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ISSUE 41 July 2010 €3 including VAT £2 NI and UK

SCIENCE

SPIN

IRELAND’S SCIENCE NATURE AND DISCOVERY MAGAZINE

BIG MOVE FOR DIT MAKIN SYNTH G ETIC CELLS

EMOTIONAL

BRAIN

3 IN 1 in

Sp Science in Sp School tive c A n i p S

THE MINES OF KILLARNEY www.sciencespin.com


Du Noyer

Geological Photography Competition 2010 Entries are invited for the 12th Du Noyer Geological Photography Competition.

Outcrop of Thor Granite near Burtonport with intrusive band of aplite, a photograph by Daragh McDonough from the 2009 competition.

George Victor Du Noyer, who served as a geologist with the Geological Survey of Ireland from 1847 to 1869, was a skilled field artist whose numerous sketches and pictures, with their combination of artistic skill and technical accuracy, were the “field photographs” of their day. This competition seeks to encourage the same blend of artistic and scientific skills through the medium of photography.

Prizes will be awarded in two categories, Irish and Foreign, and a prize fund of €800 applies. Entrants may submit a maximum of 4 photographs, illustrating any aspect of field geology or scenic landscapes. All photographs entered must be accompanied by a note giving the name and address of the photographer and a short description of the geological content. Up to four photographs may be submitted as prints or good quality scans. Submitted material will not be returned and GSI reserves the right to reproduce entries in its publications and promotional activity with due acknowledgement. Only previously unpublished photos will be accepted as entries. By entering this competition entrants are stating that they have taken the photo and that the photo is unpublished.

The competition will be judged by a panel including representatives of the Irish Geological Association, the Geological Survey of Ireland and external nominees and their decision will be final. Entries will be exhibited and prizes awarded at a GSI Cunningham Awards ceremony on 10th December. The photographs will be evaluated on the basis of creativity, technical skill, and geological content. Entries should be posted in an envelope marked “Du Noyer Competition” to: Cartography Unit, Geological Survey of Ireland, Beggars Bush, Haddington Rd, Dublin 4 or e-mailed to info@planetearth.ie Closing date for entries: Friday 8th October 2010. For full details visit the GSI web site www.gsi.ie LIVE LINK


SCIENCE

SPIN

The move to Grangegorman will bring all DIT colleges onto one parkland site.

UPFRONT

SCHOOL SPIN

Publisher DKS Ltd 5 Serpentine Road, Ballsbridge, Dublin 4. www.sciencespin.com Email: tom@sciencespin.com LIVE LINK Editors Tom Kennedy tom@sciencespin.com Seán Duke sean@sciencespin.com

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Business Development Manager Alan Doherty LIVE alan@sciencespin.com LINK Design and Production Albertine Kennedy Publishing Cloonlara, Swinford, Co Mayo Proofing and web diary Marie-Claire Cleary marieclaire@sciencespin.com

l What do scientists actually do? l Young scientist projects

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The emotional brain

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SPIN ACTIVE

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Read all about it

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The third part in a series of articles in which Veronica Miller explains all about the brain, and how it works. Collect the book length series. A supplement in Science Spin covering applied science and transfer of results into business and industry. l Green light for biggest single development in higher education. Tom Kennedy reports that more support for science is not matched by more news about research.

Battling for iron

Heather McLaughlin explains why we should starve the harmful bugs.

31 Synthetic cells 33 Roy Sleator describes the birth of the world’s first replicating synthetic cell The mines of Killarney 35 Tom Kennedy reports on how Killarney was the centre of an ancient industrial revolution

Picture research Source Photographic Archive www.iol.ie/~source.foxford/ Printing Turner Group, Longford

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Geological Survey of Ireland

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UPFRONT Bad connections

CELLS in tissues stick together, but if neurons fail to connect properly, schizophrenia or other mental disorders may develop. At Trinity College Dublin, researchers have been able to identify genes associated with cell adhesion. In a paper, published in the journal Molecular Psychiatry, the researchers explain that a study involving 15,000 individuals revealed that genetically determined variations on how cells connect to each other is linked to the development of serious mental disorders. The research group involves a number of investigators, and as they found, a number of factors are involved in cell adhesion, so coming up with a diagnostic test to assess risks is not going to be easy. However, the discovery does open up new avenues for researchers to halt, or possibly reverse the defective cell bonding processes. Commenting on the signficance of the findings, Dr Aiden Corvin, Science Foundation Ireland Principal Investigator and Head of the Psychosis Research Group at Trinity College Dublin said: “This is a really intriguing finding, which suggests that regulation of brain wiring is playing a significant role in schizophrenia and bipolar disorder. What is surprising is that some of the genes contributing to this effect have previously been implicated in disorders of language and autism, suggesting that this regulatory process is critical to the development of many different neurodevelopmental disorders which until now we have considered separately.”

Stem cells

Dr Alan Colman, Executive Director of the Singapore Stem Cell Consortium has begun working with researchers at the Regenerative Medicine Institute, REMEDI, in Galway. Dr Colman, a leading expert in the field, is helping the Galway researchers to perfect techniques in producing pluriopotent stem cells from blood, skin and other tissues donated by volunteers. Welcoming Dr Colmen’s appointment as Adjunct Professor, the Director of REMEDI, Tim o’Brien said the collaboration with Singapore will be of great benefit in developing stem cell expertise in Ireland.

Reopening of Museum

THE Natural History Museum is has returned to its home in Merrion Street. The Museum closed in 2007, following the collapse of a stone staircase, and some of the exhibits were transferred to Collins Barracks. At the end of April repairs and restoration work were completed, and the Natural History Museum celebrated the reopening with a few new features. Seats have been installed, and a new hands-on education area has been opened. While lighting has been improved, and there are plans to provide digital access to special collections, care has been taken to maintain the old Victorian ambience. Admission is free, and the Museum is open Tuesday to Saturday, 10 am to 5 pm. Sundays opening 2 pm to 5 pm. Closed on Mondays and bank holidays. www.museum.ie LIVE LINK

Bringing back the past with a 3D fossil

CoMPuTER modelling is adding value to old fossils. Instead of having to crack open a precious and possibly unique specimen, the fossil can be scanned and viewed, slice by virtual slice. Scientists at Imperial College London have made a 3D model of a Carboniferous cockroach, and as one of the lead researchers, Russell Garwood remarked, “people joke about it being impossible to kill cockroaches, and our 3D model almost brings this one back to life.” This particular specimen, known as Archimylacris effintoni, gave rise to our present day cockroaches, termites and mantisis, and then, as now, these creatures were common. “The Carboniferous period is sometimes referred to as the age of the cockroach because fossils of Archimylacris eggintoni and its relatives are amongst the most common insects from this time period. They are found all over the world,”said Russell. To create the model, 3142 x-rays were made using a CT scanner at the Natural History Museum in London. Computer modelling was then able to reveal legs, antennae and body parts in great detail. By observing appendages on the legs, the researchers were able to conclude that the insect had the ability to cling onto smooth surfaces, such as leaves. The researchers could also see that the legs had claw like hooks, which would have given the cockroach an ability to clamber up trees, and the creature could run. Long legs at a low angle to the body would have meant that it could scuttle along at speed. “We now think this ancient ancestor of the cockroach spent most of the day on the forest floor,” said Russell, ”living in and eating lots of rotting plant and insect matter, which was probably the bug equivalent of heaven. We think it could have used its speed to evade predators and its climbing abilities to scale trees and lay eggs on leaves, much in the same way that modern forest cockroaches do today.”

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UPFRONT Such an eruption would have a huge impact on the area, but, as the researchers point out, it is impossible to predict future volcanic activity. Rodríguez-González, who led the research team, said that there had been three periods of volcanic activity during the Holocene following an eruption east of the island more than 10,000 years ago. Other eruptions took place between 5,700 and 6,000 years ago, and between 1,900 and 3.200 years ago. “Archaeological evidence,” he said, “show that the most recent period of eruptions affected prehistoric human settlements on the island.” The researchers concluded that eruptions are on the increase, and the gap between them is becoming shorter. “The amount of magma releases had increased,” they state, “as has the explosivity of eruptions.”

Looking at the evidence of past eruptions. Antonio Rodríguez-González. Mapping the risks.

Time to blow

OVER the past 11,000 years there have been 24 eruptions on the north east side of Gran Canaria. This happens to be the most populated area, and, according to Spanish and French researchers, further eruptions are likely to occur. After studying the evidence, researchers, from the University of Las Palmas de Gran Canaria, and the Jaume Alme Almera Institute of Earth Sciences in Barcelona, have mapped out where the greatest risks occur. In a paper, published in the Journal of

Battle before birth

WE all have genes from our mother and our father, but do they always get on? It seems that the battle between the sexes before birth, and at a conference on early nutrition held in Munich during May, Dr Miguel Constancia from the University of Cambridge explained that genes from the father and mother may actually compete for resources.

Quaternary Science, the researchers explain that the most active areas are concentrated on the northern sector of the island. Based on field studies, eruptions there, they state, have not been at the upper scale of volcanic violence. Evenso, the next eruption, they predict, is likely to produce a cone of 30 to 250 metres in height, and flows of lava are likely to range from 100 to 10,000 metres in length. Dr Constancia said that evidence has been found to show that genes from the father have an important role in controlling how the placenta functions. This has an affect on nutrient devlivery to the growing fetus, and the consequences are likely

to last into adulthood. Dr Constancia said that some adult diseases, such as type 2 diabetes, may possibly originate from an inbalance in the placenta caused by competing parental genes.

Science on air

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UPFRONT An old water flea

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 flata, belongs to the same group as water-fleas 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.

Bedrock of history

JERUSALEM’s 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. David’s soldiers climbed down into the spring and by tunnelling under the walls got access to the city.

Later, one of David’s 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.

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Web: www.gsi.ie E-mail: gsisales@gsi.ie

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UPFRONT

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

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 findings in the journal PNAS, the researchers explain that they now have an unprecedented window into a Cretaceous woodland. This was a time when the first flowering plants began to appear. Two of the scientists involved, Matthias Svojtka and Norbert Vávra, from the University of Vienna, explained that thirteen insect families have been identified 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 significant Cretaceous amber deposits came from North America and Eurasia.

An 8mm long member of the Thysanoptera, thunder fly, family. Naturhistorisches Museum Wien

Canida albicans biofilm under attack. The fungal growth on the right has been attacked by Pseudomonas. Confocal microscope image, Gordon McAlester.

Blocking infections

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 biofilm which is difficult 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 difficult 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.

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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 biofilms 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.


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The flat-headed cat out on the prowl. Photo: Andreas Wilting.

UPFRONT Heat sensor

PLANTS cannot hide from extremes of heat or cold, but they can modify their growth. As scientists at the John Innes Centre in Norwich observed, plants can detect temperature differences of just one degree C. The knowledge that plants respond to changes in temperature is nothing new, but until now, no one could explain how this worked. To find an answer, Vinod Kumar and Phil Wigge from the Centre selectively labelled genes so that they would give off light when the temperature was increased. By screening a large number of cress, Arabidopsis, plants the researchers found a mutant that failed to detect differences in temperature. As Dr Kumar explained, this mutant was quite peculiar in that it lit up even when cold. Even when the temperature was lowered, the plant continues to behave as if it was in a hot environment. Further investigation, which the researchers published in the journal, Cell, revealed that the plant had a genetic defect that affected the behaviour of a particular histone. By wrapping itself around DNA this histone protein controls which genes are to be turned on. If that histone wrapper is loose, as in the mutant, all the genes, and not just a selected few, are turned on. Normally, when cold, the wrapper is tight, and it only loses its grip when the temperature goes up. Thus, this special histone regulates the plant’s response to changes in temperature.

        

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Jungle cats

ONE of the rarest form of cat inhabits the tropical rainforests of Thailand, Malaysia, Brunei and Indonesia. The flat headed cat, Prionailurus planiceps, is unusual in having webbed feet, which help it hunt for fish and crabs by riversides. The cat, which can weigh up to 2kg is seldom seen, and according to scientists from the Leibniz Institute of Zoo and Wildlife Research in Berlin, Germany the species needs protection if it is to survive. Fragmentation of its habitat is putting the cat under pressure, and because it lives in the lowlands, it does not inhabit the national parks, most of which are in more elevated areas. In reporting their findings in the Public Library of Science, the scientists noted that almost 70 per cent of the cat’s home territory has been taken over by plantations, and they argue that other lowland species, such as the hairy-nosed otter, are also under pressure.

Animal care

THE Athlone Institute of Technology is to collaborate with the Irish Society for the Prevention of Cruelty to Animals in delivering animal care and developing courses. Prof Ó Cathåin, president of the Institute, said that veterinary nursing students will be able to assist on special vet days at the ISPCA’s centre at Keenagh, Co Longford. Placement opportunities, he said, wll give veterinary nursing students valuable experience in animal care. At the same time, the ISPCA will benefit from a stronger focus on education.

Cancer response

TWO THIRDS of the women who receive tamoxifen following initial treatment of breast cancer benefit from the drug. However, with the other third, the drug has no benefits. At Queen’s School of Pharmacy, researchers Dr Tracy Robson and Dr Hayley McKeen have discovered a marker which shows which women are likely to respond to tamoxifen. Women with a gene, known as FKBPL have been found to respond well to the drug. The researchers hope to use this discovery in developing a test to predict the outcome of treatment. At present, many women are being treated with tamoxifen without knowing whether or not it will be of benefit to them. This can mean delaying in giving them an alternative treatment. Dr Robson said this type of research brings us closer to a more personalised approach to cancer treatment. Being able to give the most appropriate therapy early on would eliminate unnecessary treatment.

SCIENCE SPIN Issue 41 Page 6


“The sense of enthusiasm is infectious as students show their work to judges and members of the public,” said Anne. At St Patrick’s, science is taught as a practical, relevant subject inside and outside the classroom at all ages. “The primary curriculum is based on child centred, guided discovery, allowing students to find answers for themselves by thinking in a logical way,” said Anne. “It appeals to primary students, giving a sense of accomplishment, self esteem and the ability to dream outside the curriculum, without the pressure of exams or worry of failure. This builds up a love for the subject which may flourish through the teenage years.”

k c o r x o F n i ce Tradition

n e i c S d u o r P

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Some past pupils

t Patrick’s Girls School in the Dublin suburb of Foxrock has a strong tradition in science. The ‘green school committee’ has representatives from classes in the school, with a special interest in conserving water, electricity and paper. Students, parents and teachers have developed a school garden where vegetables and ‘minibeasts’ abound, with home grown compst used to boost organic growth. The students have also taken part in the Primary Science Fair - for primary schools - at the BT Young Scientist & Technology Exhibition, which their teacher Anne Doran said was a “fantastic experience, both in preparation and participation.”

i Dr Julie Mc Enery - astrophysisist at Nasa i Dr Anne Marie Healy - pharmacist and senior lecturer in pharmaceutics and pharmaceutical technology and also a fellow in Trinity College Dublin Regards

School Spin


CAREERS in SCIENCE

Ireland’s real-life ‘Batwoman’ Dr Emma Teeling, has spent her career studying bats, creatures she finds ‘fascinating’ for many reasons including flight and echo-location. Highly articulate, fasttalking and hugely enthusiastic, Emma — Director of Bat Research Ireland and a highly regarded UCD researcher — is like a walking advertisement for a career in science. A few minutes talking to her, and it’s clear, she just loves her work.

BATWOMAN SEDUCTION

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mma is one of those people that didn’t simply ‘fall into’ a scientific career, as one of several, or multiple options considered. She was fascinated by the natural world around her from when she was a little girl, and, for her, there was only one career that mattered. She can’t recall when she was seduced by science, but she clearly remembers that her father, who was fascinated by science himself, helped with the seduction process. Emma recalled a night that left an impression on her when she was about 11 or 12 years old. “I couldn’t sleep so went into my parents’ room,” Emma said. “My Dad was also awake. He had been reading a Times article about leptons, quarks and atoms, and started to tell me about these small molecules. We talked for about an hour about the wonders of the world until the rest of the house woke up. He told me I could be anything – a butterfly biologist in the Amazon, or a nuclear physicist at CERN. All I had to do was work hard at school and study what I loved, which, of course, was science. I think he was surprised when I did actually become a bat biologist working all over the world though.”

SCHOOL

It’s not a surprise to learn that Emma loved science at school, in particular physics and biology. She liked her teacher, and because she was interested, she didn’t mind studying these subjects. She also had ability, and passion, two vital ingredients for latter success. But, perhaps more than anything, her success is based on her total single-mindedness. “I did think about becoming a doctor, but I would have only done this to be able to study the science behind medicine. I always felt a little scared picking science as my career choice as I wondered if I would ever find a job. It is not quite a profession in the traditional sense. I think that studying science in school enabled me to realise that this was what I really wanted to do.”

TRAINING

One of the downsides to pursuing a career in science is the length of time it takes to actually get a job as a full-time professional scientist. A lot is made of the length of time it takes to train medical doctors, but, arguably, for scientists, the process is even longer.


the results. “This is part of my job as a lecturer. It is long and sometimes tedious, but I am very happy when it is over, and I see how my students have done.”

For example, doctors can graduate in five years, have no problem getting a job, and are on a good salary from day one. Scientists meanwhile, can spend four years doing an undergraduate degree, perhaps another three or four doing a PhD, and then maybe another two or three doing post-doctoral work. That’s about 10 years of training. Even after all of that, academic jobs can be hard to come by, and there are no guarantees. Of course for someone like Emma, the training and the hard work are all certainly worth it. “I feel lucky to have had the experiences and education that I have had. Before I got my first faculty position in UCD I had studied and been training as a scientist for over 12 years. I was reading about, learning about, and adding to mankind’s understanding of how life works. I got to travel all over the world. I lived in Canada, the US, spent time in Malaysia, Brazil, Thailand, Africa, all the while training to be an independent scientist.”

WORK

BATS

The long years of study finally paid off for Emma and she now holds a coveted position as a senior lecturer at UCD with her own research team. Her working day is somewhat different from when she was a post-graduate student, but it is still varied and interesting. “Typically my day consists of lecturing, analyzing data with my students, interpreting data, writing up these analyses as scientific articles – thinking, reading, hypothesizing,” said Emma. “When I can, I like to generate data by working in the lab, or going into the field to observe and catch the animals that we are studying. I used to do this a lot more as a graduate student and post-doc. I miss this aspect of my work. My students get to have all of the fun, most of the time. For Emma the best thing about being a scientist is those ‘eureka’ moments when some solution to a problem suddenly becomes clear. “It is 3 in the morning, you are exhausted, you have been working on a project or an idea for two years,” said Emma. “Suddenly, when analyzing a new piece of data, you finally understand. It is at that time that you know more than anyone else in the world. This makes all of the hard work worth it.” There are downsides to every job, of course, even a person’s dream job. For Emma the less appealing part of her job is having to correct “endless amounts” of exams and having to collate all of

The focus of Emma’s work is bats, and primarily addressing the question of how bats arose and developed their unique adaptations – flight and echo-location. There is also a more local focus on the bat populations in Ireland. It is not known whether bats here are increasing or decreasing in number, not even if we have identified all Irish bat species. Emma’s lab is developing new techniques to count bats, and to identify them into species. Some skeptics might question the value of spending taxpayers’ money on studying bats, and as Emma is supported by Science Foundation Ireland, she is supported by the Irish tax payer. So what do the general public get out of it? “Bats regulate insects,” said Emma. “If one species is to go extinct we have no idea what this will do to Ireland’s natural landscape. All environments depend on the species that are present in them. To remove one may cause the entire ecosystem to crumble. Therefore we must carefully monitor these environments and species.”

ADVICE

The advice Emma would give students considering pursuing a career in science is – do it. “Learn about the world, immerse yourself in things that fascinate you and study hard,” said Emma. “If it is science that drives you then spend the time studying it. I would advise you to take the subjects that you love at college level, at least for the first degree. You want to get high grades in your degree then you can study anything at fourth level.” Emma firmly believes that science and technology can help drag Ireland out of the economic mire, but there is a word of warning too for the Government. “Yes, I do think that science is our main hope. The Government will have to stick to their guns and make science funding a priority so that we can get out of this mess. However, they must not curb scientific creativity by only funding projects directly related to industry. This has the potential to kill future spectacular scientific discoveries that drive our modern world.”

School Spin


CAREERS in SCIENCE

THE FOSSIL HUNTER

TRAINING

Gareth, like all top scientists, loves his work, but he admits that getting to where he is today – a highly regarded full-time scientist, working all over the world – has been tough. There are not that many jobs in science, said Gareth, relatively to the numbers chasing them, especially in an academic field like investigating ancient dinosaur or bird fossils. “Many full-time scientists these days work for companies, like drug and oil companies. No company would hire a dinosaur specialist.” Despite the difficulty in finding the right jobs, the pursuit of a science career is worth the effort, and the years of study, he said. “The cool thing about working in science is that you are always learning and so studying more. I have always loved what I do, and so then the studying is easier.”

WORK

I

f anyone thinks that the science is boring, they should take a look at the career of Dr Gareth Dyke. Gareth is a superb young UCDbased ‘fossil hunter’. He has traveled the world for his science, and the places he has worked and researched in read like the set locations from the latest Bond film. Kazakhstan, Libya, Morocco, Russia. Gareth has been here, there, and everywhere, often spending months digging in harsh, burning hot locations looking for fossils. His main research interest is in fossil dinosaurs and the evolution of bird flight. This area of science – the study of fossils – is palaeontology and Gareth is a palaeontologist.

INTEREST

Gareth is from Southampton, a city on the south coast of England that is very close to the Isle-of-Wight. That is significant because this island is one of the best places in the UK for finding fossils, and Gareth would later become a palaeontologist, or a scientist that studies fossils. A family friend helped the young Gareth to get interested in fossils. “My parents had a friend called Roger, who used to work in the docks in Southampton. But he got sick and he couldn’t drive a boat anymore – he was a tug-boat captain. He was keen on collecting fossils, and so when he couldn’t work, he used to take me along on his fossil finding trips to the Island,” recalled Gareth. A series of ‘really cool’ teachers in school were also vital in triggering Gareth’s interest in the natural world, and science. These included a ‘biology’ teacher that was more interested in discussing physics and science fiction programmes on TV than biology. “We’d spend hours in class talking about the scientific basis of science fiction, Star Trek, and stuff like that,” recalled Gareth, of his physics-loving biology teacher. It is notable too that Gareth’s teachers did not shy away from teaching the experimental, practical side of science. “At my school in Southampton, we always did lots of experiments and went on field trips: finding insects in a local cemetery is one I remember,” said Gareth. There were other influences, such as Gareth’s friend Darren who kept reptiles at home and was forever drawing cartoons about animals. His granny also played a part, and he recalls when he was about 10 being brought by his Granny, who lives in Cardiff, to see robotic dinosaurs at the museum there. “I remember that really well,” said Gareth.

Gareth lives in Northern Ireland, and commutes up and down to UCD – though not every day. His wife works in Belfast so the couple picked a mid-way point, near the border in a beautiful scenic place to live. The commuting is not what he dislikes about his job rather it is the number of meetings that he has to attend when he is on campus at Belfield. “One thing that a lot of people that work at Universities like to do is talk a lot,” Gareth said. “When not doing that (attending meetings), I give lectures about the biology of animals, especially the reptiles and birds to students, and work with other researchers. If I am out of UCD, then I travel to museums and other fossil collections, and spend at least one a month each year doing fieldwork – looking for new fossils and digging them up.” The travel that is often involved with fieldwork, to far flung parts of the world, is not a problem for Gareth, even though he is away from home, his family and friends for extended periods of time. He loves to travel, and that was what brought him to Ireland in the first place. The chance to meet people with similar interests and to travel and get to see new places is great, as is the opportunity to find new fossils in remote places, he said.

BIRDS

The question that really interests Gareth in his work is discovering how animals flying. That means that fossil birds are obviously of huge interest to him, and the animals – dinosaurs – that birds are now thought to have evolved from. “Birds I like because I am interested in how animals fly. Working on fossil birds is a neat way for me to combine three sciences I am interested in — biology, geology and physics. Just the bits I am interested in though.” “Birds are the most diverse and successful group of land animals that we have with us today. My work is important because - I hope - I am adding information that will allow us to better understand how and why birds have evolved, and what the reasons are for their success. How did they evolve flight, that kind of thing?”

ADVICE

In terms of advice to students considering their career options, Gareth said: “Study what you are interested in: never take a course because you think it might help you to get a job, or because of the money. These motivations lead to bad karma.”

School Spin


The Young Scientists

Patrick O’Doherty and (right) Ben McRedmond with their project.

UNLEASING THE POWER OF TWITTER

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ould you like to be able to predict the outcome of a vote before it happens? Or to pinpoint exactly what people’s real opinions are? Or what people are talking about? What’s hot, and what’s not? In business and politics, there has long been a great interest in getting answers to these questions, and people have been prepared to pay vast sums for surveys that might product ‘so so’ results. Enter Twitter, the hugely popular social networking tool, that perhaps first entered the mass public consciousness during the Iran uprisings of 2009 and has gone from strength to strength since. Also, enter, two talented Gonzaga College 5th Year students, Patrick O’Doherty and Ben McRedmond. The two students showed that Twitter has immense potential to provide accurate answers to crucial questions, at the 2010 BT Young Scientist and Technology Exhibition in January. As anyone with even a basic knowledge of marketing will know, information that can accurately predict trends, of what people are saying about a product, or service, is absolute ‘gold’. In the 1980s for example, it was routine for magazines, and newspapers to commission PR companies to conduct surveys to determine what readers thought about their publications. These surveys were immensely expensive, and the results were still somewhat questionable. The beauty of Twitter, and what people like Patrick and Ben are doing, is that it contains within it, superb information about what people really think, and how people are going to behave in future. It is like listening in to real conversations between real people about what they really think. The potential is enormous, and the Gonzaga boys are to be praised for realising that potential.

PROJECT

The Gonzaga students could have analysed any one of a number of social networking tools, but they decided to stick with Twitter. Patrick explained why: “The ability to not have two-way communication between people – you can follow somebody without them following you back. That leads to a very interesting ‘ecosystem’ where people reference each other. For instance if Ben says something interesting on Twitter I would what’s called ‘re-tweet’ that. It is sent out to a wider audience, but still people get the credit.” The students created quite a few new software programmes that were in turn run through their database of information gleaned from Twitter, in other to generate different types of results. “One of the analytical methods that we use is able to predict the outcome of competitions, so, for instance, we were able to predict the winner of the X Factor, three hours before the live television final,” said Patrick. We showed that the winner was going to win with 62 per cent (of the vote) and he won with 61 per cent. It’s quite accurate.” “The second thing that we can do is what’s called ‘sentiment analysis’. This is where we to teach the computer to be able to classify things as being positive, negative, or neutral. This is particularly useful if you want to track your product through a week, and see what people are thinking about it, how they feel about it.” Patrick gave the example of 3D television, which was launched recently to a big hoopla by all the television manufacturers. However, it quickly became clear that the public didn’t really want it. There were media reports stating this, and opinion polls, and the students did a sentiment analysis of what people were talking about within Twitter to

School Spin

either confirm this view, or to contradict it. “We ran a block of data relating to 3D television through our sentiment analysis scripts and it came out 70 per cent negative and only 30 per cent positive in favour of 3D TV, so it directly lines up with what media and public opinion polls are saying,” said Patrick. “This is all based on software that we have created, and mathematics.” That is impressive enough, but the students weren’t finished. They also decided to work on ‘trend identification, using the data freely available within Twitter. “This is where we can find the most talked about phrase in a data set.,” said Patrick. “This was the hardest part of the project because computers only work on absolute definitions. You can define a word very easily, it is character, space, character, but a phrase can be any combination of words, anywhere in a sentences, that makes it really hard. We have this in a working state at the moment, we haven’t had a chance to get a huge amount of results from it yet, but it’s useful.” “For example, let’s say you want to find out who is the most talked about artist in music, for a week or a month, you can take that data, run it through this algorithm, and you will get out of it the most popular phrases and the most popular keywords that people have been discussing. “It is a way to analyse what people are doing and saying, getting a whole lot of data back from nothing basically. It is like a large passive participation survey. People are more likely to put factual information on twitter than they would agree to on a survey.”

PREDICT

The students set up a website to showcase their work at http://wepredictit.com/, and have been accepted into the BT (British Telecom) business mentoring programme, have filed a patent, and are planning to develop their idea as far as they possibly change. Certainly, their future looks rosy. “The main thing is prediction and being able to say what the public are thinking about a certain opinion,” said Patrick. “Wepredictit. com which is a website showcasing our latest results. This project would not have been possible two years ago because Twitter didn’t exist. The idea behind this is very simple, but implementing it is the tricky part. We are making sense of social ‘noise’.” Patrick O’Doherty and Ben McRedmond are 5th Year students at Gonzaga College, Dublin 6 They won two prizes at the 2010 BT Young Scientist and Technology Exhibition. 1st Prize: Senior Technology Group. Special Award: The most innovative use of technology.


The Young Scientists

Exotic pets Conor Hynes

5th Year, Confey College, Leixlip The ‘stick insect’ family, also known as the phasmida, are well known for their ability to resemble sticks or leaves and, thus, hide from predators. Conor Hynes, 5th Year student, from Confey College, Leixlip, first became fascinated with these insects when his mother brought a few of these exotic creatures home from a course that she was doing at Dublin Zoo. Stick insects are not native to Ireland, and though there are about 3,000 recognised species in the world, most inhabit the tropics, and like to live in temperatures of about 24°C. What Conor wanted to know, and he did this for his BT Young Scientist and Technology Project in the RDS in January, was to determine whether the insects could survive the Irish climate, and whether they posed a threat to native flora and fauna? These insects are herbivorous, and they feed on the leaves of trees or shrubs, and they can cause damage to plants, given their large appetites. They grow by moulting, or shedding their skin five times, said Conor. If they lose limbs, which can happen with fights in their youth, he said, then these can be re-grown following the next shedding episode. Many species are flightless, or wingless and they manage to blend in beautifully with their surroundings, by resembling leaves or sticks.

The title of Conor’s RDS project was ‘Exotic Pets Could they be a Threat?’ “I carried out five different experiments to see how much food they consume, how much eggs they lay, how low a temperature they can survive and to see if the eggs can overwinter here,” said the articulate, and personable Conor who conducted the research project on his own. Aside from the question of whether the insects – which can be classed as an ‘invasive species’ in Ireland - were a threat to native Irish species, Conor wanted to investigate: How adaptable are the insects? Can they change their food source if required? What are the lowest temperatures that they can survive? Does temperature have an effect on reproduction?

EXPERIMENTS

Conor’s insects are all female, but unlike humans, the female stick insect can breed with or without the male. The stick insects are, thus, referred to by Zoologists as being ‘parthenogenic’. Conor observed that his females laid about three eggs per day, and about 540 eggs per lifetime. That is a significant egg-laying capacity for a small insect, said Conor. In his temperature experiment, Conor found that the insects can survive temperatures as low as 10°C. From that he drew the conclusion that stick insects have the capacity to survive the Irish summer. He said that he was conducting a further

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experiment, not yet complete, that would determine whether stick insect eggs, could survive a cold Irish winter. His experiment was to cover last winter, and certainly if the eggs survived temperatures that hit -8°C last winter, that would indicate that stick insects can survive even the most severe conditions in Ireland.

CONCLUSIONS

Conor concluded that, in large numbers, stick insects certainly can do damage to local flora, as each individual insect is – remarkably – capable of chomping its way through one metre2 of plant material. If they got out during the summer they could do a lot of damage, he said, but it is unclear whether they would die out once the winter started to kick in. If the eggs his animals laid in 2009 managed to survive the winter of 2009/2010 that would indicate that stick insects, which are popular as pets because they are relatively easy to manage, could be considered a threat to native species in the same way as perhaps the grey squirrel. As for what he wants to do once he leaves school? Conor, is interested in doing science in college, but somewhat surprisingly, given his love of sick insects, he said he would be more interested in physics that in zoology.


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PART THREE

Will scientists lose control of their data? Continuing our series of special features in which Dr Veronica Miller explains what we know about the brain and how it works.

ThE EmoTIoNal BraIN T

wo black dots and another black line underneath. This could sound like a grammar instruction to German students. Yet babies can recognise these features as a smile and will attempt to smile back at you from a very early age — even if they can’t really tell the difference between you and a pot of jam from a distance. Nowadays most of us wouldn’t end a txt msg or msn conversation without the appropriate emoticon, because despite how well we can write about feelings, a simple smile and frown can communicate our feelings much better. As we grow older we become more sophisticated and unique in our emotional responses. Yet despite our individual differences, across the world there are universal emotional responses that we all recognise; laughter, tears, joy, happiness, sorrow and fear. All of these responses we are born with; few of us needed to be taught how to cry when we were born. So why is it that we have emotions and how do we feel them?

how do you feel?

How our emotions are relayed in the body was a puzzle, until two physiologists came up with similar theories to explain emotional responses in the body, both of which focused on the ability of the brain to make sense of our emotions. The two physiologists were William James (1842-1910) an American, Carl Lange (18341900) a Danish guy; the theory is known as the James-Lange theory. Their theory has three steps. Firstly it says that an emotion-producing situation elicits an appropriate set of physiological responses, such as trembling sweating or increasing your heart rate. These basic bodily responses are then coupled with behavioural responses,

such grinding your teeth or fists clenching when you’re angry. Then the physical behavioural responses send signals up to your brain which interprets these responses and behaviours as an emotion — in this case ANGER!

a body of emotion

This theory leans on the idea that our emotions and our perceptions of emotions are dependant on the feedback we get from our body. One scientist named Hohman in 1966 decided to test how important body responses for perception of emotion. So he got a group of people who had different levels of bodily sensitivity; who were paralysed to different degrees within their body. He found that those with the greatest physical sensation did indeed have the greatest level of emotional perception. Without bodily responses our brains wouldn’t be able to process emotions. While our own experience of emotion allows us also to pick out true from fake emotions. True smiles tend to result in creased eyes and lowered eyebrows with wide grins. Open eyed smiles tend to be fake; if you show people a series of smilers most of us will pick out the fake CORTICAL 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 LIMBIC brain

Three two one go

AUTONOMIC

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So despite the fact that our spines tingle and hearts rate with excitement, it’s 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 tier our emotional


Basal ganglia

Cerebrum (Cerebral cortex)

Thalmus Hypothalamus

Amygdala

Limbic System in the brain showing how the hippocampus, amygdala and hypothalamus are all connected in the middle of the brain.

responses, fears are processed within seconds in much in the way our bodies and are mainly processed that the Jame’s Lange via the autonomic and limbic systems, theory does into three the slower persistent lingering fears are made Hippocampus different levels. up of memories and inability to shut down the Firstly we have the response of our bodies to a scary situation. autonomic system response. Our instant fears, the kind that jump out at you at The primary autonomic areas night time enter our brains firstly when we make eye in the brain are the brainstem and the hypothalamus. The contact with them. Scary sights instantly fire pictures to brainstem mediates our heart rate, breathing sweating the back of our heads to the primary visual cortex. From and eyes dilating and is the first area of the brain to be the visual cortex images are then shunted back into the activated in emotional situations. Then messages are midbrain, via the thalamus and out to the amygdala on fired from it to the hypothalamus to trigger the release either side of our head, deep inside the brain just above of different chemicals into the blood stream preparing the ears. The amygdale are the walnut sized bundles of us for an emotional response. James Olds and Peter emotion processing fibres that store our innermost fears Milner discovered this in 1954 after finding that electrical and desires. If your Amygdala isn’t working properly, you stimulation of the hypothalamus in animals produced can’t process fear properly and can even lose the ability to euphoric or rage or attack behaviours. recognise fear in other folks. Secondly and up a level we have Scary sights, shuttled from the the limbic system consisting of visual cortex slot into the Amygdala the hippocampus and amygdala. which then signals to the nerve The amygdala controls our fear fibres in the midbrain responsible and anxiety responses, and the for controlling our sweating, hippocampus makes short term breathing, blood pressure heart memories, so that we know what to rate and adrenalin responses do next time the emotional response is to prepare us for fight or flight. needed . If you stop the hippocampus At the exact same time that these and amygdala working in animals by primary animalistic responses are cutting off their blood supply, you find initiated, a twin message is shuttled that the animals become very docile and from the amygdala up to the Anterior lack normal emotional responses, such as fear Cingulate Gyrus, to a porthole back to or anger. our consciousness in the cortex to tell us A cross section through the brain stem. that something scary has been spotted The third tier of emotional cake is the input to our cortex and output generated by and we are afraid. In this way both it to the limbic and autonomic areas via the relay station in our conscious and unconscious brains are alerted to the the thalamus to help us make informed decisions as to how fearful stimulus. to respond to the emotional situation. Whether to make a The unconscious response to fear is mediated by fight or take flight. the brainstem, the tube at the top of the spinal chord which contains a variety of clusters of neurons. The brainstem is responsible for controlling heart rate, blood Eye sense fear and I feel afraid pressure breathing and the release of different chemicals Fear can be fast and slow— an instantaneous fright responsible for making blood vessels squeeze and relax when somebody jumps out at you as you walk along a to shoot blood from areas like the stomach to areas that darkened corridor, and a longer lasting feeling of unease would be essential for you in a fight such as muscles as you walk home at night-time along a dark road. Quick

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to run away, or the brain to think of a way to escape. Our conscious fears are stored via the hippocampus and amygdala in through our emotional cortex where memories are consolidated.

Feeling hormonal

cause your hippocampus to shrink. Some brain imaging studies claim that soldiers who have post traumatic stress disorder or women who have been in abusive marriages have smaller hippocampi than unstressed folks. So although a little stress can be good, in the long term too much is bad for your brain.

Although it wouldn’t look so pretty on valentine’s cards, the brain really is the emotional epicenter of our bodies. Thinking of feeling It receives all the stimuli which trigger our emotions, The cortex as you know is the outer layer of our brains whether that’s a kick to the groin or a beautiful sunset, chiefly concerned with our cognitive or thinking ability. processes this information, and sends out impulses to our Dr Korbinian Brodmann, a German man, was the scientist muscles, either on our face to smile, or our throats to call who discovered what different parts of the brain do. out in pain. Some of the signals are sent out via cranial Thanks to his pioneering work at the beginning of the nerves which spring from the brainstem out to our facial, 19th century the confusion that had reigned over the throat, eye heart and gut muscles. Other architecture of the brain was cleared up. signals are sent out into the blood stream He characterised different brain areas via the pituitary gland. and found that the frontal region was most associated with behaviour and The pituitary gland is at the base of your skull and is a semi-permeable emotion. He named the area “regio bundle of cells, which are bathed in blood frontalis” and found that it had a and leak hormones out of the brain and particular granular structure which was into the blood-stream. The pituitary is unique to humans and primates such controlled and connected to hypothalamic as apes, but that rats and other lower and brainstem regions. Once it receives animals didn’t have this structure. a signal, it releases hormones, which are The “region frontalis” is now known similar to neurotransmitters, but they as the Pre-Frontal Cortex (PFC) because work over long distances from organ to it’s located just before the front of the organ, rather than just cell-to-cell. For cortex, behind the motor and premotor example hormones from the pituitary can cortex, just above the back of your ears make the kidneys release adrenalin; the in a strip from ear to ear This area is fight or flight hormone, or release cortisol also the most extensive cortical area of the stress hormone. the cerebral hemispheres accounting for Once you’ve switched on our 30 per cent of the cerebral cortex, which emotional responses it’s very important to shows you just how important emotions switch them off, otherwise like electronic are. Dr Korbinian Brodmann found gizmos, our batteries will wear out. The PFC, can be split into two major that the frontal area of the brain Usually chemical sensors in the brain sub-areas, the dorsolateral PFC, and is associated with behaviour and can sense when hormone levels are too the orbitomedial PFC each which emotions. high for too long, and they switch off have slightly different functions. production by the kidneys. But sometimes,under very The dorsolateral PFC receives sensory sound and sight stressful conditions, stress responses last too long, which input, and generates decisions relating to cognition and can have dire consequences on our sensitive emotional behaviour; whether to ask for a large or small pay rise brains. depending on the mood of your boss. The orbitomedial PFC receives input from sight, taste and bodily sources and generates decisions used for socio-emotional On the tip of your ... something responses; whether to shake somebody’s hand or hug When it comes to exams, job interviews or TV game them at a funeral. shows, cortisol can be your friend. In short bursts cortisol In order to process emotions, the PFC is hard wired activates the hippocampus and helps make and retrieve via the thalamus in the middle of the brain to a variety memories. But too much cortisol can have the opposite of different brain areas, relating to our primary emotions effect. In low levels cortisol binds to one set of receptors in the amygdala, the generation of memories in the which activates the brain, but in high levels a different hippocampus, and the brainstem for body responses like set of cortisol receptors are expressed by brain cells, sweating shaking or having dilated pupils. The thalamus and these ones actually switch off memory making and basically acts like the switchboard for the emotional calls retrieval by the hippocampus. You’ll be familiar with this of the brain. when even though its just at the tip of your tongue, you can’t remember somebody’s name or why you’ve gone into a shop when you’re super stressed and tired out. This is because high cortisol levels literally make you blank out. And over many years, some people think that chronic stress causes memory impairment and actually

Crocodile tears

In evolutionary terms the limbic system was one of the first areas of the brain to develop. Crocodiles, one of the phylogeneticaly oldest creatures on the planet have

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a forebrain that is almost entirely composed of the limbic system — which should mean that crocodiles are very emotional animals! Our primary emotions were tightly linked to our sense of smell, and the Pre Frontal Cortex is highly innervated by the hippocampus, amydala and olfactory membrane. The limbic system was originally designed many thousands of years ago to detect chemicals in the air and produce the appropriate response in the body. Literally animals could smell fear in the air and then either get ready to attack or run and hide. However gradually our limbic systems have lost their sophisticated sense of smell and our emotions have become blurred by sensory input from our environment and other areas of the body.

But even on a more literal note, its actually the ability of people to lose parts of their heads that elucidated how important our brains are for emotions and behaviour. Once classic story from neuroscience tells of a man named Phineas P Gage who was helping to lay train tracks in 1848. As the story goes an explosion sent a steel rod, measuring 3.5 foot through his left frontal cortex and out the other end of his brain, and left him still alive despite damaging a huge portion of that part of his brain. After the accident his personality changed and he became irrational, fearless, antisocial and inconsiderate. Though his story may sound extreme, it and other such incidents led people to believe that simply chopping Gut instincts The crack shows where the rod would have exited If your gut instinct tells you not Phineas’s head. From “The World Inside Your Head.” out the appropriate part of to do something, then listen to Clear Channel Exhibitions San Antonio Texas USA. the brain — a lobotomy could assuage the symptoms of it, because it’s probably the best emotional disturbance that and most reliable instinct you people experienced. If your amygdala which processes have. Impulses from your guts are hard wired into the fear is too active, because of drug effects or mutant Pre-Frontal Cortex and help you when you’re making genes, you’re more likely to be paranoid and fearful decisions in social settings. The fact that emotions are — removing the offending area could help you with vital to proper decision making is only recently coming to your problems! However, nowadays, medics are less light, with scientists only now realising that little emotion likely to cut off a broken leg than put a cast on it, so may be just as bad for decision making as excessive neuroscientists are more reluctant to cut out brain areas emotion has long been held to be. that appear not to be working properly. In fact they If you don’t have an emotional response, memories are more likely to attempt to generate the appropriate are not tagged appropriately into the amygdala and dietary or chemical intervention to help solve the hippocampus, so that when the PFC has to weighing up problem. your options next time you are in a scary situation, you won’t have enough stock of information to make the right decision. If you get angry, memories of what happened Highs and lows in the brain last time you punched somebody would be weighted Sometimes it can seem like our brains up in the PFC, which should then are a mere emotional playground generate the appropriate emotional for the different types of molecules response. Usually… However under that inhabit it. Excesses can make us the influence of drugs or alcohol hyperactive and give us wild mood people’s judgements can become swings, and too little can leave us as impaired. dull listless lifeless shells. There are a variety of types of Losing your head chemicals in nerve endings which find Sometimes when people get very their way to our emotional cortex, angry, we say that they lost their the PFC. Some are monoaminerigic, head. In the heat of the moment, which means that they are primarily when we’ve got too many conflicting made of one amine, and come from and new emotions shooting around the brainstem and upper midbrain our heads, it’s very possible that we areas. Adrenalin serotonin and can lose our ability to process our dopamine, which you may have heard feelings and make logical decisions. of, are all mono-amines, consisting We often say things in anger that we Model of a tyrosine molecule- which you eat and of one type of an amine. Cells in the wouldn’t normally say. brain and the body can make these your brain cells convert to dopamine.

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molecules by shuffling about oxygen and hydrogen and carbon molecules on ready made amines such as tryptophan and tyrosine that we get in our diet from proteins.

Why care about feeling?

If you constantly lose your temper, or can’t get rid of gut wrenching nerves just before a first date or exam, you may wonder what use feelings are at all. In fact we’re so concerned with controlling our feelings that the fastest growing legal and illegal pharmaceutical industries center on selling us drugs such as antidepressants to lift us out of deep depressions and anxiolytics to quench our fears. Yet an absence of emotional responses or apathy can be just as bad as having uncontrollable feelings.

What if you couldn’t care less?

An injury to any of the brainstem, limbic or cortical regions which regulate feelings can instantly take emotions out of our lives. This might seem like a cheaper alternative to Botox, no more frown, smile or wrinkle lines! But for your friends, family and loved ones it would be near impossible for them to tell how you felt about any situations. And knowing how others feel is an essential part of our lives. Imagine never seeing your friends or family smiling crying or showing they care. For children with autism, sensing and showing emotional responses is very difficult. The word autism itself literally means “self” ism, suggesting that the person is almost stuck within themself and unable to communicate with others. People with autism have less eye, vocal and tactile contact with friends and family alike. Although this doesn’t mean that they have no feelings, just that they don’t display emotions in the same way most people do. Some scientists think that when the brain is developing exposure to a toxin or infection interrupts the development of emotional brain regions trigger autistic symptoms. Whereas others suggest that autism involves problems with synthesising neurotransmitters that are important for human bonding. For example, oxytocin is considered the bonding neurotransmitter. It can make us feel more relaxed and settled. Married men have higher levels than single men, and new mothers have higher levels of oxytocin after giving birth to encourage bonding with their kids. Some studies claim that mice lacking oxytocin have austic-like behavior. Yet although oxytocin treatment can calm us down, it doesn’t cure all children with autism. So for now, we only have parts of the Autism emotional jigsaw.

Happiness is.....

Whether it’s a euphoric feeling after scoring a goal, climbing a mountain or simply payday , happiness is universal and triggers the same physiological and neurochemical responses in all of us. Happy people live longer and recover better from illness. And happiness, like yawning, is infectious. Studies show that knowing one happy person can make you a happier person. Happiness is also a state of mind. When you are happy, greater levels of serotonin are released within your brain. And serotonin is one of the most important neurotransmitters for

regulating your moods. Too much and you feel euphoric, too little and you can be depressed. For most people, our serotonin levels are constant, although they can depend on your diet. But even if you can make the neurotransmitter; if your serotonin receptors are low, or genetically mutated, your capacity for happiness can be reduced. It may not surprise you that people who live in the cold and omnipresent darkness of the northern hemisphere are more likely to become depressed and suicidal. However, genes are also involved. A study in Finland found that people who were suicidal had mutations in their serotonin receptors suggesting an inability to feel happy. And the drugs which are prescribed to people with depression usually work by stimulating serotonin receptors, or by slowing down the break-down of serotonin at synapses between neurons, so that what little is there, can work better for longer.

Don’t worry B happy

Coincidentally the earliest chefs in many cultures also appear to have been innovative neurochemists. Its no coincidence that whether you’re celebrating the end of Ramadan with cheese and dates, or indulging in turkey dinners over Christmas, or eating Fucku Mame (happiness beans) to celebrate spring in Japan, you are also eating foods which have extra-ordinarily high levels of tryptophan, the chemical which serotonin is made of. Tryptophan is an essential nutrient in that your body cannot make it and needs to eat certain beans, proteins and vegetables to get it. In your gut, the absorbance of tryptophan in your gut from protein rich foods is helped by the presence of B vitamins Unexpectedly many B vitamins are actually made by friendly bacteria in your gut, although not many people would credit bacteria as the key to their happiness.

If you’re sick stay home!

When you’re sick, friends and co-workers will usually tell you to stay home. They’re not the only ones. Your body will also tell you to stay home, using an ancient sickness reflex. If you infect mice with bacteria or viruses to mimic an infection, you find that the mice display a reproducible phenomena also found in monkeys and men which is known as “sickness behavior”. This means that they become anti-social, they move around less, and begin to lose weight. Sickness behavior also is associated reduced levels of serotonin, the happy neurotransmitter. Thus the desire to stay home when you’re sick is actually thought to be an evolutionarily conserved response designed to keep you safe from predators when you are ill. Therefore, even though being depressed and a little anti-social is uncomfortable, in some ways it is your body’s way to keep you safe. Whether your job will be safe from predators after days at home is a different issue!

Learning to feel

If you watch children playing, you’ll see that they’re highly emotionally charged creatures quick to laugh and smile and even quicker to throw a tantrum when things

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don’t go their way. You may wonder why it is, apart from the odd racket throwing incident by tennis players, that older people don’t play in the same way. Why it is that as we grow older we stop being submissive to our primary emotional demands. One theory suggests that it’s only at the age of 10-12 years that children start to be able to see things from other people’s point of view, and understand the consequences of their actions. They develop the ability to have ideas and understand the world more completely- known by the snappy title of hypo-thetico-deductive reasoning. So as we get older we start to learn that if we do start shouting at people because they take too long in the queue at the shop, its less likely to hurry them up and more likely to annoy them. Having a greater store of experiences and emotionally tagged memories means that we’ve a greater reserve of information to plough through before we have an emotional reaction. This is probably why children are more emotional than adults — not that they feel more strongly but perhaps they think a little less.

The thinking heart

Veronica Miller has a doctorate in neurobiology from Newcastle University, a Masters in Science Communication from DCU and a degree in Biochemistry from TCD. Previously she worked on “Scope” a popular science TV series for teenagers. Currently Veronica is working in the Wadsworth Center, New York State Department of Health laboratories, researching how environmental toxins contribute to risk of disease from womb to tomb, with a focus on autism, Parkinson’s disease and dementia.

Young boys and girls at Lucan, Co Dublin. Photo series: Tom Kennedy, Source Archives.

Love hate fear anger and happiness all are processed in the brain in brain areas that physiologists can stimulate and emulate responses from. And yet, when we remember happy thoughts, or sad events our hearts are generally the first to start letting us feel- either heavy hearted or light hearted. We know that the heart receives information from the brain via the brainstem, telling it to beat more quickly or to slow down. But this doesn’t necessarily tell us why the heart is so important when it comes to emotion and feeling. We also know that the pattern of innervation from

the brain to the heart changes over a person’s lifetime; different chemicals are used to transmit messages from infancy to adulthood. On the heart there are several clusters of neurons which act as the heart’s own neural regulator. This neural regulation, which receives input from the brainstem increases in size, like branches of a tree as you get older, changing in the areas that it touches and the chemical intensity of the signals transmitted to the heart telling it to beat more quickly or slowly. It would be tempting to suggest that our emotional responses could be wired into our hearts and simple memories of emotional responses could trigger heart felt responses, but this area still remains uncertain. What we do know is that experience can both colour and control our emotional expression, dysfunction in the areas that transmit and store our emotions results in too much or too little of an emotional repertoire. Our ability to learn and remember, to use our intellect for not only purely logical but also emotional responses is therefore a fundamental part of what makes us human. Unsuccessful job seekers will have long ago learned to hate IQ and aptitude tests, which may be why the idea of Emotional IQ tests is beginning to become popular. Love or hate it our IQ is important, and then next chapter will tell us why some have greater IQs than others and how you can improve your own.

Collect the series as Veronica Miller continues to go deeper into our amazing brain.

In our next issue — what’s behind better memory and intelligence? SCIENCE SPIN Issue 41 Page 19


SPIN ACTIVE Restoring confidence

In addressing the Engineering Ireland conference, Dr Chris Horn, co-founder of Iona Technologies, said that arrogant incompetence has resulted in a loss of confidence in government and professions. However, as he added, failures should not stop us from rebuilding a more robust economy. “As a result of the failures in our society and in our systems, many of the public are disillusioned and frankly apprehensive about the future. Professionals in many disciplines, from banking, to medicine to the religious

have been damaged by scandals. There are many investigations to be had, many fingers to be pointed and many lessons to be learnt. But life must go on too,” he said. “This time the rebuilding must be done within a framework of systems, within processes and with robust regulation.” Dr Horn, the current President of Engineers Ireland, said that engineers have a vital role to play in economic recovery as innovators. Incompetence has caused a lot of damage, but as he warned, Ireland cannot afford to lag behind emerging countries. “Emerging countries are no longer just doing

Dr Michael Walsh and Prof Tim McGloughlin, UL researchers with a model of the Prolong AV Graft

Better graft

ONE of the problems with insertion of medical devices is that they can have a limited life. People requiring regular dialysis, due to kidney failure, are fitted with a special graft, through which arterial blood is drawn off for treatment before return to a vein. Many of these graft devices have a functioning life of under two years, necessiting repeat surgery. Researchers at the Materials and Surface Science Institute at the University of Limerick examined the problem, and in collaboration with surgeons, came up with an improved design. Dr Michael Walsh, who led the project, said the new design eliminates a long standing problem caused by the growth of micro-organisms blocking the flow. Until now, the devices in use disrupted the flow of blood, and a better understanding of the haemodynamics involved, revealed that this was a problem that could be eliminated by changing the design. The team have patented the Prolong AV Graft, and it is expected to be popular in a global market estimated to be worth $300 million a year. The design, described by the researchers as non-intuitive, involves splitting the flow of blood so that the returning streams create self-correcting eddies, reducing the shear and friction that give rise to the blockages. Prof Pierce Grace, consultant vascular surgeon at the Mid-Western Regional Hospital said that once the novel device has proven its worth in dialysis, the same approach may be of benefit in peripheral bypass surgery. Restoring blood flow can, he said, make all the difference between recovery and amputation. SPIN ACTIVE

things cheaply. They’re also embracing a spirit of ingenuity and creativity. They’re innovating too by re-designing products and making commercial breakthroughs in everything from health-care to telecommunications. The BRIC (Brazil-Russia-India-China) countries are actually streamlining and improving whole business processes to achieve results even more effectively than competitors like Ireland in developed countries. Consequently, we have to innovate if we are to compete and win. Engineers are the epitome of this creativity and ingenuity and will underpin this.”

Power from grass

AT a recent conference the Environmental Research Institute at University College Cork presented a case for harvesting of biomethane. According to the Institute the abundance of grassland in Ireland constitutes an untapped source of energy. Perennial grass required little input, yet anaerobic digestion could produce a high yield of biomethane fuel. The Biofueld Research Group at the ERI has calculated that 200 anarobic digestors, costing about €7m each, could displace seven per cent of the natural gas in the national grid. Apart from providing farmers with a good income, home grown gas would help reduce dependence on imported fuels.

Education Ireland

IRELANDis being promoted as a destination for international students. Under the branding, Education Ireland, state agencies are aiming to attract more students from overseas. According to a report from Enterprise Ireland, international students are now worth up to €430m a year to the economy, and the number at postgraduate level are on the rise. 23 per cen are studying at post-graduate level, and of these 8 per cent, over 2,000, are taking PhDs. Students come from 159 different countries, one third from Europe, and 17 per cent from the US.


SPIN ACTIVE

Detecting cancer

eARLY detection of the saucer-like polyps that indicate the onset of bowel cancer has become possible using technology developed at dCU. Software tools developed by dCU researchers can highlight these polyps from a Ct scan as a 3d image. Until now, early detection of these tell-tale polyps has been difficult to achieve.

Maria Johnston, operations manager at dCU’s innovation centre, invent, remarking that “we are very excited about this development,” said that the technology has now been licenced out to Biotronics, a medical imaging company. the computer aided detection technology was developed at dCU’s image Processing and Analysis centre, and it offers a more advanced alternative to traditional endoscopic procedures. the detection, done from

Energy research centre

United technologies Corporation, an American multinational, is to conduct research at the recently launched international energy Centre at tyndall national institute in Cork. United technologies is investing €15m and funding, totalling about €35m, is also coming from Science Foundation ireland, the Higher education Authority, enterprise ireland, and the industrial developent Authority. Prof Roger Whatmore, CeO of tyndall, said the combined support is giving the new centre the critial mass to attract researchers and develop internationally recognised expertise in the field of integrated energy systems.

Community enterprise

SinCe the launch in 1989 over €61m in support has been given to 134 community enterprise centres throughbout the country. the Community enterprise Scheme involves a partnership between enterprise ireland and local communities, and the aim is to provide start-ups with a local base. One of the most recently centres, at Kilmallock, Co Limerick, is to make three new 2500 sq ft enterprise units and office space available to firms.

Power from waste

BY the end of this year a new treatment plant at Slane, Co Westmeath, will be converting 250,000 tonnes of black bin waste into fuel and compost. the Panda Waste plant, representing a private investment of €21 million, is to produce a coal substitute for use in making cement, compost for agriculture, and power which will be fed into the national grid. According to the company, recovery of high calorific material from black bin waste will be used to generate 1.3 MW of electrical power. the company, with a turnover of about €50 million a year, employs more than 200 servicing 60,000 domestic and 3,000 commercial customers. SPIN ACTIVE

a non-invasive Ct scan, gives faster and more accurate results. Maria Johnston said that dCU has become a world leader in image processing, and further collaboraqtion with industry will follow. the latest results are the result of HRB and SFi supported research led by Prof Paul Whelan working with clinicians, dr Helen Fenlon and dr Padraic Mac Mathuna.

Cameras for space

A CAMeRA, designed to monitor active galaxies at high speed in two colours has been successfully tested at the Kingsland Observatory, Co Roscommon. the dual photometer, known as tophicam, was developed by eamonn Ansboro of Space exploration with support from Cork institute of technology. Funding from Science Foundation ireland was used to build two cameras at Andor technology in northern ireland. dr nial Smith, head of research at Cork institute of technology, welcomed the fact that the whole project, from design and testing, could be done in ireland. “this is a first for ireland,” he said. the advance in camera design is expected to reveal more about a class of active galaxies known as blazars. Active galaxies emit great gets of gamma rays, and in the case of blazars, these jets are most prominent because they point towards earth. the intensity of these jets vary over a timescale ranging from just minutes to days, and one of the objectives is to determine why these variations occur. LIVE www.kingslandobservatory.com LINK


SPIN ACTIVE Recycling tyres

A DunDAlk company, Crum Rubber, was presented with a Green Entrepreneur Award for success in reducing Ireland’s waste tyre level. The company, established in 2003, collects and converts discarded tyres into a range of rubber matting products. These are widely used now in agriculture, sports, recreation and childcare locations, and the company, which employs 23, is planning to expand into exports.

Engineering students Raymond Carley, from Killiney, Sam Hajim, from Clonskeagh and Fionan O’Sullivan, from Dun Laoghaire pictured at UCD Belfield ahead of the Siemens RoboRugby.

Spin offs

Robotic rugby

lAST year 35 companies were set up to commercialise research results from third level colleges. According to the Technology Transfer Office this number is up from just ten the year before. The rise has been attributed to support provided through the Technology Transfer Strengthening Initiative. Set up by Enterprise Ireland in 2007 the iniative led to the establishment of technology transfer offices in ten third level institutions. Dr John Scanlan from nuI Maynooth, said that the latest figures prove the economic value of supporting university based research. “In the current business climate, the commercialisation of research from our universities can make an essential contribution to economic recovery, and these figures are proof of that,” he said.

Future enterprise

A ThREE year ‘Enterprise of the Future’ project has been launched by the Digital Research Institute at nuI Galway with the support of Cisco. The aim of the project is to make information more accessible to staff in organisations. At present, information is usually stored in documents, emails, scans and other formats. DERI’s search and integration technology is to be used to bring all this information together. DERI, based at nuI Galway, was founded in 2003 to develop the next generation of Internet technology.

www.deri.ie LIVE LINK

ROBOTS created by uCD students competed to win the Siemens sponsored RoboRugby Challenge at Belfield. The 19 robots were constructed by first year students of engineering. Brian Mulkeen from the uCD School of Electrical, Electronic and Mechanical Engineering, said that “between designing, building and programming their miniature robots, they have all picked up new skills, including teamwork, that have a much wider application.” Siemens, employing about 1,000 in Ireland, has been supporting the competition for the past six years.

Fingerprinting

uSInG technology developed at nuI Galway, a spin-out company, Analyse IQ, has launched a product that can identify the molecular constituents in complex mixtures. The company uses innovative software to analyse spectrocopic data, produced by scattering of laser light from the molecules in gas, liquids or solutions. The company has signed partnership deals with the manufacturers of spectroscopy instruments, such as Ocean Optics in the uS. Analyze IQ was established in 2008 after five years of collaboration between experts in spectroscopic technology, software, and machine learning. The company founder, Dr Michael Madden, said that the software was developed to facilitate the rapid but accurate analysis of complex mixtures, such as those found in drugs. In law enforcement, for example, the molecular fingerprinting can provide law enforcement personnel with valuable information on where the drugs came from. According to Dr Madden, who worked on the project while a lecturer in engineering and informatics, the technique used in the new product is more accurate than standard chemometric-based approaches.

Smarter cities

IBM is locating a smarter city technology centre in Dublin. With support from the IDA, a team of up to 200 people will focus on better integration of urban services and facilities. Traditionally, essential services in areas such as transport, water and energy, have been managed by separate systems, but with developments such as advanced modelling, better integration could be achieved. In collaboration with IBM, Dublin city is to become the test bed for new tecnology. Michael Daly, IBM’s general manager for Ireland, said that this development reflects the company’s willingness to evolve and meet changing demands. “In today’s rapidly changing world, no company can afford to stand still. IBM has been in Ireland since 1956 and, continues to evolve its presence in Ireland towards higher value, knowledge intensive activity” he said. SPIN ACTIVE


Hamilton Institute

H

ave you ever been talking in a group, and started speaking at the same moment as someone else? You stop, pause and excuse yourself. After that one of you will talk first, and the other will wait politely. Of course, no one waits for too long, to avoid an awkward silence in the conversation. Wireless communications can work in a similar way. When you use WiFi on your laptop, iPhone or other gadget, then transmissions should happen one at a time. The WiFi system uses a similar rule for polite conversation, where people pause for a random amount of time before they transmit, to give other people a chance to talk. Similar to a real conversation, there is a trade off between how long transmitters wait and how efficient the network is: if you pause for too long, the conversation moves slowly; if you don’t pause enough, then people keep jumping in at the same time. WiFi is one of the things that we study at the Hamilton Institute. You could take a guess about how long to pause for in a WiFi network. However, if you can understand what is happening theoretically, then you can say exactly how long to pause for to get the best performance from your network. Our aim is to use mathematical analysis that tells us how to understand, improve and design networks. Using the right theoretical tools lets us say how a system must behave. The nice thing about mathematical theories is that they are ‘reusable’. The algebra that you learned in school works well regardless of whether it is applied to physics, economics, electronics or any subject. At the Hamilton Institute, there are people working on problems in areas such as Communications Networks, Biology, Automotive Design and Robotics. The one thing we have in common is that we use mathematics to understand our problems. Recently, over a polite conversation at lunch, people from the biology and networks group were chatting about how some anti-HIV drugs worked. We discovered that the mathematical approach that had been used while studying wireless networks was the same approach that was needed to understand the action of the anti-HIV drug! In drug therapy, though, one does want to be as impolite as possible when interfering with the viral infection.

Another problem tackled by the network team at the Hamilton Institute relates to TCP, the protocol that is used to carry most of traffic across the Internet. One of the things that TCP does is control how fast data is sent into the network, so that the network is not overwhelmed. While traditional TCP works quite well on slower networks, people had spotted that it would have problems moving data over long distances and very fast networks. This was an important problem to solve, as many scientists now need to move huge amounts of data between research groups (one example is the data produced at the Large Hadron Collider in CERN). When the Hamilton team began working on the problem, there were several proposals on the table for how to improve TCP. By building mathematical models of how TCP works, the team was able to understand why particular problems arose with some of the proposals. More importantly, the mathematics also showed how these problems could be fixed. Hamilton’s version of TCP is now available as a part of Linux, and the mathematical tools used to design it are still being used to improve the design of TCP. The mathematics used includes linear algebra, probability theory and control theory, which we also use to understand how cars make their way through cities. At the Hamilton Institute we have a mix of projects covering both the development of advanced mathematical tools and how these tools can be used to solve real-world problems in ICT and biology. Projects at the Hamilton Institute are supported by funding from Science Foundation Ireland, the Higher Education Authority, Enterprise Ireland, the European Union and industrial companies, particularly from the ICT and pharmacy sectors. Making advances in applied research projects is driven by our advances in basic research. This is our recipe for success at the Hamilton Institute, and we believe that a successful research landscape in Ireland equally benefits from the right mix of theoretical and applied research. For more details: http://www.hamilton.nuim.ie/ http://research.nuim.ie/

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LIVE LINK


DIT comes together

A

fter years of planning, all six Dublin Institute of Technology colleges are to come together on one big site. In the biggest single development for higher education in Ireland yet, construction of a brand new campus is already underway at Grangegorman. This enormous 78 acre area is one of the last sites available for a development of this size in Dublin, yet the vast majority of people did not even know of its existence. As a former mental institution, the extensive grounds of Grangegorman were hidden behind high walls. Out of sight, out of mind, and even today there is just one modest entrance from a narrow and not very accessible street.

Tom Kennedy reports that the move to Grangegorman is the biggest single development ever for higher education in Ireland. For more than a decade, the Dublin Institute of Technology (DIT) has been planning to make this move, and now, at last, the green light has been given. At a recent meeting, held appropriately in one of the old, and soon to be demolished halls, the DIT head of campus planning, Noel O’Connor, said that work on site is to begin immediately. The overall plan, he said, involves a fairly rapid ramping up of developments in which activities, currently spread over 39 separate locations, are brought together into a single campus setting. SPIN ACTIVE

The move is big, and expensive, but as Noel points out, the plan is cost effective, and the benefits will be enormus. At present, most of the properties occupied by the DIT colleges are in need of refurbishment, some because they are not up to health and safety standards. Bringing these buildings up to an acceptable standard could actually cost more than the move to Grangegorman, and, besides, it would be a waste of money. The student population is on the rise, and Noel explained that the capacity of DIT to deliver on education is severely constrained by fragmentation of infrastructure. Each college, for example, has a canteen, and a library, and there are multiple exam halls,


SPIN ACTIVE yet they are all part of DIT. Obviously there is scope there for rationalisation, but as Noel explained, some of the problems go well beyond simple bean counting accountancy. Not alone are student numbers expected to rise by 40 per cent by 2020, but more of them will go on into industry related research. “Research, development and innovation activities,” said Noel, “are central to DIT’s mission.” This is the stage where knowledge is converted into wealth, and at present it is not as easy at it could be to bring in industrial partners. In a campus setting, stragegic partners could be accommodated on site, and, pointing out that there could be a lot more room for interaction with industry, Noel said that the present industry park on East Wall, although physically distant from any of the colleges, is already full. The 15,000 sq metre industry park is run by the Bolton Trust, which also provides start-ups with financial support. Since 2001 DIT has been running a Hothouse Ventre Programme for budding entrepreneurs. This has produced an impressive list of spin-offs, including Trezur, Amartus, Automation Intellect, Crosswins.com, ig cast, Cicero Networks, Movidia, Arconics, Grapevine Mobile, Grip Communications, GameStop, Nostra Systems, Garvivo, Enerfina, Centron System Solutionhs, Blutech, DataKraft, and Cora Systems. Providing this growing crop of innovators with more and better space, and resources that they could share with the college, would make a lot of sense, and, according to the planners, some of these developments could actually be self-funding. The fact that Grangegorman is in an area where unemployment is high means that the local impact of campus innovation could have additional significance. In surveying the surrounding area, planners were able to identify over 1,000 companies, most of them small, employing five people or less. Noel said these firms are going to be prime targets for programmes of college support and knowledge transfer. Government approval was critical for giving the transfer the go-ahead, but as Noel explained, sixty per

cent of the funding is coming from DIT itself. DIT is committing itself to raise €298 million from disposal of property, savings, sports funds, and philanthropic donations, and the 40 per cent balance, €194 million, is to come from the State either directly or via private public partnerships. Just

A great deal of work behind the scenes went on to make this move a reality, and while there are a number of stakeholders, the overall plan was drawn up by a US company, Moore Rubel Yudel, working with Irish partners, Duffy, Mitchell O’Donoghue (DMOD). Once the overall plan had been completed, and approved, DIT swung into action. Site preparation had already begun. Some of the Victorian buildings are of considerable architectural merit, and these will be spared as features, but there are unlikely to be any regrets when all other reminders of the past are swept away. SPIN ACTIVE

how successful DIT will be in raising money remains to be seen, but at least expenditure will be ramped up in relatively easy stages, €8 million this year, €11 million in 2011, and €13 million in 2010. The planners argue that the State is getting a very good deal because some of the expenditure will come back fairly quickly through VAT on construction, and the construction industry will also benefit from the anticipated generation of 450 jobs a year for the next ten years. If all goes to plan, up to 1,000 people will continue to work on in full-time jobs. In five years time 70 per cent of DIT is to be on site, and the plan, in many senses, is to break down the walls. The academic library is to be shared with a public Dublin City branch library, there are to be shops, and the educate together primary school on site is to be expanded to facilitate 400 pupils. The planners talk about retaining leafy green fingers running through the grounds, and the old classical façade of Broadstone is to take on a new lease of life. The Luas Red line already comes close, and a new Green Line is to be extended into the campus. For generations, Grangegorman was a most unhappy place, and like our prisons, more likely to a cause rather than a cure distress in the unfortunate inmates. Fortunately, this shameful era, at least in Grangegorman, was brought to an end, and instead of the stern and


SPIN ACTIVE unforgiving facades, new purposebuilt facilities are to be constructed on part of the site, and these will provide primary health care for the local community. Good for the community, good for the health authorities, and good for the college. Noel said that DIT will share clinical practice areas with the health authorities for education and training. An Optometry Centre is already part of the package, and there are plans to set up an Environmental Health Research Centre. With 22,000 students and 2,000 staff, shops, a theatre, sports grounds and who knows how many high-tech start ups on site, Grangegorman will have a huge positive impact on an area that was badly in need of a lift.

Kevin Street, founded in 1887, is the oldest of the six colleges. Formerly under the Dublin City Vocational Committee, the colleges were merged in the Dublin Institute of Technology in 1992. Alltogether, the six colleges constitute one of the largest providers of third level education in the country across a wide range of disciplines. The colleges are: Kevin Street, College of Music in Chatham Row, College of Commerce in Rathmines, College of Marketing and Design in Mountjoy Square, College of Technology in Bolton Street, and the College of Catering in Cathal Brugha Street.

How the World Bank sees Ireland’s wealth, a view that puts knowledge way ahead of natural resources.

Intellectual

CAPITAL

OVER the past few years, thousands of scientists have been added to Ireland’s population, and DIT’s move to Grangegorman is just one of the steps being taken to bring more people into higher education. Prof Paddy Cunningham, the Government’s Scientific Adviser, said that in spite of the need to keep a tight

reign on spending, the investment in education is well worthwhile. Ireland’s real wealth, he said, is not in land and property, but in knowledge. Poor countries, he added, can be rich in natural resources, but without knowledge, those resources cannot be put to good use. We often think as the land as wealth, but, as Prof Cunningham remarked, the World Bank would put this down to about three percent, way below the actual value of intellectual property. Many of the world’s poorest countries are high in resources, but low in intellectual reserves. In terms of intellectual resources, said Prof Cunningham, Ireland is actually well off, and becoming more so. “Compared to other OECD states,” he said, “Ireland’s growth in intellectual capital has been about 60 per cent faster,” and economically, this is having a significant impact. If we leave aside the reckless banking, the knowledge-based growth has been enormous. We have gone from simple low-skill assembly into advanced SPIN ACTIVE

manufacturing, and internationally traded service exports have been growing fast. Prof Cunningham said that when times are hard, as they are now, every cent of public spending has to be justified, but even so, Ireland’s investment in its future is surprisingly low. If we take public spending to be €60 billion a year, three quarters of that immediately becomes, as Prof Cunningham put it, “eaten bread.” Of the other quarter, 12 per cent goes in to the ‘hard stuff’ such as roads, 13 per cent goes into general education, and, even though spending on science has gone from €300 million to almost €1 billion, just one per cent is left over to invest in knowledge for the future. Given that growth is going to come from this knowledge, Prof Cunningham made the point that we should continue to increase, rather than decrease this spending. The students of today will be the wealth generating graduates of tomorrow, and, as Prof Cunningham commented, “in hard times you need seed corn to survive.”


communicating research outcomes to a broader audience. In effect, news about science is often locked into closed rings of specialists, and Martin said that breaking out of this ring and raising the profile of what’s going on in science would produce great benefits. Before people in business or industry can apply science they must first understand what the results mean for them.

Street life, Paris. Tom Kennedy. Source Archive.

One fit for all

Read all about it The huge increase in funding for science in Ireland has not been matched by a corresponding rise in media attention. Tom Kennedy reports that research institions would like to get a better press.

Why bother?

Before taking up his post as Government Scientific Adviser, Professor Paddy Cunningham had a long and distinguished career, and a one time he was director of research at Teagasc. Speaking on the subject of communications at a recent joint HEA-IRCSET event, he recalled how he encouraged staff to publish their results in peer review journals. More often than not, the response was “why should we?” Many of the researchers argued that it was far more important for them to communicate directly with farmers, because these were the people who needed to apply the results.

Such an argument, said Prof Cunningham, was short sighted, because without publication, good results will not get recognition and scientific approval. Citations, he said, reinforce that approval. Prof Cunningham’s point about recognition raises an issue that there is no single all-embracing channel for scientific communications. In taking up this point, Martin Hynes, director of IRCSET remarked that compared to other channels, peerto-peer communication, although it is within a closed group, is very effective. “Those who want hard facts,” he said, “know where to look,” but the same cannot be said of success in

SCIENCE SPIN Issue 41 Page 27

Peter Greene, one of the leading lights of Alpha Galileo, an international news release service, said that it is important to realise that there are many different audiences. All too often, a press release is aimed at everyone and at the same time at no one group in particular. A single release, he said, is often not the most effective way to get a message across, because different people want to know different things. Scientists need to become better at presenting their findings to the world, and to illustrate this point Peter said that in the 90s, if you had asked the average person in Britain about the British space programme, they might have responded ‘what programme?’, yet they would have known all about NASA. One of Peter’s aims in setting up the Alpha Galileo service was to change that distorted perception, and make science more accessible to the media, so that, for example, French news could get into British papers, and German news into Peruvian papers. “If we can’t do that,” he said, “we have to give way to the Americans who are very good at this, and they will fill our newspapers.” Thousands of journalists have signed up for the daily news alerts from the Alpha Galileo service, and as Peter pointed out, Irish institutions could take advantage of this to boost the export of their releases. News about research results has to be presented in a way that people can relate to, and in the case of newspapers, Cathering Murphy from the Irish Independent, said that some of the language used in scientific releases can be quite obscure, if not actually misleading. As she recalled from one such release, she first thought that the word‘theraupatic candidate’ referred to a person, and then, after checking, realised that what was being referred to was, in fact, a drug.


In newspapers editorial content has to make sense to readers. In The Irish Independent, said Catherine, coverage of science focuses on the likely impact on readers. Scientists might consider their findings important, but it’s the stories with a unusual or entertaining angle that makes readers stop and wonder ‘what’s that?’ that are more likely to get into print A good eye-catching picture, said Catherine, can make all the difference in making a story stand out, and Dick Ahlstrom from The Irish Times, agreed. As he explained, the the stories that appear in print are those that have managed to survive editorial selection, and last minute changes are part of newspaper life. Pictures, he said, are hugely important. In getting through the selection process, a good picture will be accepted much faster, and with much less bother, than the story itself. Although getting into print involves some element of luck, Dick made the point that the researchers themselves must help make this happen, and indeed, they have an obligation to explain what they are doing. In Dick’s view, the public have a right to know how their money is being spent. In thinking about outlets, science journalist and broadcaster, Mary Mulvihill said that scientists should not just confine themselves to print. Radio, she said, is a powerful medium, so when institutions issue releases, they should try to include a contact for someone who is willing to be interviewed on air. There are lots of radio outlets now around the country, she said, and as with print, “the pictures are important.” Her advice is to give a story some emotional colour, and as people in radio often say, ‘the pictures on radio are better than on television.’

Branding

EUCHARIA Meehan who heads research programmes at the Higher Education Authority said that many scientists do not appreciate how important it is to acknowledge the source of their funding. Ommitting credits, she said, can have serious consequences. Failure to mention where funds come from, she explained, can result in cuts, and to explain why, she said that agencies, such as the HEA, have an ongoing obligation to report on how the money is being

spent. The funders, such as the European Commission, regularly review these reports, and if credits are not given, funding can be withdrawn due to lack of compliance. As Eucharia explained, this might not seem all that important to researchers, but it is actually a serious problem. What happens, she said, is that when someone in the Commission asks for the reports, they see no mention of the support, so the agency involved simply gets crossed off the list.

Casting seeds on barren ground

PEOPLE involved in research often wonder why relatively little news about what they are doing gets into print yet we are being constantly reminded that science is important. As journalists at the meeting pointed out, there are often good reasons why releases are not picked up by the press. The language can be obscure, the content might not mean much to readers, but as this writer pointed out, one of the main barriers that scientists have to overcome has little to do with the quality of content, or indeed journalistic independence. Science stories have to compete for space, and space is expensive. It might come as a big surprise to most readers to learn that the price they pay at the newsagent may not even cover the cost of printing. Publishers are engaged in a constant tussel to get the balance right between attention grabbing news, editorial features to keep the readers happy, and the commercial content. How that balance is struck depends on the publisher, but even the most serious broadsheets have to watch the bottom line, and they know that reader interest alone will not keep them in business. We see proof of that in the number of recent lay-offs, due entirely to decline in income, and not at all to a decline in circulation. A science story may be very good for content, but more often than not, it will not grab enough attention to make the cover, and it will almost certainly earn no advertising income. A health care story, or a feature on travel may not be as good in quality of content, but it is much more likely to be attractive to a hard pressed editor because, even if not written with this in mind, it can be used as bait to attract advertising support. As this writer noted, this, far from ideal situation, seriously limits the capacity of publications to absorb news about science. That’s the bad news. For the good news, we could look at the rapid rise in electronic media, and many of the world’s journalists are beginning to think that this is where their futures might lie.

Some guidelines from Science Spin l Get the essentials into the first para. That grabs the attention of an editor or journalist and shows that the rest of the story is worth looking at. l Make the story relevant to nonspecialists. If possible link the story to something familiar. l Branding and acknowledgement of funding may be of vital importance to you, but keep in mind that those sort of details can bore the reader and kill a good story. l If possible include a good image. Not a dreary line up of grinning white

coats or handing over the cheque, but an informal action photo of a researcher actually doing something. l Think of going on air. Talk about your research on local radio. l Understand who your audience is, and your audience will understand you. l Don’t expect a single release to cover all the possibilities. Are you looking for local, national, or international coverage? l Inclusion of some quotable quotes can be helpful, but make them real and

SCIENCE SPIN Issue 41 Page 28

avoid the tired old politically correct cliches. l Don’t expect to get sign off. Most journalists will check back on accuracy of facts that they are not sure of, and the last thing they want is for someone else telling them how to write a story. l When a release is issued it is important to give a contact. The researcher should be available to answer questions.


Calling all scientists! Speaking Science One Day Workshop Communications training Just for you!

What is it? Speaking Science is an intensive one day communications training workshop for scientists and it aims to help you to tell your stories. If you need to explain what you are doing or if you need talk to the press, this is the course for you. Who should attend? This course is aimed at staff scientists based in academia, public bodies or industry and 4th level students, MSc and PhD candidates who need to develop a wide range of career development skills. The ability to communicate clearly is one of the most important of these skills. Who presents it? Seán Duke, Joint Editor, Science Spin magazine. Seán has fifteen years experience as a science writer and editor. He is also the creator and presenter of Ireland’s only weekly radio science slot on 103.2 Dublin City FM. Seán began the Speaking Science initiative in 2008 in response to the need for scientists to acquire better communication skills. Until now Speaking Science has only been available as an in-house course. When is it on? Tuesday 21st September 2010. Book early as there is limited availability on each date. Time: 9.00 am to 5.30 pm. Venue: Terenure Enterprise Centre, Terenure, Dublin 6. Cost: €195 per course.

ow Book n e for th r be Septem e cours

More information: To book a place simply email Alan Doherty at alan@sciencespin.com choosing either the June or September date.

l Speaking Science can also be held on your own premises for groups up to ten

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Atlantic Corridor hosts Scientists from Mesa Biotech Academy

Arizona Scientists visit schools in the Midlands AtlAntiC Corridor hosted 12 biotechnology lecturers and students from Arizona last week and facilitated visits to 9 national Schools in the Midlands to promote applied science teaching in schools. the group was led by an American Scientist, Xan Simonson and she has brought biomedical and genomics research to the high-school classroom in her home State of Arizona. She oversees the biotechnology program for Mesa Public Schools as the coordinator of the Biotechnology Academy at Mesa High School and manages the programs at the districts four other high schools. A former CSi who is now an applied biology teacher, Simonson has a grant to develop a national model to train teachers and help them implement genomic research techniques in the United States. Her work including her study visit to ireland is funded by a variety of public and private sources, including strong links with the biosciences sector in Arizona. the visitors wowed the irish students and teachers with their hands on approach to the teaching of science in schools.the students were shown how to extract dnA from their saliva using simple tools and their dnA was then put into mini test tubes and attached to a necklace to bring home as souvenirs. they were also shown how to make dnA bracelets with all of the beads and tools required, provided by the scientists. the Arizona crew also brought over a mini ‘discover Garden’ for the students. they collected moss and other organisms from a recent field trip to lough Boora and had the students replant them into their little pots and gave them the tools to make sure they grow and develop. Jackie Gorman CEo Atlantic Corridor said “these workshops proved invaluable for both teachers and students alike which will add immense value to their delivery of the Primary School Science Curriculum. Her success in Arizona in creating interest in science has been acknowledged in her own State of Arizona and at a national level. We were delighted with the opportunity to host the Xan Simonson and her crew of lecturers and students from Arizona in the irish Midlands. the continued development and promotion of science in children at a young age is necessary to nurture and develop future leaders in research and innovation in this country.”

Karen Cunningham, Projects Executive, Atlantic Corridor pictured with students at Clonown National School during the Mesa Biotech Workshop.

Cllr tony McCormack, President tullamore Chamber, attended one of the workshops and he was impressed with what he saw. Cllr McCormack said “i would like to congratulate Atlantic Corridor on this great initiative. it was great to see the interactive activities with the kids getting stuck into the projects and working with the scientists and developing their science skills. the dnA example was an excellent way to demonstrate to children how practical science is as a subject.” Mayor of Athlone Cllr Mark Cooney attended a workshop in Clonown national School, a small primary school on the outskirts of Athlone. Cllr Cooney said “it was a privilege to be part of the tour visit to Athlone and to see the interactive science activities with the kids getting stuck into the projects and working with the scientists and developing their science skills. the dnA example was an excellent way to demonstrate to children how practical science is as a subject. the group of scientists were a lovely bunch of people and the children thoroughly enjoyed the experience.” this is the second time that Atlantic Corridor has hosted a visit for the Mesa Biotech Academy, in 2008 they undertook classes in Secondary Schools in the Midlands as part of the Atlantic Science Conference 2008. the importance of this work was acknowledged by Atlantic Corridor Chairperson John Flanagan “science, technology, innovation – these subject areas are the key skills that are needed now and in the future to develop our economy and our society. it is wonderful that Atlantic Corridor has provided access for schools in our region to international best practice from Arizona.”

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Xan Simonson, Mesa Biotech Academy with President of Tullamore Chamber of Commerce Cllr Tony McCormack and Jackie Gorman, CEO, Atlantic Corridor.


Listeria monocytogenes and the

battle for Iron Gold is for the mistress -- silver for the maid -Copper for the craftsman cunning at his trade. “Good!” said the Baron, sitting in his hall, “But Iron -- Cold Iron -- is master of them all.” Rudyard Kipling – Cold Iron.

Heather Mclaughlin, winner of the UCC Science for all competition and runner up in Science Speak, explains how a harmful bacterium can steal our iron. ron is an essential element for the survival and reproduction of most bacteria and plays an import role during infection. Bacteria, such as Listeria monocytogenes, require iron to cause infection, and the body tries to prevent this infection by holding onto its iron very tightly. Because iron is vital for all living cells, including both human host cells and the invading Listeria, the stage is set for a biological war between invader and defender, with iron the prize for the victor. Listeria monocytogenes is responsible for the disease, listeriosis, which is caused by eating foods contaminated with the bacterium. In healthy individuals symptoms are usually mild, but in people with compromised

I

immune systems (e.g. pregnant women, newborns, the elderly or individuals with pre-existing illness), listeriosis can cause meningitis, sepsis, miscarriage or even death. Due to its high mortality rate and its link to food, Listeria monocytogenes has been recognized as a significant public health problem. Listeria monocytogenes is ubiquitous in nature, and is found in healthy humans, farm animals and the environment. It is a hardy bacterium and it has proven very difficult to control and completely eliminate the bacterium from the food chain. Upon ingesting contaminated food, Listeria is introduced into the gastrointestinal tract, but then quickly crosses the

Heather McLaughlin

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intestinal wall to infect the blood and the immune system. Listeria monocytogenes is a unique bacterium in that it can survive in a wide range of diverse niches such as soil, food, and blood. Through evolution, Listeria has developed strategies for coping with stresses encountered in the environment as well as in the host. One of the most significant challenges faced by the bacterium occurs during infection, when it has to battle with the host for a precious resource - iron! Iron is one of the most abundant elements on earth, and it is involved in several essential biological processes including DNA synthesis and oxygen transport. The amount of iron in bacteria and in our bodies must be tightly controlled, as too little iron can prevent normal growth and reproduction and too much iron can be toxic. Under normal circumstances, as food enters our digestive tracts, a protein called transferrin is released, binding ingested iron and transporting it to cells where it is then stored with the protein ferritin. The bodies’ largest supply of iron is found in the blood tightly bound to the protein hemoglobin, which allows for oxygen transport. By using these proteins that can bind iron with high affinity, our bodies can protect against both iron toxicity and infection caused by most invaders. Unfortunately for us, over many thousands of years, Listeria has evolved the ability to recognize transferrin, ferritin, and hemoglobin and extract iron from these protein sources. This tactic gives Listeria a significant advantage in the biological battle for iron, since it can essentially ‘hijack’ the bodies’ own defense mechanism to meet its own needs for this vital element. We have been interested in this phenomenon for several years in our laboratory located in the Microbiology Department and the Alimentary Pharmabiotic Centre in University College Cork. Using a computer based approach, previous laboratory members identified a gene in Listeria monocytogenes that could make a protein which is potentially required for the acquisition of iron. The aim of my work was to investigate the role this gene plays in iron acquisition and in infection. I created a mutant strain of Listeria in which this iron gene is deleted (and a ‘complemented’ mutant strain in which the gene has


been re-inserted). Interestingly, the mutant strain, lacking this iron gene, showed a growth defect in low-iron environments and a very much reduced ability to cause infection when compared to the parent strain of Listeria monocytogenes. While this research has been vital in helping us to understand the role of this gene and in highlighting the importance of this gene and of iron to the Listeria infective process, it has also introduced an interesting possibility which we are currently exploring. Could we use the mutant Listeria to create a vaccine delivery system? Vaccines are often preparations of weakened or inactive microbes that are used to ’kick-start’ our immune system by exposing it to a harmless version of the pathogen. For example, exposing the immune system to an inactivated polio virus can protect us against future attacks. This is because all bacteria and viruses have unique cell-surface proteins and carbohydrates, called antigens. Inside our bodies specialised immune cells recognize these antigens and deploy other immune cells to kill these foreign microbes. The immune system also

The iron thief, Listeria monocytogenes. creates a ‘memory’ of these antigens so that it can mount a rapid response in the event of a second attack. Our Listeria monocytogenes iron mutant would potentially serve as a good vaccine candidate as it can survive inside the body and present specific Listeria antigens to our immune cells without the risk of developing a fullblown infection. The mutant could not only provide immunity to Listeria monocytogenes infections, but could also serve as a platform for delivery of other antigens. For example, if we expressed antigens from viruses such as HIV which causes AIDS, or

the human papillomavirus which can cause cancer, on the surface of our mutant strain, we could use it to provide protection against a range of deadly human diseases. Our initial vaccine trials have shown promising results, as mice given two booster shots using our iron mutant were not infected, but were completely protected against subsequent infection with the parent strain of Listeria monocytogenes. Our work shows that by understanding the basic mechanisms by which Listeria acquires iron in the body, we can not only learn how to ultimately control and prevent listeriosis - but we could also take advantage of this dangerous bacterium to create vaccines which could help to conquer a range of other diseases. Heather McLaughlin, supervised by Dr Cormac Gahan and Prof Colin Hill is conducting Science Foundation Ireland supported research at the Alimentary Pharmabiotic Centre and Dept of Microbiology at University College Cork.

Flying fossil

JAW bones from a giant flying reptile have been unearthed in North Africa. The bones were found during an expedition led by Nizar Ibrahim, a PhD student from UCD. This is another significant find for the scientist who we featured in a previous issue of Science Spin for his work highlighting the great diversity of life that once existed before a lush landscape was covered by dry sand. The jaw bone was found in three pieces, and as Nizar explained, they were uncrushed, despite the fact that they had been buried for 65 million years. Nizar said the lance-like lower jaw with no teeth would have been somewhat similar to a modern heron. A partial neck vertebra found nearby is thought to have belonged to the same animal, and piecing them together, Nizar said the wing span could have been about six metres. As other finds, including some by Nizar, show, the landscape was inhabited by giants.

Reporting his find in the journal PLoS ONE, Nizar said the pterodactyl had been named Alanqua saharica in reference to the Arabic, Al Anqu, the mythological flying creature that died in a fire only to be reborn from the ashes. Although hot, dry, and bare, a great river bed ran through the Sahara, and this flying reptile came from a highly diversified environment. As

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Nizar explained, Pterosaur bones are relatively rare compared to other larger animals because their bones were light and flimsy. Like birds of today, or indeed aeroplanes, excess baggage makes it harder to take off. Above: Artist’s impression of Alanqa saharica by Davide Bonadonna.


The first synthetic cell Dr Roy Sleator tells the story of Mycoplasma mycoides JCVI-syn1.0 – the first self replicating synthetic bacterial cell.

erhaps best known as the genomics pioneer who defied all the odds to decode the book of life and publish its contents years ahead of the government funded Human Genome Project’s projected completion date; J. Craig Venter has done it again – this time in the nascent field of synthetic biology. In the May issue of Sciencexpress, Venter (an associate editor on BioBugs) and colleagues (including John Glass – also a member of the BioBugs editorial board) reported the design, synthesis and assembly of Mycoplasma mycoides JCVI-syn1.0 1 – the first bacterial cell to contain a completely synthetic genome, and as such the first citizen of synthetic biology. The story which led to the development of JCVI-syn1.0 has its origins as far back as 1995, when Venter and his team published the sequence of Mycoplasma genitalium 2. A pathogen isolated from the epithelia of primate genital and respiratory tracts; M. genitalium possesses one of the smallest genomes of any free-living organism and, as such, represented the perfect target for this research. Of the 485 genes encoded by the ~600,000 bp M. genitalium genome, approximately 100 were found to be non-essential – suggesting a minimal genome size of ~400 genes. To confirm that this did, in fact, constitute the minimum requirement for life, Venter and co-workers first had to synthesise

P

bp — base pairs

DNA is made up of base pairs, in which nucleotides are joined by a hydrogen bond. In DNA, A (adenine) pairs up with T (thymine), and G (guainine) with C (cytosine). Genome length is usually measured in terms of bp, base pairs.

the minimal genome, and then transplant it into a recipient cell to ‘boot-up’– two steps which had never before been achieved in the laboratory. The first breakthrough came in 2007, when the team finally cracked the chromosomal transplantation step 3. By replacing the genome of the bacterium Mycoplasma capricolum with the native chromosome of a different species of Mycoplasma (M. mycoides), Venter and colleagues had, in essence, changed one species of bacteria into another. Proof that the transplantation was a success was achieved when the recipient cell (M. capricolum) began to adopt the physical characteristics of its chromosomal donor (M. mycoides). The final hurdle, the chromosomal synthesis step, was overcome the following year with the publication of a paper entitled “complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome” 4. When all the essential elements were in place Venter and his team

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set out to to create the first synthetic life-form. However, the slow growth rate of the target organism M. genitalium (which has a doubling time of 16 hours) meant that a single experiment could take several weeks to complete and so, despite its tiny genome, M. genitalium was replaced with the larger (in DNA terms) but faster growing M. mycoides. The genome assembly process consisted of a painstaking assembly of 1,078 sequence ’sets‘, known as cassettes, each of 1,080 bp in length. An 80 bp overlap in adjacent cassettes, facilitating correctly orientated sequence assembly. The assembly was done in yeast cells, the DNA being put together in stages. The first stage involved taking 10 cassettes at a time to build 110, 10,000 bp segments. In the second stage, these 10,000 bp segments were taken 10 at a time to produce eleven, 100,000 bp segments. In the final step, all 11, 100 kb segments were assembled into a complete synthetic genome, and propagated as a single artificial chromosome. The complete synthetic M. mycoides genome was then isolated from the yeast cell and transplanted into M. capricolum recipient cells. Because these recipient cells were, what is termed, restriction deficient, they could accept the synthetic DNA without breaking it down. Following uptake, the synthetic genome began to encode all the proteins required for life. These proteins included restriction enzymes that then proceeded to break down, and effectively remove, the native M. capricolum genome.

Cassettes

A gene cassette is a transferable sequence of DNA that codes for one or more genes.


Dr J. Craig Venter, and Hamilton O. Smith. Right, the research team. Following transplantation and replication on a nutrient agar plate these cells formed a colony. These synthetic cells did not contain any of the proteins that were present in the original recipient cell, so, in essence the DNA ‘software’ had built its own ‘hardware’. To distinguish the synthetic genome from native DNA, the researchers incorporated four ‘watermark’ sequences to serve as markers. These were inserted into regions of DNA that are not essential in maintaining viability, so modifying these sequences would not adversely affect the cell. Apart from serving as useful markers, the researchers also inserted a bit of humour. Decode the string of bases, and you can send an email to declare your success. There are also the names of 48 authors and key contributors, as well as three famous quotations. One of these, from James Joyce, perfectly encapsulates the ups and downs of a the 15 year project - “To live, to err, to fall, to triumph, to recreate life out of life.” At a cost of about $40 million, and countless man hours, Venter and his team have achieved the unimaginable – they have created (or perhaps more correctly ‘recreated’) life from scratch; converting a digitized DNA sequence, stored in a computer file, into a living entity capable of growth and self replication. The next step will undoubtedly be to return to the minimum genome of M. genitalium – the ideal platform for analyzing the function of every essential gene in a cell, and from there;

Synthesis

Each DNA cassette was chemically synthesised from scratch by a specialised company, Blue Heron. This has great significance because it demonstrates that a functioning genome can be manufactured and this can take over the control of living, replicating cells. As many commentators put it, one of the parents of JCVI-syn1.0 was a computer. The researchers are not claiming to have created life, but that they have succeeded in reprogramming cells using synthetic DNA. Ultimately it could become possible to design and manufacture independent living cells completely from data held on computer. who knows? Perhaps the creation of completely artificial life forms – an upgrade to JCVI-syn2.0 — entirely new species designed for specific roles from biodegradation to biomedicine … the possibilities are endless. However, the ethical, legal and social implications of this new science cannot be ignored, and in a passage reminiscent of that famous understatement from Watson and Crick’s double helix paper of 19535 “it has not escaped our notice…”; Venter and colleagues conclude that “this work will continue to raise philosophical issues that have broad societal and ethical implications.” Indeed, it will.

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References

1. Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, et al. “Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome.” Science 2010. 2. Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, et al. “The minimal gene complement of Mycoplasma genitalium.” Science 1995; 270:397-403. 3. Lartigue C, Glass JI, Alperovich N, Pieper R, Parmar PP, Hutchison CA, 3rd, et al. “Genome transplantation in bacteria: changing one species to another.” Science 2007; 317:632-8. 4. Gibson DG, Benders GA, AndrewsPfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, et al. “Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome.” Science 2008; 319:1215-20. 5. Watson JD, Crick FH. “Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid.” Nature 1953; 171:737-8. Dr Roy D. Sleator is a lecturer at the Department of Biological Sciences, Cork Institute of Technology. Dr Sleator is also Founding Editor-in-Chief of the scientific journal Bioengineered Bugs on which J. Craig Venter, the lead scientist in the creation of the first self replicating bacterial cell, is an associate editor. http://www. landesbioscience.com/journals/biobugs/


The mines of Killarney

Killarney lakeside. Photo: Tom Kennedy, Source Archives.

Thousands of years ago the mine site would have been a hive of activity.

Better known now for the picture postcard views, the lakesides of Killarney were once a big attraction for prospectors in search of copper. Tom Kennedy reports that copper was being already produced in Killarney long before the discovery of bronze. lthough Killarney may well be Ireland’s best known destination, the lakes surrounded by extensive forests of mature oaks may as well be a million miles away from the touristy bustle of the town. Along the

a

forest trails all but the birds and the rustling breeze through the leaves are quiet. Bluebells and white wild garlic bloom in the dappled shade. Peaceful and pleasant, but in a way this is an idealised environment, and it has been

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so for generations. The recent row that saw jarvies banned from the extensive Muckross House grounds is just one end of a cleaning up process that began early in the 19th century with the closure of mines beside Lough Laune at Ross Island. Whatever about the poor old nags, who do what horses must do, digging holes into the landscape was a much more serious issue, and as a visitor from 1828 complained, the character of the place was being ruined by “the roar of engines, the din of hammers, and the thunder of explosives.” Landowners and their visitors valued their peace and romantic views, so the miners were banished, mine buildings were demolished, trees planted, and traces of the industry that had once brought wealth into the area were landscaped into the pools and hollows that we see today.


It might come as a surprise to most visitors that the peace and quiet by Lough Laune is relatively new, and in fact, Ross Island was originally the centre of an ancient industrial revolution. Four thousand years ago, dense clouds of acrid smoke would have billowed out from fires blazing against exposed workings, and instead

of birdsong, there would have been the constant thump thump of rock tools smashing into lumps of heat loosened ore. Much of the copper that went into ancient axe heads, not just in Ireland, but in Britain, came from Ross Island, making this one of the oldest known mines in these islands.

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Excavations

The mining activities of the 18th century were well known, but in the 1990s it became clear that some of the traces were much older. Excavation by archaeologists from NUI Galway revealed that mining at Ross Island had begun around about the time that metals first came into use in Ireland. In reporting on a decade of careful investigation, the archaeologist, William O’Brien, described how the workings had been extensive and highly organised. Ireland already had a Neolithic population when the knowledge that metals could be extracted from mineral bearing rocks filtered up from the south. More than likely, the resident population would have been familiar already with the distinctive stains of malachite and azurite, but with the arrival of new technology, those colours became a magnet for miners. To work the ore, miners relied on fire and Stone Age technology. At Ross Island, fires were lit against exposed faces, heating the rocks until


The Blue Pool, where copper was mined from an open cut.

they shattered, and it is assumed that quenching with cold water helped this process. The broken fragments were then smashed and the metal bearing ore sorted out. At Ross Island, thousands of stone cobble hammers, grooved for binding onto wooden handles, were found. William O’Brien also reported that other tools included shovels made from shoulder bones of cattle, and it is assumed that miners must have used leather and wooden implements. The excavation work camp at Ross Island, he said, provided more than a glimpse into the daily life of an ancient mining community. “The foundation traces of huts used by the miners have been identified, consisting of circular and sub-rectangular settings of stake-holes where walls once stood. Excavation here revealed animal bones, mostly of cattle and pig with some sheep, discarded by the miners after their meals. A small quantity of worked bone was found, as were flint artifacts, including arrowheads and scrapers. About 400 shards of small pottery vessels used as drinking cups by the miners were also recovered.�

A contemporary sketch of the 19th century workings housing a beam engine for pumping. Part of the dam, built to hold back lake water.


The discovery of a small ingot of copper at Knockkasarnet, near Killarney, supports the idea that some, or perhaps all, of the sorted ore concentrate was smelted on site in charcoal pit furnaces. If not smelted on site, the ore was certainly smelted locally, for the distinctive chemical signature of copper from this area shows up in an abundance of metal objects, most of which were found in Munster.

Industrial Revolution

While Killarney was part of the revolution that brought humanity out of the Neolithic and prepared them to enter the Bronze Age, it also contributed significantly to the 18th century industrial revolution. During that time thousands of tons of copper ore were extracted and sold on to smelters in Britain.

The copper folly

In 1761 minerals were discovered at Cahirnane, and the land owning Herbert family, encouraged by the extraction of a ton of ore from a trial shaft, took on a mining expert, Rudolf Raspe, to oversee expansion. What distinguishes this loss-making “copper folly” from all the other failed ventures is the involvement of Rudolf Raspe, mineralogist and author. Having fallen into debt, Raspe fled from his native Germany to England, where he worked as a mineral consultant. The Herbert family asked him to act as the consultant for Cahirmane, but within a year he died of scarlet fever, and although his grave is unmarked, he is remembered for his book, “The fabulous adventures of the Baron von Munchhaussen,” which he based on the tall tales told by a real character, who was, in fact, a baron. The adventures, such as riding on a cannonball, getting a wolf to draw his sledge, being sold

In the early 1750s copper ore, extracted from the Muckross peninsula, was being carted off along the Kenmare road for shipping to Bristol. Later, in 1757, another company, the Eastern Mine, was active, and in 1801 the mine was reopened with shafts reaching down 65 metres. Although this seems to have been a period of more intense activity, the 18th century miners were sometimes surprised to find that others had been there before them. The land-owning Brownes and Herbert families were keen to profit from the exploitation of any minerals discovered on their vast estates, and Ross Island was just one of a number of locations around Killarney where mines and rock quarries were opened. William O’Brien records that a John Asgill raised four tons of lead ore on Ross Island in as a slave, or going on a trip to the Moon, like all good tales, grew in the telling, and while Raspe may have done his share of embellishing, the baron himself may well have been repeating stories he had picked up in his extensive travels.

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1726, and a Joseph Bacon having taken up a lease in 1726, surrendered it in 1731. Advancing technology meant that speculators could dig deeper and further, but at enormous cost. Mining has always been a risky business, and in the 18th century it seems that for every company that went boom another one went bust. Metal prices, ore quality, and the cost of pumping made every operation as much a balancing act as betting on the horses. Between 1804 and 1810 it was reported that 3,200 tons of copper ore were extracted from Ross Island by Colonel Robert Hall. Shafts went down 16 metres, and tunnels branched out from these. By 1829 there were about 50 mine shafts in the area, and one open working, the Blue Hole, still remains as a deep water filled cleft by the lake shore. Colonel Hall, a military man, who had once commanded a regiment that included a number of Cornish miners, was responsible for initiating several mining ventures in Munster, and at Ross Island he had been granted a 31 year lease based on paying a royalty of one eighth on the value of ore raised. For a time, ease of open cut mining at the Blue Hole produced a good profit, but after running into financial problems, caused largely by the high cost of keeping mines dry, the mine was leased to William White in 1811, but just two years later he had to abandon it. At its height, in the early 19th century up to 500 were employed, and experienced miners were brought in from Wicklow, Wales and Cornwall. The scale and approach was industrial, but in one respect, there was no great change compared to the ancient practices of smash and grab. After crushing in the ‘bucking shed’, fragments of ore were picked out by hand In 1825 it was the turn of yet another company, the Hibernian Mining Company, to seek a fortune on


A cross section of the workings at Ross Island. Image: Geological Survey of Ireland.

Ross Island. In spite of getting expert advice and spending about £20,000 on extending the dam to hold back the lake and installing a powerful steam pump capable of drawing out 13 tons of water a minute, the company never managed to extract enough ore to make a profit. Time after time the miners were defeated by water, and the dam at Ross Island is one surviving indication of how hard they struggled to hold back the lake.

Ignorance

Mining companies were often accused of mismanagement, but lack of knowledge could be just as harmful. The geologist, Robert Kane, writing in 1845, described how one mine owner, through unwitting ignorance, lost a fortune. The owner’s concern, understandably, was to maximise the extraction of copper, so, as was normal, everything else that came out of his Muckross mine with the copper ore was simply discarded. As Kane wrote, in this spoil, “there was found in great profusion a mineral of a granulated metallic appearance.” One of the miners recognised this as a valuable mineral known as arseniuret of cobalt. Saying nothing, he managed to recover many tons of this mineral, and it seems that his employer never realised what was going on until it was too late. “Long afterwards,” write Kane, “a more candid miner, who visited the works and saw some specimens of it, told the proprietor its value.” However, the deposited had since been worked out, and as Kane concluded, “it only remained for the mine owner to ruminate on the furtune he might have made if he had possessed a proper knowledge of his business.”

Expelled

The miners had been expelled in 1829, but almost a century later they were back in the form of the Ross Island Mining Company. However, this was a short-lived revival, frustrated not so much by lack of minerals, as the same old problem, flooding from the lake. Even if that problem could be overcome, mining is unlikely ever to resume in Killarney, for this is now a national park and mineral exploration is prohibited, and visitors are even warned that it is against regulations to use geological hammers. Even so, the returns from mining heritage may well exceed anything earned from the minerals themselves and the local economy will continue to benefit for as long as walkers keep following the trail.

Copper rich

The Killarney lakes lie along the junction of Old Red Sandstone with the geologically more recent Lower Limestone of the Carboniferous period. The limestone formed as the old Devonian landscape began to sink under a shallow warm sea. Countless billions of marine organisms deposited the calcium carbonate that solidified into the

The discovery that metals could be extracted from ores spread slowly from the Near East, and that knowledge would have been carried up along the western trade routes. In Mesopotamia native copper had been

known for thousands of years, and by 5,000 BC Bulgarian and Serbian miners were smelting copper ore over beds of charcoal. A thousand years later a more technically demanding technique was being used in the Alps to convert copper sulphides into an oxide that could then be smelted in a charcoal furnace. According to Paul Bud, a specialist in archaeometallurgy from the University of Durham, the metal workers knew exactly what they were doing, and, writing in British Archaeology, he noted that they deliberately choose to include arsenic rich ores to produce harder objects of higher value. Knives and daggers were high in arsenic, but everyday objects contained less, “suggesting that arsenic quantities were being controlled.”

limestone rocks we see exposed along the lake shore. Long after these sedimentary rocks were formed, movement of the Earth’s plates pushed the horizontal beds into folds, and super-heated fluids carried dissolved minerals up through the numerous cracks and fissures. Prospectors were usually led to mineral rich veins by surface staining, and in Killarney the indications were

good enough for miners to dig in at Ross Island, the Muckross Peninsula, Crow Island, and Cahirnane. The biggest and most successful operations were at Ross Island and on the Muckross Peninsula. At Ross Island the copper is accompanied by some silver, which may once have added to the attraction. Minerals include chalcopyrite, CuFeS2, and tennantite, Cu12As4S12

Mineral staining on Ross Island rocks.

Arsenic copper

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Photo: Tom Kennedy, Source Archives.

One of the ancient mining sites at Ross Island. Another thousand years later, the miners at Ross Island in Ireland, clearly understood this process and the importance of blending. The ores of Killarney are mixed, with some having up to 30 per cent arsenic, yet the metals produced there were consistent in make up. Ores that were low in arsenic were topped up the addition or ores that had an excess of arsenic. This knowledge appears to have reached Ireland before Britain, for, as Paul Bud pointed out, flat axes of superior material suddenly appeared along the western coast of Munster in large numbers, matching similar finds in Spain and Portugal. Iberian settlers, known from their distinctive style of pottery as the Beaker People, found what they were looking for in Munster and brought their knowledge.

The same kind of flat axes have been found in England, Wales and Scotland, and Paul Bud reports that their chemical signature strongly suggests that they all came from Munster. They share the arsenic, Miners could dig deeper, but some tasks, such as hand-picking ore remained much the same.

References

antimony and silver traces that occur only in Ireland. “It seems reasonable,” he wrote in British Archaeology, “to conclude that these earlier British metal artefacts were indeed imports, not from the Continent, but from the mines of Munster.” Not that this situation could last. Within a few hundred years miners throughout Britain also knew all about blending, and if their copper was low in arsenic, they brought in a top up supply from elsewhere. Obviously there was a thriving trade in metals, and having mastered blending, the next step, adding tin, was almost a logical extension.

The Ross Island Project began at NUI Galway to investigate the history and archaeology of mining at Ross Island and Killarney. William O’Brien at University College Cork, who was then with the Department of Archaeology in NUI Galway is the author of “Bronze Age copper mining in Britain and Ireland”, and he also produced a short descriptive guide, “Ross Island and the mining heritage of Killarney”. The account of mining at Ross Island is also on an excellent web site: www.nuigalway.ie/ross_island LIVE LINK


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Science Spin 41