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.

Sunday, 13 July 2014

Some very interesting developments about my brain model

A few days ago I posted a comment on Pharyngula and duplicated it on this blog under the title

Filling the Black Hole in Brain Research

Burkhard Neidecker-Lutz commented in considerable detail and my reply is given below. It will be interesting to see how this develops.

Commenting on my comments #88 and #90 Burkhard Neidecker-Lutz #93 says
You may be surprised by what I can be interested in :-). And yes, curiosity is a very useful emotion to keep oneself motivated. But it is not even half what you need for doing science. So onto your approach.
I think we would both agree that there is no satisfactory published model of how electrical activity at the neuron level is converted to human intelligence.
Short summary: no, I would disagree (with lots of caveats).
Long version. Seriously long.
There is an awful amount of stuff packed into that sentence of yours. First the part where we agree.
There is electrical activity at the neuron level, plenty of wiring and connections and at the highest level we agree that the whole system exhibits a stunning number of behaviours we call “intelligent”.
If you mean by your statement that we do not have a concise, simple unifying theory on how you get from the former to the (ill-defined, let’s do that below) latter, then, yes, I agree.
I was talking very specifically about your last meaning – and your reference to the book by Jeff Hawkins On Intelligence is very helpful. I had not read it before, although I had picked up quite a few of the ideas from other sources. The following is my reaction, after a quick scan, and I will be re-reading his book in more detail over the next week or so. {See Comments on Jeff Hawkins' book "On Intelligence" for some highly critical comments.}

You and Jeff are looking at the same problem that I am looking at, but from a completely different viewpoint. Jeff is starting from the physical brain and asking how its components are constructed and how they work. I fully appreciate that some very detailed and sophisticated work has been done in this area.

My primary interest for more than 50 years is in communicating and processing information and I am asking the top down question – “How must neurons function in order that we think in the way we do?” What is important to me is the meaning of the information being processed and not the finer detail of the biological system that does the processing.

 Other researchers who has tried a top down approach have started by looking at natural language and there have been major disputes, for instance around the work of Chomsky, and they don’t seem to have reached anything like an agreed conclusion. Other researchers (at least in the 1970/80s) studied sophisticated logical puzzles of the type that amuse mathematics undergraduates and called it Artificial Intelligence. This period of research is now considered by many to have not been very fruitful.

My research started accidentally in 1967 after having worked with very complex manual and computer information processing systems. The first steps were made when I was examining the human interfacing problems of a working commercial system which priced orders for about 250,000 customers buying any of about 5,000 products. This lead to the idea of a “white box” computer which could work symbiotically with humans on large and open ended non-mathematical problems. In effect the system is a pattern recognition system rather than the rule based approach of the conventional “black box” computer.

What is clear to me is that Jeff’s model of what neurons can actually do, and my model of what they need to be able to do to handle complex real world information problems is very similar. If it is agreed that we are both modelling the same thing it means that in 1970 I actually had a crude working model of how humans process concepts (but not down to the neuron interface level). However that was the year I was declared redundant because the work was not compatible with the way my employer thought computers should be going.

I moved to a university and by 1988 I had a very much more powerful model, but was reluctant to start shouting “Eureka” because I knew I still had many issues to solve – and I am naturally a quiet backroom boy type of scientist who was not interested in being in the limelight. At that time I appeared to be close to a break-through with a working package being trial marketed and attracting rave  reviews, and a paper accepted in the top UK computing journal, However I was getting exhausted from banging my head against the computer establishment brick wall for years. At the same time a new head of department made it repeatedly very clear he thought I was grossly incompetent because I had not got any research money into the department in recent years.  (This was because for some years my research had been seriously disrupted by my daughter’s illness and eventual death.) Basically I folded and allowed myself to be declared redundant again (but this time with a pension) and I decided to abandoned academic life to do voluntary work helping the mentally ill.

Many years later and now very much an old age pensioner my son sensibly asked what he should do about the piles of papers (which include everything from the research project) should he find himself having to clear the house. Reviewing the options he mentioned the word “skip.” As a result I decided that I should look online to see what had happened since 1988 and realised that my research might still be of interest. I set up a blog and uploaded some of the key publications online. I also started to blog my ideas out loud and quickly realised that what I had been doing could be relevant to brain research. Comparatively recently I have worked out how CODIL (the symbolic assembly language of the “white box” computer I was working on) could be re-interpreted in a form that could work on a neural network, and I have also looked at the evolutionary implications of the model.

Clearly this string of comments is not the ideal place to discuss the matter, but if you are interested have a look at the above links and contact me through my blog.

Wednesday, 9 July 2014

Wednesday Science Limerick: Why MSG is added to food

Your food can be bitter or sweet
You sense sourness or salt when you eat
While umami's the flavour
The taste that you savour
When something is really a treat.

Many processed foods contain monosodium glutamate (MSG) and on the packets it is sometimes described as a flavour enhancer.As someone who trained as a chemist I knew that it was the sodium salt of glutamic acid (2-Aminopentanedioic acid if you really want to know) and is one of the amino acids that make up the proteins in our body. However I had no idea why it was added, or how it worked, so I decided to have a dig around on the web - and found an exciting story about taste which I had never learnt at school.

I was brought up to think that our taste buds could detect four different tastes - sweet, sour, bitter and salt, and this was complemented by the sense of smell. However about 100 years ago a Japanese researcher, Dr. Kikunae Ikeda, was trying to find out why a stock made from the seaweed kelp improved the taste of many other foods. He found that the stock contained glutamate and that it provided a distinct taste. This 5th taste is now known as umami, which is a Japanese word (うま味meaning "pleasant savoury taste" and there are special receptors in the tongue that react to the presence of glutamate in the food.

It turns out that there are four kinds of taste receptors, each found in a different parts of the tongue. If you want to dig deep into the technical aspects see the Wikipedia pages on Taste Buds and Taste Receptors.

Filling the Black Hole in Brain Research

Three years ago I posted Brain Storms - 2 - The Black Hole In Brain Research suggesting why there were problems in bridging the gap between the brain's neural network and human intelligence. Earlier this year both the E.U. and the U.S.A. announced multibillion pound projects to try and bulldoze a solution. P.Z. Myers has now posted a blog What are you going to simulate? on Pharyngula and I have posted the following comment, which may be lost among nearly 100 other comments on his site.
The research seems to be working on the assumption that if we knew all the connections we would automatically understand how the brain works and what makes us different to animals. I would suggest that the best way to understand how the brain works may well be to start at the animal end and consider the possible evolutionary pathways. For this reason I agree with P.Z. when he says

 What the hell? We aren’t even close to building such a thing for a fruit fly brain, and you want to do that for an even more massive and poorly mapped structure? Madness!” It turns out that I’m not the only one thinking this way: European scientists are exasperated with the project.

Tuesday, 8 July 2014

Chimpanzee Language - Is it a model for a primative language in early hominids

There has been a lot of online interest in the paper The Meanings of Chimpanzee Gestures by Catherine Hobaiter & Richard W. Bryne, which has just been published in Current Biology. The abstract ends: Here we present the first systematic study of meaning in chimpanzee gestural communication. Individual gestures have specific meanings, independently of signaler identity, and we provide a partial “lexicon”; flexibility is predominantly in the use of multiple gestures for a specific meaning. We distinguish a range of meanings, from simple requests associated with just a few gestures to broader social negotiation associated with a wider range of gesture types. Access to a range of alternatives may increase communicative subtlety during important social negotiations.

The researchers claim that they have decoded 66 different gestures whose meaning is the same whichever ape was making a gesture. For instance if a mother shows the sole of her foot to a baby it means "climb on me", while touching an arm is a request asking to be scratched. Interestingly chewing leaves is an invitation for sexual attention. Apparently several gestures can be strung together to represent more complex exchanges.

For the time being I feel rather frustrated, as the full paper is behind a paywall, and I would really like to assess the strength of the research for myself - rather than being dependent on the first wave of press release news reports. However there has been plenty of earlier work which establishes that a social animals such as the chimpanzee must be communicating, and I am sure that if there are any weaknesses in the current paper comments will soon turn up on various blogs elsewhere. 
Chimpanzee communication signals

However if wild chimpanzees in Uganda have a language of over 50 gestures it is interesting to  think how many gestures (or simple vocal sounds) would an early hunter-gather hominid need to be able to organise hunting by ambush or describing the location of a food source, in addition to normal social interactions. I would have thought a hundred different signals relating to actions and the ability to name a hundred objects would prove a powerful survival tool - and is not much more than appears to have been demonstrated in chimpanzees. Such a language could be far more primitive than the proto-language that is believe to have preceded all modern languages. 

Of course my estimate is only a guess. Has anyone done any research on the size of vocabulary needed to plan and execute a complex hunt?