of mathematical logic in gene regulation. Early achievements in genetic
engineering using recombinant DNA
technology (the insertion, deletion,
or combination of different segments
of DNA strands) can be viewed as the
experimental precursors of today’s
synthetic biology, which now extends
these techniques to entire systems of
genes and gene products. One goal can
be constructing specific synthetic biological modules such as, for example,
pulse generator circuits that display a
transient response to variations in input stimulus.
Advances in DNA synthesis of longer and longer strands of DNA are paving the way for the construction of
synthetic genomes with the purpose of
building an entirely artificial organism.
Progress includes the generation of a
5,386bp synthetic genome of a virus,
by rapid (14-day) assembly of chemically synthesized short DNA strands. 37
Recently an announcement was made
of the near completion of the assembly of an entire “minimal genome” of
a bacterium, Mycoplasma Genitalium. 7
Smith and others indeed found about
100 dispensable genes that can be removed individually from the original
genome. They hope to assemble a minimal genome consisting of essential
genes only, that would be still viable but
shorter than the 528-gene, 580,000bp
genome of M.Genitalium. This human-made genome could then be inserted
into a Mycoplasma bacterium using a
technique wherein a whole genome can
be transplanted from one species into
another, such that the resulting progeny is the same species as the donor genome. Counterbalancing objections to
assembling a semi-synthetic cell without fully understanding its functioning,
the creation of a functionally and structurally understood synthetic genome
was proposed, 17 containing 151 genes
(113,000bp) that would produce all the
basic molecular machinery for protein
synthesis and DNA replication. A third
approach to create a human-made cell
is the one pursued by Szostak and others, who would construct a single type of
RNA-like molecule capable of self-repli-cating, possibly housed in a single lipid
membrane. Such molecules can be obtained by guiding the rapid evolution of
an initial population of RNA-like molecules, by selecting for desired traits.
Lastly, another effort in synthetic
biology is toward engineering multicellular systems by designing, for example, cell-to-cell communication
modules that could be used to coordinate living bacterial cell populations.
Research in synthetic biology faces
many challenges, some of them of an
information processing nature. There
arguably is a pressing need for standardization, modularization, and abstraction, to allow focusing on design
principles without reference to lower-level details. 15
european artist leonel
Moura works with
Ai and robotics. the
swarm Paintings,
produced in 2001, were
the result of several
experiments with
an “Ant Algorithm”
where he tried to
apply virtual emergent
pheromone trails to
a real space pictorial
expression. in this case,
a computer running
an ant algorithm was
connected to a robotic
arm that “translated” in
pencil or brush strokes
the trails generated by
the artificial swarm of
ants. For more images,
see www.leonelmoura.
com/.
Besides systems biology that tries
to understand biological organisms as
networks of interactions, and synthetic biology that seeks to engineer and
build artificial biological systems, another approach to understanding nature as computation is the research on
computation in living cells. This is also
sometimes called cellular computing,
or in vivo computing, and one particular
study in this area is that of the computational capabilities of gene assembly in
unicellular organisms called ciliates.
Ciliates possess two copies of their
DNA: one copy encoding functional
genes, in the macronucleus, and another “encrypted” copy in the micronucleus. In the process of conjugation,
after two ciliates exchange genetic information and form new micronuclei,
they use the new micronuclei to assemble in real-time new macronuclei
necessary for their survival. This is accomplished by a process that involves
re-ordering some fragments of DNA
(permutations and possibly inversions),
and deleting other fragments from the
micronuclear copy. The process of gene
assembly is fascinating from both the
biological and the computational point
of view. From the computational point
of view, this study led to many novel and
challenging research themes. 14 Among
others, it was proved that various models of gene assembly have full Turing
machine capabilities. 23 From the biological point of view, the joint effort of
computer scientists and biologists led
to a plausible hypothesis (supported
already by some experimental data)
about the “bioware” that implements
the process of gene assembly, which is
based on the new concept of template-guided recombination. 4, 28
Other approaches to cellular computing include developing an in vivo
programmable and autonomous finite-state automaton within E.Coli, and designing and constructing in vivo
cellular logic gates and genetic circuits that
harness the cell’s existing biochemical
processes.
At the end of this spectrum of views
of nature as computation, the idea was
even advanced by Zuse and Fredkin
in the 1960s that information is more
fundamental than matter or energy.
The Zuse-Fredkin thesis stated that the
entire universe is some kind of computational device, namely a huge cellular