Monthly Archives: July 2016

Why sleep

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It would be surprising if there were a single function for sleep, but there are often articles implying that the mystery is solved and THE reason for sleep has been found. Recently there was one in the New Scientist which prompted my post (https://www.newscientist.com/article/2096921-mystery-of-what-sleep-does-to-our-brains-may-finally-be-solved/).

We can look logically at reasons why we sleep. For any biological behaviour or process, there can be a spectrum of causes. At the one end of the spectrum are the ultimate causes – the evolutionary reason, the function being carried out, and the ‘why’. At the other end are the proximate causes – the individual immediate cause, the trigger, and the ‘how’.

The thing that seems the most distance and universal ultimate cause is probably that it is evolutionarily difficult to be well fitted to two dissimilar niches at the same time. There are animals that are active in the day and adapted to that; they hid and conserve their energy at night because they are not adapted to night. Or an animal can be adapted to night and hid in the day. This idea applies to animals that hibernate through a cold season every year to which they are not well adapted. There are animals that go dormant in dry seasons and are active when it is wet. It would be a good bet that all other functions of sleep are built on this mechanism of being inactive during recurring periods. Sleep is widespread amongst animals.

If there is an inactive time, that is the time to do all the things that cannot be done easily when active. Growth and repair would be immensely easier during rest. Imagine growing new muscle cells in a walking leg – much easier to wait until the leg is not moving. Growth and repair is best done on all the organs when they are just ticking over at most. This would include any maintenance needed in the brain.

These ultimate causes produce, during evolution, a proximate mechanism: an oscillating function that produces drowsiness and than sleep and followed by awakening and activity. Hormones and signals can work this rhythm without triggers, but do use light and darkness to get the timing right. The mechanism also affects the working of the body to make it suitable for growth and repair – the temperature, heart and breathing rates and many hidden levels have different sleep and wake settings. This sort of mechanism causes sleep but it is the ‘how’ of sleep not the ‘why’.

The brain is a complex organ with many functions. It is not a simple concept to say that the brain is inactive, resting and recuperating. There may be many processes in the brain taking advantage of sleep; there are a number of different types of sleep which obviously have different functions.

One function that has been investigated is waste removal. During parts of sleep some of the brain cells become physically smaller and this allow the movement of liquid through the brain, clearing out waste. It probably would interfere with the working of the brain to have cells temporarily lose volume – better to do this during sleep.

Another function that sleep houses is REM phase/dreaming. Dreaming is not completely understood but it is clearly needed for the successful integration of new memories into the web of established memories in the cortex. In this process the memories seem to be partially activated and re-experienced in combination with previous memories. For this process to be safe (without sleep walking or worse) the brain disconnects the possibility of skeletal muscle movement. This paralysis could only be acceptable in the safe inactive state of sleeping.

Another function that is known but not completely understood is the resetting of the brain’s level of activity. This is the one outlined in the NewScientist article. Consider that during the day, there has been continuous firing of neurons as a result of continuous signaling through the synapses of the brain. The synapses that are not used do not lose any strength while the ones that are used increase in strength. We end the day with a very excitable brain. During sleep this is brought down to a lower level to start the next day. All the synapses lose strength so that the new difference between strong ones and weaker ones remains but the overall strength is lower. As a photographic metaphor, it is like lowering the ‘brightness’ while maintaining the ‘contrast’ on a washed out over exposed photo. If this is not done, due to sleep deprivation, then the brain finds it more and more difficult to function. It seems that sleep alternates between strengthening particular synapses and weakening all synapses.

Of course, this is probably only the tip of the iceberg for finding sleep functions in the brain. I would not be surprised at a number of others being identified. There may even be processes that apply to insects but not to humans, as insects can sleep too. That is why an article that implies that there is a single function, THE reason for sleep, and that single reason has finally been found, is annoying. All the causes of, reasons for, functions of sleep are important and unlikely to be all found or understood.

Click bait PR in science

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ScienceDaily reports on a recent paper (Leon Gmeindl, Yu-Chin Chiu, Michael S. Esterman, Adam S. Greenberg, Susan M. Courtney, Steven Yantis. Tracking the will to attend: Cortical activity indexes self-generated, voluntary shifts of attention. Attention, Perception, & Psychophysics, 2016) which looks at the areas in the brain involved in volition. Here is the abstract:

“The neural substrates of volition have long tantalized philosophers and scientists. Over the past few decades, researchers have employed increasingly sophisticated technology to investigate this issue, but many studies have been limited considerably by their reliance on intrusive experimental procedures (e.g., abrupt instructional cues), measures of brain activity contaminated by overt behavior, or introspective self-report techniques of questionable validity. Here, we used multivoxel pattern time-course analysis of functional magnetic resonance imaging data to index voluntary, covert perceptual acts—shifts of visuospatial attention—in the absence of instructional cues, overt behavioral indices, and self-report. We found that these self-generated, voluntary attention shifts were time-locked to activity in the medial superior parietal lobule, supporting the hypothesis that this brain region is engaged in voluntary attentional reconfiguration. Self-generated attention shifts were also time-locked to activity in the basal ganglia, a novel finding that motivates further research into the role of the basal ganglia in acts of volition. Remarkably, prior to self-generated shifts of attention, we observed early and selective increases in the activation of medial frontal (dorsal anterior cingulate) and lateral prefrontal (right middle frontal gyrus) cortex—activity that likely reflects processing related to the intention or preparation to reorient attention. These findings, which extend recent evidence on freely chosen motor movements, suggest that dorsal anterior cingulate and lateral prefrontal cortices play key roles in both overt and covert acts of volition, and may constitute core components of a brain network underlying the will to attend.”

I have not been able to read the original paper but I assume that it is a careful and useful study of how intentions and decisions happen when there is no compulsion involved. It has further evidence of the dorsal anterior cingulate and lateral prefrontal areas being involved in preparation of voluntary action. I assume that the authors do not stoop to ‘click bait’ in the original paper; I assume they use the sort of language that they use in the abstract. The press release put out by Johns Hopkins University is the problem. There are repeated uses of the phrase ‘free will’ and even the phrase “volition, or free will” implying that these words are interchangeable. And ‘free will’ is even used in the title of the press release, which seems like clear click bait to me. There is still debate on whether free will exists and if it does what its mechanism is. Because of this many people would be interested in a scientific paper that deals with free will. Mentioning free will in the PR for the paper is click bait unless the paper actually deals with the subject. Instead the paper seems to be about how decisions prepared and executed. The problem is that the study did not involve any measure of if-when-how the intention or the act was felt in the subject’s consciousness. We do not know what the subjects thought.

There are a number of definitions of free will: in religion it is lack of predestination; in philosophy it is lack of material determination (classic dualism); in jurisprudence it is owning the responsibility for an action (not coerced, accidentally or unconsciously done but in involving conscious intent); in neuroscience it has come to mean a decision taken under conscious control (an action that is started or can be stopped by conscious intent) – very similar to the legal meaning. What the last three have in common is control of intent/execution by conscious thought. Volition is a word without any necessary connection to consciousness. Unless an experiment tracks conscious events as well as other events, it has nothing to say about free will. It can have a great deal to say about volition, decision, intention, motor control, action plans etc. etc. but without involving consciousness, it has absolutely nothing to say about free will. As I said above, I have not been able to read the original paper, but if as I suspect it does not measure or time conscious feelings of intent or execution then its PR is misleading.

Synergy and Modular control

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When we learned the simple overview of the nervous system in grade school, we were taught that the brain sent signals to muscles to contract and that is how we moved. And by brain, we assumed the thinking part up high in the head. But it cannot be so.

A little deer is born and in a very short time is standing and in a little longer is taking its first wobbly step. Within a couple of days it is running and frolicking. Deer are not that special; other animals ‘learn’ to get around very quickly too. Even humans babies, if they are held upright with their feet touching a surface will walk along that surface. In a sense, the spinal cord knows how to walk by lifting and moving forward alternate legs. It does not know how to walk well, but the basics are there. Human babies are slower at managing to get around because they are born at a less developed stage and walking on two legs rather than four is trickier. In all sorts of observations and experiments there is evidence that the ability to walk is innate in the spinal cord and does not require the brain.

The spinal cord has some primitive control modules or muscle synergies. Muscle synergies are present in a number of natural behaviors; they are low-level control networks found in the brain stem and spinal cord that coordinate a group of muscles. They make common movements easier to order up. We have the ‘intent to go over there’ and without any more conscious thought we do it in an automatic way. Now if we had to trigger individual muscles in the right time sequence, it would likely take many hours to get not very far with a number of falls along the way. One could say that we would ‘get the hang of it’ as we did it. But that is saying we would make parts of it automatic (create modules and synergies).

This modularization of motor control is layered. The simplest control is in the spinal cord, but it is modified and adapted to conditions by the brain stem and especially the cerebellum. The cerebellum gets instructions from other parts of the brain and finally these modules within modules are able to execute the simple ‘intention to go over there’.

The synergies in a baby’s spinal cord are an ancient set that is similar of all mammals (probably all land vertebrates). The muscles work in a rhythm where each event triggers the next in a circle. There are two primitives that are involved in human walking that we are born with. One is to bend the leg so that the foot leaves the ground and moves forward then goes back down and straightens. Two is a forward push against the ground by the straight leg. These two complexes of muscle contractions and relaxations are wired so that their action in one leg inhibits their action in the other. When the left leg does one, the right leg cannot do one but can do two. And when the left leg does two, the right cannot do two but can do one. They are also wired so that in each leg it is the end of one that triggers the start of two and the end of two triggers the start of one. It is the same in four legged animals except there is another set of inhibitions between the front and hind legs. At this level it is not very adaptive and can only react to sensory information that comes through the spinal cord from the muscles, joints and skin. Babies cannot use this facility to get around because they do not have the strength to maintain the posture needed with such a large heavy head on such a little body, and more importantly, the spinal cord has no information from the ears about balance. Balance is very important for bipedal walking. The baby must create two other synergies: to react to balance information and to use the hips, back and arms to keep the center of gravity over the legs. In the meantime, when they don’t have the strength, they can crawl using the 4 legged modules.

The cerebellum and brain stem add the control of balance and of pace (there are relative changes to the timing of events when the whole process is sped up). They can correct for uneven ground. They can keep the direction of motion toward a target. But the coordination control of the lower brain is not just direct signals to muscles but uses the synergies built into the spinal cord. And it is much more complex than the action in the spinal cord. In fact, the cerebellum has more neurons that the whole rest of the brain. It manages the modules, timing, adjustments to modules, effects from sensory input and feedback and commands from higher levels of the brain, then packages it all for execution. Another great trick of the cerebellum is to do two things at the same time, say walk and throw a ball. Both may be deep seated modules but there are adjustment to be made where they interfere with one another.

The point I am making here is that although movement seems so easy for us to execute, that is because it is not arranged consciously, or even largely in the cerebral hemispheres. It is modularized so that a simple request in the cerebral cortex goes through layers of calculation and fine-tuning to become individual signals to individual muscles. It is synergy/modularization that gives us this flexible but easy to use system. We are surprised that it is easier to create a program to play chess in the abstract (and win) than it is to program a robot to physically move the pieces and operate the time clock in a game. When we do not understand how something is done, it appears easy. It is a common trap.

 

Metaphors and shapes

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Judith Copithorne image

Metaphors (including analogs and similitudes) appear to be very basic to thought. These are very important to language and communication. A large bulk of dictionary meanings of words are actually old metaphors, that have been used so much and for so long that the words has lost its figurative root and become literal in their meaning. We simply do not recognize that it was once a metaphor. Much of our learning is metaphorical. We understand one complex idea by noticing its similarity to another complex idea that we already understand. For example, electricity is not easy to understand at first but we have learned to understand a great deal about how water flows as we have grown up by watching it. Basic electrical theory is often taught by comparing it to water. By and large, when we examine our knowledge of the world, we find it is rife with metaphors. We can trace many ways we think about things and events to ‘grounding’ in experiences of infants. The way babies establish movement and sensory information is the foundation of enormous trees and pyramids of metaphorical understanding.

But what is a metaphor? We can think of it as a number of entities that are related in some way (in space, in time, in cause-effect, or in logic etc.) to form a structure that we can understand and think of/ remember/ name/ use as a predictive model and treat as a single thing. This structure can be reused without being reinvented. The entities can be re-labeled and so can the relations between them. So if we know water flowing through a pipe will be limited by a narrower length of pipe we can envisage an electrical current in a wire being limited by a resistor. Nothing needs to be retained in a metaphor but the abstract structure. This facility of being able to manipulate metaphors is important to thinking, learning, communicating. Is there more? Perhaps.

A recent paper (Rolf Inge Godøy, Minho Song, Kristian Nymoen, Mari Romarheim Haugen, Alexander Refsum Jensenius; Exploring Sound-Motion Similarity in Musical Experience; Journal of New Music Research, 2016; 1) talks about the use of a type of metaphor across the senses and movement. Here is the abstract:

“People tend to perceive many and also salient similarities between musical sound and body motion in musical experience, as can be seen in countless situations of music performance or listening to music, and as has been documented by a number of studies in the past couple of decades. The so-called motor theory of perception has claimed that these similarity relationships are deeply rooted in human cognitive faculties, and that people perceive and make sense of what they hear by mentally simulating the body motion thought to be involved in the making of sound. In this paper, we survey some basic theories of sound-motion similarity in music, and in particular the motor theory perspective. We also present findings regarding sound-motion similarity in musical performance, in dance, in so-called sound-tracing (the spontaneous body motions people produce in tandem with musical sound), and in sonification, all in view of providing a broad basis for understanding sound-motion similarity in music.”

The part of this paper that I found most interesting was a discussion of abstract ‘shapes’ being shared by various senses and motor actions.

“A focus on shapes or objects or gestalts in perception and cognition has particularly concerned so-called morphodynamical theory … morphodynamical theory claims that human perception is a matter of consolidating ephemeral sensory streams (of sound, vision, touch, and so on) into somehow more solid entities in the mind, so that one may recall and virtually re-enact such ephemeral sensations as various kinds of shape images. A focus on shape also facilitates motion similarity judgments and typically encompasses, first of all, motion trajectories (as so-called motion capture data) at various timescales (fast to slow, including quasi-stationary postures) and amplitudes (from large to small, including relative stillness). But shapes can also capture perceptually and affectively highly significant derivatives, such as acceleration and jerk of body motion, in addition.”

The authors think of sound objects as occurring in the time range of half a second to five seconds. Sonic objects have pitch and timbre envelopes, rhythmic, melodic and harmonic patterns. In terms of dynamics, sonic objects can: be impulsive with an envelop showing an abrupt onset and then decay, or be sustained with a gradual onset and longer duration, or be iterative with rapidly repeated sound, tremolo, or drum roll. Sonic objects could have pitch that is stable, variable or just noise. These sonic objects are related to similar motion objects – objects in the same time range that produce music or react to it. For example the sonic objects in playing a piano piece or in dancing. They also have envelopes of velocity and so on. This reminds me of the similar emotions that are triggered by similar envelopes of musical sound and speech. Or, the objects that fit with the nonsense words ‘bouba’ and ‘kiki’ being smooth or sharp. ‘Shape’ is a very good description of the vague but strong and real correspondences between objects from different domains. It is probably the root of being able to use adjectives across domains. For example, we can have soft light, soft velvet, soft rustle, soft steps, soft job, and more or less soft anything. Soft describes different things in different domains but, despite the differences, it is a metaphoric connection between domains so that concrete objects can be made by combining a number of individual sensory/motor objects which share abstract characteristics like soft.

“In several studies of cross-modal features in music, a common element seems to be the association of shape similarity with sound and motion, and we believe shape cognition can be considered a basic amodal element of human cognition, as has been suggested by the aforementioned morphodynamical theory …. But for the implementation of shape cognition, we believe that body motion is necessary, and hence we locate the basis for amodal shape cognition in so-called motor theory. Motor theory is that which can encompass most (or most relevant) modalities by rendering whatever is perceived (features of sound, textures, motion, postures, scenes and so on) as actively traced shape images.”

The word ‘shape’, used to describe corresponding characteristics from different domains, is very like the word ‘structure’ in metaphors and may point to the foundation of our cognition mechanisms, including much more than just the commonplace metaphor.