[HN Gopher] Trumpet is an operating system for simple and robust...
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Trumpet is an operating system for simple and robust cell-free
biocomputing
Author : aelnona
Score : 36 points
Date : 2023-12-17 11:27 UTC (1 days ago)
(HTM) web link (www.nature.com)
(TXT) w3m dump (www.nature.com)
| pushfoo wrote:
| > It is likely that the future of biocomputing hardware and
| software will likely include a combination of all three
| technologies [19]: live cell, enzyme-free, and enzymatic logic
| gates.
|
| This prediction has a bunch of fun implications for security:
|
| * Viruses and malware for such computers will also have a
| physical virus stage
|
| * Tradeoffs between DNA and traditional methods for data storage
|
| * A possible arms race between obfuscating and detecting unusual
| retrotranscriptases
| justinclift wrote:
| > Tradeoffs between DNA and traditional methods for data
| storage
|
| Wonder how badly it could go if the data storage container is
| ruptured while against someone's body?
|
| DNA cross contamination could be interesting, unlikely to be in
| any kind of good way.
| koeng wrote:
| > Wonder how badly it could go if the data storage container
| is ruptured while against someone's body?
|
| Nothing, really. Your body is good at fighting that sort of
| thing, because it's literally happening every second of every
| day with billions of bacteria and environmental DNA. Even
| specialized organisms have a rather tough time getting by all
| the defenses.
|
| For example, there are zero human-infecting raw-DNA
| pathogens.
| justinclift wrote:
| Cool, that makes sense. :)
| eternityforest wrote:
| Could at least some bio computers be hacked to print ebola
| viruses?
| pushfoo wrote:
| > Wonder how badly it could go if the data storage container
| is ruptured while against someone's body?
|
| TL;DR: pretty much zero unless you're immunocompromised
|
| The price tag of the broken equipment and bacterial
| infections are probably the biggest concerns.
|
| Genetic information is like software. It doesn't do anything
| unless it's in a compatible environment. Eukaryotic cells
| like those in plants, animals, fungi are delicate. Viruses
| which can write DNA into them without killing them have to be
| complicated, which makes the viruses delicate. Being this
| delicate means work with these cells and viruses can be very
| expensive.
|
| Why try to use a multi-Xeon server rack with fiber links when
| all you need is a cluster of 5 Raspberry Pis and a bare bones
| router? The latter is way cheaper.
|
| For the same reasons, well-understood bacterial models like
| tame E. Coli strains are popular in biocomputing [1]. Slime
| molds [2][3] are also popular, and they're even famously good
| at pathfinding.
|
| Your coworkers, however, might be annoyed that you broke the
| biocomputer again.
|
| [1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421265/
|
| [2] https://link.springer.com/referenceworkentry/10.1007/978-
| 3-6...
|
| [3] https://royalsocietypublishing.org/doi/10.1098/rsta.2014.
| 021...
| koeng wrote:
| > * A possible arms race between obfuscating and detecting
| unusual retrotranscriptases
|
| Why, exactly?
| pushfoo wrote:
| Using living cells as a read/write storage medium also makes
| them a target for malware. It's not limited to ransomware and
| classics, but also fun new possibilities [1]. Figuring out
| how to implement W^X should be a top research priority.
|
| [1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4270005/
| gonesilent wrote:
| Trumpet winsock
| kaycebasques wrote:
| > We have demonstrated the use of Trumpet to build all universal
| Boolean logic gates. We have also built a web-based platform for
| designing Trumpet gates and created a primitive processor by
| networking several gates as a proof-of-principle for future
| development.
|
| Sounds super cool. The website doesn't seem to be hosted on the
| web but they provide a ZIP download in the supplemental
| information section: https://static-
| content.springer.com/esm/art%3A10.1038%2Fs414...
|
| It's a bunch of Python files. No docs on how to get started but
| the filenames are reasonably semantic.
|
| Edit: the paper says it's supposed to be hosted at
| https://trumpet.bio/ but that's not working for me
|
| Edit again: http://trumpet.bio/ works (just not https)
| aconz2 wrote:
| My understanding is that they are picking a genome (in whole or
| in part synthetic / designed by them), a set of starting enzymes
| or transcription factors or the DNA sequence of those (not sure)
| (also in whole or in part synthetic), then running a computation
| by letting DNA transcription happen for some number of cycles,
| and finally read the output by some signaling protein like
| fluorescence that will either be present or absent depending on
| how you designed the initial conditions.
|
| To me, Trumpet sounds more like a compiler or circuit/program
| synthesizer than an operating system, since my understanding is
| you have some circuit in mind and the goal is to find a good
| genome (and/or the enzymes, not super sure yet) that can
| implement it. This means finding enzymes that will accurately
| promote or block transcription at a target location. And also
| checking against potential problems as the computation/reaction
| progresses since in a deep circuit depth you would presumably
| have many more kinds of things floating around that could
| interfere. I didn't see any mention on the circuit efficiency
| here, like how many base pairs per gate as # of gates increases,
| which I would guess would get larger faster than linear.
|
| They mention the signal amplification of many genomes being
| transcribed which is really neat (like error correction). Though
| makes me wonder if the output signal has a defined or expected
| duration of stability. If it is stable forever, it is like a
| fixed point or attractor, but I suspect unless under much greater
| design or control, things would change. And what is the latency
| of these gates?
|
| With cell-free, it seems plausible to design from-scratch genomes
| using a database of known proteins and that could be really cool.
| And funny to think about applying evolutionary search to
| determine the fittest genome for the job. From there we go to
| unicellular and then up to multicellular!
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