Thursday, 31 July 2014

Rural Relaxation - Graham Atkins

Graham Atkins at Book Signing
Many of my "Rural Relaxation" walks are around College Lake, a nature reserve only a few miles from where I live. It was created out of a huge chalk pit, associated with the Pitstone Cement Works, because Graham Aktins, a lorry driver who worked for the company, persuaded the management that when the quarrying finished  the site could become a wonderful home for wild life. The Site is now managed by the Berks, Bucks & Oxon Wildlife Trust (BBOWT), Graham having retired a few years ago.

Graham on College Lake Buggy
Recently a small sign has appeared at College Lake, under a picture of Graham, reporting he died at the end of June. This picture was taken the last time I saw him, in September last year when he was at College Lake when the Castle Hide was rededicated to George Goddard (the former quarry manager who supported Graham's work). In addition Graham signed copies of his wonderful book Creating a Nature Reserve. He was not well at the time and used one of the electric buggies to go to Castle Hide - and we must all be pleased that he was able to leave a written record of how College Lake came about, so that visitors can understand his foresight and achievement. It also provides important guidelines for anyone else planning to establish a nature reserve ona brown field site.

Wednesday, 30 July 2014

Wednesday Science Limerick: Smallpox

We had thought we were safe from smallpox
And that samples were safe behind locks
But a store had some vials
Left over from trials
Insecure and just placed in a box.

Edward Jenner (1749–1823)
Smallpox was a very serious contagious disease which was estimated to kill 400,000 Europeans a year in the latter part of the 18th century. It had been observed that dairymaids, who had had cow pox appeared to be immune from smallpox and Edward Jenner discovered by using cow pox it was possible to be protected against the disease by vaccination.  Following a worldwide campaign the World Health Organisation finally declared that smallpox had been eradicated in December 1979. It is the only infectious disease where this has happened.

Monday, 28 July 2014

Why using CODIL is very different to programming a computer

So you have already learnt to program a computer and you know want to understand CODIL (Context Dependent Information Language) and how it works. I suspect that you have a problem because your have learnt to think in “computer programming” type mental box. – Let me explain.

In 1971, when high level computer programming languages were beginning to be used Gerald Weinberg wrote the book The Psychology of Computer Programming. He was interested in teaching a new language PL/1 and some of the students had already learnt the commercial programming language COBOL, and others the scientific programming language Fortran. In addition some had never programmed before. He found that if a student had learnt COBOL or Fortran they tended to use PL/1 as if it was a version to the language they knew and hence failed to make full use of the novel features of PL/1. Students who had no prior experience had no such inhibitions.     Read ON ...

Sunday, 27 July 2014

Are Humans domesticated Apes?

I like "out of the box" ideas and I really enjoyed the post I like this hypothesis by P.Z. Myers about the effects of domestication on animals. When we domesticate an animal species we select for tameness and this means, in effect, we select animals which have reduced adrenal glands as in such animals their stress levels are reduced, they are generally less fearful, and they are more open to socialization.

There appear to be associated side effects. For instance Mouse, rat, guinea pig, rabbit, dog, cat, fox, mink, ferret, pig, reindeer, sheep, goat, cattle, horse, camel, alpaca, and guanaco all show depigmentation (especially white patches and brown regions). Rabbit, dog, fox, pig, sheep, goat, cattle, and donkey have floppy ears while rat, dog, cat, ferret, camel, alpaca, and guanaco have reduced ears.
He suggests that the common factor is linked to neural crest cells during the early development stage.

Image: fotolia
This would also the fact that domesticated rat, guinea pig, gerbil, rabbit, pig, sheep, goat, cattle, yak, llama, camel, horse, donkey, ferret, cat, dog, and mink have reduced brain sizes compared with their undomesticated relatives.

Myers speculates that is might be the explanation for Neanderthal brains being bigger that ours - in that the difference is due to Homo sapiens being more domesticated!

Of course this is speculation - but the whole article emphasises that evolutionary changes in one feature can have knock on effects elsewhere in the body.

Wednesday, 23 July 2014

Wednesday Science Limerick: Nightmares

The Nightmare, by Henry Fuseli (1781)

When you wake, with a shock, in dispair,
With a monster that looks like a bear
It is not what it seems
Its a beast in your dreams
So don't panic its just a nightmare

Earlier this year I attended a very interesting talk "The Psychology of Ghosts and Hauntings" by Professor Chris French, at a meeting of the Chiltern Humanists. Prior to the talk I was aware of most of the different types of human mental failings he mentioned and I was delighted with his well chosen examples and references to the kinds of research projects that have been carried out.

One thing which particularly excited me was the discussion of sleep paralysis, which provides an explanation of why, when you dream you are running down the street, your legs don't move. I had not come across this condition before and it is relevant to the model of the brain's internal language I am developing, by demonstrating that there is a well known blocking mechanism.

This lead to my reading up topics such as sleep, rapid eye movement, parasomnia, nightmares and sleepwalking on Wikipedia and I get the impression that, like other areas of brain studies there are a lot of ideas as to what is involved - nut a lot more needs to be done. What is clear is that many species of animals sleep and that the brain is clearly very active for at least part of the time were are sleeping. As such there must be a good evolutionary advantage in sleeping which involves the brain, which appears to be refreshing and rehearsing the information it has accumulated when it was awake. However it would not help if the sleeper physically re-enacted the actions of the day and the brain has a mechanism to switch off brain activity which would lead to concious awareness of the dream, and the associated bodily movements.  Sleep problems, such as night terrors and sleepwalking, can be related to these switches failing to work correctly and on one hand you imaging your brains rehearsal as real but cannot move, or that your body moves but you are not aware of what is happening.

His thoughts were so far from the floor
That he dreamed that in clouds he did soar
Till he tripped on a boulder

And so tumbled over 
And won't walk in his sleep anymore.

Tuesday, 22 July 2014

The Trouble with Brain Science - History suggests possible solutions

Professor Gary Marcus, Professor of Psychology, At New York University has just written an interesting  article "The Trouble with Brain Science" in the New York Times. This relates to the to the open letter sent by hundreds of scientists who consider the latest EU funding proposals for brain research are unsatisfactory. Gary's article clearly states views about the current state of brain studies.
Neuroscience awaits a similar breakthrough. We know that there must be some lawful relation between assemblies of neurons and the elements of thought, but we are currently at a loss to describe those laws. We don’t know, for example, whether our memories for individual words inhere in individual neurons or in sets of neurons, or in what way sets of neurons might underwrite our memories for words, if in fact they do.
This is just one of the hundreds of articles that have appear in the media in the last few weeks - and relates back to my post several tears ago under the title Brain Storms - 2 - The Black Hole in Brain Research.

Perhaps the difficulty is that when a lot of scientists have been looking very hard for a solution to an important problem it is assumed that it is a very difficult problem and more and more scientists pile in to dig the hole deeper. This approach only works if everyone is digging in the right place ...

There are some interesting precedents if one looks back in history

The Ptolemaic system of epicycles attempted to explain the apparent movement of the planets in the night sky, and tried to  explain their movements in terms of a number of linked circular motions. As measurements became more accurate the number of these epicycles needed to increase and the problem of working out what was happening - although if powerful computers had existed at the time we might still be stuck in the scientific past with epicycles within epicycles within epicycle to the nth degree.  The only reason the Ptolemaic model lasted as long as it is is that we are not dispassionate independent observers - and as the big-headed animals that we are  we considered that we must be at the centre of everything. All that was needed was to step back a bit and put the Earth on which we live in a wider context.

Ambix, cucurbit and retort
The Eighteenth Century chemists had a different problem in that they believed their eyes. At the time they were trying to isolate and identify the elements that were the building blocks of the world we live in. One of the most easily observed and spectacular elements was Phlogiston. There was no doubt that it was important and they needed to get a sample so that they could examine its properties in detail. It was very easy to make, a very large number of everyday materials contained it in profusion, and if you put animals in jars with air containing Phlogiston they died. Try as hard as they could they repeatedly failed to isolate it and put it in a bottle. However the experiments by Joseph Priestley produced a gas which was called dephlogisticated air because it didn't contain any Pholgiston. This gas caused substances which contained Phlogiston to release it very readily.

In fact the search for the element Phlogiston was fruitless – because what appeared to be Phlogiston being created was the light and energy when things burn in oxygen, and they were trying to capture heat and light as if it was a solid substance.

Perhaps the current difficulties in understanding in understanding how the brain holds and processes memories is that we have been asking the wrong questions. As regular followers of this blog will know I am currently drafting a paper describing a model which promises to bridge the gap.  Some aspects of the model have already been aired on this site, and more is in the pipeline, but the two historical examples point to two "outside the box" areas I am exploring.

Self importance

Judy Horacek(C)
We are very special. Just look at all the things we can do that other animals living on this planet can't do. We are so successful that our activities are rapidly altering the climate, and we know how to build magnificent weapons of mass destruction. But of course, if we succeed in changing the world so much that we (and many other plants and animals) become extinct, we will just be another dead end branch of the evolutionary tree of life. We have already dismissed the Ptolemaic system and realised that we are not at the centre of the universe. What we need to do is to climb down from the pedestal we have created and  try and take an objective view.

In my model of the brain I start by assuming that our brains are really no better than those of at least the higher animals, except that we have more capacity than most, if not all, other mammals. I then look at how an animal with such a brain might evolve to have the information processing powers that we have - and find that the very simple protocol the neurons in an animal brain need to process enough information to survive is sufficient to support virtually everything we do. The main difference is due to improvements in the speed of learning which allows us to exchange and remember cultural knowledge more easily. Better cultural knowledge means better tools - and the most important tool, which improves generation by generation is language.

Uncertainty and form

The Phogiston story shows we can be looking for the wrong kind of information. Phlogiston turned out to be energy waves and not a solid substance. Perhaps the questions "Where are memories stored?" and "How are they formatted?" are not the best questions to ask if you want an answer. Having got a Ph.D. in theoretical chemistry I accept without question the ideas behind Heisenberg's Uncertainty Principle and have never lost a minute of sleep over wondering whether Schrodinger's Cat is alive or dead.  After all an electron is both a particle or a wave, and only "makes up its mind" when it knows what question I am asking about it.

My brain model takes the physicist's "Ideal Gas model" as a guide - and assumes the brain can be considered as a sea of identical neurons, with different and variable strength links connecting them. You see a "Rabbit" and the eye "in effect" drops a suitable pebble of activity into the sea, generating a suitable wave of activity to spread over the surface of the neuron sea. At the same time your stomach drops a pebble of "Hunger" into the sea. The two wave trains intersect, and collapse onto a single neuron which becomes active and initiates a new wave "Rabbit Pie". The various groups of ripples represent the human short term memory - and it it is inappropriate to ask where a particular memory resides in the brain when the sea is perfectly calm. For instance my memory of my mother only exists when I am thinking about my mother - when there is an appropriate set of ripples in my short term memory.

And what about the EU proposals

Now at the start of this post I mentioned the protest letter about the E.U. funding plans. What we know is that over the years billions of man-years of effort appear to have been invested it trying to do something which every new-born child does automatically. The E.U. (and the U.S. government) have decided that we need to invest even more following our noses in the directions we have been looking because if we spend enough money going in a single direction we will eventually find the answer.

The examples of epicycles and Phlogiston show that if you have the wrong model it is very easy to waste good research resources trying to go down blind alleys. My research is trying to escape from the establishment brain research boxes which assume that we are more intelligent than animals and that you can find memory in specific locations if you look hard enough. O.K. As a scientist I know my model could be wrong (although many establishment scientists behave as if they knew they were right) but my experience with my research suggests that the current scientific world is very bad in recognising that significant out-of-the-box ideas can originate in unexpected out-of-the-box places.

Whatever your views on the E.U. proposals remember that this generation of scientists is not guaranteed to be right all the time, any more than of the previous generations were. The fact the Richard Dawkins called one of his books on evolution "Climbing Mount Improbable" should be warning enough that if we find ourselves facing a major scientific brick wall we should be prepared to step to the side and look for an out-of-the-box way round rather than waste money trying to scale impossible heights.

Sunday, 20 July 2014

Comments on Jeff Hawkins' book "On Intelligence"

When I mentioned the book “On Intelligence” by Jeff Hawkins on Some very interesting developments about my brain model I had only briefly assessed it. When I came to study it in more detail I found it took the problems of intelligence and how the brain works no further than other modern accounts I have seen. It was initially difficult to work out how successful, or otherwise, his understanding of the way the brain processed information  because of the way the book had been written. I don’t need to say any more this than to repeat his own words in Chapter 4:
You may have noticed, too, that in telling a story some people can't get to the crux of it right away. They seem to ramble on with irrelevant details and tangents. This can be irritating. You want to scream, "Get to the point!" But they are chronicling the story as it happened to them, through time, and cannot tell it any other way.
This is a perfect description of how the book itself has been written.

Have the Australians gone Mad?

Unfortunately we have no option but to live in the same planetary sized box as the Australians and there is no way we can leave the sinking ship if the Australians have decided to let their part of the bilges fill to overflowing with excess carbon emissions. 

Perhaps I am being a little unfair on Australian and there are many others I could  also blame for failing to take the future seriously. Even I don't take things as seriously as I should because sometimes I take the car when I could walk - and become healthier by working off the result of over-eating. However I have had a particular interest in the effects of climate change in Australia since 1990 (See Global Warming - To Australia in a Box) and have been watching the temperature rise (see It ain't Half Hot, Mum).

So I am distressed to hear the latest news - that the Australian Government has decided to abolish the carbon tax (see Back to 'Ground Zero' with Carbon Tax Repeal). Perhaps the politicians have noticed that the road through the Blue Mountains is currently blocked by snow and ice and cannot distinguish between "weather" and "climate". Or may be the problem is that Australia has so much desert that there is plenty of sand for the ostrich-like politicians to bury their heads in. ... I could go on and on and on about this subject ...

Our approach to the climate is rash
As rain forests are burnt in a flash
Our future ambition
Less carbon emission
Is forgotten when we want more cash 

Wednesday, 16 July 2014

Wednesday Science Limerick - Earthworms and Forests

In the States, on the old forest floor
There's a problem that we must deplore
For the earthworms at work
Bury all of the dirt
And the tree seeds won't grow any more.
It seems to be common knowledge to most of us, that earthworms are good for soils. When asked, most people express something along the lines that earthworms are good because they “mix and aerate soil” and “increase nutrients”. This concept likely comes from decades of research on the positive impacts of earthworm activity in gardens and farm fields where the soil can become compacted and less productive if it isn't broken up and organic material isn’t mixed in. But hardwood forests in the Great Lakes region developed for thousands of years since glacial retreat without any earthworms. The natural processes in these earthworm-free forests usually keep the soil loose and uncompacted. Hardwood trees produce tons of nutrient rich leaf litter each year. When leaf litter is produced faster than it decomposes, you can see the development of a thick forest floor, and beneath that forest floor a unique set of soil layers also develops…read more. As litter in the forest floor is decomposed by bacteria and fungi, nutrients are made available for understory plants and tree seedlings. The thick forest floor of earthworm-free hardwood forests turns out to be a central feature of these ecosystems since it is where most nutrient cycling occurs and where virtually all understory plants and tree seedling germinate and grow. When earthworms invade, the hardwood forest ecosystem begins to change rapidly as this forest floor is removed.

Continue reading the full story on the 

Monday, 14 July 2014

The Uniqueness of Humans among Animal Species

This afternoon's The Infinite Monkey Cage had Brian Cox and Robin Ince talking to Keith Jensen, Katie Slocombe and Ross Noble about Human evolution and comparisons with chimpanzees and other animals. Like other programmes in this series it is well worth listening to, and this one was particularly relevant to this site. It is repeated tomorrow (Tuesday) on BBC Radio 4 at 11pm and an extended version is available on the BBC web site.