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Synthetic Biology: Engineering Open-Source Software with DNA

51 points by mgh2 14y ago

samirahmed 14y ago
Synthetic 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/ http://www.clothocad.org/
- sharpshoot 14y ago
  nice you worked on Merlin
- jostmey 14y ago
  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.
  - McGinness 14y ago
    DNA manipulation would be orders of magnitude more difficult and time consuming with out computers as would anything involving chemistry, molecular biology and understanding genetic structure. Apps and programming/automation have everything to do with the future of the field, its not just test tubes.
    - jostmey 14y ago
      True, but from what I've seen biologist for the most part can get along just fine with only a basic knowledge of REGEX and spreadsheet software. The biologist I've worked with tend to be a resourceful bunch, capable of solving difficult problems with simple tools. EDIT: Granted, there is a growing need for data-scientist who can help sort through mountains of data for relevant information. But I don't think there is much need for pre-built software solutions. Each lab faces unique problems, and their software development needs, if any, are unique.
  - nmb 14y ago
    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? :)
stiff 14y ago
First, 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 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 strive very hard to make parts independent and abstract away low-level details, in biology everything is interacting all the time (even physically the molecules clash hundreds of times per second) and every low-level physical/chemical effect might be used to serve some purpose. Evolutionary "design" does not have any limits to the intellectual complexity of its results like our limited human intelligence forces us to have in our "purposeful" design process. Even predicting the outcome of a single gene being expressed is very complicated, protein folding is now a separate field putting our knowledge of physics, chemistry, biology and computer science to a test, and what to say about predicting the interactions of those proteins inside the human body. I wish people would take a good university-level biology 101 course before making nonsensical simplifications and spreading those as "science news". By the way, I do not doubt this is an interesting initiative and that some useful things will come out of it, I just strongly oppose the notion that we can all now "play with nature’s design".
- jostmey 14y ago
  I totally agree with this! I wish we could "play with nature's design" like we can program computers. But alas, our technology is woefully inadequate for the task, and our understanding of the natural world is still sadly primitive. What is needed is a generation of people willing to commit themselves to basic science research. Working in basic science is perhaps not as glamorous as working as an entrepreneur, a programmer, or whatever else. But over the course of a lifetime, the work is infinitely more satisfying.
  - redwood 14y ago
    Curious what field and capacity you're working in basic science. I'm considering pivoting out of industry. Studied physics undergrad but quite frankly couldn't cut it to do so post-grad. However I do wonder if another field would be doable for me... but without prereqs I'm not sure how to get onto that path now (I'm not a coder, getting really into bio/chem/neuro/genetics). Been out of uni 6 yrs
jergosh 14y ago
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 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.
jostmey 14y ago
How 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.
- madhadron 14y ago
  Very important point. E. coli describes a range of organisms that share about 14% of their genome. For comparison, all of primates share over 99%. The strains everyone uses for genetic engineering are derived from strains isolated many decades ago and are incapable of colonizing hosts. They've also been selected over the years to be hysterical (they over respond to any stimulus, since when you're picking colonies to study response, you select the bright, clear one...and if you do it again and again over the years, you select for hysteria). Poking around, I couldn't find the strain they used. They might have engineered a gut isolate. They might not. Doesn't appear to say anywhere.
corwinbad 14y ago
Hi, 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 <X>": http://www.youtube.com/watch?v=F8qcDQaY8Mw http://www.youtube.com/watch?v=F8qcDQaY8Mw and at Leo Laporte Twit.tv: http://www.youtube.com/watch?v=BLhU1RGTHN4 http://www.youtube.com/watch?v=BLhU1RGTHN4
- terangdom 14y ago
  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?
cdi 14y ago
Make Anthrax/Bird Flu at home! Kill billions!
gms7777 14y ago
This may be nit-picking but in their diagram the color chart, portrayed visually as a venn-diagram, is rather misleading. It seems to imply that if you have colitis and worms, you have colorectal cancer. And if you have everything, you're A-OK. Really, a color wheel would have been a far better choice of diagram.
madhadron 14y ago
Others have already said this, but let's get it out in the open once and for all: Biochemistry has no relation to computation. Neuroscience has no relation to computation. Anatomy has no relation to computation. Ecology has no relation to computation. Someone using an computational image in any of these fields is trying to impart a sense of familiarity for his audience. If you actually want to learn any of these fields, you need to build your thought processes from scratch. No part of you works like a computer.

51 points by mgh2 14y ago

Synthetic 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/ http://www.clothocad.org/

sharpshoot 14y ago
nice you worked on Merlin
jostmey 14y ago
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.
- McGinness 14y ago
  DNA manipulation would be orders of magnitude more difficult and time consuming with out computers as would anything involving chemistry, molecular biology and understanding genetic structure. Apps and programming/automation have everything to do with the future of the field, its not just test tubes.
  - jostmey 14y ago
    True, but from what I've seen biologist for the most part can get along just fine with only a basic knowledge of REGEX and spreadsheet software. The biologist I've worked with tend to be a resourceful bunch, capable of solving difficult problems with simple tools. EDIT: Granted, there is a growing need for data-scientist who can help sort through mountains of data for relevant information. But I don't think there is much need for pre-built software solutions. Each lab faces unique problems, and their software development needs, if any, are unique.
- nmb 14y ago
  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? :)

stiff 14y ago

First, 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 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 strive very hard to make parts independent and abstract away low-level details, in biology everything is interacting all the time (even physically the molecules clash hundreds of times per second) and every low-level physical/chemical effect might be used to serve some purpose. Evolutionary "design" does not have any limits to the intellectual complexity of its results like our limited human intelligence forces us to have in our "purposeful" design process. Even predicting the outcome of a single gene being expressed is very complicated, protein folding is now a separate field putting our knowledge of physics, chemistry, biology and computer science to a test, and what to say about predicting the interactions of those proteins inside the human body. I wish people would take a good university-level biology 101 course before making nonsensical simplifications and spreading those as "science news". By the way, I do not doubt this is an interesting initiative and that some useful things will come out of it, I just strongly oppose the notion that we can all now "play with nature’s design".

jostmey 14y ago
I totally agree with this! I wish we could "play with nature's design" like we can program computers. But alas, our technology is woefully inadequate for the task, and our understanding of the natural world is still sadly primitive. What is needed is a generation of people willing to commit themselves to basic science research. Working in basic science is perhaps not as glamorous as working as an entrepreneur, a programmer, or whatever else. But over the course of a lifetime, the work is infinitely more satisfying.
- redwood 14y ago
  Curious what field and capacity you're working in basic science. I'm considering pivoting out of industry. Studied physics undergrad but quite frankly couldn't cut it to do so post-grad. However I do wonder if another field would be doable for me... but without prereqs I'm not sure how to get onto that path now (I'm not a coder, getting really into bio/chem/neuro/genetics). Been out of uni 6 yrs

jergosh 14y ago

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 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.

jostmey 14y ago

How 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.

madhadron 14y ago
Very important point. E. coli describes a range of organisms that share about 14% of their genome. For comparison, all of primates share over 99%. The strains everyone uses for genetic engineering are derived from strains isolated many decades ago and are incapable of colonizing hosts. They've also been selected over the years to be hysterical (they over respond to any stimulus, since when you're picking colonies to study response, you select the bright, clear one...and if you do it again and again over the years, you select for hysteria). Poking around, I couldn't find the strain they used. They might have engineered a gut isolate. They might not. Doesn't appear to say anywhere.

corwinbad 14y ago

Hi, 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 <X>": http://www.youtube.com/watch?v=F8qcDQaY8Mw http://www.youtube.com/watch?v=F8qcDQaY8Mw and at Leo Laporte Twit.tv: http://www.youtube.com/watch?v=BLhU1RGTHN4 http://www.youtube.com/watch?v=BLhU1RGTHN4

terangdom 14y ago
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?

cdi 14y ago

Make Anthrax/Bird Flu at home! Kill billions!

gms7777 14y ago

This may be nit-picking but in their diagram the color chart, portrayed visually as a venn-diagram, is rather misleading. It seems to imply that if you have colitis and worms, you have colorectal cancer. And if you have everything, you're A-OK. Really, a color wheel would have been a far better choice of diagram.

madhadron 14y ago

Others have already said this, but let's get it out in the open once and for all: Biochemistry has no relation to computation. Neuroscience has no relation to computation. Anatomy has no relation to computation. Ecology has no relation to computation. Someone using an computational image in any of these fields is trying to impart a sense of familiarity for his audience. If you actually want to learn any of these fields, you need to build your thought processes from scratch. No part of you works like a computer.