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Comment by blurbleblurble | Hacker News Reader

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?

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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.

I don't think they mean the literal information encoded in the RNA. The fact the RNA exists is, itself, a signal. It shows that there was previously a signal that caused the RNA to be transcribed. And then once you start including concentrations and degradation times for all the various things involved in the system...

Well there's lots of information there which can be used to infer aspects of previous states. I assume it's more of this aspect that is being referenced, rather than what is encoded in the RNA.

98.8% of our DNA is identical with a chimpanzee, and 60% common with a fruit fly.

I am personally interested by the 'RNA Computer' hypothesis which posits an additional layer of differentiation in computations performed by interacting RNA.

I have also read of experiments where memories (learned behaviors) were transplanted by injecting ground-up neural material. Flatworms were the subject I think.

Of course this is all near the edge of mainstream, but I think genuine science demands openness to new ideas.

That's on a GENE level. On a nucleotide base by base we are very different.

From what I understand, most of the RNA just sits there, and people are speculating its role. Did I get that part wrong?

no. RNA is a very active molecule. It rarely sits around, nearly all organisms have RNAses which are eating RNA that is sitting around.

Protein formation is well known to be involved in at least some long term memory formation and recall: https://en.wikipedia.org/wiki/De_novo_protein_synthesis_theo...

Although I'd again argue that there is no single "true" medium or mechanism of memory.

I'd remind you that DNA is indeed memory. It's memory whose recall is heavily modified and contextualized by its environment, for example methylation, the topology of how it is currently twisted, the kinds of nutrients available for molecular synthesis, etc.

If RNA mediates memory on a sub-generational timescale, it seems that it'd provide a dynamic, contextual bridge between generational memory in DNA and shorter term kinds of memories that play out over timescales less than an individual's life. So that the molecular formation of a given memory would have a semantic basis in the longer term context. A concrete but way oversimplified example of this might work:

You go through a traumatic experience where you almost die. The specific way you almost die is related to a number of factors involving your ability to run fast enough. The long term memories of that experience are then encoded as proteins by a mosaic of genes related to certain muscles, their shape and size, certain metabolic pathways, etc. The way we might unpack or interpret that memory at any given time/context could be as a gutteral impulse that results in such realizations as "I need to get more exercise" or "my grandparents had heart disease, maybe I should go to the doctor" or "wow I'm sure hungry for fish", etc.

Btw I'm not even arguing that it's as clear cut or simple as that, just sharing how I intuitively make sense of all this evidence and these hypotheses.

WTF is "generational memory"?

the idea would be that learned behavior which is not genetically encoded is instead passed down in the form of specifically structured information molecules.

A lot of biologists these days use "generational memory" to refer to epigenetic configurations that are heritable, but in the context of my comment I was using it more to refer generally to information that is typically modified over multigenerational timescales. My point was to frame RNA as a kind of intermediary between longer term and shorter term mediums of memory.

So as an simplified analogy, the DNA would be like a dictionary of common words that could be used to encode a meaningful story about something the organism has experienced. The RNA would be like the handwritten copy of each word as the story is written down on a piece of paper. The paper with the handwritten story is analogous to the proteins that have been shown numerous times to be involved in long term memory storage and recall.

I'm not sure you can call DNA memory.

Yes, it contains information. But you can't write to it.

For most eukaryotic organisms DNA it might not be "random access memory" but it contains a record of genes that somehow managed to get through the selective pressures they were subjected to over countless generations. I'd say that this information is an imprint of history, and is memory.

My hunch is that you're thinking of memory as being equivalent to RAM in a computer. So I'll remind you that read only memory is still memory.

Some microorganisms, like viruses, do directly modify DNA. That's where CRISPR came from.

I'd encourage you to check out the full range of definitions of the word "memory".

Read only memory was written once.

An imprint of history is not memory, in much the same way that fossils, stars, the environment is not memory. Human DNA has not been written to. It is edited in only very specific circumstances - DNA repair, TCR/BCR recombination, meiosis and interestingly, and possibly relevant - LINE-1 transposons in neural tissue.

Why not? They encode state in a way that is stable over time. Any medium that preserves state over time can and likely does function as memory in some way or another.

At any rate, DNA encodes useful information related to how an organism's ancestors were able to survive their environment. If you prefer not to call it "memory" for semantic reasons, I don't really care too much, although my opinion is that memory is too deep of a concept to be narrowly confined like that. Nevertheless, even if you don't call DNA memory, it doesn't change my point in the comments above, which is that the information encoded in DNA is directly relevant to any survival related memories, and so it would make a lot of sense if such memories were formed in direct, physical reference to that information. Seeing as how it's been shown that protein formation is involved in memory formation and recall, and seeing as RNA is how proteins get their molecular structure, it's not a far reach to see the possibility that RNA is a contextual bridge for memory to be encoded in reference to survival related information provided by DNA.

None of this requires that DNA be writable in the same way that transistor based me let is writeable. DNA is written through a probabilistic, distributed process, but it still encodes information about the molecular tools its carriers successfully managed to survive and reproduce with.

Of course you can. See, for example, the Lambda switch. https://en.wikipedia.org/wiki/Lambda_phage#Induction Yeast modifies its own DNA by copying one of two passive templates into an active region to switch its own internal mating state.

Viruses integrate into the human genome, then decay and eventually become fodder for new regulatory regions and genes.

During human life, your genome is mutated, and your body repairs it, sometimes making mistakes, which are permanent (and passed down to your children if it happens to the germ line).

I could go on...

Ok, DNA changes occur, but physiological writing to the DNA does not happen in humans. I'll give you DNA repair, BCR/TCR rearrangement, meiosis, and also the more recently discovered LINE-1 retrotransposons - but they occur at specific times and usually in a random fashion. I don't think this fits any idea of what memory is.

If you're saying it's theoretically possible, I would agree that it might be, and that there is a potential for DNA to be memory. But to claim that DNA is memory without a known write process is premature I think.

Yeah, I agree- you have to stretch the concept of "brain memories" pretty far to accomodate epigenetics.

Yes... any human instinct, like the fear of spiders that you can observe in a days old baby, is a form of memory, and DNA/RNA could certainly be a storage mechanism for these.

Evolved behaviours are arguably the opposite of memory: it's the RNA of the people who avoided the spiders that got reproduced.

I mean... By definition isn't that a form of memory?

Whether it's learned or you were born with it doesn't really change that the information had to be stored and transferred which is...memory?

I guess what the OP means is that one definition of memory is that it is generated by your experiences. In this case the memory is the lack of experience (with a spider), because those genes keep you away from spiders. So it is possible that you can develop the RNA without seeing a spider, hence the opposite of memory.

In this case no information was "stored" after meeting a spider or getting bitten by it. Rather people who (by accident) had predisposition to avoid spiders happened to survive better.

Selection may be a part of it, but you may be wrong in saying no information was stored.

I remember hearing about this one really interesting experiment where they would expose mice to a specific scent (I think it was citrus), and then give them a shock. Obviously after a while, when the mice smelled that scent they would get nervous and try to hide (or something along those lines, this is from memory so forgive any erroneous details). They then bred those mice and separated the offspring from the parents so that there was no way they could learn about the smell from them.

When they exposed the offspring to the smell, they reacted in the same way their parents did. Without ever having been exposed to it before, or knowing about the shocks. Pretty interesting stuff.

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