Something I've never understood is how the nucleotides arrive to be included in the DNA strand. These animations always just show them appearing in perfect sequential order when they're needed, which is of course not what happens.
How are they delivered to the polymerase in the first place? How do they "know" where to be?
Are there just so many of them in the cytosol that through sheer numbers, there's enough random chance they'll just shuttle into place when the polymerase needs them?
I wrote a blog post a few years ago explaining how molecules get to the right place at the right time. The short answer is that cells are nothing like the nice, peaceful animations. Cells are extremely crowded and things move extremely fast. Glucose molecules, for instance, move around cells at 250 miles per hour and collides with something billions of times a second. An enzyme might collide with a reactant 500,000 times a second. And proteins can spin a million times per second. So as you suspect, by random chance molecules are in the right spot very frequently.
Thank you for writing this. I used to wonder how flies have such terrific reaction times and whip around the air with insane agility. And then I wondered if we are just seeing them in fast forward, due to the relatively slow clock in our heads. I imagined it was why they had such a short lifespan of just several days. And I imagined them seeing us as glacially moving statues—"man this guy hasn't moved in years!"
Reading your description of cells as moving imperceptibly fast only fills me more with this sense—that we are very slow moving giants, waiting on the billions of "years" of inner machinery time to tick us forward ever so slowly.
Time for you to read "Dragon's Egg", a hard sci-fi book about a civilization that evolves on a time scale far shorter than humans ultimately leading up to interaction with humans and this civilization. Awesome book which explores different time scales.
I've been having this same thought lately, about the scales of time that exist below/inside what we perceive. I agree that smaller/simpler brains probably run on a higher clock speed than those that are larger or more complex, and that impacts perception. But even within the fastest little minds, the rate at which chemical reactions take place or electrical signals propagate make them seem glacially slow in comparison.
I was actually thinking about putting a little video together about these scales of time, with the video containing nothing more than a person's blink reaction slowed down 5,000x.
I wonder if we allow enough for this in our search for alien life? Are their other life-forms out there somewhere whose timescales are radically different from ours? How would we find or communicate with them if there were?
like forests? I cannot forget the statement in 'Avatar' describing the 'tree of life'. How is it that memories have not been encoded in massively networked aspen forests? Or may they're there and we just havent looked. And with large encoded memory stores, manipulation of that data is what we call conciousness.
Thanks for the excellent blog post. This is something more people need to appreciate.
I never realized just how crowded until I saw David Goodsell's molecular illustrations[1] in Drew Barry's TED talk.[2] Goodsell's drawings show the actual density and diversity of molecules inside the cell.
People get confused because they read that cells are ~99% water by molecule count. By weight they're only ~65-70% water. One out of three atoms being part of a non-water molecule means cells are tightly packed.
> Are there just so many of them in the cytosol that through sheer numbers, there's enough random chance they'll just shuttle into place when the polymerase needs them?
Yes. Everything at that scale is very small, very close together and moving very, very fast.
This kind of thing is very common at the cellular level: have a receptor/channel/process/thing that only one precise 3d molecule can fit into - and then just wait.
As long as there's a process somewhere to make/acquire that molecule, then one will be along in a few nanoseconds or so, depending on the concentration. In the meantime the recipient will just wait.
In this way otherwise independent processes can regulate each other, and respond in a concentration dependant way to changing conditions without any central control.
I imagine there are not many things with unexpected shapes at that level that aren't accounted for somehow. Anything that doesn't slot into it perfectly will get knocked away by collisions. Bad shapes do exist however (prions) and are a cause of diseases.
Life is very much about density gradients. Ion channels, osmotic pressure, and so on.
40% of the cytoplasm is proteins (by volume), which is remarkably high, considering a naive lattice packing is just 34% (the tetrahedral lattice with a density of).
Yes, and indeed, this is why life as we know it only works in a narrow temperature range: high enough for Brownian motion to drive reactions, low enough not to unravel the results too quickly.
How are they delivered to the polymerase in the first place? How do they "know" where to be?
Are there just so many of them in the cytosol that through sheer numbers, there's enough random chance they'll just shuttle into place when the polymerase needs them?