#7. What is Intelligence? Part I. DNA as Knowledge Base [genetics, engineering]

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Red: theory; black, fact

The Known Intelligences 

There may be three intelligences: the genetic, the synaptic, and the artificial. The first includes genetic phenomena and may be the scientifically accessible reality behind the concept of God. The synaptic is the intelligence in your head, and seems to be the hardest to study and the one most in need of elucidation. The artificial is the computer, and because we built it ourselves, we understand it. Thus, it can provide a wealth of insights into the nature of the other two intelligences and a vocabulary for discussing them.

The Artificial Intelligence 

Artificial intelligence systems are classically large knowledge bases (KBs), each animated by a relatively small, general-purpose program, the "inference engine." The knowledge bases are lists of if-then rules. The “if” keyword introduces a logical expression (the condition) that must be true to prevent control from immediately passing to the next rule, and the “then” keyword introduces a block of actions the computer is to take if the condition is true. Classical AI suffers from the problem that as the number of if-then rules increases, operation speed decreases dramatically due to an effect called the combinatorial explosion.

DNA Through an AI Lens

A genome can be compared to a KB in that it contains structural genes and cis-acting control elements. The latter trigger the transcription of the structural genes into messenger RNAs in response to environmental factors and these are then translated into proteins that have some effect on cell behavior. The analogy to a list of if-then rules is obvious. A control element evaluates the “if” condition and the conditionally translated protein enables the “action” taken by the cell if the condition is true.

Avoiding Slowdowns at Scale

Note that the structural gene of one rule precedes the control element of the next rule along the DNA strand. Would this circumstance not also represent information? However, what could it be used for?

It could be used to order the rules along the DNA strand in the same sequence as the temporal sequence in which the rules are normally applied, given the current state of the organism’s world. This seems to be a possible solution to the combinatorial explosion problem, leading to much shorter delays on average for the transcriptase complex to arrive where it is needed. I suspect that someday, it will be to this specific arrangement that the word “intelligence” will refer.

A Rule-ordering Mechanism 

The process of putting the rules into an efficient sequence may involve trial-and-error, with transposon jumping providing the random variation on which selection operates. 

A variant on this process would involve the enhancement by de-methylation of recombination sites that have recently produced successful results. These results would initially be encoded in the organism's emotions, as a proxy to reproductive success. In this form, the signal can be rapidly amplified by inter-individual positive feedback effects such as competition. It would then be converted into patterns of DNA de-methylation in the germ line. DNA methylation is known to be able to cool recombination hot spots, so de-methylation should do the opposite.

Rule Creation 

A longer-timescale process involving meiotic crossing-over may create novel rules of conduct by breaking DNA between promoter and structural gene of the same rule, a process analogous to the random-move generation discussed in my post on dreaming. Presumably, the longest-timescale process would be creating individual promoters and structural genes with new capabilities of recognition and effects produced, respectively. This would happen by point mutation and classical selection.

Implementing Jump Instructions In DNA 

How would the genetic intelligence handle conditional rule firing probabilities in the medium to low range, which would call for jump instructions as opposed to merely incrementing the instruction pointer?

This could be done by cross linking nucleosomes via the histone side chains in such a way as to cluster the cis control elements of likely-to-fire-next rules near the end of the relevant structural gene, by drawing together points on different loops of DNA. The analogy here would be to a science-fictional “wormhole” from one part of space to another via a higher-dimensional embedding space. In this case, “space” is the one-dimensional DNA sequence with distances measured in kilobases, and the higher-dimensional embedding space is the three-dimensional physical space of the cell nucleus.

A Possible Mechanism of Jump Instructions 

The cross linking is presumably created and/or stabilized by the diverse epigenetic marks known to be deposited in chromatin. Most of these marks will certainly change the electric charge and/or the hydrophobicity of amino acid residues on the histone side chains. Charge and hydrophobicity are crucial factors in ionic bonding between proteins. A variety of such changes are possible.

Another way of accounting for the diversity of epigenetic marks, mostly due to the diversity of histone marks, is to suppose that they can be paired up into negative-positive, lock-key partnerships, each serving to stabilize by ionic bonding all the wormholes in a subset of the chromatin that deals with a particular function of life. The number of such pairs would equal the number of functions. Their lock-key specificity would prevent wormholes, or jumps, from forming between different functions, which would cause chaos.

Evolutionary History of Jump Instructions 

If the eukaryotic cell is descended from a spheriodal array of prokaryotes with internal division of labor and specialization, then by one simple scheme, the specialist subtypes would be defined and organized by something like mathematical array indexes. For parsimony, assume that these array indexes are the different kinds of histone marks, and that they simultaneously are used to stabilize specialist-specific wormholes. A given lock-key pair would wormhole specifically across regions of the shared genome not needed by that particular specialist.

A secondary function of the array indexes would be to implement wormholes that execute between-blocks jumps within the specialist's own program-like KB. With consolidation of most genetic material in a nucleus, the histone marks would serve only to produce these secondary kind of jumps while keeping functions separate and maintaining an informational link to the ancestral cytoplasmic compartment. The latter could be the basis of sorting processes within the modern eukaryotic cell.