5 ms·

This is super cool! People underestimate how insanely chaotic a cell is at a molecular level. Often diagrams show blobs cleanly interacting but the reality is m

by entee 8y ago

This is super cool! People underestimate how insanely chaotic a cell is at a molecular level. Often diagrams show blobs cleanly interacting but the reality is more like the images linked here: https://mgl.scripps.edu/people/goodsell/illustration/public/ https://mgl.scripps.edu/people/goodsell/illustration/public/ Everything touches everything. Everything is always moving around. This work suggests that the cell has taken advantage of this enormous challenge. If everything is always in motion, that means you have trouble controlling things, but that gives you a chance to maximally sample your environment. This makes this sort of efficient data processing possible. Downstream are a number of mechanisms that help make sense of that signaling, denoising the chaos. One example from a lab I worked in briefly (old but still cool): https://www.sciencedirect.com/science/article/pii/S0092867411002431 https://www.sciencedirect.com/science/article/pii/S009286741... https://www.ncbi.nlm.nih.gov/pubmed/18599789 https://www.ncbi.nlm.nih.gov/pubmed/18599789

jmole 8y ago
Awesome images, thanks for sharing. I wish they'd have put these in science books growing up. Are these to scale? It's interesting to see how much more particular (as in, composed of large particles) these cells look compared to the illustrations I'd seen growing up. I always imagined the proteins that made up a cell wall would be more on the order of how grass looks to a human, in terms of size respective to the cell. Or another analogy, I used to think of a cell like a room (the cell membrane) with furniture in it (the organelles). Now it seems more like just a big pile of furniture.
- improbable22 8y ago
  Another famous example: The magic of the Golgi stain, which first produced pictures of neurons, was that it stained only a tiny fraction of the cells. That's why you can obtain a picture with cells reaching out and occasionally connecting. Whereas in reality all that empty space is other cells, doing the same thing. More modern pictures are like so: http://www.conte.harvard.edu/news/2015/8/18/imaging-the-brains-jungles-a-miniscule-yet-monumental-leap-forward http://www.conte.harvard.edu/news/2015/8/18/imaging-the-brai...
- entee 8y ago
  I believe the components are indeed drawn to scale! The cell is a mess, there is virtually no central coordination, just individual molecular signals. A protein gets phosphorylated by a receptor, then its on its merry way till it hits something it interacts with and maybe because it's phosphorylated it activates that thing to do something else, or maybe, luck of the draw it doesn't. It's amazing that it even works, but it does so because billions of years have shaped life to be resilient to chaos. Some context: Unicellular life is roughly 3.5B years old Eukaryotic life is roughly 2B years old. It took 1.5B years to figure out how to build and use organelles Multicellular life is roughly 1B years old. Another billion years to figure out how to coordinate and specialize cells. Sea sponges, essentially "animals" are 700M years old Animals that can move around are about 500-600M years old, backbones in animals show up around the same time, then we're off to the races. This sort of patterning is maybe in the 700-800M year old window. It took billions of years for life to figure this out, you can do a lot by evolving that long. https://www.newscientist.com/article/dn17453-timeline-the-evolution-of-life/ https://www.newscientist.com/article/dn17453-timeline-the-ev...
  - est31 8y ago
    > A protein gets phosphorylated by a receptor, then its on its merry way till it hits something it interacts with and maybe because it's phosphorylated it activates that thing to do something else, or maybe, luck of the draw it doesn't. There are proteins that spread via diffusion, but there is also transport along microtubules in transport vesicles. Not entirely sure how the routing/navigation question is solved though, aka how does some vesicle know it needs to go to the nucleus vs golgi apparatus.
    - entee 8y ago
      Oh yes, of course there are many motorized processes, but the point is there's no inherent logic to them. A myosin grabs onto a filament and goes to the plus end of the actin filament (usually, not some of them, again it gets complicated :) but it doesn't know where that tube is going. It'll just happily move to the end and fall off/get blocked. If the destination "wants" or "needs" supra-diffusion transport, it needs to recruit the tubes to come to it. Every entity in the cell essentially acts as its own agent, and it's only through interactions that it does one thing or another. EDIT: probably more accurate to call actin "filaments" not tubes, typo
- Pulcinella 8y ago
  I believe they are roughly to scale. I remember reading how Goodsell does some back of the envelope calculations when planning an illustration. You hear in pop-science how the human body is ~50-70% water as if that is a lot. Really it’s a rather low level of solvent to run chemistry reactions in. I did some undergraduate research in a biochemistry lab and when we would perform an experiment with a protein we were studying, the proteins and other chemicals would always be very dilute, maybe ~99.9999% water or higher. Cells are very “sludgy” and it’s surprising to me that anything works at all the proteins don’t just immeadietly stick together and precipitate out of solution like egg-whites when cooked. It’s a tricky number to estimate because the orders of magnitude are so stark. Proteins are at very, very low concentrations but each protein is made of hundreds or thousands of atoms. The number of protein molecules is small but the they are almost big enough that their volume is not insignificant. There are other things that are unintuitive about chemical reactions. A lot of chemical reactions are faster than the movement of molecules. A protein maybe able to catalyze a chemical reaction faster than it can diffuse through water so it sits around most of the time waiting to collide with the molecule it will catalyze. Basically like a CPU waiting an eternity for data from a “fast” SSD to show up.
  - a1369209993 8y ago
    > You hear in pop-science how the human body is ~50-70% water as if that is a lot. Really it's a rather low level of solvent to run chemistry reactions in. For reference, gelatin is about 85% water[0], and still manages to be a solid glob you can balance utensils on top of. 0: The stuff I had on hand is 20g powder to 118g water.
- 781 8y ago
  Cells are extremely crowded. In fact, some processes like protein folding require crowdiness, if it's missing it can misfold. Realistic animation: http://www.cellimagelibrary.org/images/28234 http://www.cellimagelibrary.org/images/28234
  - Ultimatt 8y ago
    Also worth keeping in mind just how fast the motion really is. That whole clip happens in 15 micro seconds.
echelon 8y ago
These illustrations are fantastic! These need to be included alongside the simplified models so students also get the big picture. Students of biochemistry should inherently get a sense of this, but the pictures communicate this point so well. This is exactly why biochemistry is so hard. The smallest cell is a maelstrom of complexity.
- strainer 8y ago
  In recent years computer animation is being used to render astonishing bio-molecular vistas. Drew Berry seems to have pioneered this around 2010. Björk promptly used his work for her music video "Hollow". Here is an example of the 'genre' [1 - Harvard MCB : The Inner Life of the Cell ] https://www.youtube.com/watch?v=VdmbpAo9JR4 https://www.youtube.com/watch?v=VdmbpAo9JR4
- femto 8y ago
  See the book "The Machinery of Life", by David S Goodsell, the artist of the first illustration. It's an entire book of such illustrations, ordered to walk the reader though the different processes happening in a cell. I'm not a biologist, but I bought this book several years ago as it was just so fascinating and appealed to my engineering mind set of wanting to know how a system hangs together. It makes sense in my mind that a noisy system will be, on average, operating at something approaching optimality. The noise jogs the system out of local minima and is effectively a form of annealing (in the numerical sense).
  - notduncansmith 8y ago
    Off-topic, but thank for introducing me to the phrase “how a system hangs together” - it so neatly encapsulates the idea of the interactions between supporting elements of a system and the forces acting upon them. Also, great connection to annealing.
  - graycat 8y ago
    Yes, my analogy is a blind man in a room with 1000 locked doors, and he has a key that fits only one of the locks and somehow, quickly, finds that door, uses his key, and opens it.
aaaaaaaaaaab 8y ago
As my biology teacher put it: a cell is a factory in which workers are constantly kicking each other and workpieces around. Sometimes they bump into a workpiece they know what to do with, so they do some work and then throw it back into the crowd.
- dandare 8y ago
  And if I remember correctly, the elements in a cell may interact couple billion times per second.
- darkerside 8y ago
  Reminds me of an old school trading floor
- hnick 8y ago
  Hah, I just had a weird thought. I wonder if increasing motion/exercise speeds up intracellular action from wiggling it all around a bit and increasing the "random bump factor"? Or is the effect of macro movement negligible at a small scale?
  - aaaaaaaaaaab 8y ago
    Nope, but increasing temperature does speed up the chemical reactions within cells due to more vigorous motion of the constituent molecules. And this is true for not just biological processes but basically any chemical reaction: the higher the temperature, the faster the reaction.
deleted 8y ago
[deleted]
mojomark 8y ago
In your statement, based on your understanding, do you think either of the following wording substitutions are accurate? Instead of: > how insanely chaotic a cell is Perhaps: "how insanely high a cell's spatial and temporal entropy is" ? And instead of: > denoising the chaos. Perhaps: > decompressing (interpreting) the spatio-temporal activity ?
- tlb 8y ago
  If you put cells in a blender, their entropy goes up. And a crystal has lower entropy. So what’s interesting about them isn’t that their level of entropy is high or low.
  - Ultimatt 8y ago
    It sort of is related to being in between though. It's that their complexity is high. Which is essentially at the phase transition between high and low entropy states of matter. Cells regulate a system full of energy to keep themselves in that messy but information rich state.
dekhn 8y ago
literally the first thing we did in grad school (biophysics) was a journal club covering the idea that cells are so concentrated, basic things like the free energy of ATP hydrolysis doesn't match what you measure in free solution, and this has huge implications for cells. I forget the term (order parameter?) but the experiment was funny because it involved packing some lipid membranes full of PEG.

by entee 8y ago

jmole 8y ago

Awesome images, thanks for sharing. I wish they'd have put these in science books growing up. Are these to scale? It's interesting to see how much more particular (as in, composed of large particles) these cells look compared to the illustrations I'd seen growing up. I always imagined the proteins that made up a cell wall would be more on the order of how grass looks to a human, in terms of size respective to the cell. Or another analogy, I used to think of a cell like a room (the cell membrane) with furniture in it (the organelles). Now it seems more like just a big pile of furniture.

improbable22 8y ago
Another famous example: The magic of the Golgi stain, which first produced pictures of neurons, was that it stained only a tiny fraction of the cells. That's why you can obtain a picture with cells reaching out and occasionally connecting. Whereas in reality all that empty space is other cells, doing the same thing. More modern pictures are like so: http://www.conte.harvard.edu/news/2015/8/18/imaging-the-brains-jungles-a-miniscule-yet-monumental-leap-forward http://www.conte.harvard.edu/news/2015/8/18/imaging-the-brai...
entee 8y ago
I believe the components are indeed drawn to scale! The cell is a mess, there is virtually no central coordination, just individual molecular signals. A protein gets phosphorylated by a receptor, then its on its merry way till it hits something it interacts with and maybe because it's phosphorylated it activates that thing to do something else, or maybe, luck of the draw it doesn't. It's amazing that it even works, but it does so because billions of years have shaped life to be resilient to chaos. Some context: Unicellular life is roughly 3.5B years old Eukaryotic life is roughly 2B years old. It took 1.5B years to figure out how to build and use organelles Multicellular life is roughly 1B years old. Another billion years to figure out how to coordinate and specialize cells. Sea sponges, essentially "animals" are 700M years old Animals that can move around are about 500-600M years old, backbones in animals show up around the same time, then we're off to the races. This sort of patterning is maybe in the 700-800M year old window. It took billions of years for life to figure this out, you can do a lot by evolving that long. https://www.newscientist.com/article/dn17453-timeline-the-evolution-of-life/ https://www.newscientist.com/article/dn17453-timeline-the-ev...
- est31 8y ago
  > A protein gets phosphorylated by a receptor, then its on its merry way till it hits something it interacts with and maybe because it's phosphorylated it activates that thing to do something else, or maybe, luck of the draw it doesn't. There are proteins that spread via diffusion, but there is also transport along microtubules in transport vesicles. Not entirely sure how the routing/navigation question is solved though, aka how does some vesicle know it needs to go to the nucleus vs golgi apparatus.
  - entee 8y ago
    Oh yes, of course there are many motorized processes, but the point is there's no inherent logic to them. A myosin grabs onto a filament and goes to the plus end of the actin filament (usually, not some of them, again it gets complicated :) but it doesn't know where that tube is going. It'll just happily move to the end and fall off/get blocked. If the destination "wants" or "needs" supra-diffusion transport, it needs to recruit the tubes to come to it. Every entity in the cell essentially acts as its own agent, and it's only through interactions that it does one thing or another. EDIT: probably more accurate to call actin "filaments" not tubes, typo
Pulcinella 8y ago
I believe they are roughly to scale. I remember reading how Goodsell does some back of the envelope calculations when planning an illustration. You hear in pop-science how the human body is ~50-70% water as if that is a lot. Really it’s a rather low level of solvent to run chemistry reactions in. I did some undergraduate research in a biochemistry lab and when we would perform an experiment with a protein we were studying, the proteins and other chemicals would always be very dilute, maybe ~99.9999% water or higher. Cells are very “sludgy” and it’s surprising to me that anything works at all the proteins don’t just immeadietly stick together and precipitate out of solution like egg-whites when cooked. It’s a tricky number to estimate because the orders of magnitude are so stark. Proteins are at very, very low concentrations but each protein is made of hundreds or thousands of atoms. The number of protein molecules is small but the they are almost big enough that their volume is not insignificant. There are other things that are unintuitive about chemical reactions. A lot of chemical reactions are faster than the movement of molecules. A protein maybe able to catalyze a chemical reaction faster than it can diffuse through water so it sits around most of the time waiting to collide with the molecule it will catalyze. Basically like a CPU waiting an eternity for data from a “fast” SSD to show up.
- a1369209993 8y ago
  > You hear in pop-science how the human body is ~50-70% water as if that is a lot. Really it's a rather low level of solvent to run chemistry reactions in. For reference, gelatin is about 85% water[0], and still manages to be a solid glob you can balance utensils on top of. 0: The stuff I had on hand is 20g powder to 118g water.
781 8y ago
Cells are extremely crowded. In fact, some processes like protein folding require crowdiness, if it's missing it can misfold. Realistic animation: http://www.cellimagelibrary.org/images/28234 http://www.cellimagelibrary.org/images/28234
- Ultimatt 8y ago
  Also worth keeping in mind just how fast the motion really is. That whole clip happens in 15 micro seconds.

echelon 8y ago

These illustrations are fantastic! These need to be included alongside the simplified models so students also get the big picture. Students of biochemistry should inherently get a sense of this, but the pictures communicate this point so well. This is exactly why biochemistry is so hard. The smallest cell is a maelstrom of complexity.

strainer 8y ago
In recent years computer animation is being used to render astonishing bio-molecular vistas. Drew Berry seems to have pioneered this around 2010. Björk promptly used his work for her music video "Hollow". Here is an example of the 'genre' [1 - Harvard MCB : The Inner Life of the Cell ] https://www.youtube.com/watch?v=VdmbpAo9JR4 https://www.youtube.com/watch?v=VdmbpAo9JR4
femto 8y ago
See the book "The Machinery of Life", by David S Goodsell, the artist of the first illustration. It's an entire book of such illustrations, ordered to walk the reader though the different processes happening in a cell. I'm not a biologist, but I bought this book several years ago as it was just so fascinating and appealed to my engineering mind set of wanting to know how a system hangs together. It makes sense in my mind that a noisy system will be, on average, operating at something approaching optimality. The noise jogs the system out of local minima and is effectively a form of annealing (in the numerical sense).
- notduncansmith 8y ago
  Off-topic, but thank for introducing me to the phrase “how a system hangs together” - it so neatly encapsulates the idea of the interactions between supporting elements of a system and the forces acting upon them. Also, great connection to annealing.
- graycat 8y ago
  Yes, my analogy is a blind man in a room with 1000 locked doors, and he has a key that fits only one of the locks and somehow, quickly, finds that door, uses his key, and opens it.

aaaaaaaaaaab 8y ago

As my biology teacher put it: a cell is a factory in which workers are constantly kicking each other and workpieces around. Sometimes they bump into a workpiece they know what to do with, so they do some work and then throw it back into the crowd.

dandare 8y ago
And if I remember correctly, the elements in a cell may interact couple billion times per second.
darkerside 8y ago
Reminds me of an old school trading floor
hnick 8y ago
Hah, I just had a weird thought. I wonder if increasing motion/exercise speeds up intracellular action from wiggling it all around a bit and increasing the "random bump factor"? Or is the effect of macro movement negligible at a small scale?
- aaaaaaaaaaab 8y ago
  Nope, but increasing temperature does speed up the chemical reactions within cells due to more vigorous motion of the constituent molecules. And this is true for not just biological processes but basically any chemical reaction: the higher the temperature, the faster the reaction.

deleted 8y ago

[deleted]

mojomark 8y ago

In your statement, based on your understanding, do you think either of the following wording substitutions are accurate? Instead of: > how insanely chaotic a cell is Perhaps: "how insanely high a cell's spatial and temporal entropy is" ? And instead of: > denoising the chaos. Perhaps: > decompressing (interpreting) the spatio-temporal activity ?

tlb 8y ago
If you put cells in a blender, their entropy goes up. And a crystal has lower entropy. So what’s interesting about them isn’t that their level of entropy is high or low.
- Ultimatt 8y ago
  It sort of is related to being in between though. It's that their complexity is high. Which is essentially at the phase transition between high and low entropy states of matter. Cells regulate a system full of energy to keep themselves in that messy but information rich state.

dekhn 8y ago

literally the first thing we did in grad school (biophysics) was a journal club covering the idea that cells are so concentrated, basic things like the free energy of ATP hydrolysis doesn't match what you measure in free solution, and this has huge implications for cells. I forget the term (order parameter?) but the experiment was funny because it involved packing some lipid membranes full of PEG.