"Conputing"?
Biology Will Be the Next Great Computing Platform
51–60 of 73 posts
Re: Biology Will Be the Next Great Computing Platform
#52Earlier quoted context omitted.
Analog computers were just digital computers with a different computational paradigm. That is, they had the same IO mechanisms, just how the Input became Output was slightly tweaked. Biological computing will be interesting primarily because it will be able to build things, which neither analog nor digital computers are particularly good at. It's an entirely different paradigm. The act of computation can also be the…
> Analog computers were just digital computers with a different computational paradigm. No, there are fundamental differences. Digital computation is inherently error correcting because there are only two states — on or off. With analog computing, errors compound over long times and there’s fundamentally no way to fix this (it’s not just “hard”, it’s theoretically impossible). That’s why analog computation is fundame…
This is another case of "cutting off my quote too early".
Compared to the difference between what biological computation and digital computation is going to look like, what we call analog and digital computers are brothers, because they share the same basic IO. ("No, they have differences..." Yes, they do... but compare to biology. A valid input to a biological computation process will be your physical body. Not some numeric representation of it, but the actual thing. This is inconceivably foreign to either the modern digital computer paradigm or anything we've ever called an analog computer. By comparison, whether someone is typing "17.213" onto a screen or setting a dial somewhere vaguely in the region of 17 is a minor detail!)
Biological computation won't be digital. It'll have digital components, but it will neither be intrinsically digital the way current computing is as it will inevitably be operating in an analog domain, nor will it resemble our current computing paradigms.
Re: Biology Will Be the Next Great Computing Platform
#53Earlier quoted context omitted.
But what if there was a way to write algorithms that can't be expressed with a von Neumann architecture? Do you know where I can read about what categories of biocomputation there are? Is there a biological Turing machine that's ever been built, or no, I guess it'd be grown? As another commenter said, computation is a more vast category than the simplicity of one instruction and then another instruction. Fantastic th…
> But what if there was a way to write algorithms that can't be expressed with a von Neumann architecture? There almost certainly isn’t, due to the universality of computation (see the Church–Turing hypothesis). At any rate, even if this hypothesis turns out to be false (almost unthinkable), DNA won’t offer anything beyond what classical von Neumann architecture offers. > Do you think someday that biological computin…
I know it was off the track of the article, I was gravitating to the more interesting idea.
Thanks for your time!
Re: Biology Will Be the Next Great Computing Platform
#54As someone who has a PhD in biochemistry and has been coding since age 5, I find the headline rediculous. You won't be computing in biology. Consider, a transistor is about 50-100 atoms wide. A protein, which cannot itself even be a minimal unit of compute, (maybe a molecular transistor like NiFe hydrogenase has a shot) is already bigger than that. The things described in the article are not biology used for computat…
But what if there was a way to write algorithms that can't be expressed with a von Neumann architecture? Do you know where I can read about what categories of biocomputation there are? Is there a biological Turing machine that's ever been built, or no, I guess it'd be grown? As another commenter said, computation is a more vast category than the simplicity of one instruction and then another instruction. Fantastic th…
I can't answer you directly but perhaps this helps too.
I recently finished Summa Technologiae from Stanislaw Lem which does investigate a lot of these questions in many of its chapters.
I highly recommend it as it is a detailed, vivid exploration written by a very wise person so much so that it is easy to forget while reading that the book was published more than 50 years ago.
But there's also a practical reason why you might be interested in it even if you wouldn't think anything of a personal(?) recommendation from someone on the internet.
It is based on a lot of academic papers Lem read from all sorts of fields, which are all referenced (at least they were in the version I've read), so it should be easy to then start to look for more recent papers based on those.
Re: Biology Will Be the Next Great Computing Platform
#55Earlier quoted context omitted.
Do you mean the effect of the actual gene knockout, crispr specificity or off-spot mutations?
CRISPR specificity. Designing good gRNAs isn’t quite trivial, although it’s not as hard as the article makes it seem. I’m not sure about the claim of reducing the time of experiments by “month”.
http://crispr.mit.edu/about
Designing a good gRNA is quite straightforward if you compare it to any other bioinformatics tasks. Even designing a degenerate primer is more complex than this.
Re: Biology Will Be the Next Great Computing Platform
#56As someone who has a PhD in biochemistry and has been coding since age 5, I find the headline rediculous. You won't be computing in biology. Consider, a transistor is about 50-100 atoms wide. A protein, which cannot itself even be a minimal unit of compute, (maybe a molecular transistor like NiFe hydrogenase has a shot) is already bigger than that. The things described in the article are not biology used for computat…
Forgive me, but did your message not spring from a biological computing device which is arguably the most marvellous material object to exist in the known universe?
You'll have to convince me that what makes us special is hardware and not software.
Re: Biology Will Be the Next Great Computing Platform
#57As someone who has a PhD in biochemistry and has been coding since age 5, I find the headline rediculous. You won't be computing in biology. Consider, a transistor is about 50-100 atoms wide. A protein, which cannot itself even be a minimal unit of compute, (maybe a molecular transistor like NiFe hydrogenase has a shot) is already bigger than that. The things described in the article are not biology used for computat…
Clickbait aside, I think there are vast possibilities for DNA to be used as a fabrication tool. Imagine a seed you could plant and it would rapidly grow in the shape of a house, using nothing but sunlight, atmospheric CO2 and a bit of fertilizer. Also, by controlling the expression of biological features you could create bioelectronic hybrids that leverage the best of both worlds. Imagine you ship to Mars a few pound…
> I believe the idea is not using DNA for general purpose programming as much as controlling biological systems using the paradigms of the software world.
That's not a new idea. I was doing this in grad school. In my postdoc, my boss wanted to rewrite the DNA control structures of our system. I overrode him and told him that the biochemistry needed to be fixed (manipulating the amino acid sequence and not the promoters). On my branch of the track, I got a 16x improvement in yield (we started from trace). On his branch there was no effect.
Re: Biology Will Be the Next Great Computing Platform
#58As someone who has a PhD in biochemistry and has been coding since age 5, I find the headline rediculous. You won't be computing in biology. Consider, a transistor is about 50-100 atoms wide. A protein, which cannot itself even be a minimal unit of compute, (maybe a molecular transistor like NiFe hydrogenase has a shot) is already bigger than that. The things described in the article are not biology used for computat…
"As someone who has a PhD in biochemistry and has been coding since age 5, I find the headline rediculous. You won't be computing in biology.... principles from CS applied to biology which has some validity." I think it may be worth reminding people that modern-day computing is only a subset of computation, and not even necessarily a very large one. Computing with biology has extremely different characteristics from…
Computing with biology would be more like the "movable feast" computing architecture videos on YouTube. Prepare to be out-neckbearded if you watch them. Not sure how useful it would be. You don't want your bank account running on such a machine.
Part of what makes computing extremely useful is that it's a crutch that lets us do things our feeble human minds can't do. Logical purity, high numerical computation, immutable logging and provenance. At the edge we start to tolerate imprecision in some domains like hci and decision making when there's a premium attached to the process, that statistically (or if we're being cynical, projects the appearance of) yields an improvement, like being able to ingest high inhuman volumes of data, or where human interaction in the correction of erroneous processing is proximal and minimally effort inducing.
Re: Biology Will Be the Next Great Computing Platform
#59As someone who has a PhD in biochemistry and has been coding since age 5, I find the headline rediculous. You won't be computing in biology. Consider, a transistor is about 50-100 atoms wide. A protein, which cannot itself even be a minimal unit of compute, (maybe a molecular transistor like NiFe hydrogenase has a shot) is already bigger than that. The things described in the article are not biology used for computat…
"As someone who has a PhD in biochemistry and has been coding since age 5, I find the headline rediculous. You won't be computing in biology.... principles from CS applied to biology which has some validity." I think it may be worth reminding people that modern-day computing is only a subset of computation, and not even necessarily a very large one. Computing with biology has extremely different characteristics from…
It will be different, but concurrency, mutability, structured programming, and scope are very relevant.
Concurrency: Not all genes are run at all times. Gene regulation can look a lot like code. Ex: if(curr_temp > DANGER_TEMP){temperature_defense_gene.activate()}.
Mutability & Scope: Cells that have the same genome can act very differently (all of your cells have ~the same DNA, but act very differently) and some cells in your body can change roles.
Structured Programming: Biological pathways use a lot of control flows. [1]
Re: Biology Will Be the Next Great Computing Platform
#60As someone who has a PhD in biochemistry and has been coding since age 5, I find the headline rediculous. You won't be computing in biology. Consider, a transistor is about 50-100 atoms wide. A protein, which cannot itself even be a minimal unit of compute, (maybe a molecular transistor like NiFe hydrogenase has a shot) is already bigger than that. The things described in the article are not biology used for computat…
But what if there was a way to write algorithms that can't be expressed with a von Neumann architecture? Do you know where I can read about what categories of biocomputation there are? Is there a biological Turing machine that's ever been built, or no, I guess it'd be grown? As another commenter said, computation is a more vast category than the simplicity of one instruction and then another instruction. Fantastic th…