Living cells are very fast and crowded places (2012) • Hacker News Board

Re: Living cells are very fast and crowded places (2012)

#21

Post by 100ideas » Tue, Nov 07, 2017, 3:28 AM UTC

mncharity wrote: post #16

> cells are extremely crowded and busy places Cells are extremely crowded and busy... and random and violent places. Molecular biology dances in a nano moshpit from hell. The Inner Life of a Cell is badly misleading. It reinforces many educationally toxic misconceptions. Yes, the graphics technology was limiting. But the video doesn't attempt to mitigate the negative impact. For instance, adding a couple of frames of…

Here is a more realistic visual representation of a (bacterial) cytoplasm: https://www.youtube.com/watch?v=2fobDHHl11c

"The simulation shows 1000 individual macromolecules diffusing, colliding and transiently associating with each other over the course of 10 microseconds of simulation; the translational diffusion coefficient of the GFP in this model is in agreement with experimental measurements."

Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm. PLoS Comput Biol 6(3): e1000694. doi:10.1371/journal.pcbi.1000694

(Note that the proteins and other macromolecules in the visualization are all individually constructed of hundreds of atoms — tRNA is a common one and has ~729 atoms; other, bigger proteins have thousands; and h2o of course has just 3. Here is an illustration from David Goodsell’s newest book showing the scale: http://imgur.com/a/shqME)

Re: Living cells are very fast and crowded places (2012)

#22

Post by [deleted] » Tue, Nov 07, 2017, 3:30 AM UTC

mncharity wrote: post #16

> cells are extremely crowded and busy places Cells are extremely crowded and busy... and random and violent places. Molecular biology dances in a nano moshpit from hell. The Inner Life of a Cell is badly misleading. It reinforces many educationally toxic misconceptions. Yes, the graphics technology was limiting. But the video doesn't attempt to mitigate the negative impact. For instance, adding a couple of frames of…

[deleted]

Re: Living cells are very fast and crowded places (2012)

#23

Post by visarga » Tue, Nov 07, 2017, 4:15 AM UTC

nsxwolf wrote: post #8

I wish I understood where all this stuff came from. When we talk about evolution we talk about random gene mutations and natural selection, but it doesn’t seem like the machinery of the cell itself is described by DNA. How do cells themselves and all their internal machinery evolve? If all you had was a genome, could you really use it to engineer the cell required for it to go inside of?

Think about this: your body is made of protein, each protein molecule is being created by copying a sequence of DNA. So your DNA has to do a LOT of copying, and for each copy it has to be cut open and put back together. In fact DNA is working hard every single day to keep us alive - it's not just sitting there until cell division. Even duplicating itself is no small feat - the total length of DNA in a human is 10B miles, from here to Pluto and back.

Re: Living cells are very fast and crowded places (2012)

#24

Post by 100ideas » Tue, Nov 07, 2017, 4:31 AM UTC

mncharity wrote: post #16

> cells are extremely crowded and busy places Cells are extremely crowded and busy... and random and violent places. Molecular biology dances in a nano moshpit from hell. The Inner Life of a Cell is badly misleading. It reinforces many educationally toxic misconceptions. Yes, the graphics technology was limiting. But the video doesn't attempt to mitigate the negative impact. For instance, adding a couple of frames of…

When we look, our visual system comprehends in terms of boundaries and empty space.

Thus we know the location and motion of the different things we see.

But "surfaces" and corresponding "empty spaces" don't occur at the molecular scale in living things. (What makes something a discrete "thing"? What makes something "empty"?)

In cellular environments, nothing is empty, everything is touching, nothing is static, everything is in chaotic motion.

Thus molecular reality presents something of a visual paradox and a philosophical puzzle: how can we visualize something that is concpetually incompatible with how our visual system sees?

It would excellent if there was more focus on this problem in the HCI communities (looking at you ACM SIGGRAPH).

Re: Living cells are very fast and crowded places (2012)

#25

Post by 100ideas » Tue, Nov 07, 2017, 4:32 AM UTC

nsxwolf wrote: post #8

I wish I understood where all this stuff came from. When we talk about evolution we talk about random gene mutations and natural selection, but it doesn’t seem like the machinery of the cell itself is described by DNA. How do cells themselves and all their internal machinery evolve? If all you had was a genome, could you really use it to engineer the cell required for it to go inside of?

If all you had was unix kernel machine code, could you really use it to engineer the hardware required for it to go inside of?

Re: Living cells are very fast and crowded places (2012)

#26

Post by nsxwolf » Tue, Nov 07, 2017, 4:51 AM UTC

100ideas wrote: post #25

nsxwolf wrote: post #8

I wish I understood where all this stuff came from. When we talk about evolution we talk about random gene mutations and natural selection, but it doesn’t seem like the machinery of the cell itself is described by DNA. How do cells themselves and all their internal machinery evolve? If all you had was a genome, could you really use it to engineer the cell required for it to go inside of?

If all you had was unix kernel machine code, could you really use it to engineer the hardware required for it to go inside of?

That’s a good analogy. So it seems the cell evolves separately. But this doesn’t seem to be talked about as much, at least not amongst laypersons.

Re: Living cells are very fast and crowded places (2012)

#27

Post by bammytest » Tue, Nov 07, 2017, 4:55 AM UTC

nsxwolf wrote: post #8

I wish I understood where all this stuff came from. When we talk about evolution we talk about random gene mutations and natural selection, but it doesn’t seem like the machinery of the cell itself is described by DNA. How do cells themselves and all their internal machinery evolve? If all you had was a genome, could you really use it to engineer the cell required for it to go inside of?

If all you had was a genome, how could you use it to engineer the cell required for it to go inside of?

Re: Living cells are very fast and crowded places (2012)

#28

Post by 100ideas » Tue, Nov 07, 2017, 4:57 AM UTC

nsxwolf wrote: post #26

100ideas wrote: post #25

Earlier quoted context omitted.

If all you had was unix kernel machine code, could you really use it to engineer the hardware required for it to go inside of?

That’s a good analogy. So it seems the cell evolves separately. But this doesn’t seem to be talked about as much, at least not amongst laypersons.

Re: Living cells are very fast and crowded places (2012)

#29

Post by hj34 » Tue, Nov 07, 2017, 4:59 AM UTC

mncharity wrote: post #16

> cells are extremely crowded and busy places Cells are extremely crowded and busy... and random and violent places. Molecular biology dances in a nano moshpit from hell. The Inner Life of a Cell is badly misleading. It reinforces many educationally toxic misconceptions. Yes, the graphics technology was limiting. But the video doesn't attempt to mitigate the negative impact. For instance, adding a couple of frames of…

You don't have to teach everyone everything. This is a misguided belief of the modern western education system that evolved from Christian roots.

As Bruce Lee would say - I cannot teach because I don't believe in systems or methods. So how do I learn? Only when I look for the cause of my ignorance.

The masses don't spend their time looking for the cause of their ignorance.

Re: Living cells are very fast and crowded places (2012)

#30

Post by dkural » Tue, Nov 07, 2017, 5:30 AM UTC

nsxwolf wrote: post #26

100ideas wrote: post #25

Earlier quoted context omitted.

If all you had was unix kernel machine code, could you really use it to engineer the hardware required for it to go inside of?

That’s a good analogy. So it seems the cell evolves separately. But this doesn’t seem to be talked about as much, at least not amongst laypersons.

Actually it's a very misleading analogy. In biology, that's precisely what is happening: The "kernel code" i.e. our genome in fact does have all the instructions on how to build a cell, how to build tissues, how everything communicates, etc. (my education: BA in math, PhD in Biology)