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 in the Garden

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...


Surprised to see this noisy juvenile pigeon relentlessly harassing its parent for food - and the parent eventually obliging by regurgitating some dinner. Perhaps naively, would have expected the juvenile to be feeding under its own steam by this point in the year. Maybe his name is Kevin? ...

Noisy juvenile pigeon demanding food from parent, Dec 2016


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

Tree, dusk, Nottingham, Nov 2016


Realised that a number of pictures taken while cycling would fit nicely into this post...

Saw this rather groovy creature (which I believe to be a Mongolian Ringneck-type Common Pheasant) at the Park and Ride by the Trent.

A pheasant, looking cool, 2013

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

Swan taking off, Aug 2014

As close as BFTF could get to a rabbit when stopped.
In contrast, they would only move at the last minute if BFTF was actually cycling.
All a bit Heisenburg if you ask me...

Herons, Colwick Park - Jul/Aug2014

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

Fields of wheat, east of Notts, by River Trent, 2014

Beautiful Scenery, Nutbrook Trail, Sep 2016

Well, hello there Mr Teenager Swan! Nutbrook Trail, Sep 2016

Poppies by the Big Track, 2015

Field of Wheat, next to the Big Track


Garden Spider (?) Autumn 2016


Mushrooms, Autumn 2016


Mushrooms in Wollaton Park, Auumn 2016


Nov 2016
London Plane Tree leaves can be surprisingly large.
This one is about 2/3 width of bike handlebars !


Sep 2016
Field Grasshopper, Sep 2016


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!


Spring 2016
22 spot Ladybird, on a  mug of tea
Unlike ordinary ladybirds (which eat aphids), these little chappies eat mildew!


Spring 2016
Newt in a Derbyshire Garden, 
(used with kind permission from Darren Sims Photography)


Spring 2016
Field Mouse in a Derbyshire Garden,
(used with kind permission from Darren Sims Photography)


Spring 2016
Swan v Duck at Rushcliffe Country Part


Oct 2015
NSB has seen the majestic deer in Wollaton Park recently, but did not dare get as close as Ghufran Shah did to get this (and many other) awesome images...

Deer at Wollaton Park, Oct 2015, via Ghufran Shah
 * Not sure if getting this close is a good idea *


Summer 2015
Picked up a piece of wood that had been lying on a garden path for several weeks and found an ants nest, with many ants eggs, underneath. Within a few minutes the ants had taken all the eggs through cracks in the paving to a safer location underground.....

Ants taking care of business..


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


Found a rather handsome example of the Common Frog in the garden....

Common Frog


A work colleague showed NSB this leaf that had had two very neat sections cut out of it by a leaf cutter bee. For scale, that leaf is only about 1 inch long.

Leaf cutter Bee


Saw this while out cycling. Think it is a Cinnebar Moth Caterpillar..

Cinnabar Moth Caterpiller

And then, spookily, found some more in the front garden....

Cinnabar Moth Caterpiller


Sep 2013
Can you see the FISH (not the crab) in this picture taken at the Sealife Aquarium at Alton Towers...

Can you see the fish (not the crab) in this picture?

NSB also saw this rather strange plant at Alton Towers, which one of @george_gorilla's colleagues has said is a plant called "Gunnera" (worth reading the link just to learn about the plants symbiotic relationship with bacteria).


Close up of the Fruits of Gunnera

Also saw this rather handsome slug on a path in the south of England, which @george_gorilla has confirmed is probably a "Limax maximus" (commmonly called a Great Slug or Leapard Slug).

A Great Slug

Close up of the "Shield"

A work colleague NSB was cycling home with recently spotted this, bright orange, fungi on a tree. Fungi are tricky to identify, but @george_gorilla thinks this might be a type of Polyporus, which are a type of fungi that break down wood.(see also here) - and an awesome set of mushroon images can be found here

Unidentified Fungi on a tree. Can you identify it?

NSB's brother has a back garden that is perhaps a little on the overgrown side, but this has the advantage of making it something of a butterfly magnet, and NSB was enchanted to see perhaps a dozen Peacock Butterflies flitting amongst the buddlia.

Inachis Io (Peacock Butterfly)

And here is a bunch of other stuff from September....

A rather handsome Woodpigeon

A Jackdaw

A splendid, if somewhat overexposed, conker

A female mallard, looking all coy

Embarrasingly, a part of me is thinking how big a meal this would make.


May 2013
NSB found these mushrooms, a few inches in diameter, in the flower pots recently - and has no ideal what they are. Fortunately, @george_gorilla was able to put NSB in contact with a mushroom expert who commented :
"It would be useful to know the size of these mushrooms and also to dig one out to look at the base of the stem. At first sight looking at the pure white cap skin which seems to have a bloom upon it and the pale gills, I think it may belong among a genus called Clitocybe. It will not be possible to go further without a microscope as Clitocybe contains a number of species with white caps and whitish gills, some of which are very poisonous.

If the stem base has a volval bag and the gills become pink it may be a Volvariella. If the gills become pink and there is no basal bag, just a plain or bulbous stem base it may be a Pluteus which suggests there is buried wood.

There appears to be no ring on the stem so it should not be Amanita, another genus with poisonous species and volval bag at stem base.Does it smell of anything in particular by the way? Just mushroomy, sweetish, floury or mealy, mouldy?

Sorry I can't help further without actually having it to examine."

Crikey, NSB had no idea it was so tricky to identify a mushroom!

A large unidentifed mushroom. Can you help identify them?

And saw this, which @george_gorilla instantly confirmed as being a common, if rather large, House Spider

Also saw this big bad boy on a fence post.

A friend posted these pictures of a Mason Bee (his identification, NSB would not have know what type they were!) that had made a home in a hole on the lug of his childrens climbing frame.

A Mason Bee has found a home in a friends climbing frame hold
And here is the Mason Bee close up


Winter 2012/2013
Beautiful Spiders Web, lit up by raindrops

A surprisingly tame fox that wandered around work,
black legs indicate that it is a youngster

Small spider, no idea what type