This article mentions two things as if they are unrelated. That the cellular environment is crowded is exactly why you need transport proteins and vesicles. All the really fast proteins are mostly going nowhere, they're just wobbling on the spot bumping into everything crammed next to them. Sandwiched most of the time between membranes they cant diffuse through freely. Its like angry jelly not hot soup.
Living cells are very fast and crowded places (2012)
41–50 of 86 posts
Re: Living cells are very fast and crowded places (2012)
#42I highly recommend the book "The Machinery of Life" by David S. Goodsell. It isn't too long, the text is interesting with out getting too bogged down in the details (there simply would be too much to cover in detail), but the highlight is he a professor of molecular biology, he is an excellent illustrator, and the book is packed with detailed illustrations that alone make the book worth it. $18 on amazon. (get the 2n…
This book is genuinely awesome. Im not sure why its so cheap in hardback but im glad it is. I buy almost anyone I know whos interested a copy. It's very good at giving you the right impression whilst being clear and easy to learn from. David Goodsell is also a really great guy and worth supporting.
Re: Living cells are very fast and crowded places (2012)
#43I 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?
Luckily, someone did an experiment similar to this one. They wrote the genome (and ONLY the genome) of a unicellular organism synthetically. Then they've removed the genome of an existing cell of a different species. The've then inserted the genome they created from scratch. The genome worked and produced versions of everything it needed, and cell division happened etc. Everything was produced & worked. So - they boo…
Craig Venter's "playing God" experiment ?
Re: Living cells are very fast and crowded places (2012)
#44Earlier quoted context omitted.
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)
The point I was trying to illustrate was that neither operating systems nor genomes contain the information needed to specify their required operating substrate and environment.
Perhaps it may be possible to derive or infer these requirements through simulation and analysis of the OS or genome, or perhaps not.
I guess it depends on the degree to which the "code" defining the system is abstracted from its operational embodiment, i.e. is the operating system in question encoded in the form of a Hardware Description Language [1], FPGA IP cores, or more abstract high-level source code?
I assume it would be more difficult/impossible to work out the hardware requirements for an OS given the just the high-level source code (are compilers included?) vs a low-level or "bottom"-level (hardware-level?) code.
Likewise for a genome, I don't think the sequence of As, Gs, Cs, & Ts specified in an organism's reference genome [2] entail the chemical and physical particulars needed to instantiate the genome in an environment (physical, virtual, whatever) such that it functions. On the other hand, if you gave me an actual genome comprised of purified genomic DNA, then I'm getting a big hint about how the code needs to be physically instantiated for it to work. From this hint, maybe a near-omnipotent reverse-engineer could infer the biochemical requirements (i.e. cell-free expression system or a donor cell) needed to boot up the organism.
Am I just being pedantic or do you see what I'm trying to get at?
[1]: https://en.wikipedia.org/wiki/Verilog
[2]: https://www.ncbi.nlm.nih.gov/nuccore/NC_010473.1?report=grap...
Re: Living cells are very fast and crowded places (2012)
#45Although 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…
> Also, speeds like "100 times per second" should be scaled down with the size scaling, if you want a feel for mechanics.
I'm a little confused, are you saying that the real speeds and rates in the article/this thread are all too fast by a factor of 100 million, or are you saying that its useful to perform this scaling mentally when imagining these systems to get a better intuition of their mechanics...?
Re: Living cells are very fast and crowded places (2012)
#46Earlier quoted context omitted.
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.
You might enjoy: Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks. Yan KK, Fang G, Bhardwaj N, Alexander RP, Gerstein M. Proc Natl Acad Sci U S A. 2010 May 18;107(20):9186-91. doi:10.1073/pnas.0914771107. Epub 2010 May 3. https://www.ncbi.nlm.nih.gov/pubmed/20439753
Also:
Istrail S, De-Leon SB, Davidson EH. The regulatory genome and the computer. Dev Biol. 2007 Oct 15;310(2):187-95. Epub 2007 Aug 10. Review. PubMed PMID: 17822690. Full-text: http://www.sciencedirect.com/science/article/pii/S0012160607...
Abstract:
> "The definitive feature of the many thousand cis-regulatory control modules in an animal genome is their information processing capability. These modules are “wired” together in large networks that control major processes such as development; they constitute “genomic computers.” Each control module receives multiple inputs in the form of the incident transcription factors which bind to them. The functions they execute upon these inputs can be reduced to basic AND, OR and NOT logic functions, which are also the unit logic functions of electronic computers. Here we consider the operating principles of the genomic computer, the product of evolution, in comparison to those of electronic computers. For example, in the genomic computer intra-machine communication occurs by means of diffusion (of transcription factors), while in electronic computers it occurs by electron transit along pre-organized wires. There follow fundamental differences in design principle in respect to the meaning of time, speed, multiplicity of processors, memory, robustness of computation and hardware and software. The genomic computer controls spatial gene expression in the development of the body plan, and its appearance in remote evolutionary time must be considered to have been a founding requirement for animal grade life."
Re: Living cells are very fast and crowded places (2012)
#47Earlier quoted context omitted.
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…
> Also, speeds like "100 times per second" should be scaled down with the size scaling, if you want a feel for mechanics. I'm a little confused, are you saying that the real speeds and rates in the article/this thread are all too fast by a factor of 100 million, or are you saying that its useful to perform this scaling mentally when imagining these systems to get a better intuition of their mechanics...?
The latter. Maybe I should reread the post, but it invites you to visualize a cell as Times Square -- scaling the sizes -- and then the unscaled speeds give the wrong impression within that visualization. (Mechanical properties like stiffness don't vary when you scale space and time together.) Outside of it, of course the absolute speeds are what you want to know.
Re: Living cells are very fast and crowded places (2012)
#48I 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 mi…
It's 7.5 billion miles to pluto one way. Total length of all DNA strands in the human body: 744 million miles. So you're off a bit.
Re: Living cells are very fast and crowded places (2012)
#49Earlier quoted context omitted.
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)
The point I was trying to illustrate was that neither operating systems nor genomes contain the information needed to specify their required operating substrate and environment. Perhaps it may be possible to derive or infer these requirements through simulation and analysis of the OS or genome, or perhaps not. I guess it depends on the degree to which the "code" defining the system is abstracted from its operational…
No, genome contains almost all of the information about the running environment. The epigenome is the rest.
Both of these even contain information about build environment.
Given high genetic mastery you would be able to figure out the conditions for the whole organism to grow, including required feedback loops. Of course, we're not even close.
Generic code is somewhat close to a quine if you look right at it.
Re: Living cells are very fast and crowded places (2012)
#50Earlier quoted context omitted.
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.
You might enjoy: Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks. Yan KK, Fang G, Bhardwaj N, Alexander RP, Gerstein M. Proc Natl Acad Sci U S A. 2010 May 18;107(20):9186-91. doi:10.1073/pnas.0914771107. Epub 2010 May 3. https://www.ncbi.nlm.nih.gov/pubmed/20439753
That was interesting, but I think their conclusion about the linux kernel being comparatively top-heavy with relatively few "work horses" was probably greatly influenced by the fact that they only analyzed the linux kernel, not linux kernel + device drivers. IMO, device drivers should be considered part of the OS - really, the work horses of the OS, not called by any other code.