Thursday, 28 March 2013

The Arduino throws a six !

One of NSB’s earliest interviews (and easily the most popular post) was with Eben Upton from the Raspberry Pi Foundation who described the motivations that had led to the development of that tiny, rather wonderful, computer.

And so far as NSB was aware, there was no one else ploughing that particular furrow.

So NSB was surprised when Jon, a work colleague, spent some spare Christmas money on an Arduino.

“Ar-what?” said NSB

“Arduino” replied Jon calmly.

He then explained that an Arduino was a Raspberry Pi-esque computer that, he had bought together with a kit of accessories that allowed the Arduino to, well, make stuff happen. Surprisingly, the Arduino was on the scene first, and by 2011 some 300,00 had been sold.

The box containing the Arduino Uno and kit

It turns out (as you can read here and here) that whilst the Raspberry Pi is a cheap computer designed to encourage people to learn computing and programming, the Arduino is more of a microcontroller that can be used to manipulate inputs from sensors (switches, thermocouples etc) and then send instructions to outputs (lights, motors etc).

Resistors, motors, thermocouples and much more, all part of the kit (Arduino board removed)

The Arduino that Jon had bought was an Arduino Uno and came with a breadboard on which circuits could easily be constructed. Progams could be written on a PC and then downloaded onto the Arduino, which could then run independently off a 9V battery.

Once Jon had got the hang of programming the device, Jon was soon able to let his imagination take hold. As an initial project, he made an “electronic dice” which used LED’s that would, on pressing a button, light up like a random dice throw.

This time the Arduino electronic dice has thrown a "four"

Importantly, when moving on to a new project, Jon had to remember to save the circuit design as well as the program.

And this time the Arduino circuit has thrown a "six" - Don't forget to save the circuit diagram when moving on to a new project!

NSB is hugely intrigued by the device and is planning to buy one in the summer. The only question is whether NSB’s limited technical ability will be able to pay the cheques that NSB’s rather overclocked imagination will be writing…

Incidentally, you can see just what can be done with an Arduino here.

And lastly, there are actually a great many types of single board computers, as shown here

Update Oct 2014
NSB didn't, in the end, get round to buying an Arduino in the summer, but has just borrowed Jon's kit and, together with No3 Son, have had a bash at programming it.

Thus far, NSB and No3 Son have managed to become masters of the LED, able to program a set of LED's to switch off and on in any sequence desired...
LED's ... switching on and off....nice!

No3 Son programming the Arduino, bless him!
(although, strictly speaking, he should have been doing his science homework)

Tuesday, 26 March 2013

Talk : The World in 10 Fossils

A recent UoN Public Science lecture featured a fascinating talk by Dr Susie Lydon entitled “The History of the World in 10 Fossils” in which she described a series of fossils that Dr Lydon felt had been important in the evolution of life on earth.

Dr Lydon pointed out that life had been present on earth well before the earliest fossils, but its presence could only be determined by the chemical effect that it had on the environment, and one of the rules Dr Lydon had set herself was that the fossils needed to be, well, fossils.

And the second key point that Dr Lydon made was that the period of time she was covering - the last 600million years or so - was much less than the 4,600million years that the earth has been around.

So, with that out of the way, let’s see what Dr Lydon’s 10 Fossils were…

1) Doushantuo Embryos
635-551 million years old, South China, Lagoonal Sea
The fossils in these sediments are so well preserved that they can be analyzed down to the cellular level, as shown in this image of animal embryos from the webpage of Geobiologist Prof Shuhai Xiao at Virginia Tech.

Doushantuo embryos (courtesy of Prof Xiao)

It is worth noting that this period in the earth’s history is just after the time when glaciers covered all, or almost all of the earth’s surface (the “Snowball Earth” hypothesis).

2) Pikaia
515 million years old, Burgess Shale, Rockies, Shallow Sea (no land life yet)
This two inch long sea creature is significant because it is one of the earliest to have had a primitive backbone (called a “Notocord”). Pikai also had other structures, such as segmented muscle blocks, that are characteristic of vertebrates.


Incidentally, the Notocord is present in some modern day animals such as the Lancelot.

Lancelot structure, showing notocord (dark strip>

The Burgess Shale is a formation that is rich in fossils from the “Cambrian Explosion” when large numbers of, frankly plain weird, creatures swan in the oceans. NSB favourite, so far, is Opabinia.

Opainia - 5 eyes on stalks!

3) Rhymia
400 million years old, Aberdeen, silica rich hot springs
The silica rich water that covered these plants when they died diffused into the cells and resulted in fossils with unusually high levels of detail. Leaves had not evolved yet, so plants were still performing all their photosynthesis in the surface of their trunks, stems and branches

cells in a Rhymia stem

Impression of Rhymia

4) Tiktaalik
350million years ago, N Canada, Equatorial River system
Tiktaalik is an important transitional fossil that shows both fish-like and land animal(tetrapod)-like:
Fish-like features :scales,fins, half-fish,
In-between features :tetrapod like wrist joint but fish like fins instead of toes, half-tetrapod ear region
Tetrapod-like features : Rib bones, neck, lungs


5) Lepidodendron
300million years, Europe, equatorial swamp forests
This plant, which grew to some 50m tall and lived in the Carboniferous period (the trees of which formed many of the worlds coal measures). Lepidodendron is in a similar classification to todays (very small) clubmosses


Impression of bark

6) Lystrosaurus
250million years, S Africa, river systems This is a mammal type creature, but from a different evolutionary path so it is not a direct ancestor of mammals. One surprising fact is that Lystrosaurus managed to survive the Permian extinction, and event that killed of many more species than the famous asteroid impact that gave the dinosaurs their exit ticket.


While another is the the fossil distribution of Lystrosaurus was one of the pieces of evidence used to prove the existence of continental drift.

Range of Lystrosaurus consistent with continental drift

7) Iguanadon
125million years ago, Floodplain, lagoonal river system
With its spike famously placed first as horn before being given its correct location on the hand, Iguanadon is a well know dinosaur, but what is not so well known is that 38 Iguanadons were found in a Belgian coal face in 1878.

A condition known as “pyrite disease” was known to affect fossils and involved crystalline pyrite in the bones was being oxidized to iron sulphate, accompanied by an increase in volume that caused the remains to crack and crumble. Conservators tries to prevent this by impregnating the bones with gelatine and oil of cloves. Which didn’t work. So in 1935 conservators applied a mix of combination of alcohol, arsenic, and 390 kilograms of shellac. Which didn’t work. So in 2003 the previous preservatives were removed and replaced with polyvinyl acetate and cyanoacrylate and epoxy glues.


8) Nymphaeales
120million year ago, Portugal, river lakes.
This is one of the first flowering plants, similar to todays water lillies

Waterlillies, not unlike Nymphaeales

9) Darwinius (Ida)
47 million years ago, Germany, lake surrounded by forests
This little fellow is a lemur like mammal, possibly an ancestor of modern primates. It’s relatively recent discovery, in 1983, was mired in controversy due to the speed at which findings were published (in an attempt to prevent leaks and speculation)


10) Lucy
3.2 million years ago, Ethiopia, lakeshore nr forests
Lucy (named after the famous Beatles song) is an early hominid who would have stood some 1.1 m, weighed 29 kg (64 lb) and looked somewhat like a Common Chimpanzee - but walked upright

Artists impression of Lucy

Any errors in this post are almost certainly due to NSB's inability to read its own, often unintelligible, notes.

Image Sources, by fossil number)
2, 2, 2, 3, 3, 4, 5, 5, 6, 6, 7, 8, 9, 10

Papers Behind Paywalls

The government, presumably, wants a public that is educated and engaged with current scientific issues. Scientists certainly want this. And a big chunk of the public also wants this.

But when an ordinary member of the public tries to find an academic article that has been referenced by a news story or a university department, what they often find is that the paper in question is stuck behind a paywall.

So the member of the public stays ignorant of the research. Critically, this means they cannot effectively challenge media or government reports that misrepresent research (Daily Mail, I'm looking at you).

BFTF has decided to keep a log of the instances if finds itself stuck on the plebs side a of a firewall, with the intention of using the resulting examples as evidence in what will be a VERY TECTCHY email to those in Government who can change the situation.

While trying to write a report on a recent talk about less-lethal weapons, wanted to read a paper titled "Injuries caused by rubber bullets: A report on 90 patients" (British Journal of Surgery 62 (6): 480–486,Millar, R.; Rutherford, W. H.; Johnston, S.; Malhotra, V. J. (1975), but couldn't, because it is STILL, almost 40 YEARS ON, still behind a paywall. Unbelievable.

While trying to write a post about a lecture on fossils, found that relevant research is out of reach of ordinary citizens (but not anti-science creationist groups)
Relevant paper : Terminal Developments in Ediacaran Embryology, Butterfield, N. J. (2011) Science, 334 (6063). 1655 -1656.

A blog, ironically about the relationship between the public and science, references a paper entitled "Blowin’ in the wind: Short-term weather and belief in anthropogenic climate change" (published in the AMS Journal Weather, Climate, and Society 2013). But when BFTF tried to find the paper, it was hidden behind a paywall.

Trying to get hold of this paper, which was very relevant to a recent talk at Cafe Sci
Stobart, R. and Wijewardane, A. "Exhaust System Heat Exchanger Design for Thermal Energy Recovery in Passenger Vehicle Applications". IMechE, VTMS 10, Vol. 2011, Vehicle Thermal Management System Conference, Warwick, UK, 2011

While trying to write a post about the nano-motor research being undertaken at the University of Oxford (and which featured at the 2012 RS Summer Exhibition), wanted to find out more about the mechanisms involved, the paper below might have helped, but I'll never know as it is stuck behind a paywall.
Direct observation of stepwise movement of a synthetic molecular transporter.
Wickham SFJ et all. Nature Nanotechnology 6,166-169.

Whilst trying to write a post about a public lecture on nanotechnology in Healthcare, had the following issues in finding information:

Double Nanoparticle Layer in a 12th Century Lustreware Decoration: Accident or Technological Mastery?
Philippe Sciau et al., 2009, Journal of Nano Research, 8, 133
Wanted to find out more about the science of lusterware, but the paywall means that I can’t

Materials: Carbon nanotubes in an ancient Damascus sabre.
M. Reibold et al Nature 444, 286 Published online 15 November 2006
Wanted to find out more about the microstructure of Medieval Damascus steel, but the paywall means I couldn't.

Preparation of lotus-leaf-like polystyrene micro- and nanostructure films and its blood compatibility.
J. Mater. Chem., 2009,19, 9025-9029
Wanted to read about synthetic hydrophobic materials, but the paywall means that I couldn't.

Activation of complement by therapeutic liposomes and other lipid excipient-based therapeutic products.
Adv. Drug Delivery Rev. V63, Issue 12, P1020–1030.Janos Szebenia et al
Wanted to read about the mechanism used in one of drugs mentioned in the talk - but the paywall means that I couldn't.

Self-assembly of a nanoscale DNA box with a controllable lid
Nature 459, 73-76 (7 May 2009)
Wanted to read about a box made from DNA mentioned in the talk, but paywall means that I couldn't.

A visit to the outstanding Summer Exhibition at the Royal Society saw BFTF intrigued by a display by the People of the British Isles DNA mapping project. Wanting to find out more, BFTF visited their website. Finding it a bit light on information, clicked on "Papers related to the People of British Isles project" and then on the rather interesting looking "The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269"
SLAM - A paywall hits BFTF in the face. Guess I'll just have to stay ignorant.

Sunday, 24 March 2013

Science in the Park 2013 - Pt2

Following on from Part 1 of this report, here is more coverage of the rather wonderful “Science in the Park” event recently held at Wollaton Hall.

Dancing Robots and Virtual Gloves
A team from Nottingham Trent University were showcasing a variety of technologies being developed to aid those who are currently marginalised to enter the workplace or recover from injury more quickly. One example of this was a “virtual glove” that was being used to help stroke victims recover.

Virtual Glove to aid recovery of stroke victims

While other research involves using robots to help those with autism to relate better to their surroundings.

Robot to aid autistic children, but today dancing "Gangnam Style"

And information was also available on the “PAUSE” project, which is delivering real benefits in allowing refugees and immigrants to enter the workplace.

Physics Buskers
The Physics department were on hand to provide some interesting demonstrations of how the world works. Most notable of these was perhaps the fact that a potato can be pierced right through with a simple plastic straw - which highlights the effect of having a small surface area (the edge of the straw) can have on how a materials interact.

Physics Buskers !

By the end of the day it was utter carnage on the potato and straw table - is this something the ethics committee needs to be aware of? Potatoes have feeling too !

Cardboard Imagination
Rather winningly, the event had filled an area with cardboard boxes of various sizes and challenged the visitors to make bridges that crossed a long span without being very heavy or use their imagination to make other constructions. Amongst many creations on the day, perhaps the stand out construction was “Buttons”, a robot created by youngsters Lorne and Finn (together with a little help with their Dad)

Something for you to try at home?

Cardboard - the toy Lego don't want you to know about...

"Buttons" by Lorne and Finn

The Solar System at Wollaton Hall
The BSA themselves were presenting handouts that showed what the solar system would look like of shrunk down to the size of Nottingham - NSB was delighted to see that they had taken the old skool approach of including Pluto as a planet.

The Inner Planets at Wollaton

.., and here are Jupiter and Saturn

..while Pluto would go through Forest Rec!

A few other observations
Despite the very unseasonal snowy weather, the event was busy all day, which was heartening to see.

Great too see a good attendance at the event

Scientists have a pretty groovy sense of humour, a good example of which was captured on this T-shirt worn by an NTU Physicist

It's a Ferrous Wheel ! Geddit?

NSB is used to seeing posters saying “Know your healthy foods”, "Know your rights" or even "Know your traffic signs" - but was amused to see a poster at one of the stands which, winningly, asked readers to “Know your Neurotransmitters”

Know your neurotransmitters!

With a slightly different hat on, it was great to see that the teabags in the volunteers break-room were Fairtrade - showing that scientists have as much of a conscious and awareness of the environment and ethical issues as anyone else.

Scientists drink it Fairtrade

Lastly, NSB thought it might be worth mentioning that these events are a great opportunity to ask researchers the difficult questions that they might not have previously considered, as they are likely to be focussed on their immediate research. For example, NSB asked questions such as why cochlear implants weren’t cheaper, how the efficiency of solar cells has improved over the years, and how light knows when to reflect and when to refract. It is surprising how often these very simple questions put the researchers very much on the back foot, with one commenting that NSB was “asking more difficulty questions than my supervisor”. With much research being done with public funds, NSB would certainly urge the public to quiz the researchers on what they are doing.

Also some of the people manning the stands are not students in the subject the stand focuses on, so it is a great opportunity to find out more about completely different subjects. In this case, NSB had an interesting discussion with someone who was something of an expert in how Hollywood movies are made, and what it takes to convince studios to reduce unfairness or stereotypical portrayals in their movies.

Science in the Park 2013 - Pt1

This weekends “Science in the Park” event at Wollaton Hall, Nottingham was a real treat, and was a near perfect mix of activities and information that seemed to draw the interest of children and parents alike.

Timed to coincide with National Science and Engineering Week, this annual science fair is organised by the Nottinghamshire Branch of the British Science Association, the University of Nottingham and Nottingham City Council

So, lets have a look at some of the exhibits that particularly caught the attention of NSB…

Bacteria and Handwashing
A team of microbiologists from the University of Nottingham were giving children the opportunity to create their own bacteria - and had some plasticine examples of the little celled microbes to give the youngsters imagination a head start.

Plasticine microbes - and a red blood cell

Now, you might think that was just a bit of creative fun for the little ones, but NSB was surprised to see that the plasticine red blood cell was was much bigger than the bacteria - and it turns out that this is a good reflection of reality, with bacteria typically being 1-5microns while cells in humans and other multicellular life are typically 10-100micron in size.

The team were also giving advice on how to wash your hands properly, and had a fascinating practical demonstration that involves smearing a little UV fluorescent cream on your hands, and then looking at your hands before and after washing with wipes - it was often a surprise to see how much of ones hands were still fluorescing AFTER the use of hand wipes. Which just goes to show that you really need to get into all those nooks and crannies between the fingers, as well as under the fingernails to clean hands effectively

How to wash your hands

 UV fluorescent cream on NSB's hands

Increasing the level of hand-washing in the developing world is, literally, a life saver and could contribute significantly to bringing down the toll of 1.87 million children under five who die each year from diarrhoea the second-most common cause of death among children under five.

Solar Power and Electric Potatoes
The display from the “The Solar Spark” team (who hail from the SUPERGEN Excitonic Solar Cells Consortium) contained some circuits powered by electrodes inserted into fruit and vegetables and also a variety of small solar powered cars and bugs. It was fascinating to talk to the researchers on the stand and hear their views on issues such as the challenge of energy storage, the durability of solar cells in the developing world and how efficiency and cost of solar cells have changed over the years.

Budding Dr Frankensteins can start here

Solar Powered Helicopter

Imaging a Sunflower
The UoN School of Biosciences had some interesting stuff on show with visitors getting the chance to fly (via computer simulation) their “Octocoper” RPV. Despite it’s fragile look, the Octocopter can lift a 2kg camera payload which is used to scan areas of farmland.

They also had some sunflowers whose roots had grown a surprising distance in just 5 days. The team explained that they had a new “Nanotom” CAT scanning machine that could image the interior of solid objects (or hidden objects such as roots in soil) with remarkable accuracy. You can read about this here.

The Octocopter, and 5-day old sunflower seedling on the right

Your brain
The Psychology department of the UoN had a series of displays and activities including a “hook the duck” game which, far, from being a mere fairground game, gave insights into the complexity of human motor skills.

It takes years to learn the hand-eye co-ordination required to hook a duck

There was also an activity where visitors were asked to throw beanbags into net targets (which was easy enough) and then to repeat the test while wearing special goggles that shifted vision about 15 degrees to the right. Interestingly, when the goggles were removed, peoples aim remained shifted to one side, showing that the brain was still trying to compensate for the effect of the glasses. This effect has implications far beyond physical activity as it touches on how people form, change and overcompensate their views.

These glasses shift your vision to the right !

And there was more - with a presentation of work being done in the “Skills Underlying Maths” project. This research effort has looked at the skills involved in performing maths calculations, with the aim of understanding why some children find maths easy, while others struggle. Check out the results of their recent work in their January Newsletter.

Whilst No3 son was having a bash at the beanbag game, NSB asked the maths researcher how maths teaching in the UK compared to the rest of the world. The researcher commented that maths learning is a complicated skill, requiring rote learning (for formulas, times tables etc), basic understanding (why we solve maths problems in a certain way) as well as other strategies - and teaching needed to cover all these skills.

Chemistry Demonstration
“Science in the Park” featured a number of interactive talks, including talks on fossils and the Bloodhound land speed record project. NSB managed to catch the “Chemistry Demonstration” which was presented by Sam Tang who, with the help of children and adults from the audience, performed a number of entertaining experiments, as you can see below.

Sam Tang explaining the handedness of Carvone

Making a fluorescent liquid from Luminol

Any science experiemnt that requires a hammer is going to be good.

Liquid Nitrogen on water makes clouds...

... and you can never have too many clouds in a science experiment.

Read on...
Check out part two of this report, with included a dancing robot, a cool t-shirt and virtual reality gloves, amongst much else.