CHE.496/2008/Responses/a9

Biological machines

• Discussion leader: George McArthur (Discussion guide)

Kevin Hershey's Response

• Designing Biological Systems
  • This powerpoint presentation by Pamela Silver of Harvard medical school discusses systems biology, which is different from the definition used in Che 496 thus far. In the powerpoint, she discusses the idea of standardizing biology and making it modular. The powerpoint goes on to say that systems biology can try to understand organisms, things we don't know, and why things work a certain way. She then goes on to discuss inelegant design, and points out the example of the vestigial thumb.

• Biology by design: reduction and synthesis of cellular components and behaviour.
  • I was unable to load this document unto my computer. From the abstract, this article discusses the emergence of synthetic biology from the question, "how can I apply that knowledge to generate novel functions in different biological systems or in other contexts?" This is very prevalent in the iGEM participants, who use genetic parts from many organisms, standardize them, and combine them to create novel functions. While I was unable to download this document, I feel that the question it poses in the beginning is very relevant to the study of synthetic biology.
• KPHershey 00:46, 20 February 2008 (EST)

Eyad Lababidi's Response

• Designing Biological Systems
  • the power point was rather broad and i couldn't really get that much from it. We probably need to discuss the points she brings up about how evolutionary change is not planned out and does not necessarily run like a wheel oiled machine while human design we can skip intermediate steps? ya, I didn't really understand that statement. I do agree though that systems biology needs to understand the why and the how before necessarily trying to implement what we've got because without a good background its much harder to create anything useful. its almost like a short term solution versus spending the extra time on fundamentals so that in the long run we are much further on with what systems biolgy is capable of doing.
• Biology by design: reduction and synthesis of cellular components and behaviour.
  • This article i believe was just a long winded version of what we've been reading about since the beginning of the semester, although it was more encompassing then any one article weve read so far. It discusses how far synthetic biology has come along and where it needs to go and what processes the field needs to undergo to the there. The article also focused in more on the abstraction of synth bio to the level of systems and gives lots of examples and analogies like the robot to the e coli cell. although this article had some more indepth examples compared and i didnt know that cells could be wired up as the article showed.

Eyad Lababidi 12:56, 20 February 2008 (EST)

Dan Tarjan's Response

• Designing Biological Systems
  • This appears to be the slides which accompany a presentation. It deals mainly with the topic of conscious design versus systems that arise through evolution. It highlights the fact that certain things necessary for intelligent design of biological systems, like modularity in biological systems, are already present in nature. It then proposes that systems biology can work towards better understanding of (I'm assuming) gene circuits and other interactions within a biological system, intracellular and perhaps between cells also. ...Which is kind of what systems biology is about as far as I know.
• Biology by design: reduction and synthesis of cellular components and behaviour.
  • This paper is a thorough overview of the origins, current state of, and potential of synbio. It covers the technologies (DNA synthesis mainly) that enable researchers to fairly easily and more importantly in a deliberate fashion to modify existing biological systems or to restructure them. It goes over the current state of the field highlighting particular importnat achievements. Pattern formation is mentioned. This is worth mentioning because as the field of synbio progresses and its applications become more complex the techniques used to program and regulate the biological systems in question will have to grow congruently. The social implications of the field are also mentioned and they will no doubt become more important as the field grows and enters the lime light. I think the references cited in this article will be worth pursuing for further information about the details of certain projects mentioned in the paper.

Daniel R Tarjan 15:07, 20 February 2008 (EST)

Patrick Gildea's Response

• Designing Biological Systems
  • This powerpoint goes over what systems biology is and its goals – to understand evolution-based design strategies among other things. I think the main benefit (and only benefit) is the descriptions (albeit, short ones) of different parts, biological devices, the bacterial edge detector, and the synthetic biology counters. These are applications that we could possibly apply toward our project and these are part of the ethos that synthetic biology presents. A distinction is made in the powerpoint between rational and thought-out engineered design and inelegant design – trial and error kind of research that is simply abhorring to us engineers.
• Biology by design: reduction and synthesis of cellular components and behaviour.
• Patrick Gildea 17:03, 20 February 2008 (EST):