23 ms·

RNA Memory Hypothesis

156 points by nahuel0x 6y ago

nynx 6y ago
Very interesting, but also worrying, in a way. If neurons are actually reasonably large, complex computers in their own right, brain emulation is much further off than some people are thinking. It's possible that ASC brain preservation doesn't preserve the internal details necessary if this hypothesis ends up being true.
- deleted 6y ago
  [deleted]
- asdfasgasdgasdg 6y ago
  To be fair it's more than just possible that ASC brain preservation doesn't work even under any other hypothesis of cognition.
  - nynx 6y ago
    That's true. I think the fair way to put it that it's possible that ASC preserves the necessary data to simulate a brain.
- deleted 6y ago
  [deleted]
- Voloskaya 6y ago
  This is the opposite of worrying.
  - nynx 6y ago
    How so?
    - Voloskaya 6y ago
      You seemed to be saying that it is worrying, as it may indicate brain emulation is much further off than some people are thinking. This indication is the opposite of worrying to me, it's reassuring.
      - earthboundkid 6y ago
        You don’t want everything you or anyone else has loved or valued to be replaced unimaginable monsters?
        Dylan16807 6y ago
        You're going to have to explain what you're talking about. Everything be replaced? What does that have to do with brain emulation? Also I think you're implying that brain emulation will lead to more "unimaginable monsters", when it could very easily be the opposite: if you can't emulate a brain then an AI has to be even weirder and harder to understand.
        undersuit 6y ago
        Dystopian futures where you exist as only as much as your can afford. It's cheapest to download yourself into a computer and slow down your computation speed than to continue to pay have a flesh and blood body.
subroutine 6y ago
This is nonsense. Evidence collected over the last 40 years have detailed how memory is encoded by synaptic weights, but the premise... "there’s no obvious way for all that sensory data to be captured in synapses as long term memories" ...just ignores these findings. The model described in the article on the other hand, has never been observed. At the least, if you are going to propose an mRNA hypothesis don't use "T" as one of your RNA bases.
- AstralStorm 6y ago
  What is the physical realisation of the synaptic weight? (Here's trouble, we do not know. It's not in just connectivity or myelination.)
  - jrussino 6y ago
    See my response to your sibling comment; clearly we still have a lot to learn, but there is already some understanding of the biological mechanisms of synaptic plasticity (which I think is what the parent comment is referring to as "synaptic weights"). https://en.wikipedia.org/wiki/Synaptic_plasticity https://en.wikipedia.org/wiki/Synaptic_plasticity
  - subroutine 6y ago
    The physical realization is the number of postsynaptic receptors. In terms of fast excitatory transmission it is the quantity of AMPA receptors. You can potentiate or depress synapses by controlling the amount of these receptors. This has been demonstrated in vivo, and in cell culture. We are at the point where we can manipulate the strength of individual synapses. Here is a nice review article: https://royalsocietypublishing.org/doi/10.1098/rstb.2013.0136?url_ver=Z39.88-2003 https://royalsocietypublishing.org/doi/10.1098/rstb.2013.013...
- titzer 6y ago
  > have detailed how memory is encoded by synaptic weights Synaptic weights is our computational model of neural networks that seems to work pretty well. But this is a model. No one has discovered the biological mechanism by which synapses are "weighted". The actual computation going on in a cell is totally based on chemistry. There are a lot of different specialized networks in human and animal brains that don't necessarily translate easily to "weighted synaptic networks" all that well. For example, networks that process audio information have been shown to recognize individual frequencies (in fact, they pretty much solely do this!) Such networks seem to be primarily based on the firing rate across a synapse. For such networks is seems more reasonable to think of neurons as signal processors whose internal computation is more based on the time domain, e.g. some kind of Fourier transform-equivalent. In short, I think you should put less weight (pun intended) in our computational model of neurons (link weights) and look more at biology.
tokipin 6y ago
One of my theories is that this (or similar virus-like mechanism) is how some memories are transferred to offspring. The reasons are: * Prodigies which happen to be good in a field related to what their parents are good at. Often the wording used indicates a memory-like reason. For example, finding the rules of chess "familiar." * Embeddings in machine learning, which allow encoding of high-dimensional information in a low-dimensional space. This would imply that humans have a somewhat-shared embedding space at some "layers". It's interesting to wonder how similar this space would be across various animals, as it would effectively be an evolved language. * Other more subtle things, like the "cultural memory" of a society. One question would be what types of time scales these memories survive across. Maybe some forms of instinct are deep memories that have been directly encoded in DNA.
- plutonorm 6y ago
  I had to scroll a long way for an intelligent contribution! https://www.scientificamerican.com/article/prehistoric-viruses-and-the-function-of-the-brain/ https://www.scientificamerican.com/article/prehistoric-virus... I also wonder if and to what extent this information can transfer between individuals? I'm reminded of the Jungian collective unconscious. You're going to think I'm a kook now, but, there's also a panspermia angle on this. Big ifs here, but. If panspermia is true. If evolution on earth is tied to evolution of life in the wider universe via transfer of genetic material. Then it could be possible that the code in which memories (or a learned manifold, encoding useful generalisation) are encoded is compatible with life here today. You could conceivably get not just morphological/physiological changes in terrestrial organisms through viral horizontal gene transfer, but also transfer of cognitive strategy via the same mechanism. X-files kinda stuff. All kind of unlikely, but an interesting possibility.
  - type0 6y ago
    But that would imply that evolution was "directed", which I think is proven that it's not. The role of viruses in evolution is almost mainstream now, it is much more likely that virus was just a method for ancient extinct organisms to exchange genes, sort of proto-sex, and not anything else outlandish.
fabian2k 6y ago
I don't think there's any real doubt that memory is stored in neurons, this is really a fringe theory. I haven't looked at it closely, but my first objection would be that RNA would be far too slow for this purpose. It's also not stable over time, cells have mechanisms to intentionally degrade it. It just doesn't make sense. There are other weird parts in the blog post, for example claiming that a particular protein kinase is involved in mRNA transcription. That is by definition wrong as a kinase is an enzyme that transfers a phosphate, so a protein kinase transfers phosphates to proteins. And the RNA in this hypothetical memory storage would not be mRNA, as that by definition encodes for proteins. The person cited in the post is also a crackpot, I've quite a lot of experience with his exploits on the Stack Exchange network. And I haven't found a conspiracy theory yet that he didn't like. This is not hyperbole, I learned of a whole bunch of conspiracy theories I didn't know existed through his posts.
- macawfish 6y ago
  RNA is literally a form of memory. The question should not be whether or not memory is encoded in RNA, it should be "what are all the ways that creatures with RNA can experience the encoding and decoding of information encoded in RNA?" Memory is literally everywhere. There is already evidence that the brain can encode memory in dynamic molecular processes, and that interference of those process can interfere with an animal's ability to recall memory. Your point about timescales is a good one, and provides a clue: the timescales over which a given medium of information can be encoded to or decoded from and over which it decays should provide a clue about the timescales we might expect organisms to experience it in. Mammals and other creatures with RNA experience memory over a whole continuous range of timescales. Why wouldn't RNA, which is optimized for encoding information, be just one of many mediators of memory?
  - fabian2k 6y ago
    Most of the RNA in our cells simply encodes for proteins. The information is entirely redundant as it is simply copied from DNA. I would not call that memory. Of course there's a lot of other stuff RNA can do like catalytic activity, triggering RNA interference or reacting to other molecules (riboswitches). But information storage isn't really anything RNA is known for.
blackrock 6y ago
What I find fascinating, is that babies are born knowing how to suck. How? It’s not something you can teach them. They say it’s an innate thing. But what does that even mean. I think babies are born with this programmed into them. Like a genetic type of memory. Then over time, the neurons establish more connections, and learn more advanced things. But the spark for that was set off at birth.
- woeirua 6y ago
  I agree that there must be some genetic component to it, but if that were the case then by the law of large numbers we should have seen some counter examples by now too, i.e. babies that lack the instinct to suck or cry, etc. It'd be interesting to know if they show any obvious genetic changes that could explain that behavior. Casual googling hasn't turned up anything, but I'm sure someone has looked into it somewhere...
  - aeternum 6y ago
    Behaviors like sucking and grasping are considered reflexes. Those reflexes are present in all mammals and are relatively primative, the more modern parts of our brain eventually learn to suppress them and they typically disappear in most humans after around 1 year old. Interestingly, patients with brain lesions in certain places or with diseases like parkinsons sometimes lose the ability to suppress these reflexes. More info: https://www.ncbi.nlm.nih.gov/books/NBK395/ https://www.ncbi.nlm.nih.gov/books/NBK395/
- blobster 6y ago
  You might want to look into ethology, which studies innate behavior like the one you referenced. https://en.wikipedia.org/wiki/Ethology https://en.wikipedia.org/wiki/Ethology
blackrock 6y ago
> accounts of people “inheriting” memories after organ transplants This is interesting. So if you transplant a liver, you get memories of the donor’s eating habits? LOL.
- type0 6y ago
  LOL indeed. And if you eat an apple, you would become an Apple fanboy.
pippy 6y ago
There's clear evidence of epigenetics playing a role in brain activity, though these are more linked to hormonal responses such as stress. It's also been proven that RNA transcripts are used to trigger maternal instincts when a zygote is present in a mother: https://en.wikipedia.org/wiki/Epigenetics https://en.wikipedia.org/wiki/Epigenetics Scientists have already modeled memory retrieval using current neural network models. There's literally videos on youtube demonstrating this. I'd be surprised if RNA was used to encode memories to the extent OP is suggesting: there would have to be a mechanism for storing this RNA inside cells or there would be evidence of random strands of RNA floating around in the body. We would have been found it a long time ago, and scientists would also be able to decode it if these strands of RNA were standardized and could be transferred person to person. Though the way evolution works and how complicated the body is, it could be occurring in a small sub process in a neurons somewhere in the body. though this would likely be tied to hormonal responses or something equally boring.
phyalow 6y ago
Human memory is truly fascinating. I recently was trying to remember the name of a software vendor sales contact who I dealt with early last year. For the better part of the past week, try as I might I couldn't remember either his first name or last, but I had a vague feeling about the "fit" or "taste" for lack of a better word of his name. After a few days of conscious effort, yesterday I remembered his first name spontaneously and then suddenly his last name too. Almost like a AWS Glacier request.
- avaldeso 6y ago
  > After a few days of conscious effort, yesterday I remembered his first name spontaneously and then suddenly his last name too. A background process completing and notifying the result to the frontend.
mjfl 6y ago
RNA has a half life of 8 hours, so uh... no. Edit: 10 hours... https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104747 https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104747
ajb 6y ago
A similar idea was discussed in 2018: https://news.ycombinator.com/item?id=16139798 https://news.ycombinator.com/item?id=16139798 "Brain Cells Share Information With Virus-Like Capsules". It would be interesting to know how the science of that article panned out.
- greyface- 6y ago
  A relevant paper (authored in part by the subject of the Atlantic piece being discussed): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5884693/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5884693/
nabla9 6y ago
I think RNA memory hypothesis is not popular because there exist better, less controversial memory systems in the cell. For example gene regulatory network or bioelectric circuits in the cell (or, more likely a combination of them). Biswas, S., Manicka, S., Hoel, E., and Levin, M., (2021), Gene Regulatory Networks Exhibit Several Kinds of Memory: Quantification of Memory in Biological and Random Transcriptional Networks, https://www.cell.com/iscience/fulltext/S2589-0042(21)00099-7 https://www.cell.com/iscience/fulltext/S2589-0042(21)00099-7
- AstralStorm 6y ago
  The bigger problem with most of these memory systems is eliciting correct behavior of amnesia in case of both electric and chemical shock, as well as permanence or lack of permanence of those amnesic inputs.
  - nabla9 6y ago
    Short term memory and problems with recall are different issues from long term memory.
mrfusion 6y ago
I would think dna methylation would be a better candidate.
mrfusion 6y ago
It’s definitely fun to think about. Are vesicles in synapses really the whole story? It’s amazing how much we don’t know.
daemonk 6y ago
We've sequenced a lot of RNA in the past decade. A lot of that were extracted from neurons. I don't think we've seen evidence of this memory storing function through sequencing.
- robbiep 6y ago
  Not to mention the persistence of these memories over long periods of time, or the protein infrastructure that would be needed to decode them in real time
eternalban 6y ago
Assuming this speculation is correct (just for fun), then we can wonder about the memory model of the body. This would be a distributed memory system, as obviously not all RNA molecules in the body could transit from memory state M0 to M1 spontanuously. So there has to be a consensus and propagation mechanism. Wouldn't it be cool if it turned out to be something like CRDTs?
yters 6y ago
Very weird Maybe the ancients are right and the soul resides somewhere in the liver. Don’t laugh; people have led normal lives with giant pieces of their brain removed, but nobody has survived the death of their livers. The former fact; normal people getting by without much brain tissue, at least, ought to be the end of the argument: purely Hebbian models of the brain are obviously false.
breatheoften 6y ago
There was a really interesting episode of the mindscape podcast[0] recently which discusses a system in Planaria where the expression of the way the worm grows (with one head or two) is found to be encoded in an electronic structure within the tissue of the worm -- rather than within the worm's DNA. In a very real and observable sense, the 'blueprint' for the target worm is stored in the tissue system rather than as a 'plan' stored in the DNA itself. I think it feels surprising to see something that seems a lot like 'memory' influencing the action that results in the expression of the complete organism via the cellular level processes in this way. I find it easy to postulate from the example of planaria that analogous 'memory encoding' systems probably exist in all sorts of cellular systems ... though I think the information theoretic reasoning referenced by the participants in that podcast for how life creates and operates these systems makes it likely that 'the existence of information storage and retrieval' in a cellular system is not at all required to imply that 'this kind of system is therefore the storage model for long term cognition'. [0] https://www.preposterousuniverse.com/podcast/2021/02/01/132-michael-levin-on-growth-form-information-and-the-self/ https://www.preposterousuniverse.com/podcast/2021/02/01/132-...
- pharke 6y ago
  Michael Levin's work seems incredibly important and one of the most likely truly breakthrough discoveries I've heard of in a long while. I'm not so sure about RNA memory storage but the point about unicellular life possessing some form of information processing ability is certainly something more people should be thinking about. The fact that such complex behaviour is possible on that minuscule of a scale means there is really something special about the computational properties of organic chemistry. I can't help but feel a lot of the hardware that makes up macro scale life is really just used for dealing with the inefficiencies of getting so many individual cells to cooperate and interface with their environment in a coordinated manner. Single celled organisms have a shorter round trip time for their decision - action - sensation loop but are generally unable to make major modifications to their surroundings by acting or moving. Nonetheless, I think they're a lot smarter than we give them credit for.
  - jodrellblank 6y ago
ckemere 6y ago
As someone who's lab studies how memories are stored and recalled in the mamalian brain, I was excited to see a headline in the top list of Hacker News. Unfortunately, I was disappointed to see what was actually there. As is often the case, this article conflates some ideas that are truly remarkable and interesting (how are memories stored?) and mixes them with very strong statements that are clearly wrong. In this case, it is clear that synapses (connections between neurons) HAVE to be involved in memory, as the only way that a memory can ever be expressed is if a neuron triggers another neuron, etc, down the chain to a muscle. (OK, thoughts don't necessarily involve muscles, but to show your thoughts to the world.) And if synapse *dynamics* are not involved in memory, then either they never change, or they change randomly, both of which will lead to problems. (That's an exercise left to the reader.) So dynamic synapses are involved in memory, definitely, no question. The article mentions a couple of things that are interesting misdirection, like invertebrate models where "memories" are transmitted via serum. These are super cool experiments, but these are memories in the same way your immune system "remembers" a virus. Despite Tonegawa's best efforts, I think most researchers are quite confident that recalling your memory of last Christmas uses a very different mechanism than your immune system does to generate imagined tastes and smells and warm feelings. The article also talks about RNA ticker tapes. There is some super cool neuroengineering research around the idea of making a designer protein that would record a neurons activity in nucleotide chains as a readout. Definitely worth a dive if you're interested. And how neural activity drives synapse dynamics is a very big open question. It's known to involve protein synthesis (pkm-zeta, anyone?), so RNA is definitely involved. Finally, for those curious about how memories work, look up the "cognitive map" or the "index theory of memory".
- garblegarble 6y ago
  That's very interesting, thank you! Do you know of any good video series / lectures that would be a good primer for a layperson on the topics you touched on?
mjg59 6y ago
People love bringing up E. coli whenever this sort of thing comes up, but it's not a compelling argument. It generally refers to the observation that if you have a bacterium swimming towards something that's bad (ie, an increasing concentration of a toxic molecule), it'll tend to start swimming away. The obvious implication is that the bacterium has to remember that it's trying to swim away from something in order to keep doing so. In reality, we've had an alternative explanation for about 20 years. The chemical receptors that respond to the molecules E. coli wants to get away from activate and generate a cascade that causes the flagella (the stranded "tail" molecules that allow them to swim) to start rotating in the opposite direction. This causes them to become tangled, and this results in the bacterium moving around randomly rather than making any progress in one direction. If it heads away from the noxious source, the receptors stop activating, the flagella start rotating in the correct direction, and it heads off in a straight line again. But what about the memory? If the bacterium didn't remember what happened, isn't there a high chance that it would just end up doing the same thing again? Yes, but we don't need to bring RNA into this. One of the molecules involved in the cascade is activated by phosphorylation - once phosphorylated, its sensitivity changes. Over time, another molecule dephosphorylates it, but this altered sensitivity means the bacterium is more sensitive to the noxious molecule than it was previously and biases the bacterium to move away. So "memory" in this case is actually just a modification of the gain in the response to a stimulus. Does it demonstrate that responses can be influenced by something that happened in the past without requiring a nervous system? Yup, absolutely. Is it something that gives us a better understanding of how rich long term memories are stored in the brain? Not really. (Source: my first attempt at a PhD was working with https://en.wikipedia.org/wiki/Dennis_Bray https://en.wikipedia.org/wiki/Dennis_Bray who did a bunch of the computational modelling that demonstrated we didn't need anything overly complicated to understand what was going on here. Absolutely wonderful scientist, but I fell out with departmental IT staff over network security stuff. Ironic with hindsight. Also, this is my recollection from almost 20 years ago, so details may be inaccurate)

156 points by nahuel0x 6y ago

nynx 6y ago

Very interesting, but also worrying, in a way. If neurons are actually reasonably large, complex computers in their own right, brain emulation is much further off than some people are thinking. It's possible that ASC brain preservation doesn't preserve the internal details necessary if this hypothesis ends up being true.

deleted 6y ago
[deleted]
asdfasgasdgasdg 6y ago
To be fair it's more than just possible that ASC brain preservation doesn't work even under any other hypothesis of cognition.
- nynx 6y ago
  That's true. I think the fair way to put it that it's possible that ASC preserves the necessary data to simulate a brain.
deleted 6y ago
[deleted]
Voloskaya 6y ago
This is the opposite of worrying.
- nynx 6y ago
  How so?
  - Voloskaya 6y ago
    You seemed to be saying that it is worrying, as it may indicate brain emulation is much further off than some people are thinking. This indication is the opposite of worrying to me, it's reassuring.
    - earthboundkid 6y ago
      You don’t want everything you or anyone else has loved or valued to be replaced unimaginable monsters?
      - Dylan16807 6y ago
        You're going to have to explain what you're talking about. Everything be replaced? What does that have to do with brain emulation? Also I think you're implying that brain emulation will lead to more "unimaginable monsters", when it could very easily be the opposite: if you can't emulate a brain then an AI has to be even weirder and harder to understand.
        undersuit 6y ago
        Dystopian futures where you exist as only as much as your can afford. It's cheapest to download yourself into a computer and slow down your computation speed than to continue to pay have a flesh and blood body.

subroutine 6y ago

This is nonsense. Evidence collected over the last 40 years have detailed how memory is encoded by synaptic weights, but the premise... "there’s no obvious way for all that sensory data to be captured in synapses as long term memories" ...just ignores these findings. The model described in the article on the other hand, has never been observed. At the least, if you are going to propose an mRNA hypothesis don't use "T" as one of your RNA bases.

AstralStorm 6y ago
What is the physical realisation of the synaptic weight? (Here's trouble, we do not know. It's not in just connectivity or myelination.)
- jrussino 6y ago
  See my response to your sibling comment; clearly we still have a lot to learn, but there is already some understanding of the biological mechanisms of synaptic plasticity (which I think is what the parent comment is referring to as "synaptic weights"). https://en.wikipedia.org/wiki/Synaptic_plasticity https://en.wikipedia.org/wiki/Synaptic_plasticity
- subroutine 6y ago
  The physical realization is the number of postsynaptic receptors. In terms of fast excitatory transmission it is the quantity of AMPA receptors. You can potentiate or depress synapses by controlling the amount of these receptors. This has been demonstrated in vivo, and in cell culture. We are at the point where we can manipulate the strength of individual synapses. Here is a nice review article: https://royalsocietypublishing.org/doi/10.1098/rstb.2013.0136?url_ver=Z39.88-2003 https://royalsocietypublishing.org/doi/10.1098/rstb.2013.013...
titzer 6y ago
> have detailed how memory is encoded by synaptic weights Synaptic weights is our computational model of neural networks that seems to work pretty well. But this is a model. No one has discovered the biological mechanism by which synapses are "weighted". The actual computation going on in a cell is totally based on chemistry. There are a lot of different specialized networks in human and animal brains that don't necessarily translate easily to "weighted synaptic networks" all that well. For example, networks that process audio information have been shown to recognize individual frequencies (in fact, they pretty much solely do this!) Such networks seem to be primarily based on the firing rate across a synapse. For such networks is seems more reasonable to think of neurons as signal processors whose internal computation is more based on the time domain, e.g. some kind of Fourier transform-equivalent. In short, I think you should put less weight (pun intended) in our computational model of neurons (link weights) and look more at biology.

tokipin 6y ago

One of my theories is that this (or similar virus-like mechanism) is how some memories are transferred to offspring. The reasons are: * Prodigies which happen to be good in a field related to what their parents are good at. Often the wording used indicates a memory-like reason. For example, finding the rules of chess "familiar." * Embeddings in machine learning, which allow encoding of high-dimensional information in a low-dimensional space. This would imply that humans have a somewhat-shared embedding space at some "layers". It's interesting to wonder how similar this space would be across various animals, as it would effectively be an evolved language. * Other more subtle things, like the "cultural memory" of a society. One question would be what types of time scales these memories survive across. Maybe some forms of instinct are deep memories that have been directly encoded in DNA.

plutonorm 6y ago
I had to scroll a long way for an intelligent contribution! https://www.scientificamerican.com/article/prehistoric-viruses-and-the-function-of-the-brain/ https://www.scientificamerican.com/article/prehistoric-virus... I also wonder if and to what extent this information can transfer between individuals? I'm reminded of the Jungian collective unconscious. You're going to think I'm a kook now, but, there's also a panspermia angle on this. Big ifs here, but. If panspermia is true. If evolution on earth is tied to evolution of life in the wider universe via transfer of genetic material. Then it could be possible that the code in which memories (or a learned manifold, encoding useful generalisation) are encoded is compatible with life here today. You could conceivably get not just morphological/physiological changes in terrestrial organisms through viral horizontal gene transfer, but also transfer of cognitive strategy via the same mechanism. X-files kinda stuff. All kind of unlikely, but an interesting possibility.
- type0 6y ago
  But that would imply that evolution was "directed", which I think is proven that it's not. The role of viruses in evolution is almost mainstream now, it is much more likely that virus was just a method for ancient extinct organisms to exchange genes, sort of proto-sex, and not anything else outlandish.

fabian2k 6y ago

I don't think there's any real doubt that memory is stored in neurons, this is really a fringe theory. I haven't looked at it closely, but my first objection would be that RNA would be far too slow for this purpose. It's also not stable over time, cells have mechanisms to intentionally degrade it. It just doesn't make sense. There are other weird parts in the blog post, for example claiming that a particular protein kinase is involved in mRNA transcription. That is by definition wrong as a kinase is an enzyme that transfers a phosphate, so a protein kinase transfers phosphates to proteins. And the RNA in this hypothetical memory storage would not be mRNA, as that by definition encodes for proteins. The person cited in the post is also a crackpot, I've quite a lot of experience with his exploits on the Stack Exchange network. And I haven't found a conspiracy theory yet that he didn't like. This is not hyperbole, I learned of a whole bunch of conspiracy theories I didn't know existed through his posts.

macawfish 6y ago
RNA is literally a form of memory. The question should not be whether or not memory is encoded in RNA, it should be "what are all the ways that creatures with RNA can experience the encoding and decoding of information encoded in RNA?" Memory is literally everywhere. There is already evidence that the brain can encode memory in dynamic molecular processes, and that interference of those process can interfere with an animal's ability to recall memory. Your point about timescales is a good one, and provides a clue: the timescales over which a given medium of information can be encoded to or decoded from and over which it decays should provide a clue about the timescales we might expect organisms to experience it in. Mammals and other creatures with RNA experience memory over a whole continuous range of timescales. Why wouldn't RNA, which is optimized for encoding information, be just one of many mediators of memory?
- fabian2k 6y ago
  Most of the RNA in our cells simply encodes for proteins. The information is entirely redundant as it is simply copied from DNA. I would not call that memory. Of course there's a lot of other stuff RNA can do like catalytic activity, triggering RNA interference or reacting to other molecules (riboswitches). But information storage isn't really anything RNA is known for.

blackrock 6y ago

What I find fascinating, is that babies are born knowing how to suck. How? It’s not something you can teach them. They say it’s an innate thing. But what does that even mean. I think babies are born with this programmed into them. Like a genetic type of memory. Then over time, the neurons establish more connections, and learn more advanced things. But the spark for that was set off at birth.

woeirua 6y ago
I agree that there must be some genetic component to it, but if that were the case then by the law of large numbers we should have seen some counter examples by now too, i.e. babies that lack the instinct to suck or cry, etc. It'd be interesting to know if they show any obvious genetic changes that could explain that behavior. Casual googling hasn't turned up anything, but I'm sure someone has looked into it somewhere...
- aeternum 6y ago
  Behaviors like sucking and grasping are considered reflexes. Those reflexes are present in all mammals and are relatively primative, the more modern parts of our brain eventually learn to suppress them and they typically disappear in most humans after around 1 year old. Interestingly, patients with brain lesions in certain places or with diseases like parkinsons sometimes lose the ability to suppress these reflexes. More info: https://www.ncbi.nlm.nih.gov/books/NBK395/ https://www.ncbi.nlm.nih.gov/books/NBK395/
blobster 6y ago
You might want to look into ethology, which studies innate behavior like the one you referenced. https://en.wikipedia.org/wiki/Ethology https://en.wikipedia.org/wiki/Ethology

blackrock 6y ago

> accounts of people “inheriting” memories after organ transplants This is interesting. So if you transplant a liver, you get memories of the donor’s eating habits? LOL.

type0 6y ago
LOL indeed. And if you eat an apple, you would become an Apple fanboy.

pippy 6y ago

There's clear evidence of epigenetics playing a role in brain activity, though these are more linked to hormonal responses such as stress. It's also been proven that RNA transcripts are used to trigger maternal instincts when a zygote is present in a mother: https://en.wikipedia.org/wiki/Epigenetics https://en.wikipedia.org/wiki/Epigenetics Scientists have already modeled memory retrieval using current neural network models. There's literally videos on youtube demonstrating this. I'd be surprised if RNA was used to encode memories to the extent OP is suggesting: there would have to be a mechanism for storing this RNA inside cells or there would be evidence of random strands of RNA floating around in the body. We would have been found it a long time ago, and scientists would also be able to decode it if these strands of RNA were standardized and could be transferred person to person. Though the way evolution works and how complicated the body is, it could be occurring in a small sub process in a neurons somewhere in the body. though this would likely be tied to hormonal responses or something equally boring.

phyalow 6y ago

Human memory is truly fascinating. I recently was trying to remember the name of a software vendor sales contact who I dealt with early last year. For the better part of the past week, try as I might I couldn't remember either his first name or last, but I had a vague feeling about the "fit" or "taste" for lack of a better word of his name. After a few days of conscious effort, yesterday I remembered his first name spontaneously and then suddenly his last name too. Almost like a AWS Glacier request.

avaldeso 6y ago
> After a few days of conscious effort, yesterday I remembered his first name spontaneously and then suddenly his last name too. A background process completing and notifying the result to the frontend.

mjfl 6y ago

RNA has a half life of 8 hours, so uh... no. Edit: 10 hours... https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104747 https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104747

ajb 6y ago

A similar idea was discussed in 2018: https://news.ycombinator.com/item?id=16139798 https://news.ycombinator.com/item?id=16139798 "Brain Cells Share Information With Virus-Like Capsules". It would be interesting to know how the science of that article panned out.

greyface- 6y ago
A relevant paper (authored in part by the subject of the Atlantic piece being discussed): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5884693/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5884693/

nabla9 6y ago

I think RNA memory hypothesis is not popular because there exist better, less controversial memory systems in the cell. For example gene regulatory network or bioelectric circuits in the cell (or, more likely a combination of them). Biswas, S., Manicka, S., Hoel, E., and Levin, M., (2021), Gene Regulatory Networks Exhibit Several Kinds of Memory: Quantification of Memory in Biological and Random Transcriptional Networks, https://www.cell.com/iscience/fulltext/S2589-0042(21)00099-7 https://www.cell.com/iscience/fulltext/S2589-0042(21)00099-7

AstralStorm 6y ago
The bigger problem with most of these memory systems is eliciting correct behavior of amnesia in case of both electric and chemical shock, as well as permanence or lack of permanence of those amnesic inputs.
- nabla9 6y ago
  Short term memory and problems with recall are different issues from long term memory.

mrfusion 6y ago

I would think dna methylation would be a better candidate.

mrfusion 6y ago

It’s definitely fun to think about. Are vesicles in synapses really the whole story? It’s amazing how much we don’t know.

daemonk 6y ago

We've sequenced a lot of RNA in the past decade. A lot of that were extracted from neurons. I don't think we've seen evidence of this memory storing function through sequencing.

robbiep 6y ago
Not to mention the persistence of these memories over long periods of time, or the protein infrastructure that would be needed to decode them in real time

eternalban 6y ago

Assuming this speculation is correct (just for fun), then we can wonder about the memory model of the body. This would be a distributed memory system, as obviously not all RNA molecules in the body could transit from memory state M0 to M1 spontanuously. So there has to be a consensus and propagation mechanism. Wouldn't it be cool if it turned out to be something like CRDTs?

yters 6y ago

Very weird Maybe the ancients are right and the soul resides somewhere in the liver. Don’t laugh; people have led normal lives with giant pieces of their brain removed, but nobody has survived the death of their livers. The former fact; normal people getting by without much brain tissue, at least, ought to be the end of the argument: purely Hebbian models of the brain are obviously false.

breatheoften 6y ago

There was a really interesting episode of the mindscape podcast[0] recently which discusses a system in Planaria where the expression of the way the worm grows (with one head or two) is found to be encoded in an electronic structure within the tissue of the worm -- rather than within the worm's DNA. In a very real and observable sense, the 'blueprint' for the target worm is stored in the tissue system rather than as a 'plan' stored in the DNA itself. I think it feels surprising to see something that seems a lot like 'memory' influencing the action that results in the expression of the complete organism via the cellular level processes in this way. I find it easy to postulate from the example of planaria that analogous 'memory encoding' systems probably exist in all sorts of cellular systems ... though I think the information theoretic reasoning referenced by the participants in that podcast for how life creates and operates these systems makes it likely that 'the existence of information storage and retrieval' in a cellular system is not at all required to imply that 'this kind of system is therefore the storage model for long term cognition'. [0] https://www.preposterousuniverse.com/podcast/2021/02/01/132-michael-levin-on-growth-form-information-and-the-self/ https://www.preposterousuniverse.com/podcast/2021/02/01/132-...

pharke 6y ago
Michael Levin's work seems incredibly important and one of the most likely truly breakthrough discoveries I've heard of in a long while. I'm not so sure about RNA memory storage but the point about unicellular life possessing some form of information processing ability is certainly something more people should be thinking about. The fact that such complex behaviour is possible on that minuscule of a scale means there is really something special about the computational properties of organic chemistry. I can't help but feel a lot of the hardware that makes up macro scale life is really just used for dealing with the inefficiencies of getting so many individual cells to cooperate and interface with their environment in a coordinated manner. Single celled organisms have a shorter round trip time for their decision - action - sensation loop but are generally unable to make major modifications to their surroundings by acting or moving. Nonetheless, I think they're a lot smarter than we give them credit for.
- jodrellblank 6y ago

ckemere 6y ago

As someone who's lab studies how memories are stored and recalled in the mamalian brain, I was excited to see a headline in the top list of Hacker News. Unfortunately, I was disappointed to see what was actually there. As is often the case, this article conflates some ideas that are truly remarkable and interesting (how are memories stored?) and mixes them with very strong statements that are clearly wrong. In this case, it is clear that synapses (connections between neurons) HAVE to be involved in memory, as the only way that a memory can ever be expressed is if a neuron triggers another neuron, etc, down the chain to a muscle. (OK, thoughts don't necessarily involve muscles, but to show your thoughts to the world.) And if synapse *dynamics* are not involved in memory, then either they never change, or they change randomly, both of which will lead to problems. (That's an exercise left to the reader.) So dynamic synapses are involved in memory, definitely, no question. The article mentions a couple of things that are interesting misdirection, like invertebrate models where "memories" are transmitted via serum. These are super cool experiments, but these are memories in the same way your immune system "remembers" a virus. Despite Tonegawa's best efforts, I think most researchers are quite confident that recalling your memory of last Christmas uses a very different mechanism than your immune system does to generate imagined tastes and smells and warm feelings. The article also talks about RNA ticker tapes. There is some super cool neuroengineering research around the idea of making a designer protein that would record a neurons activity in nucleotide chains as a readout. Definitely worth a dive if you're interested. And how neural activity drives synapse dynamics is a very big open question. It's known to involve protein synthesis (pkm-zeta, anyone?), so RNA is definitely involved. Finally, for those curious about how memories work, look up the "cognitive map" or the "index theory of memory".

garblegarble 6y ago
That's very interesting, thank you! Do you know of any good video series / lectures that would be a good primer for a layperson on the topics you touched on?

mjg59 6y ago

People love bringing up E. coli whenever this sort of thing comes up, but it's not a compelling argument. It generally refers to the observation that if you have a bacterium swimming towards something that's bad (ie, an increasing concentration of a toxic molecule), it'll tend to start swimming away. The obvious implication is that the bacterium has to remember that it's trying to swim away from something in order to keep doing so. In reality, we've had an alternative explanation for about 20 years. The chemical receptors that respond to the molecules E. coli wants to get away from activate and generate a cascade that causes the flagella (the stranded "tail" molecules that allow them to swim) to start rotating in the opposite direction. This causes them to become tangled, and this results in the bacterium moving around randomly rather than making any progress in one direction. If it heads away from the noxious source, the receptors stop activating, the flagella start rotating in the correct direction, and it heads off in a straight line again. But what about the memory? If the bacterium didn't remember what happened, isn't there a high chance that it would just end up doing the same thing again? Yes, but we don't need to bring RNA into this. One of the molecules involved in the cascade is activated by phosphorylation - once phosphorylated, its sensitivity changes. Over time, another molecule dephosphorylates it, but this altered sensitivity means the bacterium is more sensitive to the noxious molecule than it was previously and biases the bacterium to move away. So "memory" in this case is actually just a modification of the gain in the response to a stimulus. Does it demonstrate that responses can be influenced by something that happened in the past without requiring a nervous system? Yup, absolutely. Is it something that gives us a better understanding of how rich long term memories are stored in the brain? Not really. (Source: my first attempt at a PhD was working with https://en.wikipedia.org/wiki/Dennis_Bray https://en.wikipedia.org/wiki/Dennis_Bray who did a bunch of the computational modelling that demonstrated we didn't need anything overly complicated to understand what was going on here. Absolutely wonderful scientist, but I fell out with departmental IT staff over network security stuff. Ironic with hindsight. Also, this is my recollection from almost 20 years ago, so details may be inaccurate)