Monday 27 May 2013

Talk : Prof Dunham on Viruses

A recent UoN Public Science lecture featured a fascinating talk by Steve Dunham, Associate Professor of Veterinary Virology. The talk was entitled "How do viruses cause disease? Lessons from our feathered friends and other animals" and gave an interesting overview of the nature and effects of viruses.

Prof Dunham began by explaining that viruses are very small, much smaller than bacteria for example. Viruses essentially comprise a section of DNA wrapped up in a protein coat - and needs a host cell to replicate.

The Human Rotavirus (which causes diarrhoea in children) can be used to give some examples images of a virus:

Schematic showing structure of a Virus

Computer generated model of Rotavirus


Rotavirus in childs faeces

Some examples of common animal viruses are :

Rinderpest (which has now been eradicated but previously could kill 100% of a cattle herd in a matter of days)
Bird Flu (more on this later)
Cat "Flu" (actually a form of Herpes)
Distemper in Seals
Coronavirus which cause respiratory diseases in animals
Papilloma Virus

Cattle who have died from Rinderpest, South Africa, 1896

Cat "flu"

The reason viruses cause animals to get sick is that they cause cell death and damage or can cause cancer.

Prof Dunham mentioned that, in some cases (Palilloma Virus being one) a human vaccine has been developed on the back of previous work developing a vaccine for animals

One problem in combating viruses is that they can spread in animal communities without the animals showing any symptoms, or may have delayed effects in terms of reduced fertility or later disease

Factors in the effect a virus has on animals include the virus type and load, as well as the age and condition of the host. The environment is also a factor, particularly the degree of overcrowding that the animals are living in (chicken herpes being an example of this, and is a disease that was not seen before the industrial housing of poultry that began in the 1950s)

Animals have a number of barriers and defences to viral infection, including tears/sneezing/saliva, fatty acids(which can attack viruses), Diarrhoea (to expel the virus) and Fever (to overheat the virus).

The response from the immune system is also multi-layered. Withing the first two days it is the Cytokines that are mainly doing the defensive work. Killer Cells then peak at day 3-4, with antibodies and T-cells arriving on the scene at around the one week mark.

Going back to the case of bird flu, there are many of varieties of this virus and most are carried by ducks without any ill effect - but the ducks can pass the virus on to other species who are very vulnerable to the virus. Chickens, for example, can die overnight from bird flu.

The designations given to the strains of bird flu (e.g. H5N1) relate to two proteins, hemagglutinin and neuraminidase, that are on the surface of the virus. Hence the H and the N abbreviation. The numbers that are included in the virus name signal a genetic change in the virus. Some combinations of H and N cause serious illness and death, while others only cause mild symptoms. Flu viruses that begin with H5 or H7 are highly likely to make birds and people sick.

It is the accumulation of random changes in the genetic code of the virus (which is not as stable as the genetic code of animals) cause new strains of viruses to develop. Indeed, only two genetic changes are required to get from bird flu to human flu.

Fortunately, some strains which could be more dangerous to humans lack the ability to spread via airborne droplets, reducing the chance of them causing epidemics.

Avian Flu - showing H and N protein structures


Image Sources
Virus Structure rotavirus reconstruction, Rotavirus, Rinderpest, Cat "Flu", Bird Flu

Sunday 26 May 2013

Talk : Alan Turing - The Building of a Brain

A recent talk at Nottingham CafĂ© Scientifique was presented by Prof Barry Cooper from Leeds University and was entitled “Alan Turing - The Building of a Brain ”

About half of the talk consisted of a biography of Turing. Given that Turing has a surprisingly detailed Interweb presence, this part of the talk is perhaps best covered by reference to some of the following resources for information of Turing's life:
* Alan Turing's Wikipedia Page (like, duh!)
*Andrew Hodges (author of "Alan Turing: The Enigma") website devoted to Turing.
* The Turing Digital Archive

The other half discussed the nature human and artificial intelligence, including mentions of some experts in the field, and this is covered below.

One of the many experts referenced was Nassim Taleb, a Lebanese American essayist and scholar whose work focuses on problems of randomness, probability and uncertainty. Taleb is the author of the "Black Swan" theory (and book). This theory describes the extreme impact of certain kinds of rare and unpredictable events and humans' tendency to find simplistic explanations for these events retrospectively. Taleb correctly predicted (and made a lot of money out of) the 2008 financial crash, so he is perhaps someone worth listening to!

Alan Turing

Prof Cooper posed the question of how nature computes, pointing out that the universe around us is arranged in a complicated way. A relevant expert here is theoretical physicist Dr Peter Woit, who has highlighted that "The Standard Model" of Physics only works because 17 key parameters have been given arbitrary values, suggesting that we do not have a good understanding of the forces and nature of the universe.

Fundamentally, as Dr Cooper said "The trouble is, we don't really know what reality is, do we?", instead we try and fit reality into the straitjacket of a mathematical model.

Related to this is the phenomena of "Morphogenesis" (how lifeforms take their shape). This is an area Turing looked at in an important 1952 paper, which you can read here and read about, in laymans terms, here

Also related is the idea of "Emergence" (how complex systems and patterns arise out of a multiplicity of relatively simple interactions). A good example being the way in which complex termite mounds are built by very simple actions of many termites.

Prof Cooper then went on to discuss the famous "Turing Test" as a way of determining whether a computer program genuinely had artifical intelligence (see also here). He pointed out that there was something of an "AI War" underway between those (such as Marvin Minsky) who have taken a rather analytical approach and those (such as Rodney Brooks) who take a more experimental path to developing AI technologies.

The consensus seems to be that AI may work well in specific, narrow, applications (such as chess computers) but will be more difficult to implement in the wide ranging way that humans, for example, have intelligence.

Things got pretty heavy and philosophical at this point, with the talk looking at the relationship between mind and body. One person to note here is Jaegwon Kim

A rebuild of a WW2 "Bombe" Codebreaker at Bletchley Park
Turing was a key figure in its development

Prof Cooper made quite a few mentions of "data types". For example, in a typcial living room there is a lot of high level data. All the items have a temperature, texture, size, shape, smell, sound, hardness, porosity etc. But when a human looks at that room, all they do is sample a very small part of the available information (largely visually) and construct a mental model of the room from that.

In addition, there is something special about the human brain that allows us to appreciate the "higher level" nature of complicated structures such as Mandlebrot sets or termite mounds - something that computers find difficult to do.

In the (always interesting) question and answer session, Prof Cooper commented that people were starting to realise that context is very important to data. For example, a person might give very different answers to a question depending on his or her perception of the environment (is is threatening, do they feel safe, it is warm or cold, who is asking the question, why are they asking the question)

Prof Cooper felt that this developing understanding of the complexity of intelligence are likely to result in a lot of algorithmic code being junked over the coming years, perhaps being replaced by "Evolutionary Algorithms".

The final word should perhaps be given to one of the last quotes of the evening, from American inventor, scientist, engineer, entrepreneur, and author Danny Hillis, who said "Maybe we'll evolve evolutionary machines before we understand them"

Image Sources
Turing, Bombe

Saturday 25 May 2013

Wildlife,Cycling and Other Uplifting Stuff

NSB thought it might be nice to record some of the wildlife that is seen in the (not very big) NSB garden, and also a little wider afield whilst out cycling...

Note1 : Includes posts about scenery, buildings and other non-wildlife stuff!
Note2 : See also : https://nottinghamscience.blogspot.com/2012/05/pictures-of-sky.html

Gorleston-on-Sea, Norfolk


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What a difference six months makes! View of River Erewash from Awsworth Rd, Ilkeston, Feb and June 2019

View of River Erewash Nov 2019

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Some images taken while out cycling winter 2018/ 2019

Shipley Woodside Colliery, Sunset 2018/19

View from Awsworth Rd, Ilkeston, Feb2019

Nottingham Embankment, early 2019(?)

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Shipley Park, chilly morning Dec 2018

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Very lucky that part of the daily commute looks like this

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Nice row of Citibikes!

Cycling in Shipley Park in 7am moonlight! - Oct 2018

This is a colour picture - Oct 2018

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Check out the Nottingham Councils Cycling Page: https://www.transportnottingham.com/cycling/

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Always lovely to see horses in Shipley Park!

Shipley Park Jul 2017

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2015 : Visited the incredibly beautiful Rhossili Bay recently. The image below really doesn't do it justice.

Rhossili, deservedly voted best beach in the UK

Rhossili Bay has been voted Britan's most beautiful beach. Not a surprise really...

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Autumn leaves, 2017

Rather like how this has turned out, but wish had paid more attention to the composition!

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Very still Trent, Autumn 2017

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Sky, Barmouth, 2017

Beach, North Wales, 2017

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Not something you see every day...

Drought Horse, Near Beeston Weir, Jun 2017

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Spotted this handsome chap (and his other half, out of shot on the right) whilst cycling along the Big Track in Nottingham.

Pheasant, Big Track, May 2017

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View across the Trent, from the South Side, Apr 2017

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Not strictly wildlife, but rather like this contrasting picture of a tree against a dusk sky...

Tree, dusk, Nottingham, Nov 2016

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Spring 2016
Emden Geese, by the Nottingham and Beeston Canal
Emden geese have long since been domesticated. They grow quickly and mate for life... ahh, how sweet!

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Summer 2015
Didn't really know where to put this, so have shoehorned it into this post - lovely vision of green while driving on the A6 (it's ok, the picture was taken from a layby!)

Wall of trees, next to A6, Derbyshire

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Field of Wheat, next to the Big Track


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HGV's on the Nutbrook Trial, 2014

Several times each day, traffic on the Embankment has to stop for this....
Aug 2014

Very handsome indeed ! Nutbrook Trail, Derbyshire, Aug 2014

Lovely colours as bright sun behind BFTF plays on the fields and dark clouds ahead.
Near Beeston Weir - Jul/Aug2014

Fields of Wheat, between Stapleford and Bramcote- Jul/Aug2014

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Another very quite day on the Trent - Jul/Aug 2014

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BFTF's bike - it is a thing of beauty


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NSB did once share ownership of a Giant African Land Snail, which would gnaw on peoples fingers in a gentle can't-really-do-any-damage kind of way). The snail was called Sammy, by the way, because that works for both males and females, and snails are notoriously sexually ambiguous.

Sammy as a baby, on a slice of cucumber


Sammy a few months later, trying to give someone a manicure


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Sunday 19 May 2013

May Fest 2013 in Pictures (Part 2)

Following on from Part 1, here is the Part 2 of the post of the awesome May Fest event at the University of Nottingham

Fashion Award of the day goes to the BioSoc


University Radio Nottingham opened their doors and allowed yougsters to have a go at being a DJ!

No3 son spent quite a bit of time with a charming first year student who explained the intricacies of the Audacity audio editing software. No3 son was so entranced by this that on arriving home, he immediately started having a bash at being a mix-master on the home laptop!

Meanwhile, NSB talked to some of the presenters about how the studio worked, and about their excellent "Science Show" programme which features interviews with some of the UoN most sciency movers and shakers. NSB hopes to have the chance to work more closely with URN in the future.

A radio dude demonstrates the Audacity audio software to No3 Son

A regular at May Fest is the "Wattbike" on which visitors are encouraged to see how much energy they can generate over a 6 second period.

NSB manged to generate a peak of 735Watts on the Wattbike
#stillgotthemagic 

Physics Buskers - possibly the most active outreach group at the University. Respect and...er... "word".

Of course, the Physics Buskers were on hand to amaze and educate.

The History department also had a strong presence at the event, including some rare and old documents. The department does research in a wide range of areas, ranging from the 1100s to the 1950s

The Hstory Dept had some fascinating pictures and documents on show,
including this Dig For Victory pic


The Biology department's outreach group has some pretty cool large scale models of biological structures...

22 Researchers used this (partly constructed) model to
explain the differnet components of a cell

Meanwhile, the Sensory Science Centre were showing how taste and other senses work.

The Sensory Science Centre were explaining how taste works

The Human Rights Law Centre (who last year, quite rightly told NSB that one of the biggest human rights issues in the UK at the moment was the lack of housing) were this year asking people what they thought the rights of the child included. Chatting to the researchers, NSB found out that that Centre had recently been providing training to the Sudanese Human Rights Commission.

The Human Rights Law Centre was asking children
what they thought they had the right to

The School of English had a strong and very engaging presence at May Fest. No3 Son loves writing his name in Viking runes, while NSB was very interested in the reearch the department had undertaken on the messages transmitted by medical advertising.

A member of the English Dept explaining to No3 Son
how he could write his name in Viking Runes

The English Dept also had some though provoking stuff
on the psychology of adverts

The Psychology department were exhibiting some interacitve phyisical tests that showed how the mind interprets and interacts with the physical senses to understand and interact with the world around us.

27 The Psychology Dept had a cool bunch of games that
demonstrated how malleable the mind is.

What can one say, it is always heartening to see a 5.25inch floppy drive. From the days when 360k meant something. Sigh... At the other end of the technological spectrum, the drives were being controlled by an Arduino.

An Arduino  making music from the motors
of a bunch of disc drives  (inc a nice old skool 5.25 inch floppy drive)

Mind Control !

When a headset detects beta waves in the brain it
makes this ball rise up. Its mind control!!!


The Centre for Plant Integrative Biologies had some fascinating displays and technology on view, including a project to develop a "virtual root" and also their impressive "octocopter" that can carry a 2kg camera payload to image the biology of fields (see here for more info and videos). The Centre's website also has a cool set of biological resources for those who want to learn more about the subject.

The Centre for Plant Integrative Biologies is developing a virtual root!...

...and they have an Octocopter than can lift a 2kg paylod
for analysing the biology of an entire field

No3 son looking down a microscope at some Botox Cells

As mentioned earlier, there simply was not time to check out all the exhibits and demonstrations (in particular, NSB did not get a chance to visit the Trent Building at all). so, sadly, the last exhibition that NSB had the chance to see was that of the School of Geography.

But it was a doozer.

Whilst No3 Son tried his hand at catching rubber lizards on a tree (which is what researchers have to do when investigating the relationship between animal and plant environment), NSB had a go a the 3-D viewers. These gave an incredible 3D image of Nottingham's city centre, perhaps similar to the kindof view that the aerial reconnisance analysts of WW2 had when viewing images from occupied Europe. Fascinating !

 The Geography Dept had this great 3D model of the Lake District
onto which they could project a variety of images
(eg what it looked in the Ice Age)

Also from the Georgraphy Dept, you could see Nottingham from the Air in 3D
with these special viewers and photos