Hacker News Board Hacker News, browsed like a classic message board
Live data from Hacker News

Living cells are very fast and crowded places (2012)

righto.com

Post reply on HN
Print view View original

51–60 of 86 posts

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

#51

Post by AstralStorm »

abecedarius wrote: post #34
dkural wrote: post #15

Although there is truth in the post, this is not entirely correct. Many chemical and biological processes take place in a much slower timescale than hundreds of thousands per second, many miles per hour etc. These processes include DNA synthesis/cell division, transcription, the transmission of electricity / ions between neurons, and many other basic processes. Also, Many proteins don't simply float every around the…

Also, speeds like "100 times per second" should be scaled down with the size scaling, if you want a feel for mechanics. Times Square is about 1km long, and a eukaryotic cell around 10 microns, so scale by 100 million. (A pretty typical protein, 5nm across, becomes 0.5 meters across in Times Square.) From this perspective even the rapid purposeful actions the article talks about go extremely slowly: 100Hz becomes a mi…

Part of the reason why neurons, eyes, nose and inner ear use special superstructure and electrical ion interfaces. These vastly help organize and speed up chemical transport. Cytoskeleton (which is partly responsible for cellular transport) is implicated in being part of long term memory.

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

#52

Post by koliber »

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…

Thank you for this writeup that peels away a layer of simplification and more vividly and accurately explains what is going on. you have a way with words. The intoxicated panicked mouse will stay with me forever.

That being said, I don't agree that it is a pervasive problem that simplification and abstraction is used in teaching. New concepts have to be introduced piecemeal. If a new topic was explained to an audience of neophytes in all its gory details, the effectiveness of the knowledge transfer would be low. Some may grasp the complicated details and form a valid mental model. However, many will be put off, as it is too much stuff at once.

Teaching is about introducing a simpler model first. Such a model is a rough abstraction with tons of simplifications and inaccuracies. Once understood by the student, it is about introducing a more intricate and realistic model, while demolishing parts of the simpler one that no longer fit. Once this more intricate model is internalized, another even more detailed one can be taught. This goes on until you get to the limits of understanding of a certain system or process. At that point, the student has the option of becoming a researcher and forging new models that have not been created before.

You can not dump the most detailed and intricate model on new students. At the same time, a good teacher is cognizant of the fact when their students have a solid enough grasp of a given model to start introducing the more intricate one, while dismantling the old one. It's a tough balancing act.

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

#54

Post by ggm »

msie wrote: post #7
ggm wrote: post #6

I spoke to a colleague who had done some work in his PhD in the physical chemistry of cells. Concepts like 'liquid' do not translate well at the intra-cellular level. 'holes' or 'channels' in a membrane, again are mostly about metaphors rather than mechanistic statements of completeness. he said for some things, an Escher infinite-space filling grid was as good a metaphor, for the cellular structure that the various…

To clarify: your colleague's comment is asinine?

Ah grammar, where would we be without you.

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

#55

Post by hyperpallium »

The information processing capability of cells, and the fact that single-celled creatures have behaviour, makes it hard for me to believe that neurons (not just in humans, in all animals with neurons) don't use any of this information processing capability.

I understand researchers have claimed to replicate the brains of some very simple animals (having something like 306 neurons)... but have they replicated the behaviour, i.e. for the same initial and ongoing inputs, you get the same outputs as the modeled brain? That should show the accuracy of the neuron model.

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

#56

Post by haihaibye »

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?

This is a bad analogy - the instructions for making everything in the cell is in the dna, so you also have the blueprints for the hardware fabrication plant.

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

#57

Post by _Wintermute »

hyperpallium wrote: post #55

The information processing capability of cells, and the fact that single-celled creatures have behaviour, makes it hard for me to believe that neurons (not just in humans, in all animals with neurons) don't use any of this information processing capability. I understand researchers have claimed to replicate the brains of some very simple animals (having something like 306 neurons)... but have they replicated the beha…

They've tried, but there's definitely a lot more work to do. If you're interested check out the Open Worm project

http://docs.openworm.org/en/latest/faq/

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

#58

Post by vbuwivbiu »

"As a result of all this random motion, a typical enzyme can collide with something to react with 500,000 times every second. Watching the video, you might wonder how the different pieces just happen to move to the right place. In reality, they are covering so much ground in the cell so fast that they will be in the "right place" very frequently just by chance."

That's the problem with those visualizations - they aim to give one an intuition of what's happening, but in fact they mislead. I wonder how it's possible to give an intuition of the reality, when in addition to the crazy statistical noisyness of the scene, those molecules are also in quantum superpositions.

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

#59

Post by pdm55 »

I found Goodsell's images of the crowded intracellular environment in E. coli, useful visualisations in developing a model of a living cellular process, namely, transcription control. Transcription is the first step in gene expression: in E. coli, RNA polymerase transcribes a complementary copy of a gene, namely, messenger RNA, for further processing to protein. The transcription process is controlled by proteins that either compete with RNA polymerase for the start site of transcription (turn off the gene) or bind adjacently and promote transcription (turn on the gene). The difficulty I had in constructing a mathematical model of transcription control was that I wanted to include nonspecific binding, where RNA polymerase binds with low affinity to random stretches of DNA. While such binding occurs with low affinity, the sheer length of the DNA meant that a significant proportion of the RNA polymerase was bound in that form. Fortunately, I became aware of the work of people like Allen Minton (NIH) and Tom Record (U Madison-Wisconsin) who studied molecular crowding. To borrow a sentence from Wikipedia, "[H]igh concentrations of macromolecules reduce the volume of solvent available for other molecules in the solution, which has the result of increasing their effective concentrations." https://en.wikipedia.org/wiki/Macromolecular_crowding I found (I hope correctly) that Tom Record's quantification of crowding, as affecting a 100-fold increase in concentration, "exactly" compensated for the reduction due to nonspecific binding. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5425810/
Post reply on HN