Chemical Roadmap to Artificial Cells

There are many possible approaches to synthesizing artificial cells. In PACE we have developed a simple graphical language that enables one to characterize and classify the essential chemical features of many different protocell projects (Rasmussen et al., 2008), which is the main reference for this text. The representation achieves several ends: It allows for comparison of different achievements, it enables articulation of how targets of ongoing research fit into a larger picture containing both those targets and the work of other researchers, and it also enables a comparison between experimental results, simulation results and hypothetical scenarios. After presenting the basic vocabulary, we show how our graphical representations may be used to construct a roadmap of different paths that lead to the creation of protocells. We then use these representations to depict the important functional features of several current protocell research efforts. 


Protocell research is a combination of experimental creations in the laboratory, computer simulations of chemical systems, and conceptual schemes that guide experimental and computational efforts. Our graphical language can represent each of these kinds of achievements and express them in a common language that enables direct comparisons among all these facets of protocell research. 


Our representation scheme aims to focus on the essential features of protocell systems, and to abstract away most of their details. The general protocell vision that is expressed in the diagrams is that life is the functional integration of metabolism, containment, and information processing, and the graphical language has primitives corresponding to these three functionalities. The diagrams provide a practical and easy method for generating natural milestones by which to judge progress in protocell research. They also enable us to side-step the seemingly interminable debates about the definition of life. However, it should be noted that the vision of life as the functional integration of metabolism, containment, and information processing is not a presumption of our graphical language. There are a range of visions of life that concentrate on particular subsets of these functionalities, many of which are presented here; all of these may be diagramed to facilitate precise comparisons between different protocell visions. Likewise, the language may grow to include other functionalities if and when they become important in protocell research. 


Our graphical language represents the key causal and functional interactions chemically realized in protocell systems. Accordingly, more complicated chemical systems require more complicated diagrams. Thus, our method is cleanest when applied to the very simple protocells characteristic of pure bottom-up efforts (see e.g. Hanczyc et al., 2008 and Rasmussen et al., 2008b), for they yield suitably simple diagrams. We have made some attempt to generalize our language to represent bottom-up methods that use material from existing living cells, such as cell-free extract containing myriad structures like ribosomes, enzymes, and the basic building blocks out of which nucleic acids and proteins are constructed (see Sunami et al., 2008). But these attempts must sacrifice the fundamental clarity and precision of our diagrammatic language in order to represent much more complicated chemical systems. 


Some top-down approaches to protocells begin with fully functioning natural living cells, such as bacteria, and modify them, creating even more complicated chemical systems (see Gabaldon et al., 2008). We have not tried to represent these top-down schemes here; they are complicated enough that our diagrams might prove useless. 


In the following figures we shortly present and illustrate the usage of the grammar.

Graphical language for artificial cells

Graphical language for artificial cells

Roadmap to artificial cells

Roadmap to artificial cells

Examples of architectures for artificial cells

Examples of architectures for artificial cells

© 2004-2008 All rights reserved by PACE Consortium .   Email.   Web Managers: U. Tangen & J. S. McCaskill