Memories of positive associations get written onto DNA

http://arstechnica.com/science/2013/08/memories-of-positive-associations-get-written-onto-dna/

by LiveTheDream • 13 years ago

126 74 13 years ago

samatman4• 13 years ago

Methylation can happen in gametes also, making some epigenetic changes heritable. The precise mechanisms of methylation are under intense study, but not well understood; it doesn't appear to be a random process in general.

This points to an almost-paradox in biology, which I call Lamarck's Lemma: There may be evolutionary advantage to being able to pass on acquired traits to one's offspring, and no known physical law that prevents it. Why, therefore, would biology not develop at least some Lamarckian mechanisms, since they could offer fitness in the Darwinian sense?

Answer: there appears to be exactly that. It's an exciting time for genetics.

nollidge3• 13 years ago

I don't see why it's a paradox. Lots of things would offer fitness - why can't all animals talk? Why can't plants move? Surely these things would offer greater Darwinian fitness.

samatman4• 13 years ago

It's not a paradox, it's an almost paradox, which is kind of like being almost pregnant from a logic perspective.

Lamarckian and Darwinian evolution were debated and Darwin won. Lamarck's Lemma, which is a term I made up, points out that, were a random walk to create a mechanism for Lamarckian evolution, Darwinian evolution might well keep it around, as it could offer fitness.

That's why I phrase it as a lemma on Darwin's theory: even if it proves true, as epigenetics suggests, it doesn't make Lamarckian thinking correct. If anything, the opposite: it shows that Lamarckian effects can be explained through natural selection.

Plants can of course move, the classic example being the sensitive plant. Whether or not non-human animals can "talk" depends, basically, on whether one means "signalling" or "language proper". The bee dance can give arbitrarily complex instructions in one particular domain: there is no 'one' bee dance, each performance is roughly as unique as a sentence or so of text.

samatman4• 13 years ago

I did want to address one other total misconception here: Darwinian fitness is a result, not an effect. There is no adaptation, at all, which predictably increases fitness. Evolution is not a direction.

"Surely these things would offer greater Darwinian fitness" is as basic a mistake as "Surely we can figure out whether this program will halt without running it".

EDIT: In fact, as I think about it, there is a deep connection between the thought "Knowing the genes of this organism, we may predict its fitness" and "Knowing the instructions of this program, we may predict its halting". I'd love to see a paper on that.

sadkingbilly• 13 years ago

Why can't plants move? Surely these things would offer greater Darwinian fitness.

Not necessarily for plants. They do in fact move. They just do it differently. They have no problem spreading their DNA throughout the world via seeds and pollen. They use a lot less energy too, compared with sprouting legs and getting up to walk around. If they did this, they would likely require much greater quantities of food, including protein, which would put plants at a disadvantage.

In any case, plants have also evolved on a completely different fitness track than that of animals. Plants have evolved incredible manipulation of chemistry, far beyond what humans can produce today, let alone even understand.

I recently finished reading Botany of Desire (Michael Pollan) where he describes how plants have co-evolved with humans, appealing to our selection of flowers, fruits, and vegetables to further distribute their DNA. Who's actually farming who? Interesting stuff.

VladRussian22• 13 years ago

I don't see why it's a paradox. Lots of things would offer fitness - why can't all animals talk? Why can't plants move? Surely these things would offer greater Darwinian fitness.

this is why we have live organisms that able to move - it is called animals, and we have animals that can talk, and we'll possibly have [some milleniums later] animals that are able to efficiently transfer memory through DNA (possibly after these animals become able to calculate and select what memories they'd like to encode into their own DNAs and what of these memories they want to transfer to the offsprings)... Evolution isn't finished as of today, it is possibly only starting :)

j2d3• 13 years ago

Animals can talk --- to each other.

jonnathanson• 13 years ago

Darwinian natural selection doesn't select for absolute/universal fitness, because there is no such thing. It selects for fitness into a specific, local niche. Humans may be more fit than chimpanzees in some areas, for example, but less fit in others.

It is a fallacy to assume that evolution is linear, and that it progresses toward some sort of universal optimum. There is no universal optimum. There are only specific, local optima.

A good example is the megalodon. From all we know, the megalodon was basically a massive, faster, more badass, more ferocious version of the great white shark. Why did the megalodon die out, and the lines that led to the great white survive? Surely big-badassedness is a desirable quality in an apex predator like a shark, right? Well, not really, because circumstances changed. Ocean temperatures changed, prey got scarcer and smaller, and eventually, size became a detriment. Megalodon was too big not to fail. What fit one day no longer fit the next.

The same thing may happen to humans someday, and some other animal may step up to take our places. It seems unlikely, but nature is the one doing the "selecting" in natural selection -- not us. Environments and circumstances change, and as they change, so do the criteria that "fit" the new context. In the Darwinian sense, "fit" refers to suitability to a habitat; it does not refer to "fitness" in the modern sense of the word. Think "product/market fit," not "physically fit."

jostmey• 13 years ago

Methylation of the nerve cells has no effect on the germline. Changes in the brain are not heritable.

samatman4• 13 years ago

Relevant to the article, and worth pointing out. It has no direct bearing on my comment, which was about (heritable) methylation of the gametes.

I believe what you mean to say is "We have been able to observe no correlation between methylation of the nerve cells and methylation of the gametes". Unless you can cite detailed studies supporting this null hypothesis. My understanding is that we have no idea.

swamp405• 13 years ago

How would you explain why birds raised in isolation can still build nests? And sing the songs of their species?

I would propose that it is possible that some animal "instincts" are really inherited memories from their ancestors.

And that if we look hard enough and deep enough, we may find similar human "instincts".

Have you ever seen a baby with a fear of spiders? Whose parents swear the child has never even seen a spider before?

gizmo6862• 13 years ago

Even without Methylation, we have another mechanism for passing on traits to offspring, raising them. Admittedly, there are many species where this is not relevant, but for species where the young live with their parents, or other members of the older generation, it seems reasonable that information and traits could be passed by cross generation interactions.

The most obvious example of this is humans, who have minimal (if any) genetic advantage over cave-men. I suspect we can find simmilar instances in other species.

bencollier49• 13 years ago

Dodgy newspaper pop-sci interpretation involving past lives in 3..2..1..

pnathan• 13 years ago

While snarky, you're right. Also see the 1910-1940 idea of "Racial Memory". One of the more popular and weird ideas to come out of Lamarkian concepts.

awda2• 13 years ago

Interesting that they could also block memory formation in addiction centers. I wonder if there is a preventative treatment possible in that direction, by blocking addiction before it happens? It's a nice dream, anyway.

contingencies• 13 years ago

Err, err, centralized government bureaucracy imposing own will-of-committee between world and consciousness to inflict totalitarian conformance to pre-approved homogeneity ... not good, even if: drugs/childporn/terrorism/etc.

awda2• 13 years ago

What makes you think this is pushed by the government? I'm envisioning opt-in.

rflrob2• 13 years ago

I'd need to read the paper, but the write up seems to ignore the possibility that methylation is required to express the genes necessary to form memories, and not that the methylation itself is, in any meaningful sense, the memory itself (as in "memories [...] get written onto DNA).

karpathy• 13 years ago

This was my first reaction as well. Blocking methylation is a drastically global operation for a cell as methylation is involved in so much of the epigenetic regulation. Turning it off probably disabled much of the normal functioning of those cells and could have had all kinds of downstream effects.

It doesn't seem fair to jump to the conclusion that the memory is actually encoded in the methylation pattern somehow. Based on a skim of the paper, the researchers don't seem to claim this either.

dekhn• 13 years ago

Ah, I only skimmed the article describing it, and originally jumped to the conclusion they had actually claimed that "memory state" (IE factual encoding) was being stored in methylation.

Modification of gene expression of genes associated with memory (in the form of changes to neuronal toplogy and excitation thresholds) seems like a more mundane and reasonable explanation.

dnautics2• 13 years ago

the title in the write up is unnecessarily sensational, your impression is exactly the model proposed in the paper. You could not read out the methylation pattern in a cell and retrieve the memory, the memory is the methylation + the cells.

JunkDNA• 13 years ago

This is fascinating but unsurprising given all the things that have come out lately with regard to epigenetics. If your mental model of DNA involves some image of a pristine blueprint that is followed with clockwork-like precision in the exact same way by every cell in your body, your model needed updating quite some time ago.

I feel that many researchers, even geneticists who should know better, still have not internalized the idea that epigenetics is pretty good evidence that somatic DNA is a read/write medium. This leads to sloppy thinking about genetic causes of disease as well as continued persistence of the idea that if we can just collect enough sequences, all genetic causes of disease might be found.

hobbes78• 13 years ago

The DNA doesn't sport standard read/write access, what's happening is that the expression or not of some genes can occur on an individual and be inherited by its offspring. The DNA doesn't change (save for the chance of a tiny few random changes, as usual)...

Blahah• 13 years ago

(de)methylation is DNA read/write. The DNA does change, although the sequence of bases doesn't.

total__C• 13 years ago

In the situation described by the article, the changes in gene expression are happening in the rat's brains. These changes aren't going to make it into the rat's gametes.

mathattack• 13 years ago

By this argument, culture can be imprinted into DNA too, no?

This also implies that it would be much tougher to do a Jurassic Park recreation, because the environment is different. You can't just start from scratch with the DNA.

Or am I misinterpreting?

MacsHeadroom• 13 years ago

You are absolutely correct.

Retric• 13 years ago

It's a mistake to think there is only one correct path when talking about DNA. Often, there is quite a bit of redundancy involved so Jurasic Park dinosaurs may be slightly different than there historic counterparts but that would not prevent them from being sufficiently viable to pass on there DNA. Because, biology is PASS / FAIL not some pursuit of perfection.

3am• 13 years ago

You are misinterpreting. As others have noted, this is DNA in the nuclei of nerve cells, not gametes. It is not heritable.

pygy_• 13 years ago

Culture is related to implicit and explicit memories shared by many people.

So (supposing that the results of this study can be generalized), yes, culture ends up imprinted in neuronal DNA, one cell at a time.

Since the imprinting is distributed and varies among the billions of neurons in your head it will not be passed to descendants (which inherit half a cell's worth of DNA).

bdg2• 13 years ago

My understanding seems to be at conflict with how I'm reading your description here. Please help me out?

DNA is comprised of four specific nucleic acids which are always the same molecular combination. These acids form into base-pairs which must always be some combination of those four acids.

The DNA itself cannot be 'written to' as if it stores information no less than the following string x = "ACGTACT" can contain additional information beyond those bytes already stored in the string. We could alter the DNA, just as we can alter the string x, but this isn't writing additional data to the binary values, but changing what's stored in those memory locations.

When we're talking about reading/wrting to the DNA, are we actually speaking about modifying the sequence of any given strand, thus "reading/writing to DNA" is a misnomer ? I know there are presently ways to produce DNA synthetically, but what you've said seems to indicate there's room here for any pre-defined sequence I print to end up doing different things in a cloned cell than their synthetic duplicates might.

Renaud• 13 years ago

To cite Kwikipedia on the Epignetics article: http://en.wikipedia.org/wiki/Epigenetics

[Epigenetics] refers to functionally relevant modifications to the genome that do not involve a change in the nucleotide sequence.

There was an eye opening documentary on the subject produced by BBC Horizon a few years ago: The Ghost in your Genes, http://www.youtube.com/watch?v=ehwFVgQ82ZY

new299• 13 years ago

The "epigenetics" they're talking about is the chemical modification of the DNA. So while we usually talk about sequences of A,T,G,C we've actually got an additional symbol e.g. M. Which might be "methylated C".

So, these "base modifications" are actually increasing the alphabet size, you have the normal A,T,G,C bases and then a set of modified bases.

I know there are presently ways to produce DNA synthetically, but what you've said seems to indicate there's room here for any pre-defined sequence I print to end up doing different things in a cloned cell than their synthetic duplicates might.

yes, or they might get modified so they are similar to the sequences already present.

XorNot3• 13 years ago

I'm hoping this turns out to be incorrect - a false lead. It would really suck if in order to download mindstates, we needed to get inside the chemistry of neuronal cells.

We can conceivably find an imaging technique that would let us 3D snapshot a brain and all it's connections. But its a big step from that big step down to getting nanoscopic views of the chemistry in every cell.

gizmo6862• 13 years ago

If you want to download a mindstate, you will almost have to deal with details at a molecular level. I am not familiar with the details of how the brain works, but consider that their is likely a huge evolutionary advantage to storing data more densely.

StandardFuture• 13 years ago

I really like the potential implications of this to future A.I. research. ;)

nateabele• 13 years ago

The takeaway: ASSASSIN'S CREED WAS RIGHT!!oen1

:-D

xzrrwe• 13 years ago

Genetic memory.

nsxwolf• 13 years ago

So... the premise of Alien 4 might not be as ridiculous as it seemed at the time? :O

ust• 13 years ago

There was an interesting article in the Discover magazine about epigenetic changes: http://discovermagazine.com/2013/may/13-grandmas-experiences...

Memories of positive associations get written onto DNA

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