[HN Gopher] "We argue that mitochondria are the processor of the...
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"We argue that mitochondria are the processor of the cell" (2022)
Author : breck
Score : 57 points
Date : 2024-06-23 12:15 UTC (10 hours ago)
(HTM) web link (www.cell.com)
(TXT) w3m dump (www.cell.com)
| macawfish wrote:
| From one machine analogy to the another... Mitochondria have been
| observed moving between cells. These are living organisms!
| Reducing their role to that of "microprocessor" seems
| suffocating.
|
| https://www.quantamagazine.org/social-mitochondria-whisperin...
| epgui wrote:
| For my masters' degree I studied extracellular free
| mitochondria and extracellular vesicles containing
| mitochondria. It's a wild world.
| breck wrote:
| Very interesting.
|
| Can you tell more? What was that like? What was your day to
| day? Wet lab/dry lab, etc?
|
| What % are extracellular? Did you study mitoribosomes at all?
|
| No detail is too small!
| epgui wrote:
| Wet lab. It was horrible. 6 years of dishwashing and
| monotony. I write software now and am much happier.
|
| The numbers were very difficult to reproduce and sensitive
| to tiny variations in experimental conditions, to the point
| of mystery. My MSc took me 6 years rather than 2, and
| that's with a >90% scope cut.
|
| I can say that there was a "comparable" proportion of
| freeMitos to mitoMPs in the samples I was studying, which
| were induced from 786-O and 786-O/VHL cell cultures using a
| variety of agonists (atypically low concentrations of
| A23187, compared to literature, and serum-starved cell
| culture medium, seemed to work best; usual concentrations
| of A23187 seemed very violent on the cells, which is
| relevant if you're trying to ascertain anything about
| physiologic conditions). Shockingly, a very sizeable
| proportion (10-50% of EVs above a certain detection
| threshold, probably near 100-150nm) of total EVs were
| either mitoMPs or freeMitos.
|
| I did not study mitoribosomes.
|
| I was trying to optimize conditions for the generation of
| EVs (literature is lacking here) and flow cytometric
| techniques for measuring EV subpopulations. Mitochondria
| gum up the tubes and require special care. Experiments that
| measure EVs without controlling for the presence of
| mitochondria are IMO inherently suspect.
|
| There is a really great paper published by L Boudreau in
| the journal Blood with better results than anything I ever
| achieved, it's very interesting stuff:
| https://pubmed.ncbi.nlm.nih.gov/25082876/
| mathgeek wrote:
| The idea of comparing evolved structures to the current height
| of technology is usually an oversimplification. It's amusing to
| think back to when the switchboard was compared to the brain,
| for example. It wasn't that long ago that we considered the
| brain and a computer to also be quite similar, but we know it's
| only in certain aspects.
| exe34 wrote:
| it's called a model. all models are wrong but some are
| useful. the plugboard model of the brain was useful in the
| sense it suggested pieces working together and functional
| connections varying for different activities.
|
| nobody is suggesting the brain runs an instruction set or a
| compiler - but it does compute in a general sense.
| soloist11 wrote:
| Everything computes in a general sense, even atoms. But one
| could just as easily say everything is "just" mathematics
| because all models of reality are mathematical. In general
| I think it's important to be wary of totalizing ontologies
| and metaphysics of reality that reduce everything to a
| single universal substance (monadology) or activity like
| computation (computationalism).
| sublinear wrote:
| > nobody is suggesting the brain runs an instruction set
|
| What happened to all those idiots saying the universe is a
| simulation and we have no free will?
| edmundsauto wrote:
| Those people still exist alongside all those idiots who
| think we have free will and that the universe is the
| embodiment of existence ;)
| EnigmaFlare wrote:
| It's an analogy, not a model. It's useless for making
| predictions or testing hypotheses. Even pretty useless for
| conveying understanding.
| Teever wrote:
| An analogy is a way of expressing a model in a highly
| compressed verbal state.
| mathgeek wrote:
| The term we're looking for is likely "analogical model"
| https://en.wikipedia.org/wiki/Analogical_models
| stefan_ wrote:
| Except sometimes you lose control and you grifters
| pretending your model is the real deal and the singularity
| is near.
| akira2501 wrote:
| The cellular environment is such a mess it's not a surprise that
| environmental changes are observed by many types of bodies within
| the cell. It's hard to think of it like a "processor," though,
| when almost all of it's messages are non specific broadcasts and
| not direct targeted messages.
|
| To me it seems like RNA is the processor, DNA is the RAM, and
| mitochondria are voltage regulation modules. That they're all
| environmentally sensitive is a consequence of how the machine is
| constructed.
| fsloth wrote:
| "To me it seems like RNA is the processor, DNA is the RAM,..."
|
| Is there anything resembling a von Neumann machine in the
| biochemistry, though?
|
| Would Turing machine analogues be more useful?
| tomlue wrote:
| Epigenetic modifications, such as methylation, are made to
| DNA by specific proteins. These modifications alter the
| transcription process from DNA to RNA, which in turn affects
| protein expression. This includes the expression of the
| proteins responsible for epigenetic changes themselves. In
| essence, the proteins that modify DNA also control the
| expression of their own building instructions through a
| feedback loop.
|
| I guess that feels a bit like a von neumann machine to me,
| but I'm not sure the analogy is super helpful.
| WJW wrote:
| Both Turing and Von Neumann machines (and the lambda calculus
| by Church) were designed to be minimal implementations that
| were still powerful enough to be provably complete in a
| mathematical sense. Mother Nature is under no such
| constraints: she happily constructs massively parallel
| "computers" with millions of global variables, each being
| written to by every core. That human minds cannot debug such
| systems is not Her problem. The only constraint is if it
| works, and it does.
| dtech wrote:
| Wouldn't RNA be the RAM and DNA be long term storage? Most of
| the work and "decision making" - at least in current organisms
| - is done by proteins.
| akira2501 wrote:
| There are many different types of RNA with different
| purposes. They all act in concert to produce proteins. mRNA
| encodes proteins, tRNA brings the proteins into
| transcription, rRNA actually acts as a protein itself to help
| drive this machine.
|
| DNA is environmentally sensitive and it can be altered. Your
| entire genome is not being produced all the time. Different
| proteins are copied based upon the conformal structure of DNA
| which changes based upon the cellular environment. The entire
| structure is copied often and no one particular set of DNA in
| your body is "the original."
|
| It has aspects of long term storage but then it's utilized in
| a way that long term storage almost never is. And all cells
| get their own copy which may be unique in several ways. So
| RAM seems like a better metaphor to me.
| acchow wrote:
| Given the billions of years of compression involved, these
| structures could occupy any number of latent spaces with all
| sorts of different meaning.
| carrozo wrote:
| Mitochondria is the powerhouse of the cell!
|
| https://knowyourmeme.com/memes/mitochondria-is-the-powerhous...
| xanderlewis wrote:
| and a monad is a monoid in the category of endofunctors.
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