Screen recording of the reading experience of an article which runs in the browser

The title probably needs parsing:

SCREEN RECORDING {

READING {

PROGRAM EXECUTION {

RESEARCH ARTICLE }}}

An article which runs in the browser is a program (ex. html and javascript)  which is executed by the browser. The reader has access to the article as a program, to the data and other programs which have been used for producing the article, to all other articles which are cited.

The reader becomes the reviewer. The reader can validate, if he wishes, any piece of research which is communicated in the article.

The reader can see or interact with the research communicated. By having access to the data and programs which have been used, the reader can produce other instances of the same research (i.e virtual experiments).

In the case of the article presented as an example, embedded in the article are animations of the Ackermann function computation and the other concerning the building of a molecular structure. These are produced by using an algorithm which has randomness in the composition, therefore the reader may produce OTHER instances of these examples, which may or may not be consistent with the text from the article. The reader may change parameters or produce completely new virtual experiments, or he may use the programs as part of the toolbox for another piece of research.

The experience of the reader is therefore:

  • unique, because of the complete freedom to browse, validate, produce, experiment
  • not limited to reading
  • active, not passive
  • leading to trust, in the sense that the reader does not have to rely on hearsay from anonymous reviewers

In the following video there is a screen recording of these possibilities, done for the article

M. Buliga, Molecular computers, 2015, http://chorasimilarity.github.io/chemlambda-gui/dynamic/molecular.html

This is the future of research communication.

____________________________________________________________

A neuron-like artificial molecule

This is a neuron-like artificial molecule, simulated in chemlambda.

neuron

It has been described in the older post

https://chorasimilarity.wordpress.com/2015/03/04/how-to-put-a-y-combinator-into-a-neuron-and-lock-it-with-a-quine/

Made with quiner.sh and the file neuron.mol as input.
If you want to make your own, then follow the instructions from here:

https://github.com/chorasimilarity/chemlambda-gui/blob/gh-pages/dynamic/README.md

It is on the list of demos: http://chorasimilarity.github.io/chemlambda-gui/dynamic/neuron.html

__________
Needs explanations, because this is not exactly the image used for a neuron in a neural network.

_________
1. In neural networks a neuron is a black box with some inputs and some outputs, which computes and sends (the same) signal at the outputs as a function of the signals from the inputs. A connection between an output of one neuron and an an input of another has a weight.

The interpretation is that outputs represent the axon of a neuron, which is like a tree with the root in the neuron’s soma. The inputs of the neuron represents the dendrites. For a neuron in a neural network, a connection between an input (leaf of a dendrite) and an output (leaf of an axon) has a weight because it models an average of many contact points (synapses) between dendrites and axons.

The signals sent represent electrical activity in the neural network.

2. Here, the image is different.

Each neuron is seen as a bag of chemicals. The electrical signals are only a (more easy to measure) aspect of the cascades of chemical reactions which happen inside the neuron’s some, in the dendrites, axon and synapses.

Therefore a neuron in this image is the chemical reactions which happen.

From here we go a bit abstract.

3. B-type unorganised machines. In his fundamental research “Intelligent Machinery” Turing introduced his  B-type neural networks
http://www.alanturing.net/turing_archive/pages/Reference%20Articles/connectionism/Turing%27s%20neural%20networks.html
or B-type unorganised machine, which is made by more or less identical neurons (they compute a boolean function) which are connected via a connection-modifier box.

A connection modifier box has an input and an output, which are part of the connection between two neurons. But it has also some training connections, which can modify the function  computed by the connection modifier.

What is great is that Turing explains that the connection modifier can me made by neurons
http://www.alanturing.net/turing_archive/archive/l/l32/L32-007.html
so that actually a B-type unorganised machine is an A-type unorganised machine (same machine without connection modifiers), where we see the connection modifiers as certain, well chosen patterns of neurons.

OK, the B-type machines compute by signals sent and received by neurons nevertheless. They compute boolean values.

4. What would happen  if we pass from Turing to Church?

Let’s imagine the same thing, but in lambda calculus: neurons which reduce lambda terms, in networks which have some recurring patterns which are themselves made by neurons.

Further: replace the signals (which are now lambda terms) by their chemical equivalent — chemlambda molecules — and replace the connection between them by chemical bonds. This is what you see in the animation.

Connected to the magenta dot (which is the output of the axon) is a pair of nodes which is related to the Y combinator, as seen as a molecule in chemlambda. ( Y combinator in chemlambda explained in this article http://arxiv.org/abs/1403.8046 )

The soma of this neuron is a single node (green), it represents an application node.

There are two dendrites (strings of red nodes) which have each 3 inputs (yellow dots). Then there are two small molecules at the end of the dendrites which are chemical signals that the computation stops there.

Now, what happens: the neuron uses the Y combinator to build a tree of application nodes with the leaves being the input nodes of the dendrites.

When there is no more work to do the molecules which signal these interact with the soma and the axon and transform all into a chemlambda quine (i.e. an artificial bug of the sort I explained previously) which is short living, so it dies after expelling some “bubbles”  (closed strings of white nodes).

5. Is that all? You can take “neurons” which have the soma any syntactic tree of a lambda term, for example. You can take neurons which have other axons than the Y-combinator. You can take networks of such neurons which build and then reduce any chemlambda molecule you wish.
__________________________________________

Artificial life, standard computation tests and validation

In previous posts from the chemlambda collection  I wrote about the simulation of various behaviours of living organisms by the artificial chemistry called chemlambda.
There are more to show in this direction, but there is already an accumulation of them:
jellyfish
20_20_hyb
9_9_hyb
As the story is told backwards, from present to the past, there will be more about reproduction later.
Now, that is one side of the story: these artificial microbes or molecules manifest life characteristics, stemming from an universal, dumb simple algorithm, which does random rewrites as if the molecule encounters invisible rewriting enzymes.

 

So, the mystery is not in the algorithm. The algorithm is only a sketchy physics.

But originally this formalism has been invented for computation.

 

It does pass very well standard computation steps, as well as nonstandard ones (from the point of view of biologists, who perhaps don’t hold enough sophisticated views as to differentiate between boring boolean logic gates and recursive but not primitive recursive functions like the Ackermann function).

In the following animation you see a few seconds screenshot of the computation of a factorial function.

facto

Recall that the factorial is something a bit more sophisticated than a AND boolean gate, but it is primitively recursive, so is less sophisticated than the Ackermann function.

 

During these few seconds there are about 5-10 rewrites. The whole process has several hundreds of them.

How are they done? Who decides the order? How are criteria satisfied or checked, what is incremented, when does the computation stop?

That is why it is wonderful:

  • the rewrites are random
  • nobody decides the order, there’s no plan
  • there are no criteria to check (like equality of values), there are no values to be incremented or otherwise to be passed
  • the computation stops when there are no possible further rewrites (thus, according to the point of view used with the artificial life forms, the computation stops when the organism dies)

Then, how it works? Everything necessary is in the graphs and the rewrite patterns they show.

It is like in Nature, really. In Nature there is no programmer, no function, no input and output, no higher level. All these are in the eyes of the human observer, who then creates a story which has some predictive power if it is a scientific one.

All I am writing can be validated by anybody wishing to do it. Do not believe me, it is not at all necessary to appeal to authority here.

So I conclude:  this is a system of a simplified world which manifest life like behaviours and universal computation power, in the presence of randomness. In this world there is no plan, there is no control and there are no externally imposed goals.

Very unlike the Industrial Revolution thinking!

This thread of posts can be seen at once in the chemlambda collection
https://plus.google.com/u/0/collection/UjgbX

If you want to validate this wordy post yourself then go to the github repository and read the instructions
https://github.com/chorasimilarity/chemlambda-gui/blob/gh-pages/dynamic/README.md

The live computation of the factorial is here
http://chorasimilarity.github.io/chemlambda-gui/dynamic/lisfact_2_mod.html

Which means that if you want to produce another random computation of the factorial then you have to use the file
lisfact_2_mod.mol and to follow the instructions.

________________________________________________________

It is time to cast doubt on any peer reviewed but not validated research article

Any peer reviewed article which does not come at least with the reviews has only a social validation. With reviews which contain only value judgements, grammar corrections and impossible to validate assertions, there is not much more trust added.

As to the recourse to experts… what are we, a guild of wizards? It is true because somebody says some anonymous experts have  been consulted and they say it’s right or wrong?

Would you take a pill based on the opinion of an anonymous expert that it cures your disease?

Would you fly in a plane whose flight characteristics have been validated by the hear-say of unaccountable anonymous experts?

What is more than laughable is that it seems that mathematics is the field with the most wizards, full of experts who are willingly exchanging private value opinions, but who are reluctant to make them in public.

Case by case, building on concrete examples, in an incremental manner, it is possible to write articles which can be validated by using the means they provide (and any other available), by anyone willing to do it.

It is time to renounce at this wizardry called peer review and to pass to a more rigorous approach.

Hard, but possible. Of course that the wizards will complain. After all they are in material conflict of interests, because they are both goalkeepers and arbiters, both in academic and editorial committees.

But again, why should we be happy with “it’s worthy of publication or not because I say so, but do not mention my name” when there is validation possible?

The wizardry costs money, directed to compliant students, produces no progress elsewhere than in the management metrics, kills or stalls research fields where the advance is made harder than it should because of the mediocrity of these high, but oh so shy in public experts who are where they are because in their young time the world was more welcoming with researchers.

Enough!

_____________________________________________________________

Bemis and the bull

Bemis said:

“I fell at the foot of the only solitary tree there was in nine counties adjacent (as any creature could see with the naked eye), and the next second I had hold of the bark with four sets of nails and my teeth, and the next second after that I was astraddle of the main limb and blaspheming my luck in a way that made my breath smell of brimstone. I had the bull, now, if he did not think of one thing. But that one thing I dreaded. I dreaded it very seriously. There was a possibility that the bull might not think of it, but there were greater chances that he would. I made up my mind what I would do in case he did. It was a little over forty feet to the ground from where I sat. I cautiously unwound the lariat from the pommel of my saddle——”

“Your saddle? Did you take your saddle up in the tree with you?”

“Take it up in the tree with me? Why, how you talk. Of course I didn’t. No man could do that. It fell in the tree when it came down.”

“Oh—exactly.”

“Certainly. I unwound the lariat, and fastened one end of it to the limb. It was the very best green raw-hide, and capable of sustaining tons. I made a slip-noose in the other end, and then hung it down to see the length. It reached down twenty-two feet—half way to the ground. I then loaded every barrel of the Allen with a double charge. I felt satisfied. I said to myself, if he never thinks of that one thing that I dread, all right—but if he does, all right anyhow—I am fixed for him. But don’t you know that the very thing a man dreads is the thing that always happens? Indeed it is so. I watched the bull, now, with anxiety—anxiety which no one can conceive of who has not been in such a situation and felt that at any moment death might come. Presently a thought came into the bull’s eye. I knew it! said I—if my nerve fails now, I am lost. Sure enough, it was just as I had dreaded, he started in to climb the tree——”

“What, the bull?”

“Of course—who else?””

[ Mark Twain, Roughing It, chapter VII]

Like Bemis, legacy publishers hope you’ll not think the unthinkable.

That we can pass to a new form of research sharing.

In publicity they say that the public is like a bull.

When you read an article you are like a passive couch potato in front of the TV. They (the publishers, hand in hand with academic managers) cast the shows, you have the dubious freedom to tap onto the remote control.

Now, it is possible, hard but possible and doable on a case by case basis. It is possible to do more. Comparable to the experience you have in a computer game vs the one you have in front of the TV.

You can experience research actively, via research works which run in the browser. I’ll call them “articles” for the lack of the right name, but articles they are not.

An article which runs in the browser should have the following features:

  • you, the reader-gamer, can verify the findings by running (playing) the article
  • so there has to be some part, if not all of the content, into a form which is executed during gameplay, not only as an attached library of programs which can be downloaded and run by the interested reader (although such an attachment is already a huge advance over the legacy publisher pity offer)
  • verification (aka validation) is up to you, and not limited to a yes/no answer. By playing the game (as well as other related articles) you can, and you’ll be interested into discovering more, or different, or opposing results than the one present in the passive version of the article and why not in the mind of the author
  • as validation is an effect of playing the article, peer review becomes an obsolete, much weaker form of validation
  • peer review is anyways a very weird form of validation: the publisher, by the fact it publishes an article, implies that some anonymous members of the research guild have read the article. So when you read the article in the legacy journal you are not even told, only hinted that somebody from the editorial staff exchanged messages with somebody who’s a specialist, who perhaps read the article and thought it is worthy of publication. This is so ridiculous, but that is why you’ll find in many reviews, which you see as an author, so many irrelevant remarks from the reviewer, like my pet example of the reviewer who’s offput by my use of quotation signs. That’s why, because what the reviewer can do is very limited, so in order to give the impression he/she did something, to give some proof that he/she read the article, then it comes with this sort of circumstantial proof. Actually, for the most honest reviewer, the ideally patient and clever fellow who validates the work of the author, there is not much else to do. The reviewer has to decide if he believes it or not, from the passive form of the article he received from the editor, and in the presence of the conflict of interests which comes from extreme specialisation and low number of experts on a tiny subject. Peer review is not even a bad joke.
  • the licence should be something comparable to CC-BY-4.0, and surely not CC-BY-NC-ND. Something which leave free both the author and the reader/gamer/author of derivative works, and in the same time allows the propagation of the authorship of the work
  • finally, the article which runs in the browser does not need a publisher, nor a DRM manager. What for?

So, bulls, let’s start to climb the tree!

Related: https://chorasimilarity.wordpress.com/2015/04/28/one-of-the-first-articles-with-means-for-complete-validation-by-reproducibility/

_________________________________________

Visit the chemlambda collection

You don’t have to possess a Google+ account to visit the new

chemlambda collection

Kind of a micro-blogging place where you can read and see animated gifs about autonomous computing molecules, about the MicrobiomeOS in the making and easy clear intros to details of chemlambda.

If you are on G+ then don’t be shy and add it to one of your circles!

__________________________________________

Personal reasons for all these threads

 As you see, I’ve updated the post on the no semantics stance with the content from various g+ posts. So now there is a all-in-one post which I shall keep updated if necessary. A better idea would be to use the chorasimilarity big post as main source from now on.
Mind that in the g+ stream I have several posts which are related, although they are technically about various details of chemlambda.
Coming to that, perhaps it has been a psychological error to show you first very complex cascades of hundreds or thousands of rewrites, hoping you will be amazed that they eventually work to give a meaningful result even if the intermediary steps have no (global) meaning.
That is why I changed the strategy and now I make clear some very simple mechanisms which emerge, all from the unique random stupid algorithm consisting in the random application of rewrites.
All this is part of the ideas which I hope some will appreciate, that’s why maybe you throw a second longer look of some of the demos
http://chorasimilarity.github.io/chemlambda-gui/dynamic/demos.html
and why not hoping that among those who start making sense of it are also some chemists who might start to believe that is actually possible to build real molecules which compute autonomously exactly like in chemlambda, or even better that at the molecular level life functions verbatim by a version of chemlambda, which is perhaps a proof of principle for that.
So chemists may take a longer look at the article Molecular computers
http://chorasimilarity.github.io/chemlambda-gui/dynamic/molecular.html
Ending with that, I just want to show that all the apparently disparate threads (chemlambda, no semantics, open access) from chorasimilarity meet: this article is perhaps the first one from a series of future versions of a research article. What is written there can be validated not socially, as in the actual peer review system, but much more rigorously by using the github repository which contains the scripts (which work thus they prove that the algorithm behind them is sound) which were used for the said work.
That is why I try my best not to go on beaten paths of publication, even if it’s hard, with the hope that using some good science as argument, having an achievable project, which can only work collaboratively, and insisting that the future is validation of the kind attached to this article, all this will make a strong enough impression on you, with benefits for all parts involved.

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