Showing posts with label Reviews. Show all posts
Showing posts with label Reviews. Show all posts

Tuesday, 7 October 2014

Synapse Review: Sir David Attenborough opens the Life Sciences Building by Daisy Dunne

On my first visit to Bristol’s Biological Sciences School back in 2011, I was marched across campus to stare at a giant empty crater on the corner of Tyndall Avenue, which I was assured would soon become the most impressive building the university has ever attempted to construct. Now, some three years later, the end result of the £54 million project is staggering – and who better to welcome in the new build than Biology’s biggest living legend, Sir David Attenborough.

At just gone 11am on Monday, I waited excitedly with an assortment of 200 distinguished guests, including senior lecturers and the city’s Mayor, for the esteemed naturalist and wildlife broadcaster to arrive and officially open Bristol’s new world-class Life Sciences Building. The university’s Vice-chancellor Professor Sir Eric Thomas welcomed us all before the now retired Vice-chancellor Professor David Clarke, who oversaw the building’s construction, regaled us with stories of some of the project’s difficulties – including the discovery of ancient gun powder under the old physics workroom that occupied the site.
Soon after, Sir David took to the microphone to deliver a compelling and personal speech, centralised around the importance of understanding the Natural Sciences to tackle the world’s most pressing problems. He stressed:
“The only way we will deal with the problems on this planet of ours that we have created is to understand what goes on… nothing, nothing could be more important in the area of scholarship than this.”
“Unless we understand the very systems on which we live, the food we eat, the air we breathe, unless we understand how our world affects us, we’ll be in real trouble.”
What’s more, he highlighted the importance of bridging the gap between science and the wider community, to make them realise “how important it is for us to do something”.


In addition to this passionate message, he also spoke of “the joy, resonance and delight” that can be conjured from the natural world, adding “understanding the natural sciences will give you joy for the rest of your lives, it brought great joy to me.”   
To finish, he professed: “I’m proud to be a freeman of this great city and also to hold an honorary degree from this very, very distinguished university”, before unveiling the building’s new plaque and declaring the building officially open.

After Sir David’s awe-inspiring speech, guests were given tours around the building to see some of the breath-taking features – including a 20 metre living wall, which houses 11 different species of plant as well as roosting spots for birds and bats. Also, guests visited the GroDome, a state-of-the-art tropical greenhouse that resides on top of the 13,500 square metre building.
For me, the most impressive aspect of the building is the five-storey glass laboratory wing, which supports ground breaking research from a multitude of different disciplines – from bat bioacoustics studies to virtual-led palaeontology. 
The new Genomics Facility is set to transform the university’s world class study into understanding the evolution and mapping of entire genomes. Professor Keith Edwards, a cereal genomics expert from the School of Biological Sciences, says:


"From the outset the new building was designed to have a state of the art genomics facility; including two next generation sequencers and a range of genotyping and robotic platforms. The new laboratories have been designed to minimise sample to sample contamination via the use of controlled air flow between rooms operating at different pressures.”

Image Credit: Nick Smith | University of Bristol

Saturday, 8 March 2014

Royal Society Wikipedia Editathon Celebrates Diversity in Science

by Julie Lee

On the 4th of March, I attended an event known as an ‘editathon’. This particular event gathered women in order to encourage them to contribute to Wikipedia. It was hosted by The Royal Society in London, in advance of International Women’s Day (today - 8th March). Among other reasons, the editathon was organised to increase the quality and quantity of articles on female scientists on Wikipedia. In addition, the event hoped to encourage women to be longer-term editors of Wikipedia.

The editathon took place over half a day, with an afternoon and an evening session. In the afternoon, Dame Athene Donald, fellow of the Royal Society and professor of physics at the University of Cambridge, provided a thought-provoking talk on diversity in science. In all other respects it was identical to the evening session, which I attended.

The event was led by John Byrne, Royal Society Wikimedian-in-residence, former Treasurer and trustee of Wikimedia UK, and 2012 ‘UK Wikimedian of the year’. Byrne gave a presentation introducing himself, Wikipedia, and good practice when editing. Additionally, his talk highlighted some problems in Wikipedia which the editathon endeavoured to fix - namely, the lack of female editors in Wikipedia (reports estimate about 9%) and the lack of quality articles on female scientists. These problems are likely linked and, further, contribute to the low public profile of esteemed female scientists. 

During the event, a group of 15-20 women worked on their laptops to help those problems, while expert Wikipedia editors roamed the room, providing advice as needed. We were encouraged to start our own articles on prominent women scientists - such as those featured by Discover Magazine. A few of us had some Wikipedia experience; however, most attendees were completely new to the game. By the end of the night, we came away with an enriched understanding of Wikipedia, better skills in editing, and a sense of accomplishment. While some critics may claim that the relative infrequency of good Wikipedia articles on female scientists is due to a simple lack of good female scientists, the event certainly challenged that view. The women we wrote about had held various directorial and professorial roles. 

Another problem Byrne described was that, in recent years, the public understanding of Wikipedia as a resource that anyone can edit has diminished. At the end, the event’s Wikipedia page showed several new articles had been made, in the span of only a couple hours. So, the event hopefully illustrated that anyone with a laptop and something to contribute can create meaningful resources for others to explore. In particular, scientists tend to grasp good editing principles right off the bat. I chatted to one of the Wikipedia volunteers, who noted that scientists are usually quick to understand why and when to cite articles - an invaluable part of making Wikipedia credible.

For those Wikipedia sceptics out there: yes, it is really easy to edit Wikipedia. Yes, there sometimes may be inaccuracies. However, Wikipedia is all about crowdsourcing, and within minutes most vandalism disappears. The editors on the wiki work tirelessly, on their own time, to make it great. So, before you criticise Wikipedia, think about how amazing it is that people around the world came together to make a highly-valued resource that print encyclopedias can only dream of. 

All in all, it was an enjoyable evening spent meeting other women and learning about the inner workings of Wikipedia. I would encourage people to visit the Wikipedia event page to examine the fruits of our labour: click here

Lastly, feel free to dive in and do some editing yourself! After all, that is the appeal of Wikipedia. 

Friday, 20 December 2013

The Musical Brain

2013 BNA Christmas Symposium overview

by Jonathan Smith

How does the human brain distinguish music from noise? What brain regions are active when we react to music? Do we all share an intrinsic musicality? How do you make a duck into a soul singer?

These important questions were discussed this month in an annual Christmas symposium held by the British Neuroscience Association (BNA). Speakers from all over the UK were invited to present their findings on the special relationship between Homo sapiens and music. These talks were also interspersed with live music, refreshments and humorous ‘Christmas Crackers’ such as the latter question asked above. In this article I summarise the research discussed in this exciting symposium.

Distinguishing music from noise by pattern-detection
It’s rare to be in a completely silent environment, even in university exams! Being able to tell apart rhythm from random noise is very advantageous. This is because we can be alerted to someone’s footsteps for example, which can let us calculate all sorts of useful information such as the proximity, speed and even mood of the walker.

Dr Maria Chait from the University College London (UCL) demonstrated that humans are incredibly sensitive to rhythmic, repeating sounds. This is even the case when our attention is diverted to other tasks - showing that there is continuous, sub-conscious processing that is very effective at detecting rhythms in our auditory inputs. This might go some way to explaining why all human societies feature some form of rhythmic musical tradition, including genres like polyrhythmic African drumming and thumping dance floor beats.

The Beat in society
It’s clear that an important component of most music is a regular pulse, or beat. The beat provides a regular structure on which we can build harmonies, rhythms and melodies. As demonstrated by the audience in a clapping task, humans are very good at detecting the beat of a piece of music and then moving in sync with it - in other words, dancing. Any Youtube video search would also reveal that our fascinating ability starts at an early age. What is happening in the brain when we detect a beat?

In studies by Dr Katie Overy of the University of Edinburgh, participants were tested to see if they could tell if the beat was repeated in patterns of fours, threes or twos, corresponding to 4/4, 3/4 and 2/4 times for musicians. Using fMRI scans to show active brain regions, Dr Katie Overy showed that groups of neurons deep inside the brain called the Basal Ganglia are very active when carrying out this task. The Basal Ganglia are highly connected regions that are really important in both sensory and motor processing, so this might be an interesting link between listening and moving to a beat. Not only this, but diseases involving the Basal Ganglia, such as Parkinson’s Disease, result in impaired beat detection. Perhaps by using music in more therapies we can provide better ways of treating Parkinson’s Disease and other Basal Ganglia disorders.

The emotional response to music
As most would agree, the soundtrack to a film deeply influences how a scene is portrayed. For instance, dissonant melodies convey discomfort and fear whereas smooth, major keys give a sense of calm and peace. At its most extreme, a piece of music can literally make our hairs stand up on end and give us the ‘chills’. This strong emotional response was measured by Dr Alan Watson of Cardiff University.

Dr Alan Watson’s lab used lie detectors to find out when we get the chills from a piece of music. This is due to the fact that lie detectors are very sensitive to changes in autonomic nervous system activity, such as sweating and pulse rate. Since our autonomic nervous system changes in response to strong emotions, the lie detector is a nifty way of showing when we get the chills! Using various imaging studies, the researchers were able to show that the chills are accompanied by a huge release of dopamine in the ‘pleasure’ circuits in the brain. This thus helps to explain why we can react so strongly to music.

Congenital Amusia and musicality
Some individuals are unable to enjoy music. Some, for example, even have trouble distinguishing between Happy Birthday and the National Anthem. These people may suffer from a condition called Congenital Amusia, a disorder of interpreting musical patterns. Yet, studies of these unique individuals may uncover just how innate musicality can be in the human brain. Dr Lauren Stewart from UCL collaborated with the BBC to carry out some of these studies.

Using a test called the Montreal Battery, the researchers found that people with this disorder have difficulty distinguishing musical tones compared with controls. They even have some trouble in detecting changes in speech tones, such as a question or a command. The research got more elaborate. The experimenters designed an artificial nonsense language and asked participants to detect if they heard a particular word in a phrase e.g. Pa-ti-ba. Interestingly, amusics were no different to controls, even when the ‘language‘ was replaced by musical tones! This indicates that amusia-sufferers may not have an absolute deficit in distinguishing pitches, but rather a lower confidence when doing so. This also indicates that a form of musicality is present in all individuals but can be honed by constant practice.

Dementia and music
Most of us are acquainted with someone who is going through the pain of dementia. It’s a very isolating ordeal for all involved and it’s expected to get much more common within the next few decades. Is music a good way of maintaining contact with sufferers who are gradually losing other precious memories?

Dr Jason Warren from UCL began by emphasising the complexity of music as a cognitive function. It’s encoded in many brain regions and evokes strong emotional and associative memories of events of that concert, party etc. All types of dementia have unique patterns of brain region damage. For example, Frontotemporal dementia (FTD) has specific damage in the knowledge-encoding temporal regions and the motor and emotion-encoding frontal regions of the brain. It turns out that FTD patients have selective impairments in identifying scary and angry music. This may prove to be an effective diagnostic tool because music is a much more robust memory than current tests using the memory of faces.


Peter Todd of the Alzheimer’s Society gave a fascinating talk about his experiences. He organises weekly singing groups called Singing for the Brain. The only difference here is that the participants are dementia sufferers at all stages of the disease. While it might not seem easy to pull off a group session with this requirement, the results of these groups are very encouraging. The groups have even performed at festivals and for BBC Radio 4! The aim of the groups is to include everyone at a personal level, no matter what level of dementia they are suffering. One heartwarming example of the good effects of these groups is of one patient who had lost his short-term memory. He couldn’t even remember that he had been in a singing group for the last hour! However, after every session, it was clear from his posture and manner that he was very upbeat from singing with the group, despite not being able to remember why! Examples like this emphasise the importance of music in social bonding for potentially lonely individuals going through dementia.

Wrap-up
It’s clear that music has been an integral part of human history. This shown by the presence of music in every human culture on Earth and the sheer amount of processing power devoted to music in our brains. The brain is a pattern-seeking machine and it has progressed from interpreting primitive vocalisations in forests to sophisticated music forms. Our emotional connection to music and musicality is preserved to a certain extent in everyone. It also proves to be an effective tool for identifying dementia symptoms and also encourages social inclusion for dementia sufferers.

Oh, and if anyone was curious about how you turn a duck into a soul singer, the answer is: Put it in the microwave until its Bill Withers.

Sunday, 13 October 2013

@Bristol Space Odyssey

by Laura Rogers


Ever wanted to play on all the exciting exhibits at the At-Bristol science centre, but felt too embarrassed as they are surrounded by children? Ever wanted to stargaze on the roof overlooking Millenium Square? Ever wanted to drink alcohol whilst at a museum? Well, adult-only nights at the At-Bristol are the perfect excuse.

I was lucky enough to attend ‘A Space Odyssey’, the adult-only night that enabled you to adventure into the depths of the sky and discover how we explore them. The night was from 6:30 to 10:00pm, however, this was not enough time to explore the whole venue and experience everything they had to offer. An insightful talk was given, in which experiments were conducted to show how satellites work. A personal favourite was when a spring was placed in hot water and immediately straightened. This phenomenon was applied to a model of a satellite, enabling it to open its wings via a current being passed through the wire, heating it up and straightening it. The welcoming Bristol Astronomical Society exhibited their telescopes, allowing us to observe stars in the sky. It was fascinating to see how a tiny spec in the sky was actually 2 stars, one orange and one blue. We had the chance to explore a recreated Martian landscape and analyse rock samples which was incredible.

At-Bristol has hundreds of interactive exhibits including: a giant hamster wheel, a walk in tornado, various water activities, exhibits to learn about the human body and many more. They were great fun to play with and helped to develop my scientific curiosity. We aimed to play with as many interactive exhibits as possible; my favourite was ‘startle’. This involved air suddenly spraying into your face, the reactions were recorded and played back in hilarious slow motion.

One of the latest exhibits, in the Zone, gives information on the science behind being a top athlete. It involves completing 5 challenges where you are set against an opponent. It was enjoyable and exciting, however, the only challenge I won was the final sprint finish! 

If you have seen the strange silver ball in Millennium Square, you may or may not know it is in fact a planetarium. You can take my word that it is much larger inside than it appears outside (Bristol’s Tardis) with a majestic screen spreading over the top of the sphere. We were transported from a view of the sky affected by light pollution to an astonishing view of the sky from a nearby countryside area. Just by listening to the audience’s ‘ooo’ and ‘ahh’ it was clear that everyone found the view spectacular. The autumn constellations were shown and a fantastic Astronomer, Lee, described the constellations and their associated Greek myths. This experience was breath-taking and is something I would highly recommend. I even recognised some constellation patterns and can now show off as I know the names and stories. 

The adult-only nights are great fun and enable you to experience the thrills of science through interactive exhibits, talks and demonstrations. The next adult only night is on Monday 9th December so keep an eye out for it.

Monday, 24 December 2012

The Neuroscience of Navigation - Christmas Symposium Review


by Jonathan Smith

On the 19th December in the Royal Society, the British Neuroscience Association (BNA) held a special Christmas symposium on the subject of the neuroscience of navigation, featuring topics ranging from ants and bird flocks to computer simulations for rodents! After these exciting talks, a concluding session of wine and mince pies went down a treat!

Not being overly familiar with the area around Pall Mall, I was forced to put my own neglected navigation skills to the test in order to arrive at the prestigious venue, the Royal Society, in time for the introduction by Professor David Nutt who is the current president of the BNA. In the introduction, he explained some of the background of research into navigation and outlined some of the latest developments that were being made by researchers. These covered a wide range of life, embarking from more basic organisms like the ant, passing through flocks of birds, crossing the development of navigation in mammals, traversing the fields of mammalian cognitive maps and arriving at the age-related changes in human navigation. Here, I try to summarise some of the fascinating presentations which deserve much more than a single article to review!

The first speaker, Dr Paul Graham from the University of Sussex, talked about the humble ant. Ants need to find food. They also must know where their own nest is in order to transport the food back home. But how do they remember where it is? In a series of experiments on the Australian desert ant, Dr Graham’s team worked out that these ants use visual panoramic cues to encode the locations of the nest and of food sources. Not only that, but they quickly set up a route between the two locations that becomes hard-wired and idiosyncratic, just like a human travelling the same route to work and back. That way, it seems that ants do not have a cognitive map of the area around the nest, but instead store information of food sources in relation to familiar cues (e.g. the location of the nest). It is thought that this system could even be the origin of our spatial cognition!

Dr Laura Biro from the University of Oxford presented her research into flock navigation. The research began with studies of individual pigeons establishing routes and expanded into simulating the flight paths of over 10 pigeons! How do these flocks decide which route to take? Firstly, individual pigeons develop idiosyncratic routes, similar to those in ants, that are based on visual landmarks. If you train two individuals with different routes and release them as a travelling pair, the results vary from either bird compromising its own route to them falling out and going their separate ways! Clearly there are complex leadership issues at work here. In flocks of more than two pigeons, there is a definite leader whose route is followed by the rest. This leader is not always at the top of the pecking order in social issues, but may possibly be the most efficient navigator of the flock.

But how do the flock decide who is the leader? This is a complex decision-making process that Biro et al have made strides in simulating. It may be that there is a hierarchy of each pigeon asserting its dominance over another in a similar fashion to winning Wimbledon - the champion proves that he plays better than the runner up and all of the runner up’s previous opponents. There is still much work to be done. Biro et al are currently working on good simulations for flocks of thousands such as those of starlings that form incredible shapes in the sky!


We then moved on to mammals. Next to present was Dr Emma Wood from the University of Edinburgh who dealt with the subject of encoding an intended destination into a memory. Firstly, mammals have neurons that fire only when the organism is in a specific location in an environment. These are called “place cells” and it is thought that these help to encode our location in space. There are also many types of these place cells e.g. some that fire at a boundary and others that fire when the mammals are travelling to an intended destination, called goal-dependent place cells.

Wood et al found through many behavioural experiments that these goal-dependent place cells were more active when the animal (in this case, a rat) was strategically planning to run to an area containing a reward. Additionally, through further experiments, they found that instead of mainly encoding the location of the destination, the goal-dependent place cells principally encoded the route to the destination. From this, a pattern is emerging that remembering routes is easier for an organism than just remembering locations and recalculating the route every time!

Dr Francesca Cacucci from University College London then talked about her research into the development of spatial cognition in rats. After birth, a rat takes roughly three weeks to develop skills needed for exploration of its surroundings. Interestingly, at approximately 19 days after birth, rats shift from being couch potatoes to intrepid explorers practically overnight! Cacucci et al think that somewhere in this transition the capacity for encoding spatial maps is developed. Rats are able to perform spatial memory tasks after around 20 days of age. This is largely dependent on a brain region called the hippocampus, so the implication is that the hippocampus is sufficiently developed to encode spatial maps. As navigation and memory uses many other navigational functions such as orientation, distance and boundaries, place cells (encoding the rat’s current location) in the hippocampus must be connected with orientational cells called head direction cells, map-encoding cells called grid cells and boundary-encoding cells called boundary vector cells. Work by Cacucci et al shows that these are not all connected before 20 days of age and could be the reason why spatial memory and exploration only kicks in at this age.

Dr Carlo De Lillo from the University of Leicester made a presentation based on searching systems in space. This was based on the concept that when making an efficient search of objects in an area, you can either form a structured way of searching them e.g. from left to right, depend on simply remembering which objects you have already visited or a bit of both. Experiments investigating how efficiently different species searched a set of objects in a room found that in comparison with rats, four-year-old children and capuchin monkeys made the most structured searches. Other experiments by De Lillo et al showed that humans in fact use structured searching as a complement to memory retention much more than other species. Put another way, it is like someone is searching through boxes and doesn’t have to remember exactly which boxes he has searched because he is working through them from left to right. This research could lead to many new tests of memory and executive function that could help in the diagnosis of conditions such as dementia and schizophrenia.


Next to present was Dr Jan Wiener from the University of Bournemouth. His research consisted of giving human participants the task of navigating a virtual maze with a set route and then retracing and rejoining the route from unfamiliar directions. Egocentric navigation is the strategy of recalling a route and exploring until your surroundings resemble this route. On the other hand, allocentric navigation involves being able to consider the spatial map independently from your own location and is needed for retracing a route and rejoining it. Experiments by Wiener et al on younger and older participants indicate that as we age, we become less able to use allocentric navigation than younger people and use egocentric navigation more and more, even when it fails to help us navigate well. Don’t panic just yet though - this ageing effect can be reduced by regular training!

The final speaker that day was Professor John O’Keefe from University College London who discovered hippocampal place cells in 1971 and was a member of the BNA in its infancy as a pub meet up! He outlined his most recent research into virtual reality for rodents. In order to generate a virtual reality for mice, his group set up a floating ball on which the animal is placed. Two screens project a scene which the mouse can move in while walking on this ball, similar to a hamster ball except with a virtual backdrop! O’Keefe et al found that a virtual scene resulted in similar amounts of place cell activity to an actual environment. Additionally, the team found that passively moving the mouse through the scene resulted in much less place cell activity, suggesting that place cell activity is largely based on active movement through a location. O’Keefe hopes now to expand the experiments to record hundreds of place cells in future as a better measure of encoding location.

Overall, the day was fascinating to attend and the discussions afterwards were very engaging. I benefited from the presentations as a way of glimpsing the world of neuroscience outside of my own studies to get the bigger picture of our progress. Oh, and the mince pies and wine afterwards didn't hurt either!

Tuesday, 16 October 2012

Website review - Codecademy


by Jonathan Smith

Being able to code is quickly becoming a useful skill to have, whether you want to write web programs or would just like to expand your CV! For many without a background in computer science, learning to code in a programming language can be extremely intimidating. For those who want to learn, there are many resources available on the web that offer to teach you how to write code in whichever programming language you want. In this review, the focus will be on Codecademy, a cool site that contains many free courses in an ever-expanding range of programming languages.


Codecademy is run by a group of hackers and programmers that aim to improve programming education worldwide without cost to the learner. It is an engaging and interactive site with a simple interface for easy use. The variety of examples offered is impressive – from learning HTML code to coding a game of Blackjack in Javascript! Courses exist for complete beginners that take you through the basics of writing code, step by step. The courses are made up of exercises that get you to input code into the browser in order to complete the exercise. By doing this, you progress to the next exercise and earn points for correct answers. This can get very addictive!

If you get hellishly stuck on an exercise, the creators do not step in. Instead, forums related to the exercise are easily available so you can find help from the community of users that are in the exact same boat. This works surprisingly well as users are always willing to help out. Speaking of users, you are encouraged to learn as a group as you can pool ideas. With this in mind, there is a 'follow' function that lets you link with other users and keep track of their progress. So if you and a friend want to learn together, then have fun! 


There are one or two issues that I would like to see improved in this site. Firstly, while it is beneficial to troubleshoot your own problems, it would be nice to see more feedback inside exercises as to where you went wrong. There is always the problematic exercise that fails because of a typo! Secondly, the obvious observation is that bugs still exist in some tasks though these are very rare and are sorted out very quickly when brought to the staff's attention.

In summary, Codecademy offers free, interactive courses designed to help you learn to code with lots of help from the community and I recommend giving it a try - that is if you can spare the time from your already busy university schedule!