Red: theory; black, fact.
I have concluded that the world contains three
intelligences: the genetic, the synaptic, and the artificial. The first includes (See Deprecated, Part 10) genetic phenomena and
is 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 presumably understand it. Thus, it can provide a wealth of
insights into the nature of the other two intelligences and a vocabulary for
discussing them.
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.
A genome can be compared to a
KB in that it contains structural genes and cis-acting control elements.(CCEs). The CCEs
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 CCE evaluates the “if” condition and the conditionally
translated protein enables the “action” taken by the cell if the
condition is true.
Note that the structural gene of one rule precedes the CCE of the next rule along the DNA strand. Surely, 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.
The process of putting the rules into such a sequence may involve trial-and-error, with transposon
jumping providing the random variation on which selection operates. A variant on this process would involve stabilization by 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. It would then be converted into DNA methylation signals in the germ line. (See my post on mental illness for possible mechanisms.) DNA methylation is known
to be able to cool recombination hot spots.
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.
How
would the genetic intelligence handle conditional firing probabilities in the
medium to low range? This could be done by cross linking nucleosomes via the
histone side chains in such a way as to cluster the CCEs 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.
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. The
variety of such changes that are possible.
Mechanistically, there seems to be a great divide between the handling of high and of medium-to-low conditional probabilities. This may correspond with the usual block structure of algorithms, with transfer of control linear and sequential within a block, and by jump instruction between blocks.
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. If the eukaryotic cell is descended from a glob-like 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.
