Information Technology Reference
In-Depth Information
20. Loci (Latin word for “places”) as localization mechanisms more general than
membranes, could be added. For example, if specific zones of membrane skin
are defined, the position of objects could be given in terms of coordinates which
refer to them. Moreover, implicit forms of localization could be based on con-
centration gradients along some directions.
By using some of the features mentioned in the list above it is possible to prove a
great number of results of computational universality [50]. We will mention only
two results of this kind:
cat
2
)
that is, the recursively enumerable sets of natural numbers coincide with the set
of numbers which can be generated by P systems with one membrane and rules
allowing at most two catalysts. Moreover:
NRE
=
NOP
1
(
NRE
=
NOP
3
(
sym
1
,
anti
1
)
that is, the recursively enumerable sets of natural numbers coincide with the set
of numbers which can be generated by P systems with three membranes and rules
allowing one
symport
rule and one
antiport
rule.
2.8
Informational Analysis of Genomes
Genomes are containers of biological information, they direct the functions of the
organisms and they are what is transmitted to the generations of their organisms.
During their transmission variations are introduced, which change the organisms
hosting them. Therefore, according to the evolutionary mechanisms, genomes are
selected indirectly through the effects they produce in the organism they direct.
The selective force driving this process pushes genomes of organisms with the best
capacity of spreading in the environments and of reproducing abundantly. From
this point of view, we could see organisms as means for selecting genomes, instead
of genomes as means for realizing organisms. The situation is a typical case of
duality, in the sense that each of the two realities needs the other one. However,
what it is essential to stress here, is the specific informational nature of genomes.
If they are responsible for the most important part of biological information, then
they have to follow the general rules which information mechanisms follow. This
simple statement implies some important informational perspectives in the analysis
of genomes, which we will outline in the following.
Many seminal works were developed in recent years where concepts from in-
formation theory and computer science [198, 200, 64, 22], formal language theory
[213], and linguistics [16] were used in the investigation of genomes considered as
particular texts ([19, 37, 52, 57, 59, 60, 24, 33, 31, 54]). These researches applied
information theoretic notions (information, entropy, mutual information, encoding,
compressibility, complexity measures, and randomness), or formal language theory
(grammars, automata, patterns), or linguistic concepts (words, dictionaries, lexical
