Wednesday, 31 December 2014

Error Bars and how they can be improved

Interesting paper entitled "Error Bars Considered Harmful: Exploring Alternate Encodings for Mean and Error" by Michael Correll and Michael Gleicher, both from the Department of Computer Sciences, University of Wisconsin-Madison, USA.

Essentially, their work tackles the public perception of error bars, noting that bar charts using conventional error bars suffer from two main problems :
Within-the-bar bias: the glyph of a bar provides a false metaphor of containment, where values within the bar are seen as likelier than values outside the bar.

Binary interpretation: values are within the margins of error, or they are not. This makes it difficult for viewers to confidently make detailed inferences about outcomes, and also makes viewers overestimate effect sizes in comparisons.

Their proposed solution is that a more nuanced way of representing error probability is used, summarised in this image from the paper:

Ways of representing probability of error

It's all interesting stuff, and it is great to read that the public comes as being able to robustly interpret data - so long as the data meets them half way!

Sunday, 21 December 2014

Liverpool Life Sciences UTC Blog by Prof Dave Hornby

Recently became aware (by the magic of Twitter) of the Blog run by Prog Dave Hornby at the Liverpool Life Sciences University Technical College.

It has some interesting stuff on it.....

How fish make their own antifreeze

An Interview with (Nobel Prize winning) Sir Richard Roberts who talks about GMO, pointing out that the opposition of some groups to GM organisms such as Golden Rice is preventing their introduction. It would have been nice, however, to have seen him questioned on some of the more dubious GMO business practices of Monsanto et al.

How fluorescent genes have transformed research by allowing target molecules to be visible under microscopy.

Lots of important points in this post about infectious diseases.

Some interesting comments see here, and here on things to consider when starting up a life science business

Green Fluorescent Protein

Image Source
GFP

Saturday, 20 December 2014

Top 10 posts of 2014

Really enjoyed writing the Nottingham Science Blog in 2014 and learnt lots of stuff!
Here are the top 10 most popular posts this year....

1 : UoN's Professor Philip Moriarty talking about 3D printing....with atoms.
Prof Moriarty moves around a lot, this is about as clear as it got...


2 : Sheffield Uni's Professor Michael T Siva-Jothy on bedbugs.
Quality reposte from Prof Michael Siva-Jothy


3: Plymouth Uni's Hazel Gibson on the public perception of fracking.
US Fuel consumption by type, history


4: UoN's May Fest 2014
Very clever stuff involving pendulums and lights !


5 : UoN's Sara Goodacre on Spiders
Erigone Atra, obviously


6: History of Train Manufacture in Derby
1377 Class, 1878


7 : UoN's Ian Fisk on the Flavour of Food
Wood and Cucumber aroma - from the same chemical !


8 : Sheffield Uni's Duncan Cameron on Soil Science
World Percapita Fertilizer Use & Available Grain Area
Derived and simplified from USDA data
http://people.oregonstate.edu/~muirp/fertlim.htm


9 : Bath Spa's Snezana Lawrence on Mathematics in Society
A sign from Bourbaki


10 : UoN's Emily Kostas on Fuel from Seaweed.
target="_blank"
Kelp Forest


Talk : Blue-Green Cities - Managing Urban Flood Risk

Recently went to an interesting UoN public lecture talk by Dr Emily Lawson, who is a Research Fellow, UoN Faculty of Social Sciences.

The talk was entitled "Blue-Green Cities - Managing Urban Flood Risk the blue-green approach" and compared traditional "grey" flood protection methods with alternative "blue-green" approaches. The talk was based on work being done by the "Blue-Green Cities" project, whose website is www.bluegreencities.ac.uk. This post is based on the talk, with a little extra linkage thrown in.

Dr Lawson began by providing a helpful glossary of some of the terms used:

Grey Infrastructure: Traditional flood defenses such as barriers, storm drains etc etc

Blue-Green Infrastructure: Natural, multi-functional defenses (e.g. replacing concrete, which rain runs straight off) with grass (which soaks up rain). More examples later!

SuDS:Sustainable Drainage Systems, which aim at use cost effective solutions with low environmental impact to drain away dirty and surface water run-off through collection, storage, and cleaning before allowing it to be released slowly back into water courses. Absolute SHEDLOAD of resources about SuDS available here. SuDS is now mandatory for new housing developments, although whether developers use it in a token or a wholehearted fashion is source of debate.

Infiltration:The process whereby water soaks into the ground (or doesn't if the ground is concrete)

Fluvial Flooding: Flooding from rivers, usually into their floodplain (not a problem unless the floodplain has been built over!)

Coastal Flooding: Usually caused by a combination of high tides, storm surges and wave action.

Pluvial Flooding: Surface water flooding, can happen unexpectedly, usually from intense rainfall. See "Toon Monsoon"

Dr Lawson then described what had happened in the winter of 2013/14, when many parts of the country received 2-3 times as much rainfall as usual (see image below and also this ,and this).

The averaging period used for the following assessment was 1981-2010

UK Rainfall Jan 2014
According to the MetOffice report on the events, the unusual weather was:

"...part of major perturbations to the Pacific and North Atlantic jet streams driven, in part, by persistent rainfall over Indonesia and the tropical West Pacific. The North Atlantic jet stream has also been unusually strong; this can be linked to exceptional wind patterns in the stratosphere with a very intense polar vortex."
This caused flooding in many regions, with much media coverage being given to the flooding in the (low lying) Somerset Levels. Dr Lawson pointed out that flooding in this area has happened many times before. For example, in 1919, flooding covered 30% of the farmland in the area, compared to the 10% that was flooded in 2013/4.

Grey Infrastructure
Dr Lawson commented that, whilst grey infrastructure did its job in terms of combating floods, and was sometimes the only solution (e.g. there is no "blue-green" alternative to the Thames Barrier) is also had a number of disadvantages.

In particular, it treats water as "a nuisance" that has to be got rid of as quickly as possible, via drains etc. This causes problems during intense rainfall, for example, as the drains simply can't cope with the volume of water, resulting in water backing up and flooding onto the streets.

Although modern drains and sewers separate rainwater from domestic foul water, old drains do not, so flooding can result in the escape of diluted sewage onto the streets or into local rivers. Not good.

In addition, grey infrastructure is being put under more pressure by continued building of new houses etc, which result in more land being covered in impenetrable surfaces. For example, 92% of Newcastle city centre is covered in impervious materials such as concrete.

Grey infrastructure is also relatively inflexible - expanding the size of existing sewers simply isn't going to happen - so can be vulnerable to changes in climate or population. As Prof. Antje Stokman from Liebnitz University explains in this paper:
"It is hard to believe that also Tokyo still in the 19th century used to be a very open, green and wet city. A system of segmented rice fields was planned as an integral partof the urban tissue, which did not only provide food to the citizens, but at the same time performed as a system of preventing floods and irrigation"

Incidentally, populations may go down as well as up. Hannover city centre, for example, has seen a reduction of population from 300,000 in 1970 to just 140,000 today, resulting in a decrease in wastewater from 3000 litres/sec to just 520 litres/sec. The effect of this is explained by Prof Stokman:
"...the amount of wastewater flowing through the pipe systems is much reduced due to decreasing urban density with sparser populations distributed over larger areas. As a result in many German cities the under-loaded sewers need to be flushed constantly to avoid smell and the accumulation of pathogens."

And finally, the point was made that flooding only happens for a short time of the year, the rest of the year the grey infrastructure just sits there looking ugly Maybe there is a better way?

Concrete flood barriers can be pretty ugly

Although these in Kentucky have been brightened up

Blue-Green Infrastructure.
In contrast to Grey Infrastructure, the Blue-Green approach (see also here, and here) aims to protect and restore natural water courses and infiltration processes, and also to introduce planted areas to improve soil water retention. Critically, Blue-Green measures aim to deliver benefits other than just flood control - they may increase biodiversity; improve soil quality; remove pollutants from the air; or be visually attractive. A leader in developing Blue-Green approaches to water management is the City of Portland, Oregon, US (see here). Here are a few examples of Blue-Green infrastructure :

A school in Portland, Oregon, US, installed a "rain garden" (a SuDS system) that performed the flood control function of allowing rain to infiltrate into the ground rather than running off into drains - but it also allowed the school to reduce their air-conditioning costs, as the plants reflected less of the light and heat from the sun than the concrete had. In addition, the rain garden was a valuable resource for the schools science students.

School Raingarden

A related feature is a "Bioswale" (another SudS system) which aims to capture rain and run-off water, slow it down, and remove pollution from it. These can work well when used around car-parks, as the the surface run-off from these areas is often contaminated with oil, rubber and other contaminants. Another common application for these is alongside roads, where they can, again, filter and slowdown rain water runoff.

Roadside Bioswale/td>

Bioswale in construction (foreground)
Completed Bioswale in background

"Green roofs" are not a new idea, but have been getting renewed interest as a SuDS approach. Their weight, however, makes them difficult to retrofit. Nice article about their use in Portland here.

This is not a field, this is the roof of the Canadian War Museum

Permeable paving can, due to the area covered, make a huge difference to the amount of rainwater that is infiltrated back to the ground instead of running off into drains. Positive economic findings in this report from Portland.

Permeable paving

And one final example, disconnecting domestic rainwater downspouts reduced water going into drains and provides water for plants. Portland have disconnected 56,000 domestic downspouts in recent years, reducing rainwater runoff significantly.

Disconnected downspout

One in "X" years
Flood defenses are, in part, defined by the kind of flooding that they are expected to be able to deal with. This is expressed in how often the most extreme event it is designed for might happen. Typically, defenses are designed as follows:

River defences : 1 in 100 years event protection
Sea defenses : 1 in 200 years event protection
Barrier defences : 1 in 1000 years event protection
Blue-Green defences : 1 in 30 years protection

It can be seen, as mentioned earlier, that blue-green defences will often need to be used in conjunction with traditional grey infrastructure. However, the use of blue-green can significantly reduce the cost of constructing grey defenses, for example by reducing the diameter of sewer piping required.

The Environment Agency published flood maps for the UK (see here) and some examples are shown below. In each case, the colour coding is as follows:
Dark Blue : >1 in 30yr event; Medium Blue : 1 in 30 to 1 in 100 yr event; Light Blue : 1 in 100 to 1 in 1000 yr event.

Nottingham river flood risk

Nottingham surface water flood risk

Nottingham surface water flood risk - significant at bottom of valley 

Somerset Levels river/coastal flood risk

Somerset Levels surface water flood risk

Show me the money.
A recent government note on flood defense spending states that :

"Some 5.2 million properties are at risk of flooding in England. Annual flood damage costs are in the region of £1.1 billion. These costs could rise to as much as £27 billion by 2080. It has been estimated that maintaining existing levels of flood defence would require flood defence spending to increase to over £1 billion per year by 2035.

Central Government spending on flood defences will reduce in real terms over the spending review period. The Government has introduced a new flood defence funding system, which it believes will help to meet the shortfall. The new funding arrangements seek to encourage more local investment in flood defences, so that schemes that might not be funded nationally may still go ahead.

There are concerns about the extent to which local communities are able to contribute to flood defence funding. While the number of properties at risk of flooding may not rise in the short term, there could be a significant increase in the longer term if current spending levels do not increase."
And also comments that :

"There was a significant increase in flood defence spending from 1997 to 2010—spending increased by three-quarters in real terms. Central Government spending on flood defence in 2010-11 was cut soon after the Coalition Government was formed. Spending was reduced in year by £30 million or 5%. In the 2010 Comprehensive Spending Review (2011-12 to 2014-15), a total of £2.17 billion in central government funding was provided for flood and coastal defence. This represented “a six per cent fall in central government funding”. The Committee on Climate Change calculated that this represented a real term cut of around 20% compared to the previous spending period."
See also this very recent BBC article.

Regarding the question of whether blue-green approaches are of economic benefit, a recent DEFRA report which looked at the application of blue-green approaches instead of a proposed large "grey" project in London, basically says "We don't know". This was due to a variety of factors, including that many of the benefits of blue-green approaches are qualitiative.

On the other hand, another DEFRA report, looking at the use of SuDS in new housing developments comments, amongst much else, that:

The differences in the costs between each drainage Standard is scale related, with SuDS costs showing greater benefit against the other Standards at large sites, with reduced cost benefit for small sites.

"SuDS have very great advantage for developments on permeable catchments where rainfall runoff can be infiltrated compared to the drainage designs based on the other Standards.

...In these [impearmeable site] situations SuDS, particularly with the use of permeable pavements, are generally advantageous over the other Standards...

SuDS generally have little cost advantage for medium and large sites where ground conditions require lining.

The issue of whether SuDS can or cannot be considered as contributing to public open space is very important to clarify, as costs associated with loss of land for dwellings is significant where vegetated systems are used.

There is a significant cost advantage in using SuDS for flat sites, but in contrast their use on steep sites tends to constrain site layout and may cost more than drainage schemes designed using the other Standards.

The study found that the approach of the design team in developing a development layout and the SuDS strategy will have a large impact on the capital costs and only small changes in both the approach will have a large impact on the cost and affordability of the SuDS scheme."


Related Content
Talk - Bedbugs
Talk - From Soil to Supper
Dr Sara Goodacre on Spiders
Green Fuel from Seaweed
Living on Frack-tured Earth

Image Sources
2014 Jan Rainfall, Flood Wall, Painted Flood Wall, RainGarden, Bioswale, StreetsideBioSwale, Canadian War Museum, Permeable paving, Disconnected Downspout

Sunday, 14 December 2014

Talk : A Defence of the Monte Carlo Simulation

Interesting Cafe Sci talk recently by Dr Nira Chamberlain on the "Monte Carlo" Simulation and how, in Dr Chamberlains view, it had been unfairly blamed for the 2008 financial crisis. This post is based on the talk, with a little extra linkage thrown in.

Dr Chamberlain is a professional mathematician, has been named as one of the UK's 100 leading practical scientists, and is an advocate for mathematics (see also here).

The Monte Carlo simulation is a way of solving mathematical problems by taking multiple random samples rather than trying to "calculate" the answer. For example, rather than trying to calculate the average time to complete a maze, say, a Monte Carlo Simulation would repeatedly try to go through a maze, taking random decisions at each junction, and see how how long it took, on average, to get to the other side.

Perhaps the first use of a Monte Carlo simulation was by French polymath Pierre-Simon Laplace, who used it to estimate the value of pi.

But it was only with the advent of electronic computers, which could quickly perform many thousands of calculations, that Monte Carlo simulations really came into their own, most famously to help the design of the first nuclear bombs in the Manhatten project. It was here that it was given the name "Monte Carlo Method" as it reminded one of the researchers of gambling behaviour in the famous Monte Carlo casino.

After WW2, Monte Carlo simulations were used in applications ranging from engineering to computational biology

An important use of the Monte Carlo simulation is in financial modelling. Dr Chamberlain explained their use, using the "maze" as an analogy for a financial product. Imagine two traders, Trader A and Trader B...

Trader A to Trader B : Here is a maze, and here is £60million pounds on the table. When the clock starts, you begin the maze and I'll start taking away £1million very minute. If you get through the maze in less than an hour, you keep any money left on the table - but if it takes you MORE than an hour, you have to give me £1million for every minute over an hour that it takes you. Do you want to take this bet? (optional evil laugh here)

Trader B (thinks) : The question I need to know the answer to, right now, is how long it takes on average to get through the maze.

And this is where the Monte Carlo simulation comes in. The simulation will have many attempts to get through the maze, and the results are likely for form some kind of frequency distribution like this :


That is all well and good - the problem comes if, in real life the maze is more complicated than the one in the simulation, and the probability distribution is actually like this :


Dr Chamberlain explained that this mismatch between theory and the real world is exactly what happened to financial models in the wake of the 2008 sub-prime defaults, and was a big factor in the resulting financial crisis.

And, worse that this, when the trades lost money the traders thought they had just been unlucky (because their simulation was wrong), so bet again...and again.

Dr Chamberlain commented that JP Morgan had released the Monte Carlo method to the financial marketplace in 1992 [as part of their RiskMetrics methodology] but, in doing so they failed to adequately warn the market about some of the dangers in using the method. The 2008 crisis left many wondering whether Monte Carlo simulations were to blame. Dr Chamberlain gave examples such as an article entitled "Is Financial Monte Carlo Simulation Dead"

However, as suggested in the talks title - Dr Chamberlain was here to defend the Monte Carlo method, and felt that the problem was more to do with poor inputs and assumptions rather than the method itself, commenting that :

i) When the underlying conditions change, so should the assumptions in any relevant Monte Carlo simulations.

ii) A crisis similar had previously occurred in 1998, when LTCM went bust having lost $4.6billion due to the Russian and Far Eastern economic crises distorting the market. [NCB notes that LTCM was dripping with Economics Nobel Prize winners and that the subsequently bought out company went bust again in 2009].

iii) The market had been warned about the risks of unexpected marked events, for example in the Black Swan theory and in a paper presented at the International Congress of Mathematicians 2002

iv) The Winner Effect, where testosterone fuels increasingly risky trading behaviour.

Talk : Maths in Society

Went to an interesting Cafe Sci talk recently in which Dr Snezana Lawrence (Senior Lecturer in Mathematics Education at Bath Spa University) discussed how mathematics was perceived in society and how it was taught to schoolchildren.

This post is based on the talk, with some added linkage thrown in.

Dr Lawrence began by describing how she had once addressed an audience of around 70 people from the London Mathematical Society to raise their hands if they were mathematicians and was surprised to find that only one person did so - it turned out that only the most "pure" mathematics researchers were actually regarded by their peers as actual mathematicians, with everyone else believing themselves to be a specialist of some sort!

The Dr continued by noting that, although mathematics was often viewed as a "universal language", there were often significant differences in how it was taught in different countries. For example, the eastern european countries are still heavily influenced by the practical style of mathematics developed by France after the revolution, in contrast to the much more theoretical work that was undertaken in next door neighbour Germany. Many of the key figures of the period, as well as the major trends, are covered in this excellent article at The Story of Mathematics.

One of the greatest awards that a mathematician can get is a "Fields Medal", which are awarded every four years. The most recent recipients, in 2014, were Artur Avila, Maryam Mirzakhani, Manoj Bhargava and Martin Hairer.

Artur Avila - top mathematician

Other mathematician who were mentioned included Paul Erdős and Andrew Wiles who discovered a proof to Fermat's Last Theorem and whose work is described here.

Andrew Wiles - aimed high, scored big time!

Dr Lawrence also played a few clips showing how mathematicians were portrayed in films (e.g. Good Will Hunting, Pi) and commented that the portrayals were generally as mathematicians being aloof, mentally on-the-edge and geniuses.

These themes were also explored in the rather awesome documentary "Dangerous Knowledge" (see also here) which looked at the lives of the great mathematians Georg Cantor, Ludwig Boltzmann, Kurt Gödel and Alan Turing. The documentary describes how Europe at the end of the 19th century was moving from an age where science was all about certainty (e.g.Newtons Laws of Motion) to one that was driven by uncertainty (e.g. Brownian motion). The program shows how mathematicians such as Cantor and physicists such as Boltzmann who were grappling with ideas that involved uncertainty faced very significant resistance from their peers. Cantor's work which dealt with infinity not as an abstract idea but as a concept that could be worked with and had infinities of different sizes, led him to a nervous breakdown.

Some idea of the paradoxes involved in thinking about infinities can be seen by considering Galileo's Paradox , which goes something like this :

1) In a number line, there are fewer square numbers (4,9,16,25,36...) than there are numbers in total (e.g. 4,5,6...34,35,36...)
2) Yet for each number there is also a square (4 has 16, 5 has 25, 6 has 36 etc) - so there should be as many squares as there are numbers.

The way mathematics was portrayed in society was also discussed, with reference being made to the infamous "Maths Class is tough" Barbie and Dr Lawrence explaining that mathematics was perceived as a "high stakes" subject to study, although it did provide some kudos to those who were good at it - and that the current fascination with millionaire IT geek entrepreneurs had also raised the standing of the subject somewhat.

Governments of all colours have long been concerned about the national skills base in mathematics (as well as in other STEM subjects), with a report on the issue being issued by Prof Adrian Smith in 2004 (Government response here)

Dr Lawrence also described the work of Nicolas Bourbaki, who has published many papers, despite the fact that there is not actually a mathematician called Nicolas Bourbaki.

Winningly, Bourbaki was also the inventor of the "dangerous bend" symbol. A fact that made the talk worthwhile for NSB all by itself!

A sign from Bourbaki

A theme that recurred throughout the talk and the subsequent Q&A was that students would often ask how mathematics was relevant to them. One example of how this can be answered is the "Taking Maths Further" podcasts, which look at how mathematical concepts are practically used in science and industry.

Also, Dr Lawrence's website, www.mathsisgoodforyou.com has a maths timeline, list of mathematicians and a lot of other, very accessible, information.

Image Sources:
Dangerous Bend
Andrew Wiles
Artur Avila

Sunday, 7 December 2014

Soyuz TMA-15M / ISS 42

There I was, idly reading through the NSB Twitter feed when this startling message from @AnneGlover_EU scrolled up into view :


26mins to launch - quick, lets head over to NASA TV

And within a few minutes NSB was glued to the NASA video feed, watching the countdown, lift off, and journey into orbit of Soyuz TMA-15M, which was carrying the crew of the ISS 42 mission. It was a heck of a ride ! And, as NSB had never watched a launch all the way to orbit, utterly fascinating - just check out these screengrabs:

21.01: Launch of Soyuz TMA15M / ISS 42

21.01 23rd Nov

21.04 : On their way to orbit. Check out the "finger-longer" used to reach control panel, and the "G-meter" stuffed toy hanging on a string.

9.04pm 23rd Nov

21.05: Still on route to orbit. Check out the manuals on the far side!

21.05 23th Nov

02.10 : Soyuz reached orbit, astronauts in Zero G.

02.27 : After a couple of rendezvous burns to align with the ISS, this is the view of Soyuz from the ISS.

02.27 Nov24th

02.28 : 551m from ISS. View from Soyuz docking display.
02.28 Nov24th

02.31 : ISS now 327m away

02.31 Nov24th

02.34 : View from ISS

02.34 24th Nov

02.35 : Now just 214m away...


02.35 24th Nov

02.38 : The whole Soyuz display. Wow! Oh, and now 182m away.

02.38 24th Nov

02.41 : 75m away

2.41 24th Nov

02.42 : View from ISS, Sun is setting on Soyuz as it, and the ISS, pass to the dark side (of the earth, not the Force).

02.42 24th Nov

02.45 : Soyuz now very close, but earth in darkness.

02.45 24th Nov

02.45: 26m away....

02.45 24th Nov

02.47 :9m away!


02.47 24th Nov

02:49 was the final docking time, and hatch opening occurred at 05.00 on 24 November.

It wasn't long before the astronauts were Tweeting some awesome images, such as this one from Sam Cristoforetti (@astrosamantha)

Wow.


Related Content
Interview with Apollo Astronaut Trainer and Geologist Prof Farouk El-Baz (a must read!)
Curiosity, Twitter and the British Connection
Interview - Chris Lintott and the Zooniverse
Apollo Programme Manuals

Image Sources NasaTV and Twitter

Thursday, 4 December 2014

Talk : Reproduction in Bedbugs

Interesting Cafe Sci talk recently by Professor Michael T Siva-Jothy from the Dept of Animal and Plant Sciences at the University of Sheffield. Prof Siva-Jothy talked on the topic of bedbugs!

This post covers some of what was covered in the talk (and the fascinating Q&A afterwards), together with a little extra linkage thrown in..

Prof Siva-Jothy began by explaining many of the extreme body forms found in nature were due to sexual selection, for example, the tail of the male Peacock, or the remarkable Peacock Spider.

It turns out that Bedbugs are another example of this type of selection.

In the case of Bedbugs, the male penis has evolved to have a shape similar to that of a hypodermic needle. This is because the male impregnates the female not via the usual route but instead by stabbing her in the abdomen. The sexual anatomy of Bedbugs is described (and illustrated) more fully in this article and also here. Incidentally, this type of sex is know as "Traumatic Insemination".

Quality reposte from Prof Michael Siva-Jothy

Prof Siva-Jothy described how on the one hand this form of insemination resulted in a shorter lifespan for the female; whilst on the other hand it was accompanied by a "donation" of Vitamin B from the male (something Bedbugs cannot make themselves) and that the male sperm delayed the onset of female menopause and allowed the females to lay more eggs overall.

The Prof went on to describe how he had been part of a team that had undertaken fieldwork in Kenya where they had looked for species of African "Batbug". This was based on research in the 1930s that had identified a number of caves in the area that contained species similar to Bedbugs. Unfortunately, the team discovered that in the intervening decades the local population had DDT'ed the insect population of most of these caves so that they (the people, not the bugs) could extract the bat guano that was there. Populations of Batbugs remained in only the most remote caves, such as those at Mount Elgon. The research is summarised in this National Geographic article.

The Q&A
As is often the case at Cafe Sci, the Q&A was just as fascinating as the main talk....

Prof Siva-Jothy commented that, before WW2, bedbugs were a fact of life in many countries, including the UK and that management of bedbugs, rather than their elimination, was usually the approach that was taken. Crevices in wooden furniture and beds was a particularly popular home for bedbugs. It was to combat this that the metal hospital beds were introduced; they provided few hiding places for bedbugs and could easily be treated with boiling water as a further precaution. Similarly, many hospitals and hotels built in the 1930s used metal framed windows and mimimalist features to reduce the number of possible bedbug hiding places. This all changed at the end of WW2 when DDT was introduced - it was a devastatingly effective insecticide and bedbugs were soon virtually eliminated from homes, hotels and hospitals through its use.

Indeed, the Prof described how some of his team had gone to the centre of Sheffield and asked people if they recognised a particular smell (which was the characteristics coriander-like smell of of bedbugs) and found that those who had been aged 10 or more at the end of WW2 recognised it immediately while those who were younger had no idea what it was.

But, in more recent times, bedbugs have started to build up immunity to insecticide effects, and infestations have again become a serious problem in many countries, especially the US. The whole story of the battle against bedbugs is told in this fascinating article by AE Potter.

A bedbug

The Prof explained how, for most insects, developing resistance to insecticides imposes a biological cost and colonies kept in a lab lose their immunity over a few generations because of this. In contrast, bedbug populations that have been kept in labs for 60 years still retain their insecticide resistance, suggesting that, for bedbugs, the immunity has a very low biological cost.

Perhaps the most practical place to end this post is with this NHS advice on bedbugs.

Related Links
Dr Sara Goodacre on Spiders
Dr Duncan Cameron on Soil Science
Dr Helen West on Dung Beatles

Image Sources
Bedbug

Friday, 28 November 2014

Interview : Dr Sara Goodacre on Spiders

NSB was hugely chuffed to have the opportunity recently to interview Dr Sara Goodacre, who is an Assistant Professor at the Faculty of Medicine & Health Sciences at the University of Nottingham. The interview was about about Spiders and the UoN Spider lab. Below is a summary of the best bits of the talk, together with some added linkage. Enjoy!....

Q: How did you get interested in Biology.
Sara commented that she had looked back at her University application forms and found that she had simply stated "I've always been interested in Biology", adding that "it was just this underlying fascination with the world around me and I couldn't imagine having done anything else and I am so pleased that I actually ended up making it into a job...I find it endlessly fascinating and it was my favourite subject at school!"

Sara added that "I actually found maths a bit easier, in biology you pick up layers of knowledge, a bit like an onion..and you never finish learning, whereas maths was sort of neater in my head, you could reach a solution to a problem"

Biology is like a box of onions,
you never know what you are going to get
Q: Earlier in your career, you were a “research fellow” - What does that mean?
Sara explained that, often a persons research path would start with obtaining a doctorate and then involve a few years of being part of a research team - during this time one would gain experience and also begin to understand what areas of research one found most interesting. Grant applications might also start to be made during this time, thus building up experience of this aspect of academic study.

With some experience under the belt, it might then possible to apply to become a research fellow, which would mean being primarily involved in running one or more research programmes, without having to do much teaching. This allows nearly all the researchers time to go towards understanding the department and getting the lab or other academic unit focus up and running. In Sara's case, the jump from researcher to research fellow involved responding to an advert from the UoN asking for lab proposals and having to convince the UoN that the Spider Lab was the right move and that Sara was the right person to run it! Amongst much else, this involved proposing research projects that were in the window between impossible and already-being-done-elsewhere.

Students at the University of Bologna in the 15th century,
some of the first research fellows amongst them?
Q: What does the Spider Lab at UoN do?
"I use it to study spiders to answer questions about why the world around us is the way it is. So, for example, I look at spiders that have different colour types..to answer questions about why do you get a number of different types within a species, why don't you get more, why don't you have fewer? And if we scroll forward 10,000years, a million years, would they all still be here? If so, why? and if not, why not? These types of fundamental questions are quite hard to study in people and in a lot of other things but in spiders you can often find very good species that you can study, that you can keep in the lab, that can help you work out why the world is the way it is."

"Spiders are particularly good [compared to fruit flies etc] because they also are useful in things like controlling pests. Your average Money Spider for example, will eat 20 fruit flies a week"

Sara also explained that understanding the behaviour of spiders might unlock some of the secrets of how they make their many different types of silk, which is of interest as researchers would like to be able to manufacture a synthetic version of this wonderful material rather that having to rely on, inevitably rather small, spiders to produce it (info on synthetic silk technologies and properties here)

Single filament of synthetic spider silk
Q: Could you give a recap of your comments (here) regarding False Widows Spiders in the UK.
Sara explained that she had been asked by a number of people to respond on whether False Widow spiders could actually harm people. Sara emphasised that the first place to look for answers was in the evidence provided by the available published science - an approach that should be used for many questions, not just in biology. In this case the evidence was "an absolute unequivocal 'NO', we shouldn't be worried about them at all".

Sara had looked at studies of people who had been bitten by False Widow Spiders (and closely related species). What Sara found was that, in the very few cases reported in the UK and France, the symptoms had appeared straight away, had been similar to those of a bee sting and had disappeared after a few hours. Although not a medic (and having access only to the media report, not the actual medical records), Sara suspected that the wounds described in recent media articles, which had appeared some hours, days or weeks after the alleged spider bite, may have been due to subsequent infection rather than the bite itself.

Sara continued by pointing out that spiders were very good at eating pest insects and yet so quickly killed off by insecticides that, if were to keep the spiders we would not need to use so much insecticide - something that is a much more environmentally friendly way of farming than using insecticides which kill off virtually all of the natural pest control!

Sara explained how this related to the work of the Spider Lab by saying "One of the reasons I work on Money Spiders is that, very helpfully for farmers, they use silk as a sail and fly back in, they go up into the air and fly back in pretty quickly - and that is incredibly helpful for us as it means they can get back into a field much quicker than if they had to walk"

"If there is no kind of a debate about how spiders can really be the good guys here, they don't cause any harm, they even eat each other if they run out of food, so they even keep themselves under control. They don't carry any diseases, I looked in the whole literature, I thought that if there is one spider who carried a harmful germ or something then someone would have written about it and it would be in the [academic] papers but it's not and that's because they don't do anything except eat pests.

"I'm not trying to be biased in favour of spiders but, if you look at the evidence, they are just great!"

Sara also mentioned that people could get over their fear of spiders at programmes such as this one run by London Zoo.

And in terms of getting building a better relationship with plants, animals and insects in ones own locality, Sara recommended the work being done by OPAL (the OPen Air Laboratories project at www.opalexplorenature.org, which is a charity Sara is involved with and which has many resources relating to spiders (such as this spider indentification pdf, or the "Spider in Da House" android app) - also worth checking out their other identification guides and their list of local activities!

Sara explained that one of the aims of OPAL is to get the everyone involved in science, by looking out to see how their local biology is faring and also to watch out for unwanted invading species. And also by suggesting projects, for example why does the number of mushrooms vary from year to year, or why are some trees doing better than others. If you have a spider related project idea, then please contact Sara directly!

Another resource is the British Arachnological Society at www.britishspiders.co.uk who have many spider experts on hand. Their comments on the False Widow Spider echo those of Sara.

If in doubt, put the spider out!

Spider Distribution Map at BAS

Q: Can you give some information on your research into Tarantula silk?
Sara explained that she was interested in Tarantula silk because Tarantulas were a very distant cousin of the spiders that are usually investigated to give ideas about manufacture of artificial silk. Tarantulas do not produce stretchy silk but do have some interesting features, including amazing feet, which allow them to walk up vertical walls !

All silk reacts with water by shrinking, which may be useful in biological switches, but we don't know much about the silk from most species of spiders. Tarantula silk appears to be water repellant, like Goretex, while House Spider silk appears to have anti-bacterial properties!

Spider Silk v Kevlar mechanical properties

Q: Any advice for youngsters thinking of studying biology.
Biology as a degree teaches you to put information together, to interact with other people, to study reports and extract information - as well as being great fun!

For young people still at school, Sara suggested that the best thing was to just dive in, and to be aware that by the time you graduate there may well be fields of biological study available that have not been invented yet! Adding that biology was a "fantastically fast moving, fun area and if you are interested in it, go for it! There will be bits where you think 'this is hard work'...but once you have done all those bits and you realise 'This is what we know, now here is all this stuff we don't know" and just dive on in there and you might just find the most fascinating place to be and that it keeps you interested forever, like it did me."

Learn Away !

Q: What is your favourite spider?
Turns out that Sara's favourite spider is a species if money spider called Erigone Atra, which is one of the best spiders at flying. Sara explained that, in the morning at around 6am, it climbs to the top of a structure (such as a gate post), tips its abdomen into the air and released about a metre of silk. This is picked up by the wind and the spider takes off, reaching heights of hundreds or perhaps thousands of metres into the air. No one knows how far they travel, but it can certainly be up to 70km per day. This is quite a risky thing to do, as the spider does not know where and in what kind of environment it will land! Because of this aerial ability, Erigone Atra is one of the UK's most important pest eating spiders.

Erigone Atra

Q: What is the geographical and climatic range of spiders
Sara commented that spiders can live in communities in the desert; that species like Erigone Atra can be blown to northern Scandinavia or the islands in the southern ocean; and that wind blown spiders are often the first species to arrive on a new volcanic island!

A few extra comments
This report does not really do justice to Sara's enthusiasm and engaging way of presenting ideas, so if any readers get the chance to hear Sara talk about spiders - grab the opportunity!

The biggest spider NSB has seen...

Related Links
Talk on Smart Materials
Talk on Natures Chemical Warface Agents
Talk on "Butterflies and Battleships"

Image Sources
Onions, University, Spider silk comparison, Silk strand, Erigone Atra