The $1000 genome

My Dad has high blood pressure and my Mum had to receive treated breast cancer but what does this say about my future health? It is possible I have a predisposition to both these conditions but I may also never develop either. The difference comes down to what combination of genes I have inherited and for me to know for sure, my genome would have to be mapped.

The U.S. Department of Energy Human Genome Project Information Web site estimates it would take "about 9.5 years to read out loud (without stopping) the more than three billion pairs of bases in one person's genome sequence"^[*]. It therefore unlikely to surprise you that the mapping of your personal genome does not come cheaply. Currently, you're looking at around $50,000 - $100,000 which only seems affordable in light of the fact the first genome to be mapped in 2003 cost $3,000,000,000.

Now, however, a new technique for gene mapping is being developed that could bring the cost down to under $1000. This would allow personal genomics to become available for predictive medicine. As our Origins' colloquium speaker, Professor David Deamer from the University of California Santa Cruz, suggested, you could imagine having your own genome stored on a thumb drive to take with you when you visited your doctor.

Professor Deamer first conceived the idea for the $1000 genome over twenty years ago. He postulated that if it were possible to create a hole in a biological cell that was sufficiently narrow that only a single strand of DNA could pass through it, then the DNA components ("nucleotides") could be analysed and recorded as they were dragged through. Combined, this pattern of DNA components make up your genes^[**]. The question was what could be used to create such a tiny channel?

The answer to this did not emerge until ten years later and turned out to be a toxin called alpha-hemolysin. As its description suggests, hemolysin is not normally remotely desirable and is released during staph infections where it burrows into red blood cells and makes them explode (not good). In this case, however, its burrowing ability is exactly what Professor Deamer's team were looking for.

Alpha-hemolysin adheres to a cell's surface and makes a hole through the cell's structure known as a 'nano pore'. When a small voltage is applied, charged particles pass through the cell to create a tiny, but measurable, electric current. When a DNA strand attempts to pass through the hole, it can only just fit. This means it temporarily blocks the channel while it is squeezing through, causing the electric current to drop. The amount the current falls by turns out to be determined by which nucleotide is currently in the way. By measuring the change in current, the genome can be mapped.

The familiar picture of DNA is not of a single strand, but of the double helix. Tied up in this manner, the DNA cannot fit through the nano pore. Instead, it enters the broader, top part of the channel and get struck. From this position, it becomes unzipped until it can finally pass through the hole and out of the cell. The very exact size of the hole is important, since to record the genome accurately, only one nucleotide at a time must exit the cell.

Genome mapping using this technique is not yet available, but Oxford Nanopore Technologies have plans to produce a commercial device using this process. That being the case, there is only really one question left:

Are you ready to know what you really are?

--
[*] In case anyone is really curious, this figure is calculated by assuming a reading rate of 10 bases per second, equaling 600 bases/minute, 36,000 bases/hour, 864,000 bases/day, 315,360,000 bases/year. So there.

[**] Nucleotides make up DNA strands and stretches of DNA strands make up genes (in case anyone else was confused about the order of the extremely small).

Networks in the brain

So your friend Ben is married to Margaret who is friends with Rachel who shares an office with Rory who worked on a planetarium show with Rob who once received a detention at school for mooning Prince Harry [*]. 

According to the theory of the six degrees of separation, you are no more than half a dozen people away from receiving that front row invite to the Royal Wedding. The idea is that you are connected to every other person on Earth through an average of six people. It is a concept huge social network sites such as Facebook have been testing, but surprisingly it is an arrangement that is reflected in the structure of your brain.

All this I learned at the Royal Canadian Institute (RCI) 2011 Gala. The RCI was formed in 1849 by Sir Sandford Fleming. One of its original roles was to publish a scientific research journal in Canada but now its emphasise is on a weekly public lecture series which covers a wide range of scientific topics. In addition, the RCI helps with grants for students wishing to study science at university and it hosts an annual Gala dinner. The Gala is an opportunity to have a discussion over a great meal with a scientist. One of the twenty five tables at this year's event was hosted by my adviser, Professor Ralph Pudritz, but I shunned his table in favour for one led by a scientist working on the structure of the brain; a topic I knew nothing about. (When I told Ralph I'd rejected his table in favour of another he assured me he 'expected nothing less'. I don't think he meant this to be a reflection of my attention in our research group meetings.)

Our table was led by Professor Mark Daley who worked on models of the brain at the University of Western Ontario. When newly arrived at his institute, Mark explained that he had known very few people.

"But, I did know Mike." He gestured towards one of the other diners seated with us. "And Mike knew everybody. So if I needed to contact somebody elsewhere in the University, I could go to Mike and the chances were he knew them. This meant although I only knew a few people, I was connected to almost everyone else via only one person."

This, Mark explained, was the premise behind the six degrees of separation. There are a few people who know a huge number of others and these individuals act like hubs. People preferentially attach themselves to hubs (since the hub is likely to meet them through their enormous list of contacts) resulting in them being connected to a great many others through a very small number of steps.

What Mark said about Mike turned out to be entirely true. When chatting to him before dinner he had declared, "Oh, you're at McMaster! Do you know Hugh Couchman and James Wadsley?" I had to confess I did.

Mark continued by explaining that the brain organises its neurons along similar principals. There are hub areas in the brain which have a huge number of neurons connected to them and these link up regions which have sparsely few connections.

This structure can be explored with two major methods. The first is to take thin slices of the brain's grey matter and the second (more desirous for live volunteers) is to watch water flows via an MRI scan.

The consequences of this neural structure have important ramifications both for the effect of brain-damage and in understanding mental illnesses. Damage to one of these hub region, for instance, can result in the head injury being fatal because the brain simply cannot rewire to compensate from such a large loss of connections. Other times, the damage can be severe but limited to one specific area. Mark cited an example of a woman with damage to one hub who was left unable to see.

In most people, the number of hub regions is small and they are found is quite specific areas. One exception to this is in the case of people suffering from schizophrenia, where many smaller hub nodes are seen and in farther flung areas in the brain than for a healthy person. 

A question I asked was whether this was the underlying concept in electric shock treatment for depression? Was the idea to try and forcibly rewire the neurons by destroying their electrical signals and thereby forcing the brain to choose another (hopefully better) structure? Mark said that while this was the correct premise, such treatments were now strongly out of favour. He compared it with chemotherapy, saying you effectively killed a lot of neurons in the hope that you destroyed the bad pathways before you took out all the good. He did describe less invasive treatments which included asking the patient to think of something pleasurable directly after thinking of a traumatic event. Over time, the association can force the brain to rewire and help with post-traumatic stress disorder.

So what is is that governs our thoughts? Is the brain, as Penrose claims in 'The Emperor's New Mind', a system governed by random probabilities via quantum mechanics? Or are we, as Mark assumes in his work, simple Turing machines whose thoughts and actions can be completely predicted based on our experiences? Neither sounded particularly appealing.

"I want another option," I told Mark. He nodded and promised me one after he'd finished his dinner. The problem with being the guest speaker at a meal was the actual food was hard to fit in amidst the barrage of questions.

The third option, he explained as the plates were cleared, was that our mind is like a Bayesian machine which using a mixture of probabilities and input from its surroundings to make decisions. So when faced with the delectable crumble for desert, there was a very high chance that I would take the logical choice and eat it. Then there was the small probability I'd lob it across the table. I love feeling I have choice.

The crumble was rhubarb, in case anyone was wondering.

At the end of the dinner, each table was allowed to pose a question to another group to allow diners the chance to hear about the different areas being discussed that evening. The most important question was posed first and was directed at Professor Jeffrey Rosenthal from the department of statistics at the University of Toronto:

"What is the probability that Kate Middleton will wear a slinky wedding dress?"

"Slinky?" Jeffrey rose to answer the question. "This isn't as close to my area of expertise as you were led to believe!"


--
[*] Editor's note: any resemblance to real people, in the Physics and Astronomy Department or otherwise, is purely coincidental and Rob has never yet admitted to knowing Prince Harry. Or mooning.

Black hole menu

It is a depressing fact that over 95% of the Universe can't be bothered to interact with you. By looking at the speed with which our galaxy is rotating, we can infer that the amount of mass present must greatly exceed what we can see in stars and gas. This 'dark matter halo' is the cocoon in which our brightly lit spiral galaxy lives.

One of the puzzling features of these galactic cocoons is their wide range of sizes. It is surprising because the size of a galaxy is proportional to its dark matter halo, yet there are no galaxies found in very small or very large halos. It's a little like looking at the cities in Ontario, and finding everyone lives in Hamilton or London, but there is not a soul to be found in Toronto or Ancaster. Additionally, the large galaxies that do exist tend to have predominantly old stars, with very little cold gas from which new stars could form. So, in our Ontario analogy, Ottawa would be populated only by people over the age of 65.

The absence of small galaxies in small halos is explainable by the violent deaths of stars. As a star such as our sun reaches the end of its life, it will throw a large fraction of its substance into the surrounding area in an explosion called a supernova. In a small galaxy, this can blow so much gas out of the halo cocoon that it destroys the galaxy, leaving behind a star-less dark matter halo.

The absence of very large galaxies in the biggest halos however, is more of a mystery. The amount of mass in these galaxies would be so large that any gas that is ejected away from the disc by supernovae will be dragged back down by the gravitational pull of the remaining matter. In the last Origins talk of the semester, Professor Tim Heckmen from John Hopkins University in Baltimore proposed that the answer lies with super-massive black holes.

The most sinister objects in the Universe, a black hole is where so much mass has been squeezed into such a tiny volume that the speed needed to escape its gravitational pull is greater than the speed of light (and that's the fastest speed there is!). For the Earth to become a black hole, it would have to be compressed down to the size of a grape. Super-massive black holes containing the mass of billions of suns, reside at the centre of galaxies. How they have formed is hotly debated but what is known is that the larger the galaxy, the larger its super-massive black hole. Of course, something that destroys everything that enters it does not have the best PR, so going to these objects for answers feels like asking a kraken to attack a single ship; the probability of having any vessels left at the end of its foraging seems rather low.

Professor Heckman's theory is that gas close to the black hole is pulled towards it like water swirling down a drain. As it approaches the edge of the hole, the energy the gas is loosing (by dropping down the black hole-drain) is converted into heat at a rate that is much more efficient than nuclear fusion. The resulting radiation is the most intense source in the Universe. If enough gas falls in, the black hole can go through a 'feeding frenzy' and produce jets that evacuate huge holes in the galaxy. These jets fill the halo with hot gas, removing all the cold star-forming gas from the disc. If the jets are strong enough, the galaxy could be destroyed completely. If it isn't, then the resulting cavity around the black hole removes its food supply and the jets turn off. Yet, as the ejected gas cools, it falls back down to the galaxy, serving up another black hole dinner.

Why though, would this mechanism not occur in our own Milky Way, destroying us and smaller galaxies along with the bigger ones, kraken style? The answer, Professor Heckman explains, is that the super-massive black hole needs feeding with a lot of gas to produce the powerful jets. One possible source of this food is from supernovae as they blow away their outer layers. This gas might initially go into the halo, but as it returns to the galaxy, it could be drawn into the black hole which would then start to feed and produce jets. Larger galaxies will have more stars and therefore more supernovae, increasing the food supply to a point where jets can be formed. This means that the lifecycle and star production of a galaxy is intimately linked to its super-massive black hole. To understand one, Professor Heckman said, you need to understand the other.

At the end of the talk, there was one important question on the audience's mind:

Which came first; the black hole or the galaxy?

A picture is worth a 1000 words

While at a conference in Italy in 2009, I attended a talk on new observations of a nearby spiral galaxy. The speaker presented several interesting results but had to confess she did not have an image of the galaxy, since they were still waiting for data from the Hubble Space Telescope. From across the room of eminent astronomers came a collective sigh of disappointment.

It was hard not to laugh. In fact, I don't think I succeeded. The idea that professionals in the field would bemoan the lack of a pretty picture was deeply amusing; surely we should all be above requiring such frivolities? 

The truth, however, is that visualisation is an intricate part of successful science. Presenting your data in such a way that the main results stand out makes for better communication, without which scientific ideas cannot be shared, tested or accepted. This was the concept behind the "Science Illustrated" conference in Toronto that Masters student, Mikhail Klassen, attended last month and was badgered into talking about at the department's weekly journal club.

Mikhail explained that the conference discussed how the way you present your results can both help and hinder the viewer. Consider, for instance, the block of letters in the image at the top of the page. If you were asked to count the number of occurrences of the letter 'v', it would take you at least a few minutes to carefully examine each line. If instead each 'v' was coloured red, the task becomes a matter of seconds. A more extreme example is that of Anscombe's Quartet which is shown in the bottom half of the image. These four data sets have statistically identical properties, including exactly the same average and spread. If these were actual scientific measurements, a glance down the columns might cause you to think that they were showing the same result. However, if you plot them on a graph, you can see at once that they show completely different trends.

On the other hand, you can also choose to visualise data in a way that confuses the viewer. A famous example of this was a power point slide showing the current situation in Afghanistan. So crowded with interlinked lines was this plot, that General Stanley McChrystal, the US and NATO force commander, remarked dryly:

"When we understand that slide, we’ll have won the war."

A common error, if slightly less extreme than the above example, is to pick a bad colour scheme. Using colours that are similar to one another can obscure the trends you are trying to illustrate. Our brains also have a 'perception priority' when dealing with visual input, placing relative position above colour. This means that if an important result is, for example, the maximum density in your galaxy, it could be that plotting this on a line graph is more effective that colouring an image of the galaxy by density.

Mikhail went on to point out that there is also an ethical side to data presentation. By plotting two quantities against one another to demonstrate a relationship, you are excluding any information about other, possibly important, factors. A non-astrophysical example of this is a reconstruction of the Air France flight 358 that crashed in Toronto in 2005. From a reconstruction of the plane landing, it appears to be a pilot mistake; the plane drifts, touches down too late on the runway and over-shoots to crash into the creek (no fatalities). However, there is no weather information in the movie and eye witnesses report strong rain and winds with terrible visibility. As scientists, it is our duty to state clearly what is and isn't shown in our plots to ensure we do not mislead our audience.

Mikhail's final point from the conference was to remind us that communication of results depends on our audience. If we are presenting our findings to the public, we will be competing with Lady Gaga for their attention! This might lead us to choose difference visualisation techniques than if we were presenting to other astrophysicists. Although, if my experiences in Italy were anything to go by, that isn't necessarily the case.

--
[Thanks to Mikhail for sharing his (very clear!) slides from his presentation. The bottom right image showing plots from Anscombe's Quartet was taken from wikipedia.]

Sneaky little hobbitses

Despite what you may have claimed over coffee this morning, 18 million years of evolution separates your landlord from a gibbon. If it's any consolation, he's only about 5 million years from a chimpanzee. After that time, our own branch of the tree-of-life evolves through a series of distinct 'hominids' before producing grad students.

But who were our ancestors and what did they look like? Is it possible to distinguish them from other branches of the ape family tree?

This was the topic of today's Origins Seminar, given by Dr Dean Falk from the School for Advanced Research in Sante Fe, New Mexico. Dr Falk is what is referred to as a 'paleoneurologist', a peculiar sounding term for someone who studies fossilized brains. Ancient remains of mammals can have a cast of their brain (known as an 'endocast') preserved via sand and other debris filling the cavity between skull and tissue. This hard coating is protected from weathering by the fossilised skull which slowly wears away, leaving the natural endocast in its wake.

The process of analysing an endocast is not an easy one since it is only an imprint of the brain's surface, so no internal information regarding the neurons or chemical structure is preserved. However, by comparing endocasts from humans and apes with those from ancient remains, much can be learnt about our own evolution.

Of course, it does help if the ancient remains you are studying are not fake. A famous example of this situation is the "Piltdown Man". Discovered in the UK in 1912 in Piltdown, East Sussex, these fossilised remains were exposed as a forgery in 1953. Rather than being the missing link between humans and chimpanzees, this skeleton was created from a human skull attached to an orangutan's jaw. The teeth had been filed down and the bones stained to look like a single specimen. In part, its success as a hoax was due to it fitting in with the preconceived idea that a measure of evolution was the brain-case size; the prevailing belief was that brains became bigger first and the rest of the body, including the jaw, changed afterwards. The discovery was also pleasing to local scientists who embraced the idea that the first human was an Englishman!

In reality, however, the first hominids were found in Africa. Ten years after the 'discovery' of Piltdown Man, Raymond Arthur Dart discovered the remains of the 'Taung Child' in South Africa; a fossil dating back 2-3 million years. With its small ape-sized brain and location far from England, the Taung Child contradicted everything seen in the Piltdown Man, making it a controversial discovery. Dart examined the brain endocast and concluded that, while the brain was relatively small, it was advanced due to its structure. In particular, he identified two groves whose positions matched those found in humans but not in apes.

Ultimately, Dart's analysis was proved to only be partially right, but the technique of examining the position of the brain's major groves (sulcal patterns) is the main way of differentiating hominid brains from our ape cousins. These differences come about as regions of the brain that were previously separated become more interconnected in humans.

Interestingly, our own ancestors were not the only bipedal species walking around Africa 300 million years ago. Paranthropus are thought to be an extinct hominid species, unrelated to us. Their brains were characterised by a prominent central ridge from which strong jaw muscles would have been attached. Our relatives were the Australopithecus africanus, of which the Taung Child is an example. The migration and spread of A. africanus is thought to be north out of Africa and then into Europe and Asia. This has been called into question recently, however, by the discovery of a hobbit.

The announcement of the three feet tall hominid remains found in Indonesia came in 2004. The attractively named, "Lb1" was female with very short legs and therefore seemingly disproportionate long arms. Her feet were genuinely long, stretching a length equal to the distance between her knee and ankle. The remains were found with primative tools, similar to those found in Africa, and she would have lived alongside giant Komodo dragons, which is a slightly unnerving prospect for someone only three foot high.

At 417 cubic centimetres, Lb1's brain was chimp sized but the endocast revealed advanced features reminiscent of a human over an ape. Her discovery opens many questions, with schools of thought differing over whether Lb1 can be a new human species from our ancestry when her brain is small and she was found so far from the picture of migration out of Africa.

One thing that appears to be clear from the endocast discoveries is that brain evolution can occur in many different ways. It is possible to rewire and reorganise our grey matter without it becoming larger. This leads to different combinations throughout the fossil history; a difficult challenge to place in logical order. So in short, size does matter, but it's not just about how much you've got. It's what you're doing with it that counts.

Can you build a transmitter?

"You claim that there are many Earth-like planets while finding none!"

"But we have found many Jupiter-sized planets and they should be rarer than Earth-sized so the trend is pointing towards a large number!"

I was sitting in the audience of "The Great Extraterrestrial Debate", an event hosted by the Centre for Inquiry in Toronto. It was part of the organisation's "Extraordinary Claims" campaign which is designed to put some of today's most controversial allegations through a critical examination. This evening's topic surrounded the likelihood of alien life interacting with us on Earth.

The debate comprised of a panel of three individuals whose profession gave them a stake in this field. The first was Astrophysics Professor, Ray Jayawardhana, from the University of Toronto, whose research focusses on planetary formation outside our Solar System. The second was science fiction author, Robert J. Sawyer, and the third was Seth Shostak, a senior astronomer at S.E.T.I. (Search for Extraterrestrial Intelligence) Institute.

Despite being labelled a 'debate', it was stated upfront that all three panellists were in agreement; to this date, there has been no strong evidence for life outside of Earth. That said, the three unique view points being brought to the table did lead to passionate discussion. The above snippet was between Ray Jayawardhana and Robert J. Sawyer and was wrapped-up by Seth Shostak who pointed out:

"Ray and Rob arguing shows how hard it is to find stupid life. If they can built a basic radio transmitter (and you should all ask yourself now if you can do that) then their biology doesn't matter!"

Apart from the thinly veiled implication that S.E.T.I. would not count most of the audience as 'intelligent life', Dr Shostak's point highlighted a fundamental difference between his work and that of many astrobiologists; S.E.T.I. is only interested in life-forms that can talk to us. This bypasses all the problems with defining what life is and how we should go about detecting it when it is likely to be nothing like our own (a problem previously touched on in this post).

But is it really likely that we will make contact with aliens who can communicate with us?

Seth Shostak and Ray Jayawardhana both discussed the recently launched Kepler mission which is uncovering a flood of planets, with 1235 possible candidates identified in the first year of operation alone. This is in comparison to the 500 planets that have previously been discovered in the last 15 years. This huge influx of data in such a short time indicates the vast number of planets there must be in our galaxy which suggests that it would be a miracle if we were the only life to have been created on any of them. Dr Shostak also added that S.E.T.I.'s current failure to find life should not be interpreted as an absence of extraterrestrial intelligence. Currently, S.E.T.I. has only searched a tiny patch of the sky and declaring the Universe baron of life based on such a survey would be the equivalent of searching a square kilometre of Africa and concluding there were no elephants on the continent.

On the other hand, even if life did evolve on another world, we might have a problem with timing. Robert J. Sawyer made the argument that while the human race has existed for a few thousand years, there is a much narrower window between the invention of radio (needed for communication with S.E.T.I.) and the creation of the atomic bomb. It could be that almost as soon as a life-form can communicate, it self-destructs. Dr Shostak counted this by stating that the invention of rockets would take place in the same time-frame to launch the bombs, which gave the possibility of members of the species leaving the destroyed planet behind them to colonise somewhere else. He suggested that, like cockroaches, a life-form such as humans would be impossible to fully wipe out.


So ... if you're not able to build a transmitter, S.E.T.I. consider you too stupid to be interesting. If you ARE able to build a transmitter, you are analogous to a cockroach. Everyone feeling good? Then I'll continue...


Then there is the problem that if aliens were to appear, how would we react? Contrary to popular movies, it was deemed unlikely that such a discovery would cause rioting in the streets. For one, the signal would be coming from so far away that it isn't going to affect your ability to buy your morning coffee from Tim Hortons any time soon. Secondly, 1/3 - 1/5 of the population believe aliens are here already doing (and I quote Seth Shostak) "experiments your mother would not approve of", so a significant fraction of the world would not even be surprised.

Robert J. Sawyer suggested that it might be unhealthy for our own future to discover a more advanced life-form. If it could be shown that most life did survive their 'technological adolescence', then the human race might not strive as hard to solve its own problems, being content to let time take its course. Dr Shostak took this idea to a more personal level by saying that tenured professors might find it depressing to know all their scientific research had been solved a million years ago by this advanced alien race. Professor Jayawardhana, however, seemed to think this would save on having to publish more papers!

Finally, Robert J. Sawyer pointed out that S.E.T.I. did make one very big assumption:

That life, if it's out there, would be remotely interested in us.

Moving through a living cell: a mystery

It was a suspicious case.

To all appearances, the motion within the living cell looked thermal; a movement of particles caused by heat. Yet the temperatures needed to produce that degree of motion exceeded 30,000 K. That would equal one very very dead cell.

So what was going on?

A question about living cells was a surprising one for a Physics colloquium. The visiting speaker was biophysicist Professor David Weitz from Havard University, and he assured us that he was constantly reminded by his biologist colleagues that he still thought very much like a physicist. Evidently, this had not been meant as a compliment, but it was a relief to his current audience who looked slightly fretful when cells were mentioned in the talk title.

He started off by reminding us of the random walk that particles will perform if they are suspended in a liquid. The famous experiment in which this was first observed was performed by Robert Brown in 1827 who was examining pollen grains in water. There is a rather nice demonstration of what he saw here. This effect became known as 'Brownian motion'. The cause of Brownian motion is the water molecules that are buffeting the larger pollen particles as they move around. The temperature of the water dictates how much energy the water molecules have and therefore how much they will bump around the pollen particles. Since this motion is entirely dictated by heat, it is an example of thermal motion.

There is one thing, however, that must be true for Brownian motion: the liquid must be in equilibrium and not undergoing any overall changes such as heating or cooling.

And if there is one thing known about living cells it is that they are not in equilibrium.

So how was it that when tiny beads are placed into a cell, they move in the same way as pollen grains on water?

It was strange and a closer inspection of the situation proceeded to reveal two more mysteries: Firstly, between steps in their random walk through the cell, the beads would appear trapped. They would vibrate slightly as if caught on a spring before freeing themselves to move to their next location. This small-scale movement was not seen in normal Brownian motion, so did it have a different cause or was the same force responsible on both scales?

The second oddity was that if the temperature of the cell was fixed, but all chemical activity ceased, the motion stopped. Brownian motion, being thermal, is entirely dictated by temperature. If the temperature remains constant, all Brownian-type movement should continue. Here in the cell, though, the lack of chemical activity was a clearly a key factor.

It was looking more and more as if this motion only looked thermal, but was driven by something else entirely.

Professor Weitz's group then studied the motion of the cell's microtubules. These are the most rigid structures within a cell and their movements, like that of the beads, can be measured. By creating a controlled cell-like environment in the lab, conditions within the cell could be changed to monitor their effect on the microtubules.

Really, it was a lot like simulations where I turned on physical processes such as star formation one by one to see their effects on an evolving galaxy. Galaxies ... living cells ... clearly they were all the same!

The results from these experiments pointed to the presence of a driving force that was shaking up the cell's internal network. In addition to the microtubules, the cell has a support structure of smaller filaments and it was these thinner components that were being moved about. The shaker was molecular motors; large molecules found in all living organisms. These can change their shape when they come into contact with ATP --an energy transmitting chemical-- causing material around them to deform. This motion of the smaller filaments pulls in different directions around the microtubules causing them to undergo the small-scale trapped vibrations that were seen in the beads. As the microtubules grow, they bend under this jiggling surrounding movement causing them to distort or perform a random walk, just like the pollen grains in the water.

So the cause for the microtubules or beads movement was not so different from Brownian motion in that it was the motion of the small-scale surrounding material that was having an effect. However, the reason for the background motion was not heat, but the driving force from the molecular motors.

Case closed.

On the worries of graduate students

"I worry about flying."

It was lunchtime, although we were a reduced crowd due to it being reading week at the University. No classes were held this week and, with Monday being a public holiday, many people had taken the opportunity to go away for a few days. The rest of us were looking ahead to our plans in the coming months. Graduate student Tara Parkin would be flying out to Hawaii to observe on the James Clerk Maxwell Telescope on Mauna Kea in March. She is planning to observe several relatively nearby galaxies and trace the sites of cold gas where stars are forming. Depending on the weather, Tara is hoping to collect data not just for her own research, but also for projects being investigated by two other graduate students in her research group. Starting in Toronto, the flight to Hawaii will be a long one, taking a little over twelve hours.

"There's always the possibility of health risks," Tara elaborates. "Such as blood clots in your legs."

Deep Vein Thrombosis (DVT), sometimes known as 'economy class syndrome' can occur on long haul flights due to the long periods of immobility that entails. While the risk is not high, DVT can lead to the development of a blood clot, so it is important on flights more than five hours to move a little around the cabin.

"I also worry about giving talks. Even if the people are friendly, it's sometimes worse to know you are talking to your peers!"

I had definitely felt this way before, as I mentioned in this post a few weeks ago.

"So," I clarified. "flying and giving talks are the main worries?"

"And velociraptors," interjected Max Schirm, a graduate student working with Christine Wilson. "They are not good either."

An eye to the sky

Altitude sickness, the safety liability waver form told us, was unlikely to be severe below 3000 m. At 2715 m, the location of the Gemini South telescope in the Chilean Andes should be fine for most visitors but if it wasn't, we were commanded to mention it to observatory personnel. The two hour drive down the steeply descending narrow dirt track from the mountain top was not the place to make mistakes.

When the observatory heard our plans to accompany Gemini Fellow, Dr Michelle Edwards, on a tour of the telescope, they suggested this could be counted as an official visit since many of our group were astronomers. Such listing would enable us to stay on the mountain for longer if we wished. Michelle explained that three non-astronomers were also attached to our party but it wasn't until she added that a theorist was also present did Gemini write the whole idea off and give us tourist passes.

Set on the foothills of the Andes and backing onto one of the driest deserts on Earth, Gemini's position in Chile is an ideal location for astronomers to study the southern sky. The domes of three telescopes could be seen as we ascended the mountain. The 4.1m Southern Astrophysical Research Telescope (SOAR), the Blanco 4m telescope and our destination, the 8m Gemini South.

Half-way up the mountain is a look out point with three slender metal tubes mounted on the stone wall. These resembled smaller versions of the instruments we were going to see but in fact proved to contain no magnifying lenses and were just used to guide your eye to the appropriate glittering silver hemisphere. Strangely, one was pointing at an entirely empty space which turned out to be the planned site for a new telescope, the Large Synoptic Survey Telescope (LSST).

Gemini, as its name suggests, is one of two identical telescopes both with primary mirrors that are 8m in diameter. Its twin sits on the dormant volcano, Mauna Kea, in Hawaii where it points towards the northern sky. Currently, the governments of the USA, Canada, UK, Chile, Argentina, Brazil and Australia share Gemini's operational costs to enable their astronomers to observe at the two sites.

It was swelteringly hot when we reach the mountain top, but the inside of the Gemini dome is cool. It is important, Michelle explains, to keep the inside temperature to approximately what it will be at night when the dome is rolled back to expose the telescope to the night sky. If this isn't done, the hot air rises out of the dome and over the aperture to create a phenomenon known as 'dome seeing'; the distortion of an image from turbulence due to the hot air rising. This turns the telescope's sharp view of the stars into fuzzy blobs, a waste of the excellent view the observatory has from the mountain top.

The huge mirrored dish of the telescope is supported high above us as we stand at the telescope's base. Its silvered surface is refreshed every five years by a large saucer-shaped device that is stored in the observatory's basement. The story goes that when this equipment was delivered to a port in Chile, the locals believed it to be a discovered UFO.

Climbing up the blue frame work, it was possible to peek under the mirror cover and see the surface that would, in another 8 hours, be pointed at the heavens. This giant star-studying cyclops made my eyes seem weedy by comparison.

Over to the far right was Gemini's newest tool; GeMS, a five beam laser guide star system. Stars 'twinkle' because the Earth's atmosphere is distorting the star light, an effect that is much worse for an 8m telescope than for your 1inch eyeball. To compensate for this, a system called 'adaptive optics' was developed that allows the telescope's mirror to deform depending on the atmospheric conditions to produce the best possible image. These adjustments can occur at a rate of 100s of times per minute. To measure what changes the mirror should make, most telescopes use 'guide stars'. These are stars of a known brightness that show minimal variations and can be used to calibrate the system. Gemini's new instrument goes one better than this; by firing lasers up at the sky, they can build an extremely accurate picture of how the atmosphere is distorting the light over a very wide area. While four guide stars are still needed, they can be much fainter objects and an area of the sky 2-3 times that of traditional adaptive optics systems can be 'corrected' for in a single measurement. This allows for far sharper images, especially in crowded areas of the sky --for instance near the galactic centre-- where locating a reliable, bright guide stars is difficult.

Of course, shooting light up into the sky does come with some associated risk to other, non-celestial, objects that might be in its path. If care is not taken, the laser beam could blind either an aircraft or a spy satellite.

The latter, ladies and gentlemen, is an act of war.

The average observing run tries to avoid such inconveniences by co-ordinating the times they wish to use the laser system with US space command (totally didn't make that name up). They then receive a list of times they may not use the laser system in particular directions.

Avoiding aircraft is a less sophisticated business. Although in theory, the flight paths and times of planes are known, this information is not accurate enough to be used. Instead, 'spotters' are employed to stand in regions close to the telescopes with a device like a hula hoop with which they can estimate the distance to the plane and whether the laser system will pose a risk. When an aircraft approaches, the spotters can contact the observatory and ensure the lasers are not being used.

This ... advanced ... aircraft detection technique that is apparently used by million dollar telescopes all over the world seemed so completely implausible that I demanded its verification from both Michelle and two other observers who were in our group. Their stories were consistent. I decided no observer was ever in a position to criticize an approximation I made in my simulations ever again.

--
(Left image is the Gemini dome, top right is SOAR and the bottom right is the view over the mountains. Many thanks to Michelle for taking the time to proof-read this piece!)

Talk

While I was a graduate student at Oxford, the astronomy department ran something they called 'the secret seminars'. These were talks given by students for students as practice at presenting their research to an audience without feeling intimated by the far more knowledgable faculty.

I hated these.

The problem was that preparing a talk is time consuming, giving it is stressful and to do both the above without a seriously good reason when there is beer to be drunk down the local pub is hardly to be desired.

However, looking back, I think learning to enjoy giving talks is one of the most useful skills I have developed as a researcher.

Scientific papers are the currency of academia. Largely, the more papers you publish, the more successful you are considered to be and therefore the chances of procuring that next job or research grant are that much higher. While there is no substitute for this means of assessment, many of the people whose work I know best I became familiar with because I had heard them give a great talk at a conference or as a visiting speaker.

For me, once I realized that my audience were interested, not critical, and no one minded if I made the odd mistake, I relaxed and started to enjoy my presentations. As a speaker, you get to hog everyone's entire attention for the duration of your talk and if you're lucky, someone will be so excited that they'll invite you to their tropically-located institute to give a seminar when your own home is waist deep in snow. What's not to like?

I also feel that giving talks has done more to publicize my work than even my published papers.

With this in mind, I took the opportunity while visiting Santiago in Chile to give two talks; one at the European Southern Observatory (ESO) and a second at one of universities in the city; the Pontificia Universidad Catolica (PUC). While I was keen to visit both institutes, these talks did present two slightly unusual problems:

The first was that my entire audience was likely to be observers. That was, astronomers who actually looked through telescopes at real stars and did not just build them in a computer.

In my theorist's opinion, that is one weird idea.

Chile is home to many of the world's telescopes for studying the southern sky. ESO itself operates three observatories in the country to give European astronomers access to the second hemisphere. Chile's high mountains and the mercilessly dry conditions of the Atacama desert make it an excellent location for getting the most out of the instruments. This makes the Chilean capital of Santiago an observers' domain with few researchers familiar with --or possibly even interested in-- my own field.

However, I was confident. I had made a couple of movies from my latest simulation results and who doesn't like movies? Nobody. Plus, movies are almost impossible to do with observational data because you'd have to observe for millions of years to cover a reasonable period of time on astronomical scales. Despite what it may feel like, this is longer than your average PhD.

So there was no doubt about it; all those observers would be jealous.

The second problem was that my audience would primarily have English as their second language. English is the language of choice for astronomy (a fact for which I am eternally grateful) with all major journals across the globe published in that language. This meant that despite being in Spanish-speaking Chile, my talk was expected to be in English. While this was probably fortunate (I only knew three words in Spanish, one of which 'bano' --meaning bathroom-- I had only learnt that morning), it was harder for the younger students who were not yet used to receiving English at speed.

This I found a more difficult problem to tackle. If I spoke very slowly, then the talk would seem stilted to the more fluent English speakers. I'd also be able to cover much less material. On the other hand, if I spoke at normal speed, it might be too quick for the students to all follow.

In the end, I spoke normally but tried to ensure the key points were clearly visible on the slides for people to read. Plus, I had movies. Who doesn't like movies?

There is always a tense moment after talks where you wonder if anyone is going to ask a question or if you lost your whole audience after slide number two. In some ways, having no questions is great since they can be annoyingly insightful at picking up holes in your work. On the other hand, it might also imply your research was too uninteresting for comment, which doesn't bode well for people wanting to read your paper or remembering to invite you out for a drink after the next conference. To my pleasure and possible surprise, both ESO and PUC were very tolerant of the theorist who had arrived in their midst and sparked an interesting discussion after I had finished speaking. Not only was this beneficial to my work, it was also a relief to know what I had presented was interesting to this broad audience.

As to the second problem, one of the students had the solution himself:

"Could I have a copy of your presentation as a PDF document? .... Though I suppose that won't allow me to see the movies."

Everyone likes movies.

Catch a falling star

Observational astronomy normally conjures up images of sparkling white domes set on the edge of cliffs above ethereal views morphed out of cloud tops. For the Canadian Automated Meteor Observatory (CAMO), however, the reality ... is a pig farm. Literally. I couldn't help feel that southern Ontario had been a bit short changed. 

This particular swine-based observatory is one half of a twin set (the second is located a pig-free field 50 km away) of telescopes operated by the University of Western Ontario (UWO) that are used to measure the position and velocity of meteors. Paul Wiegert from UWO visited McMaster to give last week's Origins Colloquium and explained why they were searching for shooting stars.

A 'shooting star' or 'meteor' is the name of the flash of light in the sky caused by an extraterrestrial rock heating up as it falls through the Earth's atmosphere. Typically, a meteor will only be 3 mm in size but travelling at a notable speed of 30 km/s. Prior to its atmospheric entry, the rock is known as a meteoroid and if it actually reaches the Earth's surface before being completely burned up, it becomes a meteorite. To complete the journey, a starting meteoroid must be larger than sizeable 1 m in diameter. The biggest meteors are called fireballs, with the Peekskill fireball being one famous example. This fell over the United States in 1992 and was recorded on the camera of a woman who happened to be filming her son's football match at the time. The resulting meteorite struck a car that was for sale, raising its price from a few hundred to a quarter of a million dollars. A second example was the Grimsby fireball which fell in 2009 and was filmed here at McMaster by an instrument owned by Professor Doug Welch from the top of the Physics department.

Where, though, do these Earth-bound rocks come from? Professor Wiegert explained that there are three possible sources. The first is from comets in our Solar System; dirty snowballs that heat up as they approach the Sun, producing a tail of rocky particles. These objects are usually trapped by the Sun's gravitational pull in the same way that the Earth is, but are on highly eccentric orbits so their passes by the Earth can be up to thousands of years apart. Should the Earth's orbit intersect the orbital path of a comet, the extended trail of debris left in the comet's wake can produce a meteor shower, such as the annual Perseids shower each summer: a more attractively stunning version of the trail of slime left by a departed slug.

A second source of meteors is a collision between two asteroids or a planet with an asteroid; rocky bodies that are smaller than planets, but also orbit around the Sun. The larger meteors that survive their decent to become meteorites typically come from this source. Contrary to what you might expect, a meteorite is typically cold when it reaches the ground. This is because it consists of the core of the meteor that is not burned up travelling through the atmosphere. The end part of the meteorite's journey is known as the 'dark flight' where it falls from the average height of a commercial aircraft without burning. The fact that this rock is not heated to high temperatures has important implications for the transmission of life across space; it could be possible that microbes shielded safely in the cold core of meteors might survive to populate a new world.

This consideration leads to the question as to whether there is a third source of meteorites: solid particles that originate from outside our Solar System. Since we find evidence of asteroid collision debris from the Moon and Mars, might we not also have received material from further away? From star systems billions of kilometres from our own?

Material from Mars found on Earth is not uncommon. It is estimated that around 500 kg or 15 individual meteorites per year hit the Earth from the red planet. However, the vastness of space makes interstellar rock transfer a whole new game. Approximately 100 rocks with diameters greater than 10 cm (the minimum size needed to protect biological molecules in space) are estimated to leave our Solar System from a terrestrial planet every year. Unfortunately, that only equates to the chance of striking another terrestrial planet to be a minute 10^-4 per billion years. Even if you were to lower your requirements and ask what the probability was of such a rock merely being captured by another star system, in the hope that this would eventually lead to a collision with a planet, the chance is only 1 per billion years. This makes the odds of us receiving biological material from another star system incredibly unlikely.

What though, asked Professor Wiegert, about smaller meteorids? Ones that are too small to be biological carriers but might still arrive in the Earth's atmosphere? Are we able to detect these and get a handle on how many we receive? It was this goal of finding such tiny object that CAMO was designed. Such small pieces of material will be very hard to detect, especially since they will burn up long before you have the chance to hold them in your hand and put them under a microscope. However, if they come from outside the Solar System, their expected velocity is very high, equal to around 20 km/s on arrive in our Solar System which will be accelerated to 46.6 km/s as they are drawn towards the Sun.

So has CAMO detected any of these interstellar visitors?

Possibly; but it's very hard to confirm. One of the problems is the giant planets in our Solar System, namely Jupiter and Saturn, are able to sling shot rocks to much higher speeds that they would otherwise obtain, making it look like they originate from further afield. It is important for CAMO to get an accurate measurement for both the meteor's position and velocity to rule out this possibility.

CAMO began taking data only last summer but perhaps soon we will know if our atmosphere is receiving the most distant of visitors.

Mission to Mars

"Would you go?"

The question was from my office mate, Kelly Foyle, a postdoc working with Christine Wilson on observations of star formation in disk galaxies. We were discussing the first Origins Institute Colloquium of the year which had been given by Canadian astronaut, Dave Williams, on the prospect of a manned mission to Mars.

I considered my answer carefully. To be one of the first humans to set foot on another planet; what an incredible prospect! I could practically hear my eight year old self, fresh from my first trip to a planetarium, jumping up and down shouting 'take me, take me!' And yet ….

"No," I said slowly. "There's too much here I couldn't leave behind for so long."

The problem with Mars is that it's really far away. Both the Earth and Mars are on elliptical orbits around the Sun, which means that their distances from each other changes continuously. The closest they have been recently was in 2003, where they were 55,000,000 km apart. While that makes even a trip round the Earth (40,075 km) seem like peanuts, the furthest Mars and Earth can be apart is 401,000,000 km. This difference is why Mars is sometimes easy to see in the sky and at other times very hard to find.

Because of this distance, an expedition to Mars would take of order three years. It would comprise of 6-7 months travel time to reach the red planet, two years on the planet surface and another 6-7 months for the return journey. For comparison, the moon can be reached in three days while journeys to the International Space Station are quicker still. This presents any would-be expedition with a problem that has never had to be tackled before; what do you do when something goes awry and you can't just come back? All previous space trips have been able to have the back-up plan of returning to Earth quickly if necessary, but a Mars-bound vessel would have to 'abort to Mars' once it was sufficiently far away from Earth. Any repairs or necessary adjustments would therefore have to be able to be performed while in space with the tools and supplies already on-board. Even though advice could be received from Earth, the twenty minute latency on communications from Mars to Earth would be too long for medical procedures to be conducted via this method; the knowledge as well as the equipment would have to be with the astronauts themselves.

In addition to this, Dave Williams placed a lot of emphasis on the problems of keeping the astronauts healthy, both in body and mind. In the low gravity of space, the human body can start to waste away which causes problems when the astronauts return to Earth. For instance, while astronauts use their arm muscles to propel themselves around the space craft, their leg muscles get little use and loose their strength. The heart muscle deconditions and bone density drops at a rate of 15% per month. Astronauts can also suffer from lower back pain as their body elongates in an environment free of the downward pull of a planet. Dave revealed that he is 6' 1'' on Earth but almost 6' 3'' in space. There is also the unknown long-term effects from exposure to cosmic ionizing radiation; high energy particles that we are shielded from on Earth by the protective cocoon of our atmosphere. Dave explained that when you close your eyes in a dark room in space, you can still 'see' flashes of light that come from this radiation passing through you. What damage they might do over a long period of exposure is unknown.

There is also the mental strain of being contained in a confined area in extreme isolation for such a prolonged period of time. Entertainment and variation in food will also be difficult, since astronauts will grow bored of eating the same meals for several years.

Once on Mars, the astronauts will be in a strong gravity field once again, although Mars' gravity is only 40% that of Earth. However, unlike on Earth, there will not be people able to help the new arrivals until they can re-adjust to the forces on their body and there will be much work to do.

To combat these problems, exercise machines have been developed specifically to keep astronauts in shape while in space. Harnesses are used to pull the user down onto the running machines and a DVD player screen help maintain a sense of orientation. Meanwhile, the University of Guelph is researching into producing crop yields on another planet and NASA are exploring different possibilities for transportable shelters to take to Mars. Dave mentioned the idea that the perfect candidate for this mission might be different than for previous expeditions into space, due to the long duration and uncertainties being faced. He suggested that older people in their 70s might potentially prefer to make the journey, since their families would be grown and long-term health effects that could occur 10-20 years later would be less of an issue.

While the space program may not yet be recruiting astronauts specifically for the Mars mission, Dave thinks there is a high chance in it happening within our lifetime. It was a strange thought to think that you could be sitting beside the first person who will set foot on an alien world. Who knows? When I reach 70 I might even change my mind and be signing up myself!

So what is it really like in space? Dave told us that he gets the most questions about how astronauts shower and use the toilet when they stay at the International Space Station. He describes the shower, which looks like a cylinder with a lid. Soapy water is used to cover your body which is then vacuumed away. The toilet, he said, uses another vacuum system. The basic idea of such a device is that you want things to go away from you. On Earth, gravity does all the work when you flush, but in space a vacuum has to be used to remove the bodily waste from the toilet bowl, where it is then stored and returned to Earth. This final point left Masters student, Mikhail Klassen, with one question:

"Why, oh why do they bring human waste back to Earth when there is infinity on all sides of you?"

It was a mystery that would have to be left for another day.

Merry Christmas

There was a caveman named 'Ogg' who lived in Waterloo. Everyday, Ogg would drive to his job in Ikea, stopping first in Hamilton to pick up his work colleague, caveman 'Thor'. As the weeks went by, Ogg noticed the rest of the people he worked with were changing. They were becoming taller, their heads looked different and they started wearing more clothes. Eventually, he decided to ask about it.

"Don't you know?" his work colleague replied. "If you commute with a Hamiltonian you don't evolve."


No, this was not in fact an episode of the TV sitcom, 'The Big Bang Theory', but the Physics and Astronomy holiday party. Yes, I found the conformation to stereotypes alarming as well.... I also laughed at that joke. This was even more alarming. It was clearly time for another beer.

For those for whom quantum mechanics has not become part of their humour repertoire, the above joke plays on the name of a maths function called the Hamiltonian that is used to calculate the energy of a system, e.g. a particle attached to a spring. If another property of that system, for instance the amount of rotation it has (angular momentum), does not change as time passes, it is said to 'commute' with the Hamiltonian. Of course, the term 'Hamiltonian' could also mean a person from the city of Hamilton. So our caveman friend Ogg was commuting with the Hamiltonian, Thor, and therefore couldn't change over time or evolve.

... Yeah. The explanation doesn't make it a more excusable joke.

Merry Christmas everyone.

It's life Jim, but ..... 5/6 how we know it

Nov. 29, 2010:

NASA to Hold News Conference on Astrobiology Discovery
Science Journal Has Embargoed Details Until 11 a.m. PST On Dec. 2

It was to be three nail biting days of anxious waiting. Stress levels in scientists across the globe rose to values only previously seen the week before Apple's iPad release. At least half of Oregon packed a suitcase ready to be told alien Spock had made first contact and his buddy Tuvok had a spare room for guests. Kentucky loaded their shot guns.

Then the moment of truth dawned:

There's a bacterium 1/100th of the size of a human hair that hangs out in some pond in California and lives off arsenic.

Whereupon approximately half the audience fell asleep, half went into a state of frenzied excitement and the one person to actually understand its implications commented that this complicated matters. To know exactly why this one person felt this way, we need to understand what makes you and the microbes in your kitchen sink blood brothers.

We have long known that life can exist in some pretty unlikely places. Organisms aptly known as 'extremophiles' have been found to thrive in temperatures exceeding 100°C (hyperthermophiles), in solutions more acidic than lemon juice (acidophiles) and under bombardment of powerful ionising radiation (radioresistent). So while California's Mono Lake with one of the highest concentration of the deadly toxin arsenic on the planet might not make a swim resort, it is perhaps not astonishing that it should still harbour life.

However, the extremophiles, you, me and the microbes in your kitchen sink are all composed of six major elements; carbon, hydrogen, nitrogen, oxygen, sulphur and phosphorus, with trace other ingredients as icing to the biological cake. Until the NASA press release, these six fundamental building blocks were common to all forms of known life. In fact, while one could speculate otherwise, there was no evidence that life didn't require these six elements to exist. This meant that searches for life on other planets seemed to necessitate the detection of the presence of these seemingly essential ingredients.

The difference with the bacterium found in Mono Lake is that it is the first living entity to have been discovered that violates this cardinal rule. Instead of phosphorus, this microbe can use arsenic in its DNA. Since phosphorus is vital to cell reproduction, it might be considered a controversial move to substitute it for the second most favourite poison in Agatha Christie's famous crime novels (the first is cyanide, in case anyone was interested). It turns out that arsenic is actually chemically similar to phosphorus, sitting directly below it in the periodic table. This makes it a viable alternative.

The discovery that life can form using a different fundamental base of elements is immensely important for scientists who have been trying to imagine what life on other worlds would be like. However, there is one thing that this discovery is not which, if it were, would cause every astrobiologist in the world to pass out for at least a week.

It is not an unrelated form of life to us.

All currently known forms of life have a common origin. Nevertheless, it is possible to conceive that life might develop in multiple places on Earth independently of one another. An occurrence of a second genesis of life on Earth is known as a 'shadow biosphere' and could evolve in a completely different way to life that we know. If such a system were found, it would be evidence that life is not difficult to produce in the right conditions. That being so, it would increase the odds of life being present on other planets considerably.

Basically, it would be time to check that your best friend isn't from a small planet somewhere in the vicinity of Betelgeuse.

The case of the bacterium in Mono Lake is not a shadow biosphere. While this microbe can use arsenic, it can also use phosphorus and indeed will prefer to when given the choice. Moreover, Mono Lake has only become heavy in arsenic over the last 50 years. Prior to that, it had a source of fresh water, removing the environment in which an arsenic-dependent microbe could develop. This points to an organism that originally conformed to the established six building blocks of life, but evolved to survive in the increasingly hostile environment of Mono Lake.

While it may not be a new form of life, this tiny microbe opens the door to a huge number of questions in astrobiology. It particular, its discovery proves that we will have to be significantly more open minded when searching for life outside our planet. If there is no core pattern that nature cannot adapt when required, then what signatures can we design our detectors to search for? In fact, this microbe hasn't so much as opened a door as ripped it off its hinges.

References: the original paper for this research is science.1197258. There are also two excellent reviews at 'Not Rocket Science' and 'Bad Astronomy'.

When stars collide

"I have a visitor, Fabio Antonini, from the Rochester Institute of Technology who is here to work on the evolution of stellar collisions."

The email from Evert Glebbeek, a postdoc in the department working with Alison Sills, popped into my inbox and nearly made me pop out my chair. What did he mean this researcher worked on stellar collisions? Stars didn't collide! All the models I had made governing their motions through my simulated galaxy assumed this was the case. If it turned out not to be ... if it turned out stars did regularly slam into each other ... if it turned out that ALL MY RESEARCH WAS WRONG ...!

The email continued by saying that they were going for dinner at a local Indian restaurant that evening. I cast aside my keyboard and told Evert I would be taking the chicken vindaloo.

In fact, I need not have been so worried. The ratio between the size of a star compared to the distance between them is normally so large that even when galaxies merge, the stars do not run into one another. The chance of a star like our Sun hitting another star is so remote that we would have to wait for the entire age of the Universe for it to occur.

There are, however, other places in our galaxy where the probability of two stars colliding is much higher. The first is in dense clusters of stars and the second is in the centre of our galaxy, close to the super-massive black hole. Over dinner, Fabio explained to me that it was the latter scenario that he was investigating; looking at a population of stars close enough to the central black hole that they could be strongly affected by the force of its gravity.

Despite the frightening images that a black hole conjures up, if you remain outside its event horizon there is no particular cause for alarm. Objects that drift past this point can never be seen again, but stars at a greater distance can orbit the super-massive black hole safely in the same way as the Earth goes around the Sun. Yet Fabio told me there is something very strange about a few of the stars very close to our galaxy's super-massive black hole; namely, that they are very young.

Stars form when clouds of gas become dense enough that they collapse under their own gravity. Once this has happened, the object produced is very hard to break apart, but during its formation the cloud can be more easily disrupted by an outside influence. Close to the super-massive black hole, clouds are not able to form stars before the black hole's gravity rips them to pieces. Stars that are found in this region are therefore usually older objects that were born further out in the galaxy and have been scattered in over time. How there could be young stars so close to the black hole was consequently a mystery, but one Fabio thinks he has found a solution to during his PhD work.

Fabio postulates that a known mechanism for breaking apart binary stars might sometimes go the opposite way, and cause two stars to merge. In a binary system, two stars are born so close together that they orbit about a common point between their centres. When such a pair approach the super-massive black hole, the black hole's gravity can disrupt the binary, resulting in one star orbiting the black hole and the other being ejected out of the galaxy at high velocity. In Fabio's models, a similar event occurs but instead a star being ejected, the black hole's influence makes the binary stars collide and merge to form a single object. This new composite star has the same chemical composition as the two old stars, but is now twice the mass. This makes it appear to observers to be much younger than it truly is, since more massive stars evolve faster than their lighter counterparts.



This movie shows the results of one of Fabio's simulations[*] of a binary merging due to the gravitational influence of a super-massive black hole. The black hole is not shown directly, but its effects can be seen upsetting the orbit of the two stars which get steadily closer and collide, before settling into a single object. [Click on the movie to play and if that sadly fails click here. If you weren't concentrating and want to start the movie from the beginning but 'reload' is treating you badly, try hitting 'shift' at the same time as 'reload'.]

This was an exciting look at one of the most dangerous areas of the galaxy. Nevertheless, from the point of view of the fate of the Earth, I was rather glad we were hanging out in a quieter suburb.

--
[*] Journal reference: Antonini, Lombardi & Merritt, 2010, astro-ph/1008.5369 .

Answering the ultimate question

"That computer learnt word associations from Wikipedia. So it knows that 'opus' goes most commonly with 'Rome', 'sushi' with 'fish' .... and therefore 'robot' with 'violent genocide of the human race'?"

We were discussing the latest colloquium from the Origin's Institute which this week had been given by Geoffrey Hinton, a specialist (and indeed founder) on neural networks from the University of Toronto. Apparently, we had inadvertently stumbled across the cause of the downfall of humanity; that the tool used to teach computers about language also happens to include a scene-by-scene description of the 'Terminator' series.

An artificial neural network is like an electronic brain; it is a computer program that is designed to work in a similar way to biological neurons. Like the brain (and unlike most other types of computer programs), neural networks can 'learn' to do a particular task by being given many examples. They are used in pattern recognition (e.g. reading a person's handwriting) and for finding complex relationships (e.g. stock market predictions or medical phenomena, where the outcome is the result of many combining factors). 

In his talk, Professor Hinton took us through one of the early algorithms for teaching a neural network. In this technique, the computer is given data --for instance an image of a hand-written number-- that it must identify. It looks for specific features in the pixels, such as the presence and position of curves or straight lines, and then makes a guess. The guess is then compared with the correct answer and the relative importance of the different features being detected is adjusted to improve the algorithm. For example, a double loop would be very important since it identifies an '8', whereas a single loop is less significant since it could belong to a '0', '6', '9' or even squiggly drawn '4'. After this training, the computer program can be used to identify a wide range of hand-written numbers accurately.

This method works, but it has its drawbacks. Having a large number of fixed features that must be programmed for the code to identify makes the process slow, inflexible and results in poor scaling. Additionally, the fact it requires labels (e.g. 'number 1', 'number 2') to apply to the data differs from the way our brain works. Each image that our brain processes can rarely be categorised by a single label. For instance, a cow in a field has a colour, a position and key tell-tale signs that indicate it might actually be a man-eating Minotaur -- all of which are not encompassed in the label 'cow'. 

An improvement to this was to replace the pre-defined features that were given to the computer to identify an object with a set of criteria it created itself based on experience. This meant the computer no longer needed to know anything about the data it was being given. It could be a series of drawings of the number 2, pictures of houses or Minotaurs disguised as cows, and the algorithm would find common collection of characteristics that it could use to identify them. An example of such an identified feature for a '2' would be a wedge of light coloured pixels in the top left corner of the image, followed by a diagonal dark line -- the start of the 2's top arch.

Left to do this, the features identified by the neural network fell into two main categories; a small set of coarse criteria based on colour and a much larger set of finely tuned criteria based on shade. An example of both these types of characteristics would be a person standing against a wall. The sharp line between the white of the wall and the darkness of their hair would form a colour-based feature. Their facial features, meanwhile, would be picked out in a multitude of different shades in the same 'skin' colour. Interestingly, the resultant map of these computer-identified features closely resembles that of a monkey's brain.

Algorithmically, the set of data defining characteristics is honed by the computer program calculating first a set of features, then set of features of the features.... then a set of features of the features of the features. This leaves a collection of basic patterns that can be used to accurately identify the type of object for which the network has been trained.

An interesting question Professor Hinton than proposed was could such a neural network use its pattern recognition to predict the next stage of a sequence, rather than just identify objects? In particular, could a program predict the next word in a sentence?

To tackle this problem, the philosophical sounding question 'what is a word?' had to be answered. It turned out to be easiest to consider a word simply as a sequence of characters and to train the neural network to predict the 11th character in the string fed to it. This process could be continually repeated to build up entire sentences.

To teach the network about how words are formed, PhD student Ilya Sutskever gave the computer 5 million strings of 100 characters each from wikipedia. At the end of this training, the computer was told to build entire paragraphs of text to assess what it knew. It turned out to almost always produced real words. In the few occasions where it made some up, they sounded like they ought to exist. For example, 'ephemerable' or 'interdistinguished'. It was also good at semantic associations. It knew that many words that started 'sn' were connected with the upper lip and nose, e.g. 'sneeze', 'snarl' and, uh, 'snow' when used as a synonym for an illegal drug. (A fact noted by the speaker, not the author of this blog). Likewise, it knew that sentences containing 'opus' often also contained 'Rome' and that ones mentioning 'Plato' frequently went on to say 'Wittgenstein'. Similarly to the human brain, however, it often did not know why these connections existed. This produced sentences that made sense grammatically, but would not actually be found. For example, it talked about the "several Irish intelligence agencies in the Mediterranean' which is geographically unlikely.

A fact I found most surprising from this work was the length of information the computer program drew from. When deciding what the next character should be, it did not just look at the few before it, but at the long pattern of characters (that is, entire words) that preceded it. This allowed it to almost always use a consistent tense and to close parenthesise.

The knowledge could be applied to words it had never seen before. Upon being given two uses of the fictitious verb 'to thrunge', it guessed that the next character in 'Shelia thrunge' would be an 's' whereas the one following 'people thrunge' would be a space.

At the end of the day though, all Douglas Adams fans will agree that there really is only one question of any importance for a neural network trained on language. The computer was therefore asked to complete the ultimate question:

'The meaning of life is ...'

To which it replied:

 '.... literacy recognition.'

Clearly, it had been listening to students and postdocs panic about their paper count in the laboratory.

So are we close to really understanding how the human brain works? Professor Hinton took the opinion:

"It's a device with a few trillion parameters ..... how hard can it be?"

The littlest astrophysicist

While many a Disney princess had gifts bestowed on her at birth by magical fairy godmothers, the graduate student community offered their own type of benefaction to our newest department member, postdoc Evert's baby son, Arthur.

"If we all start speaking in Klingon, then the baby will become fluent!"

"How many actually speak...?" I cut-off my own question, deciding I didn't wish to know the answer.

Fortunately for Arthur, the languages he is most likely to first adopt are English and Dutch, since his parents are both from The Netherlands. (After which, a bazillion more will be added; because the Dutch roll like that.) Unlike his parents however, Arthur is also a Canadian, by virtue of him being born in the hospital here in Hamilton. As I counted the fingers of the tiny boy, I wondered if an equivalent term to 'army brat' should be created for children who seemingly have a random extra nationality, unconnected to any in their family. Perhaps 'postdoc spawn'. It could catch on!

In celebration of their son's birth, Evert and Tine brought in a traditional Dutch treat for the arrival of a newborn, "beschuit met muisjes" or "biscuits with little mice". This tradition stretches back to the 17th century and consists of a rusk-like biscuit sprinkled with sugar coated anise seeds. Blue and white seeds are used to celebrate the birth of a boy and pink and white are used for a girl. The name 'mice' comes from the little stem on the anise seed that resembles a tail.

Naturally, the birth of a baby results in many challenges for all concerned. For me, it was working out what the hand-made card announcing Arthur's birth said, since it was all written in Dutch. For Evert, new techniques that simultaneously supported stellar evolution investigations and baby evolution support needed to be developed. The currently favoured method is a one-handed devotion to each task. It could be that while Arthur's first spoken language is Dutch, his first written one is going to be FORTRAN.

[While no comment is made in the text, the reader is left to determine the gender-related split between primary interest in baby / food that the above photos suggest.]

When I was your age, Pluto was a planet

“A girl came up and told us that her teacher had said there were nine planets in the Solar System but she had tried to tell her that she was wrong, since Pluto wasn’t a planet, it was a dwarf planet!”

I looked up from browsing the photos that Rachel Ward, a Master’s student working on modelling the early stages of star formation, had taken at the Ontario Science Centre’s ‘One World, One Sky’ event in the middle of October. “How old was she?”

“Five.”

Huh. I was pleased to learn that someone was keeping up with the astronomical publications, even if it was not always me.

The event this had occurred at, and the pictures from which I was now perusing, had been an outreach initiative by Toronto’s astronomical community. It built on the success of the ‘International Year of Astronomy’, a year-long celebration in 2009 to mark the 400th anniversary of Galileo Galilei’s use of the first telescope. Throughout that year, institutes around the world had made a particular effort to hold public seminars, observing nights and (in the case of Japan) to create an astronomically-informative toilet roll. (For the curious, yes, I do have one. I refuse to comment on whether I have used it, although I will say that the first sheet is dedicated to the topic of my research).

The international nature of astronomy was the continuing focus for the ‘One World, One Sky’ event, which included talks about the role of astronomy throughout history as well as in society today. The ancient Egyptians, for instance, were very familiar with the night sky and used their knowledge to predict the annual flooding of the Nile, an essential part of their agricultural cycle. They recognised that the flood occurred when the dog star, Sirius, rose just before the sun, an event that took place each summer in late June. 5,000 years later, we see the heliacal rising of Sirius in early August due to our change in position as we move through the galaxy.

Modern day agricultural issues were later blamed on astronomy when the subject of crop circles arose during a panel discussion for ‘Ask an Astronomer’. Rachel, with fellow graduate students Aaron and Mikhail, took on the barrage of question from the public that ranged through profound (“What is space?”), taxing (“What is dark matter?”) and into the fictional (“What about UFOs?”). For the rurally curious, incidentally, the origin of crop circles is more likely to sit with the alcohol-fuelled back row of students than with an out-of-space phenomenon.

Rachel’s small solar system expert approached her while she was manning one of the booths demonstrating various astronomy based concepts. Included in this section of the day was the opportunity to build a comet out of frozen ice, carbon dioxide, dirt and (more surprisingly) windex, which was apparently used as a source of ammonia. There was also a race to build a space station, a meteorite collection and displays on the astronauts from around the world.

After hearing about all this, I realised I had to get back to work. There was at least one five year old eagerly waiting for my results.


[Photo caption from left to right: (1) Aaron answers a question during the 'Ask an Astronomer' panel discussion (2) Rachel demonstrates how to build a comet (3) Mikhail shows features on the surface of Venus to astronomers-in-training.]

Questioning the standard

Around 13.7 billion years ago, a hot, dense and infinitesimally small point started to expand rapidly in an event known as the 'Big Bang'. As it inflated, the matter within it cooled, condensing into galaxies and stars until it became the Universe we see today.

Ironically, the man who coined the term 'Big Bang' was not one of the founders of the theory, but one of its opponents. Sir Fred Hoyle was an astrophysicist at the Institute of Astronomy in Cambridge and is possibly better known for his naming of the theory he did not believe than for his ground breaking work on stellar nucleosynthesis; the mechanism by which stars form the heavy elements such as carbon and oxygen. Hoyle favoured a 'Steady State' cosmological model, whereby matter is continuously created as the Universe expands, so there is no absolute beginning. In 1949, he used the term 'Big Bang' (some claim derisively) while discussing his research on the radio, and the striking image this conjoured caused the name to stick for both its supporters and opponents alike. Since then, the Big Bang theory has become accepted as part of the standard model for cosmology and very little is heard of alternative theories outside historical reviews of the field.

For me, the first time I head anyone talk on a different model was this semester when Professor Jayant Narlikar was invited to speak at McMaster, giving talks both at the Origins Institute and in the Astronomy department. Professor Narlikar worked with Fred Hoyle while he was at Cambridge in the 1960s and, like his mentor, is a proponent of steady state theories. His affiliation with Hoyle and subsequent astrophysical career would have made him a speaker not to be missed, but I was also intrigued and (I admit) skeptical. Few people nowadays questioned the Big Bang theory, so was it not time for Hoyle's old team to drop their searches for an alternative explanation?

With this in mind, I listened as Professor Narlikar began his talk by explaining what had driven himself and his colleagues to seek out a new cosmological model. He explained that in 1948, the Armenian scientist, Viktor Ambartsumian, raised ideas about astronomical objects known active galactic nuclei (AGN). These highly compact regions were seen to be pumping energy into space, suggesting that they were violating two of the sacred rules in physics; the conservation of energy and momentum.

To explain these systems, Narlikar, Hoyle and a third astrophysicist, Geoffrey Burbidge, developed a variation on Hoyle's original Steady State theory which become known as the 'Quasi-steady State’ theory in 1993. Like the standard picture, Narlikar's universe contains dark energy that permeates all of space. In the Big Bang theory, however, the presence of dark energy causes the Universe to expand, whereas here it has the opposite effect, pulling the Universe in on itself. To off-set this, Narlikar introduces a second energy type called the "C-field". When the C-field energy gets very high, it creates both matter and space via Einstein's equation for the equivalence of matter and energy, E = mc², thereby continuing to conserve energy.

The C-field's strength increases around very compact, massive objects (such as AGN), causing a mass production of particles such as what Ambartsumian described. The standard picture of AGN is that they are black holes that are accreting mass that radiates furiously as it is accelerates. In Narlikar's model, black holes do not exist in the traditional sense, but are places where the C-field is exceptionally strong, producing explosive creation events of matter and space.

The resultant creation of space dilutes the C-field, eventually causing it to become much weaker than the dark energy which takes over and starts to pull the Universe back in. As space collapses, the C-field density rises until it once again dominates the dark energy and forces the Universe to perform another change of direction. It is a giant heart beat, lasting billions of years.

So can this be tested? Professor Narlikar's idea was straight forward; while most of the galaxies and stars would be destroyed as the Universe contracts, a few would survive into the next heart beat. Therefore, if we could find stars older than the Big Bang model gives for the age of the Universe (that is 13.7 billion years), it is possible that they came from a previous expansion phase in a universe that is better fitted by Narlikar's model.

Professor Narlikar's team conjectured that such surviving stars were likely to be ejected away from our galaxy during the turmoil caused in the contraction and expansion of the Universe. They therefore searched for old stars near one of our Milky Way's satellite galaxies, the Large Magellanic Cloud. Examining data from the Hubble Space Telescope, the astronomers found a number of candidates that appeared to be abnormally old. However, Narlikar's group were cautious; could there be alternative theories as to why these stars might appear much older than they really were? For instance, if the star was really not a single object, but two stars orbiting one another closely in a binary, it would be redder (and therefore seem older) than either twin actually was. Alternatively, their candidate might be not very old, but very young, too young to be accurately dated by the techniques they were employing. Finally, they might have made incorrect assumptions about the composition of the star, causing the age estimates to be off.

After considering all these points, Professor Narlikar concluded that, while they had possibilities for stars whose age exceeded 13.7 billion years, it was impossible to prove conclusively at this time.

I continued to think about Jayant Narlikar's talk for the rest of that day. It stayed in my mind not because he had convinced me that the Big Bang theory was wrong, or even because the talk had been well presented and interesting (although it had been). It was because it reminded me strongly why I became a scientist; to question all and every idea in the search for the truth.

In the 17th century, Galileo Galilei was condemned for his support of the Copernican model of the Solar System which placed the Sun, not the Earth, at its centre. (Amusingly, the Catholic Church only publicly vindicated him in 1992). This history is evidence for how easy it is to become complacent with established theories and loose track of what science is about. After listening to Professor Narlikar's talk, the direction my own research could go in seemed to double and triple before my eyes. I remembered that I should not be be confined by what people had done before, but rather use the ideas as stepping stones to go in any number of directions.