Talk:CH391L/S12/Introduction

In regards to the debate over genetically engineered food, the vehement protests against it are intriguing considering the fact that we've been naturally altering the content of our food since the beginning of domestic agriculture. I wonder how it would change if people actually understood the benefits of the genetically engineered foods rather than dismissing all genetically modified food as evil regardless of its purpose. Midhat Patel 14:20, 26 January 2012 (EST)

Commenting on Midhat’s statement, I was entirely against genetic modification of food before I read more about it and learned how common it is in crops and food we eat every day. I believe that by educating ourselves people can see the benefit of genetically engineered foods, but at the same time it should be regarded with caution when considering possible environmental impact. "Razan Alnahhas 18:49, 29 January 2012 (EST)"

Razan makes a very good point. For example, Monsanto's Roundup Ready technology is incorporated in over half of all crops grown in the US[1]. Effectively, Monsanto engineered their plants to resist Glyphosate, the active ingredient of their trademark herbicide, Roundup. One of the potentially damaging side-effects of the widespread adoption of Roundup thanks to this genetic modification is that at least 19 invasive weeds have developed Glyphosate resistance[2]. Genetic engineering is a fantastic field, but as the saying goes: "With great power, comes great responsibility." As future members of this field, we should take into account the repercussions of our work. *Peter Otoupal 23:21, 29 January 2012 (EST)

• Peter Otoupal 22:58, 5 February 2012 (EST):EDIT: Added links to my data. I was technically incorrect; glyphosate resistant weeds are grown on 50% of US cropland. However, 93% of soybeans, 78% of cotton, and 70% of corn acres grow glyphosate resistant weeds, which is pretty huge.

With regards to the introduction, why has this field not progressed as quickly as others like computer technology or polymers? Is it due to the complexity of the basic parts and our lack of total understanding, or could it be that experiments involving synthetic biology are very sensitive to human error, making it difficult to reproduce and/or scale up? Jeremy McLain 12:01 p.m. January 28, 2012

Relating to Jeremy's questions, I found it very interesting to view synthetic biology as more or less competing against evolution since it's so difficult to connect natural and synthetic modules. These processes have been refined over and over for an amazing long time and it is feat for science to be able to replicate such complexity in only a few decades. I think that using these evolutionary pathways as templates for advancement will be the best way to make progression in this field. I am looking forward to trying to connect the vast amount of natural modules and make a functioning organism. Logan Bachman 01:36, 30 January 2012 (EST)

Interesting observations regarding evolution, Logan. I like to think of using evolution in synthetic biology as a way of making up for our slight ignorance of biological complexity. We can use it to tune circuits and genes that we designed to have a certain behavior as a module, so that they cooperate and communicate properly.

As a further comment, often evolutionary processes can lead to "complexification" for no reason (i.e., without increasing biological fitness)! [3]

I think our reading for today comments quite a bit on the analogy between computer technology and synthetic biology. They start out drawing a comparison between the hierarchy of computer parts (Physical Layer - Gates - Modules - Computers - Networks) and of a biological parts (Molecular Layer - Biochemical Reactions - Pathways - Cells - Tissues/Cellular Communities). However, as we read on, we see that this analogy is really very shakey at best. There are a couple main problems. The first is that computer systems are made of parts - transistors, capacitors, and resistors - that behave reliably and largely deterministically... I think. I'm not an electrical engineer. Biological parts like RNA and protein molecules are not like this. They behave stochasitcally and have system-wide effects at a much longer time scale than electrical components. In many (most?) cases, they are also necessarily located in direct physical proximity to the molecules/processes they effect at all times. This all means that the system behaves chaotically, and very small differences to system input can drastically effect the system output.

In addition, cells are not rationally designed like computers. They are evolved. Each cellular component or "module", to use their terminology, has evolved in the context of many, many other components and likely plays multiple roles in the cell. As a result, it can be difficult or impossible to separate one aspect of a component or module's behavior from its context in the cell as a whole.

Hereis a link to a flyer for a talk next week Friday that is definitely of interest to everyone in the class. Dr. Chang of UC Berkeley will be talking about her work engineering "new chemical function in living organisms". --Michael Hammerling 13:54, 30 January 2012 (EST)

One challenge of synthetic biology is breaking this computer-organism analogy and thinking about things that messy "wet-ware" organisms can do better than digital computers! Mike is referring to stochastic noise in gene expression in his comment, and this randomness could potentially be harnessed to give rise to useful phenomena. Recent studies are showing that this type of noise allows organisms to encode probabilistic developmental rules like: sporulate 30% of the time. Jeffrey E. Barrick 14:36, 30 January 2012 (EST)

Is there any certain patterns for this kind of noise, it seems to me that if an organism can translate the noise to fill in its gap of certain metaboli activity then this noise is not stochastic in nature.*Yi Kou 12:59, 31 January 2012 (EST):

I think that it's largely due to the complexity of the parts involved. One one level this is the complexity of knowing what you need to pay attention to when you create a DNA sequence from scratch. The same sequence is often instantiated at the DNA, RNA, and Protein levels, and there are different constraints on each of these systems and fairly fuzzy notions of what exactly needs to be avoided and specified in each case. On another level, the technology for building synthetic biology contraptions is really in its infancy, equivalent to at least in the vacuum tube age, if not the era of mechanical computers. The field is rapidly developing new methods, but these difficulties in just making what you imagine definitely limit the field. Furthermore, in many cases the parts themselves can degrade (due to mutating) when you grow them in lab. When this happens, it can take a lot of effort to track down when things went wrong because you can't directly "see" the problem in a DNA sequence. Jeffrey E. Barrick 14:05, 30 January 2012 (EST):

References

1. Micheal Owen. Herbicide-Resistant Weeds in Genetically Engineered Crops

2. Emily Waltz. Glyphosate resistance threatens Roundup hegemony. doi:10.1038/nbt0610-537

3. ISBN:0878934847