6 ms·

It seems like there has been more hype around synthetic biology in the tech press the last year or so, but it still feels like this field is being slept on a bi

It seems like there has been more hype around synthetic biology in the tech press the last year or so, but it still feels like this field is being slept on a bit. AGI gets a lot of press but is at best decades out, however one could argue that the potential (for good and bad) of synbio is close to as large, but the tech is much more real. In many cases it already exists -- we can modify human embryos, the first human study of CRISPR in the US kicked off a few weeks ago -- and in others it doesn't seem too far out I'm a non scientist and have been excited to learn more about this field, but to find out the most exciting stuff you need to read scientific papers. The details are the coolest parts IMO. A bit of self promo here, but I recently wrote a blog post summarizing a Stanford synbio paper in layman's terms [0]. [0] https://www.baybridgebio.com/blog/synbio-laymans-terms.html https://www.baybridgebio.com/blog/synbio-laymans-terms.html

deleted 7y ago
[deleted]
wetpaws 7y ago
Field stuck permanently in limbo because "ethics".
- amelius 7y ago
  Ethics are a good reason to postpone research in a certain direction. However, the frightening part is that countries with lower ethical standards can still do whatever they want and over time even gain a technological advantage over the US. We need to figure out how to deal with this.
  - wetpaws 7y ago
    Ethics is absolutely not an argument to postpone any kind of research. It does not solve the problem, it just hides it under a rug, essentially creating two problem out of one.
- The_rationalist 7y ago
  Why doesn't "ethics" account deaths caused by not allowing human DNA editing? Ethics is not a complex thing despite what most people believe. Utilitarism is scientifical ethics.
dhash 7y ago
(Full disclosure, i run a YC startup selling to synbio + think that it's undervalued) The field really doesn't do blog posts, it's a shame. For some interesting stuff in synbio that's approachable to your prototypical HNer, check out [1], a Verilog-to-DNA compiler that works with small logic circuits. [2] (Not really synbio) but using reed solomon codes to better do High-Throughput Screening. [3] PACE, a way to ask evolution to implement a particle filter for us. [4] A remapping of the base pair 3-tuple to amino acid that maximizes edit distance, filling in the gaps with STOP codons - stopping something from evolving, and [5] some cool people working on wholly synthetic cells. [1] Nielsen, A. A. K., Der, B. S., Shin, J., Vaidyanathan, P., Paralanov, V., Strychalski, E. A., … Voigt, C. A. (2016). Genetic circuit design automation. Science, 352(6281). https://doi.org/10.1126/science.aac7341 https://doi.org/10.1126/science.aac7341 [2] Erlich, Y., Gilbert, A., Ngo, H., Rudra, A., Thierry-Mieg, N., Wootters, M., … Zuk, O. (2015). Biological screens from linear codes: theory and tools. BioRxiv, I(1), 35352. [3] Dickinson, B. C., Leconte, A. M., Allen, B., Esvelt, K. M., & Liu, D. R. (2013). Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-assisted continuous evolution. Proceedings of the National Academy of Sciences, 110(22), 9007–9012. https://doi.org/10.1073/pnas.1220670110 https://doi.org/10.1073/pnas.1220670110 Esvelt, K. M., Carlson, J. C., & Liu, D. R. (2011). A system for the continuous directed evolution of biomolecules. Nature, 472(7344), 499–503. https://doi.org/10.1038/nature09929 https://doi.org/10.1038/nature09929 [4] https://www.biorxiv.org/content/10.1101/695569v2 https://www.biorxiv.org/content/10.1101/695569v2 [5] http://buildacell.io/ http://buildacell.io/
- The_rationalist 7y ago
  Well if you have time to waste (or to invest) I've made an analysis of how to cure ageing. I have some unanswered questions about what is feasible in DNA editing, maybe your knowledge could enlighten me? https://github.com/LifeIsStrange/An-algorithm-for-curing-ageing/blob/master/README.md https://github.com/LifeIsStrange/An-algorithm-for-curing-age... I would like an answer for e.g: https://github.com/LifeIsStrange/An-algorithm-for-curing-ageing/issues/4 https://github.com/LifeIsStrange/An-algorithm-for-curing-age...
- bigmit37 7y ago
  Thank you for this. I am also interested in this field and it’s hard to fib good info.
The_rationalist 7y ago
I agree with all you said and I wish more people would think like that. You might be interested by my analysis on how to cure ageing. https://github.com/LifeIsStrange/An-algorithm-for-curing-ageing/blob/master/README.md https://github.com/LifeIsStrange/An-algorithm-for-curing-age... >AGI gets a lot of press Does it? Yes AGI in sci-fi (e.g matrix) is not new. But the medias and even the AI journals do almost 0 press about AGI. Narrow (specialized) AI is now mainstream, especially the deep learning paradigm. But clearly solving an NLP task is not building an AGI.. At best it's solving a constituent of an AGI. But many constituents of an AGI does not have an NLP task, which means mostly nobody work on it. An AGI, to be implemented need a big, sound, cognitive architecture. AGI gets a lot of press So, can you name at least one AGI architecture? Nobody knows nor talk about them. To name the two most promising: Cyc and opencog. https://www.google.com/url?sa=t&source=web&rct=j&url=https://wiki.opencog.org/w/OpenCogPrime:Cognitive_Architecture&ved=2ahUKEwj-_9-w66vkAhUIzIUKHVtqC8kQFjAAegQIAxAB&usg=AOvVaw3K4xu7OYxKMw70CyEN47Yy&cshid=1567211136741 https://www.google.com/url?sa=t&source=web&rct=j&url=https:/... Well currently the website is down... But it is enlightening to read such an architecture.
- space_fountain 7y ago
  I'm no biologist, but I think you're missing some causes of aging. DNA isn't the only thing that has to stay mutation free for an organism to not age. Lots of the cellular machinery will propagate error to future generations. For a simple example see prion diseases. Sure they seem big scary and rare, but I'd suspect in reality this sort of thing happens way more often than we probably realize just in ways that can't be spread person to person even via cannibalism or that has much lower consequences. Keep in mind also that ending aging is striving against not just entropy but evolution. Cancer cells are selected for. Obviously not on a species level, but if even just one cell messes and starts reproducing out of control it will quickly take over. You can implement more checks along the way and repair damage as it comes up, but the point remains that if even just one cell somehow isn't effected, it will be selected for among all the cells that make you up.
  - The_rationalist 7y ago
    Thank you for the feedback! DNA isn't the only thing that has to stay mutation free for an organism to not age. Could we draw a list? Your example on prion is incorrect as prion are misfolded proteins made by buggy DNA genes. https://en.m.wikipedia.org/wiki/Prion https://en.m.wikipedia.org/wiki/Prion Another thing that I identify as contributing to aging other than cell DNA is mitochondrial DNA (it's weird to realize we have two different DNA in each cells) Does other organelles apply? I fking don't know and how could I? :(

deleted 7y ago

[deleted]

wetpaws 7y ago

Field stuck permanently in limbo because "ethics".

amelius 7y ago
Ethics are a good reason to postpone research in a certain direction. However, the frightening part is that countries with lower ethical standards can still do whatever they want and over time even gain a technological advantage over the US. We need to figure out how to deal with this.
- wetpaws 7y ago
  Ethics is absolutely not an argument to postpone any kind of research. It does not solve the problem, it just hides it under a rug, essentially creating two problem out of one.
The_rationalist 7y ago
Why doesn't "ethics" account deaths caused by not allowing human DNA editing? Ethics is not a complex thing despite what most people believe. Utilitarism is scientifical ethics.

dhash 7y ago

(Full disclosure, i run a YC startup selling to synbio + think that it's undervalued) The field really doesn't do blog posts, it's a shame. For some interesting stuff in synbio that's approachable to your prototypical HNer, check out [1], a Verilog-to-DNA compiler that works with small logic circuits. [2] (Not really synbio) but using reed solomon codes to better do High-Throughput Screening. [3] PACE, a way to ask evolution to implement a particle filter for us. [4] A remapping of the base pair 3-tuple to amino acid that maximizes edit distance, filling in the gaps with STOP codons - stopping something from evolving, and [5] some cool people working on wholly synthetic cells. [1] Nielsen, A. A. K., Der, B. S., Shin, J., Vaidyanathan, P., Paralanov, V., Strychalski, E. A., … Voigt, C. A. (2016). Genetic circuit design automation. Science, 352(6281). https://doi.org/10.1126/science.aac7341 https://doi.org/10.1126/science.aac7341 [2] Erlich, Y., Gilbert, A., Ngo, H., Rudra, A., Thierry-Mieg, N., Wootters, M., … Zuk, O. (2015). Biological screens from linear codes: theory and tools. BioRxiv, I(1), 35352. [3] Dickinson, B. C., Leconte, A. M., Allen, B., Esvelt, K. M., & Liu, D. R. (2013). Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-assisted continuous evolution. Proceedings of the National Academy of Sciences, 110(22), 9007–9012. https://doi.org/10.1073/pnas.1220670110 https://doi.org/10.1073/pnas.1220670110 Esvelt, K. M., Carlson, J. C., & Liu, D. R. (2011). A system for the continuous directed evolution of biomolecules. Nature, 472(7344), 499–503. https://doi.org/10.1038/nature09929 https://doi.org/10.1038/nature09929 [4] https://www.biorxiv.org/content/10.1101/695569v2 https://www.biorxiv.org/content/10.1101/695569v2 [5] http://buildacell.io/ http://buildacell.io/

The_rationalist 7y ago
Well if you have time to waste (or to invest) I've made an analysis of how to cure ageing. I have some unanswered questions about what is feasible in DNA editing, maybe your knowledge could enlighten me? https://github.com/LifeIsStrange/An-algorithm-for-curing-ageing/blob/master/README.md https://github.com/LifeIsStrange/An-algorithm-for-curing-age... I would like an answer for e.g: https://github.com/LifeIsStrange/An-algorithm-for-curing-ageing/issues/4 https://github.com/LifeIsStrange/An-algorithm-for-curing-age...
bigmit37 7y ago
Thank you for this. I am also interested in this field and it’s hard to fib good info.

The_rationalist 7y ago

I agree with all you said and I wish more people would think like that. You might be interested by my analysis on how to cure ageing. https://github.com/LifeIsStrange/An-algorithm-for-curing-ageing/blob/master/README.md https://github.com/LifeIsStrange/An-algorithm-for-curing-age... >AGI gets a lot of press Does it? Yes AGI in sci-fi (e.g matrix) is not new. But the medias and even the AI journals do almost 0 press about AGI. Narrow (specialized) AI is now mainstream, especially the deep learning paradigm. But clearly solving an NLP task is not building an AGI.. At best it's solving a constituent of an AGI. But many constituents of an AGI does not have an NLP task, which means mostly nobody work on it. An AGI, to be implemented need a big, sound, cognitive architecture. AGI gets a lot of press So, can you name at least one AGI architecture? Nobody knows nor talk about them. To name the two most promising: Cyc and opencog. https://www.google.com/url?sa=t&source=web&rct=j&url=https://wiki.opencog.org/w/OpenCogPrime:Cognitive_Architecture&ved=2ahUKEwj-_9-w66vkAhUIzIUKHVtqC8kQFjAAegQIAxAB&usg=AOvVaw3K4xu7OYxKMw70CyEN47Yy&cshid=1567211136741 https://www.google.com/url?sa=t&source=web&rct=j&url=https:/... Well currently the website is down... But it is enlightening to read such an architecture.

space_fountain 7y ago
I'm no biologist, but I think you're missing some causes of aging. DNA isn't the only thing that has to stay mutation free for an organism to not age. Lots of the cellular machinery will propagate error to future generations. For a simple example see prion diseases. Sure they seem big scary and rare, but I'd suspect in reality this sort of thing happens way more often than we probably realize just in ways that can't be spread person to person even via cannibalism or that has much lower consequences. Keep in mind also that ending aging is striving against not just entropy but evolution. Cancer cells are selected for. Obviously not on a species level, but if even just one cell messes and starts reproducing out of control it will quickly take over. You can implement more checks along the way and repair damage as it comes up, but the point remains that if even just one cell somehow isn't effected, it will be selected for among all the cells that make you up.
- The_rationalist 7y ago
  Thank you for the feedback! DNA isn't the only thing that has to stay mutation free for an organism to not age. Could we draw a list? Your example on prion is incorrect as prion are misfolded proteins made by buggy DNA genes. https://en.m.wikipedia.org/wiki/Prion https://en.m.wikipedia.org/wiki/Prion Another thing that I identify as contributing to aging other than cell DNA is mitochondrial DNA (it's weird to realize we have two different DNA in each cells) Does other organelles apply? I fking don't know and how could I? :(