

Scientists claim to crack brain memory code - janecoder
http://www.jpost.com/LandedPages/PrintArticle.aspx?id=262191

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polyfractal
The paper itself can be found here:
[http://www.ploscompbiol.org/article/info:doi/10.1371/journal...](http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002421)

First reaction was a serious, audible "Ughhh". I'm skimming the paper now but
this looks a lot like "we played with some _in-silico_ models and came up with
a nifty thing"

Edit: Christ, I don't even know where to begin. Seriously.

First of all, there is no mention of the fact that microtubles don't innervate
dendritic spine heads. Actin is the primary cytoskeletal support for synapses.
I can think of several plausible explanations to get around this fact, but
they don't offer any which immediately put me on edge for the whole paper.

Second, there is zero in-vitro experimentation. It is extremely possible that
none of this happens anywhere, let alone in the brain. Granted, in-silico
experiments are often used to guide future benchwork...but I would have liked
to see some preliminary wet-bench tests.

Here is a gem from the paper:

 _MTs appear to have intrinsic electro-mechanical vibrations, e.g. coherent
oscillations in the low megahertz range. [...] Signal propagation will be
influenced by, and depend on MT lattice vibrations and related effects._

 _In LTP, high frequency inputs (e.g. 50 to 100 Hz) are required for prolonged
post-synaptic response. Kumar et al [58] showed that memory formation in
dendrites depends on synchronized inputs, with an optimal frequency near 50
Hz. Density and patterns of CaMKII-induced tubulin phosphorylation in post-
synaptic MT lattices would depend on frequency and synchrony of inputs._

Wait, what? They are correlating electro-mechanical oscilations (MT
vibrations) with electro-chemical oscilations (synaptic firing)?

 _‘Scale-free’ implies self-similar information patterns repeating at
different spatial and temporal scales (following 1/frequency power laws).
Similar to ‘fractals’ and holograms, scale-free structures and processes arise
commonly in nature and technology, and are inherently robust and resistant to
disruption. In the brain, evidence suggests neuronal network structure,
temporal dynamics, and representation of mental states are all ‘scale-free’,
with self-similar patterns repeating at various temporal and spatial scales
and locations [68]–[71]. Interference patterns of periodic, coherent reaction-
diffusion waves in cytoplasm and larger spatial scales could account for
scale-free information patterns regulating biological systems including the
brain. Microtubules can generate three-dimensional reaction-diffusion patterns
[70], and we suggest such patterns operate at multiple time scales to regulate
biological systems._

Translation: There are fractals in the world and we see the brain structured
in certain ways, so those patterns must apply to smaller things, right? We
showed some dubious computer modeling of microtubules vibrating and a kinase
phosphorylating. Therefore, the vibrations are encoding brain information.
QED.

There's more, but I need to get to work. Let me just put it this way: there is
a very good reason this paper is not in Nature Neuroscience.

~~~
zerostar07
Rightly said (there's more indeed). When people talk about the dangers of open
publishing this will be their canonical example.

~~~
alex_stoddard
On the contrary, this is a excellent example of the benefits of open
publishing. A very dubious paper is hyped in the press and the actually
published work is available to all to be read and critiqued as thoroughly as
it deserves. This, in my opinion, is completely independent from issues with
the benefits and problems of peer review.

~~~
zerostar07
PLoS articles are peer reviewed as well. I was commenting about the standards
PLoS sets for itself by allowing this article with this title.

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zerostar07
That's a load of hogwash. They found that some molecules match and the press
is going all "brain code cracked". The authors, of course, provoked all this
by linkbaiting the article (talk about modesty; also, WTF PLoS?). Nobody
believes these things but these people. We have optogenetic tools to probe
memory functions much more efficiently and people do that already. This came
up a some time ago btw: <http://news.ycombinator.com/item?id=3688953>

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alt_
I can't connect to www.jpost.com and had to use a proxy to read it.

The original article seems to be [http://www.newswise.com/articles/scientists-
claim-brain-memo...](http://www.newswise.com/articles/scientists-claim-brain-
memory-code-cracked)

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andreasvc
Hameroff, the author, also subscribed to the quantum brain hypothesis, along
with Roger Penrose; an idea which was widely dismissed as wildly implausible,
if I recall correctly. The topic itself is fascinating though.

~~~
Dn_Ab
It is still widely dismissed. And while coherence seems to be relevant for a
particular stage of energy conversion in photosynthesis and also in allowing
sensitivity to magnetic fields, the mechanisms for leveraging these are
incidental. They are used passively to achieve an effect and not actively to
perform computations as would be required for Penrose's hypotheses.

To claim the brain leverages quantum effects at biological scales is going far
but still plausible. But to say that quantum computations are going on in the
brain and are expressed at the level of thinking we acheive (evinced by
claiming that we are not Turing machines), that is something that would
require a lot of data to support (something that this theory sorely lacks).
Much of what we know about quantum mechanics and neurobiology would have to be
redressed. Indeed if such were true there would be indirect evidence - I
expect we would find quantum mechanics, heck ordinary probability theory, more
intuitive for example .

Far more interesting are the epigenetic like effects that occur in memory
formation.

~~~
andreasvc
> claiming that we are not Turing machines

There are independent arguments for that position, namely that it's quite
likely that the brain does not everywhere operate digitally, with well-defined
discrete states. And even if it did in a trivial sense because the whole of
physics operated that way it wouldn't really help with describing how the
brain works (wrong level of abstraction).

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mikecane
If it turns out to be true that the brain encodes in 6-bit bytes, isn't our
8-bits for a byte extravagant?

I'm reminded that "nature is lazy" and always goes for the easiest and
quickest route for efficiency.

~~~
sp332
Information is defined in terms of bits, not bytes. You can define a byte to
be any number of bits, <https://en.wikipedia.org/wiki/Byte#History> But the
amount of information is determined by the number of bits, not the number of
bytes.

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andreasvc
Regardless of the speculation about the number of bits, what basis do they
have for the idea that memory is digital & discrete? I thought analog would be
more plausible.

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givan
Pure speculation, until we understand how the brain works we can't know for
sure what is what and if that stuff is used for information encoding.

~~~
alan_cx
So don't read anything about it until some one mysteriously pops up with the
complete brain specification?

It is not speculation, its a hypothesis and theory which has some evidence to
support it. Now they and others will go off and try to build on it, or
disprove it.

I don't understand why anyone would be scornful and dismissive of this?

~~~
Daniel_Newby
Saying that CaMKII probably associates with microtubles to form memories is
discovery, a reasonable extrapolation.

Calling the molecule's arms _is_ the purest and most unwarranted speculation.

~~~
pygy_
I believe you accidentally the _byte_?

~~~
Daniel_Newby
Yes. Thanks.

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16s
I think there may be something to this. I write pattern/word generation
software for use in password cracking and some of the most common English
consonant vowel patterns are six characters long. For example, the CV pattern
cvccvc matches these proper words and slang words (batman, defcon, summer,
winter, bigboy, number, fatdad, hotmom, badguy, soccer, etc). This is just one
example of a popular six character pattern, there are more.

~~~
pygy_
It's not six bytes patterns but six bit bytes, that can store 2^6 == 64
different values.

Computers nowadays standardized on eight bit bytes, synonymous with _octet_ ,
but the definition of a byte is actually hardware-dependent.

~~~
16s
The point is segmenting things by six. No need to think of the 'things' in
terms of bits or bytes (of which I'm very familiar). In my example, it is
popular English word patterns. In the article, it's bits in memory. Both of
which are 'things' of six.

~~~
andreasvc
That's called numerology and it's nonsense. Six is just a conveniently small
number, nothing special about it.

