Extraterrestrial

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Delving into the meaning of artificial life
Consortium's report aims to define, classify synthetic biology's many branches
EETimes.com, Chappell Brown, (03/20/2006 9:00 AM EST)

Peterborough, N.H. -- The ability to engineer artificial biological components, and one day perhaps artificial organisms, puts a new spin on the ongoing debate about artificial life, which has been linked mainly to silicon circuits. It has been argued that when VLSI systems reach a high enough level of complexity, they will essentially be alive in the same sense that biological systems are alive.

A study that is being conducted by a consortium of companies delves into the issue of artificial life in detail, since it is fundamental to defining and classifying different branches of synthetic biology. Loosely defined as the engineering of systems using mechanisms and principles from molecular biology, synthetic biology could have a wide impact on the field of engineering and on society as a whole, according to a report of the study.

The report was written principally by Hubert Bernauer of ATG:Biosynthetics (Feiburg, Germany) for consortium leader Sociedade Portuguesa de Inovação (Baltimore).

The first phase of the study was completed last October. The next phase, which is seeking to identify new research efforts and startups in the field, will be completed this June. Using research papers as a measure of activity in the field, it says that the United States leads such endeavors with 68 percent of all papers written in the world. The European Union comes in second at 24 percent, and Israel and Japan are next with 3 percent each. Most of the work in the United States was performed in California, with Massachusetts coming in second.

Because it's such a new field, the report's authors had to come up with a working definition of exactly what activities should be included in the term "synthetic biology." In doing so, the report may have an impact on the field simply through its attempts to define it.

According to the report, "Synthetic biology is the engineering of biological components and systems that do not exist in nature and the re-engineering of existing biological elements; it is determined on the intentional design of artificial biological systems, rather than on the understanding of natural biology."

MIT's BioBrick project (see www.eetimes.com, article ID: 21800320)--a catalog of standard DNA sequences that code for specific cell functions--is emblematic of the new field. DNA is a digital code that natural systems use to assemble themselves. A recent technical capability that has propelled synthetic biology is the ability to synthesize a strand of DNA reliably from any predetermined digital sequence. Companies providing that service have sprung up, allowing anyone in biomedical research or bioengineering to work with artificial DNA.

Elements for life

Such current computer-related fields as genetic algorithms, autonomous agents, neural networks and artificial intelligence mimic aspects of living systems. But just how close are they to actual living organisms? The gap is not just a matter of complexity, the authors argue; it also critically depends on the relationship between information and the physical system that represents it.

Biologists have identified three critical principles that must be present in any living system: They must be self-creating, self-organizing and self-sustaining. The self-sustaining capability includes the ability to replicate components, process information and steadily consume energy from the environment. While electronic systems are highly adept at information processing, they are not self-replicating except at the software level, and they consume only one type of strictly defined electrical energy. In contrast, biological systems have excelled at self-replication, and their strategies for consuming energy from the environment are extremely varied.

The report is pessimistic about the possibility that silicon-based systems can ever be able to duplicate the versatile repertoire of information processing and physical replication required by living systems. This is mainly due to the nature of the materials upon which artificial and biological life are based: silicon for the former and carbon for the latter. Carbon has a high degree of flexibility in forming novel configurations with itself and with other common elements such as hydrogen, allowing complex information-processing systems to be represented in a corresponding materials system. In contrast, artificial-life systems realized in electronic systems do not have a corresponding molecular configuration associated with them. While software programs that realize all the basic elements of living systems can be run on silicon circuits--and they might become highly complex programs in the future--the artificial systems will never be closely integrated with corresponding silicon molecular systems.

Synthetic biology will be able to remedy that problem by creating artificial-life systems employing the same flexible molecular strategy of living systems. Several avenues of attack are being developed to do that.

In a top-down approach, researchers are trying to find the evolutionary principles that create various components of living systems, and apply them to nanostructures to create new lines of artificial organisms.

Another method uses a bottom-up, building-block tactic. Specific cell functions are identified, standardized and then coded in DNA sequences. As in inorganic engineered systems, more complex functions are built out of simpler building blocks. The hope is that at some point, self-sustaining systems will result from this classic engineering route.

The authors expect this approach to create a new biological paradigm. Instead of "molecular biology," the new field would be called "modular biology."

In a third procedure, the regulation approach, researchers are trying to identify the signaling systems with which cells modify their growth and behavior. By making those systems program-mable, it might be possible to repurpose biological systems for engineering objectives.

In another branch of synthetic biology, researchers are using the combinatorial properties of DNA and RNA to run test tube experiments to build nanostructures. These molecules can be combined with nanoclusters or other artificially created structures to build systems for specific applications in medicine and biological research. This area is known as "in vitro" synthetic biology.

Complex computer-based simulations of biological systems are also classed under the synthetic biology umbrella, although the object with those systems is to provide a kind of CAD system for modeling and predicting the behavior of natural or engineered biology. These are called "in silico" systems, in which computer models will be an integral part of the evolution of engineered biological systems.

The vision within silico computer systems is similar to that of the EDA industry, where standard fabrication processes make it possible for someone with circuit design expertise to try out a concept on a computer, simulate and specify how it should be laid out--with the confidence that an actual working silicon IC can be produced from the design. In the world of synthetic biology, that kind of capability would greatly speed up the entire field, allowing researchers and engineers to rapidly field artificial-life systems based on past experience and experiments.

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