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