Sunday, 31 August 2014

Rural Relaxation: The Twist at College Lake

The Seat at the Top of The Twist
When I want some exercise and a breath of country air well away from a computer key board (and with the mobile phone switched off) I frequently go to College Lake. The place has many different habitats and I have been taking photographs of the Reserve for 9 years - recording the changing seasons - and the improvement made by BBOWT, who run the reserve. 

I have decided that at the end of each month my "Rural Relaxation" post will concentrate on one feature of the reserve and include pictures taken at a range of dates. 

This month I visit The Twist, a winding path with a seat at the top, giving good views across the Lake. There is also a seat at the bottom (at present) which is currently the only place in the Reserve where you can stand really close to the water of the Lake. I say  "at present" because only three months ago the water was covering the path in front of the seat, while the other seat near the Octagon hide is already under water. 

For more pictures and descriptive text CLICK HERE

The Twist and nearby features of the College Lake Nature Reserve
Posted in Memory of Graham Atkins

Thursday, 28 August 2014

The Limitations of Conventional Programming Languages

Under the heading Trends in Programming Dr Geoffrey Sharman, chair of the British Computer Society Advanced Programming Specialist Group, sums up the current trends in programming and developing applications. He writes:
    Overall, programming languages have been relatively stable for several decades. Almost all modern languages are derived originally from Algol and, more directly, from C.
    While there continues to be development of existing languages such as C++ and Java, and of new languages such as Python, Ruby and Groovy, these are recognisable as incremental improvements on an existing paradigm, rather than new paradigms, and therefore exploit widely available programming skills. Notable exceptions are COBOL and FORTRAN, which are firmly established in particular industries, but also stable providing that skills are maintained.
    Similarly, programming tools such as compilers, interpreters and debuggers have improved over many years. The introduction of integrated development environments (IDEs) just over a decade ago provided a significant increase in programming productivity, which continues to be improved year on year.
    No other technologies are in sight that might offer significant productivity increases and, therefore, current attention is focussed on ‘agile’ development methodologies, which seek to offer shortened development cycles and increased confidence in the outcomes of development projects. 
    For the most part, these methods are based on iterative development techniques in which a subset of function can be demonstrated early in a development project and then reviewed against user needs, and enhanced or refined as the project progresses. The success of these techniques is based primarily on refining specifications rather than the development process itself. In other words, answering the question ‘am I developing the right thing?’ rather than ‘am I developing the thing right?’ ... ...

Basically little has really changed since I retired in 1988. The real problem, which has not been tackled relates to the fact that modern computers are black boxes. If a user is running a black box system of any kind they have a serious (and in some cases catastrophic) problem when something goes wrong, because they do not know what has gone wrong or how to correct it. This means that every effort has to be made to ensure that the black box always works correctly - and the more complex the task the harder it is to pre-define and implement every possibility. The article suggests that what are now needed are not better programming languages but better ways of specifying the task and ensuring that the program does what the task requires.

No one appears to have realised that the fundamental problem results in having a black box. What is really needed is a white box system where the user can work with symbiotically with the automated system. Of course things can still go wrong but now the user can see what is wrong and take appropriate remedial actions. As CODIL is a preliminary attempt to build a white box computer I decided to write the following letter in reply to Dr. Sherman's article.
     As a long retired Fellow of the Society I read about the comparative lack of progress during the years since my retirement, and I am not really very surprised. The conventional rule based programming approach lacks the flexibility of the human mind and has problems with the messier aspects of the real world. An analogy with the railways of Victorian times illustrates the problem. Both railway lines and programs need to be planned in advance and only when they have been built can “fare-paying customers” (goods/passengers in the case of trains, data for programs) use the systems. Both are prone to considerable disruption if faults occur in key places, and both are unable to cater for low volume non-standard “journeys” (which do not justify the up-front building costs) and unpredictable real world events. Many bigger and more successful computer systems work because people are more flexible and change their behaviour when offered a limited but very much cheaper service – moving to live in houses built near railway stations in late Victorian times, and using hole-in-the-wall banking today.
     However there are many problems where there are very hard to fully pre-define requirements and where low volume and unpredictable requirements cannot be ignored, We still read of projects in such areas running into trouble. Medical records are a good example. They involve active participation of many people to gather the data, which relates to the real life problems of many people who each have an assortment of medical issues. At the same time medical advances lead to changes in our understanding of the diseases, new ways of monitoring the patients, new drugs and medical experiments, and problems such as the development of drug resistance.
     I have recently been looking back into the relevant computing history. Many of the early experimental programming languages got squeezed out in the rush to develop better conventional programming tools and one of the “lost” languages seems of particular interest in this context. CODIL (COntext Dependent Information Language) was conceived as the symbolic assembly language of a radically new human-friendly “white box” computer architecture, as an alternative to the human-unfriendly Von Neumann “black box” computer. The research was triggered by a study of the 1967 sales accounting package of one of the biggest commercial computer users, Shell Mex & BP, at a time when many of the sales contracts had been drawn up in pre-computer days. The initial research work into CODIL was financially supported by the LEO pioneers, David Caminer and John Pinkerton, but was axed when the old LEO research labs were closed and ICL was formed. A short talk on the first preliminary research was given to the Advanced Programming Group 45 years ago, and several papers were later published in the Computer Journal describing work with a simulator, as no hardware was ever built.
     A re-examination of the CODIL project papers suggests that the real reason for its failure was that the research concentrated on looking into the possibility of producing a competitive computer package and failed to do any essential unrushed blue sky research into why it worked!
    My current assessment is that the CODIL approach represented an alternative mathematical model of information processing to the “Universal Machine” approach of the conventional stored program computer. Instead of a top down rule based approach which uses numbers to represent instructions, addresses and data, within a precisely defined mathematical framework, CODIL takes a bottom up approach using recursive sets rather than numbers as the basic storage unit and makes no formal distinction between program and data. It uses associative addressing and automatically compares patterns to find and fill up “gaps” in incomplete patterns. It appears that the approach could be implemented on a simple neural network and work done 40 or more years ago may prove to be relevant to understanding how the brain works.
     Of course further examination may show that the CODIL approach is not the answer to building complex human-friendly open-ended systems but its very existence could indicate that there are other interesting research gems which were lost in the mad rat race in the early days of computing to capitalise on the market potential of this new invention. 

Wednesday, 27 August 2014

Wednesday Science Limerick: Buckminsterfullerene

A bucky-ball has to be seen
It's called buckminster (dash) fullerene
It is like a football
It's a cage, that's not all
It traps atoms in ways unforeseen.

When I studied Chemistry at university there were three known forms of the element carbon, diamond, graphite and amorphous carbon (such as charcoal). I became very interested in carbon atoms which contained unsaturated hexagonal rings and ended up doing a Ph.D. linking theoretical calculations with their measured properties. It was over 25 years later, in 1985, that the first "Buckyballs" were discovered.
Buckmasterfullerene (chemical formula C60) consists of a sphere of 60 carbon atoms arranged as 20 hexagons and 12 pentagons forming a truncated icosahedron. The pattern is same as the leather faces on an association football and the name was given because an architect Buckminster Fuller designed buildings with spherical domes called geodesic domes. It opens up an exciting new field of carbon chemistry including materials with very interesting properties. Metal atoms can be trapped inside the cage, and bucky-balls laced with potassium are superconductors up to a temperature of 18 degrees Kelvin. In addition the discovery has lead to many other fullerenes being discovered - the most important being nanotubes which can be likened to sheets of graphite being rolled up into a tube.

Note about the limerick below the fold.  

Health, diet and the understanding of what science can do.

A good old fashioned English Breakfast
The Independent newspaper today has an article The science of saturated fat: A big fat surprise about nutrition? which seemed very relevant to me at the moment for family reasons.

Earlier this I was given a very robust talking to by the nurse at my doctor's surgery and as I result I have already lost 7 kg by reducing portion sizes, eating more fruit and vegetables, and cutting out between the meals nibbles. I am taking the need for a daily walk more seriously, and spend an hour a week in our local swimming pool. I am well on track to achieve  my target of 10 kg lost by Christmas, with further losses in the New Year. However my current eating habits may need further  modification when I hear the result of a blood test next week.

Over the bank holiday weekend I had planned several further posts on this blog but was distracted by a urgent phone call - as a close relative was rushed to hospital four days ago with a heart attack. Fortunately it was more of a sharp warning and after an angioplasty the signs are good - but he is even more overweight than I was and one of the matters he will have to address is his weight. We have already had some discussions about what the doctors might recommend.

And so to the newspaper article, its statement that saturated fats do not cause heart disease, and the discussion of why the earlier research was wrong. The article suggests that Our fear of saturated fats began in the 1950s when Ancel Keys, a pathologist at the University of Minnesota, first proposed that they raised cholesterol and therefore caused heart disease. It then goes on to review the findings of Ronald M Krauss when he reviewed the literature on the subject and was able to show that the evidence of a link is inconclusive. The story sounds plausible and he may be right.

The problem is knowing what one can believe. There must be many possible links, some strong, some weak, between the food we eat and our health and in theory science can look for and measure the effects. I know enough about science to know that in theory I could look into the literature in detail and assess the reliability of the information for myself. I could but I don't have the time or motivation to do so. I also realise the very real difficulties of carrying out long term dietary research over several decades in a way that will return statistically significant results. My father was, for a time, a tobacconist and can remember the years it took to get people to accept that smoking could damage your health.

However I have noted that the article is linked to a publication of a book, and there are many different books on the market, articles in magazines and on web sites, and programmes on television which give conflicting advice. Most would claim they are backed by science and a very significant number have commercial interests which could influence their objectivity. 

All this must influence what people think about science. Every one has to eat to live and is interested, in the short term at least, in their health. Good science has difficulties in providing reliable predictions about long term effects of diet - and there is much pseudo-science, such as homeopathy, which has no scientific foundations. This gives Joe Public the impression that science is unreliable, and the lack of understanding could well encourage people to take up issues which have no sound basis. 

Wednesday, 20 August 2014

Wednesday Science Limerick - Comet 67P

There’s a comet named 6 7 P
That Rosetta has wanted to see
And it looks like a duck
Though with plenty of luck
They’ll find water among the debris

Comets are astronomical objects consisting of a mixture of rocks, dust, water ice and frozen gases which orbit the sun in an extended orbit. When they approach the sun they heat up and some of the water and frozen gases evaporate, releasing some of the dust. The escaping material  is blown by the solar wind (caused by plasma escaping from the sun) to form a tail which can sometimes be visible to the naked eye - although the central rocky body is too small to see. Every time it comes close to the sun it loses more material and may break up into fragments. Meteor showers can be associated with some comets - representing small fragment which have become detached and spread out along the orbit over millions of years.

In recent years robotic space craft have approached and photographed comets and at the present time the spacecraft Rosetta is in orbit round the comet 67P/Churyumov–Gerasimenko. (Sorry for the long name - and the fact that I didn't include the full name in my limerick - but comets are named after their discoverers.) It has proved to be most interesting in that it is anything but spherical - and its shape has been likened to that of a rubber duck. Before 1959 it didn't approach the sun closer than about 400 million kilometers but a "close" approach to the planet Jupiter altered its orbit so that it now comes to within 190 million kilometers. Obviously the closer it comes the hotter it gets and the more material it looses each orbit. Some of the smoothest areas appear to be in the "neck" and if the comet consists of two large rocky masses cemented together with water ice it may not be that far from splitting into two. 

There will be much more active research over the next couple of years, with much more detailed photographs plus other scientific measurements of the material escaping from the surface. In addition there will be an attempt to land a probe and sample the surface. I will be following the discoveries with interest and I note that the Wikipedia page is being kept well up-to-date - the last amendment being yesterday.

Monday, 18 August 2014

Do Chimps have a bigger Short Term Memory than we do?

In thinking about the brain's internal language one of the interesting features relates to the size of our short term memory, and the number of thoughts we can handle at any one time. This video suggests that chimps may be better equiped in this area than we are!

Saturday, 16 August 2014

The Wiring of the Human Brain

A bird’s-eye view of nerve fibres in a normal, healthy adult human brain. The back of the brain is on the left of the image and the left side of the brain is at the top of the image. 
I am impressed with what can be done using MRI Scans.
Picture and more information from the Welcome Trust Blog

Thursday, 14 August 2014

Last month I criticised Jeff Hawkes book because he used the term "invariant" when discussing human memory. I pointed out.
Since when has the world been invariant? And even if it was our memories change continually with time, and my memory of my mother when I was six would not have been the same as my memory of her forty years later, or my memory of her 15 years after her death at the age of 90. One of the well-known limitations of the human mind is that long term memory is not a reliable record of what happened.
If you want to know how unreliable our memory can be watch the above lecture by Elizabeth Loftus.

Wednesday, 13 August 2014

Wednesday Science Limerick: Helium

They say one degree Kelvin is cold
Liquid Helium’s quite uncontrolled
When put in a jar
It’s behaviour’s bizarre
It climbs out – that’s a sight to behold

Helium is a most interesting element. It is the lightest of the chemically inert noble gases and the second commonest element in the universe. It was first discovered because of its spectrum in sunlight – which is why it is called Helium – after the Greek word for the sun ἥλιος (helios). The nucleus, the alpha particle, is also a product of radioactive decay.

It has the lowest boiling point of any substance (4.22 degrees Kelvin) and it is still a liquid at absolute zero, although a solid can be formed at high pressure. Below 2.1768 degrees Kelvin it become superfluid. This is a strange property where a thin film spreads out over all surfaces connected to the liquid and the liquid flows through the film from higher to lower levels. In the diagram the film covers all surfaces of the sealed container and from the outer to the inner bowl until the levels are equal. If the container was not sealed the liquid helium would escape.

In fact there are two isotopes of helium, He4 (2 protons and 2 neutrons) – as described, and He3 (2 protons and 1 neutron) which does not become superfluid until a much lower temperature. These strange properties are hard to understand without some knowledge of quantum physics and the meaning of words like "Boson" and "Fermion" – but should you want to know more the articles on Wikipedia are well written.

For more about the background to these Wednesday Science Limericks, and this one in particular, see below the fold.

Tuesday, 12 August 2014

Rural Relaxation - Whirlwind at College Lake

On Sunday we had a bit of a storm at Tring but once it had passed I decided to got to College Lake for a walk and cup of coffee - but couldn't get there as the road was closed because power lines had been brought down near the bridge over the canal at Bulbourne. So on Monday I went to see what had happened.
OK I was a day too late to photograph the whirlwind but had come from the west and cut a gap (see above) in the tall poplar trees that border the Canal.  Between those trees and the smaller ones closer to the water there is a small hay meadow and the second photograph shows broken branches that were lifted by the wind and drop in the meadow. Other branches could be seen on the track leading back to the Visitors Centre.

The whirlwind swept across the lake, a visitor's photograph showing the water whipped up by the island on the right in the first photograph. It then crossed out of the reserve and brought down a tree in Northfield Road, about quarter of a mile away.

Saturday, 9 August 2014

The Brain and the Evolution of Human Intelligence (Comments Please)

I am currently drafting a paper on the Evolution of Human Intelligence which will bring together three interacting models, each representing different levels of activity and abstraction. The jumping off model I am calling the “Brainwave Model” which looks at simple decisions at the human short term memory level. Above this is an “Intelligent Pattern Recognition Model” which examines the relevant CODIL research and its relevance to culture, natural language and intelligence – and in effect defined the brain’s “Symbolic Language”. Below the Brainwave Model” there is the “Ideal Brain Model” (early draft to be rewritten) which looks at what the neurons need to be able to do in order to support the two higher models. The paper will continue looking at the evolution of the brain and human intelligence, using the models as a guide, starting with the requirements of a simple animal and looking at how the brain’s power increases as culture evolves.

Draft Section: The "Brainwave Model

The Brainwave Model forms a short term memory bridge which links the complex high level mental activities which we associate with human intelligence, with electrical and chemical activities at the neuron level, and the objects in the real world we are thinking about.  It is best described by a simple example.

Imagine the brain as a sea of interconnected neurons and into this sea we drop pebbles of information. This creates ripples of activity which spread out across the sea, and eventually die away. For instance our eyes see a rabbit and result in a “rabbit” ripple becoming active. This process could well involve many hundreds or thousands of neurons becoming active as the ripple develops and this activity can only pass between neurons which are linked. Each ripple can be considered as an active thought in the short term memory and at this level of modelling we are not interested in the fine detail within a wave of activity.

At the same time the body becomes hungry and a “food” ripple becomes active. The two ripples spread and meet and combine to generate a new brainwave – “rabbit pie”. At the point at which they coalesce there will be a neuron which is linked in such a way that it can be activated by either the “rabbit”, the “food” or “rabbit pie” ripples. What has happened at the thought/concept level could be represented as:
rabbit, food à rabbit pie

We can generalize this to model the human short term memory. At any one time there are a maximum number of ripples (about seven) which can be active at any one time. Each ripple can be given a concept name, which for convenience in this text will be shown in bold brown font. Where two or more ripples intersect there will be a neuron (or a group of neurons) which can be activated by the relevant concept and this can “take a decision” by activating a new ripple.

Of course it is important to realise that a concept name, such as rabbit, is not a precisely defined entity as the ripple through the neurons would be different depending on the colour of the rabbit, or whether it was a real rabbit or a rabbit in a children’s story book. It may well be that in some situations the sight of a wild rabbit, or a carcase in a butcher’s shop will trigger the rabbit pie decision, while the sight of a domesticated rabbit, or a picture of Beatrix Potter’s Peter Rabbit will not. At the same time the strength of the food concept will vary depending on how hungry you are. Other minor factors might affect whether you imagine the pie to be topped with short crust or puff pastry – or whether instead you think of rabbit stew. Such differences are an essential features of how the brain works.

The brain is a dynamic learning (and forgetting) system which is not concerned with any externally defined global models. In a relation such as
rabbit, food à rabbit pie
the “meaning” of rabbit is defined only by the ripples active at the time the rabbit pie decision is made. As part of the brain’s learning process the mental activity involved will have a feedback effect which could modify the way the activated neurons are linked – so the meaning of rabbit could be slightly different the next time a similar rabbit is seen in a similar situation.

When we come to the exchange of information between people using natural language we need to agree stable long term concept names for objects, such as rabbits, but our individual brains will associate the concept rabbit with different memories which will develop over time. Later in the paper, when I look at CODIL as a model of brain activity, the same situation arises. CODIL was conceived as a practical working tool which did what its human user wanted – and by default items (the equivalent of concepts) have to be stable – although options were built in to allow CODIL to dynamically alter its behaviour over time.

Before moving on to discuss higher level models of brain activities it is necessary to understand how this simple brainwave model provides a basis for further research. The brain contains billions of neurons, and each neuron has direct (and indirect) links to many other neurons. This would represent a massive array involving tremendous computer power if one tried to look at the problem globally. The wave of activity associated with the current thoughts (concepts) in our short term memory act as an filter on the vast array selecting a minute number of entries – and in some cases none at all. When considering how the brain processes higher level “intelligent” ideas all neurons and links can be ignored apart from the tiny number which are activated in the current context.

Friday, 8 August 2014

Should we be teaching Primary School Children to Program Computers?

Of course we live in a world where computers are playing a very important part of everyday civilized life so it is important that children have some understanding of them.  But does that mean that that every child should be able to program them? Might it be just as important to teach them what is happening at the electronics level? Or to use word processing tools? Or graphic art packages? It is important to realise how fast technology is changing and existing I.T. style jobs may have become redundant within their lifetime. I am not going to enter this debate but to ask a far more profound question:

Should we teach children to “think like machines” or should we build machines that “think like people”?
Or is it already too late?

Thursday, 7 August 2014

The "Filter Problem" in locating relevant research in the on-line records

 DrugMonkey posted the following question under the title "There is no filter problem in science"
It is your job as a scientist to read the literature, keep abreast of findings of interest and integrate this knowledge with your own work.
We have amazing tools for doing so that were not available in times past, everything gets fantastically better all the time.
If you are a PI you even have minions to help you! And colleagues! And manuscripts and grants to review which catch you up.
So I ask you, people who spout off about the "filter" problem.....
What IS the nature of this problem? How does it affect your working day?
I have posted the following comment in reply:

Wednesday, 6 August 2014

Wednesday Science Limerick: POST

At Westminster you'll find a POST
Which in science is deeply engrossed
For our average M.P.
Knows no science you see
And the right facts are what they need most

You never know what you will discover when you are on the web. I often submit a limerick or two in a weekly limerick competition - and this week the first line had to end with post. Perhaps because I went to Dartington I like to think outside the box and find a slant that others will miss.

So I decided to see what organisations are referred to as P.O.S.T. and came up with the Parliamentary Office of Science and Technology. This  body provides in-house advice on current issues parliamentarians, few of whom have any significant training in science. I probed further and discovered that the organisation publishes what are called POST Notes which are available online. There are far too many to assess them all but I decided to look at a few that interest me. They are normally 4 pages long - and explain the issues without suggesting policy decisions.

My reaction is that POST is providing good support information to our Members of Parliament on science matters - but whether they actually read  it is another matter. If I have reason to write to my M.P. on any science related issue I will be checking the list of POST Notes to remind him which one he should read.

Tuesday, 5 August 2014

How to avoid being placed in a Prison Box

(Reuters) - Formula One boss Bernie Ecclestone has offered to make a $100 million (59 million pounds) payment to end his trial on bribery charges, a district court in Munich said on Tuesday, with state prosecutors saying they would accept his offer.
Judge Peter Noll asked Ecclestone if he could make the $100 million payment within a week. Ecclestone's defence attorney Sven Thomas answered "that's do-able".

The judge said the court would adjourn for four hours until 1 p.m. (12 p.m. BST) to consider whether to accept the deal. [The deal was accepted]

Of course the deal would mean that there is no formal admission of guilt in the case, which involved channelling $44 million to jailed BayernLB banker Gerhard Gribkowsky to smooth the sale of a major stake in the business by the bank to private equity fund CVC, which became the largest shareholder in Formula One in 2006
Shall I just say that I consider that any court system which is prepared to accept bribes to cancel court cases involving bribery is a corrupt court. 

Why you should stop believing in Evolution

The Week as an excellent article entitled Why you should stop believing in Evolution which I really enjoyed. And so will you.

It points out that evolution is like gravity or the fact that the world is round - it is out there and it is just an essential part of nature. Really the only question is whether you understand it or you don't.