Past participant of iGEM (International Genetically Engineered Machine, the competition mentioned in the article) here. Infuriatingly, this writeup fails to mention that the E. chromi (and all the other projects) was carried out by undergraduate students (this is the team: http://2009.igem.org/Team:Cambridge/Team), perhaps because it makes it sound less trustworthy and sellable. According to the same website, the "designer Daisy Ginsberg" was involved peripherally, at best.
Synthetic Biology: Engineering Open-Source Software with DNA
11–20 of 35 posts
Re: Synthetic Biology: Engineering Open-Source Software with DNA
#12How do they prevent the E. Chromi bacteria from eventually being displaced by other non color coding poo bacteria? It seems to me that even if the E. Chromi did work as advertised, that the bacteria would quickly (within days) disappear from your intestinal track.
If anything, I would suspect that the E. Chromi would be at an evolutionary disadvantage in the gut. This is because the E. Chromi would be expending effort trying to color code poo, while their neighboring bacteria would just be focused on digesting and reproduction. Based on the principles of evolution, I would expect the E. Chromi bacteria to disappear entirely from the gut with a few thousand generations of bacteria.
Re: Synthetic Biology: Engineering Open-Source Software with DNA
#13Hi, My name is Omri and I'm the founder of Genome Compiler (genomecompiler.com) - we built a free app for designing and ordering of synthetic DNA - check it out!
also gave a talk at Google "solve for ": http://www.youtube.com/watch?v=F8qcDQaY8Mw and at Leo Laporte Twit.tv: http://www.youtube.com/watch?v=BLhU1RGTHN4
Re: Synthetic Biology: Engineering Open-Source Software with DNA
#14Synthetic Biology is in great need for computational tools and expertise to help advance the field. Platforms like ClothoCAD are great places for those interested in open-source software and syn-bio applications. http://www.clothocad.org/
Don't deceive yourself into thinking that you can program your way into biological research. Biological research has very little to do with apps/programming/web-development. Synthetic biology requires an understanding of chemistry, molecular biology, and genetic structure.
What if I have that knowledge (in addition to software engineering) and would like to contribute in some sort of open-source capacity? Know of any other projects I could look into? :)
Re: Synthetic Biology: Engineering Open-Source Software with DNA
#15Make Anthrax/Bird Flu at home! Kill billions!
Re: Synthetic Biology: Engineering Open-Source Software with DNA
#16First, DNA is not software and second, before we all get too excited about "Arudino for organisms", have a look at the actual parts: http://partsregistry.org/Catalog The biological world is very different from the world of man-made devices and you cannot expect to easily engineer, and even more so, to "program" things using DNA the way you build something from NAND gates or computer instructions - in engineering we s…
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Re: Synthetic Biology: Engineering Open-Source Software with DNA
#17First, DNA is not software and second, before we all get too excited about "Arudino for organisms", have a look at the actual parts: http://partsregistry.org/Catalog The biological world is very different from the world of man-made devices and you cannot expect to easily engineer, and even more so, to "program" things using DNA the way you build something from NAND gates or computer instructions - in engineering we s…
While I might agree with your general point that biology is not software, I think you might be being a little too pessimistic for the field as a whole. You don't need to predict the "outcome" as you define it. You just have to get the function you want. Plenty of people, even high school students and undergraduates, are "playing with nature's design."
Re: Synthetic Biology: Engineering Open-Source Software with DNA
#18First, DNA is not software and second, before we all get too excited about "Arudino for organisms", have a look at the actual parts: http://partsregistry.org/Catalog The biological world is very different from the world of man-made devices and you cannot expect to easily engineer, and even more so, to "program" things using DNA the way you build something from NAND gates or computer instructions - in engineering we s…
While I might agree with your general point that biology is not software, I think you might be being a little too pessimistic for the field as a whole. You don't need to predict the "outcome" as you define it. You just have to get the function you want. Plenty of people, even high school students and undergraduates, are "playing with nature's design."
I am not necessarily pessimistic, I do believe smart people will be able to work those things out and some maybe even will put them to good use, I am just an opponent of oversimplifying problems and sceptical of metaphors. You say: You just have to get the function you want, I would put it more as You have to get just the function you want and I think this isn't as simple, especially when those artificial organisms start interacting with environments more complex than a test tube e.g. the human body. In this case, outside of the laboratory, I think it would be valuable to know what we are doing and not "play".
This probably depends a lot on the context you would like to use those things in, but in general there are lots of warnings about potential unexpected interactions in descriptions of some of the parts and the practical projects seem to have lots of safety precautions too.
Re: Synthetic Biology: Engineering Open-Source Software with DNA
#19First, DNA is not software and second, before we all get too excited about "Arudino for organisms", have a look at the actual parts: http://partsregistry.org/Catalog The biological world is very different from the world of man-made devices and you cannot expect to easily engineer, and even more so, to "program" things using DNA the way you build something from NAND gates or computer instructions - in engineering we s…
My prediction: We can find a subset of proteins such that they do not interfere with each other, and still large enough that they can perform useful functions.
It is possible to write threaded software in a way that everything interacts with everything and it is almost impossible to make out how anything works. That's why we don't. The halting problem never stopped us from writing software.
Re: Synthetic Biology: Engineering Open-Source Software with DNA
#20Hi, My name is Omri and I'm the founder of Genome Compiler (genomecompiler.com) - we built a free app for designing and ordering of synthetic DNA - check it out! also gave a talk at Google "solve for ": http://www.youtube.com/watch?v=F8qcDQaY8Mw and at Leo Laporte Twit.tv: http://www.youtube.com/watch?v=BLhU1RGTHN4
Very cool idea! I think you should think carefully about the use cases.
Is it for someone who wants to take a gene from one organism, move it to another and then order that organism? Is it for people wanting to manually tweak genes to improve efficiency, slightly change function? What kinds of manual tweaks? Is it for someone who wants to understand how an organism works?
When /I/ look at it, I think it could benefit from being more abstract, but I am not your target audience, so take this with a grain of salt. I don't think looking at individual base pairs is useful. Amino acids might be, but are still too emphasized in the interface. The most abstract view, showing genes in order is not abstract enough. I want to see genes grouped by function (e.g. reproductory system, energy production, acidity regulation etc). For each gene I want to see:
a) High level description of function (already there, but in a single line text field. Give more screen estate).
b) What activates the gene? i) Directly (e.g high concentration of Na+) ii) Indirectly (e.g. genes a, b, c) iii) Very Indirectly (environmental stress)
c) As exact specification as possible of what happens when it is activated: i) What does it activate in turn? ii) What does it catalyze?