The inner artificial life of a cell, a game proposal

The  inner life of a cell is an excellent, but passive window

It is also scripted according to usual human expectations: synchronous moves, orchestrated reactions at a large scale. This is of course either something emergent in real life, or totally unrealistic.

As you know, I propose to use the artificial chemistry chemlambda for making real, individual molecular computing devices, as explained in Molecular computers.

But much more can be aimed at, even before the confirmation that molecular computers, as described there,  can be built by us humans.

Of course that Nature builds them everywhere, we are made of them. It works without any external control, not as a sequence of lab operations, asynchronously, in a random environment, and it is very hard to understand if there is a meaning behind the inner life of a living cell, but it works nevertheless without the need of a semantics to streamline its workings.

So obvious, however so far from IT way of seeing computation.

Despite the huge and exponential advances in synthetic biology, despite the fact that many of these advances are related to IT, despite that more and more ways to control biological workings, I believe that there has to be a way to attack the problem of computations in biology from the basis. Empirical understanding is great and will fuel for some time this amazing synthetic biology evolution, but why not thinking about understanding how life works, instead of using biological parts to make functions, gates and other components of the actual IT paradigm?

As a step, I propose to try to build a game-like artificial life cell, based on chemlambda. It should look and feel like the Inner life of a cell video, only that it would be interactive.

There are many bricks already available, some molecules (each with its own story and motivation) are in the chemlambda repository, other are briefly described, with animations, in the chemlambda collection.

For example:
– a centrosome and the generated microtubules like in

kinesins  as adapted walkers like in

– molecules built from other ones like RNA from DNA

– programmed computations (mixing logic and biologic)

– all in an environment looking somehow like this

Like in a game, you would not be able to see the whole universe at once, but you could choose to concentrate to this part or that part.
You could build superstructures from chemlambda quines and other bricks, then you could see what happens either in a random environment or in one where, for example, reductions happen triggered by the neighbourhood of your
mouse pointer (as if the mouse pointer is a fountain of invisible enzymes).

Videos like this, about the internal working of a neuron


would become tasks for the gamer.

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Artificial life which can be programmed

Artificial life

3_27_quine_huge_short

which can be programmed

ttttt

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An apology of molecular computers and answers to critics

This is how a molecular computer would look like, if seen with a magically powerful microscope. It is a single molecule which interacts randomly with other molecules, called “enzymes”, invisible in this animation.

molecular_computer_new

There is no control over the order of the chemical reactions. This is the idea, to compute without control.

The way it works is like this: whenever a reaction happens, this creates the conditions for the next reaction to happen.

There is no need to use a supercomputer to model such a molecule, nor is it reasonable to try, because of big number of the atoms.

It is enough instead to find real molecular assemblies for nodes, ports and bonds, figured here by colored circles and lines.

The only computations needed are those for simulating the family of rewrites – chemical reactions. Every such rewrite involves up to 4 nodes, therefore the computational task is handy.

Verify once that the rewrites are well done, independently of the situation where you want to apply them, that is all.

Once such molecular compounds are found, the next task is to figure out how to build (by chemical reactions) such molecules.

But once one succeeds to build one molecule, the rest is left to Nature way of computing: random, local, asynchronous.

From this stage there is no need to simulate huge molecules in order to know they work. That is something given by the chemlambda formalism.

It is so simple: translate the rewrites into real chemistry, they are easy, then let go the unneeded control from that point on.

This animation is a screencast of a part of the article Molecular computers
http://chorasimilarity.github.io/chemlambda-gui/dynamic/molecular.html
and everything can be validated (i.e. verified by your own) by using the chemlambda repository
https://github.com/chorasimilarity/chemlambda-gui/tree/gh-pages/dynamic

Now I’ll pass to a list of critics which, faced with the evidence, they look uninformed:
1. Chemlambda is one of those rewriting systems everybody knows. Ignorant claim, while it is true that some rewrites appear all over the place, from string theory to knot theory to category theory to geometry of interaction, the family of graphs considered is not the same, because those graphs are purely combinatorial object and they don’t need a global embedding, like all other formalism do, in a schematic space-time. Moreover, the choice of the rewrites is such that the system works only by local rewriting and no global control on the cascade of rewrites. No other formalism from the family does that.

2.  Is well known that all this is already done in the category theory treatment of lambda calculus.

False, if one really reads what they do in category theory with lambda calculus, then one figures quick that they can’t do much for untyped lambda beta calculus, that is without eta reduction. This is mentioned explicitly in Barendregt, for example, but the hype around categories and lambda calculus is so pervasive that people believe more than what actually is.

3.  Chemical computing is old stuff: DNA computing, membrane computing, the chemical abstract machine, algorithmic chemistry.

Just because it is chemical computing, it does not mean that it is in the family mentioned.

The first name of chemlambda was “chemical concrete machine” and there there are comparison with the chemical abstract machine
http://arxiv.org/abs/1309.6914
(btw I see that some people discover now “catalysts” without credits in the written papers)
The cham is a formalism working with multisets of molecules, not with individual ones, and the computation is done by what corresponds to lab operation (splitting a solution in two, heating, cooling, etc)
The membrane computing work is done around membranes which enclose containers of multisets of molecules, the membrane themselves being some abstract concepts, of a global nature, whil ein reality, as well as in chemlambda, everything is a molecule. Membranes exist in reality but they are made of many molecular compounds.
DNA computing is an amazing research subject, which may be related to chemlambda if there is a realization of chemlambda nodes, ports and bonds, but not otherwise, because there is not, up to my knowledge, any model in DNA computing with the properties: individual molecules, random reactions, not lab operations.
Algorithmic chemistry is indeed very much related to chemlambda, by the fact that it proposes a chemical view on lambda calculus. But from this great insight, the paths are very different. In algorithmic chemistry the application operation from lambda calculus represents a chemical reaction and the lambda abstraction signals a reactive site. In chemlambda the application and lambda abstraction corresponds to atoms of molecules. Besides, chemlambda is not restricted to lambda calculus, only some of the chemlambda molecules can be put in relation with lambda terms, but even for those, the reactions they enter don’t guarantee that the result is a molecule for a lambda term.

Conclusion: if you are a chemist, consider chemlambda, there is nothing like it already proposed. The new idea is to let control go and instead chain the randomly appearing reactions by their spatial patterns, not by lab operations, nor by impossibly sophisticated simulations.
Even if in reality there would be more constraints (coming from the real spatial shapes of the molecules constructed from these fundamental bricks) this would only influence the weights of the random encounters with the enzymes, thus not modifying the basic formalism.
And if it works in reality, even for only situations where there are cascades of tens of reactions, not hundreds or thousands, even that would be a tremendous advance in chemical computing, when compared with the old idea of copying boolean gates and silicon computers circuits.

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Appeared also in the chemlambda collection microblog

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What if… it can be done? An update of an old fake news post

In May 2014 I made a fake news post (with the tag WHAT IF) called Autodesk releases Seawater. It was about this big name who just released a totally made up product called Seawater.

“SeaWater is a design tool for the artificial life based decentralized Internet of Things.”

In the post it is featured this picture

[source]

scoop-of-water-magnified-990x500… and I wrote:

“As well, it could be  just a representation of the state of the IoT in a small neighbourhood of you, according to the press release describing SeaWater, the new product of Autodesk.”

Today I want to show you this:

3_27_quine

or better go and look in fullscreen HD this video

The contents is explained in the post from the microblogging collection chemlambda

27 microbes. “This is a glimpse of the life of a community of 27 microbes (aka chemlambda quines). Initially the graph has 1278 nodes (atoms) and 1422 edges (bonds). There are hundreds of atoms refreshed and bonds made and broken at once.”

Recall that all this is done with the most simple algorithm, which turns chemlambda into an asynchronous graph rewrite automaton.

A natural development would be to go further, exactly like described in the Seawater post.

Because it can be done :)

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The Internet can be your pet

or  you could have a pet which embeds and run a copy of the whole Internet.

The story from this post  starts from this exploratory posting on Google plus from June 2nd, 2015, which zooms from sneakernet to sneakernet  delay-tolerant networking to  Interplanetary Internet to Nanonetworks to DNA digital data storage to molecular computers.

I’ll reproduce the final part, then I’ll pass to the Internet as you pet thing.

“At this stage things start to be interesting. There is this DNA digital data storage technique
http://en.wikipedia.org/wiki/DNA_digital_data_storage
which made the news recently by claiming that the whole content of the Net fits into a spoon of DNA (prepared so to encode it by the technique).

I have not been able to locate the exact source of that claim, but let’s believe it because it sounds reasonable (if you think at the scales involved).

It can’t be the whole content of the net, it must mean the whole passive content of the net. Data. A instant (?) picture of the data, no program execution.

But suppose you have that spoonful of DNA, how do you use it? Or what about also encoding the computers which use this data, at a molecular level.

You know, like in the post about one Turing Machine, Two Turing Machines https://plus.google.com/+MariusBuliga/posts/4T19daNatzt
if you want classical computers running on this huge DNA tape.

Or, in principle, you may be able to design a molecular google search …
molecule, which would interact with the DNA data to retrieve some piece of it.

Or you may just translate all programs running on all computers from all over the world into lambda calculus, then turn them into chemlambda molecules, maybe you get how much, a cup of molecular matter?

Which attention:
– it executes as you look at it
– you can duplicate it into two cups in a short matter of time, in the real world
– which makes the sneakernet simply huge related to the virtual net!

Which brings of course molecular computers proposal to the fore
http://chorasimilarity.github.io/chemlambda-gui/dynamic/molecular.html  ”

Let’s develop this a bit! (source)

The following are projections about the possible future of biochemical computations with really big data: the whole, global data produced and circulated by humans.

They are based on estimates of the information content in the biosphere from the article [1] and on a proposal for life like molecular computing.

Here are the facts. In [1] there are given estimates about the information content of DNA in the biosphere, which are used further.

One estimate is that there are about 5 X 10^11 tonnes of DNA, in a biomass of about 2 X 10^12 tonnes, which gives a proportion of DNA in biomass of about 1/40.

This can be interpreted as: in order to run the biochemical computations with 1g of DNA there are needed about 40g of biochemical machinery.

From the estimate that the biomass contains about 5 X 10^30 cells, it follows that 4g of DNA are contained (and thus run in the biochemical computation) in 10^13 cells.

The Internet has about 3 X 10^9 computers and the whole data stored is equivalent with about 5g of DNA [exact citation not yet identified, please provide a source].

Based on comparisons with the Tianhe-2 supercomputer (which has about 3 X 10^6 cores) it follows that the whole Internet processes in a way equivalent as a magnitude order to 10^3 such supercomputers.
From [1] (and from the rather dubious equivalence of FLOPS with NOPS)  we get that the whole biosphere has a power of 10^15 X 10^24 NOPS, which gives for 10^13 cells (the equivalent of 4g of DNA) about 10^17 NOPS. This shows that approximately the power of the biochemical computation of 4g of DNA (embedded in the biochemical machinery of about 160g) is of the same order with the power of computation of the whole internet.

Conclusion until now: the whole Internet could be run in a “pet” living organism of about 200g. (Comparable to a rat.)

This conclusion holds only if there is a way to map silicon and TM based computers into biochemical computations.

There is a huge difference between these two realms, which comes from the fact that the Internet and our computers are presently built as a hierarchy, with multiple levels of control, while in the same time the biochemical computations in a living cell do not have any external control (and there is no programming).

It is therefore hard to understand how to map the silicon and TM based computations (which run one of the many computation paradigms embedded into the way we conceive programming as a discipline of hierarchical control) into a decentralized, fully asynchronous, in a ransom environment biochemical computation.

But this is exactly the proposal made in [2], which shows that in principle this can be done.

The details are that in [2] is proposed an artificial chemistry (instead of the real world chemistry) and a model of computation which satisfies all the requirements of biochemical computations.
(See very simple examples of such computations in the chemlambda collection https://plus.google.com/u/0/collection/UjgbX )

The final conclusion, at least for me, is that provided there is a way to map this (very basic) artificial chemistry into real chemical reactions, then one day you might have the whole Internet as a copy which runs in your pet.

[1] An Estimate of the Total DNA in the Biosphere,
Hanna K. E. Landenmark,  Duncan H. Forgan,  Charles S. Cockell,
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002168

[2] Molecular computers,
Marius Buliga, 2015
http://chorasimilarity.github.io/chemlambda-gui/dynamic/molecular.html

Crossings as pairs of molecular bonds; boolean computations in chemlambda

I collect here the slightly edited versions of a stream of posts on the subject from the microblogging chemlambda collection. Hopefully this post will give a more clear image about this thread.

Here at the chorasimilarity open notebook, the subject has been touched previously, but perhaps that the handmade drawings made it harder to understand (than with the modern :) technology from the chemlambda repository):

Teaser: B-type neural networks in graphic lambda calculus (II)

(especially the last picture!)

All this comes with validation means. This is a very powerful idea: in the future validation will replace peer review, because it is more scientific than hearsay from anonymous authority figures (aka old peer review) and because it is more simple to implement than a network of hearsay comments (aka open peer review).

All animations presented here are obtained by using the script quiner.sh and various mol files. See instructions about how you can validate (or create your own animations) here:
https://github.com/chorasimilarity/chemlambda-gui/blob/gh-pages/dynamic/README.md

Here starts the story.

(Source FALSE is the hybrid of TRUE, boole.mol file used)

boole

Church encoding gives a way to define boolean values as terms in the lambda calculus. It is easy:

TRUE= Lx.(Ly.x)

FALSE= Lx.(Ly.y)

So what? When we apply one of these terms to another two, arbitrary terms X and Y, look what happens: (arrows are beta reductions (Lx.A)B – – > A[x:=B] )

(TRUE X) Y – – > (Ly.X) Y – – > X (meaning Y goes to the garbage)

(FALSE X) Y – – > (Ly.y) Y – – > Y (meaning X goes to the garbage)

It means that TRUE and FALSE select a way for X and Y: one of them survives, the other disappears.

Good: this selection is an essential ingredient for computation

Bad: too wasteful! why send a whole term to the garbage?

Then, we can see it otherwise: there are two outcomes: S(urvival) and G(arbage), there is a pair of terms X and Y.

– TRUE makes X to connect with S and Y to connect with G

– FALSE makes X to connect with G and Y to connect with S

The terms TRUE and FALSE appear as molecules in chemlambda, each one made of two red nodes (lambdas) and a T (termination) node. But we may dispense of the T nodes, because they lead to waste, and keep only the lambda nodes. So in chemlambda the TRUE and FALSE molecules are, each, made of two red (lambda) nodes and they have one FROUT (free out).

They look almost alike, only they are wired differently. We want to see how it looks to apply one term to X and then to Y, where X and Y are arbitrary. In chemlambda, this means we have to add two green (A) application nodes, so TRUE or FALSE applied to some arbitrary X and Y appear, each, as a 4 node molecule, made of two red (lambda) two green (A), with two FRIN (free in) nodes corresponding to X and Y and two FROUT (free out) nodes, corresponding: one to the deleted termination node, thus this is the G(arbage) outcome, and the other to the “output” of the lambda terms, thus this is the S(urvival) outcome.

But the configuration made of two green A nodes and two red L nodes is the familiar zipper which you can look at in this post

betazipper

In the animation you see TRUE (at left) and FALSE (at right), with the magenta FROUT nodes and the yellow FRIN nodes.

The zipper configurations are visible as the two vertical strings made of two green, two red nodes.

What’s more? Zippers, they do only one thing: they unzip.

The wiring of TRUE and FALSE is different. You can see the TRUE and FALSE in the lower part of the animation. I added four Arrow (white) nodes in order to make the wiring more visible. Arrow nodes are eliminated in the COMB cycle, they have only a fleeting existence.

This shows what is really happening: look at each (TRUE-left, FALSE-right) configuration. In the upper side you have 4 nodes, two magenta, two yellow, which are wired together at the end of the computation. In the case of TRUE they end up wired in a X pattern, in the case of FALSE they end up wired in a = pattern.

At the same time, in the lower side, before the start of the computation, you see the 4 white nodes which: in the case of TRUE are wired in a X pattern, in the case of FALSE are wired in a = pattern. So what is happening is that the pattern ( X or = ) is teleported from the 4 white nodes to the 4 magenta-yellow nodes!

The only difference between the two molecules is in this wire pattern, X vs =. But one is the hybrid of the other, hybridisation is the operation (akin to the product of knots) which has been used and explained in the post about senescence and used again in more recent posts. You just take a pair of bonds and switch the ends. Therefore TRUE and FALSE are hybrids, one of the other.

(Source Boolean wire, boolewire.mol file used )

If you repeat the pattern which is common to TRUE and FALSE molecules then you get a boolean wire, which is more impressive “crossings teleporter”. This time the crosses boxed have been flattened, but the image is clear:

boolewire

Therefore, TRUE and FALSE represent choices of pairs of chemical bonds! Boolean computation (as seen in chemlambda) can be seen as management of promises of crossings.

(Source Promises of crossings, ifthenelsecross.mol file used )

You see 4 configurations of 4 nodes each, two magenta and two yellow.

In the upper left side corner is the “output” configuration. Below it and slightly to the right is the “control” configuration. In the right side of the animation there are the two other configurations, stacked one over the other, call them “B” (lower one) and “C” (upper one).

Connecting all this there are nodes A (application, green) and L (lambda, red).

ifthenelsecross

You see a string of 4 green nodes, approximately vertical, in the middle of the picture, and a “bag” of nodes, red and green, in the lower side of the picture. This is the molecule for the lambda term

IFTHENELSE = L pqr. pqr

applied to the “control” then to the “B” then to the “C”, then to two unspecified “X” and “Y” which appear only as the two yellow dots in the “output” configuration.

After reductions we see what we get.

Imagine that you put in each 4 nodes configuration “control”, “B” and “C”, either a pair of bonds (from the yellow to the magenta nodes) in the form of an “X” (in the picture), or in the form of a “=”.

“X” is for TRUE and “=” is for false.

Depending on the configuration from “control”, one of the “B” or “C” configuration will form, together with its remaining pair of red nodes, a zipper with the remaining pair of green nodes.

This will have as an effect the “teleportation” of the configuration from “B” or from “C” into the “output”, depending on the crossing from “control”.

You can see this as: based on what “control” senses, the molecule makes a choice between “B” and “C” promises of crossings and teleports the choice to “output”.

(Source: Is there something in the box?, boxempty.mol used)

I start from the lambda calculus term ISZERO and then I transform it into a box-sensing device.

In lambda calculus the term ISZERO has the expression

ISZERO = L a. ((a (Lx.FALSE)) TRUE)

and it has the property that ISZERO N reduces either to TRUE (if N is the number 0) or FALSE (if N is a number other than 0, expressed in the Church encoding).

The number 0 is
0 = FALSE = Lx.Ly.y

For the purpose of this post I take also the number 2, which is in lambda calculus

2=Lx.Ly. x(xy)

(which means that x is applied twice to y)

Then, look: (all reductions are BETA: (Lx.A)B – – > A[x:=B] )

ISZERO 0 =
(L a. ((a (Lx.FALSE)) TRUE) ) (Lx.Ly.y) – – >
((Lx.Ly.y) (Lx.FALSE)) TRUE – – >
(Ly.y)TRUE – – > (remark that Lx.FALSE is sent to the garbage)
TRUE (and the number itself is destroyed in the process)

and

ISZERO 2 =
(L a. ((a (Lx.FALSE)) TRUE) ) (Lx.Ly. x(xy)) – – >
((Lx.Ly. x(xy)) (Lx.FALSE)) TRUE – – > (fanout of Lx.FALSE performed secretly)
(Lx.FALSE) ((Lx.FALSE) TRUE) – – >
FALSE ( and (Lx.FALSE) TRUE sent to the garbage)

Remark that in the two cases there was the same number of beta reductions.

Also, the use of TRUE and FALSE in the ISZERO term is… none! The same reductions would have been performed with an unspecified “X” as TRUE and an unspecified “Y” as FALSE.

(If I replace TRUE by X and FALSE by Y then I get a term which reduces to X if applied to 0 and reduces to Y if applied to a non zero Church number.)

Of course that we can turn all this into chemlambda reductions, but in chemlambda there is no garbage and moreover I want to make the crossings visible. Or, where are the crossings, if they don’t come from TRUE and FALSE (because it should work with X instead of TRUE and Y instead of FALSE).

Alternatively, let’s see (a slight modification of) the ISZERO molecule as a device which senses if there is a number equal or different than 0, then transforms, according to the two cases, into a X crossing or a = crossing.

Several slight touches are needed for that.

1. Numbers in chemlambda appear as stairs of pairs of nodes FO (fanout, green) and A (application, green), as many stairs as the number which is represented. The stairs are wrapped into two L (lambda, red) nodes and their bonds.
We can slightly modify this representation so that it appears like a box of stairs with two inputs and two outputs, and aby adding a dangling green (A, application) node with it’s output connected to one of its inputs (makes no sense in lamnda calculus, but behaves well in the beta reductions as performed in chemlambda).

In the animation you can see, in the lower part of the figure:
-at left the number 0 with an empty box (there are two Arrow (white) nodes added for clarity)
-at right the number 2 with a box with 2 stairs
… and in each case there is this dangling A node (code in the mol file of the form A z u u)
boxempty

2. The ISZERO is modified by making it to have two FRIN (free in, yellow) and two FROUT (free out, magenta) nodes which will be involved in the final crossing(s). This is done by a clever (hope) change of the translation of the ISZERO molecule into chemlambda: first the two yellow FRIN nodes represent the “X” and the “Y” (which they replace the FALSE and the TRUE, recall), and there are added a FOE (other fanout node, yellow) and a FI (fanin node, red) in strategic places.

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ArXiv is 3 times bigger than all megajournals taken together

 How big are the “megajournals” compared to arXiv?
I use data from the article

[1] Have the “mega-journals” reached the limits to growth? by Bo-Christer Björk ​https://dx.doi.org/10.7717/peerj.981 , table 3

and the arXiv monthly submission rates

[2] http://arxiv.org/stats/monthly_submissions

To have a clear comparison I shall look at the window 2010-2014.

Before showing the numbers, there are some things to add.

1.  I saw the article [1] via the post by +Mike Taylor

[3] Have we reached Peak Megajournal? http://svpow.com/2015/05/29/have-we-reached-peak-megajournal/

I invite you to read it, it is interesting as usual.

2. Usually, the activity of counting articles is that dumb thing which is used by managers to hide behind, in order to not be accountable for their decisions.
Counting  articles is a very lossy compression technique, which associates to an article a very small number of bits.
I indulged into this activity because of the discussions from the G+ post

[4] https://plus.google.com/+MariusBuliga/posts/efzia2KxVzo

and its clone

[4′] Eisen’ “parasitic green OA” is the apt name for Harnad’ flawed definition of green OA, but all that is old timers disputes, the future is here and different than both green and gold OA https://chorasimilarity.wordpress.com/2015/05/28/eisen-parasitic-green-oa-is-the-apt-name-for-harnad-flawed-definition-of-green-oa-but-all-that-is-old-timers-disputes-the-future-is-here-and-different-than-both-green-and-gold-oa/

These discussions made me realize that the arXiv model is carefully edited out from reality by the creators and core supporters of green OA and gold OA.

[see more about in the G+ variant of the post https://plus.google.com/+MariusBuliga/posts/RY8wSk3wA3c ]
Now, let’s see those numbers. Just how big is that arXiv thing compared to “megajournals”?

From [1]  the total number of articles per year for “megajournals” is

2010:  6,913
2011:  14,521
2012:   25,923
2013:  37,525
2014:  37,794
2015:  33,872

(for 2015 the number represents  “the articles published in the first quarter of the year multiplied by four” [1])

ArXiv: (based on counting the monthly submissions listed in [2])

2010: 70,131
2011: 76,578
2012: 84,603
2013: 92,641
2014:  97,517
2015:  100,628  (by the same procedure as in [1])

This shows that arXiv is 3 times bigger than all the megajournals at once, despite that:
– it is not a publisher
– does not ask for APC
– it covers fields far less attractive and prolific than the megajournals.

And that is because:
– arxiv answers to a real demand from researchers, to communicate fast and reliable their work to their fellows, in a way which respects their authorship
– also a reaction of support for what most of them think is “green OA”, namely to put their work there where is away from the publishers locks.

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