Category: Irish Times

Size matters …and so does scale

Star-Forming Region S106 Credit: NASA, ESA, and the Hubble Heritage Team (STScI/AURA)

My latest piece for the Irish Times Bang! magazine plus some essential links below the post to further reading on the subject of size, scale and our universe!

How big, how far, how small, how much? These are the questions about our universe, and everything in it, that have fascinated us humans for millennia. And science helps us answer them, writes MARIE BORAN.

Ever since mankind gazed up at the night sky, it has inspired questions that form the basis of modern science: how big, how far, how small, how much? If twinkling stars appear to be nothing more than tiny shimmering lights in the sky, how can we tell how big they are or what distance they are from Earth?

It’s all a matter of working out scale, as Ted patiently explains to a perplexed Dougal in Father Ted. Holding up a plastic toy cow while simultaneously pointing to a herd of cattle outside the window, Ted says: “These are small . . . but the ones out there are far away.” This is obviously a silly example. We know how big something is when we hold it on our hands.

Simply put, it is either roughly bigger or smaller than our hand. In fact, this is how the ancient Egyptians and Babylonians first measured objects in the third millennium BC. A cubit was the distance from the forearm to the tip of the middle finger, and a half-cubit was the span of the hand.

As time went on this evolved and changed into the standard inch, foot and yard that we use today.

Thousands of years later, in the third century BC, the Greek astronomer and mathematician Aristarchus took one giant leap and attempted to work out the distance to the moon. He did this by observing the size of the Earth’s shadow in relation to the moon during a lunar eclipse.

Aristarchus also estimated that the moon was a quarter the size of the Earth, and was about 60 times the radius of Earth, which is fairly close to modern calculations. He wasn’t so successful with his guess on how far we are from the sun but he was ahead of his time – and 17 centuries ahead of Copernicus. He suggested that the Earth was not the centre of the universe but instead moved around the sun.

Unlike physically measuring something in cubits, these kinds of calculations showed that it was possible to infer the size or distance of an object indirectly by using information about related objects. Unfortunately there is only so much you can observe and calculate with the naked eye.

The next great leap in understanding the scale of the world around us came with the invention of the telescope and microscope. These instruments appeared around the same time in the 17th century, when Dutch lens-grinder Jan Lippershey is documented as having made the first telescopic device. Galileo, however, was the Steve Jobs of his time: while he didn’t invent the telescope he was the one who made it popular, and improved upon its design.

Galileo was not only busying himself with bringing us beyond the solar system by unveiling the Milky Way, he also turned the lens down upon more earthly things with the microscope. Illustrations of the legs, wings and other body parts of bees from 1625 are the first documented use of this scientific instrument.

Besides asking how big the universe is we were now asking how small things were. The first measurement for things smaller than the human eye was the micrometer, which was scientifically quantified in the mid 18th century.

The micrometer fits into a scale of universal measurements alongside the millimetre, the centimetre and so on. It can be difficult to conceptualise micrometres and even smaller subatomic measurements but you can use order-of-magnitude reference objects to visualise very small or very large scales.

Imagine you are 1mm tall, even tinier than the Lilliputians in Gulliver’s Travels . The eye of a needle now becomes a doorway and a single hair is as thick as a tree trunk. If you were to pick up red blood cells they would be the size of MMs.

Another quick way to visualise scale is to substitute microscopic objects with stuff you have lying around the house. Take those MMs again and think of them as red blood cells, roughly 10 um (micrometers) in size. If you placed a sugar grain beside the MM that’s what a bacteria would look like in comparison.

Additionally, a hair from your head would be the size of a poster tube and an actual sugar grain would be the size of an A4 cardboard box.

The reason we can “see” so much of the universe is because of powerful telescopes such as the Hubble Space Telescope. This telescope was launched into space on April 24th, 1990 aboard the space shuttle Discovery and is almost the size of a large school bus.

It is so powerful that it can lock onto a target within the accuracy of 7/1000th of an arcsecond, or the width of a human hair seen from one mile away.

Hubble not only sees many magnitudes farther than the human eye but also sees wavelengths not visible to us: near ultra-violet to near infrared wavelength. It has given us staggeringly beautiful images of galaxies billions of light years away and allowed scientists to observe the birth of stars and the prevalence of black holes.

The telescope, and the astronomer it’s named after, Dr Edwin Hubble, helped us learn more about the size of our universe, that it is expanding, and introduced us to the Big Bang theory.

The Big Bang theory tells us that between 12 to 14 billion years ago the universe was only a few millimetres across but expanded in a hot dense state into all matter in the known universe today.

Studying this matter helps us understand how the universe came about and this means going small. The job of particle physicists is to examine a world we cannot see: the subatomic world of quarks, leptons and bosons.

If you remember protons from class then imagine that this is comprised of smaller particles: two up quarks and one down quark to be precise.

On this scale, it becomes tricky to quantify matter. Scientists don’t know exactly how small quarks are but because 99.999999999999 per cent of an atom’s volume is empty space, if you were to scale an atom’s diameter to the length of 30 American football fields, electrons and quarks would be less than the diameter of a human hair.

Calculating anything on the back of an envelope

Physicist Enrico Fermi (1901-1954) was famous for his back-of-the-envelope calculations. He delighted in thinking up tricky mathematical problems and working out approximate answers with a pencil and paper. These are now known as Fermi questions.

A Fermi question uses limited data and asks further questions in order to work out a fairly accurate answer that doesn’t require any specialist scientific knowledge. For example, what is the circumference of the Earth?

The most famous Fermi question, and one the physicist posed to his students, is the piano tuner problem. He challenged his class to work out the number of piano tuners in Chicago given a single piece of information: the city’s overall population.

Back in those days you couldn’t do an internet search for such an obscure question, which was just as well because Fermi was teaching his class to become scientists and mathematicians by using the most powerful computer in their possession: the human brain.

Fermi knew from census figures that Chicago had a population of about 3 million. He then assumed that the average family has about four members, which makes 750,000 families in Chicago. If we assume that one in five families owns a piano there are 150,000 pianos in the city.

The average piano tuner would: 1. Service four pianos each day; 2. Work a typical five-day week; 3. Take two weeks of holidays a year. We can now begin calculating. In one year the average piano tuner would service four (pianos) x five (days) x 52 (weeks) minus the 10 days off (40 pianos-worth). That’s 1,000 pianos serviced in a year. If there are 150,000 pianos in the city then 150,000/1,000 gives us 150 piano tuners to meet demand.

Using this method you can work out the circumference of the Earth in a few minutes. First, we take something we already know. Using an atlas we can see that the distance between New York and Los Angeles is roughly 3,000 miles. In those 3,000 miles we pass through three different time zones. From this we work out there are roughly 1,000 miles per time zone. But how many time zones are there in the world? There are 24 because there are 24 hours in the day.

This means that it takes 24,000 (24 x 1,000) miles to travel around the Earth. From class, you will remember that the formula for the circumference of a circle is 2 Pi r where r is the radius and Pi is 3 (we’re using rough numbers here because we’re doing it with pencil and paper). So we have: 24,000/6 = r = 4,000. The diameter is twice the radius, so the diameter of the Earth is 8,000 miles. The scientifically accurate diameter of the Earth is 7,901 miles so for the back-of-an-envelope calculation you can be pretty accurate.

Further Reading

Siri, AI and robots

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Here’s a piece – iRobot – that I wrote for Bang! science magazine in the Irish Times. It’s on one of my favourite subjects: robots.

Tell me a joke Siri. ‘Two iPhones walk into a bar . . . I forget the rest.”

It turns out that Siri, the new virtual digital assistant on the iPhone 4S, has a (bad) sense of humour. Does the ability to tell jokes make Siri intelligent in any sense of the word? Or is it just a clever piece of software with a vast bank of canned responses?

Can machines think?

Alan Turing, the father of modern computer science, addressed this question as far back as 1950 when he asked, “Can machines think?” To devise the first measure of machine intelligence, Turing tweaked a Victorian parlour game, where the player had to guess, based on the responses, whether they were talking to a man or woman who remained concealed behind a curtain.

If you converse with someone behind a computer screen and you can’t tell if this is a person or a machine, then the machine has truly demonstrated “artificial intelligence”, he concluded. This became known as the Turing Test and is still used to gauge how naturally an artificial agent can converse.

Each year the Loebner Prize competition gathers a panel of expert judges to see if they can be tricked by AI (artificial intelligence) software known as chatbots, which are programmed to mimic human conversation. To date, despite using quite sophisticated programming, these chatbots tend to give away their silicon-based nature. Their responses range from slightly off to utter gibberish, and most humans can spot that their sentence structure isn’t quite right.

Try that for size!

Here’s an example of one of the many bizarre exchanges that a judge had with a chatbot known as Do-Much-More at the 2009 Loebner Prize contest. Judge: “What do you make of the Arctic Monkeys?” Do-Much-More: “Well, here’s a clue: I make what a keeper in a zoo would make. Try that for size!”

Despite his seemingly playful nature Do-Much-More hasn’t spotted that in this context the judge was talking about a band, and the brave chatbot doesn’t even consider admitting to the judge that it doesn’t understand. It simply ploughs ahead.

This is because a test like this is about guesswork and trickery rather than gauging true intelligence, according to Jason Hutchens, an academic who entered the Loebner Prize twice. There are, however, many other measures of machine intelligence and the iPhone’s Siri doesn’t just try to hold conversations. The AI behind Siri is quite complex and its roots lie in US military research.

Adam Cheyer created Siri after working as the chief architect at Calo (Cognitive Assistant that Learns and Organises), one of the largest artificial intelligence projects in US history. Siri listens to voice commands and tries to make sense of them. The first step is voice recognition software but once Siri “hears” what you’re saying it must then make sense of it. This is where the AI comes in.

Siri like to learn

The information passed along to Siri is put in the context of a process or request that it must evaluate and carry out, which is not very different from how most computer programmes work. On the surface intelligent agents like Siri are making decisions, or at least that is how the complexity of the programming makes it appear.

Perhaps the most important piece of AI that Siri has is adaptability.

Explaining how it works on Quora.com Cheyer said: “Siri learns over time (new words, new partner services, new domains, new user preferences, etc).”

Robots that walk the walk

Artificial intelligence, however, isn’t all about the software. Some intelligent agents talk the talk while others walk the walk. The most interesting and cutting edge robots of this kind aren’t just programmed to walk; they’re programmed to learn to walk.

Josh Bongard from the University of Vermont in the US has designed robots that start out a bit like human babies; they begin by crawling, slithering or dragging their bodies along the floor. Over time, they learn to balance better, graduate to walking confidently on two legs and can travel much faster.

Interestingly, these robots experience a form of “super evolution”: in the beginning they are using anguilliform locomotion (they wiggle like fish or eels) but then progress to many legs and finally two.

One of the more famous real-life robots is decidedly more appealing due to its humanoid form. Asimo is a robot developed by Japanese company Honda Robotics and was first created in 2000. Its name is an acronym for Advanced Step in Innovative Mobility, which is appropriate as it can both walk and run.

The most recent version of Asimo was unveiled earlier this month and is probably one of the most advanced robots in the world. Standing at a mere 4ft tall, this Hobbit-like robot has advanced AI that allows it to navigate around people by predicting where they will move next. This is something that you and I do without thinking every day when we walk down a crowded street but is an amazingly complex task for a robot.

Due to both a tactile sensor and a force sensor embedded on the palm and in each finger Asimo can now open bottles and pour drinks. Intriguingly, it now has the ability to run backwards and hop on one or two legs. When this diminutive robot eventually becomes available to buy it will be like having Rosie the maid from the Jetsons but with legs instead of a set of wheels.

Honda Robotics has suggested that we are now one step closer to having an office robot as Asimo can perform simple tasks while being able to navigate around a stream of people walking about.

Emotional and mechanical

But what about that which makes us human? Something that no robot, it seems, may ever be able to replicate is human emotion. Emotion is hard wired into the human experience and is evolutionarily advantageous in terms of species survival.

For humans to really bond with machines they must connect on an emotional level says Dr Cynthia Breazeal, a roboticist with the Massachusetts Institute of Technology.

In 1999 Breazeal created Kismet, the first emotionally intelligent robot. Kismet doesn’t have a body but its head is kitted out with sensors, cameras and motors. It not only interprets what you are saying but also reacts in quite a human fashion. The robotic head swivels towards the human participant and depending on the movement of its lips, eyebrows, ears and even how it hunches or hangs its head will convey surprise, happiness, anger or disgust.

Kismet’s AI is busy interpreting the tone of your voice, your eye movement and body language to figure out the emotional context of your conversation. It then attempts to respond in kind.

These fields of robotics will have therapeutic benefits, according to Breazeal: children with autism can experience pressure-free social interaction with Kismet-like creatures.

Uncanny likeness

If robots are too human-like, however, we can enter what is known as the Uncanny Valley, a phrase coined by Japanese roboticist Dr Masahiro Mori. This is a situation where robots look almost but not quite human.

Psychologically speaking, this kind of robot tends to scare or disgust us more than something that looks like Optimus Prime or WALL-E.

“There are good reasons why robots shouldn’t look too human,” says futurologist Prof Michael Hulme. “Recent research on avatar images showed that we prefer to look at faces that look clearly like an avatar rather than a pale imitation of a human being.”

An example of a creepy-looking humanoid robot is the Actroid, developed by Osaka University. Robots like this may mimic blinking, nodding and even breathing but it is likely that we will always know that there is something not quite human about them.

The future of robots…

Robots and other artificially intelligent machines will come in various different forms in 10 years’ time says Prof Michael Hulme: “I’m very interested in the notion of specific robots for specific purposes; the idea of a robot as a companion, or one that helps with housework. Take guide dogs for example, they’re very important to the individual and perform a single task extremely well; this is how I see robots fitting into society in the future.”

There will also be emotional robots in the future, he says, but they will be context-based. Science fiction scenarios of robots programmed with emotions often end in disaster, the most famous being HAL 9000 from 2001: A Space Odyssey. Perhaps HAL should not have been given emotions or the ability to acquire feelings; Hulme says that emotional behaviour will inevitably be assigned to robots that need them as part of their function.

One of the most important issues in 10 years’ time will be the world’s aging population and this is where caring, emotionally aware robots come in. We’re all living longer and part of elderly healthcare will inevitably involve robot aides.

“Given the demographics this is one of the areas where robotics will become very significant,” Hulme says.

There are already prototype units that can carry people up stairways, issue reminders to take medication and take blood pressure. There are also robots like Paro, a robotic baby seal who promotes social interaction among the elderly and is being tested by the National Institute of Advanced Industrial Science and Technology in Japan.

Hulme also thinks that AI will come into its own in the era of TMI (too much information). New research predicts that the total amount of information created in 2011 will reach 1.8 zettabytes (or 1.8 trillion).

If this data was stored on a 32GB Apple iPad it would fill 57.5 billion units; enough to build the Great Wall of China comprised of these iPads, but at twice the height of the original. In 10 years’ time we may not be able to cope with this data but we could have intelligent agents doing so on our behalf.

This AI would be “representative of the individual” and “almost performing as if it was part of the human being”, says Hulme, asking me to imagine a virtual facsimile of myself that will find the information you want on your behalf.

This kind of complex AI is more likely 50 than 10 years down the line but has its roots in the kind of “recommendation” systems like the one Amazon uses.

Will we have truly intelligent machines in 10 years time? Probably not, although the computer scientist who coined the phrase “artificial intelligence” estimated that it could be anywhere between “five to 500 five years” before real AI would emerge. So while we will have our robot butler just don’t expect it to be any good at telling jokes.

Here comes the brain again

This is a reproduction of a piece I wrote recently (June 9, 2011) for the Irish Times. It’s taken from here.

The next time you find yourself in a taxi, ask the driver to tell you about the last movie he watched. If he has a foggy recollection, you can always blame it on how his brain is wired.

It is not that taxi drivers have especially bad memories. Like everyone else, their brains are “wired” as a direct result of repeated behaviour and experiences and this can have interesting results.

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A famous brain-imaging study by Dr Eleanor Maguire, formerly of University College Dublin and now at London City University, looked at a group of London taxi drivers and observed that parts of their brain literally grew due to their job.

“The study suspected that because these men had to get to know London streets like the back of their hand, parts of the brain responsible for this function might be larger than in the average person,” says Dr Richard Roche, lecturer in psychology at the National University of Ireland, Maynooth.

It was found that a part of the brain known as the posterior hippocampus was larger than average, especially in the right half or right hemisphere of the brain. Roche explains that as this area grew, it expanded into a nearby part of the brain.

“As a result, when these taxi drivers were asked to recall the plot of a film, they weren’t as accurate as the average person. There is a bit of a cost when you enhance a particular brain function and the neurons expand into another area,” Roche says.

Plastic Fantastic

This shows that the brain is not a hard-wired organ that is incapable of change. It is plastic and the wiring is changed slightly every time we perform a new thought or action, says Dr Kevin Mitchell, neurogeneticist at Trinity College Dublin.

Experience literally shapes the brain, says Mitchell. “The major function of the brain is to adapt itself to the environment, form memories of what has happened in the past and better predict the future. This happens at the level of brain cells connecting with each other.”

We know that neuroplasticity occurs early in development when the young brain is organising itself, says Dr Lorraine Boran, lecturer in cognitive psychology at Dublin City University.

This plasticity continues throughout our lives in response to learning, and also in the case of brain injury where rehabilitation focuses on compensation of lost function or maximising spared function, she says.

“Brain connections form and reform in response to our environment,” explains Boran.

Cells that fire together wire together

In order to describe how connections are formed and fixed in the brain, Boran, Mitchell and Roche all use the mantra: cells that fire together wire together.

Roche says that the phrase “use it or lose it” also applies. He explains that one of the reasons that people seem to experience cognitive decline as they get older is because their brains aren’t getting the same workout as they used to.

“A lot of people get to retirement age and cognitively, they hang up their boots. Something as simple as reading can keep neurons firing.”

Dr Niall Pender is head of the department of psychology and principal clinical neuropsychologist at Beaumont Hospital. He works with a “memory clinic” that involves older people who are not suffering from cognitive decline such as vascular dementia but who are pre-empting this by getting involved in activities that will keep the brain as active as possible for as long as possible.

He explains that it’s not just crosswords or brainteasers that keep the mind active. Exercise and socialising and especially learning new skills keep neurons firing and create new neural pathways in the brain.

A finely tuned orchestra

Forming new connections is the key to recovery in stroke patients and others who have suffered brain trauma of some sort, explains Pender. Borrowing an analogy from psychologist Barbara Wilson, he says we should think of the brain as a finely-tuned orchestra.

If the string section disappears there are two choices: the rest of the musicians can improvise and attempt to play the same piece of music or they can adapt the sheet music to work with the remaining orchestra.

Similarly, when sections of the brain are damaged or destroyed by an injury, this does not spell disaster. “The brain is very plastic and its capacity to recover from damage is vast,” says Roche. “This is contrary to what people thought until relatively recently. For a long time the received wisdom was that if you damaged your brain there wasn’t much you could do.”

“Use it or lose it” comes into play when the brain has been damaged, says Roche. “The more active your brain is pre-stroke, the more resilient it will be afterwards.”

How the brain is pre-wired also has a profound effect on how each individual processes information and approaches problems.

Wired differently

Mitchell says: “When the brain has developed in a different way the wiring is different than normal. This is most likely what happens in conditions such as autism and schizophrenia. “If that’s the case, you’re probably not going to be able to fix the problem itself but you can compensate,” he says.

With autism, there are some differences in areas of the brain that are wired to mediate social cues, explains Mitchell. People with autism can find it difficult to maintain eye contact. They may not look at people simply because their wiring means that they are not interested in looking at people.

Mitchell emphasises that because the brain is pre-wired to behave in a certain way does not mean this cannot be changed consciously. “It is possible for those with autism to compensate by learning social rules in an intellectual fashion.”

Despite all our current knowledge, we are still learning how the brain works, says Pender. There are many different parts and they all have a role to play – from keeping us breathing and waking to high-level executive skills and the parts that give us a sense of humour.

We also have to take into account elements of our genetic history and our environment. We are born with certain predispositions that help shape our personality and intelligence, and experience changes this further.

People often ask if some brains are wired better than others, says Mitchell. “Not better but they are certainly wired differently.”

Bad to the bone?

DO WE CHOOSE a life of crime or does it choose us? Dr Kevin Mitchell, neurogeneticist at the department of genetics in Trinity College Dublin, says that certain individuals are more likely to end up behind bars because of the way their brain is wired.

Psychopathic individuals in particular are estimated to make up 20 per cent of the prison population and are three to four times more likely to re-offend than the average criminal. They don’t respond particularly well to rehabilitation either.

The psychopath is defined by a particular personality profile, explains Mitchell. “They are superficially charming, egocentric, calculating, manipulative and have a deficit in what you might call moral reasoning or a conscience. “Someone with a psychopathic personality knows the difference between right and wrong but doesn’t feel it,” he adds.

Research in neuroscience and genetics has found that this behaviour is due to underlying structural differences in the brain.

The prefrontal cortex and the amygdala are parts of the brain that are responsible for impulse control and emotional responses such as empathy. In the brain of the psychopath these regions have been found to be reduced in size.

“When we are shown faces of other people expressing fear, a part of the brain known as the amygdala becomes active as we feel sympathy. This area does not activate in the brain of a psychopath,” Mitchell points out.

“Brain imaging shows that people classed as psychopathic don’t even show an emotional response to pain they might receive themselves such as an impending electric shock.”

Mitchell talks about a psychopath who was asked why he didn’t care if he caused pain to others. “He said he could sense pain as physical stimulus but it didn’t carry negative emotional weight. It was something to avoid but not in a visceral way. “Brain imaging would seem to support this clear disconnect between the intellectual and the emotional,” says Mitchell. Psychopathy may be the result of faulty brain wiring but it is not all that rare. It is estimated that about 1 per cent of the general population have this condition, so you’re probably on first-name terms with one.

Thankfully, most psychopaths aren’t like Dexter. “In fact, many do very well in jobs where these kinds of personality traits are seen as useful,” adds Mitchell.

What lies beneath

This is a copy of the piece I wrote for the Irish Times on all the strange and wonderful microbes found in the human body.

Forget what the ads for cleaning products would have us believe, bacterial micro-organisms are crucial for our wellbeing, writes MARIE BORAN

THE HUMAN BODY is a busy place teaming with alien life. Right now there are about 100 trillion micro-organisms inside you, tiny creatures that are living, dying, feeding, fighting, multiplying and happily occupying your inner space.

It is not one or two varieties but a whole host of organisms, known as microbes or micro-organisms to scientists but bugs to the rest of us.

“Microbes are virtually anything of microscopic size: parasites, moulds, yeast, and bacteria,” says Prof Colin Hill from the Alimentary Pharmabiotic Centre at University College Cork. “To date we’ve categorised over 2,000 of these wild and wonderful creatures that live in the average healthy human body.”

These microbes, mostly bacteria, are not harmful to the human body. In fact we enjoy a co-operative relationship with our native microbes. We provide them with a warm environment and food. In exchange they help us digest our food in order to absorb certain nutrients. “If you had no microbes you would be a very unhealthy individual. You wouldn’t be able to digest food and your immune system would be extremely weak. They live in harmony with us and with each other. One species can break down certain materials in the digestive tract and the other will harvest this.”

It’s not all harmony, however. There is a constant battle being waged inside all of us, says Dr Stephen Smith from Trinity College’s department of clinical microbiology.

“Thankfully most of us have a healthy immune system that protects us on a minute-by-minute basis. Every time we brush our teeth we introduce outside bacteria to the bloodstream but they are killed almost instantly.”

The immune system differenciates between friendly microbes, or “commensals”, and the disease-causing ones known as “pathogens”. Bacteria reside outside the protective layer of cells on the human body and once they start invading it sets off danger signals, says Smith.

Our body also naturally flushes out potentially dangerous microbes. This is one of the reasons we have tear ducts, explains Dr Conor O’Byrne from the Bacterial Stress Response Group at NUI Galway. “The surface of the eye is not a particularly great place for microbes to live because our tears contain antibacterial substances. Otherwise our eyes would become cloudy with bacterial growth.”

The importance of the good bacteria living inside us is highlighted when pathogenic bacteria make us ill. Many bacterial infections are treated by broad-spectrum antibiotics that kill the bad guys but a lot of the good guys too, says Dr Christine Loscher from the school of biotechnology at DCU.

“When you take these antibiotics orally they go straight into the gut. They tend to wipe out a lot of the friendly bacteria there. This is why many people experience cramping, digestive problems and suffer from diarrhoea afterwards.”

Not all good bacteria are wiped out and they rapidly multiply to repopulate your digestive system, Loscher says. “Dairy foods, especially yogurt, can help maintain the balance of good bacteria. This is something humans have been aware of on some level since ancient times. Fermented foods containing bacteria were eaten for this purpose.”

Modern science further understands the role that many of these microbes play in human health by profiling their DNA, the genetic material from which they are composed.

“Because of advancements like the Human Genome Project it has become easier to extract DNA from organisms. This is a bit like collecting evidence at a crime scene,” says Hill, explaining part of his work at the Pharmabiotic Centre. “If you want to examine bacteria from the gut or mouth you take a swab or a biopsy or perhaps scrape plaque off teeth. Putting it crudely what you then do is take the live sample, smash open the microbes, extract genetic material and sequence this to identify them.”

In the past microbial samples were placed separately on agar plates in a lab, but Hill says that this missed out on the complex interactions happening between different species. “These micro-organisms inside our bodies work together so when we separated them in the lab they didn’t grow.”

Microbiologists thought they had inner space figured out but were wrong, says Hill: “We thought we knew what was there but it was much more complicated than we expected. You could say microbiology has had a big shock over the last 10 to 15 years.”

One of the reasons for studying the behaviour of these microbes is that it could lead to the development of therapies or treatments, says Hill. These bacteria produce things and communicate with the immune system. “If we can extract these compounds and try to reproduce them in the lab maybe they can be used in development of new drugs.”

Despite all of this, bacteria get a lot of bad press, especially in commercials for cleaning products, says Prof Wim Meijer from the Conway Institute at UCD. “People don’t seem to realise that without microbes we wouldn’t even be here.”

Your body – a colony for trillions

IF YOU’RE ONE of those people who doesn’t like sharing your dessert keep this in mind next time a friend reaches over for a forkful. Each bite of chocolate cake you take is also being enjoyed by more than 100 trillion others, the microscopic life forms living happily in your gut.

Micro-organisms don’t just live in our digestive tract. They’re found in every nook and cranny of the human body from our eyelashes to between our toes. There are more than 2,000 known species and they have been colonising us from the moment we were born.

The vast majority of these microbes (more than 99 per cent) are strains of bacteria and most of these live somewhere in our digestive tract. There are also some viruses, fungi and protozoa too.

Overall there are thought to be about 1,000 different species present in the gut alone. They are so many microbial cells in the human body that they outnumber our own cells 10 to one.

“They’re everywhere. It doesn’t make a difference if you frequently wash your hands. The entire surface of your skin is teeming with them,” says Prof Wim Meijer from the Conway Institute of Biomolecular Biomedical Research at University College Dublin.

This does not mean that they pose a threat to our health. The opposite is true. “Our body’s native species are quite beneficial and provide us with certain vitamins and amino acids as well as forming a protective layer against disease-carrying micro-organisms,” he says.

“If you were somehow able to remove all of these microbes from the gut you would die rapidly and horribly,” Meijer points out.

We could theoretically survive without these co-operative micro-organisms if it were possible to live in a completely sterile, germ-free environment. This would bring on its own problems, however.

“The immune system would begin to misbehave and you would be hypersensitive to disease,” says Prof Colin Hill from the Alimentary Pharmabiotic Centre at University College Cork. “You’d also have to eat 50 per cent more food just to maintain energy because these microbes help us break down food and extract nutrients.”

Not all of our fellow travellers are harmless or beneficial, however.

“The most negative impact of microbes living in the oral cavity is the damage they cause to your teeth,” says Dr Conor O’Byrne from the Bacterial Stress Response Group at NUI Galway.

It’s not sugar that causes tooth decay. Bacteria love to “eat” sugar, producing tooth-unfriendly acids as a result, explains O’Byrne. The less sugar they find, the less acid is produced – another reason to share your dessert!