The bottom-up and the top-down approaches in synthetic biology
The bottom up approach consists of assembling minimal living systems from biological and/or non-biological building blocks. Our work belongs to this bottom up approach. This approach is pursued in the spirit of Richard Feymann maxim: "What I cannot create, I do not understand”. Said in other words: To really understand life, we need to be able to create life.
Our protocell design only utilizes non-biological materials as building blocks (Rasmussen et al., 2003). This means that none of our molecular building blocks are used or found in modern cells, although our components all have similar functionalities as the components found in biological systems. We use alternative, simpler and specially designed molecules because they allow us to realize the same fundamental functionalities using a dramatically simpler blueprint for the protocell compared to what we see in modern cells.
The bottom up approach to creating minimal living cells can also be pursued by assembling existing biological building blocks in simplified ways (see e.g., Sunami et al., 2010). Our lab also has efforts in this area.
It should be emphasized that although our team is predominantly occupied with the bottom up approach, much more effort within synthetic biology today is devoted to modify existing living organisms than to create minimal living cells from scratch (Porcar et al., 2011). The approach based on modifying existing cells is called the top downapproach. The top-down approach reached an important milestone in 2010, when Craig Venter’s team was able to transplant an artificially synthesized genome into another cell without a genome and thereby “reboot” the other cell and bring it back to life (Gibson et al., 2010; Life after the synthetic cell Nature, 2010; Artificial Life: Scientific Revolution? Or end of life as we know it?, J. of Cosmology, 2010).
Another important line of research within the top down tradition is the effort to develop so-called “bio-bricks" (BioBricks 2011) that can be composed and inserted into cells, in similar ways as electrical engineers make and compose electronic components in modern information and communication technology devices. Our iGEM undergraduate student teams at SDU utilize this approach when they go to MIT and compete with other teams each year.
Porcar, M., Danchin, A., Lorenzo, V., dos Santos, V. A., Krasnogor, N., Rasmussen, S. and Moya, A. (2011), Ten grand challenges for synthetic life, to appear in Synthetic Biology.
Sunami, T., Caschera, F., Morita, Y., Toyota, T., Nishimura, K., Matsuura, T., Suzuki, H., Hanczyc, M.M., Yomo, T. (2010) Detection of Association and Fusion of Giant Vesicles Using a Fluorescence-Activated Cell Sorter, Langmuir 26 (Oct. 2010), 15098–15103.
Gibson, D.G., et al. 2010 Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 5987, (July 2, 2010), 52-56. DOI: 10.1126/science.1190719.
Life after the synthetic cell, Nature 465, 27, (May 27, 2010), 422-424.
Artificial Life. Scientific Revolution? Or the End of Life as We Know It? Journal of Cosmology (June, 2010) 8,http://JournalofCosmology.com/ArtificialLife100.html.
BioBricks 2011, see http://biobricks.org
Rasmussen, S., L. Chen, L., Nilsson, M. and Abe, S., Bridging nonliving and living matter, Artificial Life 9 (2003) 269.
Richard Feymann, Quote found on his blackboard at time of death in 1988; as quoted in The Universe in a Nutshellby Stephan Hawking. Richard Feymann (1918-1988) was a physicist and Nobel Prize Winner.