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25 Jan The Chromophore as Digital Bit

Microtubule Structure I have opined in prior posts that the skeletal components that give structure to axons and dendrites, especially microtubules, may play a larger role in cognition than previously thought. The illustration of microtubule structure at right shows how the alpha and beta tubulin dimers string themselves together to make protofilaments, which further join one another to form microtubules. Both the filaments and the tubules have positive and negative ends which serve to help them in growth. Today, I want to discuss a biological structure that may also contribute to the way in which microtubules participate in cognition: the chromophore’s soliton switch.

The Chromophore

One change that affects tubulin dimers in MT is called tyrosination. Tyrosination, acetylation and phosphorylation actually change the molecular structure of the component. In designing molecular computers, scientists have formulated a model using a molecular structure called a chromophore.

Chromophore 1

In the chromophore, changing molecular bonds can act as gates or single-bit data storage registers. A particle called a soliton can be used to activate and inactivate the switch, and light can be used to transfer single electrons from one nitrogen atom to the other (Van Brunt, 1985, p. 212).  The illustration above shows a possible structure for a chromophore.

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Section 3 #13

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Table of Context

A soliton switch in a molecular computer can be used to represent binary logic like a flip-flop in a digital computer. Though one might use a soliton switch to resemble a single neuron, it is possible that multiple such switches could reside on a single MT, thus affecting the flow of impulses within a neuron.

The Soliton

Soliton switching in molecular computers is analogous to the interaction of spreading patterns of activation between neurons in a neural network and data stored in data registers in individual neurons. A chromophore model of molecular computing is far simpler than that proposed here in that the solitons and electrons are single particles while neurons pass E/I between themselves in large and variable quantities. As an analogy, the comparison may yield interesting insight because the effect of tyrosination on a tubulin dimer is somewhat similar to the effect of a soliton on a chromophore.

Soliton

Chromophore Switched

Thus the effect of tyrosination is similar to the effect of “burning” (writing data to) a ROM. A microtubule, then, could contain information, and that information may be accessed through an ON/OFF type switching mechanism where the patterns of ONs and OFFs indicate the content of the pattern. In the chromophore model, there are two different mechanisms affecting the information value of the register: solitons for switching and light for flipping electrons. In the neural model, both chemical and electrical influences are in effect continually, so ionization and gate properties could be altered in a similar way. The soliton is a charge on the end of a chromophore.

Chromophore Enabled Disabled

Describing state changes as flip-flops suggests a digital interpretation of information processing in the brain. Since neurons are capable of more than just two states, this data can also be applied to analog processing. An analog model is actually as plausible, if not more likely, than a digital one because of the analog nature of spreading E/I and the quantity of MT isoforms.

Information Storage

As indicated in prior posts, many properties and characteristics of MT and IF could enable them to store and process information in the brain. One interpretation of this data could be used to support current neural models if it is assumed that IF and MT provide for the learning and storage of weights of links between cells. This is a plausible theory, though there are other mechanisms that are more directly involved at synaptic junctions and seem more likely to fill this function. The intriguing possibility is that intracellular components such as MT and IF actually store symbolic information that can be used to encode, decode, relay, filter and interpret stimuli.

Brain Data

Intermediate Filaments

Intermediate filaments have properties which are analogous to the chromophore model. The variable terminal-domain structures of IF segments represent ON/OFF switches or binary flip-flops. Because a single intermediate filament has a large number of segments, the capacity of information in IF is similar to that in a single microtubule. However, the quantity of IF in neurons is many times greater than that of MT, so the potential capacity does not lend itself well to speculation. In addition, since IF have a lower turnover rate than MT, the term of memory would be longer in IF.

IF Terminal Domains

Certainly there are many properties and characteristics of MT and IF that could enable them to store and process information in the brain. One interpretation of this data could be used to support current neural models if it is assumed that IF and MT provide for the learning and storage of weights of links between cells. This is a plausible theory, although there are other mechanisms that are more directly involved at synaptic junctions and seem more likely to fill this function.

IF Protofibril

IF Protofibril

That intracellular components such as MT and IF actually store symbolic information that can be used to encode, decode, relay, filter and interpret stimuli is an intriguing possibility. Does this mean that MT and IF are like computer memory (RAM) or data storage devices (disks)? Nothing in our physical brain has yet been shown to be fast enough to record information in real time. Therefore, the biological basis of our ability to memorize things quickly is not yet apparent. But the ability to store information on a persistent or long-term basis may be easier to ascribe to components of neurons.

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