7 ms·
A little while ago, a patent for high throughput DNA synthesis using silicon chips went off-patent, so I have been learning analog IC chip design to build an op
by koeng 4y ago
A little while ago, a patent for high throughput DNA synthesis using silicon chips went off-patent, so I have been learning analog IC chip design to build an open source high-throughput DNA synthesis chip. If it works, and I sold them at cost, it would reduce the cost of oligo pool synthesis by ~100x and possibly gene synthesis by 10x.
For about 8-9 years now my goal has been to build a cell from scratch for less than $1000 and enable anyone to be able to do so. While I’m handling the other bits elsewhere, DNA synthesis is a key technology primed for open source disruption.
- iron2disulfide 4y ago(Digital) chip designer here: this is super cool. What tech node are you targeting? Have you checked out any of the free open-source tools and PDK from Skywater, Google, eFabless and co?
- koeng 4y agoI'm planning on using the chip ignite program! They can build the chip I need - the harder bit is figuring out the coatings needed (sputter coating post-processing is needed to be compatible with the chemistry). I am pretty new to chip design but know the DNA space quite well - I would love to do a call, if possible, because I have lots of noob questions about chip design and chip design tools. Happy to share anything about the biological side in exchange!
- peteradio 4y ago
- LunarCamper 4y agoIs there a page, blog, twitter account, newsletter, Github repo or anything to follow this? I have no knowledge in this space so I'm of no help, but I'm very interested in the prospect of this stuff becoming more accessible!
- dialdial 4y agoLikewise, piggybacking!
- koeng 4y agoGithub here - https://github.com/koeng101/dnachips https://github.com/koeng101/dnachips It is a bit dead when it comes to a git, since I am trying to get the first machine needed, which is a DNA synthesizer (asked about that here https://groups.google.com/g/diybio/c/V3OYVBxaH04 https://groups.google.com/g/diybio/c/V3OYVBxaH04 for example). The idea is that with a traditional DNA synthesizer I can have positive controls of the chemistry, and develop a chip that can fit inside the flow cell of the existing synthesizer. In biotech, everything goes wrong a bit more often than in computer science, so the focus lately has been getting my hands on a working synthesizer. This is a tried and true method of getting chip synthesis working. If that works, I'd like to provide the chip at cost for integrators, as well as develop a functioning full product for integration with some bots I'm building for my official work. Personal website is here - http://keonigandall.com http://keonigandall.com
- natch 4y agoSounds fascinating, what could possibly go wrong? “Your scientists were so preoccupied with whether or not they could, they didn't stop to think if they should.” —Dr. Ian Malcolm (Jurassic Park).
- neodypsis 4y agoWhat's your point? The technology already exists and is being used.
- natch 4y agoYour name, password, and the names and addresses and phone numbers and emails of all your family members already exist and are being used. So, by your logic, you have no reason to share them to everyone? The logic doesn’t hold up. You can make the same argument for anything. It makes sense to think about the dangers, not pretend that bad logic is an excuse to do anything you want.
- algoatecorn 4y agoNo, actually your first sentence's logic doesn't hold up as it isn't a fair comparison at all. You can already order custom oligos and synthesized genes for relatively cheap. The chip idea would just reduce the cost more.
- durkie 4y agothis sounds so cool! i wish you the best luck with it.
- neodypsis 4y agoPretty cool. May I ask, what is your background? And, what resources are you using to learn about analog IC chip design?
- koeng 4y ago~10yr of synthetic bio, did 4yr of mitochondrial engineering + directed evolution at UCI, then ran the FreeGenes Project for 3yr at Stanford. Chisel for programming it (great little lang/project) https://www.amazon.com/Digital-Design-Chisel-Martin-Schoeberl/dp/168933603X https://www.amazon.com/Digital-Design-Chisel-Martin-Schoeber... Efabless PDKs - https://efabless.com/ https://efabless.com/ Other than that, lots of trial and error. Hardware people are brutal with their acronyms, so it really comes down to a lot of stumbling around and reading whatever I can.
- neodypsis 4y agoVery cool. Best of luck!
- PontifexMinimus 4y agoHow will you prevent people from using this technology to create DIY pathogens? If the answer is "I won't" or "it'll be open source, I won't be able to", consider doing something less harmful instead.
- algoatecorn 4y agoSynthesizing oligos is not the same thing as creating an infectious clone. This technology would be used to synthesize primers and custom promoter+gene fragments.
- thfuran 4y agoHow far down this road do you go? Someone engaged in bioweapons manufacturing probably uses laptops and chairs too.
- bqmjjx0kac 4y agoThe difference is that those already exist. I think concern about the development of new technology is valid. Suppose nuclear weapons did not exist and someone was concerned about the Manhattan project — would you say that chairs enable people to build regular bombs, so we shouldn't worry about nuclear bombs?
- f1shy 4y agoThe technology already exist. The OP stated, patents are over, and that is why (s)he is working on it. Even if it not exist, security by obscurity is no security... if anybody can do the tech, the bad guys are going to be as fast, or faster than the good guys... So I hope the good guys do the tech for everybody...
- EricMausler 4y agoYou are severely underplaying how chaotic people can be, and how valuable a barrier to entry is at deterring that chaos from causing damage.
- jfim 4y agoNot knowing anything about this field, what could someone do with such a chip? Is it something like a 3D printer where you can get a rough but usable finished product, or is it more like a "if you want to make bacterium X produce Y product, you need to do X, Y, Z, W, etc." and the chip is used to do one of the steps.
- koeng 4y agoIt is more like the X Y Z W. However, the X Y Z W bits I am working on as well (https://github.com/TimothyStiles/poly https://github.com/TimothyStiles/poly , https://github.com/TimothyStiles/allbase https://github.com/TimothyStiles/allbase , trilo.bio, freegenes.org). Going for fully automated "make bacterium X produce molecule Y", but still a while away (but surprisingly not THAT far off)
- jfim 4y agoThat's really cool! I was about to ask how to get started on that field, but I also noticed that you have that covered in https://github.com/TimothyStiles/how-to-synbio https://github.com/TimothyStiles/how-to-synbio
- Dracophoenix 4y ago> so I have been learning analog IC chip design to build an open source high-throughput DNA synthesis chip. Any resources and books you'd recommend?
- elicash 4y agoThis is not at all an area I know anything about, but a podcast I was listening to (Moore's Lobby) recently mentioned on chip design broadly: https://www.zerotoasiccourse.com https://www.zerotoasiccourse.com And also: https://www.udemy.com/user/anagha/ https://www.udemy.com/user/anagha/
- Dracophoenix 4y agoThank you!
- koeng 4y agoAs a software engineer, verily and the like just didn't make as much sense to me as chisel. Got this book and have been very slowly working through it - https://www.amazon.com/Digital-Design-Chisel-Martin-Schoeberl/dp/168933603X https://www.amazon.com/Digital-Design-Chisel-Martin-Schoeber... Efabless's chip ignite program is also great - check it out! https://efabless.com https://efabless.com
- O__________O 4y agoFor anyone interested, found following blog post on OP’s website, which is linked to from their HN profile: _____ How to make DNA synthesis affordable https://keonigandall.com/posts/affordable_dna_2.html https://keonigandall.com/posts/affordable_dna_2.html
- waiquoo 4y agoHaving worked at the largest synthetic DNA manufacturer (at least they were, I think they still are)... a lot of his information is just wrong. There is a huge incentive to lowering the cost of producing oligos and synthetic genes. This is actually a very interesting time in the space (shoutout AnsaBio). I encourage him to continue explore new ways of making DNA, but understanding the market is very different from building off an expired patent.
- koeng 4y agoI’ve spoken to the CEO of Ansa bio about this topic and they aren’t focused on lowering prices, but increasing what can be built. I would like to know what specifically you think I am wrong about, though. Always happy to improve my thinking.
- imnotreallynew 4y agoDo you mean completely from scratch? If so, why would one want to do that versus taking an existing cell and injecting custom DNA?
- koeng 4y agoYou can't jump over fitness troughs. For example, full tRNA recoding. Plus, it is neat to make life from chemicals.
- hcks 4y agoI don't understand why, if it really worked, the org holding the patent didn't do anything of it.
- cultofmetatron 4y agokodak invented digital photography
- koeng 4y agoThey did. This runs genscript's high throughput DNA synthesis platform. They actively sell the result as their oligo pool product.
- eezurr 4y agoI'd just like to echo (verbally "vote") my concern. Every great step forward comes with the potential for an order of magnitude steps backward, i.e. destruction. The amount of man hours to e.g. blow up a building is far fewer than the amount needed to build it. Will the output of your product add a suicide timer to a cell? Will the output of your product prevent the cells from procreating/multiplying? Will the output of your product prevent pathogen creation? Will the output of your product require a specific, unnatural energy source that can only be man made? Professionals take great care in thinking about those problems, and sometimes still fail. (IIRC, a synthesized breed of mosquitos that were released in Brazil failed to die off and are now a part of the biosystem). [0] https://www.dw.com/en/genetically-modified-mosquitoes-breed-in-brazil/a-50414340 https://www.dw.com/en/genetically-modified-mosquitoes-breed-...
- FerociousTimes 4y ago> Will the output of your product prevent the cells from procreating/multiplying? How would unicellular organisms procreate exactly?! I am not being pedantic here but procreation usually entails sexual reproduction and I don't see how this is possible for these organisms.
- zxexz 4y agoI'm pretty sure procreation just refers to the process of reproduction, sexual and asexual inclusive.
- FerociousTimes 4y agoMy understanding of the pertinent terms in this specific context is as follows: 1) Multiplying: Asexual reproduction only. 2) Reproduction: Sexual and asexual reproduction. 3) Procreation: Sexual reproduction only.
- zxexz 4y agoI appreciate the way you understand the terminology. However, I'm not sure everyone else understands it the same way. Although, I do admit the terms can be confusing. BTW: I don't see how 'multiplying' could refer to just asexual reproduction. People often use it in sentences like 'the deer population near here multiplied the last couple years'.