Month: October 2016

What the frack?: An exploration of hydraulic fracturing in the UK.

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For many years I’ve been skirting the sidelines of the debate on hydraulic fracturing (commonly known as fracking), occasionally dipping in and out of articles but usually concluding that I don’t know enough to make an informed decision. However fracking has now come to me, placing itself firmly on my doorstep – so I’ve decided it’s about time I did my research!

I live in Bury, a region in the north of Manchester which, according to the amusingly named website ‘Frack Off’, sits within what is known as an oil exploration block. This being an area of land, typically 1000s of square kilometres in size, which has been ‘awarded’ to an oil drilling and exploration company by the government. Apparently the lucky exploration company with control over my home turf is Hutton Energy.

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The reason my home county is such hot property for energy companies is because the ‘British Geological Survey Gas-In-Place Resources Assessment of Bowland Shale’ has suggested that it sits above a large amount of, possibly gas rich, shale rock. Shale is a fine-grained sedimentary rock formed by compression of mud (mineral particles and organic matter) over time. It is also incredibly common, forming over 35% of the world’s surface rock. Over millions of years shale becomes buried deep within the Earth and, when it reaches depths of over 2 kilometres, heat and pressure cause organic matter within the shale to release methane gas – it is this ‘natural gas’ which can be harvested to generate electricity for domestic use. The problem with shale gas is that, unlike conventional gas supplies (such as those harvested in the North Sea) which collect in large reservoirs, the methane in shale is trapped by the fine grain structure of the rock. It is only when shale rock is drilled and fractured that the gas is released and can be harvested. This process of fracturing shale rock to harvest methane gas has caused an enormous stir, with supporters on both sides of the debate campaigning ferociously.

But what are the debates for and against this process and how relevant are these to fracking in the UK?

To understand these arguments it is first important to know what hydraulic fracturing really entails and there is no doubt that the process sounds particularly invasive. For starters, shale gas exploration companies will drill large boreholes down into gas-bearing shale rock. These holes will stretch thousands of miles below the surface of the ground and, in many cases, will continue horizontally through the shale rock. These boreholes are then lined with steel and concrete for stability and to limit leakage of fracking-related materials into the surrounding land. Next, a perforating gun is used in the lower segments of the borehole to make a number of small holes in the concrete casing – these holes are concentrated in the parts of the pipe sitting within the shale rock. Finally, a mixture of water, sand and chemicals is pumped under high pressure down the borehole and out of the small holes in the concrete piping. This high pressure water mix causes fractures to develop in the shale rock, while sand within the water lodges in these cracks ensuring that they remain open and porous. This process allows gas trapped within the shale to flow out of the rock and then travel back up through the borehole to the surface for harvesting.

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Image credit BBC: http://www.bbc.co.uk/news/uk-14432401

Supporters of this process argue that fracking in the US has significantly boosted domestic oil production, driven down the cost of gas and created many job opportunities. Those in favour also suggest that fracking can generate electricity at half the CO2 emissions of coal – but, be aware that this figure varies depending on sources and that some argue that the atmospheric pollution caused by fracking is actually no better than that of traditional coal extraction. The benefits here are attractive for the UK, especially since our North Sea gas fields are reaching the end of their lives, most of our nuclear plants are planned to close by 2023 and a third of our coal-fired power stations are set to close by 2016 to meet European air quality regulations. So, we are undoubtedly in need of an energy boost. However, it is interesting to note that oil and gas industrial representatives recently told ‘New Scientist’ that “ it would take at least 10 years for the UK to produce a meaningful amount of shale gas, making it a poor substitute for dwindling North Sea production in the short term”

So is fracking fit for purpose, especially considering that many academics agree that a move towards renewable sources of energy is preferable?

Those opposed to the process argue strongly that fracking introduces too many health and environmental concerns to be a viable and safe source of energy. Specifically, many are concerned that methane gas and fracking chemicals could travel upwards through natural fractures in the rock, polluting underground aquifers and further contributing to global warming. It is also suggested that leaks in pipelines could lead to further aquifer pollution. These concerns are certainly valid, however to date there have been very few peer reviewed articles published suggesting that chemicals and methane released by the fracking process have reached local aquifers. It is also argued that these risks can be significantly minimised by strict regulations and regular monitoring. For example, thorough geological surveys should be carried out prior to exploratory fracking to detect pre-existing fractures, pipelines should be strongly reinforced and regularly monitored and chemicals used in the fracking process should be assessed and approved by the environmental agency.

Many opponents to the process also raise concerns that fracking may trigger earthquakes. Again, to date there have been few proven links between fracking and earthquakes. However, one of the few instances where this has been the case was in 2011 when two small earthquakes struck Blackpool close to an exploratory fracking site. Experts suggest that these quakes were caused by lubricated rocks slipping along a small fault line. Cuadrilla, the company in charge of the Blackpool site, propose that they will now monitor seismic activity around all their fracking sites and, if small quakes begin to occur, they will reduce the flow of water into the borehole, or even pump it back out preventing bigger quakes.

Indeed, many of the environmental and health concerns raised against fracking seem to be manageable given stringent regulation and proper monitoring – something which the UK government claim to take very seriously.

In my view more research is still needed to explore the validity of existing environmental concerns while stringent regulations must also be put in place before going forward with further exploratory work. This all leads me to one big question: can we trust those involved in the process to ensure this happens?

On a personal level I’m still not convinced, there does seem to be a strong vested government interest in moving fracking forward – in some cases this is happening to the detriment of local councils and areas of natural beauty. In my mind urgency is the mother of mismanagement so, until I’m convinced that fracking in the UK will be properly managed, local communities will be consulted and engaged as part of the process and this will not be used as an excuse to slow down on development of more sustainable energy resources I think I will remain skeptical.

Post by: Sarah fox

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Light pollution – are we losing the night sky or is there still hope?

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I guess it was inevitable that I would eventually write a post about light pollution – the modern day scourge which reduces the visibility of celestial objects and forces astronomers to travel hundreds or sometimes thousands of miles in order to avoid it. There’s even a saying that an astronomers most useful piece of equipment is a car! Probably the most damaging effect of light pollution is not that it makes faint galaxies and nebulae difficult to spot and photograph (there are ways of overcoming this), but that whole generations of children grow up not knowing what a truly dark sky looks like!

Figure 1. The effect of light pollution on the night sky. This split image shows how artificial light washes out most of the faint detail in the constellation Orion.
Figure 1. The effect of light pollution on the night sky. This split image shows how artificial light washes out most of the faint detail in the constellation Orion.

 

I am one of those children. I grew up in suburban England (about 60 miles north west of London) where the night sky had a beige/orange tinge, the constellations were difficult to spot and the Milky Way was something you either looked up in a book or ate. I was about 14 when first I saw a proper night sky; on holiday in North West Scotland. I was so fascinated with the sight that an interest in astronomy embedded itself in me and never left! I was lucky, I was still quite young and my interest could be nurtured before the realities of life (exams, chores, jobs…) stepped in. Many aren’t so lucky. I always wonder, how many inquisitive people never experience the joy of observing the universe because of that orange glowing veil of light pollution (LP). It is the barrier that light pollution creates that prompted me to write this post.

I will now concentrate on the issues LP poses to astronomy. Before I do so, I should say that good evidence exists showing that LP can negatively affect human health (such as disrupting sleep cycles) and the natural environment (changing bird migration patterns etc), detailed discussions can be found here. Regarding astronomy, light pollution is

Figure 2. Direct light pollution. These street lights in Atlanta radiate light across a wide area, stargazing near these will be very difficult. Image taken from http://www.darkskiesawareness.org
Figure 2. Direct light pollution. These street lights in Atlanta radiate light across a wide area, stargazing near these will be very difficult. Image taken from http://www.darkskiesawareness.org

problematic for two main reasons. (1) Unwanted light can travel directly into your eyes ruining the dark adaption they need to observe faint celestial objects. It can also invade telescopes causing washed out images and unwanted glare. This form of light pollution involves light traveling directly from an unwanted light source (such as a street lamp) to your eye/telescope.

The second source of LP comes from the combined effect of thousands of artificial lights, known as sky glow. Sky glow is form of LP most people are familiar with; the orange tinge that

Figure 3. Skyglow in Manchester. This light is scattering off the atmosphere and falling back to the ground. As a result, the sky looks bright orange. Image taken from https://commons.wikimedia.org/
Figure 3. Skyglow in Manchester. This light is scattering off the atmosphere and falling back to the ground. As a result, the sky looks bright orange. Image taken from https://commons.wikimedia.org/

in some places can be bright enough to read by! Sky glow exists because the Earth’s atmosphere is not completely transparent, it contains dust, water droplets and other contaminants that scatter man made light moving through it. Some of this light is scattered back down towards the Earth, it is this scattered light that drowns out the distant stars and galaxies. It is a visual reflection of the amount of wasted light energy we throw up into the sky.

You may be thinking that LP spells the end for astronomy in urban areas. Well luckily there are ways around the problem. One way is to  filter it out. The good thing about skyglow is that it is produced mainly by street lamps that use low pressure sodium bulbs. The light from these bulbs  is almost exclusively  orange with 589nm wavelength. Figure 4 shows a spectrum of the light given out by one of the lamps.

Figure 4 - Different colours of light produced by a typical low pressure Sodium street light. The vast majority of the light is orange (589nm) as shown by the bright orange bar. Image taken from: https://commons.wikimedia.org/
Figure 4 – Different colours of light produced by a typical low pressure Sodium street light. The vast majority of the light is orange (589nm) as shown by the bright orange bar. Image taken from: https://commons.wikimedia.org/

Since this light is comprised of essentially one colour, we can use a simple filter to cut out this wavelength whilst leaving other wavelengths unaffected. In addition, the wavelength of the sodium lights is quite different from the colours produced by many nebulae. Therefore when we filter out the orange light, we don’t also block the light coming from astronomical objects.

So…what am I worrying about then? If light pollution can be overcome by filtering out certain wavelengths of light then astronomy should be possible from anywhere. Well, not quite. Filters are not perfect, even the best filters will block other colours and dim our view of the stars. There is also another reason to worry – street lights are changing. As you may

Figure 5 - LED and sodium streetlights outside my house. LEDs produce light that is harder to block using conventional filters, Sodium lights (seen here as orange) shine lots of light into the sky contributing to sky glow. (Image is my own)
Figure 5 – LED and sodium streetlights outside my house. LEDs produce light that is harder to block using conventional filters, Sodium lights (seen here as orange) shine lots of light into the sky contributing to sky glow. (Image is my own)

already know, street lights are being altered from the sodium bulbs to LEDs. These LEDs are more energy efficient and produce a more natural white light. However, this white light is harder for astronomers to filter out without also blocking light coming from deep space. Luckily, these newer lights are better at directing their glow downwards towards the ground rather than allowing it to leak up into the sky. Figure 5 shows the LED and Sodium lights outside my house. The LED lights appear darker because most of their light is directed towards the ground.

There is still debate in the astronomy community about whether the new street lighting will be beneficial for astronomy. At the moment, LEDs are being introduced slowly so it is difficult to make a clear comparison. My hunch is that when Sodium lights are replaced completely, there will be an improvement in our night skies and finally young people will grow up seeing more of the night sky.

Post by: Daniel Elijah

 

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Could fruit flies help defeat HPV-derived cancers?

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In 2012 528,000 cases of cervical cancer were diagnosed worldwide. In the same year, more than half this number were estimated to have died as a result of this condition. The cause? A virus of the Papillomaviridae family, specifically one of the High Risk Human Papillomaviruses (HR-HPVs). Although mainly associated with cervical cancer in women, HR-HPVs cause an ever increasing number of head and neck, throat and genital tumours in both sexes.

Human Papillomaviruses lack an envelope, a coat made from the membrane of the host cell, possessing only an icosahedral capsid – a sturdy protein bubble that protects the viral DNA within. Viral DNA hijacks the host’s cellular machinery to produce new viral proteins which both continue virus assembly and cause cancer. It is still uncertain exactly how these proteins interact with our cells to cause cancer but some major players and pathways have been identified. Specifically, scientists believe that two particular proteins (the E6 and E7 proteins) may play an important role in this process.

These two E6/7 macromolecules can be referred as “oncoproteins”. Although quite scary, this term simply defines proteins which are involved in mechanisms that could cause a cell to behave abnormally, increasing the chances of them becoming cancerous. Specifically, these two proteins interfere with a wide variety of mechanisms that will trigger conversion to malignancy. Respectively, they either boost or block the activity of p53, Rb and E2F, three molecules that control a cell’s life cycle.

Considering the huge impact such cancers have on human life, it may seem unusual that we are still in the dark about so many aspects of HPV associated pathophysiology. Our limited knowledge is in part due to constraints implicit in this type of research. Specifically, for obvious ethical reasons, researchers are not able to study HPV associated cancers in living human subjects or deliberately induce cancers in subjects. Therefore, they must rely on model systems when studying these disorders. In the past, researches have used artificial keratinocytes (skin’s cells) and mouse models, to understand how processes work in living tissues. However, this work raises a few questions, such as: How do you compare findings in tissue alone to what you would find in a dynamic and complex living system and how well can we compare mouse models to human conditions?

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Picture credits: By Botaurus, via Wikimedia Commons – CC BY-SA 2.5 (open access/open use).

We now have an answer to these questions, or at least something that marks the start of a deeper understanding. Researchers at the University of Missouri have been able to successfully develop and use living, fruit fly models. Mojgan Padash’s research team injected fruit flies with the E6 protein along with a human-derived one needed by the E6 to function. The first results show that, although abnormalities in the fruit flies’ skin were noticed, another molecule was needed in order to fully trigger cancer. Following the hypothesis that mutations in a human molecule called Ras, a family of “switch” proteins which activate cell growth-specific genes, the team introduced the latter into the fruit flies. Those “simple” abnormalities turned into malignant cancers, just as they would do in humans.

The results, published in the open access journal PLoS Pathogens, allow scientists to monitor biochemical pathways similar, if not identical, to those found in human sufferers. But why flies and not mice? Although further away from humans, sharing only 60% of the human genome against the 97.5% of mice, flies are easier to use than their murine counterpart. Fruit flies are easier to breed (so to quickly obtain new generations) and their genes can be mutated quicker than mice. Moreover, little to no ethical approval is needed to use them (they can be ordered online, with just one click!) and their easier to monitor development allows researcher to effectively model disease development. These fruit fly models, which are continuously refined and developed, have the potential to help in discovering new molecules involved in such processes.

It comes to no surprise that such information could impact heavily on future treatment, and even the prevention of pathologies caused by this increasingly dangerous family of viruses. So, next time you think about killing a fruit fly in your kitchen … maybe think twice.

Post by: Paolo Arru – @viraleclair

screen-shot-2016-10-10-at-19-43-41Paolo is currently a final year student in Microbiology at the University of Manchester, UK. Science communicator wannabe, he has a keen interest on everything related to HPV, viral oncology and parasitic infections to just say a few. Every bit of his free time is used for planning and getting involved in new projects, baking and getting lost in museums. You can follow him talking about science festivals, geeky stuff and bake off on

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Symbiosis – harmony or harm?

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We have all experienced relationships which are beneficial and others that are not. The same can be seen throughout nature. Originally defined by German scientist Heinrich Anton de Bary, symbiosis describes a close association between two species, principally a host and a symbiont, which lives in or on the host. While some partnerships may be advantageous or neutral to one or both parties, others may have a more detrimental effect.

Mutualistic symbiosis:

screen-shot-2016-10-02-at-22-27-45The first of the symbioses involves relationships between two different species which benefit both organisms. Mutualistic symbiosis can involve organisms of all shapes and sizes from stinging ants and bullhorn acacia trees, a relationship where the tree provides the ants with food and shelter in return for protection from herbivores, to the alliance between oxpeckers and zebras, in which the bird enjoys a readily available food source while the zebra has any parasites living on it removed.

One of the most well studied forms of mutualistic symbioses is that of the ruminant (i.e. cattle and sheep etc.), as these organisms play an important role in our agriculture and nutrition. Ruminants host an extensive microbial population in the largest of their four stomachs, the rumen. A mutually beneficial relationship exists between these two organisms because the rumen microbes are able to digest the plant matter consumed by the ruminant. In doing so, they produce fatty acids, which can be used by both parties for energy. Carbon dioxide is also released in this process, providing the rumen microbes with the oxygen-free environment they need to survive (these microbes are predominantly anaerobic so are poisoned by oxygen).

Parasitic symbiosis:

screen-shot-2016-10-02-at-22-27-52In contrast to mutualistic symbiosis, the interaction between two organisms may be less savoury in nature. Parasitic symbiosis describes a relationship between organisms where the symbiont benefits at the expense of its host. Unfortunately for the host, this generally causes it harm, whether this be in the form of disease, reduced reproductive success or even death. The symbiosis between birds, such as the cuckoo and the reed warbler, known as brood parasitism, is a characteristic example of a parasite-host relationship. Rather than building her own nest, the parasitic cuckoo will lay her eggs in a reed warbler’s nest, leaving the warbler to raise this egg along with her own offspring. Once hatched, the cuckoo chick then ejects the warbler’s young from the nest, allowing it to receive all the food that its “adopted” mother provides.

Unsurprisingly, this antagonistic relationship has led scientists to question why warblers raise these parasitic chicks if the practice is so harmful. It has been suggested that cuckoos engage in a kind of “evolutionary arms race” with its chosen host, based on the host’s ability to recognise a parasitic egg. In this ongoing contest, the evolution of a host species to become more adept at spotting and rejecting a parasitic egg may result in a subsequent evolution in the cuckoo to counter this change. This may be to lay eggs with greater similarity to the host’s or to move towards a new host species. Such a process could continue indefinitely.

screen-shot-2016-10-02-at-22-28-01An even more detrimental relationship exists between the parasitoid wasp and its hosts, which include a range of insects from ants to bees. Similarly to cuckoos, these wasps rely on their host to facilitate the development of their young, but do so by either laying their eggs inside the host or gluing them to its body. Once hatched, the wasp larva will feed on the host, usually until it dies.

Commensal symbiosis:

Symbiosis does not necessarily have to be beneficial or detrimental to the host organism. Commensal symbiosis describes a relationship in which one organism benefits while the host is unaffected. This may be in the form of shelter, transportation or nutrition. For example, throughout their lifecycles small liparid fish will “hitch a ride” on stone crabs, providing them with transportation and protection from predators while conserving energy. The crabs, meanwhile, appear to be neither benefitted nor harmed.

One case of commensalism which may come as a surprise involves Candida Albicans, a species of yeast known to cause the fungal infection Candidiasis in humans. Contrary to popular belief, C. Albicans can be pathogenic or commensal depending on which phenotype it has. Under normal circumstances, C. Albicans reside in our gastrointestinal tract undergoing a commensal symbiotic relationship with us (i.e. causing us no harm). This interaction is actually the default existence for C. Albicans. When changes occur in the body’s environment, however, a “switch” in phenotypes to the pathogenic form can occur, placing a temporary hiatus on the usual commensal relationship.

A plethora of symbiotic relationships exist throughout the natural world, from the tiny microbes inhabiting the ruminant gut to the large acacia trees housing ants. They can offer both organisms the harmony of a mutually beneficial association, as is the case with the oxpecker and the zebra, or be parasitic and work in the favour of one player while harming the other, as seen with the parasitoid wasp. In some instances, one organism can gain benefit without impacting the other either positively or negatively. As illustrated by C. Albicans and cuckoos, a symbiotic interaction may change or evolve according to the environment or evolution of the host, respectively. Symbiosis is clearly a highly important aspect of nature which many organisms rely on for survival, and one that will continue to fascinate scientists and non-scientists alike both now and in the future.

Post by Megan Barrett.