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The essential point here is probably related to some forms of biological memories
which are not genetically driven. Of course, different phenotypes determine different
individuals, and different individuals determine different ways which the natural se-
lection can act on them. However, are there some kind of execution memories which
add kinds of articulation to this basic evolutive dynamics?
These questions raise, in biological terms, a problematic which relates to well-
known philosophical debates going back to Aristotle, full of implications with many
contexts and disciplines. In this sense, the dichotomy genetics/epigenetics relates
to Aristotle's potency/act or potentiality/actuality distinction, and more recently to
Rene Thom's salience/pregnance in the form emergence and development [156].
A form emerges in a context which is necessary to its identification. An object in
space is a form of discontinuity, as different from what is external to it, but at the
same time, a form becomes a center of pertinent relations which determine its func-
tion giving sense to its existence. If genes encode forms, the functions they activate
are related to the forms they provide, after transcription and translation, and to the
forms which are involved in these processes. Here an essential difference with pro-
grams is due to the conformational, geometric, and physical character of the forms
these programs realize. In this sense the dialectics genetic/epigenetic links naturally
to
morphogenesis
,
embryogenesis
, and developmental mechanisms of form emer-
gence in biological organisms. Perhaps, a unified logic underlies these phenomena,
and discovering the main rules of this logic will be a great gain in knowledge of life.
An important field of application of synthetic biology is the so-called
gene ther-
apy
. This means synthetic methods that transform portions of genomes, aimed
at contrasting or blocking pathological phenomena. In particular, oncolytic aden-
oviruses are an emerging therapeutic approach for cancer [124, 123, 120, 159, 157,
135, 136]. The general schema of this method is based on the specific relationship
between a gene and its promoter region. An activation
regulative configuration
is
realized in the promotion region of a gene, in terms of protein and regulative RNA
fragments binding to sites (at the end of a complex network of intermediate levels,
where for example, A promotes B that inhibits C, and so on, through a chain of ef-
fects and counter-effects). When this happens, then the transcription process of the
corresponding gene starts, in several phases, from the DNA unpacking to the gene
transcription into pre-mRNA (performed by RNA-polymerase enzyme of a specific
type).
Let us consider an adenovirus
having a gene X controlling the virus prolifera-
tion in the infected cells (causing their destruction). The cancer cells are the selective
target of the therapy, by avoiding, at same time, the viral effect against the normal
cells. Let us assume that some cancer cells express a specific protein, for example
a marker of cancer proliferation. Let us suppose also, for the sake of simplification,
that this protein occurs only in these cancer cells. Let Y be the gene that expresses
this marker protein. Now, let us replace the promoter region P(X) of the gene X of
A
A
with the promoter region P(Y) of the gene Y.
In this synthetic virus
A
, the gene X is promoted by P(Y). Therefore, if a pa-
tient with cancer is infected by the engineered virus
A
, then it remains silent in
the normal cells, because its promoter is absent and the regulative configuration
