Anaerobic digestion · 01273 562139 or [email protected] Science and explanations S cience is about observing things and then explaining them. Take the experience we all have of

Volume 22Number 1October 2012

Secondary Science Review

Anaerobic digestionDealing with food waste

Contents1 Food waste recycling Vicky Wong

4 Circadian rhythms John O’Neill

7 Plant responses Gary Skinner

9 The big picture The sand beneath your feet Vicky Wong

13 Metals in the body Mary Finnegan

16 Bad Science Ed Walsh

19 Try this: Make your own lava lamp Vicky Wong

20 The next step Tom Denbigh

22 Volcanoes from space David Sang

Subscription informationCatalyst is published four times each academic year, in October, December, February and April. A free copy of each issue is available by request to individuals who are professionally involved in 14-19 science teaching in the UK and who are registered with the National STEM Centre. Teachers should visit www.nationalstemcentre.org.uk to find out how to register.

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David Sang PhysicsBrighton

Vicky Wong ChemistryDidcot

Gary Skinner BiologyHalifax

Editorial team

Editorial contact: 01273 562139 or [email protected]

Science and explanationsScience is about observing things and then

explaining them. Take the experience we all have of daily cycles in our bodies. At night, we become sleepy; eight hours later, our bodies wake us up. We say that we have a ‘body clock’. If you travel across several time zones, you may suffer from jet lag, because your body clock has not adjusted.

The idea of a body clock is an explanation at a very simple level. At a deeper level, scientists were able to show that the levels of various hormones in our bodies change up and down during each 24 hours. Later, they discovered some of the mechanisms in cells which caused these changes. Now, as John O’Neill shows in his article on pages 4-6, we are beginning to understand how genes operate to control these daily cycles. That’s a much more profound explanation than simply talking about body clocks.

As Gary Skinner points out (pages 7-8), there are many other phenomena in Biology still waiting to be explained.

Published by the Gatsby Science Enhancement ProgrammeGatsby Technical Education ProjectsAllington House (First Floor)150 Victoria StreetLondon SW1E 5AE

© 2011 Gatsby Technical Education ProjectsISSN 0958-3629 (print) ISSN 2047-7430 (electronic)

Design and Artwork: Pluma Design

The cover image shows food waste in a college canteen. It is estimated that over 8 million tonnes of food is discarded each year in the UK. Find out how we can make better use of this waste in the article on pages 1-3.

Volume 22 Number 1 October 2011

The Catalyst archiveOver 200 articles from past issues of Catalyst are freely available in pdf format from the National STEM Centre (www.nationalstemcentre.org.uk/catalyst).

Students: We have now created a website specially for you where you can browse hundreds of articles from past issues of Catalyst and find out how to subscribe.www.catalyststudent.org.uk

1Catalyst October 2011

Vicky Wong

Key words

composting

bacteria

anaerobic digestion

methane

Food waste recyclingPower from potato peelings

methanogenic means methane-producing

A kitchen food waste container A lorry load of food waste arrives at the plant

Food waste is generated by virtually every household and has to be got rid of, but a debate is raging about how this should be done. In some parts of the country, food waste bins have been used for a few years now...but what is a food waste bin like and what happens to the collected scraps?

In most places which collect this type of refuse, households have two food waste bins. The smaller one is designed to be kept in the

house and have the rubbish put into it as it is generated. The bin is lined with a compostable liner rather than a standard plastic bag. These are not inexpensive and are made from a special plastic which can decompose much like the food waste. These bags are then emptied into the larger bin which is kept outside. This has a lockable lid to keep out animals. In warmer weather the inside bin needs to be emptied more frequently to prevent smells and flies, but it is not unpleasant.

There are various ways of dealing with the collected waste. In Oxfordshire, the food waste is collected and then sent to an anaerobic digestion plant for treatment.

Anaerobic digestionAnaerobic digestion uses methanogenic bacteria to break down the food waste. This produces biogas which is mainly methane. The gas is collected and can be used as a fuel, to produce transport fuel or to generate electricity. At the Oxfordshire plant, electricity is generated from the methane on site.

On arrivalDelivery lorries bring the waste onto the anaerobic digestion site. They enter a large building which has a negative pressure (which ensures air will tend to enter rather than leave) and doors which open and close very quickly. The air in this building is changed 2 or 3 times an hour and is passed through a filter and an alkali scrubber to remove acidic gases before being released. This helps to prevent any bad smells escaping and polluting the local atmosphere.

2 Catalyst October 2011

The food waste then needs to be treated prior to being fed to the bacteria. This is necessary to separate out contaminants such as plastics which the bugs cannot digest as well as to break the food down into small pieces. The solid waste is passed through a macerator. This breaks all of the incoming material down into smaller bits and produces a gloopy ‘soup.’ The gloop is left in a settling tank where the heavier fragments sink to the bottom and can be removed. This includes denser materials such as metals, glass and grit.

BlendingThe material that is fed to the bacteria needs to be carefully controlled to ensure that they stay in optimal health to achieve the best break down of the material. To achieve this, the materials which will be fed into the digester are analysed regularly.

Food waste being macerated

As the processing facility can accept a wide variety of wastes, the material going into the digester sometimes needs to be supplemented with silage. This is an energy crop which helps to stabilise the composition of the material. It also produces a high yield of gas.

The material is then pasteurised by being heated to 70˚C and the temperature held there for an hour. Similar to the process for pasteurising milk, the aim of this is to kill unwanted bacteria and reduce the risk to health. The sludge can be passed warm into the digesters to help keep the bacteria in them at optimal temperature.

The digestersAnaerobic digestion relies on living organisms: bacteria. If they are not looked after well they will die and the plant will cease to function. New cultures of suitable bacteria can take 3 months to grow.

The digestion takes place in large concrete tanks and here the methane begins to be produced. The tanks hold up to 4200 m3 of waste and are heated to the optimal temperature of about 40˚C. The tank has a double membrane for the roof. This allows the methane to be stored above the digesting material. The inner membrane fills and empties as methane levels rise and fall while the outer membrane is fixed and protects the interior from the weather.

The waste is chopped up again and re-mixed before spending further time in a digester. Altogether waste spends around 120 days being digested.

Box 1 - What they say

What do you think?

‘The government has no plans to force households to put food scraps into slop buckets.’ Caroline Spelman, Government Environment Secretary

‘Calling the food waste container a ‘slop bucket’ is ill-worded and provocative for a system which is sensible and positive.’ A voter


Generating electricityThe point of the plant is not just to get rid of food waste, but to turn it into something useful. The gas is used in the generation of electricity in gas turbines. The biogas produced in the digesters is not pure methane, though. It naturally contains other gases which contaminate it and may harm the turbines. These include sulfides such as hydrogen sulfide which must be removed before the gas is pumped to the turbines.

The sulfides are removed by being oxidised to sulfates:

The sulfates will form solids which will not contaminate the gas. The sulfides can be oxidised to sulfates by adding oxygen or another suitable oxidising agent into the methane.

When it is clean enough, the gas can be passed to the generators. The gas turbine engine burns the methane from the biogas to drive a generator. The output of the generator is dependent on the speed at which the gas turbine turns. The electricity produced is used for all the power needs of the plant and also supplies enough energy to the national grid to power 4200 homes.

If more gas is produced than the gas engines can cope with then the excess biogas is burnt at a flare stack some distance from the plant.

The effect of the digested waste as a fertiliser. The dark green area shows the

strong growth where the fertiliser has been sprayed.

It is estimated that wasting food costs the average family with children £680 a year.

Two of the digesters at the anaerobic digestion plant

The gas engines have a cooling system and hot water from this is used to heat the pasteurisation tanks and to keep the digesters at the optimal temperature.

The gas engine is in a soundproof building to minimise noise disruption to those living nearby.

The left over waste is kept in special tanks. When it conforms to regulation standards and at the right time of year it can be used as a fertiliser on agricultural land. This then helps a new generation of food crops to grow, which in time end up in kitchen waste bins....

Vicky Wong is Chemistry editor of Catalyst.

S2- SO [O]

sulfide sulfate

2-4

4

John O’Neill

Key words

body clock

circadian rhythm

hormones

health

We all have body clocksIf you have ever flown across time zones you may have experienced symptoms such as headaches, fatigue, irritability and constipation which are generally referred to as ‘jet lag’. We know this is not simply the result of flying abroad, because the same effects are seen in people who do shift work.

What actually happens is that, unlike your wristwatch, the body’s master timekeeper (the suprachiasmatic nucleus or SCN, based in the brain’s hypothalamus) can only advance or delay by about an hour each day in response to the light levels you experience when awake. So until this clock in the hypothalamus has caught up with the new time zone you’re in, it will send muddled hormone signals to other parts of the body. Therefore, for example, even though it might be lunchtime at your destination, your digestive system might think you should be sleeping and is not prepared for food - meaning your meal isn’t digested properly.

We know that, although the SCN is very important for co-ordinating rhythms across the body’s many organs, in fact every cell and tissue in the body has its own clock – explaining the many observable physiological rhythms such as core body temperature, and the oscillating levels of hormones such as melatonin (that makes us sleepy at night) and cortisol (that wakes us up in the morning).

How the ‘clock’ in your brain controls your daily cycle.

Rising levels of melatonin bring sleep, during which

your core body temperature falls. Then rising cortisol

levels wake you up.

In some countries, you can buy melatonin tablets

which may help you get over jet lag; ‘anti-energy’

drinks contain melatonin and claim to help you relax.

Disturbingly, there is now a lot of evidence in humans who do shift-work, and from experiments in rodents, to suggest that long-term disruption of the body clock significantly increases the risk of many chronic diseases such as diabetes, cardiovascular disease and various types of neurodegenerative disorder and cancer. This seems to be because the body clock is hard-wired into so many aspects of cellular biology and physiology that when it goes wrong, it impacts upon numerous systems e.g. the body clock controls what time of day cells are able to divide, so when the clock is disrupted, this control is lost and cells become more likely to develop into tumours.

Circadian rhythmsHow your body clock works

An internal biological clock within every cell of your body helps to co-ordinate and organise human behaviour and metabolism into approximately 24-hour rhythms – allowing organisms to synchronise with, and anticipate, day and night. When the body clock is disrupted in humans it can have serious short- and long-term health consequences, and so understanding how biological time-keeping works has become an important question for medical research. As often happens in science however, the answer just keeps getting more complicated!

Catalyst October 20114

5Catalyst April 2011 5

Body clocks = circadian rhythms‘Circadian rhythm’ is the term that researchers use to describe this daily biological timekeeping. As with many scientific phrases ‘circadian’ comes from Latin, meaning ‘about daily’ (circa–dian). Fascinatingly, circadian rhythms can be observed in most organisms on the planet (including plants, fungi and even some bacteria).

Circadian timekeeping was first observed in 1729 by a Dutch astronomer, Jean Jacques d’Ortous de Marian. He isolated mimosa plants in dark rooms for several days and found that even in the absence of sunlight (or other environmental cues), the plants continued to open their leaves during the day and close them during the night. He concluded that the observed cycle was not a result of external forces but was an innate property of the plant.

Mimosa plants open their leaves during the daytime –

even when they are kept in the dark.

Subsequently behavioural rhythms were observed in humans and many other organisms under similarly constant conditions. Indeed, when measured in the laboratory or underground caves over several weeks, the intrinsic period in humans is slightly longer than a day (~24.2 hours), and slightly shorter in mice (~23.7 hours) meaning that humans would be able to live on Mars without adverse clock impairment (day length of 24.6 hours). In the natural world, the circadian clock is subtly reset each day by cues such as dawn and dusk meaning that the observed period is almost exactly 1 day. It is presumed that the reason for our intrinsic period never being exactly 24 hours, is to provide some flexibility to cope with variable day length over the seasons of the year.

Michel Siffre is a French geologist who has spent

long periods underground in experiments to

investigate the length of his natural circadian rhythm,

which is longer than 24 hours. Sensors on his skin

detect his physical condition.

Why be rhythmic?We think biological rhythms exist because from the beginning of life on Earth (around 3.7 billion years ago) there have always been daily cycles of light and dark (day and night) due to the approximately 24 hours it takes the Earth to rotate on its axis. Therefore organisms which use light from the Sun (directly through photosynthesis, or indirectly due to vision, or for heat) developed the capacity to keep time internally, and thereby anticipate the transitions between day and night. Such organisms would have had an evolutionary advantage over those that did not and so were more likely to reproduce e.g. plants display daily cycles of chlorophyll production which peaks just before dawn, not in response to it, allowing more efficient use of resources. Improved fitness due to internal timekeeping has been confirmed in the lab i.e. plants with an internal clock whose period matches the natural light/dark cycle out-compete plants carrying mutations that result in longer or shorter (28 vs 20 hour) intrinsic periods.

A familiar example of rhythms in humans would be the cycle of sleep and wakefulness which tends to coincide with night and day – this makes sense because humans cannot see well at night. In contrast nocturnal animals like mice, that rely more on smell, do the opposite, sleeping during the day.

Mice show a circadian rhythm in both activity and body temperature.

Catalyst April 20116

A number of clock genes have now been identified, and the way that they work seems to be quite simple, namely: transcriptional-translational negative feedback loops. Put simply, clock genes in our DNA (within the cell’s nucleus) are turned on around dawn and transcribed into messenger RNA (mRNA). The clock gene mRNA is then translated to become clock proteins (in the cell’s cytosol), and the levels of clock proteins build up during the day. Around dusk the clock proteins enter the nucleus and turn off their own clock genes. Because there is no longer any transcription (mRNA), no more clock proteins are produced. Overnight, the clock proteins keep clock genes inactive but are slowly broken down so that, by the following dawn, none remain. The clock genes now reactivate and the cycle begins again.

The activity of ‘clock genes’ varies during the day.

The author found that even red blood cells, which have

no cell nucleus, exhibit circadian rhythms.

A genetic basis for circadian clocksMolecular genetics has been a powerful tool for identifying ‘clock genes’ which are relevant to circadian rhythms and has taken us several steps towards understanding how organisms keep time. The basic principle is the same whether you are looking at single cells in culture, or whole organisms i.e. when timekeeping is affected by mutating or altering the activity of a gene, then that gene must be involved in clock’s mechanism and is labelled a clock gene. For example, a rare human mutation that results in a naturally shorter period (around 23 hours) was shown to be due to a single base pair change in DNA within a gene called Period2, this mutation changes a single amino acid of the encoded protein (PERIOD2) meaning that is broken down more rapidly.

New findingsAlthough these genetic explanations for circadian rhythms can explain large amount of experimental data, we noticed several clues suggesting that the real mechanism might be more complicated. For example, when other researchers have altered a clock gene’s activity so that it is permanently switched on, often the clock does not stop, at the behavioural and/or cellular level. Therefore, to test whether cycles of gene activity in DNA are required for circadian rhythms, we looked in a cell that has no DNA – the red blood cell. Human red blood cells, or erythrocytes, naturally have no nucleus or DNA. We thought that if we could detect circadian rhythms in blood outside of the body, then a transcriptional-translational mechanism could not be the explanation for it.

To test our hypothesis we looked at rhythms in oxidation of an evolutionarily ancient family of proteins called peroxiredoxins, since we had previously found that these proteins are oxidised with 24-hour cycles in cultured mouse cells and mouse liver and so would be a good ‘marker’ for rhythms in the absence of gene activity. We therefore took blood samples from three volunteers and purified the erythrocytes, to remove white cells of the immune system, and then incubated the red cells for several days in simple salt/sugar solution.

We observed robust rhythms of peroxiredoxin oxidation that persisted for at least 3 days in vitro (outside the body). Amazingly, we observed similar rhythms in a simple marine alga (called Ostrecoccus tauri). This suggests that purely genetic mechanisms are not sufficient to account for cellular timekeeping, and the hunt is now on to determine what additional systems in the cell are able to sustain the remarkable and medically-important phenomenon of circadian rhythms.

John O’Neill is a Wellcome Trust Career Development Fellow at the Institute of Metabolic Science, University of Cambridge.

Morning

Evening

Midnight

Midday

Dawn Dusk

clock proteindegraded

clock genes active

clock genes inactive

clock mRNA

Translation

Transc

riptio

n

Feedback repression

clock protein

Delayed relaxation of repression

Gary Skinner

Plant responsesGetting to the root

(and shoot) of a

problem

It comes as a surprise to many people that plants show sensitivity and movement. Gary Skinner explains how scientists first came to understand this topic, and why more experiments are needed to provide a complete explanation.

The sensitivity of plants to external stimuli and their ability to move are often shown with the example of the sensitive plant (Mimosa pudica), which folds its leaves in response to touch or heat. However, the folding movement of the leaves here is very unusual and not found in many other plants. In fact, all plants do move and show sensitivity, but they do it very slowly. Place a house plant on a windowsill so it is illuminated from one side and it will bend in the direction of the light over a few days. Lay a plant on its side and the roots will curve downwards and the shoots upwards.

A sensitive plant

(Mimosa pudica)

growing in the wild

in Madagascar. The

leaflets at top left

are in the process of

folding up.

Cress seedling growing in a vertically mounted Petri

dish, the roots are showing positive geotropism,

growing towards gravity, and the shoots negative,

growing away from it.

Lentil seedlings growing towards the light – this is

phototropism



In 1913, Boysen-Jensen showed that the 'message' sent down the coleoptile is chemical. If you cut the tip off and put it back on again with permeable gelatine in between, the response still happens, but with mica, which is impermeable, it does not.

Finally, in the 1920s Frits Went extracted the chemical and called it auxin. A theory was then developed by Went and Nicolai Cholodny, working independently. This is the Cholodny-Went or C-W theory, and has been the standard explanation for both geotropism (response to gravity) and phototropism (response to light) ever since. Auxins are plant hormones which stimulate cell division and growth – see Figure 2.

New ideasHowever many biologists have been questioning the theory for some years and it is now widely believed that a strict application of the C-W theory is not acceptable. The basic point is that the movement (redistribution) of auxin can no longer be thought

of as the sole controller of curvature but rather just one controller of several. Other controlling elements are involved which may include calcium ions, electrical charges, a variety of inhibitors and the sensitivity of cells to all of these. In addition, some research has shown that there is a great deal of variability between individual shoots (and roots) and it is possible that shoots not responding in the normal way may have been dominant in batches used in experiments. This may have led to many unexpected results and be behind some of the controversies.

Whatever the truth, it is clear that the simple textbook explanation as summarised in Figure 2 is unlikely to be sufficient to explain all that has now been found. In many areas of science, we are a long way from complete answers to important questions. But this can be seen as a benefit for the aspiring scientist! It just shows that many questions still remain to be answered and that the research can be done with much historical material to help and support it. As Isaac Newton said, “If I have seen further it is only by standing on the shoulders of giants.”

Gary Skinner is Biology editor of Catalyst.

Figure 1 The Darwins’ experiment on phototropism: Coleoptiles with no tinfoil cap and free along their whole length bend toward light. With a foil cap they do not bend, but when buried in fine sand up to the tip they do bend. So, as long as the tip can ‘see’ the light, it will ‘tell’ the stalk what to do.

How do they know?So, how do plants know up from down, light from dark, and how do they move toward or away from these and other things? The fact is, we still do not really know! But Charles Darwin and his son Francis had laid the foundations of understanding in 1881 with the publication of the book The Power of Movement in Plants, where they said “…we were impressed with the idea that the uppermost part determined the direction of the curvature of the lower part.” They tested this idea (we might call it a hypothesis) with some simple experiments. The work was done on canary grass (Phalaris canariensis) which, like all grasses, has its youngest leaves protected inside a tubular structure called a coleoptile. Their experiment is summarised in Figure 1.

Figure 2 How auxins account for phototropism. When a growing shoot receives light from above, auxins are produced evenly and cause the shoot to grow straight up. When light comes from one side, auxins migrate to the dark side and cause those cells to grow faster so that the shoot bends.

The standard textbook account of phototropism

in plants. A very similar mechanism accounts

for geotropism too.

Light Light

Fine Sand

Soil

Tinfoil Cap

light

light

light

auxin moves down the stem

auxin makes cells grow faster here

9Catalyst October 2011 9

Last time you visited a sandy beach what did you do? Lie on the sand? Make sandcastles? Get annoyed at sand in your sandwiches or stuck to your suncream? Did you pay much attention to the sand itself and marvel at how beautiful it is? The chances are that you did not – but magnified pictures of sand show just how amazing it really is.

The picture on pages 10-11 was taken by Dr Gary Greenberg who was a biomedical researcher at University College London.

The sand grains are viewed at magnifications of up to 250 times so that each grain is shown up in stunning detail.

The delicate and colourful grains include fragments of crystals, tiny portions of shells – including some spirals – and splinters of volcanic rock. Sand can also include remnants of volcanic explosions, dead organisms and even degraded man-made structures. If you didn’t notice all this when you were on the beach it is not surprising as these structures are well beyond the limits of human eyesight.

Dr Greenberg says, “It is incredible to think when you are walking on the beach you are standing on these tiny treasures. Every time I look through my microscope I am fascinated by the complexity and

The sand beneath your feet

Dr Gary Greenberg

individuality created by a combination of nature and the repeated tumbling of the surf on a beach.”

Gary searches through thousands of tiny rocks with acupuncture needles to find and arrange the most perfect specimens, and then uses a painstaking technique to create his images.

He says, “Extreme close up photography normally gives a very shallow depth of field so I had to develop a new process to make the pictures that I wanted. I take dozens of pictures at different points of focus then combine them using software to produce my images.

“Although the pictures look simple each grain of sand can take hours to photograph in a way that I am happy with. The beach nearest my lab is Haiku, Hawaii but my pictures show sand from all round the world from Japan to Ireland.”

This stunning image shows that there can be a lot of art in science and science in art.

The Big Picture

High-power microscopy reveals that

grains of sand may be fragments of

shell, rock or crystal.

www.catalyststudent.org.uk

Photo: G

ary Greenberg (S

WN

S G

roup)


Sand from Pismo

Beach, California.

The grains are mainly

chert, quartz and other

igneous rock and shell

fragments.

Studying sand can reveal both the geological and biological history of a local environment as sand varies from place to place. Sand from near a copper smelter can contain grains of copper; grains can contain worm trails from microscopic worms living in the ocean. Even the grains themselves can contain clues as to where they are from – grains from a desert environment tend to be pitted and pock-marked from where they collide with each other whereas grains from the ocean tend to be worn to a smoother surface.

Can you identify for the following grains in the picture on pages 10-11?

• To the left of the centre is a glassy Y-shape. This is a sponge spicule from the internal skeleton of a sponge. These are made of silica (as is glass) and are hard and sharp enough to cut through your skin.

• Near to this are two microscopic spiral shells. Shells are largely composed of calcium carbonate, CaCO3. By making these shells, the organisms are removing carbon dioxide from the ocean – and form a crucial part of the carbon cycle in the process.

• Below them, some circles on a white fragment are a piece of sea urchin shell which has been eroded by the waves. The circles are the sites where the spines would have been attached.

• Just to the right of the glassy Y is a brown striped tube which was once part of a sea urchin spine.

Look here!For further information on the work of Gary Greenberg see www.sandgrains.com

For a gallery of some of his other images see http://tinyurl.com/63kjvy

• A fragment with a lot of holes is a piece of coral. Centre right is a tiny, white, tube-building worm.

• The pink and white bit which looks like a piece of seaside rock is a splinter of shell.

Brightly coloured sand grains are often pieces of metamorphic rock. Colour alone is not enough to identify exactly what each mineral is as a tiny addition of a different chemical (often a transition metal compound) is often sufficient to change the colour.

Moon sandDr Greenberg is currently studying lunar sand which was brought to earth by the Apollo 11 Moon landings 40 years ago. Microscopes now are much more powerful than they were back then, allowing the sand to be studied in new ways. The environment on the Moon is very different to that on Earth, having no atmosphere and no water, so the rocks erode in a different way to that found on Earth.

Vicky Wong is Chemistry editor of Catalyst.

Clues in sand


Could the presence of iron in brain cells

help to explain why some people suffer from

Alzheimer’s disease, a form of dementia?

Mary Finnegan of the University of Warwick

hopes to shed some light on this question.

The most common elements in the body are oxygen, carbon, hydrogen and nitrogen, but other elements including many metals

are found at lower concentrations and are just as important. A well known example is iron which is a key component of haemoglobin in the blood, essential for transporting oxygen around the body. But iron is also important in cells, acting as a catalyst for many chemical reactions. Copper, zinc, potassium, manganese, magnesium and many others are also critical for our bodies to stay healthy. Most of these metals are at such low levels in the body, around 1 in a million or even 1 in a billion atoms, that they are known as trace metals.

Although these metals are essential, they can be harmful if the levels become too high or they are in a dangerous chemical form. To be used properly by the body iron needs to switch between the more reactive Fe2+ and the less reactive Fe3+. However too much reactive Fe2+ can be toxic to cells and so proteins are used to transport iron around the body and store it as the less reactive Fe3+.

If the way that metals are managed by the body is disrupted, this can cause disease. For example, subtle changes in iron and other metals have been observed experimentally in diseases such as Alzheimer’s disease, and these changes may be involved in the disease process.

Alzheimer’s diseaseAlzheimer’s disease affects around 465 000 people in the UK and the number of sufferers is growing as our population ages. It is a form of dementia that causes cell death in the brain and leads to memory loss and mood swings. Many people with Alzheimer’s disease become unable to look after themselves. There is currently no cure for the disease and although we know many details about what is happening in the brain in Alzheimer’s disease, the underlying causes – why some people get it and others don’t – are not well understood.

Researchers have found small changes in the quantity of iron in some of the regions of the brain affected by Alzheimer’s disease and also changes in the quantity of proteins that regulate iron. There has also been some work to observe what happens to other metals, such as copper and zinc, in the diseased brain compared to normal healthy brains of the same age.

However it is very difficult to measure changes in trace metals in the body as the quantities are so small. Traditional methods involve taking a block of tissue, dissolving it and using a spectrometer to measure the total concentration of the different metals in that block. However this does not provide any information about where the changes in the metals occur or what form the metal is taking. Is there more iron, copper, and/or zinc in the cells that are dying? Is there more reactive, and therefore more toxic, Fe2+ present in Alzheimer’s disease than in people with healthy brains?

This is where the Diamond Light Source can help. Diamond is the UK’s synchrotron and scientists can use the special X-rays produced at Diamond to detect metals in biological tissues.

Key words

Alzheimer’s

disease

synchrotron

radiation

X-ray fluorescence

Mary Finnegan

Fe2+ and Fe3+ are iron ions, atoms which have lost 2 or 3 electrons. Fe2+ can be harmful.

The Diamond Light Source is housed in this giant circular building in Oxfordshire.

Iron and Alzheimer’sStudying metals in the brain


Specimen thicknesses are measured in micrometres (µm); 1 µm = 10-6 m

X-ray energies are measured in electron-volts (eV); 1 eV = 1.6x10-19 J

How synchrotron light can ‘see’ metal in tissues

To detect metals in biological tissues scientists can make use of a phenomenon called X-ray fluorescence. X-ray fluorescence occurs when high energy X-rays lose some of their energy as they strike atoms in the sample. The atoms emit lower-energy X-rays. The useful thing is that each element emits X-rays of a specific energy so, by measuring the energies of these X-rays, we can find out which elements are present.

Post mortem brain tissue, left to medical research by someone who had Alzheimer’s disease, is cut into thin sections of around 30 µm thick and X-ray fluorescence is used to look for metals in the tissue. The beam of X-rays is tuned to an energy of 10 000 eV and focused to a square spot size of between 60 and 3 µm. The X-ray beam scans across the sample and a detector collects the X-rays emitted at each point. The detector can detect X-rays across a wide energy range and so produces a spectrum of emitted energies. The spectrum has peaks where there is an element fluorescing at that energy. For example, iron fluoresces at an energy of 6403 eV so if there are X-rays detected at this energy we know iron is present. By looking at how the intensity (brightness) of the X-rays at 6403 eV changes across the sample, the variation in iron concentration can be observed.

This schematic diagram of Diamond shows the beam lines radiating out from the large accelerator storage ring.

Diamond Light SourceA synchrotron is a particle accelerator designed to produce very bright light. There are four steps to producing the synchrotron light at Diamond:

• Electrons are produced by an electron gun, and a linear accelerator (linac) uses high voltages to accelerate the electrons.

• These electrons are fed into a small booster synchrotron and accelerated until they are travelling close to the speed of light.

• The electrons are now passed into the storage ring of the main synchrotron. The storage ring is not actually a circle, but a pentagon made up of straight lines. At the junction of these straight sections are bending magnets which change the direction of the electrons and cause them to give off energy in the form of light.

• This light can be channelled out of the storage ring, at points called beamlines, and used for experiments.

Different bending magnets mean that Diamond can produce light with a range of wavelengths from infra-red, to visible, to ultra-violet to X-rays. The synchrotron light is extremely bright – up to a 100 billion times brighter than the sun – and can be tuned to a very narrow range of wavelengths (energy) at each beamline, depending on what experiments are to be carried out.

Control Cabin

Experimental hutch

Optics Cabin Beamline

Storage ring

Linac

Electron gun

Boostersynchrotron

The ‘light’ produced by the Diamond accelerator is not just visible light. It covers much of the electromagnetic spectrum, from infra-red to X-rays.


The X-ray fluorescence spectrum of brain tissue has

peaks which show which metal elements are present.

Look here!Health Q&A video at www.youtube.com/watch?v=MTZyUlfBrlA

The Alzheimer’s Society funds Mary’s research: www.alzheimers.org.uk

More about how Diamond works: www.sep.org.uk/catalyst/articles/catalyst_16_1_255.pdf

These ‘maps’ show the distribution of iron and zinc in a section of brain tissue from

a person who had Alzheimer’s disease.

Understanding Alzheimer’sWithout the intensity of synchrotron X-rays it would be extremely difficult to detect these metals while maintaining the spatial information. By studying the changes in iron and other metals in Alzheimer’s disease compared to people who died with a healthy brain, researchers hope to improve understanding of the disease that will hopefully lead to better treatment and ways of diagnosing Alzheimer’s disease.

Looking at iron in the Alzheimer’s diseased brain is not the only example of how synchrotron X-rays are being used in medical research. Some other examples include looking at metal changes in other brain diseases, such as Parkinson’s disease and looking at inflammation around metal implants such as hip replacements.

Mary Finnegan is studying for a PhD in biomedical engineering at the University of Warwick.

Sample preparationThe way the samples are prepared is very important as this technique is very sensitive and any contamination on the sample could give false results or ‘shine’ much more brightly than trace metals in the tissue, masking their signal. The tissue must be cut in a very clean environment with a non-metal knife. The section is mounted onto a slide made of quartz – glass slides cannot be used for most of these measurements as glass often contains randomly distributed inclusions of the metals being examined.

The elements that can be detected by this technique depend on the energy of the X-ray beam focused on the sample. With an electron beam of 10 000 eV, zinc, copper and iron can be detected. Maps of these different elements can be created to compare the distribution of the metals in the tissue. For example, in X-ray fluorescence maps from the hippocampus, a region of the brain important in memory that is badly affected in Alzheimer’s disease, does the iron distribution vary across the cell population in the same way zinc does?

Choosing the spot size is also important. With a bigger spot size a larger area of tissue can be mapped, but many cell bodies in the brain are around 10 µm in diameter so choosing a smaller spot size may allow the metals to be pin-pointed to specific cells. Experimental time at Diamond is very limited for the scientists who get to use it, maybe only a few days a year, so it is important that experiments are planned carefully!

X-ray fluorescence mapping will detect atoms of an element no matter what chemical form it is in and no matter what other elements it is bound to. However, at Diamond the way the tissue absorbs X-rays can also be measured to provide information about what form a metal is in. For example is iron in the safer Fe3+ form that we expect the body to store it in? Or is there evidence for the more toxic Fe2+?

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Key words

patterns

medical trial

double blind

publication

Ed Walsh

One of the things that we do as scientists is to look for patterns in data. Ed Walsh explains how this can go wrong.

Patterns are useful because, if we do a number of tests and the results fall into a pattern, it probably means we’re doing something

right. Then we can look for an explanation of the pattern. For example, you’ve probably seen alkali metals reacting with water. Alkali metals are in Group 1 of the Periodic Table and are in a column over at the left hand side. The first three are lithium, sodium and potassium. They all react with water and are increasingly reactive as you go down the group. The next one down, rubidium, isn’t allowed in schools and the one after that, caesium, is even more dramatically explosive.

You can see why by searching for caesium reaction on YouTube and watching the Open University clip. It takes you through all five in three minutes and you can see a simple pattern. (Don’t trust the Brainiac clip –they added explosives to spice things up!)

Bad SciencePatterns, trends and dastardly traps

Misleading patternsPatterns can be dangerous though. Sometimes we can convince ourselves that we’re getting a pattern. Imagine you were doing a simple test, tossing a coin and writing down the results. (It’s an unbiased coin, with an equal chance of coming up heads H or tails T.) You do eight flips and then try to work out the ninth. What would you guess as being the ninth flip from each of these?

a) H T H T H T H T?b) H H T T H H T T?c) H H H H T T T T?

The answer is, of course, you’ve no way of knowing. Any of these, on the ninth flip, could just as easily be heads as tails. Patterns can be misleading.



So how do we tell if there’s really a pattern, or whether it’s just chance? And does it matter? Well, yes, it does matter. It can be a matter of life and death. We’ll see why in a minute, but let’s play some cards first. This is a very simple (and, I mean, very simple) game. It’s called “Play your cards right” and used to be a TV programme, featuring Bruce Forsyth (now on Strictly Come Dancing). In the programme Bruce would present a contestant with a row of cards, face down. He would then turn the first one over. Let’s say it was a two. The contestant would then be asked whether the next card was going to be higher or lower (Ace = 1, Jack, Queen, King = 11, 12, 13) and the audience would call out “higher” or “lower”.

Let’s apply this, however, to fatalities on a road. The graph shows the annual figures for crashes on a freeway in the Australian state of Victoria. Starting in 1991, they go: 8, 6, 10, 13, 9. Not good, but it’s a long, busy, fast road. It then jumps the following year to 21. The authorities, stung into action, declare it to be an ‘Accident Black Spot’ and the figures drop to 16 the next year. The following year warning signs, road markings and a speed camera are installed. The next year the figure is 8 and the following year 5. Everyone breathes a sigh of relief: the preventative measures have worked – or have they? Well, applying the principle of ‘Regression to the Mean’ it’s not obvious that they have. Road accidents are random events and will rise and fall year by year – who’s to say they wouldn’t have dropped anyway?

Medical testing

Of course, if your last card was lower than seven, you’d predict “higher”; if it was higher than seven you’d predict “lower”. This neatly demonstrates a principle called “Regression to the Mean”. You don’t know what the next card will be but you do know the values rise and fall around a mean (in this case, of seven). A contestant would be ill-advised, following a sequence of five, seven, nine, Jack to call “higher” even though there might seem to be a pattern of the value increasing by two every time.

Spot the patternScientists are pattern-spotters, but the underlying patterns in nature are often difficult to see. Can you spot the patterns in the sequences of cards below? Each sequence runs from left to right.

The problem is to decide which features are relevant and which are irrelevant. For cards, this could be their numbers, suits or colours – or a combination of these. The answers are at the end of the article.

This also applies when it comes to testing medicines and other treatments. Surely, if you come up with something that you think will work, you give it to someone who’s ill and see if they get better? Do that a few times, publish the results and collect your winnings from big pharmaceutical company. Actually, no. People get better for lots of reasons. Imagine someone told you that a guaranteed cure for a cold is to treble your chocolate intake and after a few days you won’t have a cold. You try it and, after a few days, your cold has gone. You remain, however, sceptical, and rightly so.

When you receive

medication, you expect

it to have been tested

correctly against other

possible treatments.

Annual road crashes on the Tullamarine Freeway,

Victoria, Australia. Source: Victorian Government

Statistical black spot


Bad science, better scienceBen Goldacre is a doctor and a journalist. He’s written a book called Bad Science, he writes a newspaper column called Bad Science and runs a website called … you’ve guessed. He’s really hot on why, when you’re testing a new medicine, you have to get it right. If you don’t, then people die. So if you have a new drug that you’re itching to try out and prove, what do you do?

Well, three things, so that you end up with a randomised controlled double-blind trial:

• Firstly you compare it against another treatment. The big question is not whether your drug works but if it works better than the current treatment, so run a comparison. Head to head.

• Secondly, you set up two groups of patients to try the drugs on (one for the new treatment and a control group for the current treatment) but the patients in each group are selected at random. Randomisation doesn’t cost anything but it’s essential.

• Thirdly, you don’t tell people which treatment they are getting. In fact, you don’t tell the people who are administering the treatments which they are using. This is called double blinding.

Actually there’s a fourth thing. You publish the results. All of them. Scientific understanding doesn’t just develop from little bits of information discovered like bits of a jigsaw that have dropped on the floor and have been found, but from arguments. Real, stand-up-and-shout arguments. Sea floor spreading, evolution and the periodic table all came from arguments. Arguments over what the evidence shows.

Science – use and abuseBad Science is about how science is used – and abused. Many of these abuses are not difficult to detect if you’re given a few pointers. That’s what Ben’s book is about. Some of these ideas have been turned into classroom activities; they’re on the web at www.collinsnewgcsescience.co.uk/badscience along with video clips of pupils trying the ideas out and Ben Goldacre talking about why these are important.

Ed Walsh is a science adviser in schools in Cornwall

Solutions to card sequences on page 17:Sequence 1 – numbers increase from left to right; Sequence 2 – even numbers are followed by red, odd numbers are followed by black.

Bad Science – the author, the book and the website.

1919

You will need:Small plastic drink bottleVegetable oilFood colouringFizzing tablet such as Alka-seltzer or Disprol

What you do:• Quarter-fill the drinks bottle with water and add

a few drops of food colouring. Shake gently to ensure they are well mixed.

• Fill the rest of the bottle with the vegetable oil.

• Add half of one of the fizzing tablets and watch what happens. You can add more tablet when the first one has all dissolved.

Make your own

‘lava lamp’

Vicky Wong is Chemistry editor of Catalyst

Try this

Making a model lava lamp Bubbles of gas at the interface

between the oil and waterIs this like a real lava lamp?The model lamp is similar to a real lava lamp in that it contains two liquids of different densities which do not mix. Real lava lamps are usually powered by heat which sets up convection currents in the mixture. The more dense liquid at the bottom (blue in the lamp shown at the right) is heated, causing it to expand. This expansion reduces the density so that it rises and bubbles up through the other liquid (purple in the lamp shown) to the surface. When it cools, the density increases again and the liquid sinks.

Why does this happen?The water is denser than the oil so usually sinks to the bottom of a mixture of the two. Combined with a bubble of carbon dioxide, however, it is less dense and so rises through the oil. Once the bubble bursts and the carbon dioxide is released, the water is again denser and so sinks back through the oil.

Catalyst October 2011

What you see:The fizzing tablet releases carbon dioxide as it dissolves. The bubbles of carbon dioxide attach themselves to some of the water and food colouring mixture and pull it up to the top as they rise. When the bubbles reach the top they pop and the water mixture sinks back through the oil to the bottom.


An odd mix of A-levels, a useful gap year and beyond – Bristol University Biology student Tom Denbigh talks about his step up to University.

I never knew that bacteria could talk. I was in a lab (one of those big white ones, looking just like a

CSI set) when my supervisor calmly told me this – old news to her. Days later, I saw it happen.

While my friends had gone straight to University, I’d done my best to avoid having to decide anything while studying for A-levels. Decisions, decisions. I can’t remember a more stressful time. So out of indecision I delayed applying to uni and took a gap year. I worked in a research lab; lived in New York; and got a tan surveying by the sea.

Tom Denbigh

Box 1 - VolunteeringIf you would like to volunteer, but don’t

know where, here are a few ideas to get you started.

Have a look for any science institutes in your area, and email as many as possible (be willing to travel).

Whenever you meet anyone involved in science, be prepared to follow them up – even if they can’t help, they may know someone who can.

Conservation organisations are always looking for help (try the BTCV).

Your school might be able to let you shadow/help a science teacher after you have left sixth-form. Your science teachers may also know old uni friends who now work in research.

Contact your local field centre! They do both research and conservation.

There is always voluntary stuff at your local hospital. This mainly involves talking to patients, and helping with little jobs, it’s good for anyone interested in medicine, and shows you’re willing to devote your time to the community, which looks good on the personal statement on your university application form.

Tom surveys and records invertebrates on the beach.

Tom examines snails in the lab.

At first trying to get any work experience seemed pretty intimidating – all I had was a mixed bag of A-levels and still a fair bit of doubt over whether I wanted to do Physics, Biology or even English Literature, as my degree! Secondly, work experience isn’t obvious, widely available, or advertised. But then since all that costs money, why would it be? I volunteered at my local aquarium (there are always conservation positions available somewhere - see Box 1) and then emailed the public relations

Where next?


Box 2 - Choosing a university for science

Tom Denbigh offers his own thoughts on choosing a university for science. He says it’s good to look at both the institution, and where your own interests lie.

Most of the universities with the best research, and commitment to science research belong to either the Russell Group or 1994 Group. Both groups are research intensive, though the universities in the 1994 group tend to be smaller institutions.

With 60% of the “world leading” research taking place in e.g. the Russell group, you can know that while you may not be involved in it at degree level, you will be taught by the top researchers!

When it comes to choosing your course, it is good to know whether you want to be general, or specialise, and choose an institution that supports that.

Often a general first year at university allows tasters of different areas, to help you choose where to focus. This is great for those undecided, but can be tedious for those lucky enough to know where they want to head!

One option at some universities also allows you to spend about a third of your first year taking units from other departments (from chemistry to French, or even law). This can be something to look out for as it can help you build on skills (such as a language) that could come in handy later in life, and can even just satisfy your interest in an arts subject before focusing on science.

Once you have a rough list of universities, it is also pretty important to decide if you like the location – you won’t want to end up living somewhere you don’t like. Remember; the happier you are, the more you enjoy your degree, and ultimately the better you will do!

Tom uses modelling clay to make replicas of fossils

from the stonework of the Cabot Circus shopping

centre in Bristol.

A Portland screw

department of my local science institute (Plymouth Marine Laboratories). My fingers were tightly crossed that I would even get the dignity of a rejection.

What they don’t tell you at school is that sometimes all you need is enthusiasm. I got a reply, and that’s when I got to work with bacteria that, yes, talked to each other! (Their method of communication is called quorum sensing, so you can look it up for yourself). Simply by asking around I got my next placement, in the same organisation where they first looked at nerve impulses – the Marine Biological Association (MBA).

A year on I was lucky enough to be offered my current summer job, surveying and data entry, but this time for a wage. Fantastic! And best of all, I might even be named on an academic paper.

I finished my trinity of experience at Rockefeller University in New York, all thanks to a chance meeting with a microbiology professor. Work experience doesn’t have to mean being desk-bound, and I ran round the Big Apple, at the same time as pimping up my CV. Of course this cost a fair amount of money, but thanks to working weekends in a shop in the first part of my year, I could afford it.

I can count on one hand the number of people on my course who have lab experience, and when it comes down to navigating my way around unit choices, it can really help, and even give you an edge in practicals!

The best thing, my year out gave was that it bought me time enough to give my degree and my university choice a real think-over. I learnt that if you want to work in science, getting a good degree counts for a lot, and going to a good university (Box 2) counts too. A pretty serious consideration though is showing enthusiasm – science can go wrong, and if your drive runs out when your first experiment doesn’t go to plan, you are no good whatsoever. Ultimately by volunteering and getting involved you can show off your energy and interest, and who knows, one thing may lead to another; you’ll have contacts and a foundation in science before you even know it!

Tom Denbigh is a 2nd-year Biology student at Bristol University.


The distribution of volcanoes across the Earth’s surface tells us about the underlying pattern of tectonic plates. Much can been learned about volcanoes by observing them from orbiting spacecraft.

Olympus MonsThe biggest volcano in the solar system is Olympus Mons, on Mars. This photograph, taken by ESA’s Mars Express, shows the six calderas which make up its summit.

ASTER is an instrument that detects thermal (infra-red) emissions and reflections from the ground. Different land surfaces show up as different colours.

SarychevSarychev Peak in the far east of Russia erupted on 12 June 2009. Observers on the International Space Station saw how the plume of ash and gas pushed aside the cloud layer above.

Vesuvius, the volcano that destroyed Pompeii in AD79, dominates the bay of Naples, Italy. This night view shows how close people live to the active volcano.

NASA’s EOS-AQUA satellite uses infra-red measurements to analyse atmospheric gases. This map shows the concentration of sulphur dioxide in Etna’s plume.

Volcanoes from space

A plume of ash and gas rises from Etna, on Sicily, off the ‘toe’ of Italy. Photographed on 11 January 2011 by NASA’s Terra satellite.

Etna

Vesuvius

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Anaerobic digestion · 01273 562139 or [email protected] Science and explanations S cience is about observing things and then explaining them. Take the experience we all have of