Growing up on the small island of Gozo, it was inevitable that the sea would exert a powerful influence on me. As a child I never tired of the sea, swimming, cooling off and floating on it in little boats. As I grew older, I came to see the sea as more than just a pretty playground. ‘Where do waves come from?’ ‘What generates sea currents?’ ‘How can I surf a wave?’ Were some questions that aroused my curiosity and motivated me to study the oceans, and eventually to choose to study physical oceanography and fluid dynamics.
Before commencing this journey, I read a B.Sc. (Hons) in Mathematics and Physics (University of Malta), graduating in 2008. Afterwards, I read an M.Sc. in Physical Oceanography, pursuing this qualification while working at the International Ocean Institute — Malta Operational Centre (IOI-MOC, University of Malta). One of the most interesting aspects of my research was studying storm surges around the Maltese Islands. The aim was to develop components to forecast variations in sea level around Malta.
In 2011, I was offered a scholarship at the School of Environmental and Industrial Fluid Mechanics (University of Trieste) in Italy. My Ph.D. research focused on the numerical modelling (Large Eddy Simulation) of coastal areas, in particular, the Barcelona harbour in Spain and the Bay of Taranto in Italy. My objective was to simulate the turbulent water mixing in the ports in order to understand the sea currents and circulation within the bays and thereby to quantify the water renewal within the basins.
Trieste, characterised by the bracing air of the famous Bora wind and by its splendid views of the Adriatic Sea, hosts many world renowned institutions and international organisations. Living in such a ‘city of science’ has allowed me to meet many celebrated scientists at seminars, workshops, and scientific conferences.
Through video conferencing I deliver a weekly physics study unit in Fluid Mechanics at the University of Malta. I am pleased that the beautiful blue Mediterranean waters are still motivating other Maltese students.
My interest in the sea has brought me a long way, not only academically but by experiencing new cultures and indulging my love of cycling along the karst (garigue) coastline.
But I remain at heart that same boy with a love of the sea. I look forward to climbing aboard my trusty kayak, revelling in the ebb and thrust of the rolling waves to continue exploring the rugged coastline of my beloved Gozo.
I chose to study Chemistry and Physics simply because they were the subjects I enjoyed most, so I enrolled on a B.Sc. (Hons) degree at the University of Malta without having a clear idea about what I would be doing once the four years are over. I was not the best brain in the class but in 2004 I graduated with a 2:1 grade and it was quite obvious that I needed a plan. A couple of opportunities to embark on a Ph.D. in Britain came along through local contacts and applications on jobs websites. Despite not knowing much about the subject, I decided to go with the Ph.D. at Exeter University because it was about Nuclear Magnetic Resonance, a subject that sits right on the verge of Chemistry and Physics.
Obviously the idea of moving abroad, living away from my parents and starting this amazing new adventure was incredibly exciting. From the start of my Ph.D. things went incredibly well, it was immediately obvious that I was much better at doing research than studying for exams. I started with looking into dynamics in solid materials on the microsecond timescale, which is the less studied type of motion. It bridges the gap between very fast (spin-lattice relaxation motions, nanosecond) and slow (millisecond to second) timescales. I published my first scientific paper a year into my Ph.D., and five more followed by the time I defended my thesis.
Because of the contacts I built during my Ph.D. as soon as I finished I was offered a post at University College London, Institute of Child Health, working as a research fellow in renal imaging. I carry out research at Great Ormond Street Children’s Hospital using novel non-invasive Magnetic Resonance Imaging (MRI) techniques. I work mainly with children requiring a kidney transplant. The aim of my work is to eventually be able to furnish doctors with information about their patients, which is currently either unavailable to them or they can only get through invasive clinical techniques such as biopsies. My work here has produced six peer-reviewed papers and I am currently working on a few more.
The research I carried out during my Ph.D. involved dealing with basic scientific concepts like Quantum Mechanics — that studies sub-atomic phenomena — and I was at liberty to experiment as I saw fit, which I enjoyed. However, despite being much more restrictive, I find clinical research extremely rewarding. Coming face to face with the people benefiting from all your hard work is really priceless.
Just after my Ph.D. I married my husband. We are now very proud parents of a two-year-old son. Any working mum would tell you that raising a family while maintaining a career is not easy, but I believe that if you like your job enough, combing the two is very worthwhile. Obviously research does not wait for anyone, and luckily for me, having colleagues that supported me meant that I was able to carry on publishing while I was on maternity leave.
Research — that would be the simplest way to answer the question above. Really and truly this answer would only apply to a small niche of individuals throughout the world.
It is a big challenge to explain to people what you do with a science university degree. The questions “Int għal tabib?” (Are you aiming to become a doctor?) or “Issa x’issir, spiżjar?” (Will you become a pharmacist?) are usually the responses. The thing is, people have trouble understanding non-vocational careers — if you are not becoming a lawyer, an accountant, a doctor or a priest, the concept of your job prospects is quite difficult to grasp for the average Joe.
In truth, it is not really 100% Joe Public’s fault — research is a tough concept to come to terms with, ask a good portion of Ph.D. students about that. There seems to be a lack of clarity in people’s minds about what goes on behind the scenes. If you boil it down, everything we use in our daily lives from mobile phones to hand warmers are the spoils of research — a laborious process with the ultimate goal of increasing our knowledge and, consequently, the utility of our surroundings.
“People need to stop feeling threatened by big words and abstract concepts they cannot grasp”
So, then, why exactly is it such an alien concept? I think the reason is that research is very slow and sometimes very abstract. Gone are the days when a simple experiment meant a novel, ground-breaking discovery — research nowadays delves into highly advanced topics, building on past knowledge to add a little bit more. I have complained about this to many of my colleagues on several occasions — and it is more complicated when you are studying something like Chemistry and Physics, or worse, Maths and Statistics — people just do not get it!
Research is exciting. The challenge is how to infect others with this enthusiasm without coming off as someone without a hint of a social life (just ask my girlfriend). It is nice to see initiatives like the RIDT and Think magazine trying hard to get the message out there that research is a continuous process with often few short-term gains. It can be surprising when you realise how much is really going on at our University, despite its size and budget.
To befriend the general public researchers still need to do more. The first step is relaying the message in the simplest terms possible — people need to stop feeling threatened by big words and abstract concepts they cannot grasp. There also needs to be increased opportunities for interaction with research — Science in the City is the perfect example. Finally, I think MCST needs to start playing a larger role — it must work closer to University and take a more coordinated role at a national level. Only then can we begin to explain what us researchers do.
Producing Food products, pharmaceuticals, and fine chemicals leads to hazardous waste and poses environmental and health risks. For over 20 years, green chemists have been attempting to transform the chemical industries by designing inherently safer and cleaner processes. Continue reading
There are over 100 billion galaxies in our universe. Each galaxy has billions of stars. Each star could have a planet. Planets can breathe life. Alessio Magrowrites about his experience hunting for E.T. Illustrations by Sonya Hallett
In 1982, 4 years before I was born, the world fell in love with Spielberg’s E.T. the Extra-Terrestrial. Fifteen years later, the movie Contact, an adaptation of Carl Sagan’s novel, hit the big screen. Although at the time I was too young to appreciate the scientific, political, and religious themes I was captivated and it fired my thoughts. I questioned whether we are alone in this vast space. What would happen if E.T. does call? Are we even listening? If so, how? And, is it all a waste of time and precious money? Instead of deflating me, these questions inspired me to start a journey that led me to my collaboration with SETI, the Search for Extra Terrestrial Intelligence. I participated in ongoing efforts to try and find intelligent civilisations on other worlds.
The debate on whether we are alone started ages ago. It was first debated in Thales, Ancient Greece. Only recently has advanced technology allowed us to try and open up communication channels with any existing advanced extraterrestrial civilisations. If we do not try we will never answer this question.
For the past fifty years we have been scanning the skies using large radio telescopes and listening for signals which cannot be generated naturally. The main assumption is that any advanced civilisation will follow a similar technological path as we did. For example, they will stumble upon radio communication as one of the first wireless technologies.
SETI searches are usually in the radio band. Large telescopes continuously scan and monitor vast patches of the sky. Radio emissions from natural sources are generally broadband, encompassing a vast stretch of the electromagnetic spectrum — waves from visible light to microwaves and X-rays — whilst virtually all human radio communication has a very narrow bandwidth, making it easy to distinguish between natural and artificial signals. Most SETI searches therefore focus on searching for narrow band signals of extraterrestrial origin.
Narrow bands are locked down by analysing a telescope’s observing band — the frequency range it can detect. This frequency range is broken down into millions or billions of narrow frequency channels. Every channel is searched at the same time. SETI searches for sharp peaks in these small channels. This requires a large amount of computational resources, such as supercomputing clusters, specialised hardware systems, or through millions of desktop computers. The infamous SETI@home screen-saver extracted computer power from desktops signed up to the programme, which started as the millennium turned.
E.T. civilisations might also transmit signals in powerful broadband pulses. This means that SETI could search for wider signal frequencies. However, they are more difficult to tease apart from natural emissions, so they require more thorough analysis. The problem is that as broadband signals — natural or otherwise — travel through interstellar space they get dispersed, resulting in higher frequencies arriving at the telescope before lower ones, even though they both were emitted at the same time. The amount of dispersion, the dispersion gradient, depends on the distance between the transmitter and receiver. The signal can only be searched after this effect is accounted for by a process called dedispersion. To detect E.T. signs, thousands of gradients have to be processed to try out all possible distances. This process is nearly identical to that used to search for pulsars, which are very dense, rapidly rotating stars emitting a highly energetic beam at its magnetic poles. Pulsars appear like lighthouses on telescopes, with a regular pulse across the entire observation band.
For the past four years I have been developing a specialised system which can perform all this processing in real-time, meaning that any interesting signals will be detected immediately. Researchers now do not need to wait for vast computers to process the data. This reduces the amount of disk space needed to store it all. It also allows observations to be made instantaneously, hence reducing the risk of losing any non-periodic, short duration signals. To tackle the large computational requirements I used Graphics Processing Units (GPUs) — typically unleashed to work on video game graphic simulations — because a single device can perform tasks of at least 10 laptops. This system can be used to study pulsars, search for big explosions across the universe, search for gravitational waves, and for stalking E.T..
The Electromagnetic Spectrum. Higher frequencies mean higher energies but shorter wavelengths. X-rays and Gamma rays are on the higher end of the spectrum making them so dangerous.
E.T. we love you
Hunting for planets orbiting other stars, known as exoplanets, has recently become a major scientific endeavour. Over 3,500 planet-candidates were found by the Kepler telescope that circles our planet, about 961 are confirmed. Finding so many planets is now leading scientists to believe that the galaxy is chock-full of them. The current estimate: 100 billion in our galaxy, with at least one planet per star. For us E.T. stalkers, this is music to our ears.
Life could be considered inevitable. However, not all planets can harbour life, or at least life as we know it. Humans need liquid water and a protective atmosphere, amongst other things. Life-supporting planets need to be approximately Earth-sized and orbit within its parent star’s habitable zone. This Goldilocks zone is not too far away from the sun, freezing the planet, or too close to it, frying it. These exoplanets are targeted by SETI searches, which perform long duration observations of exoplanets similar to Earth.
“The big question is: where do we look for E.T.? I would prefer rephrasing to: at which frequency do we listen for E.T.?”
By focusing on these planets, SETI is gambling. They are missing huge portions of the sky to focus on areas that could yield empty blanks. SETI could instead perform wide-field surveys which search large chunks of the sky for any interesting signals. Recent development in radio telescope technology allows for the instantaneous observation of the entire sky, making 24/7 SETI monitoring systems possible. Wide-field surveys lack the resolution needed to figure out where a signal would come from, so follow-up observations are required. Anyhow, a one-off signal would never be convincing.
For radio SETI searches, the big question is: where do we look for E.T.? I would prefer rephrasing to: at which frequency do we listen for E.T.? Imagine being stuck in trafficand you are searching for a good radio station without having a specific one in mind. Now imagine having trillions of channels to choose from and only one having good reception. One would probably give up, or go insane. Narrowing down the range of frequencies at which to search is one of the biggest challenges for SETI researchers.
The Universe is full of background noise from naturally occurring phenomena, much like the hiss between radio stations. Searching for artificial signals is like looking for a drop of oil in the Pacific Ocean. Fortunately, there exists a ‘window’ in the radio spectrum with a sharp noise drop, affectionately called the ‘water hole’. SETI researchers search here, reasoning that E.T. would know about this and deliberately broadcast there. Obviously, this is just guesswork and some searches use a much wider frequency range.
Two years ago we decided to perform a SETI survey. Using the Green Bank Telescope in West Virginia (USA), the world’s largest fully steerable radio dish, we scanned the same area the Kepler telescope was observing whilst searching for exoplanets. This area was partitioned into about 90 chunks, each of which was observed for some time. In these areas, we also targeted 86 star systems with Earth-sized planets. We then processed around 3,000 DVDs worth of data to try and find signs of intelligent life. We developed the system ourselves at the University of Malta, but we came out empty handed.
A camera shy E.T.
Should we give up? Is it the right investment in energy and resources? These questions have plagued SETI from the start. Till now there is no sign of E.T., but we have made some amazing discoveries while trying to find out.
Radio waves were discovered and entered into mainstream use in the late 19th century. We would be invisible to other civilisations unless they are up to 100 light years away. Light (such as radio) travels just under 9.5 trillion kilometres per year. Signals from Earth have only travelled 100 light years, broadcasts would take 75,000 years to reach the other side of our galaxy. To compound the problem, technology advances might soon make most radio signals obsolete. Taking our own example, aliens would have a very small time window to detect earthlings. The same reasoning works the other way, E.T. might be using technologies which are too advanced for us to detect. As the author Arthur C. Clarke stated, ‘any sufficiently advanced technology is indistinguishable from magic’.
The Wow! signal is a brief, strong radio burst of unknown origin detected by the Big Ear Telescope, SETI search, 1977. If it originated from deep space, it could either be a new astrophysical phenomena or an alien signal.
At the end of the day, it is all a probability game, and it is a tough one to play. Frank Drake and Carl Sagan both tried. They came up with a number of factors that influence the chance of two civilisations communicating. One is that we live in a very old universe, over 13 billion years old, and for communication between civilisations their time windows need to overlap. Another factor is, if we try to detect other technological signatures they might also be obsolete for advanced alien life. Add to these parts, the assumed number of planets in the Universe and the probability of an intelligent species evolving. For each factor, several estimates have been calculated. New astrophysical, planetary, and biological discoveries keep fiddling with the numbers that range from pessimistic to a universe teeming with life.
The problem with a life-bloated galaxy is that we have not found it. Aliens have not contacted us, despite what conspiracy theorists say. There is a fatalistic opinion that intelligent life is destined to destroy itself, while a simpler solution could be that we are just too damned far apart. The Universe is a massive place. Some human tribes have only been discovered in the last century, and by SETI standards they have been living next door the whole time. The Earth is a grain of sand in the cosmic ocean, and we have not even fully explored it yet.
“Signals from Earth have only travelled 100 light years, broadcasts would take 75,000 years to reach the other side of our galaxy”
Still, the lack of alien chatter is troubling. Theorists have come up with countless ideas to explain the lack of evidence for intelligent alien existence. The only way to solve the problem is to keep searching with an open mind. Future radio telescopes, such as the Square Kilometre Array (SKA), will allow us to scan the entire sky continuously. They require advanced systems to tackle the data deluge. I am part of a team working on the SKA and I will do my best to make this array possible. We will be stalking E.T. using our most advanced cameras, and hopefully we will catch him on tape.
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!
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
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.
The particle beams circulating in the CERN Large Hadron Collider (LHC) have enough energy to melt 500kg of copper. How can we protect the machine from itself?
My phone rang, waking me up in the middle of the night. It is 2 a.m., and I (Dr Gianluca Valentino) am driving from the sleepy French village where I live at the foot of the snow-capped Jura mountains to the CERN Control Centre. As groggy as I feel, I am trembling with excitement at finally putting months of my work to the test.
The operators on night shift greet me as I come in through the sliding door. These are the men and women who keep the €8 billion Large Hadron Collider (LHC) running smoothly. The LHC produces 600 million particle collisions per second to allow physicists to examine the fundamentals of the universe. Their most recent discovery is the Higgs boson, a fundamental particle. In 2012, this finding appears to have confirmed the Higgs field theory, which describes how other particles have mass. It helps explain the universe around us.
The empty bottles of champagne on the shelves of the CERN Control Centre are a testimony to the work of thousands of physicists, engineers, and computer scientists. The LHC has now busted record after record rising to stratospheric fame.
The LHC is an engineering marvel. A huge circular tunnel 100 m underground and 27 km in circumference. It straddles the Franco-Swiss border and is testimony to the benefit of 50 years of non-military research at CERN, the European Organization for Nuclear Research. CERN is also the birthplace of the World Wide Web.
The LHC works by colliding particles together. In this way physicists can peer into the inner workings of atoms. Two counter-rotating hadron (proton or heavy-ion) beams are accelerated to approach the speed of light using a combination of magnetic and electric fields. A hadron is a particle smaller than atoms, and is made up of several types of quarks, which are fundamental particles (there is nothing smaller than them — for now). The beams circulate at an energy of 7 TeV, which is similar to a French TGV train travelling at 150 km per hour.
For the magnets to work at maximum strength, they need to operate in super-conducting mode. This mode needs the collider to be cooled to -271°C using liquid helium, making it the coldest place in the universe. It is also the hottest place in the universe. Collisions between lead ions have reached temperatures of over 5 trillion °C. Not even supernovae pack this punch.
The two separate beams are brought together and collided at four points where the physics detectors are located. A detector works by gathering all the information generated by the collisions which generate new sub-atomic particles. The detectors track their speed and measure the energy and charge. ‘Gluon fusion’ — when two gluons combine (a type of boson or particle that carries a force) — is the most likely mechanism for Higgs boson production at the LHC.
My role in this huge experiment is to calibrate the LHC’s brakes. Consider a simple analogy. A bike’s brakes need to be positioned at
the right distance from the circulating wheel, and are designed to halt a bike in its tracks from a speed of around 70 km/hr. Too far apart, and when the brakes are applied, the bike won’t stop. Too close together, and the bike won’t even move. In the LHC, the particles travel at nearly 300,000 km/s.
Equipment called collimators act as the LHC’s brakes. The LHC is equipped with 86 of them, 43 per beam. They passively intercept particles travelling at the speed of light, which over time drift from the centre outwards. The machine is unprotected if the collimators are placed too far away from the beam. The beam’s energy, equivalent of 80 kg of TNT, would eventually drill a hole needing months or years to repair. If the collimators are too close to the beam they sweep up too many particles, reducing the beam’s particle population and its lifetime.
Dr Ing. Nicholas Sammut
The LHC has four different types of collimators, which clean the particles over multiple stages in the space of a few hundred metres. These collimators also protect the expensive physics detectors from damage if a beam were to hit them directly. If the detectors were hit the LHC would grind to a halt.
What does it take to calibrate these brakes? Each brake or collimator is made up of two metre-long blocks of carbon composite or tungsten, known as ‘jaws’. The jaws should be positioned symmetrically on either side of the beam, and opened to gaps as small as 3 mm to let the beam through. They can be moved in 5 µm increments— that is 20 times less than the width of a typical human hair. The precision is necessary but makes the procedure very tedious.
The beam’s position and size at each collimator are initially unknown. They are determined through a process called beam-based alignment. During alignment, each jaw is moved in steps towards the beam, until it just scrapes the edge. Equipment near the collimator registers the amount of particles they are mopping up. Then, the beam position is calculated as the average of the aligned jaw positions on either side, while the beam size is determined from the jaw gap.
The problem is that there are 86 collimators. Each one needs to be calibrated making the process painfully slow. To calibrate the jaws manually takes several days, totaling 30 hours of beam time. To top it all, the alignment has to be repeated at various stages of the machine cycle, as the beams shrink with increasing energy, and imperfections in the magnetic fields can lead to changes in the beam’s path. This wasted time costs millions and makes the LHC run slower.
Previously, one had to click using a software application for each jaw movement towards the beam. With a step size of 5 µm and a total potential distance of 10 mm, that is 2000 clicks per collimator jaw! Extreme precision is required when moving the collimator jaws. If the jaw moves too much into the beam, the particle loss rate will exceed a certain threshold, and the beam is automatically extracted from the LHC. A few hours are wasted until the operators get the machine back and the alignment procedure is restarted.
Dr Ralph Assman
Over the course of my Ph.D., I automated the alignment, speeding it up by developing several algorithms — computer programs that carry out a specific task. The LHC now runs on a feedback loop that automatically moves the jaws into the correct place without scraping away too much beam. The feedback loop enables many collimators to be moved simultaneously, instead of one at a time. A pattern recognition algorithm determines whether the characteristic signal observed when a jaw touches the beam is present or not. This automates what was previously a manual, visual check performed by the operator.
The sun’s rays begin to filter through the CERN Control Centre, and the Jura mountains are resplendent in their morning glory. The procedure is complete: all collimators are aligned in just under 4 hours, the fastest time ever achieved.
In early 2013, the LHC was shut down for a couple of years for important upgrades. Before then my algorithms helped save hundreds of hours; since the LHC costs €150,000 per hour to run, millions of euros were also saved. This software was part of the puzzle to provide more time for the LHC’s physics programme and is now here to stay.
The morning shift crew comes in. The change of guard is performed to keep the machine running 24 hours a day, 7 days a week, while I head home to catch up on lost sleep.
Research — that would be the simplest way to answer the question above. Really and truly this answer would only apply to a small niche of individuals throughout the world.
