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Anybody knows why we cant just write a cell simulator and start experimenting that way with DNA manipulation? I mean I have no idea what the first nucleotides a

by JepZ 9y ago

Anybody knows why we cant just write a cell simulator and start experimenting that way with DNA manipulation? I mean I have no idea what the first nucleotides are for, but when I have a simulator I can try changing them and see what happens? This may sound like a naive approach, but is there anything special hindering us from building such a simulator or is it just that scientists will not find it useful as it will take too long before we know which nucleotides are important for our goals?

landryraccoon 9y ago
> Anybody knows why we cant just write a cell simulator This is hard. To my knowledge we can't even write most basic components of a cell simulator yet. One of the obvious requirements would be a protein folding simulator. Nobody has been able to come up with a working one of those yet. > when I have a simulator I can try changing them and see what happens? If you write a simulator that does this you will be a billionaire and probably win a Nobel prize in medicine while you're at it.
- hoelle 9y ago
  Yep. I recently met a team working on this stuff at the Allen Institute for Cell Science. The problem space is huge and the field is totally in its infancy. If anyone is interested in this work, check their job site. Last I heard they were looking to hire a programmer to help write the sim. Cool team + science.
  - jjjensen90 9y ago
    Out of curiosity I checked their jobs site. What a cool opportunity, working in a nascent field of science at a prestigious institution. It was funny to notice that they seem to value a Bachelor's degree at a rate of higher than 1:1 with career experience: > 4-5 years of experience in a software development team AND a bachelor’s degree in computer science or a related field | OR 15+ years of relevant working experience... > 6-9 years of experience in a software development team AND a bachelor’s degree in computer science or a related field | OR 20+ years of relevant working experience That is a pretty heavy premium to put on those years during undergrad. I certainly wasn't as good by undergrad + 5 years as at 15+ years in the field, but maybe they know better than me.
- SimbaOnSteroids 9y ago
  What is the major hurdle that needs to be cleared in order to be able to get a NN to figure out protein folding, I understand that protein folding is complex but its also the sort of problem I perceive, perhaps extremely naively, a NN being good at solving.
deleted 9y ago
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viewtransform 9y ago
To build the cell simulator you would have to model all the biochemical pathways in a cell. This is a bit of a problem http://biochemical-pathways.com/#/map/1 http://biochemical-pathways.com/#/map/1 http://biochemical-pathways.com/#/map/2 http://biochemical-pathways.com/#/map/2
- JepZ 9y ago
  Thanks, cool links. I didn't even know you can use Leaflet for something else than just maps.
  - constantlm 9y ago
    Didn't even notice Leaflet there, nice spot. TIL
- deleted 9y ago
  [deleted]
fsloth 9y ago
I'm not sure if you could do that without a full quantum dynamic simulation of each cell organelle. Is there anything better than DFT method for quantum chemistry? You can look it up and see how much effort it takes to simulate just a few molecules. I'm pretty sure full cell level simulation would revolutionize biology and medicine.

by JepZ 9y ago

landryraccoon 9y ago

> Anybody knows why we cant just write a cell simulator This is hard. To my knowledge we can't even write most basic components of a cell simulator yet. One of the obvious requirements would be a protein folding simulator. Nobody has been able to come up with a working one of those yet. > when I have a simulator I can try changing them and see what happens? If you write a simulator that does this you will be a billionaire and probably win a Nobel prize in medicine while you're at it.

hoelle 9y ago
Yep. I recently met a team working on this stuff at the Allen Institute for Cell Science. The problem space is huge and the field is totally in its infancy. If anyone is interested in this work, check their job site. Last I heard they were looking to hire a programmer to help write the sim. Cool team + science.
- jjjensen90 9y ago
  Out of curiosity I checked their jobs site. What a cool opportunity, working in a nascent field of science at a prestigious institution. It was funny to notice that they seem to value a Bachelor's degree at a rate of higher than 1:1 with career experience: > 4-5 years of experience in a software development team AND a bachelor’s degree in computer science or a related field | OR 15+ years of relevant working experience... > 6-9 years of experience in a software development team AND a bachelor’s degree in computer science or a related field | OR 20+ years of relevant working experience That is a pretty heavy premium to put on those years during undergrad. I certainly wasn't as good by undergrad + 5 years as at 15+ years in the field, but maybe they know better than me.
SimbaOnSteroids 9y ago
What is the major hurdle that needs to be cleared in order to be able to get a NN to figure out protein folding, I understand that protein folding is complex but its also the sort of problem I perceive, perhaps extremely naively, a NN being good at solving.

deleted 9y ago

[deleted]

viewtransform 9y ago

To build the cell simulator you would have to model all the biochemical pathways in a cell. This is a bit of a problem http://biochemical-pathways.com/#/map/1 http://biochemical-pathways.com/#/map/1 http://biochemical-pathways.com/#/map/2 http://biochemical-pathways.com/#/map/2

JepZ 9y ago
Thanks, cool links. I didn't even know you can use Leaflet for something else than just maps.
- constantlm 9y ago
  Didn't even notice Leaflet there, nice spot. TIL
deleted 9y ago
[deleted]

fsloth 9y ago

I'm not sure if you could do that without a full quantum dynamic simulation of each cell organelle. Is there anything better than DFT method for quantum chemistry? You can look it up and see how much effort it takes to simulate just a few molecules. I'm pretty sure full cell level simulation would revolutionize biology and medicine.