Monday 31 December 2012

Science in 2012

Ryan Hamnett

“As a layman, I would now say, ‘I think we have it.’ Do you agree?”

These were the words of Rolf-Dieter Heuer, director-general of the particle physics laboratory CERN in Switzerland, on July 4th 012, and officially announced the discovery of the long-sought Higgs Boson particle. But while evidence for the existence of the ‘God particle’ may have been the breakthrough of the year (if not the decade), there have been plenty of science stories grabbing headlines, both for innovation and controversy. Read on for a reminder of the stories you saw, and a few that may have slipped past you as well.

Physical Sciences 
The discovery of the Higgs Boson particle has not been easy – it took months of gathering data from over 500 trillion particle collisions at the Large Hadron Collider (LHC) at CERN. The staggering amount of data collected finally allowed the researchers to confidently claim that the new boson they had found, with a mass of 125 gigaelectronvolts, was indeed the elusive Higgs Boson, as predicted by theorist Peter Higgs almost 50 years ago. The existence of this particle is crucial to the Standard Model of physics – although somewhat unfortunately no other particles have yet been discovered. Baby steps, I suppose. For an opinion about the coverage and reception of the Higgs Boson, check out Issue 3 of Synapse.

Sometimes, though, the understanding of our world, solar system and universe just cannot be achieved with a particle accelerator; sometimes you need a hovering sky crane gently lowering a rover in the middle of a crater. Only NASA could have achieved a feat such as this, and in August the first low-resolution images from the Curiosity rover were received. While no signs of life have yet been confirmed, soil samples analysed by Curiosity reveal a surprisingly close composition to that of Hawaii. Further afield, more and more exoplanets are being discovered, with the closest one yet a mere 4.4 light years away orbiting Alpha Centauri, while another exoplanet 40 light years away is believed to be made entirely of diamond.

Despite these successes, NASA’s monetary support from the US government continues to dwindle, even resulting in NASA holding a cake sale to highlight this. Their lack of funds may pave the way for more commercial enterprises – this year saw SpaceX’s Dragon spacecraft rendezvous with the International Space Station, and of course Red Bull made Felix Baumgartner’s ascent (and rather more rapid descent) to the stratosphere possible.

Life Sciences
CERN was not the only organisation to acquire large amounts of data this year – the Encyclopedia of DNA Elements (ENCODE) project collected 15 terabytes of data over 5 years in order to characterise all of the ‘functional’ parts of the human genome. They predict that at least 20% of the genome is involved in regulating gene expression – with genes for proteins themselves making up just 1% of the total DNA. Another ambitious project was the start of mapping the wiring of the mouse brain, a project which complements the Human Connectome project also currently underway. With mouse models being common throughout neuroscience, understanding the similarities and differences between human and mouse brains will be invaluable in elucidating the mechanisms behind conditions such as Alzheimer’s disease and schizophrenia.

In medical science, stem cells continue to show their potential in treatment with the (controversial) discovery of stem cells in women’s ovaries which are capable of producing new eggs; this alongside the creation of egg cells from stem cells in mice by Japanese scientists in October. A powerful new painkilling substance with fewer side effects than morphine has potentially been found in a truly unexpected place – the venom of the Black Mamba snake. It appears to work by a different mechanism to conventional painkillers, although in its current form (being transmitted along with incredibly potent neurotoxins when bitten by one of the deadliest snakes in Africa), it probably isn’t quite ready for mass release.

The death of Lonesome George, the last known individual of the Pinta Island tortoise subspecies and symbol of the Galapagos Island conservation effort, occurred in June. But as extinction occurs, so too does the discovery of new species, with two of the world’s smallest vertebrates being found this year – Paedophryne amanuensis, a frog of just 7mm from Papua New Guinea, and Brookesia micra, a dwarf chameleon from Madagascar (juvenile pictured).

And, of course, no life sciences review would be complete without mentioning at least one GM story. University of Wyoming scientists genetically engineered silkworms to produce large amounts of spidersilk, which has higher tensile strength than that of steel. Future applications may include sutures and body armour.

Out of the Lab
While this year may have seen major scientific advances, controversy has never been far behind. A paper describing mutations to an H5N1 avian flu strain so that it was able to infect ferrets by air was initially only allowed to be published if certain details were left out. Only 5 mutations were required, and the US National Science Advisory Board for Bio-security was concerned that the information could be dangerous in terrorist hands. Eventually, the paper was published some months later.

At the same time, there has been a huge push for more transparency and open access to peer reviewed work. A key spark in this explosion was the boycott of Elsevier, Dutch publishing giants who critics claim charge too much for their papers, and are opposed to open access. While the campaign may have seen scientists stepping up to be heard, another story this year may cause the reverse – in October, 7 men were convicted of manslaughter for providing falsely reassuring statements before a major earthquake hit the area around L’Aquila, resulting in over 300 deaths. 

So there you have it – 2012, a year dominated by Olympic sport, has come to an end, and with it a year of discoveries, inventions and exploration. If there is one concept and, in the case of 2012, one headline-grabbing event, to sum up some of the biggest breakthroughs of the year, and to sum up science in general, it must surely be: Curiosity. Here’s looking forward to 2013. Happy New Year!

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!

Thursday 20 December 2012

Synapse Issue 3

Here is the third issue of Synapse Science Magazine. You will be able to find the printed magazine around the University of Bristol campus.

Monday 17 December 2012

Virgin Births in the Animal Kingdom

Louise Brown

Christmas is fast approaching, a tradition celebrating the tale of the ‘miraculous’ virgin birth of Jesus Christ. However in the animal kingdom, ‘virgin’ births are actually commonplace. This was brought into context with the now classic report of a captive female Boa constrictor giving birth to 22 offspring in two different litters; offspring that did not have a father. What makes this story so extraordinary is that although asexual reproduction is common in invertebrate species, such as insects and many marine creatures, it only occurs in less than 0.1% of vertebrate species.

There are a number of amazing forms of animal reproduction, and most of these are far from the “Male+Female=Baby” convention we humans are used to.  Asexual reproduction in invertebrates is simply a cloning process, with offspring being genetically identical to the parent. However, the way in which the Boa constrictor mother produced her young was by a special form of asexual reproduction known as Parthenogenesis. This term comes from Greek mythology; the goddess Artemis, called Parthenos ‘the Virgin’, was associated with nymphs who became pregnant. Parthenogenesis occurs as a female egg sex cell develops into an embryo without being fertilised by a male; although this is well documented in bees, wasps and ants, for this to happen in a vertebrate species is something very unusual indeed.

The Boa offspring were atypical in themselves; every single one was a female and bore a rare type of pale-sand coloured scales. This colouration is a genetic trait that is only passed down from the mother. This was the unexplained fact that alerted her keepers that something different was going on. During sexual reproduction, one copy (allele) of each gene is passed to offspring, one from each parent, so they end up with two copies of every single gene in their DNA. Therefore, for the new-born snakes to carry the sand-colouration, they must receive two rare forms of the gene causing it from their mother and father. The female Boa had been living with males, so this would be a plausible explanation for unusual coloured-scales in young produced by typical sexual offspring. However, there was a complication; the males present were known not to carry the rare form of the gene. This means that they could not have passed it onto offspring, meaning there is no way that the young could ever have carried that colouration via simple sexual reproduction. The only way the new snakes could have been that colour was if they have received two copies of that gene from their mother, meaning they must have received two copies of every single gene making up their DNA from their mother. This left only one surprising explanation; Parthenogenesis.

Further proof for this was the fact they had unique sex chromosomes; instead of the X and Y that humans carry, snakes have Z and Y. Usually, males carry ZZ and females carry ZW, but the young produced in this case had WW. This meant they must have inherited both of these chromosomes from a female parent.  No vertebrate in which the female carries the odd copy of the sex chromosome (in this case, W) has ever been recorded to carry both copies of this, meaning this story disproved what was thought to be impossible.

This is not the only piece of evidence that Parthogenesis amongst vertebrates is more common than ever believed. Other examples exist, such as the case of a Hammerhead shark female who gave birth to one pup despite there being no males or sperm present. There have also been cases of female Komodo dragons laying clutches of eggs independently.

Overall, Parthenogenesis has been described in about 70 species of vertebrates, including snakes, fish, lizards and even a turkey! However, it has never been documented in mammals and until not long ago, cartilaginous fishes. It was first suggested that it must never occur in animals that have a womb. Then, the Hammerhead shark, a species of cartilaginous fish, case that appeared a few years disproved this idea, illustrating further that we still have a lot yet to discover and learn about reproduction in the animal kingdom. Mary still has a lot to answer for…

Sunday 16 December 2012

Synapse science news #11

Too busy to keep track of all the science news during the week? Don’t fear Synapse is here. Check out this week's news.

New primate discovered -  Scientists have found a new species of slow Loris in Borneo. Read more.

Handy fish - Zebrafish are being used to study the evolution of limbs from fins. Scientists have been able to make them develop 'pre-hands' instead of fins by controlling their genes. Read more.

Norovirus in hospitals this winter - Wards closed to visitors due to vomiting bug.  For more information.

Global meteor show - The annual Geminids meteor shower took place this week, peaking on Thursday 13th. Don't worry, it is not related to the end of the world! More information here.

Felicity Russell and Tom Stubbs

Tuesday 11 December 2012

Festive or Digestive?

This image may look like some kind of neon winter wonderland, but it is actually a microscopic view inside a human intestine. More specifically, the image represents the cells that make up intestinal tissue. They just so happen to look like Christmas trees, together with a bit of snow from Photoshop! Dr Alex Greenhough and Paloma Ordonez Moran from the School of Cellular and Molecular Medicine at the University of Bristol created the image.

Sunday 9 December 2012

Synapse science news #10

Too busy to keep track of all the science news during the week? Don’t fear Synapse is here. Check out this week's news.

Urban adaptation - Birds are taking and using cigarette butts to repel pests. Read more.

Earth at night - NASA releases night-time satellite images of Earth. Check out what city lights look like from space here. See them here.

Catch-up with Curiosity - Curiosity is yet to find complex organic carbon-rich compounds essential for life. Check out the analysis of the Rover’s soil sample and the future plans for its Mars adventure. Read more.

Super solar power - Ghana government uses Feed-in-tariffs to incentivise building of largest African solar energy plant. It plans to provide electricity to 100000 homes, wow! More information.

Earth timeline from the BBC - Check out these stunning images illustrating the amazing events that changed our world through time here.

Invisibility cloaks coming soon? - Invisibility cloaks getting a step closer for all you Harry Potter fans. Scientists have been able to design a two-dimensional, unidirectional cloak. For more information, click here.

The life of a woolly rhinoA preserved woolly rhinoceros body reveals insights into how, the once most abundant mammal in Eurasia, lived. Read more.

Elephant concernsKenyan elephant numbers drastically decline in last 4 years. Check out how the demand for Ivory is threatening the existence on one of our planet’s most spectacular animals. Read more.

Saraansh Dave and Felicity Russell

Friday 7 December 2012

Batteries Breakthrough

Hannah Bruce Macdonald

Having been around for 200 years, you wouldn’t think that there would be much room for improvement in the field of Batteries. However, scientists at Massachusetts Institute of Technology (MIT) have managed to outdo themselves (and Duracell) by designing a battery large enough for grid-scale storage. Currently, the National Grid is playing the balancing act between the output of their generators and the consumer demand; which is particularly difficult when maintaining an alternating current (AC) of 50 Hz. This can’t be taken lightly with the responsibility of more than a slight fluctuation in this AC can cause electronic devices to fail in power surges.

The storage of energy would ease the stresses of this supply management, but the scales of energy concerned are huge and it is not as simple as building a comedy-sized battery. A normal dry-cell battery scaled up would require the combination of thousands of individual, can-sized, cells to be linked together; a complex and expensive solution. 

Liquid metal batteries may be the answer to this. In very basic terms the battery can be explained as a sandwich of three metals, a molten-salt electrolyte with a sunk, dense positive electrode and a light, floating negative electrode. The difference between the floating and sunk metals is what causes the voltage. This design is much reduced in complexity, making it a much more feasible option. With the figure of $15 million in investments from Bill Gates, Total and others, this new battery has been described as a cheap potential. This clever battery would be capable of charging from the Grid during the night while acting as a secondary generator at peak times during the day. Terrifyingly, the demand for electricity is predicted to exceed its supply in Manhattan in less than three years. This electricity crunch could be solved by these batteries storing excess energy at low times and then releasing it again when required. These batteries also lend a hand to renewable energy sources, such as wind and solar power, which cannot be relied on for consistent 24 hour supply.

The structure of a liquid metal battery

These batteries are still in relatively early development and the company Ambri are playing their cards close to their chest while they fine-tune and scale up their batteries to protect their design. The development in this area is still open with no front runner between liquid batteries and other options such as redox flow, lithium-ion and sodium-ion batteries. There may not be enough letters in the alphabet to label these batteries, but all I know is that I wouldn’t try licking it.

Wednesday 5 December 2012

Synapse team visits @bristol

The Synapse Team had a fantastic evening yesterday exploring the @Bristol Science Centre in the heart of Bristol, as we attended the centre’s first ever evening event. For those of you who have never been it really is a ‘must see’. With the children all tucked up in bed, we got the chance to fulfil some of our childhood endeavours, creating huge bubbles and Christmas decorations with LED lights, interacting with and occasionally squishing some animated bugs, moving water down a dam, running in a giant hamster wheel and even dressing up as dinosaurs. We were amazed by the tornado tunnel and were proved weak compared to the magnitude of atmospheric pressure.

If that was not enough to keep everyone entertained, there was the extra bonus of a science show in which a Christmas pudding went up in flames. The Planetarium left most of our members star struck as it took students out of the city into the countryside to view and enjoy the autumn night sky in its full glory. Not only did we learn about constellations, but were reminded of a few Greek myths at the same time. Some of us even had a go on ‘animate it’ and I witnessed a few sending their animated videos back to their housemates or even their parents (although they may not admit it). Some were also caught on camera as they enjoyed drawing the Aardman animations.

The human body section kept the majority of us entertained as the evening drew to a close. Members got to have a go at designing proteins, learning about microsatellites and reading through the genetic code of the X chromosome. After eating shortbread shaped like conical flasks and test tubes and enjoying the odd drink, the team finally headed off home in the cold, gazing at the stars, still buzzing with excitement. Thank you so much @Bristol for a wonderful evening, we will be back.

Monday 3 December 2012

Weird and Wonderful: Ladybird Mimic Spider, another real life Pokémon!

Tom Stubbs 

Meet Paraplectana duodecimmaculata, nicknamed the Ladybird Mimic Spider (or Ladybug Mimic Spider to our American friends). Despite belonging to the same group as tarantulas and black widows, this cute little critter looks just like a ladybird! In addition to resembling a ladybird this spider is also reminiscent of the Pokémon Parasect, from back in the day! Why, you ask, would a spider, that most people find scary, chose to look like a ladybird that is not associated with such fear. Well in the animal kingdom the bright colouration and spots of a ladybird represent a warning sign; they are what is termed aposematic. This visual warning system is designed to discourage predation by informing any potential trouble makers that the animal is not edible. In the case of the ladybird, they are filled to the brim with toxic and foul-tasting alkaloids. By mimicking the ladybird, the edible spider is using this colour system to avoid predators, this is known as Batesian mimicry. Intriguingly this spider is not alone in mimicking the ladybird, you also find other edible beetles using their colour patterns.

The ladybird mimicking beetle (right) has adopted the same tactic as the spider (left)

Saturday 1 December 2012

Synapse science news #9

Too busy to keep track of all the science news during the week? Don’t fear Synapse is here. Check out this week's news.

Men are from Mars and women are from Venus - New evidence suggests men and women view and interpret the world very differently. Evidence comes from a study conducted here at Bristol University. More information.

Long lasting bread - Wouldn't bread that can last 60 days be amazing. No more trips to Sainsbury’s just to make some toast! An American company says it has invented a way to make bread last 60 days by zapping it with microwaves to remove spores. Read more.

Holy moly! - The second largest black hole ever has been found. It resides in the galaxy NGC 1277, that is just a quarter the size of our own Milky Way. Find out more

Snooze you win - More sleep is the way forward. Even 2 hours can be as effective as a painkiller. Read more.

Imaging the famous corkscrew - Scientists have been able to take a photograph of a double helix for the first time, using an electron microscope. More information

Ice on the scorched world - What are the chances of finding ice on the planet closest to our sun? Very high according the NASA! Data from the Messenger spacecraft has recorded over 100 cubic kilometres of ice at the planet’s poles. Read more.

Overdosing on grapefruit - Research suggests that mixing grapefruit with prescription drugs can have very adverse effects. Find out more.

Pac-man on Saturn’s moon - Astronomers have identified variable heat signatures on Saturn’s moon Tethys that look like Pac-man! Read more.

Mary Melville and Katherine MacInnes