Biochemistry 9


the chemistry of awareness


We live on earth in a REAL universe.  But our understanding of that real world is drastically limited to information detected by our senses which provide only very incomplete, sometimes misleading information about our immediate surroundings.  Our nervous system associates together information from our senses, and uses that mechanism to construct memory, understanding, and consciousness.  That is mediated by language which has been developed by nervous systems and passed from one individual to another.  Humans have used their limited understandings to augment their senses with instruments and now computers.  Groups of humans have attempted to select what is considered the most useful information and understanding and pass that to other individuals through what is called education.  But this elaborate process is fraught with problems due to
    • misinterpretation of nerve signals from the senses,
    • incomplete memory and memory losses over time,
    • imperfect mental concepts and ideas used to interpret observation and memory,
    • uncertainties and multiple meanings and implications in verbal language and its usage, and
    • poor selection and communication of what is passed from one individual to others via education.


Most human beings seem to have some level of self-awareness.  But consciousness remains a vague concept.  One experiment investigates if an individual viewing via a mirror an otherwise invisible spot (say on her or his forehead) recognizes that the spot is actually on that individual's self.  Only a few other animals beyond humans have clearly shown such self recognition.

The individual neurons which provide consciousness are roughly as complicated as individual single-cell bacteria which almost certainly lack consciousness.  It appears that consciousness occurs as a result of thousands of such neurons forming memory by associating internally consistent self observations by the sense organs in a collection we label as self.  Such brain activity is currently (at this writing) understood very poorly.  Awareness probably requires the ability to correlate nerve responses via multiple pathways.  For example if you touch your knee with a finger, sensory nerves in both the finger and knee report the touch.  You may also see the location of the contact.  And many other nerves in both the arm and leg may send signals which help indicate locations of each appendage.  The result is the brain constructs a map correlating the multiple signals so that a future touch to that spot on the leg will allow the brain to determine that location on the body.

Early in life when a baby hears itself cry, its brain can correlate sound levels from each ear with visual placement.  Later when the baby hears another person talk and sees that person talking, the brain can correlate differences in sound levels from each ear to widen the concept of location.  Subsequently receiving similar sound levels, the brain is able to assign a location of the sound source compared to the head even without vision.  Such mapping by correlating information from multiple neurons may be the essence of awareness.

Reality verses our perceptions of reality

When information is provided by alternative means, the perception may be less accurate.  It is likely that information provided by language, and other symbols is also incorporated into developing awareness.  While today many people likely believe their thinking brain resides in the top of their heads, earlier cultures perceived such functions resided in the torso or even in extremities.  Since there is little sensory information about the location of such function, it is likely that language provided the basis for those aspects of awareness.  It seems difficulty, perhaps impossible, to form concepts without associated vocabulary.

It is not clear that consciousness is even the same for all humans.  And it is unlikely we all have the same level or amount of consciousness.  Those who understand frames of reference as part of the physics concept of relativity likely find it easy to accept that the awareness of others is different from their own since each person perceives the world from their unique frame of reference.  While all humans possess essentially the same neuron hardware necessary to form consciousness, because each of us has a different collection of experiences, we likely construct different awareness.  That stated, there are likely thousands of similar experiences which can develop nearly equivalent awareness.

Necker CubeSeldom used sensory neurons may send signals which have not previously been well mapped.  For example, people experiencing a heart attack or pain from a gall or kidney stone often report experiencing pain some distance from the location of the actual physical cause.  A damaged shoulder might cause pain perceived to be lower in the arm or even in their finger tips.

Visual awareness experiments suggest that consciousness involves the filling in of incomplete associations.  For example we recognize incomplete shapes where a portion seems to be hidden from view.  (Do you see the cube?  Do you see parts of the white lines extending across the white space?  How many different perspectives do you see?  Is the front of the cube towards the upper left or lower right?  Is the cube behind the holes in a white swiss cheese, or in front of black dots?) We are even more likely to associate such visual objects when they move in unison.  Conversely the study of how we distinguish visual images containing a few differences also provides clues as to what we associate together.  The ability to associate and distinguish are skills that themselves can be honed by practice.  So our consciousness and awareness are themselves learned characteristics of our brains.

Because of the limitations restricting how out brains develop understanding of the world around us, all of us develop what might be accurately described as a fantasy understanding of reality.  Because of the very limited sensory data upon which our understandings are developed and the need to guess or fill in for missing information, our understanding is grossly different from reality in ways we rarely if ever realize.  But to the extent that our fantasy understanding roughly approximates reality, we are able to meet our primary needs and usually survive in this world.  This imperfect and often erroneous understanding guides our every thought and action.  Most people live their lives as if little in their understanding of the world could be significantly improved.  Yet there is abundant evidence that errors in our understanding extending on the individual level from arguments between those we meet and live with to continuing large scale wars.  Our fantasy understanding controls, restricts and empowers our lives.  For example, a young woman who understands she can only be compatible with a skinny 9 foot tall man may never find a boyfriend or spouse.  The restrictions of our fantasy understanding might be appreciated by considering how difficult it is for most people to find a spouse they can live happily with for the rest of their lives.  (Were it not for restrictions our fantasies place upon us, nearly EVERY possible couple would be biologically compatible!)  A person who believes that every individual who is a Moslem must believe in using violence to achieve change may choose to never allow any meaningful discussion with any Moslem.  A man who believes that every properly self-respecting woman must wear a face, hair and body hiding burqa could find it difficult to work near women with other attire.  Our visual impressions such as a rock is solid (consider the emptiness inside and between atoms) may be easier to change than parts of our fantasy understanding formed from information not gained directly by our senses.  It is likely that our experiences, discussions, television shows, movies, and computer games are can modify our understanding of reality, sometimes with disastrous results.  But as we grow older, it is likely that we subconsciously reject information which might contradict our fantasy understanding while using consistent information to reinforce our understanding.  So a movie might modify the understanding of one person one way and another person much differently.  Religious teaching such as love your neighbors and even your enemies may have a limited ability to modify our understanding; but many people who claim that belief still send their sons to war to fight those whom they fear could bring them harm.  It is not clear whether an awareness of limitations in our fantasy understanding opens the possibility of improving that understanding.  While few people would step off a cliff, visually perceiving that would endanger their life, many people are still willing to stand in a suspended tram with a glass floor which gives the same visual perception.  So we have some ability to modify our understanding of our perceptions.

Physical and chemical mechanism of consciousness

Unlike most 2-dimensional computer chips, the brain is a 3-dimension tangle of neuron cells.  But those neurons in different regions on the brain assume different hierarchical functions.  Although functional development of the brain is not yet clear, perhaps function determination is as simple as utilization of the nearest available neuron as a signal arrives from a sensory detector neuron.  And to a limited degree, neurons apparently can be re-purposed if needed.  The junction between neurons is key to the formation of memory and associations which bring awareness and consciousness.

When a stimulus sends a signal along neurons to the brain, the neurotransmitter serotonin is released at the synapse where a signal is transmitted from one neuron to an adjacent neuron.  This activates receptors which release cyclicAMP which functions as a secondary messenger.  The cyclicAMP activates protein kinases which, by adding phosphate groups, prepare more neurotransmitter for release, boosting the capacity to carry the signal across the synapse with the adjacent neuron.  No new proteins are synthesized, but for a short time the sensory neuron will have heightened sensitivity.  If the stimulus is more forceful the response is stronger.  This amplification lasts only for a few minutes, demonstrating what is called short-term memory.

memory diagramBut if the neuron is repeatedly stimulated, long-term memory is created.  Converting short-term memory to long-term memory requires appropriately spaced repetition of the nerve stimulation.  When repeatedly stimulated, the additional serotonin (or other neurotransmitter) releases higher concentration of the second messenger (cyclicAMP) which activates additional protein kinases.  These along with another enzyme migrate into the nucleus of the neuron.  There they activate genes in the sensory neuron resulting in production of new protein used to construct additional synaptic connections.  When the stimulus is repeated several times, the sensitization may remain for weeks.  What we call memory is actually additions in synapses that form the contact points between the neurons.  While genes are involved in the growth of new synaptic connections, it is the stimulation by the environment that governs the expression of the genes and causes the learning.  The connections between neurons in our brains actually grow and change when we have experiences and learn.

When nerve impulses arrive nearly simultaneously from several different detectors (such as discussed earlier when you touch your knee) the associated signals mutual reinforce encouraging the development of new synaptic connections.  Nearby neurons which are not adequately stimulated essentially learn to discriminate and not response.  It appears that such associations due to the physical construction of new synapse are the primary mechanism for memories of all sorts and consciousness on the higher levels.

Our limited understanding of how we gain and maintain consciousness conforms what teachers have long known helps learning:

Investigation: Consciousness

Are there different levels, degrees, or kinds or consciousness?

What kinds of experiences teach or encouraged development of consciousness?

What are the capabilities, advantages, or possibilities for consciousness?

Are there other tests which can be constructed to determine consciousness or self awareness?  Are there ways to quantify and measure consciousness?


Try mapping a touch where it is not visible, perhaps by leaning back against an object or having someone touch you.  Previous experiences may have mapped the location.  But can you determine if some areas of your skin or better mapped than others?

Communicating technical information such as observations and findings is a skill used by scientists but useful for most others.  If you need course credit, use your observations in your journal to construct a formal report.

Investigation: Intelligence

The French psychologist Alfred Binet published in 1905 the first modern intelligence test intended to identify students needing additional help in coping with assigned school tasks.  Since then a wide variety of tests have been developed for predicting success in education, employment and various roles in society.  Such tests have been criticized for results biased by the language ability, economic and family status, and prior training of the person being tested.

But in the procedure which follows, the goal is to develop your ability to think creatively rather than be measured.


Design an intelligence (IQ) test using only a standard piece of writing paper and a sharpened pencil.  To to restrict directions to use no special or advanced vocabulary and only simple mathematical directions.  (Mathematics may be the closest we currently have to a universal, low ambiguity language.)  Try to think of all the things one could do with a pencil and piece of paper, then construct a series of directions that might require intelligence to successfully accomplish.  If possible try to construct a means of mathematically evaluating the degree of intelligence demonstrated by a person taking your test.

Communicating technical information such as observations and findings is a skill used by scientists but useful for most others.  If you need course credit, use your observations in your journal to construct a formal report.


Dan Dennett. Can We Know our Minds? a TED talk, Feb. 2003.


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created 26 November 2006
latest revision 30 January 2010
by D Trapp
Mac made