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I wonder would it be possible to accelerate a synthetic cell's evolution via software? If you already know exactly what's in the cell (you built it!) could a c

I wonder would it be possible to accelerate a synthetic cell's evolution via software? If you already know exactly what's in the cell (you built it!) could a computer speed up its life via a software model and jump ahead to something more complex which you build as version 2?

daveguy 11y ago
That would be awesome, but it is unlikely with current software and hardware. Even small scale simulations (nanoseconds to microseconds of a single protein molecule) require hours of sim time (on large clusters).
- saalweachter 11y ago
  To elaborate, time is the problem. The number of atoms in the smallest viable cell is actually reasonably small, less than a billion atoms, such that you could hope to store it all in memory on a single beefy computer. Meanwhile, you need something like picosecond resolution in the simulation, while you need seconds of simulated time to see interesting macro-level things happen. If you want to see cell division, you're probably talking a minimum of thirty minutes of simulated time.
- ealloc 11y ago
  Not to mention that the molecular dynamics simulations you're describing can't actually simulate chemical reactions. (the covalent bonds can't change in the sim, unless you do a much more intensive QM calculation and even that's iffy).
gpvos 11y ago
If you want evolution, you would also have to simulate the cell's environment. Without an environment, there's no natural selection and thus no evolution.
adrianN 11y ago
It would be cool to play with this idea using the OpenWorm platform.
sixdimensional 11y ago
Actually, I was wondering if a learning algorithm could be coupled with a builder that uses real synthetically created biological components in an automated system. This way, the builder comes up with new combinations, automates all the science around evaluating the combination as quickly and automatically as possible, and the software/learning algorithm controls the development towards some generalized goal. Ok, I admit this sounds ridiculously sci-fi, but, why do I feel like this is actually possible (just really, really hard)? EDIT: To clarify, I am actually suggesting a real living system coupled with software/hardware, not a simulation. The idea is, I realize real life can't be "sped up" like a simulation, but if it's truly automated and kept running/fed/operational, the system could just sit there and keep trying things as long as it runs - over a long period of time, humans could monitor its progress.
- zardo 11y ago
  I don't see why it couldn't be done, that's kind of a goal of programmable microfluidics. http://groups.csail.mit.edu/cag/biostream/ http://groups.csail.mit.edu/cag/biostream/ It is sci-fi though, a biolab that operates like aws for biology experiments is featured in 'Rainbows End'.
toufka 11y ago
You'd be hard pressed to beat biological evolution... A liter of e. coli can have upwards of 100s of billions of cells. Which can double every 90 minutes. Try to run that many instances of a full environmental simulation in software. That's 1L of bacteria. Scaling that up to 100L is pretty easy. Try to do that on your super computer... A straightforward evolutionary experiment to find resistance to an antibiotic can literally run trillions of trials in a stupid simple overnight culture. Slowly increase the dose of an antibiotic in a few liters of bacteria over the course of a day or two and see what survives.
- louprado 11y ago
  To take it a step further, I wonder if it is possible to engineer better catalysts to speed up cell division. Evolutionary pressure should bias towards maximum reproduction rates (given a the right environmental conditions). But I wonder how much variation there is in cell division times between different species of bacteria.
  - superdaniel 11y ago
    I think you're describing the field of [bioprocess engineering](https://en.wikipedia.org/wiki/Bioprocess_engineering https://en.wikipedia.org/wiki/Bioprocess_engineering). A lot of time is spent trying to balance cell growth with the possibility of mutations being introduced into the system. Even between different strains of E. coli the doubling rate can vary. Moreover, one also needs to contend with the fact that prokaryotes typically cannot produce very complex proteins. This leads some processes to need to use eukaryotes such as CHO cells, which are much slower.
- x5n1 11y ago
  Not to mention millions of years of evolution.
- meric 11y ago
  Perhaps it would be more practical to use biological components to accelerate software...
ctdonath 11y ago
Somebody did do a software-style analysis of a simple cell. Fascinating article, amazing results, pity I don't recall it. Worth looking for, shouldn't take long to find.
- pak 11y ago
  You're probably thinking of this paper by Jon Karr et al.: "A Whole-Cell Computational Model Predicts Phenotype from Genotype" http://www.cell.com/abstract/S0092-8674(12)00776-3 http://www.cell.com/abstract/S0092-8674(12)00776-3
  - dnautics 11y ago
    Note the hit rate on predicting lethal knockouts - not much better than flipping a coin
narrator 11y ago
Cells make proteins. Proteins fold up to do their jobs. Protein folding is O(2^N) to simulate in software, so probably not.
- CreRecombinase 11y ago
  If only it was O(N^2). Seconddary, tertiary and quaternary structure definitely is not the same complexity as bubble sort
  - narrator 11y ago
    You didn't read my post. I said O(2^N) which means basically computationally intractable for large N and even if Moore's law were to continue indefinitely it would still be computationally intractable for large N. O(N^2) problems, on the other hand, are far more approachable by software.
jcoffland 11y ago
I've been a programmer at the Folding@home project for about 8 years now. It takes massive computing power and a lot of time to simulate even one reasonably sized fast folding protein using the state of the art methods. Simulating a whole cell ab initio is way beyond the reach of current technology.

daveguy 11y ago

That would be awesome, but it is unlikely with current software and hardware. Even small scale simulations (nanoseconds to microseconds of a single protein molecule) require hours of sim time (on large clusters).

saalweachter 11y ago
To elaborate, time is the problem. The number of atoms in the smallest viable cell is actually reasonably small, less than a billion atoms, such that you could hope to store it all in memory on a single beefy computer. Meanwhile, you need something like picosecond resolution in the simulation, while you need seconds of simulated time to see interesting macro-level things happen. If you want to see cell division, you're probably talking a minimum of thirty minutes of simulated time.
ealloc 11y ago
Not to mention that the molecular dynamics simulations you're describing can't actually simulate chemical reactions. (the covalent bonds can't change in the sim, unless you do a much more intensive QM calculation and even that's iffy).

gpvos 11y ago

If you want evolution, you would also have to simulate the cell's environment. Without an environment, there's no natural selection and thus no evolution.

adrianN 11y ago

It would be cool to play with this idea using the OpenWorm platform.

sixdimensional 11y ago

Actually, I was wondering if a learning algorithm could be coupled with a builder that uses real synthetically created biological components in an automated system. This way, the builder comes up with new combinations, automates all the science around evaluating the combination as quickly and automatically as possible, and the software/learning algorithm controls the development towards some generalized goal. Ok, I admit this sounds ridiculously sci-fi, but, why do I feel like this is actually possible (just really, really hard)? EDIT: To clarify, I am actually suggesting a real living system coupled with software/hardware, not a simulation. The idea is, I realize real life can't be "sped up" like a simulation, but if it's truly automated and kept running/fed/operational, the system could just sit there and keep trying things as long as it runs - over a long period of time, humans could monitor its progress.

zardo 11y ago
I don't see why it couldn't be done, that's kind of a goal of programmable microfluidics. http://groups.csail.mit.edu/cag/biostream/ http://groups.csail.mit.edu/cag/biostream/ It is sci-fi though, a biolab that operates like aws for biology experiments is featured in 'Rainbows End'.

toufka 11y ago

You'd be hard pressed to beat biological evolution... A liter of e. coli can have upwards of 100s of billions of cells. Which can double every 90 minutes. Try to run that many instances of a full environmental simulation in software. That's 1L of bacteria. Scaling that up to 100L is pretty easy. Try to do that on your super computer... A straightforward evolutionary experiment to find resistance to an antibiotic can literally run trillions of trials in a stupid simple overnight culture. Slowly increase the dose of an antibiotic in a few liters of bacteria over the course of a day or two and see what survives.

louprado 11y ago
To take it a step further, I wonder if it is possible to engineer better catalysts to speed up cell division. Evolutionary pressure should bias towards maximum reproduction rates (given a the right environmental conditions). But I wonder how much variation there is in cell division times between different species of bacteria.
- superdaniel 11y ago
  I think you're describing the field of [bioprocess engineering](https://en.wikipedia.org/wiki/Bioprocess_engineering https://en.wikipedia.org/wiki/Bioprocess_engineering). A lot of time is spent trying to balance cell growth with the possibility of mutations being introduced into the system. Even between different strains of E. coli the doubling rate can vary. Moreover, one also needs to contend with the fact that prokaryotes typically cannot produce very complex proteins. This leads some processes to need to use eukaryotes such as CHO cells, which are much slower.
x5n1 11y ago
Not to mention millions of years of evolution.
meric 11y ago
Perhaps it would be more practical to use biological components to accelerate software...

ctdonath 11y ago

Somebody did do a software-style analysis of a simple cell. Fascinating article, amazing results, pity I don't recall it. Worth looking for, shouldn't take long to find.

pak 11y ago
You're probably thinking of this paper by Jon Karr et al.: "A Whole-Cell Computational Model Predicts Phenotype from Genotype" http://www.cell.com/abstract/S0092-8674(12)00776-3 http://www.cell.com/abstract/S0092-8674(12)00776-3
- dnautics 11y ago
  Note the hit rate on predicting lethal knockouts - not much better than flipping a coin

narrator 11y ago

Cells make proteins. Proteins fold up to do their jobs. Protein folding is O(2^N) to simulate in software, so probably not.

CreRecombinase 11y ago
If only it was O(N^2). Seconddary, tertiary and quaternary structure definitely is not the same complexity as bubble sort
- narrator 11y ago
  You didn't read my post. I said O(2^N) which means basically computationally intractable for large N and even if Moore's law were to continue indefinitely it would still be computationally intractable for large N. O(N^2) problems, on the other hand, are far more approachable by software.

jcoffland 11y ago

I've been a programmer at the Folding@home project for about 8 years now. It takes massive computing power and a lot of time to simulate even one reasonably sized fast folding protein using the state of the art methods. Simulating a whole cell ab initio is way beyond the reach of current technology.