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Archive for December 2008

Summary of posts to the end of 2008

This blog has been going for a little over 6 months; it is coming to a new year; so I intend to do a little housekeeping. The object is a make it easier for my visitors to find what they want among the posts. I have made a list of general ideas/questions that I am trying to investigate, and then, for each heading, I list the posts that apply to that idea.


Purpose of the blog

The aim of this blog is to prepare people for the revolution that is going to happen soon in neuroscience. The very first post (1 Jun aims ) outlined the scope of the blog. The aims are enlarged on later in (10 Aug scientific shocks). To give an indication of the type of material that was intended in the blog an early post gave a list (12 Jun what do we know about consciousness) and another gave probable functions (2 Jul does sconsciousness have a function). Putting consciousness in context was the purpose of  (9 Oct one way to look at consciousness).


A different way to look at consciousness

Some posts have been specifically written to help people come to grips with a different way of viewing their mental life. These posts hardly contain any quotes or links to scientific material. I have used some descriptions of my own way of seeing myself: (6 Jun living without a conscious mind) (10 Jul decisions) (15 Aug who is watching) (18 Oct why make problems) (15 Nov metaphors for consciousness) (30 Nov metaphor) (15 Dec a few definitions)   


Some posts look at more specific problems in understanding consciousness

·        The question of how qualia or the quality of our experience is produced has been a problem, especially for philosophers. (13 Jun why not) (21 Sep the wrong questions)  

·        Consciousness includes awareness of fringe events. (25 Oct a certain feeling) (12 Nov fringe consciousness) (3 Dec confidence)  

·        There is also a problem of what to do about free will. M Gassaniga has put forward the idea of an interpreter that makes sense of our actions. (26 Jul the interpreter) Other posts on this subject:  (17 Sep the problem of free will) (15 Oct a feeling of will) (31 Oct virtual agency) (3 Nov Llinas) (6 Nov more Llinas) (18 Nov decisions without frontal lobe activity)  

·        A spatial construction is basic to consciousness. (19 Aug  the 3D world) (30 Sep built-in sat-nav)

·        There is one is probably one mechanism for various types of awareness. (4 Sep shared workspace) (8 Sep what goes on in dreams) (3 Oct consciousness in Zen meditation) (21 Nov default network) (9 Dec hypnosis) Thinking can be different when it does not have to be tied to awareness of the thinking. (27 Sep eureka)  

·        An important question is how we live in the present when it takes time for the brain to process information and render it part of consciousness. (24 Jun living in the present) Changizi explains some visual illusions by projection into future (26 Aug living in the present 2) It affects tennis refs (9 Nov prediction).  Not only does it take time to produce conscious experience, the process is like frames of a movie, so it is discontinuous rather than being continuous. (19 Jul watching the movie)

Old ideas that get in the way

There are ways of thinking that interfere with understanding the brain. (12 Dec a different angle)  

·        Some people take the metaphor between computers and brains a little too seriously. (19 Jun brain-computer metaphor)

·        Many people are resistance to there being a continuity between our brains and those of other animals. (4 Aug are animals conscious?) (23 Aug a birds eye view) (28 Oct dogs) (24 Nov Occams razor and rules of thumb) (12 Dec hangover from the Great Chain of Beings)  (27 Dec not just a few animals)

·        I have encountered a strict identification of language with consciousness that I think is counterproductive. (7 Aug the inner voice) (24 Sep unconscious meaning).

·        A leftover from Freudian theories is a distrust of unconscious thinking. (6 Oct bad press for unconscious)

·        The idea that the neo-cortex is the only part of the brain involved in producing consciousness is counter production. The thalamus as well as the cortex is important in producing consciousness (11 Sep Grand Central Station)  (21 Dec thalamus waves)


Some ‘how’ hypotheses

There are some hypotheses that seem very convincing. So far we have taken a quick look at the following:

·        Bayesian calculations create consciousness. (2 Jun is the brain bayesian) (24 Dec  Friston’s law ) looked at the possibility put forward by K Friston.

·        R Rensink has a hypothesis that there are two aspects of consciousness, the big picture without detail and the focus with a few items in detail. (29 Jul change)

·        R Llinas puts forward a hypothesis that the thalamus controls consciousness (6 Dec yet more Llinas)   

·        My own hypothesis for many years has been massively parallel overlapping feed back loops within the cortex and between the cortex and the thalamus. (4 Jul ambiguous perceptions) (14 Sep feedback)


Miscellaneous bits and pieces

(23 Jul smell is different),  (30 Aug do grandmother cells fly?), (12 Oct metaphor to embodiment), (22 Oct the homunculus problem), (27 Nov not inside us)  

Not just a few animals

Article in the Scientific American Mind site by Paul Patton on intelligence in animals, One World Many Minds, talks about goldfish learning mazes with the skill that rats show.

“By performing tests on goldfish after parts of their forebrain had been destroyed, the Spanish team showed in a study published in 2006 that the spatial abilities of goldfish derive from a part of the roof, or pallium, of the forebrain that may correspond to the hippocampus in mammals. Together these new studies indicate that the common ancestor of cartilaginous fishes, bony fishes and land vertebrates may already have possessed a hippocampuslike structure and the spatial cognitive abilities it confers. The hippocampus, which is also involved in processing emotions, is the main pallial component of the limbic system; in MacLean’s triune brain scheme, it was supposed to have originated with mammals. A variety of other limbic system structures are now known to exist in nonmammals.”

Goldfish are part of the teleost fishes that first evolved 200 million years ago - and well after land vertebrates appeared. Their brain structures therefore developed independently from those of the land vertebrates from common early fish structures. The two main branches of land vertebrates have evolved separately for about 300 million years. The one branches evolved into modern mammals and the second into birds and modern reptiles. They have evolved different brain plans, again based on the plan of their common ancestors. The difference in anatomy was first interpreted mistakenly so that it was thought that birds and reptiles did not have a well developed pallium. It is now known that the dorsal ventricular ridge in birds and reptiles is a pallium structure and is similar in function to the mammalian pallium structure, the cortex. Both the cortex and the DVR are involved cognition, planning, learning, remembering, perceiving, and controlling fine movements. Similar connections with other areas of the brain and between areas within the pallium are found in the cortex and the DVR. The neuroanatomical terminology for birds was revised in 2002 to reflect this new understanding.

“Far from being “birdbrains,” our feathered friends have displayed clever behaviors. Among birds, the largest forebrains are those of parrots and corvids (a group that includes crows, jays, ravens and jackdaws). Relative to body size, the brain of a parrot is as large as that of a chimpanzee, although, in absolute terms, it is about the size of a walnut. In recent years researchers have documented stunning cognitive abilities in these two groups of birds.”

In another Scientific American Mind site item by Nicole Branan there is a report on self-awareness in magpies, Magpies Recognize their faces.

“When you look in the mirror, you know you are seeing yourself. Your dog, on the other hand, thinks its reflection is a fellow canine (if anything). So far scientists thought this lack of self-recognition was ubiquitous in the animal kingdom—with the exception of apes, elephants and dolphins. But a new study presents evidence that self-recognition has also evolved in a bird species.

Helmut Prior of Goethe University in Frankfurt, Germany, and his team tagged magpies with a brightly colored mark below their beaks, where the birds could not see it directly. When the magpies looked in the mirror, some of them tried to reach the mark with their beak or touch it with their foot, which shows that they recognized their own mirror image, the researchers say.”

If that isn’t enough, we also have the invertebrates. Some such as the octopus long known to be quite intelligent with some remarkable talents. But now there are indications that bees may have some consciousness. A Scientific American Mind site article by Christof Kock looks at the talents of bees,

Exploring Consciousness through the Study of Bees.

“And contrary to assertions made by philosophers, novelists and other literati, by and large this stream of consciousness does not relate to quiet self-reflection and introspective thoughts. No, most of it is filled with raw sensations… I suspect this feeling is not that dissimilar to the way animals consciously experience their world. Except perhaps for the great apes and a few other privileged big-brained animals, most species do not posses the highly developed sense of self, the ability to reflect on oneself, that people have. Most biologists and pet owners are willing to grant consciousness to cats, dogs and other mammals. Yet our intuitions fail us completely when we consider fish and birds, let alone invertebrates such as squid, flies or worms. Do they experience the sights and sounds, the pains and pleasures, of life? Surely they can’t be conscious—they look too different from us, too alien.

Insects, in particular, were long thought to be simple, reflexive creatures with hardwired instinctual behaviors. No more. Consider the amazing capabilities of the honeybee, Apis mellifera….”

Experiments are described using glass mazes and sugar-water rewards that show that bees can be taught to run glass mazes using the delayed matching-to-sample paradigm. For example, the bee can be shown a green patch and will remember this in the maze and will turn right if the T has a green patch and left if it has a different colour. Having mastered this skill it can quickly learn to run a maze with different colours to match and with different stripe patterns.  

“Bees live in highly stratified yet flexible social organizations with group decision-making skills that rival academic, corporate or government committees in efficiency. In spring, when bees swarm, they choose a new hive that needs to satisfy many demands within a couple of days (consider that the next time you go house hunting). They communicate information about the location and quality of food sources using the waggle dance. Bees can fly several kilometers and return to their hive, a remarkable navigational performance. Their brains seem to have incorporated a map of their environment. And a scent blown into the hive can trigger a return to the site where the bee previously encountered this odor.

…What this dilemma highlights is that there is no accepted theory of consciousness, no principled theory that would tell us which systems, organic or artificial, are conscious and why. In the absence of such a theory, we must at the very least remain agnostic about consciousness in these creatures.”

It seems to me easier to explain the intelligent actions of animals if they have some form of consciousness then if they haven’t.

Friston’s Law

The New Scientist magazine had an article by G Huang about Friston’s theory,

is this a unified theory of the brain.

“…The brain is much messier than a physical system. It is the product of half a billion years of evolution. It performs myriad functions - reasoning, memory, perception, learning, attention and emotion to name just a few - and uses a staggering number of different types of cells, connections and receptors. So it does not lend itself to being easily described by simple mathematical laws. That hasn’t stopped researchers in the growing field of computational neuroscience from trying. In recent years, they have sought to develop unifying ideas about how the brain processes information so that they can apply them to the design of intelligent machines.

Until now none of their ideas has been general or testable enough to arouse much excitement in straight neuroscience. But a group from University College London may have broken the deadlock. Neuroscientist Karl Friston and his colleagues have proposed a mathematical law that some are claiming is the nearest thing yet to a grand unified theory of the brain. From this single law, Friston’s group claims to be able to explain almost everything about our grey matter…

Friston’s ideas build on an existing theory known as the “Bayesian brain”, which conceptualises the brain as a probability machine that constantly makes predictions about the world and then updates them based on what it senses…”The brain is an inferential agent, optimising its models of what’s going on at this moment and in the future,” says Friston. In other words, the brain runs on Bayesian probability…

This is where Friston’s work comes in. In the 1990s he was working next door to Hinton. At that time Hinton was beginning to explore the concept of “free energy” as it applies to artificial neural networks. Free energy originates from thermodynamics and statistical mechanics, where it is defined as the amount of useful work that can be extracted from a system, such as a steam engine. It is roughly equivalent to the difference between the total energy in the system and its “useless energy”, or entropy.

Hinton realised that free energy was mathematically equivalent to a problem he was familiar with: the difference between the predictions made by an artificial neural network and what it actually senses. He showed that you could solve some tough problems in machine learning by treating this “prediction error” as free energy, and then minimising it…

Friston developed the free-energy principle to explain perception, but he now thinks it can be generalised to other kinds of brain processes as well. He claims that everything the brain does is designed to minimise free energy or prediction error. “In short, everything that can change in the brain will change to suppress prediction errors, from the firing of neurons to the wiring between them, and from the movements of our eyes to the choices we make in daily life,” he says.”


Thalamus waves

Here is more from that article in the New York Times about Rodolfo Llinas’ by Sandra Blakeslee (here). This part is about conditions that appear to involve the loss of thalamus driven brain waves.

“When the brain is awake, neurons in the cortex and thalamus oscillate at the same high frequency, called gamma…. .Such coherent activity allows you to see and hear, to be alert and able to think…But at day’s end, cells in the thalamus naturally enter a low-frequency oscillation… .You fall asleep. Your brain is still tapping out slow rhythms, but consciousness is suspended.

So if a small part of the thalamus gets permanently stuck at a low frequency, or part of the cortex fails to respond to the wake-up call, Dr. Llinás said, an abnormal rhythm is generated, a so-called thalamocortical dysrhythmia….a maintained, abnormal low frequency in a part of the brain can generate what is called an attractor. Think about a tornado. It’s just wind that is turning on itself. In doing so, it becomes a thing that, while made out of air, has a life of its own.

“A thalamocortical dysrhythmia also has a structure. It is a thing. And it leads to the symptoms seen in a wide variety of brain diseases.”

Dr. Llinás believes that these disrupted rhythms can be set off by a variety of causes — faulty genes, brain injury, chemical imbalance…. dysrhythmias can be treated with deep brain stimulation, drugs or tiny surgical lesions that return brain oscillations to normal, he said. The goal is to wake up parts of the brain that have fallen into low-frequency sleep mode.

In Parkinson’s, chemical changes send bits of the thalamus into a low-frequency mode. If the affected part of the thalamus connects to the brain’s primary motor center, a slow tremor, at four cycles per second, appears. The patients shake at the same frequency as the oscillating motor thalamus.

If the abnormal bit of thalamus connects to a region that plans movements, the patients cannot initiate movement.

And if the piece of thalamus is involved in making smooth movements, the patients experience increased muscle tone. They become rigid.

Dr. Llinás says a patient can experience several of these symptoms or only one, depending on the site of the abnormal rhythm. By the same token, he says, normal function can be restored by acting on the right spot.

Deep brain stimulation, in which slender electrodes are implanted directly into the cortex or thalamus, has been used in 40,000 patients around the world, mostly for movement disorders, and is now being tried for schizophrenia, epilepsy, Tourette’s syndrome, dystonia, chronic pain, depression, phantom pain and traumatic brain injury.”


The interesting thing here, for our concern with understanding consciousness, is that the thalamus appears to control the existence of consciousness. It may also control the focus and nature of the conscious experience.

A different angle

Many people come to look at the brain from some variation on a particular set of preconceived attitudes.

  1. Most and all important thinking happens in the neo-cortex.
  2. There are two independent thinking systems: unconscious and conscious.
  3. There is a big divide between how humans think and how animals think.
  4. Introspection is a trustworthy means to understand ‘conscious thought’.
  5. Without human language it is not possible to have concepts.
  6. It is impossible to have morality and responsibility without free will and impossible to have free will without a ‘conscious mind’.


All of these notions are probably false. They may not be but they certainly can be mistaken. The important thing is to keep an open mind when interpreting research results. It hampers us to carry Freud, Descartes, Chomsky and others like millstones around our necks.


The more reasonable way to look at things can be laid out.

  1. The whole of the forebrain and parts of the midbrain are important in normal thinking. In particular the cortex does not work without the thalamus and vice versa. The more ancient parts of the cortex, such as the hippocampus, are extremely important to thought and memory, not just the neo-cortex.
  2. Being conscious of thoughts should not be confused with the actual thinking any more than being conscious of a tree should be confused with the actual tree. It may be that there is one undivided thinking process and that we are aware of some of the process but not all of it (or even most of it).
  3. In evolutionary history, we have only recently, diverged from our sister species. There is no reason our brains differ in kind, rather than degree, from other animals.
  4. Introspection may be largely an exercise in spin or self deception. We would not know if it was from within introspection.
  5. There is non-verbal thinking even though some people resist and downplay the idea. You can think something and not be able to find words to express the idea.  
  6. We make decisions and that should be sufficient for owning our actions and accepting responsibility for them. What that means morally and legally needs to be decided as it has been in the past. Conscious free will is a red herring.

A few definitions

I am not a great one for coining new terms. But when talking about consciousness, the existing terms can have a variety of meanings and so using them can mislead. So…I am going to give my readers some definitions of how I use some very vague words. That does not mean that I disapprove of other meanings for the words – I am just trying to clarify how I have been using them.


Reality and Model/s of Reality:

This is like the pair of concepts that

Hang-over from the Great Chain of Beings

 “Medieval naturalists placed living things along a linear scale called the great chain of beings, or scala naturae. This hierarchical sequence ranked creatures such as worms and slugs as lowly and humans as the highest of earthly beings. In the late 1800s the enormous mass of evidence contained in Charles Darwin’s masterwork, On the Origin of Species, convinced most of his scientific contemporaries that evolution was a reality. Darwin explained that modern species were related by physical descent and saw the relations among species as resembling the diverging branches of a family genealogical tree.”


This quote is from Scientific American Mind Article . The idea of the chain of beings lingered on. The immediate interpretation of evolution was ‘humans are descended from monkeys’ when it should have been ‘humans and monkeys have a common ancestor’.


“Over the past 30 years, however, research in comparative neuroanatomy clearly has shown that complex brains—and sophisticated cognition—have evolved from simpler brains multiple times independently in separate lineages.”


We do not just need to look at what other mammals can do with their brains but also birds, fishes, mollusks and even insects. In our outlook on other animals we should teach ourselves not to think in terms of the ‘chain of beings’. In a sense all living things with us today are approximately the same in terms of newness or oldness, and approximately the same in terms of being well adapted to their environment. There is no clear criteria for ranking species into higher and lower along a chain of beings. Some are bigger, some are faster, some of smarter, some can stay under water longer, some are more fearsome, some are better fliers, some live longer, some have more offspring, some have larger ranges, maybe some are happier, but all of them are approximately equally successful.


Is hypnosis a distinct form of consciousness? It isn’t that special according to an article in Scientific American Mind. (here). Lilienfeld and Arkowitz also point to a number of false beliefs about hypnosis.

“…having failed to find reliable markers of trance after 50 years of careful research, most researchers have concluded that this hypothesis [that hypnosis is a unique state of consciousness] has outlived its usefulness. Increasingly, evidence is suggesting that the effects of hypnosis result largely from people’s expectations about what hypnosis entails rather than from the hypnotic state itself. …”


They list a number of misconceptions: relaxation is not necessary and people have been hypnotized while pedaling vigorously on a stationary bicycle; subjects are awake not asleep; subjects can resist suggestions and are not mindless automatons; posthypnotic amnesia only occurs when subjects expect it; literalism is not displayed to any higher degree than in people simulating hypnosis; trance logic is also a function of people’s expectations; the increased theta band activity is probably due to quiet concentration; increased anterior cingulated cortex activity is present whenever contradictions are perceived; suggestibility is only increase by something like 10%.


Perhaps the only thing that is happening is that when we guess as to the reasons for our actions, we make a different sort of guess when we think we are in a ‘hyponotic trance’ then we would make normally.


Yet more Llinas

There has been an article in the New York Times about Rodolfo Llinas’ ideas (here). I have blogged before about his insights – they are worth many visits. Here is part of the NYT piece by Sandra Blakeslee.


“Dr. Llinás, the chairman of neuroscience and physiology at the N.Y.U. School of Medicine, believes that abnormal brain rhythms help account for a variety of serious disorders, including Parkinson’s disease, schizophrenia, tinnitus and depression. His theory may explain why the technique called deep brain stimulation — implanting electrodes into particular regions of the brain — often alleviates the symptoms of movement disorders like Parkinson’s.

…Unlike neuroscientists who study the brain’s outer layer, or cortex, he has focused his attention on the thalamus, a paired structure in the midbrain. He has found that each walnut-size thalamus has 30 or more nuclei, each of which specializes in one type of information collected from the senses — sights, sounds, movements, external touches, internal feelings and so on.

Each nucleus sends its message to a specific area of the cortex for initial processing. But then the information is shuttled back down to the thalamus, where it is associated with other senses. And then it is returned to the cortex in a richer, multisensory form that is constantly elaborated, reverberating into a symphony of life experiences.

The thalamus and cortex work dynamically by passing loops of information back and forth, Dr. Llinás said. “If you think of the brain as an orchestra, the thalamus is the conductor. The players are in the cortex. When the conductor makes a move, the players follow. The conductor then hears their sounds and makes new moves, resulting in a continuous dialogue.”

Cells in the thalamus and cortex rely on intrinsic electrical properties to keep the music going. “Groups of neurons, millions strong, act like little hearts beating all their own,” Dr. Llinás said. They can oscillate at multiple frequencies, depending on what is happening in the outside world.

When the brain is awake, neurons in the cortex and thalamus oscillate at the same high frequency, called gamma. “It’s like a Riverdance performance,” Dr. Llinás continued. “Some cells are tapping in harmony and some are silent, creating myriads of patterns that represent the properties of the external world. Cells with the same rhythm form circuits to bind information in time. Such coherent activity allows you to see and hear, to be alert and able to think.”

But at day’s end, cells in the thalamus naturally enter a low-frequency oscillation. They burst slowly instead of firing rapidly. With the thalamus thrumming at a slower rhythm, the cortex follows along. You fall asleep. Your brain is still tapping out slow rhythms, but consciousness is suspended….” 

This is a very convincing description to me. This is probably because it seems close to the MPOFBL idea – massively parallel over-lapping feedback loops.


A few months ago there was an item in ScienceDaily (here), Neuroscientists Glimpse How The Brain Decides What To Believe. This deals with that is probably the source of a fringe feeling in consciousness indicating how sure we are of some idea.

‘You’re driving to a restaurant for the very first time. At a crossroads, you make a turn. You drive for several minutes, and then several minutes more. Nothing in sight. The disturbing thought creeps into your mind: “I should be there by now. Did I make the wrong turn?” At what point will you make a u-turn and go back? It all depends on how confident you are of the decision you made at the crossroads. Having a sense of what we know — and don’t know — is a universal human experience, and has often been assumed to be the hallmark of self-consciousness. But new research by neuroscientists at Cold Spring Harbor Laboratory suggests that the estimation of confidence that underlies decisions may be the product of a very basic kind of information processing in the brain, shared widely across species and not strictly confined to those, like us, that are self-aware.

…They found that neurons in a part of the brain known as the orbitofrontal cortex (an area of the brain found in both rats and humans) signal the uncertainty of the decisions,… “We tested several alternative explanations but the best explanation for the neural activity we observed was that these neurons were signaling the confidence of the animal about its decisions.”… This showed that they could not only calculate their level of confidence in a given decision, but also use that calculation in subsequent decisions to guide behavior… Taken together, these experiments reveal “that confidence estimation is not a complex function specific to humans but a core component of the process of decision-making probably found throughout the animal kingdom,”…’