofmann, he said.
What was so important about
this discovery is that it revealed the
existence of a key trigger that sets
of the fys initial defences against
infection. While the discovery
that fruit fies have the ability to
withstand an assault might not
have the impact of prime-time
news, the signifcance became
more obvious when it was found
that the same trigger is universal. All
animals, including humans, depend on
this trigger, known as Toll, to set of our
innate immune system. Without it we
would be overwhelmed by invading
bacteria and fungi.
In recognition for this enormously
signifcant discovery Jules Hofmann
was awarded a Nobel Prize for Medicine
in 2011. Hofmann shared this award
with two other scientists, Bruce
A Beutler and Ralph M
Steinman because they had
also made closely related
discoveries on how the
immune system actually
works. As Hofmann
made clear, when
speaking at the ESOF event
in Dublin, collaboration
between many diferent
scientists has always been a
feature of this research, and during his
years of research on fruit fies he often
relied on the genetic, biochemistry or
other expertise of others to fll in the gaps
that would, in efect put the jig-saw of a
complex chain of reactions together into
one coherent system.
Jules, who grew up on the border
between Luxembourg and France, said
that his own interest in insects began
because of his father, a teacher of biology,
who enjoyed collecting and identifying
the various species in the surrounding
countryside. It fascinated him that insects
make up most of the species on the
planet, and it was a natural progression
for him to study Zoology at Strasbourg
University. For his PhD he worked under
Professor Pierre Joly who had a special
interest in grasshoppers, particularly the
troublesome Locusta migratoria. These are
the locusts that swarm into enormous
clouds, causing starvation
because they devour
everything in their path.
Jules Hofmann was
struck by a remark that
his supervising professor
made one day. In all his
studies, said Jules, he
had never encountered
an opportunistic microbial
infestation in these insects in
spite of the fact that he had not
taken any precautions to prevent this.
This was a defning moment in my
life, said Jules. He began to look for
reasons why these insects had such a
good defence, painstakingly examining
every step in what was then known
about their immune system. It was
known that engulfng micro-organisms
in a process known as phagocytosis
was involved, but techniques and
analytical equipment at that time were
not as advanced as they are now. Blood
from many thousands of blow fies was
collected in an unsuccessful attempt
to identify components, known as
peptides, that might be involved in
alerting the defensive cells to go in
for the kill.
Even so, Jules Hofmann
persisted, going from one species
of insect to the next, before
concentrating on fruit fies. His aim
was to identify the peptide trigger
that set of the immune reaction
and to link this to the genetic code
responsible for producing it. Many
Big discovery from little flies
Who could have anticipated that looking at fruit fies would
produce such signifcant results? Tom Kennedy reports on
how fundamental research led to a major discovery on how
the body defends itself against disease.
You cannot
underestimate
the importance of
basic science.
Jules A Hofmann
and Bruce Beutler
of the hormones that set of reactions are
chemical compounds consisting of amino
acids in a chain, and these molecules,
which are usually quite small, are known
as peptides.
Hofmans persistence eventually
paid of, and a peptide known as Toll,
originating in a dorsal region of the
insect, was found to be the elusive switch
that turned everything on.
Experiments with insects with a
mutation for the Toll gene revealed that
fies without this trigger were rapidly
overwhelmed by invading microbes.
It was then found that Toll is far from
unique, and Bruce A Beutler, working in
the US, was able to demonstrate that a
number of similar Toll triggers exist in
mammals. Since then Toll-like triggers
have been found to be a universal part
of our immune system, a discovery that
would probably never have been made
without Hofmanns dedication to fruit
fies.

Immunity has two lines of defence, the frst, an innate response, comes into play
immediately a micro-organism is recognized as an invader. The innate response
attempts to destroy the invaders by mounting a defence, and in evolutionary terms, this
is the older system and it is general in that it is non-specifc to any particular pathogen.
If the invaders manage to break through the innate barrier, an adaptive system
comes into action in which killer cells attack specifc targets. What are known as T and
B cells seek out particular micro-organisms for destruction in what is literally a fght to
the death. Unlike the innate response, the adaptive system learns from one attack that
another one could be on the way. Second time around, the adaptive immune system is
primed and ready to respond quickly, and for this reason we can acquire a high degree
of immunity by deliberately introducing disabled versions of common pathogens
through vaccination.
How important is immunology?
Apart from the obvious importance to general health, Irish researchers are among the world leaders in
this feld. Based on the number of times that scientifc papers are quoted, Ireland is in the best three
top-performing countries, and Science Foundation Ireland has acknowledged that Trinity College
Dublin is currently stands out as in the top one per cent worldwide for immunology research.
Other universities such as NUI Maynooth are actively involved in immunology research, and this
is a feld that attracts substantial funding from private and institutional sources.
Immunology is regarded as one of the key elements in maintaining Irelands position as a good
place to invest in science. For this reason SFI, in collaboration with industry, is a big supporter of a
high-powered Strategic Research Cluster at TCD headed by Professor Kingston Mills.
St Vincents Fairview
Hidden away in an area with lots of historical associations, St
Vincents Hospital in Fairview has an fascinating history. Aidan
Collins tells how so many colourful fgures, such as the Sham
Squire, Grose the antiquarian,
and James Joyce all have close
connections to St Vincents,
and the hospital itself began
with a scandal, so shameful
that for years the truth was
suppressed.
Available, paperback 25 or
hardback 35
Postfree from
www.sciencespin.com
Te Exemption
An amazing story of survival through some of the darkest years
of Europes recent history. Vera Hajnal tells of how invasion soon
shattered an idyllic childhood. Growing up in a secure and loving
family, going to school and sometimes being allowed help her
father, a doctor, Veras frst shock came when, accompanying her
grandmother to the railway station, she was stopped by men
wearing armbands who asked: Are you Jewish?
Vera describes how she survived the years that followed, and
amazingly, her account has no trace of bitterness and throughout
it all she never lost faith in the
underlying goodness of people. Her
own survival, as people were being
literally rounded up and shot by
paramilitary thugs, was remarkable
in that on being contronted on the
street she happened to be carrying a
piece of paper exempting her father
from military service.
Hardback 25
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T
enrecs are interesting and fascinating
mammals which, outside of the
realms of zoology lectures, remain
unknown to many people. A select group
of just 31 species, these Madagascar
natives have evolved into incredibly
diverse individuals that resemble moles,
shrews, hedgehogs and even otters! Their
striking similarities to other species are
so strong that early taxonomists didnt
recognise tenrecs as being sister species.
However, molecular studies established
tenrecs as a clearly defned mammalian
family which is more closely related
to elephants and sea manatees than to
hedgehogs or shrews!
Members of the tenrec family display a
whole host of quirky traits. For example,
the common tenrec (Tenrec ecaudatus), an
animal which is only around 30 cm and
2kg, holds the record for the largest litter
size of any mammal at an astounding 32
babies!
In terms of sheer weirdness, my
personal favourite tenrec oddity is the
lowland streaked tenrec (Hemicentetes
semispinosus). At just 15cm long and
weighing 80-150g, these cute, yellow and
black-striped critters are unobtrusive
inhabitants of tropical rainforest areas
in eastern and northern Madagascar.
Their detachable, barbed quills are
both a formidable defence to would-be
predators and comprise a weird and
wonderful means of communication.
In the centre of their backs a special
set of quills have been modifed into
a stridulating organ. Reminiscent of
grasshoppers or crickets the stridulating
quills are rubbed together to produce
high-pitched sound. They are the
only mammals to have evolved this
strange communication method, a
skill which is used to maintain
contact within family groups.
Look up David Attenboroughs
BBC series on Madagascar to
see a wonderful clip of the
stridulating tenrecs in action.
In short, although relatively
understudied and poorly known
outside of specialised circles, tenrecs
are an awesome family flled with
evolutionary oddities. The ingenious,
unique communication found in H.
semispinosus is just one trait which more
than justifes tenrecs inclusion into
the annals of weird and wonderful
animals.
Left: The tailless tenrec, Tenred ecaudatus,
or Common Tenrec. Photo: Markus Fink.
Sive Finlay, a Zoology graduate is currently
working as a postgraduate scholar with the
Macroecology and Macroevolution group at
TCD.
Weird and
wonderful animals
Sive Finlay introduces us to the Lowland
Streaked Tenrec
Above: Lowland Streaked Tenrec, Hemicentetes semispinosus
IN
World War II a statistician called
Abraham Wald was employed to
analyse US planes returning from air
combat. Metal was scarce, and the idea
was to only reinforce the most vulnerable
parts of the planes. The parts of returning
aircraft that made it home full of bullets
must be the toughest parts, Wald
reasoned, and so a decision was made
not to reinforce these areas, but to use the
scarce metal to strenghten the other parts
of the aircraft.
Dr Aoife McLysaght, geneticist at
TCD, understands Walshs logic and
applies it to her own gene hunting
eforts. Dr McLysaght is identifying genes
that are most sensitive to being hit with
bullets - which in genetic terms means
being hit with random gene mutations.
This is important because it is known that
THE GENE HUNTER
Sen Duke talked to Aoife McLysaght about sharing her passion for science.
in certain sensitive genes right across all
living species having too many copies
of a particular gene, or too few, can result
in a disease.
School
Dubliner Aoife attended her local
national school before attending St
Andrews College, on Booterstown
Avenue. She recalled that although
there wasnt too much science taught in
primary school, she was very interested
and engaged by such science as was on
ofer. In particular, Aoife remembers
presenting a science project with her
best friend in sixth class, which involved
explaining aspects of the weather to other
pupils and teachers.
I had fun little demonstrations, to do
with the power of wind and air, Aoife
recalled. We had a plastic bag with a
book on top of it. We got the opening of
the bag and blew into it and showed that
it would lift the book. We also had a glass
milk bottle, with a balloon on top that
was not infated. We placed the bottle
into a jug of really hot water, and the air
would expand and infate the balloon.
I remember having loads of fun doing
that, she said.
Her interest in science was strongly
established by the time she attended
St Andrews. She remembers that she
was always engaged with science, and
actively listened to the teachers, so that
information went in, making life much
easier when it came to passing the exams.
When the Leaving Certifcate rolled
around Aoife chose to do Biology and
Chemistry, but not Physics. She believes
that was a mistake in hindsight as she
always enjoyed physics.
Instead she chose to study geography,
because it was regarded as a science
subject by the universities. This was a
mistake, she says now, because while
she enjoyed physical geography - such
as explanations of why earthquakes
occur she did not at all like social
geography, which for her involved too
much memorising of lots of very dull
information. Her experience has told her
in the years since that people will succeed
at what they enjoy. That was proven
when her geography result proved her
worst Leaving Certifcate result.
At St. Andrews, she was inspired by
the eforts of a great teacher, Dr Nick
Frewin, a PhD holder, who taught her
science and biology. He was just really
good, recalled Aoife. He spent a lot
of time clearly explaining things, had
well planned lessons, and there was a
lot in it beyond the course. He was well
liked enough for people to write him
letters when he was retiring. When I did
genetics, there was a class of 12 people,
and three of those have been his [Dr
Frewin] students, and the year behind me
we had another one, said Aoife.
The role of the teacher is crucial, says
Aoife, and she cited the example of
the many people that say they cant do
maths. The number of people who think
they cant do maths is too high there
are a lot of people that have been put of
maths. They stop trying because they
think they cant do maths. The students
underestimate their own abilities.
Students should be allowed have a bit of
fun with maths. Games and puzzles for
example, said Aoife.
Recently, Aoife received a prestigious
European Research Council grant
which are only given to the top tier
of scientists in Europe to try and
identify disease-causing genes. The aim
she said is identify those genes that
are vulnerable to changes in quantity.
This might involved a reduction in the
copies of genes, or too many copies.
There is a certain amount of variation in
the number of copies of genes between
people, and its common. However, in
some people certain variations in gene
quantities increase disease vulnerability.
This is an evolutionary approach
to genetics, explained Aoife. The goal
is to see which genes have tolerated
changes in amount high or low
over evolutionary time and which have
not. The identifcation of those genes
that have proven intolerant to change
over evolution can provide a key to
which genes are linked to disease today,
the reasoning goes. There is variation
in [gene] copies, because mutations
happen, explained Aoife. DNA is a
chemical that copies itself in cell division,
and this is an easy mistake that happens
a lot.
Once the sensitive genes that have
been linked to disease have been clearly
identifed, then it becomes possible to
develop better and more precise ways
to diagnose disease. Following on from
that, if there are improved methods to
diagnose disease at an earlier stage, then
it should become possible for medical
scientists to develop better disease
treatments and therapies.
Communicator
Aoife is also one of the best scientist-
communicators in Ireland, and is
regularly invited to speak in schools and
at public lectures about her work and
its implications for society. She believes
that it is important that some scientists
communicate with the public, but she
also acknowledges that although she
enjoys this activity, not every scientist
will feel the same.
It is important that some of us do
it, and there is support for that. I mean
that it is recognised as a valid part of the
job. A valid activity, that it is respected.
Sometimes people might think it is a trivial
activity. I dont think that. I see science
as part of our culture, we should all have
access to that. A lot of people love music,
but dont have the intention of being a
musician. Its the same with science
people should have access to it, she said.
Aoife McLysaght talking to a packed house as one of the TedX events at the Bord Gis Theatre
in Dublin.
Photograph, TCD Science Gallery.
For Aoife, science is about the ability
to learn, to deduce, to understand
something, even when it is not visible to
the naked eye. It involves being able to
think long-term, beyond our own lives.
Science is exciting, interesting, dynamic,
but it is a big mistake to try and push
it onto people. It is also a mistake, she
believes, for the Irish government, or any
government to get too closely involved in
deciding how funding for science should
be spent. It would be better to fund the
best people than to fund certain areas,
she said.
She has some advice for young people
that might be considering science as
a career. When I was young, I didnt
know you could be a scientist, I didnt
know any scientists. I didnt know what
I would end up being if I studied science.
My mum said to me, do what you enjoy
the job will follow. Its very optimistic,
but I kind of subscribe to that, she said.
SCIENCE SPIN
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Lets learn more!
Friction works on a moving object
to slow it down or stop it.
When an object slows down it loses
energy - this energy is convered
into heat or sound.
When you rub your hands together
friction causes heat and your
hands feel warm.
When you pull hard on the brakes
of your bicycle it is friction that
stops the bike.
Sometimes we hear a screech when
we pull the breaks - some of the
energy lost due to friction is
converted to sound!
If you want to know HOW something works why not write to Dr. How and ask? Send your e-mail to naomi@sciencespin.com
Science Wows!
Dr. How's
Friction can often be a help to us...
if there was no friction between
our shoes and the surface beneath
us then we would not be able to stay
on our feet.
It is friction between our food and
the fork or spoon that allows us lift
the food to our mouth.
Brakes in cars use friction to allow
us to control the speed of the car.
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Lift a jar of rice with a pencil!
Friction
You will need...
an empty plastic
jar,
a pencil,
a bag of dry
rice
Fill the jar with the dry rice and insert the pencil
(point side down).
Raise the pencil slowly up towards the top of
the jar but do not remove it completely.
Now slowly push the pencil back into the jar
again and repeat several times.
You should feel it getting harder to push the
pencil down.
If the level of rice in the jar drops then top it up
with more rice. After a few goes you should find that
when you try to lift the pencil up out
of the jar, the whole jar lifts!
So what is happening?
Each time you push down the
pencil the rice in the jar is
compressed. When this is done
repeatedly the grains of rice are
squashed tightly together and
cannot move. This increases the
friction between the rice and
the pencil until eventually
the pencil can lift the
jar of rice.
...exploring Friction!
The coefficient
of friction (CF) is a
measurement of the
amount of interaction
between two surfaces.
The CF is the ration of
the friction to the
weight of the
object.
What is Friction?
Frction is the force
that acts on two objects
that rub off each
other.
Dynamic friction
is the force that
acts on an object
as it moves over
a surface.
Static friction
is the force that
holds something
still and prevents
it from
sliding.
The CF is
always a value
between zero
and one.
Some musicians
use friction to make
music. Violin players
rub rosin on their
bow to help it stick
better to the
strings.
There are three types of friction:
1. DRY or SLIDING friction...
where two solid objects rub off
each other
2. FLUID friction...
friction formed when an object
moves through a liquid or a gas
3. ROLLING friction...
friction produced between a
rolling object (like a wheel) and
a surface
Friction works
on an object in the
opposite direction
to which the object
is moving!
Sometimes friction works against
us... such as slowing down an
object that we want to move
faster or wearing down the moving
parts of a machine.
To prevent friction we might use
an oil to lubricate moving parts
to reduce wear and tear.
We also use small balls called ball
bearings within machines and other
moving parts. The ball bearings
move more easily on a surface -
reducing friction.
If we reduce the surface area of
an object we can rduce the friction
acting on that object - this is how
ice skates work!
Skis on snow
have a low CF
value of about
0.15
Metal
moving over
metal has
a CF of
0.74
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Friction
You will need..
a balloon, an old
CD,
a drinking bottle top,
and glue
Glue a bottle top over the whole in the
CD and leave it until the glue has dried.
Make sure that the drinking bottle top
is closed.
Inflate a balloon and pinch the neck of
it while you place it over the bottle top.
Place the CD on a smooth surface and
open the bottle top.
Give the CD a little push and see what
happens!
So what is
happening?
The air from the balloon gets
released and forms a cushion of
air under the surface of the CD.
This allows the CD to travel
across the surface with a lot
less friction - just like a
real hovercraft!
Make a hovercraft!
Factors that
influence friction
include: the roughness
of the surfaces, the
weight of the object
and surface
area
Fractal Ireland
Figure 1: The perimeter of an object may
be estimated by superimposing a square
grid and counting the number of boxes that
contain sections of the perimeter. In the
case of a smooth object, such as the S-shape
shown on the right, the estimated length of
the perimeter, i.e. the number of these boxes
multiplied by the width of a box, is essentially
independent of the box width (computation by
D. Whyte, TCD).
Y
ou are contemplating taking a holiday.
How about a canoe trip around the
island of Ireland, keeping as close to the
shore as you can? How long will it take at
an average of, say, 20 kilometres a day?
A quick Google search gives the length
of the coast line as 1448km (CIA - The
World Factbook), 3171km (Ordnance
Survey Ireland) and 5631km (http://
www.goireland.com/about-ireland.
htm). So the trip might take nearly all of
summer (72 days) or indeed, you might
barely be able complete it within a year
without canoeing in the winter (282
days)!
How can it be that these numbers
difer so wildly? The answer is that an
estimate of the length of the coastline
depends on the map that you use, in
particular on the fne scale at which it
gives up reproducing the wriggles of
the real coastline. Such an object is called
a fractal. How then are we to describe
it? And how does the work of a group of
second year Theoretical Physics students
at Trinity College Dublin [1] help to
realistically plan a canoe trip?
This kind of problem lay largely
unrecognised, except in the minds of
deep-thinking mathematicians, until in
the 1960s and 70s the mathematician
Benot Mandelbrot brought the topic into
the scientifc mainstream [2, 3]. Helped
by the huge advances in computer
graphics, fractals had an enormous
popular impact from the 1980s onwards.
So what is a fractal? Consider a
smooth object, such as the S-shape shown
in Figure 1 (right). An approximation
of its perimeter may be determined as
follows: overlay the object with square
boxes of equal side length; count the
number of boxes that contain a bit of
the perimeter; multiply this number by
the side length of each box and record
this product. Repeating this procedure
for smaller and smaller square boxes
(corresponding to an ever fner grid),
shows that the product is roughly
constant, independent on the box size, as
shown in Figure 1 (below).
The situation is diferent, however,
when this procedure is applied to
a coast-line. Using maps from the
almighty maps.google.com site and
GIMP image manipulation software
(http://www.gimp.org), the four TCD
students superimposed various grids
of decreasing box length onto a map of
Ireland. This is illustrated in Figure 2 for
the coast between Dingle and Skibbereen.
Using Click Counter software (http://
www.murgee.com/) , they then counted
the number of boxes which contain bits
of the coast.
Again we can estimate the length of
the coast by multiplying the number of
coastline containing boxes by their width.
The result is shown in Table 1 and Figure
3. Unlike in the example of the smooth
S-shape, the length of the coast-line is
seen to increase as we decrease the box
sizes. The value given by the Ordnance
Survey Ireland is reproduced for a box
How long is Irelands coast? Stefan Hutzler explains why the
answers to this question vary so wildly.
The rugged and indented western coast,
infra-red image from the Marine Institutes
National Coastline Survey.
width of 1.8km. But using an even fner
grid would eventually result in a line-
length of infnity! Coastlines and indeed
also rivers, clouds, ferns, etc. [3] are
examples of self-similar objects which
display structure at all length scales.
Mathematically speaking, the
determined length of the circumference
is proportional to w
1-D
, where w is the box
width and D is called the fractal dimension
D of the object under scrutiny. In the
case of our smooth S-shape example of
Figure 1 the value of D is one, i.e. the
dimension of a line. (Note that this makes
L independent of w, as observed in fgure
1.) The fractal dimension of the Irish
coast-line, however, turns out to be about
D = 1.20 0.01, as a numerical analysis of
our data shows (see solid line in Figure
3). Since D measures the raggedness of an
object, we also expect diferences when
comparing the relatively smooth east to
the wild west coast. And indeed the
students found D = 1.1 and D = 1.26,
respectively.
How do these numbers compare with
values for other countries? The South-
African coast-line appears smoothest,
with D = 1.05, while Norway with
its fjords tops the bill with D=1.52.
Mandelbrots value for the West coast of
Britain, determined in 1967, was D=1.25
[2].
So what about your canoe trip? In
consulting Fig. 3 you might use the
length of the canoe as your scale, and
get an estimate of more than 12000
kilometres! But that would correspond
to unduly meticulous navigation. Lets
say you will stand of the coast enough
that you mostly steer straight for about
100 metres at a time: let us use that. Now
we get 5667km ... Maybe you should
just stay at home and read Mandelbrots
magnifcent Fractals: Form, Chance and
Dimension (3), opening your eyes to our
fractal world?
References
[1] The TCD students carrying out the
project were Killian Walshe, Stephen
Burke, John Mark Geary and Liam Kelly.
[2] B. Mandelbrot, How long is the coast
of Britain? Statistical self-similarity and
fractional dimension, Science, 156, 636-
638 (1967).
[3] B. Mandelbrot, Fractals: Form, Chance
and Dimension, W. H. Freeman (1977).
Stefan Hutzler is Associate Professor at the
School of Physics, Trinity College Dublin.
36 49 1764
27 69 1862
18 112 2016
14.4 147 2116
10.8 203 2192
7.2 363 2613
3.6 777 2797
2.7 1102 2975
1.8 1752 3153
Box width in Number of Estimated
kilometres boxes containing total
section of length of
coast-line coast-line
Table 1: Summary of data obtained for the coast-line of the island of Ireland. The estimated
length of the coast increases with decreasing width of the boxes making up the grid.
Figure 3: Unlike the case of our
smooth S-shape in Figure 1, the
estimated length of the Irish coast
increases with the accuracy at
which it is mapped. This feature
of fractal shapes is written in
mathematical terms as L(w) ~
w
1-D
, where L(w) is the box width
w dependent length and D is the
fractal dimension. Determining
D numerically (using a least-
square ft) from our data of Table
1 as D = 1.20 0.01 enables us
to interpolate between measured
data points to obtain coast lengths
for any grid size (box width).
Figure 2: Irelands coast-line between Dingle and Skibbereen, superimposed with square
grids of box-width 10.8km (left) and 2.7km (right), respectively. Only boxes containing a
section of the coast are shown. It is seen that the fner the grid, the more details of the coast
become visible.
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Box width in kilometres
M
apping rocks is like a rite of
passage for young geologists.
By going out into the feld they gain
confdence and return better equipped
to see the connection between theory
and practice. As Aoife Blowick,
now studying for her PhD at UCD
observed, geological charts and
book illustrations can create the
impression that everything is neat
and tidy, but the reality is not so well
defned.
Aoife was one of the two
winners of the Cunningham Award
presented each year to those who
had completed the most outstanding
geological mapping projects. Like
the other winner, Myles Watson,
Aoife had chosen to map an area in
the Haute Provence of south-east
France. What makes this area so
interesting, and at the same time
so challenging to geologists, is that
sedimentary basins were formed
millions of years ago while the
underlying rocks were being pushed
and deformed by movement of the
earths crust.
In simple terms, said Myles, Africa
had started to push up against Europe, so
the crust began to fex. Where the crust
went down, sediments poured in, and
this did not happen all at once, but in
waves, so the geological structure
now is complex.
After submitting his maps and
feld notebooks, Myles had started
working in an oil exploration
company, Providence Resources,
and was soon so immersed in the
business that he had almost forgotten
about his mapping project when news
that he had won the Cunningham
Award came out of the blue. The
company is small enough for Myles to
become involved in diferent aspects of
the business. I have tried my hand at
seismic interpretation and I am getting
to grips with geomodelling software, he
said. It is an interesting business to be
in and you get lots of opportunities to do
really fun geological stuf.
Geology has always appealed to
Myles, ever since he picked up a rock
near his home in County Monaghan
and wondered why there seemed to
be something shaped like a spring
embedded inside. Years later he found
out that this was not a spring, but a
fossilized crinoid.
At UCD he began studying science,
and after remarking that I really liked
the broad approach, he added that I
always gravitated towards modules that
were geology based. Partly this was
because he had a strong preference for
feld work, and he still has no desire
to embark on a career that would
turn him into a desk jockey.
Aoifes interest in geology began
with geography and chemistry, both
subjects she enjoyed at school in
Wexford, and like Myles, she was
glad to have the opportunity to keep
up with chemistry and biology up
to second year at UCD. That meant
she could hold of on making a fnal
decision in favour of geology, rather
than chemistry which she had been
considering. Now, with a good
grounding in both, she can combine
the two.
Like Myles, Aoife spent six or
seven weeks tramping around an
area of about 54 square kilometres.
I love hiking and trekking, she
said, so was in her element, even
if appearing as an oddity in the
landscape. At frst the local farmers
Mapping
ancient basins
Tom Kennedy reports that two young award-winning geologists
headed out to south east France to examine how some ancient
sedimentary basins had been pushed about and deformed as Africa
drifted north.
All observations are entered into
the notebook which serves as a
permanent record that can be
revisited at any time. Here, Myles
has sketched out some features to
accompany his notes.
Myles Watson displaying
his Cunningham Award
mapping project.
farmers were a bit suspicious of this
hammer-wielding fgure wandering
about with no apparent purpose
in a hard hat and high-vis jacket.
However, once the locals knew what
Aoife was doing, they were eager to
help, pointing out features that she
might have missed, and advising
her how best to get around the more
difcult terrain.
The basins ride on top of a great
thrust, and Aoife described this as
like resting on a giant blanket. As
the rocky blanket is moved, the
basins on top are deformed. The
basin itself is quite fat, said Aoife,
but the edges, east and west, were
mountainy.
Every feature had to be examined,
and as she commented, its no good
going up to a rock and glancing at
it for fve seconds. Every feature
means something, so, as she said,
you need to think about it.
Most of the rocks that Aoife
encountered were limestone, but as she
explained, this is not like the limestone
we are familiar with from the Irish
midlands. There are diferent types
of limestone, she said, and what she
was looking at had grains so small
that the rock was like solidifed mud.
Distinguishing between these rocks in
the feld, she said, can be quite difcult,
so its not always possible to take a snap
decision on identifcation, especially
as appearances, such as colour, can be
misleading. In cracking open one of these
fne grained limestones, she said, you
see that it is very hard, and it gives of
a characteristic smell. These are the sort
of clues that enable a geologist to work
out what they are looking at even when
outcrops are far apart. There is a lot of
guesswork involved, but as Aoife said,
its educated guesswork.
Everything that is likely to have
signifcance is noted down, and like
Myles, Aoife was not convinced
that an electronic pad might be
better than pencil and paper. New
technology has its place, she said,
but with a notebook there is less
chance of essential information
being lost, and it is always possible
to check back on the original
observations.
The one technical advance that
Aoife is really keen on is the camera.
I take lots of photographs, she
said, and these form an important
part of her records.
Both Aoife and Myles are
well and truly hooked by geology,
but while Myles is happy to get
involved in the applied side, Aoife
has chosen to immerse herself in
research. I have started my PhD at
UCD, she said, and that involves
studying the sandy deposits made
by the Nile. So, from the ancient basins
in France, Aoife is going to study the
geologically much more recent deposits
made by a major river. There are lots of
parallels, she said, and when it comes
to sedimentary deposits, its an ongoing
story. She is quite excited about this
study, particularly as a lot of what she
learns from the Nile could be applied
to other river systems, such as those in
South America.
Aoife Blowick is now going to study geologically
more recent sediments laid down by the Nile.
UPFRONT
www.sciencespin.com
Bedrock of history
JERUSALEMs fate was determined by the underlying geology.
At the annual Geological Society of America meeting last
October, Michael Bramnik from Illinois University explained
that underground passageways in the karst limestone enabled
King David to take the city. Water was drawn from the Spring
of Gihon, which lay just outside the city walls. Davids soldiers
climbed down into the spring and by tunnelling under the
walls got access to the city.
An old water fea
A 450 million year old Crustacean, complete with fossilized soft
parts, has been found in Herefordshire. One of the scientists
involved in the discovery, Prof David Siveter from the University
of Leicester, said that what made the 5mm long fossil so special
is not that it is a previously un-named species, but that the soft
parts have been preserved so well that eyes and the antennae can
be made out.
The fossil, named Nasunaris fata, belongs to the same group
as water-feas and shrimps. Their descendants are common
today in lakes and oceans, and geologists often use the fossils as
indicators of past climates.
Internal image of the fossil showing the soft parts and eyes. Image:
David J. Siveter, Derek E. G. Briggs, Derek J. Siveter and Mark D.
Sutton.
Later, one of Davids successors, King Hezekiah, fearing that
the Assyrians would take Jerusalem using the same approach,
rerouted the water into the city via a 550 metre long tunnel. It
proved to be a good decision, for in 701 BC, Jerusalem was the
only city that the Assyrians failed to take.
Water still remains a major factor in shaping modern history
in the region, and Michael Bramnik said that when he went in
search of hydrological maps for other towns and settlements
he was often rebuffed with a claim that such maps do not
exist.
UPFRONT
www.sciencespin.com
Window into the ancient past
A REMARKABLY detailed snapshot of the Cretaceous period has
been preserved in amber. Amber, almost as clear as glass, is fossilized
resin, the sticky substance exuded by pine trees.
A team of twenty researchers from Germany, France, Austria,
Ethiopia, Italy, the UK and USA, have been examining the 95 million
year old plants, insects, nematodes, fungi, and even bacteria encased
in Ethiopian amber. The amber was found within sandstone from the
northwestern plateau of Ethopia. In reporting their initial fndings
in the journal PNAS, the researchers explain that they now have an
unprecedented window into a Cretaceous woodland. This was a time
when the frst fowering plants began to appear.
Two of the scientists involved, Matthias Svojtka and Norbert
Vvra, from the University of Vienna, explained that thirteen insect
families have been identifed so far. These include hymenopterans,
thrips, barklice, zorapterans, and remains of moths and beetles.
During the lifetime of these animals, Ethiopia was part of the ancient
continent, Gondwana. As the researchers pointed out, amber from
this region is rare, adding greatly to the value of the fossil record.
Until now the most signifcant Cretaceous amber deposits came from
North America and Eurasia.
A chalcid wasp
(Trichogrammatidae) in Ethiopian
amber, body length 0,6 mm
A wasp, just under half a cm long, from the
famiuly Mymarommatidae. Naturhistorisches
Museum Wien
An 8mm long member of the Thysanoptera,
thunder fy, family. Naturhistorisches
Museum Wien
MEDICAL implants, such as cathers
and prosthetics can save lives, but they
can also become an unintended host
for fungal infections. Thehe yeast,
Candida albicans, can form a bioflm
which is diffcult to eradicate, and
as researchers at University College
Cork report, this is the most common
hospital-acquired infection.
Normally, the yeast is not a
problem, but in certain circumstances
it causes a severe infection. Acquired
resistance to antibiotics is making it
more diffcult to keep these fungal
attacks under control, but as the Cork
researchers report in the journal,
Microbiology, another pathogen could
provide a solution to that problem.
The bacterium, Pseudomonas
eruginosa, invades burn wounds, so
it is seen as a troublesome pathogen.
However, as the researchers found,
it inhibits the growth of Canida
albicans.
Dr John Morrissey, who led the
research team, commented that if we
can exploit the same inhibitory strategy
that thre bacterium P aeruginosa uses,
then we might be able to design drugs
that can be used as antimicriobials to
disperse yeast bioflms as they form.
He also said that it might be possible to
incorporate such inhibitory drugs into
the implants.
The next step, he said is to
determine what kind of chemicals are
being produced by the bacterium, and
to discover how and where it targets
the yeast.
Blocking infections
Canida albicans bioflm under attack.
The fungal growth on the right has been
attacked by Pseudomonas. Confocal
microscope image, Gordon McAlester.
SCIENCE SPIN
Irelands science, nature and discovery magazine
6 issues a year covering science at home and abroad
In newsagents throughout Ireland, and on subscription
Subscribe on line from our website. 30 post included Ireland, UK and EU
www.sciencespin.com
Europes role in food security
Dr Shenggen Fan,
Director General,
International Food
Policy Research
Institute, speaking at
the third in Teagascs
lecture series Grand
Challenges for
Global Agriculture
and Food.
G
lobal hunger and malnutrition remain persistent as nearly 870 million people are
currently undernourished and more than two billion sufer from micronutrient
defciencies. What is more, many current and emerging challenges, such as natural
resource constraints, climate change, and a growing, more afuent, and urbanised
global population, threaten food and nutrition security further. Dr Shenggen Fan,
Director General, International Food Policy Research Institute, speaking at the third
in Teagascs lecture series, said: An integrated approach is needed to sustainably
improve food and nutrition security for the worlds poorest and most vulnerable.
Europe has a key role to play in advancing this task going forward as well. In his
lecture, Dr Fan made policy recommendations on the role of Europe in achieving the
above, including: increasing development assistance to food and nutrition security;
expanding investment in agricultural R&D and support technology transfer; reforming
domestic agricultural policies and promote open trade; building national capacities in
developing countries; and, promoting South-South and North-South learning.
SNP chips
genomic
selection
A
paradigm shift in dairy cattle
breeding programmes occurred very
recently with the direct inclusion of
DNA information in the Irish national
genetic evaluation of dairy animals.
The inclusion of DNA information,
in a process called genomic selection,
results in greater accuracy by which
genetically elite animals can be identifed
and thus subsequently used as parents
of the next generation. Other uses of
DNA information include parentage
verifcation and the screening of animals
for known lethal or congenital genetic
mutations. A new low-cost genotyping
platform, the International Dairy & Beef
(IDB) genotyping platform, developed
by Irish scientists in collaboration with
US scientists, was released in February
2013. Within three weeks of a hair sample
from an animal been taken on-farm, the
producer will receive information on the
sire of the animal, whether it carries any
genetic defects, as well as an accurate
estimate of the genetic merit of the
animal. This information will infuence
the producers decision on whether or
not to retain the animal as a parent of the
next generation. As well as contributing
valuable information to the producer to
make more informed breeding decisions,
the information generated it is also a vital
component of food traceability.
A
dvanced DNA sequencing technologies
have led to a revolution in almost all
felds of biological research. Sequencing
of all or part of the genome has had an
enormous impact on research relating
to human and animal health, food and
agriculture. For example, studies within
Teagasc have focused on identifcation
of microorganisms within the human
gut that contribute to health or disease.
Incorporating benefcial microorganisms
into foods can help restore and maintain
good digestion in the
gut.
Advanced DNA
sequencing has a big
role to play in this kind
of research, and in the
coming years this area
will become even more
critical in producing
results.
Teagasc, and the Alimentary
Pharmabiotic Centre (APC) recently
secured funding to greatly expand the
DNA sequencing facilities at Teagasc
Food Research Centre, Moorepark. Three
additional state-of-the-art sequencing
platforms, an Illumina MiSeq, an Ion
PGM and an Ion Proton, will greatly
expand the number of options open to
researchers. A combination of a Teagasc
equipment grant and Science Foundation
Ireland infrastructure funding has made
it possible for this
centre to be one of
the few around the
world to have access
to such a full range of
sequencing resources.
Teagasc researcher Dr
Fiona Crispie.
Next generation sequencing
Taking a hair sample from a calf during
flming of the Science Squad television
series.
T
he Alimentary Pharmabiotic Centre
(APC) was formed a decade ago with
the help of Science Foundation Ireland
(SFI) funding. Since then it has become
a vibrant research centre with, over 150
scientists and clinicians from research
areas including gastroenterology,
microbiology, psychiatry, food science,
neuroscience, immunology, biochemistry,
gerontology, cardiovascular and
paediatrics, among others.
Researchers at the
APC investigate the
close links between
gut microbiota and our
general health. While it
is generally known that
good health depends on
having a well balanced
gut microbiota, the APC
researchers aim to provide
a proper scientifc basis
for selection of benefcial
bacteria. These health-
promoting bacteria and
their metabolic products
can be incorporated
into what are known as
functional foods. These
are foods that have an
extra health beneft.
Benefcial microorganisms can also
be used to produce health-promoting
pharmabiotics.
APC researchers have been
identifying novel substances produced
by these microorganisms, known as
bioactives. These are of great interest.
particularly to the pharmaceutical
industries, because they have a lot of
potential to develop treatments for a
variety of diseases.
Because this type of research covers
a wide spectrum between health with
nutrition APC works in partnership with
the food and pharmaceutical sectors. In
particular APC has become a leader in
probiotics, a fast-developing feld that is
of intensive interest to food producers.
The APC researchers at UCC and
Teagasc have in fact been ranked number
two in the world in probiotic research
by the independent international ratings
agency Thomson Reuters
Science Watch Global Analysis.
A large and well equipped
scientifc team includes
professors Paul Ross and
Catherine Stanton as APC
Principal Investigators; Dr Paul
Cotter leads the Next Generation
Sequencing Platform, Dr Mary
Rea leads the Culture Curation
and Applications Platform and
Dr Mark Fenelon is an APC
Faculty member. All are based
at the Teagasc Food Research
Centre, Moorepark.
The APC recently received
funding from SFI for a third term.
Teagasc/APC researchers Dr Rebecca
Wall and Dr Catherine Stanton.
Environmental footprint of livestock supply chains
W
hich country produces
the greenest milk and
meat? How do you measure
the carbon footprint of
lamb meat? Can we reduce
the water footprint of
beef production around
the world? Can dairy
production co-exist with
biodiversity?
These hot topics of
discussion in the food
industry are driven by
increasing demands in
the marketplace for more
sustainable products.
But measuring
sustainability across complex
animal supply chains is not
easy. And, in the absence of
internationally-agreed rules
to guide robust and fair measurement,
there is the risk that the debates about
how sustainability is measured start
to detract from the task of driving
real improvement of environmental
performance.
The urgent need for coordinated
approach based on international best
practice led the FAO to initiate the
Partnership on Livestock Environmental
Assessment and Performance (LEAP).
LEAP brings together industry,
governments, civil society representatives
and leading experts from
around the world to develop
science-based, transparent
and pragmatic guidance
to measure and improve
environmental performance
of livestock products, for
example, beef and lamb meat
or poultry (chicken and eggs).
Teagasc and the
Department of Agriculture,
Food and the Marine are
key participants in the
LEAP Partnership providing
leadership on the Steering
Committee, input into
technical guidance being
developed and through
the direct support for a
doctoral student to work
on developing indicators
for nutrient use efciency in animal
production systems. A Walsh Fellow PhD
student has been appointed, under the
joint supervision of Teagasc, the FAO and
Wageningen University and Research.
Follow @RogierSchulte on Twitter for
updates.
Alimentary Pharmabiotic Centre
Teagasc, Head Ofce, Oak Park, Carlow. Tel: (059) 917 0200
Website: www.teagasc.ie
The partnership is developing methods for
environmental footprinting of livestock farms
that apply equally to farms on all continents.
Marine biodiversity
Diatoms like this may be
microscopically small, but
they are abundant and
form an important part
of the food chain.
At sea, animals have a
lot more freedom to take
on forms that would be
impossible to support on
land. Tis colourful deep
sea Acorn Worm was
photographed by David
Shale during the MAR-
ECO programme which
explored the mid-Atlantic
ridge as part of the
Census of Marine Life.
A Basking Shark with mouth wide open to feed. Photographed
by Chris Gotschalk. Until early in the last century these sharks
were hunted from Achill, Co Mayo.
W
e spend most of our time on land, but 95
per cent of the habitable space on Earth
is in the oceans. Life began in the oceans, and
diversity is much greater at sea than on land,
yet we still know little about the creatures that
inhabit most of our planet. As the European
Marine Board has pointed out, over 33,000
species have been identifed in the seas around
Europe, and only 760 of these have been known
since the last century.
The European Marine Board is an organisation
established in 1995 to represent 34 member
organisations including Irelands Marine
Institute. In a recent scientifc briefng the Board
stressed how important it is for us all to realise
that the greatest genetic diversity is not on land,
but in the sea. Biologists divide life into broad
categories, known as phyla, and while 13 of these
are exclusively marine, just one is on land only.
In an ambitious bid to catalogue the richness
of life at sea, a ten-year long global census
of marine life project was organied. About
2,700 sientists from 500 institutions pooled
their resources to create this listing which
now, without counting in bacteria, identifes
240,000 species. There are, literally, countless
microorganisms, many of which thrive under
extreme conditions.
Not alone are there many species, but
collectively the smallest organisms make up 90
per cent of the living biomass in the oceans.
Very little is known about these organisms, and
the same can be said of most of the larger species.
According to the Marine Board briefng for
most species in European waters hardly anything
is known about their life cycle or how they
interact with other species or the environment.
To put it mildly, there are enormous gaps in our
knowledge, and to address this the Marine Board
has called for greater collaboration between
existing marine research stations. There are many
such stations around the coasts of Europe, some
big, others small, and as the Boards briefng
points out, lots of them have been established
for over a century. Acting alone there is only
so much they can do, but through the European
Marine Board all of these stations can become
part of a multi-disciplinary network drawing on
each others knowledge and sharing resources.
As on land, biodiversity at sea has to be
protected, and in this the Marine Boards briefng
highlights the need for a signifcant shift in
policy. At present just two per cent of the worlds
oceans have ofcial protection, and under the
EU Habitat Directive nine marine areas are
listed, all close to land and none of which are in
open water. In contrast to this there are over 200
areas listed on land. As the briefng reminds us,
bottom trawling and overfshing provide enough
evidence to show that the marine environment is
fragile and cannot be taken for granted.
www.marineboard.eu
Tom Kennedy

Tis tiny
Coccolithophore,
Emilania huxleyi has
a calcite shell unlike
diatoms which encase
themselves in silica.
Te Atlantic Cod, Gadus morhua, has been put at risk by
overfshing. Photograph, Hans-Petter Fjeld.
The Antarctic Krill, Euphausia superba, An image by Prof Uew
Kils from the virtual microscope, a fascinating site where details
of this animal can be viewed at high magnifcation. Visit the site
at http://www.ecoscope.com
Giants of the deep
SeafarerS of old often came back telling stories about
giant creatures emerging from the depth and wrapping their
tentacles around ships. These stories, which undoubtedly
grew in the telling, were based on the real-life Giant Squid
which can grow to 13 metres, weight 900 kg and lives in
depths of down to 1000 metres below the surface.
The fact that the Giant Squid has rarely been observed
live adds to the mystery surrounding this strange creature.
about a year ago the crew of a Japanese submarine managed
to make a video record of the squid at a depth of 630 metres,
but scientists still have a lot to learn about this animal.
Dr Louise allcock from the ryan Institute at NUI Galway
was among a team of international scientists, led by PhD
student, Inger Winkelmann from the Natural History
Museum of Denmark, seeking to fnd out more about the
Giant Squid from its genetic code. from this study of 43
squid remains from around the world the scientists have
concluded that they are all genetically uniform, so belong to
one species.
It is thought that the adults remain in fairly restricted
areas, but the young drift with the currents, and on reaching
deep water they dive down to begin the next life cycle. as
yet, no one knows how long these creatures live or how
quickly they grow.
VISITorS going out for some fresh air on the way out
to the Poolbeg lighthouse in Dublin were presented
with a strange sight as thousands of cockles came
to the surface. The great stretch of sand between
Sandymount and the Half Moon swimming club was
traditionally known as the Cockle Banks, but normally
these bivalves stay hidden below the sandy surface,
opening to flter-feed only when the tide comes in.
for some reason the cockles recently failed to cover up,
and thousands of them died.
Professor Jim Wilson from TCDs Zoology
Department said that this was an unusual event,
but was inclined to rule out pollution, anoxia or a
plankton bloom. The most likely explanation, he
suggested, is that the cockles were literally frozen out
of it. Just before this mass die-back, conditions in this
very exposed area were more extreme than usual, and
it is highly likely that the cockles were not down deep
enough to excape the frost.
Photographs: Marie-Claire Cleary.
Alive, alive oho ...
After being
attracted by bait
this giant squid
was captured of
Tokyo in 2006.
Photo, Tsunemi
Kubodera, Japanese
Science Museum.
Right, a 19th
century French
paddle steamer
hauling in a giant
squid of Tenerife.
Gas for the lab
If anyone wants to set up a lab,
but has no gas supply Sinead Clarke,
transition year student at St Marys in
Ballina, County Mayo has a solution.
Running a modest 13 volts through water
with a dash of calcium hydroxide to help
the current fow, can produce enough gas
to keep a Bunsen burner in action.
a conversation about injecting
hydrogen into car engines frst got Sinead
interested in the idea that useful fuel
could be generated from water, so she
began to investigate the possibilities. It
struck her that gas can be a problem for
labs. There is a certain amount of risk
attached to having gas on tap, and of
course for some labs there might be no
supply at all.
So, with the help of her technically-
minded dad, Sinead built a gas
generating unit. In this a direct current is
fed into stainless steel plates immersed
in water within a closed system. The
well-made and very professional looking
unit, said Sinead, took forever to make,
and with a 13 volt supply it can generate
an impressive half a litre of hydrogen a
minute.
The gas, a mix of hydrogen and
oxygen, bubbles out through a water
flled chamber, and as Sinead explained,
this is an essential safety feature because
it stops fash-back from ignited gas if
the pressure drops. The gas can be used
in a modifed Bunsen burner and as
Sinead explained, the unit is safe to use,
and probably safer than a conventional
system.
as far as I know, she said, there is
nothing like it on the market.
Sinead , who did the project at home,
helped by her dad, said she likes science,
but tackling a project like this really gets
her fred up. I would really like to do
more on this project. (TK)
Wood pellets
Simple device boost
performance
Shauna Dixon, secondary school
student at Mount St Michael in
Claremorris, discovered a simple way
to boost the performance of wood-pellet
boilers. Shauna was one of the winners
at this years BT young Scientist and
Technology exhibition for her project
showing how fltering out the dust can
bring efciency up by over 15 per cent.
Shauna said that wood pellet boilers
have become very popular, but dust
from the fuel is creating serious
problems. Surprisingly, it is not the dust
from combustion thats the problem.
The dust, she explained, comes with
delivery, and she frst became interested
in this because the boiler that has been
heating her home for the past six years
needed extra maintenance. We had to
keep servicing it, she said. Deciding to
investigate, Shauna found that the auger,
a screw-like device, that feeds pellets
down into the boiler, was becoming
clogged with dust.
It struck her that removing that build-
up of dust would solve a lot of problems,
and it also occurred to her that the
solution was simple. as she explained,
Shauna went of to the supermarket and
got an ordinary bin. Turning the bin on
its side below the hopper, she stuck a
shoe box inside to act as a dust collector.
as she remarked, there was nothing
complicated involved, and anybody
with a wood-pellet boiler could rig up a
similar home-made flter.
Shauna has a strong practical streak,
but she was also very keen to fnd out
a lot more on how and why dust is
such a problem. Wood Pellet boilers
have become quite common around
Claremorris, and as she discovered,
most of her neighbours also had similar
problems with dust.
The problem, she found, begins with
delivery. Pellets, which come from a
supplier in northern Ireland, are fed
into the hopper at high pressure, and
naturally with all the vibration and
mixing involved, a considerable amount
of dust is generated. (TK)
BT YOUNG SCIENTIST AND TECHNOLOGY EXHIBITION
Yourboilerissettohaveafxed
airtopelletratio,saidShauna,and
whenthatisincorrectlotsofgasesare
produced.Thosegasesarecorrosive
tometal,andtheycanbebadforthe
environmentaswell.So,notaloneis
burninglessefcient,buttheboileritself
islikelytosufer.
Shaunacarriedoutsometests,
comparingperformanceofherown
homeboilertothoseofaneighbour.
Theaverageboilerrunsatabout75
percentefciency,shesaid.The
boilernextdoorwasrunningat73per
centefcencywithoutaflter,while
ourswasrunningatabout89percent
efciency,Thismeantthattherewas
anenormousdiferenceofover15per
centinperformancefromthesamefuel.
Inaddition,carbonmonoxideemissions
weredecreasedbyabout60percent.
Anotheraspectoftheproblem,she
added,isthatthedustitselfcanbea
hazard.Finedustmixedwithaircanbe
explosive,andinindustrygreatcarehas
tobetakentoavoidelectricalsparksin
enclosedspaceswheredustislikelyto
occur.Ifwoodpelletboilerswereinan
industrialsetting,saidShauna,these
precautionswouldbeinplace,andthis
isanothergoodreasonwhyflteringout
thedustissoimportantwithdomestic
boilers.
Shaunacalculatedthatabout14
percentofthefueldeliveryislostas
dust,andagain,Shaunagavethissome
practicalthought.Iputthedustinold
milkcartons.Inastoveoropenfre,they
burnperfectly.Thatmadeherwonder
ifthedustcouldberecycled,butasshe
remarked,tomakethemintopellets
orlogs,youcouldneedapowerful
compressor,andyouwouldalsoneeda
bondingagent.
Shaunathoughtitwouldbeagood
ideatopatentheridea,but,withsome
wryamusement,sheremarkedthat
flteringoutthedustissoeasythat
everyonecandoit.Evenso,Shaunais
wellonherwaytobecomingquitean
expertinthisfeld,andsheiscertainly
notshortofideas.
Thefutureofwoodfuelisbright,and
Shaunaremarkedthattheobligationto
meetenergytargetsishelpingtopush
updemand.By2020fortypercentof
Irelandsenergyneedsaretocomefrom
renewablesources,suchaswood.(TK)
This report frst appeared on the local forestry
site www.forestgrowers.com
Laundered
diesel
ThErEisabigpricediferencebetween
dieselforuseonthefarmanddieselfor
useontheroad,yetthefuelisalmost
exactlythesame.Farmersdonothaveto
payaheftytax,sotopreventroadusers
fromtankingupwiththecheaperfuela
dyeisused,greenintherepublicandred
inNorthernIreland.Notsurprisingly,this
hasledtoablackmarketforlaundered
diesel.Whenthedyeisremovedthefuel
looksnormalenoughforunsuspecting
motoriststopaythefullprice.
Whattheydonotseeistheby-product
oflaundering,adirtysludgethatthe
criminalgangsengagedinthistrade
simplydumpbytheroadside.Giant
industrialsizedcontainersflledwith
sludgeareacommonsightbyborder
countyroadsides,andasMarlena
Drobniewska,afourthyearstudent
atBalbrigganCommunityCollege
explained,localauthoritiesarebeing
forcedtopayforexpensiveclean-ups.
Becausethesludgeisanenvironmental
hazardithastobecollectedandexported
fortreatmentanddisposal.Thecostto
LouthCountyCouncilalone,where90
sludgefndsweremadein2011,isabout
1millionayear.
Whentheirscienceteacher,Tom
ODonoghue,broughtupthesubject,
Marlenaandtwoofherclassmates,
rossMcGrathandCianhollandagreed
thatlookingatwhatcouldbedonewith
thesludgewouldmakeagreatYoung
Scientistproject.
AsMarlenaexplained,themarked
dieselistreatedwithbentonite,amineral
familiartomanypeopleasanabsorbent
catlitter.Mixedwithsulphuricacidthe
bentonitedrawsoutthedye,andthis
becomesthesludgethatnoonewants.
Atleast,thatshowthesituationis
now,butastheyoungscientistsargue,
thatsludgecouldususedasfuel,and
thisiswhattheysetouttodo.
Onitsown,explained,Marlena,the
sludgewillburn,butnotverywell.
Mixedwithsawdustorcornfower,
performanceimproves,andtoshow
howthestudentsconductedaseries
oftests.Fivegramsofthepuresludge
wasobservedtoburnfor376seconds.
Eightypercentsludgewithtwentyper
centcornfowerburnedfor580seconds,
whileraisingthecornfowerpercentage
tofortypercentmadethemixburnfor
602seconds.Beyondthat,increasing
thepercentageofcornfowerledtoa
decreaseinburntime.
Thesametestswererunusingsawdust
insteadofcornfower,buttheresultswere
notasgood.
Thestudentsmademini-briquettes
fromthemix,andgiventhatthesludge
isanenvironmentalhazard,theywere
pleasantlysurprisedtolearnfromthe
EnvironmentalProtectionAgencythat
burningtheirbriquetteswouldposeno
problem.
AsMarlenaobserved,cornfowerisnot
expensive,andevenifitisacost,itwould
bealotcheaperthanhavingtoexport
thousandsoflitresofhazardouswaste.
Thestudentsgotahelpfulresponse
fromtheEPA,butsofar,saidMarlena,
nowordbackfromthelocalauthorities.
Maybetheyjustdidntwanttodealwith
abunchofstudents,sheremarkedwitha
shrug.
(TK)
BT YOUNG SCIENTIST AND TECHNOLOGY EXHIBITION
Ross McGrath, Marlena Drobniewska and
Cian Holland at the RDS.
O
ne of the main reasons why a great
civilization emerged and survived
for thousands of years in China is that
everyone valued brown gold. David-
Toews, a veterinarian and author of
The origin of feces points out that
until relatively recent years China had
the most intensive and sustainable
agricultural system in the world. This
was possible because almost all human
excreta, 90 per cent, was returned to the
soil as fertilizer.
Over in Japan, farmers
left buckets out for
travellers to make their
contribution, and in the
seventeenth century,
before the city of Edo
became Tokyo, boatloads
of fresh vegetables were
shipped back from the
countryside in return
for night soil. Excrement
became so valuable that
traders were able to
demand money as well as
food, and for apartment
dwellers the rent went up
if neighbours moved out.
Stealing shit became a
crime.
As the author of this informative book,
due out in June, tells us, the fact that it
is a bit impolite to use the word says a
lot about our failure to think about how
important shit is to our survival. As he
remarks, there are things we dont talk
about, even if we are sitting on a pile of
it, and with a neat turn of phrase he
gives us an important message: How
can we unleash the incredible power of
excrement if we dont know shit?
He certainly has a point, and my own
great-great grandfather would have
agreed with it. As in John B Keanes
wonderful play The Field two lush
meadows here still stand out from the
surroundings because he arranged for
them to receive the night soil from the
nineteenth century Swinford work-house.
I sometimes think, not so much of the
stinking cart-loads as they bumped and
rattled out over the road, but of how
much these poor unfortunates gave back
to the land.
Nodoubt,ifIweretoheadoftothe
nearest big hospital in Castlebar with the
same idea in mind, I would need a slurry
tanker, and my unwelcome arrival would
be treated as an emergency. Furthermore,
the Environmental Protection Agency
would come down on me like the
proverbial ton of bricks, and rightly
so.NotonlywouldIbefllingupmy
tanker with excessively watered-down
excrement, but I would be picking up
bugs galore, antibiotics and goodness
knows what other powerful drugs.
Dumping that back on the
land, bordered by a stream
that meanders back into
town, would not, alas, be
such a good idea.
This kind of situation,
the author notes, has come
about because we humans
have become so good
in solving one problem
without considering the
fact that we are creating
another. This is the sort of
linear thinking that has
earned dam engineers,
road builders, intensive
farmers and others, such a
bad name.
He makes a telling
observation, familiar from his own
experience as a vet. Farmers make
intensive use of antibiotics, such as
ivermectin, which as he remarked is
regarded as something of a miracle
because it keeps the bad bugs at bay.
However, one of the problems this creates
at the other end of the cow is that the
drugs also suppress the dung eaters.
Thus, you might say, the shit is no longer
worth shit.
By comparison, an animal in the wild
will feed a host of followers. An elephant,
we are informed, only digests about 40
per cent of the food it consumes. What
comes out is a feast for dung-beetles and
other assorted creatures, and from their
point of view, it is the elephants role
to bring down the nutrients from high
above so that they can go back to enrich
the soil.
Not that the author is preaching to
us like an eco-warrior. As a practicing
vet he clearly has his feet on the ground,
and he well aware of the fact that lots
of pathogens and parasites depend on
excrement to move from one host to the
next. Contaminated water is a killer.
About two million people a year die from
diarrhoea, most of them children. One
particular parasite, Toxoplasma gondii,
inhabiting the gut of cats, has given rise
to concern because it has managed to
spread into some of the remotest parts
of the world. This particular parasite
can cause pregnant women to miscarry,
andtheinfammationitcausesis
suspected of contributing to depression.
The explanation for its spread is simple
enough. There are lots of cats, and no one
is really bothered about where the smelly
contents of the litter tray is dumped.
Before anyone is tempted to grab and
strangle the family pet, bear in mind that
cats are only a tiny part of the problem.
Strangely enough, while everybody is
concerned about the extinction of so
many species, the global population of
all animals has actually increased. Heres
how the author puts this in perspective:
In 10,000 BCE there were about a
million people on the planet. Thats 55
million kilograms of human excrement
scattered around the globe in small
piles, slowly feeding the grass and
fruit trees. In 1800, there were about a
billion people on the planet, so about
55 billion kilograms. By 1900, we had
a world human population around 1.6
billion, which would have been 88 billion
kilograms of human shit.
We now have more than 7 billion
people living on Earth, and not alone
has the population shot up, but more
and more people are living in densely
populated cities. Intensive farming
means that more and more animals are
being packed into smaller spaces.
I do not think we need an
internationalscientifcstudytotellus
that there is a whole lot more excrement
in the world than ever before in history,
he writes, and as he explains, it is
notsodifculttoworkoutwhatthe
consequences of simply dumping all or
most of this means. In the UK, David
estimated that humans discard 135 tons
of nitrogen and 58 tons of phosphorus
a year. The output from cattle is even
greater, 280,000 tons nitrogen, 50,000 tons
phosphorus and 100,000 tons nitrogen.
Then come the chicks, hidden away
in big sheds, producing 40,000 tons of
phosphorus.
Obviously, this is not the smartest
way to use our resources, but as the
author explains, the aspiration to get a
chicken in every pot goes back a long
way. Even in what we might think of the
bad old days, no one was happy to see so
many people starve. Intensive farming
Replacing a heap of trouble with a
mountain of opportunities
REVIEW
was the way to deliver on that promise,
and maybe that should give us pause
for thought. As the author observes, we
should not rely on the technology that
gave rise to the problems in the frst place
to provide us with the solutions. Yet,
what we are getting is often just more of
the same linear type solutioneering, and
I cant help but wonder why the chosen
solution for Dublins growing volume
of sewage is to pump the treated waste
further out into the bay. I understand
that recovery of nutrients would have
been a much more expensive alternative,
but it does seem to suggest that all local
authorities are frmly locked into systems
that have no future.
Interestingly, the city systems that we
have inherited did not begin as sewers at
all. It is true that the Victorian engineers
made an enormous impact on public
health by bringing in clean water and
removing sewage, but way back in 600
BC the famous Cloaca Maxima in Rome
was designed, not for sewage, but to
carry away rainwater. The author informs
COLOUR
The science and art of colour explained by Margaret Franklin and
Tom Kennedy. A colourful and informative paperback. 15 post free
from www.sciencespin.com
INK
M
anuscripts can often be
traced back to a
particular monastery through
an analysis of the inks used by the scribes.
For writing a wide variety of substances have been
found to meet the basic requirements; freedom of flow,
clarity, and a high degree of permanency. Boiled tree
bark, the black mush produced by ink-cap mushrooms,
blue from cornflowers, powdered root of the yellow
flag iris, and even strong coffee have been used. A
black ink was made from the winter blackened bark
of blackthorn twigs mixed with milk or glue. One
common type of ink was made from oak galls, the
round balls formed by insects on oak trees. One
formula for preparation was five pounds of iron
sulphate, five pounds of gum, 12 gallons of water,
and measuring by volume, 12 gallon of oak galls.
Collecting enough oak galls for 12 gallons must
have been difficult but it just shows how big the
demand for ink was. On an even more extensive
scale Indian ink was made from lampblack and gum, and
producing fine grained soot became a big, although very dirty
industry in parts of south eastern Europe. The soot, lampblack,
was mixed with linseed to make printers ink.
COLOUR
The
quality of
medieval
inks had
to be high
for
manuscripts
such as this
to survive.
This is a page
from a medical
manuscript,
the Book of the
OLees,
preserved at the
Royal Irish
Academy.
63
Colour has hue, saturation, and
brightness, and three dimensional
modelling, although harder to
visualise, led to more accurate
systems of classification.
The colour wheel gives a good idea of how colours
relate to each other. By subtracting the colour from
one side of the wheel we get the opposite hue.
event. The exception is the Mourne Granite which is
only 55 million years old and it developed during initial
opening of the Atlantic Ocean, possibly due to the melting
of the Earths crust by the ascending Antrim basalts (see
Basalts and other Volcanic Rocks earlier).
The generation of hot molten granite in the base of
the Earths crust is driven by the movement of plates:
where they collide, the over-ridden crustal plate sinks to
a depth where it melts to form liquid granite (see Figure
3). Where those plates pull apart they release extremely
hot basalt from the mantle which in turn melts the crust it
Vegetation covered schist lying up against a granite cliff above
Lough Oular, Co Wicklow.
Figure 15. Ireland is well-endowed with granite rocks. The granite
of the Mourne Mountains is the northeast stands out from the
others in being signifcantly younger only 55 million years old.
67
Carboniferous plants
A. Palaeopteris hibernicus,
from Kiltorcan, Co Kilkenny.
B. Alethopteris loachitica,
Ballynstick, Co Tipperary.
C. Alethopteris lonchilides,
from Drumnagh colliery, Co
Cork.
D. Root of Lepidodendron,
Towerstown, Co Laois.
Photographs: Tom Kennedy.
ROCK AROUND IRELAND
Peadar McArdle guides us around Irelands diversifed geology.
Paperback 15 postfree from www.sciencespin.com
Gold Frenzy
The story of Wicklows gold
Peadar McArdle
ISBN 0 906002 08 7
In 1795, the chance discovery
of a nugget was immediately
followed by a gold rush as
people were drawn by the
prospect of picking up instant
wealth from Wicklows
Goldmine River.
In this entertaining and
highly informative book,
Peadar McArdle, former
Director of the Geological
Survey of Ireland,
describes how the frenzy
has never really died down,
and to this day, panners
hope to be rewarded by the
glimmer of gold.
Hardback 20
From Dubray, GSI, and
selected bookshops, or buy
post free from
www.sciencespin.com
Open access
HunDReDs of scientifc papers reporting on Teagasc research are now
available to everyone free online. Teagasc reports that almost 300 papers
have been uploaded providing a picture of agricultural research from 2012
onwards.
Traditionally it would only have been possible to read published articles
after paying a subscription, and for many journals these charges put the
information out of reach to most people.
The Teagasc Open Access repository has been named str, a direct
translation into Irish.
For more information:
http://t-stor.teagasc.ie
us that in most european cities sewers
were not sewers at all, and it is only
when a rising population made back-
yard cesspits overfow that permission
was granted to allow them to discharge
into the public system. Thats only half
the story, because it was the availability
of piped water that caused so many of
the cesspits to overfow.
The author has lots more to say about
a subject that whether or not we like it,
we do have to learn how to live with it.
Review, Tom Kennedy
The origin of feces, David Waltner-Toews.
ECW, June 2013. 220 pages, paperback.
12.99
Gold Frenzy is available from the
Science Spin website, Dubrays,
Kenny, Hannas, the GSI store and
from other sselected bookshops.

Hardback 20
IBSN 0 906002 08 7
Albertine Kennedy Publishing,
Cloonlara, Swinford,
County Mayo
GOLD FRENZY
IN
1795, following the chance discovery of a nugget, there was a
gold rush as people were drawn by the prospect of picking
up instant wealth from Wicklows Goldmine River. Gold has
always been mankinds enduring passion, and long after the
initial rush which the Government tried to crush, the belief
persisted that great wealth remained undiscovered
among the Wicklow hills. Charles Stewart Parnell was
among those eager to support the prospectors, and with
independence, nationalists were convinced that Ireland was
about to rediscover its source of ancient gold.
In his entertaining and highly informative book, Peadar
McArdle, former Director of the Geological Survey of
Ireland, describes how the frenzy has never really
died down, and to this day, panners dream that
one day they might strike it rich.
The story of Wicklows gold by Peadar McArdle
Searching for gold in County Wicklow, by
the late 18th century Irish landscape artist,
Thomas Sautell Roberts.
Courtesy of the National Library of Ireland.
Order on line from
sciencespin.com
for post-free delivery Ireland, UK and EU
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