Why should public, private, and non-profit entities invest in research? Several reasons exist.
Firstly, research is key for our future. Research helps drive new knowledge that will improve the world. Society depends on research, across a wide range of disciplines, to strengthen our quality of life and sustain economic stability. By raising funds for University research the RIDT is surely not trying to reinvent the wheel. On the contrary, throughout Europe, the US and Asia public universities are enhancing their Government funding through various initiatives to sustain important research. Universities all across the globe appeal to public entities, private individuals and NGOs to fund research and invest in our society’s future.
Locally, we have just started scraping the surface of fundraising for research. Recently, the RIDT received a number of important donations which shall serve to continue fostering local research. In the first of its kind, we received €55,000 from local NGO ‘Action for Breast Cancer Foundation’ (ABCF), raised through the ALIVE Cycling Challenge. They are being used to launch a Ph.D. studentship in breast cancer research. The Lifecycle Foundation has also donated €70,000 towards kidney disease research. These NGOs have followed a stream of public and private entities, as well as students, who have been donating money for research for the last three years.
Secondly, don’t you want to be part of something bigger? You probably cannot find the cure for cancer yourself, but everyone can contribute to make that a possibility. As the University’s Research Trust, we do not only want to attract big corporate companies or NGOs to donate money, but we also want you — the students, the alumni, the professionals, the workers, the parents, to realise that donating for research is a noble cause. A recent Christmas campaign at the University of Malta that was spearheaded by KSU, the UoM staff and the Chaplaincy managed to raise €12,000 from students, staff, and academics on campus. A third of these funds were donated to the RIDT, which were devolved to the Department of Anatomy. They will be invested in specialised research projects focusing on specific strands of cancer, such as leukaemias, sarcomas, brain tumours, breast and colon cancer.
Research affects our day-to-day lives. Though research discoveries take time and need constant investment to benefit our society, we can come together as a Maltese community by investing in research for good causes. Ultimately, let us imagine a world where we have cured all major diseases, where we can move objects with our thoughts, and unravel the mysteries of the universe.Imagine, and let’s make it happen!
RIDT is the University’s Research Trust aimed towards fostering awareness and fundraising for high-calibre local research. We aim to achieve this by raising funds for various research projects undertaken at the University of Malta. Please visit www.ridt.eu to donate and our Facebook page on www.facebook.com/RIDTMalta for more information about our latest events and initiatives.
Made infamous by Sigmund Freud, the idea is that we spend one third of our lives dreaming about what we would like to do. Our rational brain suppresses these feelings.
On the other extreme, our brain is just as active in certain sleep stages. These neural firings express themselves in dreams. There are no deep hidden emotions behind them.
Somewhere in between lie recent studies that show that dreams are important in memory, learning and emotions. If you sleep without dreaming these qualities will suffer. For example, rat studies in 2001 showed how while dreaming they replayed solutions to mazes to commit them to their long-term memory.
Send your questions to think@um.edu.mt and we’ll find out if it’s the truth or just a fib!
In 2011 an IBM computer called Watson made the headlines after it won an American primetime television quiz called Jeopardy. Over three episodes the computer trounced two human contestants and won a million dollars.
Jeopardy taps into general world knowledge, with contestants being presented with ‘answers’ to which they have to find the right questions. For instance, one of the answers, in the category “Dialling for Dialects”, was: While Maltese borrows many words from Italian, it developed from a dialect of this Semitic language. To which Watson correctly replied with: What is Arabic?
Watson is a good example of state of the art technology that can perform intelligent data mining, sifting through huge databases of information to identify relevant nuggets. It manages to do so very efficiently by exploiting a grid architecture, which is a design that allows it to harness the power of several computer processors working in tandem.
“Maltese has been described as a language in danger of ‘digital extinction’”
This ability alone would not have been enough for it to win an American TV show watched by millions. Watson was so appealing because it used English as an American would.
Consider what it takes for a machine to understand the above query about Maltese. The TV presenter’s voice would cause the air to vibrate and hit the machine’s microphones. If Watson were human, the vibrations would jiggle the hairs inside his ear so that the brain would then chop up the component sounds and analyse them into words extremely rapidly. The problem for a computer is that there is more to language than just sounds and words. A human listener would need to do much more. For example, to figure out that ‘it’ in the question probably refers to ‘Maltese’ (rather than, say, ‘Italian’, which is possible though unlikely in this context). They would also need to figure out that ‘borrow’ is being used differently than when one says borrowing one’s sister’s car. After all, Maltese did not borrow words from Italian on a short-term basis. Clearly the correct interpretation of ‘borrow’ depends on the listener having identified the intended meaning of ‘Maltese’, namely, that it is a language. Watson was equipped with Automatic Speech Recognition technology to do exactly that.
To understand language any listener needs to go beyond mere sound. There are meanings and structures throughout all language levels. A human listener needs to go through them all before saying that they understood the message.
Watson was not just good at understanding; he was pretty good at speaking too. His answers were formulated in a crisp male voice that sounded quite natural, an excellent example of Text-to-Speech synthesis technology. In a fully-fledged human or machine communicating system, going from text to speech requires formulating the text of the message. The process could be thought of as the reverse of understanding, involving much the same levels of linguistic processing.
Machine: say ‘hello’ to Human
The above processes are all classified as Human Language Technology, which can be found in many devices. Human Language Technology can be found everywhere from Siri or Google Now in smart phones to a word processing program that can spell, check grammar, or translate.
Human-machine interaction relies on language to become seamless. The challenge for companies and universities is that, unlike artificial languages (such as those used to program computers or those developed by mathematicians), human languages are riddled with ambiguity. Many words and sentences have multiple meanings and the intended sense often depends on context and on our knowledge of the world. A second problem is that we do not all speak the same language.
Breaking through Maltese
Maltese has been described as a language in danger of ‘digital extinction’. This was the conclusion of a report by META-NET, a European consortium of research centres focusing on language technology. The main problem is a lack of Human Language Technology — resources like word processing programs that can correctly recognise Maltese.
Designing an intelligent computer system with a language ability is far easier in some languages than it is in others. English was the main language in which most of these technologies were developed. Since researchers can combine these ready-made software components instead of developing them themselves, it allows them to focus on larger challenges, such as winning a million dollars on a TV program. In the case of smaller languages, like Maltese, the basic building blocks are still being assembled.
Perhaps the most fundamental building block for any language system is linguistic data in a form that can be processed automatically by a machine. In Human Language Technology, the first step is usually to acquire a corpus, a large repository of text or speech, in the form of books, articles, recordings, or anything else that happens to be available in the correct form. Such repositories are exploited using machine-learning techniques, to help systems grasp how the language is typically used. To return to the Jeopardy example, there are now programs that can resolve pronouns such as ‘it’ to identify their antecedents, the element to which they refer. The program should identify that ‘it’ refers to Maltese.
For the Maltese language, researchers have developed a large text/speech repository, electronic lexicons (language’s inventory of its basic units of meaning), and related tools to analyse the language (available for free). Automatic tools exist to annotate this text with basic grammatical and structural information. These tools require a lot of manual work however, once in place, they allow for the development of sophisticated programs. The rest of this article will analyse some of the on-going research using these basic building blocks.
From Legalese to Pets
Many professions benefit from automating tasks using computers. Lawyers and notaries are the next professionals that might benefit from an ongoing project at the University of Malta. These experts draft contracts on a daily basis. For them, machine support is still largely limited to word processing, spell checking, and email services, with no support for a deeper analysis of the contracts they write and the identification of their potential legal consequences, partly through their interaction with other laws.
Contracts suffer from the same challenges when developing Human Language Technology resources. A saving grace is that they are written in ‘legalese’ that lessens some problems. Technology has advanced enough to allow the development of tools that analyse a text to enable extraction of information about the basic elements of contracts, leaving the professional free to analyse the deeper meaning of these contracts.
Deeper analysis is another big challenge in contract analysis. It is not restricted to just identifying the core ‘meaning’ or message, but needs to account the underlying reasoning behind legal norms. Such reasoning is different from traditional logic, since it talks about how things should be as opposed to how they are. Formal logical reasoning has a long history, but researchers are still trying to identify how one can think precisely about norms which affect definitions. Misunderstood definitions can land a person in jail.
Consider the following problem. What if a country legislates that: ‘Every year, every person must hand in Form A on 1st January, and Form B on 2nd January, unless stopped by officials.’ Exactly at midnight between the 1st and 2nd of January the police arrest John for not having handed in Form A. He is kept under arrest until the following day, when his case is heard in court. The prosecuting lawyer argues that John should be found guilty because, by not handing in Form A on 1st January he has violated the law. The defendant’s lawyer argues that, since John was under arrest throughout the 2nd of January he was being stopped by officials from handing in Form B, absolving him of part of his legal obligation. Hence, he is innocent. Who is right? If we were to analyse the text of the law logically, which version should be adopted? The logical reasoning behind legal documents can be complicated, which is precisely why tools are needed to support lawyers and notaries who draft such texts.
Figuring out legal documents might seem very different to what Watson was coping with. But there is an important link: both involve understanding natural language (normal every day language) for something, be it computer, robot, or software, to do something specific. Analysing contracts is different because the knowledge required involves reasoning. So we are trying to wed recent advances in Human Language Technology with advances in formal logical reasoning.
Illustration by Sonya Hallett
Contract drafting can be supported in many ways, from a simple cross-referencing facility, enabling an author to identify links between a contract and existing laws, to identifying conflicts within the legal text. Since contracts are written in a natural language, linguistic analysis is vital to properly analyse a text. For example in a rent contract when making a clause about keeping dogs there would need to be a cross-reference to legislation about pet ownership.
We (the authors) are developing tools that integrate with word processors to help lawyers or notaries draft contracts. Results are presented as recommendations rather than automated changes, keeping the lawyer or notary in control.
Robots ’R’ Us
So far we have only discussed how language is analysed and produced. Of course, humans are not simply language-producing engines; a large amount of human communication involves body language. We use gestures to enhance communication — for example, to point to things or mime actions as we speak — and facial expressions to show emotions. Watson may be very clever indeed, but is still a disembodied voice. Imagine taking it home to meet the parents.
“Robby the Robot from the 1956 film Forbidden Planet, refused to obey a human’s orders”
Robotics is forging strong links with Human Language Technology. Robots can provide bodies for disembodied sounds allowing them to communicate in a more human-like manner.
Robots have captured the public imagination since the beginning of science fiction. For example, Robby the Robot from the 1956 film Forbidden Planet, refused to obey a human’s orders, a key plot element. He disobeyed because they conflicted with ‘the three laws of robotics’, as laid down by Isaac Asimov in 1942. These imaginary robots look somewhat human-shaped and are not only anthropomorphic, but they think and even make value judgements.
Actual robots tend to be more mundane. Industry uses them to cut costs and improve reliability. For example, the Unimate Puma, which was designed in 1963, is a robotic arm used by General Motors to assemble cars.
The Unimate Puma 200
The Puma became popular because of its programmable memory, which allowed quick and cheap reconfiguration to handle different tasks. But the basic design was inflexible to unanticipated changes inevitably ending in failure. Current research is closing the gap between Robby and Puma.
Opinions may be divided on the exact nature of robots, but three main qualities define a robot: one, a physical body; two, capable of complex, autonomous actions; and three, able to communicate. Very roughly, advances in robotics push along these three highly intertwined axes.
At the UoM we are working on research that pushes forward all three, though it might take some time before we construct a Robby 2. We are developing languages for communicating with robots that are natural for humans to use, but are not as complex as natural languages like Maltese. Naturalness is a hard notion to pin down. But we can judge that one thing is more or less natural than another. For example, the language of logic is highly unnatural, while using a restricted form of Maltese would be more natural. It could be restricted in its vocabulary and grammar to make it easier for a robot to handle.
Take the language of a Lego EV3 Mindstorms robot and imagine a three-instruction program. The first would be to start its motors, the second to wait until light intensity drops to a specific amount, the third to stop. The reference to light intensity is not a natural way to communicate information to a robot. When we talk to people we are not expected to understand how the way we put our spoken words relates to their hardware. The program is telling the robot to: move forward until you reach a black line. Unlike the literal translation, this more natural version employs concepts at a much higher level and hence is accessible to anybody with a grasp of English.
The first step is to develop programs that translate commands spoken by people into underlying machine instructions understood by robots. These commands will typically describe complex physical actions that are carried out in physical space. Robots need to be equipped with the linguistic abilities necessary to understand these commands, so that we can tell a robot something like ‘when you reach the door near the table go through it’.
To develop a robot that can understand this command a team with a diverse skillset is needed. Language, translation, the robot’s design and movement, ability to move and AI (Artificial Intelligence) all need to work together. The robot must turn language into action. It must know that it needs to go through the door, not through the table, and that it should first perceive the door and then move through it. A problem arises if the door is closed so the robot must know what a door is used for, how to open and close it, and what the consequences are. For this it needs reasoning ability and the necessary physical coordination. Opening a door might seem simple, but it involves complex hand movements and just the right grip. Robots need to achieve complex behaviours and movements to operate in the real world.
The point is that a robot that can understand these commands is very different to the Puma. To build it we must first solve the problem of understanding the part of natural language dealing with spatially located tasks. In so doing the robot becomes a little bit more human.
A longer-term aim is to engage the robot in two-way conversation and have it report on its observations — as Princess Leia did with RT-D2 in Star Wars, if RT-D2 could speak.
Lego Mindstorms EV3 brick
Language for the World
Human Language Technologies are already changing the world. From automated announcements at airports, to smartphones that can speak back to us, to automatic translation on demand. Human Language Technologies help humans interact with machines and with each other. But the revolution has only just begun. We are beginning to see programs that link language with reasoning, and as robots become mentally and physically more adept the need to talk with them as partners will become ever more urgent. There are still a lot of hurdles to overcome.
To make the right advances, language experts will need to work with engineers and ICT experts. Then having won another million bucks on a TV show, a future Watson will get up, shake the host’s hand, and maybe give a cheeky wink to the camera.
Richard Feynman is my new idol. He’s hallucinated, he’s chatted up call girls, and he’s won a Nobel Prize. Realistically, I’ll probably only manage one of those achievements.
Surely you’re joking Mr Feynman!: Adventures of a Curious Character is as amazing a book as was Dick himself. He died of cancer in 1989, three years after the book was published.
The book is a great read and insight into his mind. It is compiled from a series of taped conversation that Feynman had with drumming partner Ralph Leighton. It haphazardly goes through his life from young radio mechanic to Professor at Caltech where he achieved most of his discoveries.
Throughout the book he randomly switches from girls, mathematics, academic life, to his adventures. This nicely sums up his life.
Take Brazil. He travelled there from Caltech during a sabbatical. There he learnt to play Samba music choosing the frigiderisa — a metal stick banged on a toy metal frying pan. ‘I practiced all the time. I’d walk along the beach […] practicing, practicing, practicing. I kept working on it, but I always felt inferior.‘ Insecurity that culminated in him walking down Brazil’s main streets, cars diverted, while his samba band made the streets dance.
“Once Feynman overcame his social awkwardness, he became a famous womaniser”
Feynman didn’t hold back his punches; if he didn’t agree with something he said it. He heavily criticised the Brazilian education system. ‘I tried to show them (students) how to solve problems by trial and error. […] I could never get them to ask […] questions.’ When surrounded by Brazil’s big shots, he said: ‘no science is being taught in Brazil. […] It’s amazing you don’t find many physicists in Brazil. Why is that?’ Magically, government listened.
Once Feynman overcame his social awkwardness, he became a famous womaniser. Girls crop up throughout most of the book. And he’s good. They would even buy him champagne and sandwiches. As most things in his life, he did it for fun and loved the game.
He writes a lot more about experiences with other women than with his three wives. His first wife’s death touched him deeply, however. ‘I didn’t cry until a couple of months later […] walking past a department store with dresses in the window.’ His other wives aren’t mentioned much.
Feynman also dabbled in drugs. He took ketamine, smoked marijuana, and might have taken LSD — denied in this book but suggested elsewhere.
He also had a short art career and managed to sell his paintings, though he lost his drive to paint by having a solo exhibition too early in his art career.
Another highlight of the book is Feynman’s colourful descriptions of the Manhattan Project that made the first atomic bomb, including how he lock-picked the project’s secrets. He also mentions his great discoveries but is incredibly humble and dismissive about his Nobel Prize — too much hassle. He beautifully describes how he came to his findings and his nervousness when meeting Einstein and Pauli.
Feynman’s genius and eccentricity is clear throughout the book. It will have you in fits. He went on all fours to sniff the world to see how much better dogs can sniff than us — apparently, not much. Life was his game, and boy did he play well.
It was a cold and grey February afternoon. Snowflakes were pelting the dreaming spires of Oxford. This gloomy weather did nothing to impede the warmth and buzz exuding from the laboratories crammed in the iconic Sherrington building. Less than a century earlier, this labyrinthine edifice was the habitat of Sir Charles Sherrington whose experiments shaped our understanding of the ‘synapse’ or the minute gaps between one brain cell (neuron) and another. The Sherrington building (part of the Department of Physiology, Anatomy, and Genetics at Oxford University) has undergone several expansions over the years. In its newest wing, nowadays it houses the research group of Dr Ji-Long Liu, a rising star in the field of genetics and cell biology.
For me, this was no ordinary afternoon. Together with Liu’s lab teammates, I was perched on a stereomicroscope whilst holding a delicate brush in my hands. On one side was a tray jammed with vials populated with fruit flies and the usual good strong cuppa. Fruit flies are no house flies: each adult fly is only a few millimetres long, their beautiful bodies are pale with black zebra-like stripes and their eyes a bright apple-red colour. I grabbed a vial, fired a puff of carbon dioxide gas through its fluffy plug and then firmly rapped the upended vial to shake its sleepy occupants onto an illuminated pad. I took a deep breath before peering at them through the eyepieces.
At the time, I was more than mid-way through my doctoral studies, and the results of my experiments were far from extraordinary. I was researching the most common genetic killer of human infants, a neuromuscular degenerative disease known as spinal muscular atrophy or SMA in short. I was exploiting the tiny fruit fly to gain new insight into this catastrophic disease.
I decided to up my efforts by generating a series of mutants or faults in Gemin3, the gene that I was investigating. I was targeting these mutants to different organs such as brain, muscle, or gut. The results of this screen were due today. With a few flicks, I deftly flipped and sorted the minuscule fly bodies into neat piles taking note of differences that are invisible to the untrained eye. The mutants did not produce any dramatic effect. Damn! Another experiment down the drain! Frustrated by the result, I mistakenly knocked over a vial, dislodging its plug. Usually, released flies would happily escape by flying. Strangely, my flies were jumping as if attempting flight but just couldn’t make it into the air — an unexpected but interesting trait or phenotype. I checked the tag on the vial. In these flies the mutant was targeted to that part of the body that powers movement, the so-called ‘motor unit’. Following that afternoon, which will remain forever etched in my memory, the results just flowed in and a few months down the line I would find myself donning my subfusc (Oxford-speak for academic dress) to defend my doctorate.
Fly Superstar
The rise to biological stardom for the fruit fly, scientifically known as Drosophila melanogaster, began in 1907 when my great-great-grandfather (by academic lineage) Thomas Hunt Morgan adopted this organism to understand heredity or genetics. Morgan was the first to harness the major advantages of working with this organism: they have an insatiable sexual appetite and a speedy development (only 10 days) from embryo to adult. This means that large-scale experiments are doable in record time. Morgan’s infamous ‘Fly Room’ at Columbia University in New York set the stage for a new ‘religion’ practiced and preached across the globe.
Morgan spent years searching unsuccessfully for flies with clear, heritable differences so that he could investigate how they are inherited. A breakthrough happened in April 1910 when he discovered his first mutant, a white-eyed male fly amongst many red-eyed flies. Morgan took great care of this special fly: he kept it in a bottle and after a day’s lab work he used to take it home! At the same time his wife Lilian, who also became a famous geneticist, gave birth to a child. And such was the excitement surrounding Morgan’s discovery that on his first visit to the hospital, Morgan’s wife said: ‘How’s the fly?’ To which, Morgan replied: ‘How’s the baby?’.
When the white-eyed fly was bred or crossed with a virgin red-eyed female, their offspring were all red-eyed. When sisters and brothers were crossed, half of the male progeny gained back their white-eye colour. This hereditary pattern is typical for a sex-linked (recessive) variation, since the gene for eye colour in Drosophila, named by Morgan as the white gene, is on the X chromosome which determines sex. Similar to us, male flies are XY whereas females are XX. This key experiment and numerous others that followed expanded on the knowledge gained through the ingenious cross-breeding experiments of pea plants by the Austrian monk Gregor Mendel half a century earlier. Importantly, this fly-based work found that characteristics like eye colour are inherited from parents through chromosomes — large structures which package DNA in our cells. Furthermore, Morgan and his gifted students uncovered that the thousands of genes in our genome are arranged along chromosomes in a precise order, like beads in a necklace. Each gene can be identified by its specific location on a chromosome.
“Flies could be used as models of human disease”
In 1933, Morgan won the Nobel Prize for these great discoveries. The first of six awards was to recognise seminal insights into our biology through this tiny fly. Hence, in 1946 one of Morgan’s protégés, Hermann Muller, was recognised for his fly research demonstrating that X-rays can damage chromosomes. Then in 1995, Ed Lewis, Christiane Nüsslein-Volhard, and Eric Wieschaus shared the Nobel Prize for their herculean efforts in discovering the genes that controlled early development in Drosophila. In the embryo, waves of master genes are triggered that lead to eyes, brains, and the body’s patterning. Similar genes were later found in humans doing the same function. In 2011 Jules Hoffman received the Nobel Prize for finding how the body’s inbuilt immunity works through the use of the fly model organism. I suspect that there is still room for more trophies in the fly triumph cabinet.
At the dawn of this century, the genomics revolution led to the complete DNA sequencing of an organism including fly and human. These monumental projects revealed that an astonishing number (more than two-thirds) of human genes involved in disease have counterparts in the fly. This development meant that flies could be used as models of human disease. It sparked off a renaissance of Drosophila research. The fly was good at modelling neuro-degenerative conditions because their nervous system has stunning similarities to ours. Neuro-degenerative diseases including Alzheimer’s, Parkinson’s, Huntington’s, and Motor Neuron Disease occur when neurons in the brain and spinal cord begin to die slowly. Patients may lose their ability to function independently or think clearly. Symptoms progressively worsen and ultimately, many die. Most neuro-degenerative diseases strike later in life, so we should expect their frequency to soar as our population ages — Alzheimer’s disease may triple in the US alone by 2050.
Malta: the right time to fly?
Together with my students in my lab at the University of Malta I am working with flies to learn more about neuro-degenerative disease. We continue to focus on SMA, a genetic disorder arising from the deterioration of motor neurons which are nerves that communicate with and control voluntary muscles. As the motor neurons die, the muscles weaken with drastic effect on the walking, crawling, breathing, swallowing, and head and neck control of unfortunate children afflicted by this condition. The child’s intellectual capacity is unaffected but vulnerability to pneumonia and respiratory failure means that many patients die a few years after diagnosis.
The underlying cause of SMA is usually a gene flaw that results in low levels of a protein called SMN for survival of motor neurons. Inside cells, SMN is bound to other proteins called Gemins. The SMN-Gemins alliance is involved in building the spliceosome, which is the chief editor of messenger RNA molecules. Messenger RNA carry the DNA code that instruct cells how to fabricate proteins. If SMN is absent spliceosomes do not form, correctly-edited messenger RNA are not produced and protein synthesis is heavily disrupted — the cell should shut down. Spliceosomes are required in each of the 120 trillion cells forming our body. Yet, in the disease SMA only motor neurons die. The reason has baffled researchers for decades and remains unsolved.
Is it possible that SMN has another function in motor neurons? And does it act alone? Our flies were crucial in providing some answers to these questions. Our work showed how the SMN-Gemins family is tightly-knit. In this regard, we recently demonstrated that both SMN and Gemins can be detected in prominent spherical specks in different cellular compartments. Within the cytoplasm, these organelles are known as U bodies because they probably are the factories of spliceosome components, which themselves are rich in the chemical Uridine. In the nucleus, the structures containing the SMN-Gemins family hug the mysterious Cajal bodies — discovered over a century ago by Spanish Nobel laureate Santiago Ramón y Cajal.
“We are feeding these flies the Mediterranean diet derivatives to see whether Alzheimer’s can be stopped in flies, which will bring us one step closer to treating it in humans”
And what about the flightless flies? Think about it. Considering that SMA is a neuromuscular disease, it makes perfect sense that on loss of SMN, muscles become so weak that flies are unable to flap their tiny wings fast enough to fly. Our latest work reveals that flightlessness is seen in flies without enough Gemin proteins. This means that SMN does not function alone but hand in hand with the Gemins. Our next step was to find out the pathway connecting the SMN-Gemins family to the motor defects. We linked the Gemin mutant which did not work properly to a tag called green fluorescent protein or GFP. GFP glows under the right light in cells. We managed to create genetically-modified flies with this modified gene — a first for Malta and a powerful tool to solve the mysteries of this disease.
Fluorescent proteins let researchers figure out a protein’s location. And by knowing the location of proteins we gain of lot of information about what they do. Consider this analogy with a VIP. If we tagged the Prime Minister of Malta we would find that he is most probably found in Valletta most time of the year. If we were aliens from another planet, this knowledge would allow us to refine our understanding of the Prime Minister’s function. Therefore, we can eliminate a function in the entertainment industry (weak signal from Paceville) but we cannot exclude a function in government (strong signal from Valletta). Likewise, we found that our GFP-Gemin mutant is mostly found in the cell’s nucleus. The nucleus houses life’s instruction manual: DNA. Our work now needs to zero in on the other proteins the SMN-Gemins family works with in the nucleus. Doing so will open new therapies to halt neuro-degeneration in children. Back to our analogy, we need to zoom in on Valletta until Auberge de Castille, the Prime Minister’s office, is clearly in focus.
Several neuro-degenerative diseases occur because of sticky protein clumps that wreak havoc inside, and outside, neurons. This is typical in Alzheimer’s disease, Parkinson’s disease and Motor Neuron Disease. With Dr Neville Vassallo’s research group, and local industry (Institute of Cellular Pharmacology), we are testing chemical derivatives of the Mediterranean diet and flora on fruit flies to see whether they can curb the protein clumps’ toxicity. They definitely do in a test tube. Flies mutated to be remarkably similar to human Alzheimer’s lose their ability to climb up the sides of their vial habitats and die prematurely because of neuro-degeneration. We are feeding these flies the Mediterranean diet derivatives to see whether Alzheimer’s can be stopped in flies, which will bring us one step closer to treating it in humans.
Through flies we have understood human biology. Apart from choosing Mr and Mrs Right, a good geneticist must learn to focus and listen to what flies are really saying. This is easier said than done but achievable. Flies have spurred me to pursue unexpected but interesting paths. In the years to come I, together with my students, will continue to flip, sort, screen and tag, looking for fly mutants who will continue to teach us about ourselves. And yes, we will be all ears!
The author is indebted to colleagues at the UoM and worldwide for their constant support and inspiration. The research of Dr Ruben Cauchi (Department of Physiology & Biochemistry, UoM) is funded by the Faculty of Medicine and Surgery, the University of Malta Research Fund and the Malta Council for Science & Technology (MCST) through the National R&I Programme 2012 (Project R&I-2012-066). For more about Dr Cauchi’s research click here.
Public cord blood banking is recommendable. Local authorities should consider setting up a national bank once the use increases, making it more cost effective. Hopefully this can happen within a few years.Continue reading
Not a 50 hour-long blockbuster, not a 30 second casual game: Attack of The Friday Monsters is an experiment with a new, middle-sized format. The game presents a day in the life of an 8 year old kid. The oneiric, nostalgic storyline is a masterfully paced intense adventure that feels just right.
Downloadable from the Nintendo 3DS eShop, the game is set in a ‘70s Japanese town, where our hero Sohta and his family just moved in. Told from the kid’s perspective, the events are open to interpretation: apparently, Godzilla-like monsters attack every Friday. On the same day, a TV show also packed with monsters is produced and aired in town. What is the secret behind these attacks? And is there a connection between fact and fiction?
Don’t expect to engage in massive monster fights in Attack of The Friday Monsters. The game focuses on talking with villagers, meeting new friends, and strolling in a beautiful countryside town. It really makes you feel like a kid again encouraging a relaxed kind of roleplay.
At €7.99, Attack of The Friday Monsters proves that digital downloads can be a great way to introduce audiences to new formats and concepts. It introduces a poetical take on games.
Unlikely, for the next 100 years. Academics and sci-fi writers take three rough approaches. We will become one with the bots by integrating computers into our body achieving the next stage of evolution. Or, robots will become so powerful so quickly that we’ll become their slaves, helpless to stop them — think the Matrix. Or, robots have certain technological hurdles that will take ages to overcome.
Let’s analyse those hurdles. Computing power: no problem. Manufacturing expense: no problem. Artificial intelligence: could take decades, but we are already mapping and replicating the human brain through computers. Energy: very difficult to power such energy-hungry devices in a mobile way; battery or portable energy generation has a long way to go. The desire to enslave humanity: would require Asmiov’s trick or a mad computer scientist to programme it into the bot’s code. Conclusion: unlikely, sleep easy tonight.
David K. Randall woke up on his back, his leg bent at an awkward angle, in excruciating pain. To figure out why, he wrote a book about the science of sleep. Clever. Clever doubles as a nice summary of the book.
Another book summary: sleep rules your life. Get a good night’s sleep or else everything suffers: your creativity, memory, attitude, ability to think straight, control your emotions, react to emergencies, sex life, and work. Lack of sleep has cost lives; to sleep is to live.
An extreme statement but Randall holds a very good argument. Zlatko Glusica, an Air India pilot, woke up just before landing and tried to bring a plane down safely with a sluggish brain whose higher brain functions were down. In this state we might talk to lamps, Glusica instead killed himself and 157 others. Lack of sleep and truck drivers are another bad idea, while battles have been lost because of sleep. Sleep prevents disasters.
“Randall covers an immense range of research and topics. This is where the book’s problems start. He did a lot of research and wants us to know that.”
The book is well researched. Randall fires factoid after research study at the reader in a pleasant easy to read style. You’ll learn about the dangers of the first sleeping pill that is now a 30 billion dollar industry, how one in five sleepwalk, and how one in four middle aged men have sleep apnea.
Sleep apnea happens when the airway collapses in either obese people or those with a narrowed throat. A minute can pass before the sufferer briefly wakes up and desperately gulps down some oxygen. Most apnea patients are unaware of their condition. It leads to disrupted sleep and less productivity, memory loss, and heart attacks. Sufferers can use a simple device that gently pushes air into the lungs as an instant cure.
The book is filled with great advice like the above. It’s simple, without hocus pocus, and doesn’t need overly expensive equipment. Relax. Don’t try to sleep too hard. Your brain must disassociate itself from the rest of your body. Don’t drink alcohol or coffee. Expose yourself to light, but not late at night, at night dim lights, avoid screens. Don’t sleep too hot or too cold, the body is meant to cool after 10 pm — let it. Exercise. Simple.
Randall covers an immense range of research and topics. This is where the book’s problems start. He did a lot of research and wants us to know that. At other times, he rambles. A stricter editor would have helped the book.
The author only glosses over hardcore scientific studies. He mentions some science behind daily rhythms in Chapter 9. The book only has 13 chapters. He hardly even mentions the genes or molecular biology related to sleep. The scientist inside me died a little death. There are some amazing stories he missed out on by focusing on the lighter human studies.
Don’t take the above too harshly. Dreamland is a great book to learn more about sleep, just avoid late night tablet reading. You have been warned.
Over summer Dr Edward Duca visited the beautiful Island of Gozo, meeting Prof. Ray Ellul and his team based in Xewkija and the Giordan Lighthouse. Gozo is a tourist hotspot because of its beautiful landscapes, churches, and natural beauty. These same reasons attracted Ellul to obtain baseline readings of air pollutants; human effects should be minimal. Their equipment told them a different story.
They’re very big, anything from 10,000 tonnes to 100,000 tonnes,’ atmospheric physicist Prof. Ray Ellul is telling me about the 30,000 large ships his team observed passing between Malta and Sicily over a year. This shipping superhighway sees one third of the world’s traffic pass by carrying goods from Asia to Europe and back.
The problem could be massive. ‘A typical 50,000 tonner will have an engine equivalent to 85 MW,’ Malta’s two electricity plants churn out nearly 600 MW. You only need a few of these to rival the Islands’ power stations.
Ellul continues, ‘this is far far worse. We are right in the middle of it and with winds from the northwest we get the benefit of everything.’ Northwest winds blow 70% of the time over Malta and Gozo, which means that around two thirds of the time the pollutants streaming out of these ships are travelling over Malta. Even in Gozo, where traffic is less intense, air quality is being affected.
“Ships currently use heavy fuel oil with 3.5% sulfur; this needs to go down to at least 0.5%. The problem is that it doubles cost”
Malta is dependent on shipping. Malta’s Flag has the largest registered tonnage of ships in Europe; shipping brings in millions for Malta. We cannot afford to divert 30,000 ships to another sea. Yet Malta is part of the EU and our politicians could ‘go to Brussels with the data and say we need to ensure that shipping switches to cleaner fuels when passing through the Mediterranean.’ Politicians would also need to go to the Arab League to strike a deal with North Africa. Ships currently use heavy fuel oil with 3.5% sulfur; this needs to go down to at least 0.5%. The problem is that it doubles the costs. Malta’s battle at home and abroad won’t be easy, but the Baltic Sea has already taken these measures.
German Dreams
The research station in Gozo is a full-fledged Global Atmospheric Watch station with a team of five behind it. Now it can monitor a whole swathe of pollutants but its beginning was much more humble, built on the efforts of Ellul, who was drawn into studying the atmosphere in the 80s when he shifted his career from chemistry to physics.
In the early 90s the late rector, Rev. Prof. Peter Serracino Inglott, wanted the University to start building some form of research projects. ‘At that time, we knew absolutely nothing about what was wrong with Maltese air and Mediterranean pollution,’ explained Ellul. Building a fully fledged monitoring station seemed to be the key, so Ellul sent ‘handwritten letters with postage stamps’ to the Max Planck Institute in Mainz. Nobel prize winner Paul J. Crutzen wrote back inviting him to spend a year’s sabbatical in Germany, but their help didn’t stop there. ‘He helped us set-up the first measuring station, [to analyse the pollutants] ozone, then sulphur dioxide, then carbon monoxide. That’s the system we had in 1996 — […] 2 or 3 instruments.’
They lived off German generosity until 2008 when Malta started tapping into EU money. After some ERDF money and an Italy-Malta project on Etna called VAMOS SEGURO (see Etna, THINK issue 06, pg. 40), Ellul now manages a team of five. In homage to his early German supporters he has structured the research team around a Max Planck model — ‘one of the best systems in the World for science’.
Paradise Lost?
Getting data about ships is not easy. ‘It is very sensitive information and there is a lot of secrecy behind it,’ explains Ing. Francelle Azzopardi, a Ph.D. student in Ellul’s team. It is also very expensive. Lloyd’s is the World’s ship registry that tracks all ships, knowing their size, location, engine type, fuel used — basically a researcher’s dream. However, they charge tens of thousands. Ellul took the decision that they gather all the data themselves.
After 2004, all international ships above 300 gross tons need to have a tracking device. Automatically, these ships are traced around the world and anyone can have a peek on www.marinetraffic.com (just check the traffic around Malta). Every half hour the team’s administrator Miriam Azzopardi saves the data then integrates it into the Gozitan database. This answers the questions: where was this ship? which ship was it? how big is it? Easy.
“Ship emission expert James Corbett calculates that worldwide around around 60,000 people die every year due to ship emissions”
If only! The problem is that the researchers also need to know fuel type, engine size, pollution reduction measures, and so on. Then they would know which ship is where, how many pollutants are being emitted, and how many are reaching Malta and Gozo. To get over this hurdle, they contacted Transport Malta (more than once) to ask for the information they needed. ‘About 50% of the ships passing there [by us or Suez are] Malta registered,’ explained Ellul. With this information in hand they could put two and two together. They could create a model for ship emissions close to the Islands and use the model to get the bigger picture.
Enter their final problem: how do you model it? Enter the Finns. Ing. Francelle Azzopardi travelled to the Finnish Meterological Institute. They had already modeled the Baltic Sea, now they wanted access to the Maltese data, in return the Maltese team wanted access to their model called STEAM.
STEAM is a very advanced model. It gathers all the ships’ properties like engine power, fuel type, and ship size. This is combined with its operating environment including speed, friction, wave action, and so on. STEAM then spits out where the team should be seeing the highest pollution indicators. Malta was surrounded.
Apart from the model, the team have seen a clear link between ships and pollution. At the Giordan lighthouse they can measure a whole host of pollutants sulphur dioxide, various nitrogen oxides, particulate matter, black and brown carbon levels, ozone, radioactivity levels, heavy metals, Persistent Organic Pollutants (POPs) and more. When the wind blows from the Northwest, they regularly show peaks of sulfur dioxide, nitrogen oxides, carbon dioxide, carbon monoxide, hydrocarbons which are all indicative of fossil fuel burning either from ships or Sicilian industry. They also picked up relatively high levels of heavy metals especially Vanadium, a heavy metal pollutant. Such metals are more common in heavy fuel oil used by ships.
Alexander Smyth is the team’s research officer who spends three months in Paris every year analysing filters that capture pollutants from the atmosphere. Two different filter types are placed in the Giordan Lighthouse. One filter for particles smaller than 2.5 micrometers and another filter for particles around 2 to 10 microns. ‘With the 2.5 filter we can see anthropogenic emissions or ship emissions because they tend to be the smaller particles. The filters are exposed for three to four days, and then they need to be stored in the fridge. Afterwards, I take them to Paris and conduct an array of analyses,’ continued Alexander. The most worrying pollutant he saw was Vanadium.
Vanadium is a toxic metal. When inhaled, ‘it can penetrate to the alveoli of the lungs and cause cancer, a worst case scenario,’ outlined Alexander. It can also cause respiratory and developmental problems — none are good news. The only good news is that ‘they are in very small amounts’. Quantity is very important for toxicity, and they are seeing nanograms per cubic metre, a couple of orders of magnitude more are needed to cause serious problems. No huge alarm bells need to be raised, although Vanadium does stick around in bones and these effects still need more studies.
Vanadium seems to be coming from both Malta and shipping traffic. ‘The highest peaks of vanadium are from the south [of Malta, but the largest number of times I detected came] from the northwest, [from ships],’ said Smyth. ‘There is a larger influence from ships compared to local pollution at the Giordan lighthouse.’
Vanadium is not the only pollutant that could be affecting the health of Maltese citizens. Smyth also saw lots of different Persistent Organic Pollutants (POPs). At low concentrations these compounds can affect immunity leading to more disease, at higher concentrations they can lead to cancer. The local researchers still need to figure out their effect on Malta’s health. Francelle Azzopardi also saw peaks of sulfur dioxide and nitrogen oxides. No surprise here as shipping is thought to cause up to a third of the World’s nitrogen oxides and a tenth of the sulfur dioxide pollution.
Inhaling high levels of sulfur dioxide leads to many problems. It is associated with respiratory disease, preterm births, and at very high levels, death. It can affect plants and other animals. Nitrogen oxides also cause respiratory disease, but can also cause headaches, reduce appetite, and worsen heart disease leading to death. These are pollutants that we want to keep as low as possible.
Ship emission expert James Corbett (University of Delaware) calculates that worldwide around 60,000 people die every year due to ship emissions. Most deaths come from the coastlines of Europe, East Asia, and South Asia. Shipping causes around 4% of climate change emissions. This is set to double by 2050. In major ports, shipping can be the main cause of air pollution on land.
Another unexpected pollutant was ozone, normally formed when oxygen reacts with light. Yet the Giordan lighthouse was not the first to start measuring this gas. It all started with the Jesuits, scholarly catholic monks.
Monks at work
A lot of time is needed to see changes in our atmosphere. Researchers need to gather data over years. To speed up the process, Ellul was hunting around Malta and Gozo for ancient meteorological data about the Islands’ past atmosphere.
He was tipped off that there were still some records at a seminary in Gozo. ‘We expected to find just meteorological data and instead we also found ozone data as well. It was a complete surprise and a stroke of very good luck. We were able to find out what happened to ozone levels in the Mediterranean over the last hundred years.’
Jesuit monks meticulously measured ozone levels from 1884 to 1900. They analysed them seeing that the concentration of ozone was a mere 8 to 12 parts per billion by volume, ppbv. Ellul compared these to a 10-year study he conducted from 1997 to 2006. ‘We measure around 50ppb on average throughout the year,’ which is nearly 5 times more over a mere 100 years.
The situation is quite bad for Malta. In the past, the minimum was in summer and the maximum in winter and spring. Now, this has reversed with spring and summer having the highest ozone levels because of the reactions between hydrocarbons and nitrogen oxides. These come from cars, industry, and ships.
Over the Eastern Mediterranean ozone levels have gradually decreased. Over Malta, in the Central Mediterranean, they remained the same. Ellul thinks this could be because of an anticyclone over the central Mediterranean bringing pollutants from Europe over Malta and Gozo. The levels of ozone in Malta and Gozo are the highest in Europe, and it could be mostly Europe’s fault. Our excessive traffic doesn’t help.
Ozone can be quite a mean pollutant. While stratospheric ozone blocks out harmful UV rays, low-level ozone can directly damage our health or react with other pollutants to create toxic smog. It’s been known to start harming humans at levels greater than 50 ppbv. It inflames airways causing difficulty breathing, coughing and great discomfort. Some research has linked it to heart attacks — a pollutant not to be taken lightly.
Over those 10 years Ellul and his team saw 20 episodes in summer where ozone levels exceeded 90 ppbv. Some were during the night, unlikely to be of local origin but due to transport phenomena in the central Mediterranean and shipping. Ellul does nod towards the possibility of air recirculation from Malta. The atmosphere is a complicated creature.
Plants also suffer from ozone. Above 40 ppbv yield from fields decreases. Gozo is definitely being affected; we could be producing more.
The devil is in the details
Ellul and his team have found a potentially big contributor to the Islands’ pollution. This would be over and above our obvious traffic problem. Yet Ellul admits that ‘there is no particular trend, it’s too short a time span. What it tells us is that what we think is a clean atmosphere is not really a clean atmosphere at all. The levels are significant.’ Azzopardi honestly says ‘I can [only] give you an idea of what is happening’.
The team needs to study the problem for longer. It needs some statistics. Clearly they see a link between ships passing by Malta and peaks in pollution levels, but the Islands need to know if shipping pollution levels beat industry, traffic, or Saharan dust. What is ships’ contribution to Malta’s health problems?
When the team knows the extent of pollution, they can see whether they go above European standards. Ozone already does, and likely to be due to pollution from the European continent. If they can extend it to a whole host of other pollutants that skyrocket above European standards due to ship traffic, then ‘our politicians,’ says Ellul, can go to Brussels to enforce new legislation. That could control Mediterranean shipping traffic to clean up our air. At least it would solve one significant problem that Malta cannot solve on its own.
The main problem is economic. A ship can be made greener by reducing its sulfur fuel content. Low sulfur fuels are double the price of the bunker fuel they currently use. New legislation would need enforcement, which is costly. Ships could also be upgraded, again at a price. Passing these laws is not going to be easy.
Ships have been a pollution black hole for a while. The fuels ships burn contains 3,000 times more sulfur than cars are allowed to burn. Quite unfair. Going back to Corbett’s figures estimating European deaths at 27,000, the current rise in shipping pollution could end up killing hundreds of thousands if not millions before new legislation is enforced. Now that would be truly unfair.
Take the language of a 
