
Octopuses and squids can rewrite their RNA - daegloe
https://www.washingtonpost.com/news/speaking-of-science/wp/2017/04/06/octopuses-and-squids-can-rewrite-their-rna-is-that-why-theyre-so-smart/
======
dluan
Original paper:
[http://www.cell.com/cell/fulltext/S0092-8674(17)30344-6](http://www.cell.com/cell/fulltext/S0092-8674\(17\)30344-6)

Does anyone know if RNA recoding happens in other species, or where it started
from? The paper mentions that RNA recoding sites slow down genomic evolution,
so what species out there have the most conserved genomes + recoding sites?

This paper was freaking fascinating.

~~~
rflrob
According to [1, probably paywalled], it's present in both vertebrates and
invertebrates, but not plants or fungi, indicating that it's animal specific,
but still quite ancient. What the authors have found is not that cephalopods
can edit their RNA, but that they do it a lot more than has previously been
reported in other animals.

I assiduously avoid studying the brain and behavioral complexity because that
stuff is incredibly complicated, but I'm pretty skeptical about the authors'
claims in the popular press that this is likely responsible for---or even
particularly connected to---cephalopod intelligence or learning. My bet would
be that in general, you get intelligence by complicated wiring, but that you
don't necessarily need complicated neurons to do that wiring. By analogy, what
makes the latest Intel processors so much better than an 8086 has a little bit
to do with the 64-bit architecture, but a lot more to do with the radically
smaller transistors.

[1] [http://www.annualreviews.org/doi/pdf/10.1146/annurev-
biochem...](http://www.annualreviews.org/doi/pdf/10.1146/annurev-
biochem-060208-105251)

~~~
AnimalMuppet
> By analogy, what makes the latest Intel processors so much better than an
> 8086 has a little bit to do with the 64-bit architecture, but a lot more to
> do with the radically smaller transistors.

I'm not sure you can draw that distinction. I don't program the transistors, I
program the architecture, and the 64-bit architecture is massively better than
the 8086 architecture. But the 64-bit architecture would not be possible
without the radically smaller transistors, because it requires so many more of
them, and that wouldn't be possible (on a realistic die size) without the
smaller transistors.

~~~
Retric
Alternatively, on on 3,000 nm a scaled up 64 bit CPU would actually be slower
due to latency issues for many workloads than the 8086. Further a scaled down
8086 would be slower on modern transistors than a 64bit CPU on most but not
all workloads so transistors are the most important difference.

------
itchyjunk
Taking inspiration from the cephalopods, our definition of intelligence also
needs to be revised more frequently. Recently, we've started acknowledging
more of the complexity in other animals, like dolphins for example.

I like their color changing behaviors as well[0]. It's is a form of
communication we don't fully understand yet.

[0] [http://ocean.si.edu/ocean-news/how-octopuses-and-squids-
chan...](http://ocean.si.edu/ocean-news/how-octopuses-and-squids-change-color)

~~~
orthecreedence
I've thought for a long time that before we focus on communicating with
extraterrestrials, it makes more sense to find ways to communicate more
fluently with existing beings on our planet, starting with ones we share a
common intelligence with (dolphins, raccoons, cephalopods, etc).

We take the animals on this planet for granted, as "lesser than," but what's
to say they aren't as intelligent and just express it in different ways? You
could say "well dolphins don't build cars or xboxes!" and I would say
"dolphins also aren't systematically destroying the planet they live on."

I know we're slowly bridging the gaps of communication with animals (for
instance, dogs who can understand verbal language or dolphins who can
associate objects with words), but it would be interesting if there were more
fluent ways of communication besides verbal. I think it would do us well to
master these.

~~~
xherberta
I agree, learning to really communicate with some other species on earth seems
like a worthwhile challenge that would push us in interesting directions.

On another thread (about dolphins finding ways to eat octopi without getting
suffocated by still-alive-and-fighting disembodied tentacles), some similar
thoughts came up.

I have to wonder if one reason for slow progress is that we've bored our
subjects. Maybe we should send poets and musicians as ambassadors, not
literal-minded scientists.

I read of a researcher who played recorded dolphin sounds for dolphins, and
she wanted to teach dolphins to say names she made up for three objects. I
don't think the results were very encouraging. But that might be because the
dolphins found it pointless.

Dolphins are aware of one another's sonar. So, they would never need to
vocalize "Look at that over there." They already know what pod-mates are
paying attention to. Why would they verbalize about things that are already
obvious on the pod's echolocation radar? They might not have a use for
concrete nouns. Dolphins' vocal communications might deal with abstract things
like social dynamics, emotions, intuition, and humor.

One other clue: I read of a recording of an upset, irate dolphin. When slowed
down significantly, it was clear the dolphin was mimicking it's trainer's
reprimands. So, we have to start by admitting that their processing speed is
way higher than ours. They're also the only animal with a more highly folded
cortex than ours.

These are creatures that can be taught a command that means "innovate" \- do
something different that you haven't shown me yet today. Maybe innovation is a
key aspect of their language. Maybe we need to think way outside the box about
what a language could be.

As for dolphins and building ... they don't need protection from sun, rain,
and snow; vast swaths of ocean are just the right temperature for them; they
can sleep with half their brains at a time while swimming; and they are not
interested in stockpiling food for later. What do they stand to gain from
building?

What dolphins lack in material culture, they might make up for in social life,
poetry, philosophy, and music. Maybe they're looking at us with pity: "Their
pod dynamics wouldn't be such a mess if only they didn't waste so much time
and effort building stuff..."

~~~
thinkmilitant
-What do they stand to gain from building?-

I would assume dolphins still die from lack of food, disease, and predation.
One(human) would assume they might want to build something to reduce those
odds?

~~~
darpa_escapee
You're assuming another intelligence values the same things as humans.

> I would assume dolphins still die from lack of food, disease, and predation.

Hell, we can find humans that don't value such things. Take a look at
Christian Scientists, they'll forgo treatment of disease out of fear of
rejecting the "divine Principle".

Dolphins use tools to hunt and catch prey. They also engage is pretty complex
behaviors to eat.

It took humans roughly a hundred thousand years to find a solution to death
from a lack of food through agriculture and we have opposable thumbs.

------
Mz
I really don't like their cookbook metaphor. It does nothing to really
illuminate the crux of what this allows the creatures to accomplish. As a lay
person with a strong interest in such things, I very much wish this article
were written with more of an eye towards "Because they can edit their own RNA,
they can do thus and such in real terms." instead of hand-wavy metaphors that
"it is like the scribe was changed to a master chef and now he can alter
recipes."

~~~
tgb29
Do you have a better metaphor?

~~~
Mz
No. That would require understanding what this means and I don't understand it
because their explanation is lame.

------
RickHull
Isn't more that that their RNA is constantly being rewritten than the
cephalopods themselves doing writing? What force is responsible for choosing
the new RNA?

I would not say it is the animals themselves doing the writing as a force of
will, sentience, or consciousness, which is what the headline implies.

The article itself says:

> _Their RNA is extensively rewritten, particularly the codes for proteins
> found in the animals ' neurons._

Tune in next week for more headline pet peeves

~~~
dluan
That's a valid question, for which you shouldn't be downvoted, but you should
know that it's not anything about it being a force of will by the animals,
more that it's a new behavior of how the animal cells are diverse. In other
words, maybe the animal is in higher temperatures that trigger a gene to begin
executing this particular 'circuit', which causes proteins to form that make
slightly more responsive nerve cell ion channels. Where previously we assumed
that variation was spread mainly through genes in DNA, this headline shows
that there are other ways beyond just DNA-> RNA-> protein.

I may have totally borked this attempted analogy, so hope that helps.

------
waynecochran
Self modifying code! Maybe nature uses Common Lisp macros.

~~~
azrazalea
[https://www.xkcd.com/224/](https://www.xkcd.com/224/)

------
Herodotus38
Original Article (thankfully not behind a paywall):

[http://www.cell.com/cell/fulltext/S0092-8674(17)30344-6](http://www.cell.com/cell/fulltext/S0092-8674\(17\)30344-6)

~~~
jfarlow
Looks like cephalopods have useful, active, and conserved ADAR activity that
changes an Adenosine to an Inosine in many RNA transcripts.

ADAR (Adenosine Deaminase acting on RNA) is a protein that recognizes specific
RNA sequences (likely, specific structures) [1]. And upon recognition it
switches an RNA's 'A' to an 'I' (a non-canonical base pair (RNA is usually
made of A, C, U, & G only)). The ribosome compiles a non-canonical 'I' as if
it were a 'G'. So this process effectively intercepts some DNA sequences prior
to compilation and swaps some (very particular) A's to G's with respect to
coding a protein. This process was found by noticing this very consistent
'mistake' between DNA and and expected sequences in high-throughput analysis.

So during the minification of the genetic code prior to compiling, under
certain conditions some very specific characters are swapped for out-of-bounds
characters that are read-through as an alternative character (if the
surrounding code suggests it should). So you can have alternate builds without
changing either the source code or the compiler, but instead by turning on/off
a bit in the the minifier (expression of ADAR protein).

This process happens a bit in humans and flies, but seems to happen a lot in
squid - specifically in the code around compiling neuronal proteins.

Curiously they show that this editing process slows down the evolution around
those neural proteins that utilize this mechanism. Because the ADAR protein
recognizes the structure of an entire sequence set in order to perform its
A->I swap, if there is any mutation in the entire sequence set, no A->I swap
occurs. And if no A->I swap occurs, the neural protein likely doesn't work as
well, lowering the fitness in any individual that has sequence drift anywhere
in that entire recognized region. In organisms that do not have this A-I shift
mechanism there is more evolutionary sequence drift in similar proteins than
in Cephalopods which utilize the A->I swap. Super cool!

[1] [https://en.wikipedia.org/wiki/ADAR1](https://en.wikipedia.org/wiki/ADAR1)

~~~
Herodotus38
Thanks for the summary. You should be happy to know that because of this I
went to your company's website, and realized it was the second time I have
done so after reading a good in-depth comment of yours (or perhaps another
cofounder).

------
amelius
Does that mean that techniques such as RNA-Seq ([1]) will fail on these
species?

[1] [https://en.wikipedia.org/wiki/RNA-Seq](https://en.wikipedia.org/wiki/RNA-
Seq)

~~~
arrosenberg
RNA Seq will still work, but you'd probably notice more variation over time
within a specific individual if you did multiple sequencings.

------
tonto
there was a 2015 paper (same lab I think) that showed very widespread A-to-I
editing in squid also
[https://elifesciences.org/content/4/e05198](https://elifesciences.org/content/4/e05198)

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mannykannot
I wonder if this might account for the relatively short life-span of
cephalopods?

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JaggerFoo
Pfft! Altering RNA. That's nothing. Once I was in a Los Angeles book store,
named Bodhi Tree, where a woman was giving a lecture on altering human DNA
using psychic power.

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dnprock
Do this mean we need to eat more of them? I'm all for it :)

