Sleeping in a dish

Neuroskeptic has an interesting posting (here) on a paper, Key electrophysiological, molecular, and metabolic signatures of sleep and wakefulness revealed in primary cortical cultures, by Hinard and others.

We and other animals regularly lose our normal awake consciousness and go to sleep. Why this happens has been a question for a long time. There are many proposed reasons and many could be correct even at the same time. So we have evolutionary, psychological, and physiological scenerios. Now there is a surprising development.

The ability to mimic sleep in a random network of cultured neurons in a petri dish is surprising. The neuron cultures go to sleep on a sort of circadian timetable. When these neurons go to sleep they can be wakened with a mixture of neurotransmitters and therefore the scientists can produce sleep-deprived neurons. They can look at the difference in the chemistry of well-rested and sleep-deprived neurons.

One change is that lysolipids build up in the neuron cell membranes during the ‘awake’ time and are reduced during the ‘asleep’ time. Lysolipids are harmful to the cells.

So neurons seem to have had a problem for all of their existence. When they communicate they accumulate lysolipid and they need a period of non-communication to rid themselves of this type of chemical.

You will be relieved to know that there is no sign of dreaming in cultured neurons, just slow wave deep type sleep. Here is the abstract:

Although sleep is defined as a behavioral state, at the cortical level sleep has local and use-dependent features suggesting that it is a property of neuronal assemblies requiring sleep in function of the activation experienced during prior wakefulness. Here we show that mature cortical cultured neurons display a default state characterized by synchronized burst-pause firing activity reminiscent of sleep. This default sleep-like state can be changed to transient tonic firing reminiscent of wakefulness when cultures are stimulated with a mixture of waking neurotransmitters and spontaneously returns to sleep-like state. In addition to electrophysiological similarities, the transcriptome of stimulated cultures strikingly resembles the cortical transcriptome of sleep-deprived mice, and plastic changes as reflected by AMPA receptors phosphorylation are also similar. We used our in vitro model and sleep-deprived animals to map the metabolic pathways activated by waking. Only a few metabolic pathways were identified, including glycolysis, aminoacid, and lipids. Unexpectedly large increases in lysolipids were found both in vivo after sleep deprivation and in vitro after stimulation, strongly suggesting that sleep might play a major role in reestablishing the neuronal membrane homeostasis. With our in vitro model, the cellular and molecular consequences of sleep and wakefulness can now be investigated in a dish.

The cause question

Someone on a television nature program says something like, “the stag feeds, he needs to eat well in preparation for the mating season.” My husband’s anger rises and he shouts at the screen that the stag eats because it is hungry and is not thinking about preparation for the mating season. And I answer that what the stag thinks or feel has nothing to do with the ’cause’ of his action, they are the ‘how’ not the ‘why’. The why is the probability of success in mating, the how is the chain of – being in good shape by eating well due to hunger etc. We have this argument often. I admit that the voice-over was not that clear and could be misinterpreted but I will not accept that the commentary was wrong. The, THE, cause of biological behaviour is evolutionary and not about mental activity. The mental activity is the means.



I was reminded of this difference in how to look at cause, when I read a blog posting on sleep. It was Bora Zivkovic’s blog in the Scientific American (here). He was pointing out that the primary reason for the evolution of sleep is to be inactive when it is dangerous to be active.

Let me put it simply: sleep makes you sit still and be quiet at times when it is dangerous to move around and there is nothing else important to do. All the other functions were added later due to either timing (some things are better done at certain times of day that coincide with either sleep-time or wake-time and the two processes get linked) or particular brain states (i.e., some functions, for instance the consolidation of memory, are easier to perform at times when the brain is NOT receiving much input from the outside environment):

The theory does not so much contradict other theories about the role of sleep as much as place them in context: “What I am saying is that it is not that sleep has been adapted to allow some vital function to be fulfilled, but the core function of sleep is to adapt animals to their ecological niche,” Siegel said. “Given the animal is inactive for a certain period of the day, certain functions will migrate to that period because it is more efficient” to perform them at that time.


So I wonder, what about consciousness? Is it something that has been added to the non-sleep state after sleep was established? Or was it something that existed that has been migrated out the sleep period to be concentrated in the wake period? After all, an organism could be inactive but still aware. Awareness would be not very useful during enforced inactivity but could become more elaborate if confined to the period of activity. We have no answers of course but they are interesting questions.


(This is this blog’s fourth birthday – it does not seem that long)



Dreaming update

Note: Sorry this is short and late. I am having computer problems. Encephalon is back – #81 is at

Christof Koch has written an article on dreaming for the Scientific American ( here ). It discusses common ‘facts’ about dreaming that have been shown to be in error. This put a different light on the relationship between dreaming and consciousness.

  1. There is not an absolute mapping between REM sleep and dreaming. Non-REM dreams are more static snapshots then narratives in the first person – but not always. Sleepwalking dreams are during non-REM sleep (not too surprising as REM sleep includes a sort of paralysis.

  2. The pons in the brainstem is required for REM sleep but not for dreams. Areas in the temporoparietal-occipital junction in the neocortex are required for dreaming.

Further, we do not smell during dreams, like we see, hear, touch. This fits with our low awareness of smell in consciousness. And there are many more interesting observations in the article, so I recommend reading it.

“they (dreams) bear witness that the brain alone is sufficient to generate consciousness. We dream with eyes shut in the dark, disconnected from the outside world. The brain regions responsible for basic sensory perception are deactivated. Nor is behavior necessary, as we are motionless except for our breathing and eye movements”

Turning off consciousness

Mind Hacks (here) has reported on a recent study of how the brain goes to sleep. M. Magnin and his group asked permission of patients with inserted electrodes (in preparation for epilepsy surgery) to record from the electrodes during normal activities. In this case the activity was falling asleep.

They found that as people drifted off to sleep, the deep brain area the thalamus wound down several minutes before the cortex. This is surprising because the thalamus has traditionally been considered a structure that regulates alertness and ‘relays’ information to the rest of the brain from the body and the spinal cord. It was often assumed that it would ‘shut down’ the cortex first, because this is often considered to be where our ‘higher’ conscious functions like abstract thought and complex perception lie, while continuing with its minimal vigilance functions. A bit like a neural ‘standby’ setting. Instead, what seems to happen is that the thalamus ‘disconnects’ itself and leaves the cortex freewheeling before it finally settles down into inactivity. Indeed, freewheeling is, perhaps, a good description here. The researchers found lots of uneven activity in the upper brain areas as they were left to drift off. Interestingly, sleep onset is one of the times when we are most likely to experience hallucinations. In fact, they are so common as to have been given their own name – hypnagogic hallucinations – while this drifting off period is known as hypnagogia.

How interesting.

What goes on in dreams?

With our senses more or less turned off, where do the conscious-like ‘perceptions’ of dreams come from?


Science Daily reported Nov 16 2007 on McNaughton and Euston’s research:

“…during sleep, the reactivated memories of real-time experiences are processed within the brain at a higher rate of speed. That rate can be as much as six or seven times faster (than) “thought speed.”

Memory stores patterns of activity in modular form in the brain’s cortex. Different modules in the cortex process different kinds of information – sounds, sights, tastes, smells, etc. The cortex sends these networks of activity to a region called the hippocampus. The hippocampus then creates and assigns a tag, a kind of temporary bar-code that is unique to every memory and sends that signal back to the cortex.

Each module in the cortex uses the tag to retrieve its own part of the activity. A memory of having lunch, for example, would involve a number of modules, each of which might record where the diner sat, what was served, the noise level in the restaurant or the financial transaction to pay for the meal.

But while an actual dining experience might have taken up an hour of actual time, replaying the memory of it would only take 8 to 10 minutes. The reason… is that the speed of the consolidation process isn’t constrained by the real world physical laws that regulate activity in time and space.

The brain uses this biological trick because there is no way for all of its neurons to connect with and interact with every other neuron. It is still an expensive task for the hippocampus to make all of those connections. The retrieval tags the hippocampus generates are only temporary until the cortex can carry a given memory on its own…

The initial creation of the tag is made through existing connections. In order to do the rewiring necessary to have the intermodular connections carry the burden takes time. What you have to do is reinstate those memories multiple times. Every time you reinstate the memory, the modules make a little shift in the connection . . . something grows this way, grows that way, a connection gets made here, gets broken there. And eventually, after you do this multiple times, then an optimal set of connections gets constructed…

His previous research has show that cells that fired during activity prior to sleep, also fired in the same sequential patterns during sleep. During sleep, the hippocampus sends little, 100-millisecond bursts of activity to the cortex as much as three times per second.”


This may be a way to explain dreams. There are other ways too. In this hypothesis, memories are first stored in a consciousness like form, a working memory. Then they are stored in a temporary form in the hippocampus, and then during sleep they are ‘replayed’ until they are stored in throughout the cortex. This ‘replaying’ produces dreams (at least if you are awoken during the process). The hippocampus probably has a limited capacity to store unconsolidated memories and therefore sleep is required at some point or the memories begin to be lost.


The hippocampus is essentially the edge of the cortex in the temporal lobe region and it is associated with two important functions: forming new memories / consolidating recent ones, and processing spatial information. People without an intact pair of hippocampi suffer anterograde amnesia, variable retrograde amnesia and an inability to navigate through a cognitive spatial map. 


Shared workspace

When we imagine something fictitious or remember something that happened, it is very much like experiencing it now. It is not an identical conscious experience but very similar. Things can slip from the future to the present to the past without much change in them. Even dreams, which are none of these things, seem to be constructed with the same building blocks. It is as if the brain uses the same workspace, tools, methods and materials whether it is constructing a fantasy, a forecast, a perception, a memory or a dream.


Two differences between dreams and the other experiences is that dreams do not seem to have the same narrative sense and they are not usually remembered. Sensory input is inhibited, action is inhibited and the brain seems to just free wheel in a state that is protected from the real world. What is going on is a mystery but probably it is a form of essential neural housekeeping.


Windt and Metzinger’s contribution to The New Science of Dreaming:

“…dreams are conscious experiences because they can be described as the appearance of an integrated, global model of reality within a virtual window of presence. From a purely phenomenological perspective, dreams are simply the presence of a world. On the level of subjective experience, the dream world is experienced as representing the here and the now. And even though it is a model constructed by the dreaming brain, it is not recognized as a model, but is experienced as reality itself. Put in philosophical terms, one can say that the reality-model created by the dreaming brain is phenomenally transparent; the fact that it is a model is invisible to the experiential subject.

Of course, the same point can also be applied to waking consciousness: even in wakefulness, our experience of the external world is mediated…since we never recognize that the reality-model experienced in wakefulness is, in fact, a model, we have the impression of being in direct contact with external reality – we live our lives as naïve realists. In this very general sense, the conscious experience of dreaming is no different from waking consciousness.”


The fact that waking consciousness must be turned off before dreaming consciousness begins and the fact that we cannot be conscious of more than one reality at a time in waking consciousness does imply that the same neural machinery is used to construct all types of consciousness.