Features

Tomorrow at 2pm Susan Cheyne will be updating listeners to Radio Oxford on the progress of her conservation work in Borneo.

Susan, of Oxford University's WildCRU, is leading research into the agile gibbon and wild cat species for the OuTrop project.

We've blogged about her work before, including the amazing images and sounds of gibbons swinging through the trees and how camera traps set up in the forest have snapped photos of elusive species, such as the clouded leopard.

Above are a selection of the latest photos from her work: this year, the 8th they have been studying orangutans and the 7th agile gibbons, has seen the birth of 2 orangutans and 3 gibbons in the groups studied.

The project is hoping to make a real difference, not just to the forest apes but to the overall ecology of the rainforest: Susan has already raised over £7,000 to provide equipment to help combat forest fires and this year the team have started the first ever long-term regeneration project to re-forest the degraded peatland.

They are also offering a new training programme for the project's Indonesian staff to help pass on the skills needed to continue and expand the scientific and conservation work.

On Thursday she'll be explaining more about her research, and how members of the public can help, at an event at Science Oxford.

Dr Susan Cheyne is a member of the WildCRU, part of Oxford University's Department of Zoology.

Oxford start-up Plink Search Ltd has become the first UK company to be purchased by Google Inc.

The firm was founded in 2009 by Mark Cummins and James Philbin, two graduate students from Oxford University’s Department of Engineering Science, to commercialise technology stemming from their doctoral research.

‘Mark and I were both involved in developing visual search during our DPhils,’ James tells me. ‘Mark's research focused on visual place recognition for robot navigation, which culminated in the FabMap software. My own research looked at how visual search could be scaled robustly and efficiently to handle millions of consumer images crawled from sites such as Flickr.’

During their doctoral research, with supervisors Paul Newman and Andrew Zisserman, they realised that, although they were approaching visual search from different angles, their combined skills could reap dividends: making it possible to build a visual, rather than text, search engine that could power a mobile phone application.

James comments: ‘Our research really showed that large scale, accurate visual search was possible even with the poor imaging conditions of mobile phone cameras.’

‘By the end of our DPhils it was clear there was a great commercial opportunity,’ Mark explains. ‘The fact that there were two of us in the same lab with matching expertise and an interest in starting a company was pretty ideal.’

They decided to form a company to develop an application that could recognise art work from photos taken by mobile phones, using the FabMap code licensed from Isis Innovation as a starting point. Mark tells me: ‘It was a good baseline to start building Plink. The technology that a robot uses to recognise places versus how we do painting recognition on a mobile phone is really very similar.’

The start-up went from strength to strength with the PlinkArt application winning first prize in Google's Android Developer Competition, which identified the best applications for the Android phone operating system. It was announced today on the company blog that Plink Search is the first UK firm to be bought by Google.

‘We're both delighted with the acquisition and very pleased to be moving to Google,’ James reveals. ‘Being engineers at heart, working at Google will allow us to tackle some really interesting large scale vision problems with the computing power to back up our ambition!’

So how did their DPhil at the Department of Engineering Science prepare them for life as high-tech entrepreneurs?

Mark tells me: ‘I think doing a DPhil is actually a great route into starting a company. You get very deeply into some interesting technology, but at the same time you have the space to keep an eye on what's happening in the market.’

‘At heart we're engineers and absolutely did our DPhils for the love of it, but we were always aware of the commercial possibilities too. I think starting a company feels much more like a natural continuation of doing a DPhil than taking a job would be.’

A team, including Oxford University scientists, has achieved a new record for storing and retrieving data from an optical quantum memory, our friends PhysOrg.com report.

The researchers achieved a data rate in excess of 1GHz, 100 times what is possible with existing quantum memories, they explain in Nature Photonics. Such a speedy memory would be a key component of any future quantum computing or communications device.

The result was achieved by firing pulses of thousands of photons encoded with data into a cesium vapor cell. The vapor turns the pulses into a spin wave, and the information can be retrieved by a read pulse that converts the spin wave back into an optical signal that is picked up by a detector.

Ian Walmsley, of Oxford University's Department of Physics, told PhysOrg's Lisa Zyga: 'There are a few steps that are required [to achieve high bandwidth], but the main approach is to use atoms with a higher energy storage state, and to apply more sophisticated control pulse methods.'

'Our plans are to demonstrate the operation of the memory at the quantum limit, using an external source of nonclassical light.'

The team note that the bandwidth was limited only by the response time of the detector, so in theory the quantum memory could be capable of even larger bandwidths. Their method, based on a Raman interaction, could be applied to other storage media (such as cold gases and solid state).

Ian adds: 'Challenges for the future in general are to increase the number of bits the memory can store and the readout efficiency of the memories to the point when they can be used in applications such as quantum communications links.'

In films and books black holes capture unwary spaceships and planets, gobble up whole galaxies or offer portals to other parts of the Universe.

So the idea that, with the start of the Large Hadron Collider (LHC), physicists finally had a machine powerful enough to, potentially, create ‘mini’ black holes caused some alarm.

But what do we really know about black holes? And how would a ‘mini’ one be different from their giant cousins lurking out there in space?

‘The simplest black holes are objects with a singularity in the centre and that are surrounded by an ‘event horizon’,’ explains Cigdem Issever of Oxford University’s Department of Physics. ‘Once something comes closer to the black hole than the radius of the event horizon, it is not able to leave: even light can’t escape and so the name ‘black hole’ was given to these objects by John Archibald Wheeler back in 1967.’

A hole in the Sun
Producing black holes turns out to be about mass (energy): squeeze mass into a sphere with a radius equal to what’s known as the ‘Schwarzschild radius’ – a threshold beyond which gravity causes an object of a certain density to collapse in on itself – and a black hole will form.

‘In fact the size of the Schwarzschild radius is directly proportional to the amount of mass that is squeezed in, as well as being directly proportional to the strength of gravity,’ Cigdem tells me.

‘For example, in order to form a black hole out of our Earth, you would need to squeeze its mass into a sphere about the size of a marble (radius 8.9 mm). By comparison the Schwarzschild radius of the sun is about 3 km.’

So what would happen if we swapped our Sun for a black hole?

‘If we replaced our Sun with a black hole of the same mass, surprisingly, not much would change in our solar system. The planets’ orbits would stay the same because the gravitational field that the black hole would produce would be exactly the same as that of the Sun. Although, admittedly, the solar system would be a bit dark and cold!’

But Cigdem’s interest in black holes isn’t theoretical, as a particle physicist she will be searching for signatures of ‘mini’ black holes in the LHC collisions:

‘I became interested in them as a particle physicist back in 2003 because extra dimension models predicted that they may be produced in high-energetic cosmic rays and, if so, even in particle accelerators. If we are really able to produce them, they could give us experimental insights into quantum gravitational effects.’

She hopes that studying them may lead to a formulation of a theory of quantum gravity: marrying Einstein’s theory of general relativity (which describes gravity on large scales) with quantum mechanics (which describes physics at very small distances).

The LHC is colliding protons on protons. These protons are made up of smaller constituents, the so called ‘partons’ which are actually the particles the LHC is colliding. The Schwarzschild radius of two colliding partons – quarks and gluons for example – at the LHC is at least fifteen orders of magnitudes below the Planck length - the smallest distance or size an object can achieve in our conventional universe.

‘This means that, in conventional models of physics, there is no way a black hole could be produced in a collision of two partons. However, there are models on the market suggesting that the strength of gravity could become significantly larger at very small distances, up to 10 to the 38th [10 with 38 zeroes] times stronger,’ she comments.

‘If this is true then the Schwarzschild radius of two colliding partons becomes large enough that, at the LHC centre-of-mass energy, two partons passing each other at their Schwarzschild radius is not so unlikely anymore. So, we may be able to produce microscopic black holes after all.’

Who's afraid of a 'mini' black hole?
So what would these tiny black holes be like? Should we be worried about them?

Cigdem tells me: ‘According to Stephen Hawking, they will not be that black in fact. They will evaporate with time approximately following a black body radiation spectrum. The evaporation rate will be inversely proportional to the black hole mass.’

‘Astronomical black holes are so massive that their evaporation rate is negligible. In contrast, mini black holes are hot: unimaginably hot. The core of our Sun is at around 15,000,000 degrees Kelvin - to get close to the temperature of a mini black hole you would need to add another 42 zeroes.’

‘What this incredible temperature means is that mini black holes of tiny mass ‘evaporate’ into the far, far colder space around them almost infinitely fast. Their expected lifetime is around one octillionth of a nanosecond – so that they pop out of existence again almost as soon as they are created.’

If they do appear they will almost instantaneously burst into many particles which the ATLAS detector should pick up.

‘These particles will have very striking features. The total energy deposited in the detector will be of the order of a few TeVs [Tera electron volts] and the number of final state particles will be large. Black hole signatures can hardly be imitated by any other new physics so, if they are being produced, it will be hard to miss them,’ Cigdem adds.

So the hunt begins: on 30 March the LHC is aiming for collision energies of 7 TeV that may enable us to see some quantum gravity effects for the first time.

At the beginning of this year Dr Cigdem Issever moved to CERN to coordinate the efforts of the ATLAS Exotics physics group.

Read more about this topic in What black holes can teach us by Sabine Hossenfelder and the LHC Safety Assessment Group report.

In the second of a series of articles marking the 10th anniversary of the Human Genome Project [HPG], OxSciBlog talks to Professor Chris Ponting of the MRC Functional Genomics Unit at Oxford University.

Chris explains what we can learn about ourselves by comparing our DNA with the genomes of other animal species.

OxSciBlog: What genome efforts have you been involved with?
Chris Ponting: It all started when I was phoned up and asked whether I’d like to help coordinate a set of analyses for the Human Genome Project. Of course, I jumped at the chance but still feel it ironic that, as someone who gave up biology at school at 16 to focus on a training in physics, I was offered this chance. Since then I’ve worked with many people and groups from around the world on the genomes of the mouse, rat, dog, marsupial, duck-billed platypus, chicken, zebra finch, fruit fly and lizard.

OSB: What can all this genetic information from different species tell us?
CP: Having DNA from different species is crucial to understanding the human genome. Each additional genome is an evolutionary yardstick against which human DNA can be compared.

For example, when you ‘walk’ down each chromosome you see DNA letters that are the same in us and in mice – they have stayed unaltered over tens of millions of years because of their biological importance. This is because spontaneous changes (mutations) in important, conserved DNA tend not to be carried over into subsequent generations as they cause illness or even death.

By separating DNA that has remained relatively unaltered across animal evolution from DNA that has changed rapidly, we efficiently separate ‘functional’ DNA from ‘junk’ DNA. One of the biggest surprises has been the amount of ‘junk’ DNA. Only about 10% of the human genome appears to ‘do’ something, the rest appears not to be important at all.

OSB: What does your own research focus on?
CP: Genomics is rapidly permeating into many areas of biology and medicine, and we have tried our hand at many things over the past few years. My group is trying to understand which genetic changes cause disorders such as autism, intellectual disability or Parkinson’s disease, whilst thinking about how zebra finches learn how to sing or how the platypus senses its prey under water.

It has been particularly enjoyable discovering that there are no more genes making protein in the human genome than they are in a microscopic nematode worm. Science is good like that: its perspective is often humbling.

We can learn a lot just from the gene sequences, seeing how they’ve been conserved or have changed across the millennia and across the tree of life. But most of what we do is to solve puzzles: putting together pieces of information drawn from diverse areas such as evolution, genetics, natural history and clinical medicine. Synthesising this information is often very rewarding and tells us something new.

OSB: What can we look forward to in the future?
CP: As sequencing becomes cheaper, some are advocating sequencing the DNA from all animals. Certainly, most of the species that are important to biology and medicine are being, or have been, sequenced. I look forward to seeing soon the DNA sequence of many animals, from ants to zebras.

Nowadays, we’re looking past the DNA that encodes protein to the hundreds of millions of DNA letters that appear to be doing something, but certainly don’t make protein. It is this ‘genomic dark matter’ that we need to illuminate if we are to better understand the differences between ourselves, or even between us and other animals.

OSB: Might this research hold benefits for human health?
CP: Sequencing DNA is becoming cheaper and cheaper. The first human genome, sequenced ten years ago, cost a staggering $3 billion. Soon one genome will cost $1000. With these plummeting costs come the realisation that individuals’ genomes can be sequenced to try and understand the DNA changes that cause rare or common diseases.

Some might be fearful of what their own genomes could tell them: might they, and perhaps their children, carry some genetic change that predisposes them to disease? In the vast majority of cases, the outcomes aren’t likely to be as simple or as clear cut as that.

I think there are two things to be said here. First, everyone’s genomes carry many changes (‘genetic blemishes’) that give marginal changes to disease susceptibility. In this sense, everyone’s genomes are far from ‘perfect’. Second, despite being able to read someone’s genomes, we are a long way from understanding them so, as scientists and clinicians, we are usually far from assigning single DNA changes to diseases.

OSB: You suggest that these approaches could lead to fewer animals being used in research. How?
CP: All our work is done in the computer and, as time has gone on, we’ve become more sophisticated at spotting genes that do equivalent things in different species. As a result, we have separated genes which are less informative from others which, if studied in model organisms such as fruit flies and mice, immediately provide insights into human biology. Also, evolutionary approaches can now make good guesses of what a gene’s functions are, all of which reduces the number of uninformative experiments. Computational studies are certainly doing their bit to reduce the use of animals in science.