One related thing that would help is bringing back the Roche biochemical pathways chart, especially the online version. It has been offline for quite some time for "revisions"; it's a shame Dr. Michal's work is unavailable; it is such a rich resource!
This implies that the cytoplasmic medium isn't just a passive substrate - it's an active computational environment where signal propagation and processing occur simultaneously. This is fundamentally different from engineered systems where computation and transmission are typically separated. In cells, it looks like the medium itself computes as it transmits. This seems to have parallels both with the Traveling Salesman and handshake problem.
I've always been amazed that identical twins - chaotic sacs of molecules unfolding over *decades* - end up being identical. it says that there is basically no randomness, no noise in cells or the developmental program - save maybe fingerprints. you would expect even very small perturbations in these diffusing molecules would compound...nope
Can you explain how the processes of a cell rely on random collisions? Like how much would the functioning of the cell degrade if you like turn down the collision rate?
Also, looking at the paper, it seems they *predicted* the diffusion coefficients of proteins from measuring some dye-labeled particles of various sizes. I don't think they actually *measured* the whole E. coli proteome. So it's not surprising at all that their graph is linear on a log-log plot, if that's the model they're using to predict the diffusion.
https://bionumbers.hms.harvard.edu/Search.aspx?task=searchbyrecent
Cheers
One related thing that would help is bringing back the Roche biochemical pathways chart, especially the online version. It has been offline for quite some time for "revisions"; it's a shame Dr. Michal's work is unavailable; it is such a rich resource!
Can you point out what are those outlier proteins on the graph? Great read!
This implies that the cytoplasmic medium isn't just a passive substrate - it's an active computational environment where signal propagation and processing occur simultaneously. This is fundamentally different from engineered systems where computation and transmission are typically separated. In cells, it looks like the medium itself computes as it transmits. This seems to have parallels both with the Traveling Salesman and handshake problem.
https://www.sciencedirect.com/science/article/pii/S0006349523000899
I've always been amazed that identical twins - chaotic sacs of molecules unfolding over *decades* - end up being identical. it says that there is basically no randomness, no noise in cells or the developmental program - save maybe fingerprints. you would expect even very small perturbations in these diffusing molecules would compound...nope
Can you explain how the processes of a cell rely on random collisions? Like how much would the functioning of the cell degrade if you like turn down the collision rate?
There's a video that helps to visualize this. Start at about 1:11:05 to see it.
https://youtu.be/YxU0ZTt_3YY?si=it6sioQO9jeNLtLo&t=4267
I'm curious, what are the 2 outlier proteins in that chart that seem to diffuse more slowly than expected for their size?
Also, looking at the paper, it seems they *predicted* the diffusion coefficients of proteins from measuring some dye-labeled particles of various sizes. I don't think they actually *measured* the whole E. coli proteome. So it's not surprising at all that their graph is linear on a log-log plot, if that's the model they're using to predict the diffusion.
See the Methods section of the paper you linked: https://pmc.ncbi.nlm.nih.gov/articles/PMC3496334/