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...

Note : Includes posts about scenery, buildings and other non-wildlife stuff!

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Common Garden Spider, Autumn 2017

Suspect this is a female Garden Spider

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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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Cycle track

Love the new cycle training area in Wollaton Park!

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Tottle Brook Flood Barrier

Intrigued by this flood barrier - on the Trent near the retail part. Presumably it is to stop the Trent from flooding Tottle Brook - but if the barrier is in operation then where does the Brook flow to? You can find out more about the brook hereand also at this map from Rushcliffe Council

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Coypu seen in a German park recently

Rather enchanted by these Coypu seen in a German park recently - much tamer than rabbits, would love to see them in the UK.

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Beetle,  Summer 2017

Flowers, West Bridgeford, Autumn 2017

Horses, close to A52 Ring Road, Summer 2017

Lovely wildflower, no idea what type, Nottingham, 2017

Common Red Soldier Beetle, Carsington Water, Summer 2017

Very still Trent, Autumn 2017

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Odd beach structures (eroding soil?) Newborough Beach, Anglesea, Summer 2017

Ladybird, Summer 2017

Sky, Barmouth, 2017

Beach, North Wales, 2017

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NSB passes a fungi covered tree stump on the way to work and, one day, decided to take some pictures and try to identify the fungi. There were more fungi species than NSB expected and, as NSB knows nothing about mushroom identification, some help was required. The help came via Twitter from kind (and very clever) souls @Nottswildlife, @curataceae, @susieoftraken and @stu_rock who, between them, provided the information attached to the pictures below:

3 types of mushroom at the base of the stump 1/3

The small light ones to the bottom left are possibly Coprinus micaceus or Coprinus silvaticus. The darker ones on lower right are Coprinus disseminatus (fairies bonnets). The grey ribbon like fungus might possibly be Bjerkandera adjusta.

Fungi on the other side of the stump, Nottingham, 2017 2/3

This large fungi is Cerioporus squamosus (see also here)

Fungi on the top of the stump, Nottingham, 2017 3/3

Same ribbon-like "bracket" fungus as in the first image so possibly Bjerkandera adjusta.

As UoN's Craig Sturrock (@stu_rock) commented, "Nice multi species community structure!"

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Blackberries - food on the go! Various locations Nottingham Summer 2017

Manky Looking Granthan Canal, nr Holme Pierrepont, Summer 2017

Corn by the Big Track, Summer 2017

Combine Harvesting, by Holme Pierrepont, Summer 2017

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Weather Station near Queens Drive Park and Ride, Summer 2017

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Not something you see every day...

Drought Horse, Near Beeston Weir, Jun 2017

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Rather beautiful flower - even did a U-turn on the bike to come back and take this picture!

Thistle flower,  Nottingham & Beeston Canal, near Boots, June 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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According to the RSBP, Egyptian Geese "was introduced as an ornamental wildfowl species and has escaped into the wild, now successfully breeding in a feral state."

Egyptian Goose, Highfields Park, April 2017

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Interesting initiative by #GetFitNotts to "to get fit together, and make a dent in Nottingham's obesity crisis!"

Also check out Nottingham People on Bikes who are a "group of individuals who passionately believe that our city needs to become a safer place to get about on a bike. By achieving this goal, we will improve the health and happiness of Nottingham residents, ease congestion, improve air quality and make our communities more liveable for people."

Of course, the daddy of all Notingham Cycling organisations is PEDALS. Founded in 1979, Pedals is "a member of Cyclenation (the former Cycle Campaigns Network) and also works closely with the CTC (national cyclists’ organisation) and Sustrans. We also work closely with other cycle campaign groups and individual cycle campaigners in the East Midlands, through the informal East Midlands Cyclists Forum, with occasional meetings as well as email contact and exchanges of information between the meetings.

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Link to an informal cycling group in Nottingham, who last year did a "coast-to-coast" ride for charity - No1 Son participated on a number of their rides in 2016.

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

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Wollaton Park Lake, Mar 2017

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Love that Nottingham Council trim the foliage by the Big Track
sent an email to Council to say thanks!

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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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Beautiful Scenery, Nutbrook Trail, Sep 2016

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

Field of Wheat, next to the Big Track


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Garden Spider (?) Autumn 2016

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Mushrooms, Autumn 2016

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

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Ride along parts of the Nutbrook Trail and Erewash Valley Trails (Sep 2016)

By pure chance it turned out that BFTF was cycling to work on National Cycle to Work Day, so took the opportunity to ride home the scenic way, via the Nutbrook Trail and Erewash Valley Trails. Some pics and bloggage below!

BFTF joined the Nutbrook trail at Shipley Country Park. The Nutbrook Trail follows the route of the dismantled Stanton railway branch line, which no doubt explains is gentle gradients...

The Nutbrook Trail takes you away from the traffic and into the countryside

The Erewash Valley Trail is the result of funding and development by a range of partners, including :

Erewash Trail Development Partners

BFTF is very grateful for their foresight and perseverance in making this wonderful trail a reality.

Sometimes the scenery is too pretty for words

Well, hello there Mr Teenager Swan!


Setting sun at Trent Lock - better get a move on if want to get home before dark!

Cracks me up every time!


Now I know I'm nearly home!

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

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

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

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Spring 2016
Swan v Duck at Rushcliffe Country Part

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NSB has been impressed with the efforts of a number of people to start up an informal cycling club in the Wollaton area of Nottingham.

Starting in the summer with short 10-20 mile rides, which initially had so many punctures and mechanical failures in the group that one of the leaders, Ajaz, commented on the need for "due diligence" on riders and bikes in future rides - and then moving towards longer rides of 30-50miles - yet being able to also retain short rides for any newcomers or those who felt the full monty was a bit much for them...

Brutal 50 miler to Belvoir

...and culminating in a "coast to coast" ride in October (complete with back up logistics team). At the end of this 3-day event, Ajaz commented that :

"Highlights of C2C challenge for me was being able to ride up all the hills without stopping, while I was also watching out for others along the way. No major incident or injury we had over £150 worth spare parts but only had 5x punctures, they were fixed at roadside within minutes. A truly amazing experience of riding on different terains (gravel stones, tarmac, mud, puddles, leafs, grass) through country roads, villages, over dual carridgeways, under and over bridges. experiencing all types of weather ( rain, wind, sun, mist, drizzle). Seeing crack of dawn each day as we left the hostels at 6am."


Coast to Coast - Day 1




Coast to Coast - in the lanes

Coast to Coast - off road

Coast to Coast - Signage

Coast to Coast - highest point

Coast to coast - mission completed

The Coast to Coast route
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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 *

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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..

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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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May2015
Found a rather handsome example of the Common Frog in the garden....

Common Frog

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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

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

Aug2014
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

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Jul2014
Saw this while out cycling. Think it is a Cinnebar Moth Caterpillar..

Cinnabar Moth Caterpiller

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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

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Sep 2013
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

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)

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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?"


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

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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

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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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