# Google translate helps the scholarly poor

Do you know what “scholarly poor” means? I saw this formulation some time ago and it made me ask: am I scholarly poor?

You find this expression in the writings of those who praise Gold Open Access, or in the articles which try to understand the Sci-Hub phenomenon.

Recall that Gold OA means practically that authors pay to publish from funds they receive for research. It’s all in the language: Green OA is not for publication, no sir! Green OA is for archiving. Gold OA is for publication and it may incur costs, you see, which may be covered by the authors. (The readers can no longer be forced to pay, so who’s left?) And the authors pay, not from their pockets, because they are not crazy rich to create and moreover to pay thousands of $to publish their article. They pay from the funds they receive for reseach, because their bosses, the academic managers, ask them to. These academic managers just love the publishers, be them the traditional ones or this new modern Gold OA blend. They don’t like the Green OA, there’s no money involved, pooh! no value. Sci-Hub made available practically any scientific article, therefore there is no longer any difference between an article published gratis, but behind a paywall, and an article published for 2000$ and free to read. Both are as easily accessible. IANAL but this is the reality of the world we are living in.

This reality upsets the Gold OA proponents, so they use this expression “scholarly poor” to denote those scholars which don’t have institutional access to the paywalled articles. Because Gold OA proponents love academic managers who are not poor, they ignore the reality that the researchers, in poor or rich (crazy?) academic institutions, all of them would rather read either from Green OA (like arXiv) or from Sci-Hub or from their colleagues who put online their work.

In itself, to name a researcher “scholarly poor” is distasteful.

But Google comes to the rescue! When I first saw this expression I was curious how it translates to French, for example, another language I understand.

Thank you Google Translate! And HAHA. And so poetical!

I checked again, today, when I decided to write this post. I recorded myself using the translate:

Yes, OK, a bit more bland, less poetical, but more  comical for the public at large.

So right, though!

# A project in chemical computing and Lafont universality

The post Universality of interaction combinators and chemical reactions ends with the idea that Lafont universality notion, for interaction systems, may be the right one for chemical computing.

These days are strange, every one comes with some call from one of my old projects. (About new ones soon, I have so many things.) Today is even more special because there were two such calls.One of them was from what I wrote in A project in chemical computing page from april 2015. It ends with:

If you examine what happens in this chemical computation, then you realise that it is in fact a means towards self-building of chemical or geometrical structure at the molecular level. The chemlambda computations are not done by numbers, or bits, but by structure processing. Or this structure processing is the real goal!
Universal structure processing!

There is even this video about an Ackermann function molecular computer I forgot about.

The idea is that the creation of a real molecule to compute Ackermann(2,2) would be the coolest thing ever made in chemical computing. If that is possible then as possible as well would be an Ackermann goo made from Ackermann(4,4):

In Graphic lambda calculus and chemlambda (III) I comment again on Lafont:

• Lafont universality property of interaction combinators means, in this pseudo-chemical sense, that

the equivalent molecular computer based on interaction combinators reactions (though not the translations) works

for implementing a big enough class of reactions which are Turing universal in particular (Lafont  shows concretely that he can implement Turing machines).

In the series about Lafont interaction combinators and chemlambda (1) (2) (3), as well as in the paper version of the article Molecular computers, an effort is made to reconnect chemlambda research with much older work by Lafont. [UPDATE: I retrieved this, I forgot about it, it’s mostly chemlambda v1  to chemlambda v2, see also this post ]

# The numberphile microbe and the busy beaver

This is another weirdly named, but contentful post after this one, During an attempt to launch myself into video explanations, I made a post on the numberphile microbe.

The numberphile microbe is the chemlambda version of a multiplication of two Church numbers, in this case 5X5=25. I called the creature evolving in the video a “numberphile microbe” because it really consumes copies of the number 5, metabolizes them and produces eventually 25. In a very careful way, though, which inspired me the following description (but you have to see the video from that post):

“The numberphile microbe loves Church numbers. His strategy is this: never one without the other. When he finds one Church number he looks around for the second one. Then he chains the first to the second and only after that he starts to slowly munch the head of the first. Meanwhile the second Church number watches the hapless first Church number entering, atom by atom, in the numberphile mouth.

Only the last Church number survives, in the form of the numberphile’s tail.”

The  mol file used is times_only.mol.  Yes, allright, is the mol version of the AST of a lambda term.

You can see the numberphile also in this animation, together with a busy beaver Turing machine (the chemlambda version explained here):

In the first half of the animation you see the “numberphile” at the left and the busy beaver as a reddish loop at the right.

What happens is that the lambda term like 5X5 reduces to 25 while in the same time the busy beaver machine works too. In the same time, the Church number 25 in the making already makes the small loop to replicate and to grow bigger and bigger, eventually 25 times bigger.

So that explains the title.

The mol file used is times_only_bb.mol. Open it and see how is it different than the first.

You can see a simulation (js) of Church number applied to a busy beaver here.

And the most important is: during the making of this short movie, no human director was present to stage the act.

# Blockchain categoricitis 2, or life as an investor and a category theory fan

… or the unreasonable effectiveness of category theory in blockchain investments.

A year ago I wrote the post Blockchain categoricitis and now I see my prediction happening.

Categoricitis is the name of a disease which infects the predisposed fans of category theory, those which are not armed with powerfull mathematical antibodies. Show them some diagrams from the height of your academic tower, tell them you have answers for real problems and they will believe.

Case in point: RChain. See Boom, bust and blockchain: RChain Cooperative’s cryptocurrency dreams dissolve into controversy.

Update: Epilogue? (28.02.2020)

Yes, just another cryptocurrency story… Wait a moment, this one is different, because it is backed by strong mathematical authority! You’ll practically see all the actors from the GeekWire story mentioned in the posts linked further.

Look:

Guestpost at John Baez blog: RChain (archived)

“Programmers, venture capitalists, blockchain enthusiasts, experts in software, finance, and mathematics: myriad perspectives from around the globe came to join in the dawn of a new internet. Let’s just say, it’s a lot to take in. This project is the real deal – the idea is revolutionary […]”

RChain is light years ahead of the industry. Why? It is upholding the principle of correct by construction with the depth and rigor of mathematics.”

__________

Another one, in the same place: Pyrofex (archived). This is not a bombastic guestpost, it’s authored by Baez.

Mike Stay is applying category theory to computation at a new startup called Pyrofex. And this startup has now entered a deal with RChain.”

Incidentally (but which fan reads everything?) in the same post Baez is candid about computation and category theory.

“When I first started, I thought the basic story would be obvious: people must be making up categories where the morphisms describe processes of computation.

But I soon learned I was wrong: […] the morphisms were equivalence classes of things going between data types—and this equivalence relation completely washed out the difference, between, say, a program that actually computes 237 × 419 and a program that just prints out 99303, which happens to be the answer to that problem.

In other words, the actual process of computation was not visible in the category-theoretic framework.” [boldfaced by me]

(then he goes on to say that 2-categories are needed in fact, etc.)

In Applied Category Theory at NIST (archived) we read:

“The workshop aims to bring together two distinct groups. First, category theorists interested in pursuing applications outside of the usual mathematical fields. Second, domain experts and research managers from industry, government, science and engineering who have in mind potential domain applications for categorical methods.”

and we see an animation from the post  “Correct-by-construction Casper | A Visualization for the Future of Blockchain Consensus“.

________________________

I never trusted these ideas. I had interactions with some of the actors in this story   (example) (another example), basically around distributed GLC . Between 2013-2015, instead of writing programs the fans of GLC  practically killed the distributed   GLC project  because it was all the time presented in misleading terms of agents and processes, despite my dislike. Which made me write chemlambda, so eventually that was good.

[hype] GLC and chemlambda are sort of ideal Lisp machines which you can cut in half and they still work. But you have to renounce at semantics for that, which makes this description very different from the actual Lisp machines.  [/hype]

# Let’s make an invisible conference

An invisible conference is a small community of interacting scholars who assemble suddenly in a public place, acquire knowledge through experimental investigation, then quickly disperse.

UPDATE: I made a page which will be  updated with details, in time.

I made up this description by copy-paste from wikipedia flash mob and invisible college.

The definition is not complete yet, there has to be included something from a key signing party.

Before the conference.       [TBA]

During the conference.     [TBA]

After the conference.     [TBA]

In case you want to meet and talk seriously, what if we organize an invisible conference? I have to think more about the place, say Bucharest, Romania? or maybe this summer at a nice camp by the sea (you need a tent)? other idea?

I put this contact also on my alternative homepage.

The “invisible” word points to the idea of an invisible college, mentioned in another post.

This post will be updated many times probably, so bookmark it because it will be less visible when other, newer posts will appear.

# An extension of hamiltonian mechanics

This is an introduction to the ideas of the article arXiv:1902.04598

UPDATE: If you think about a billiard-ball computer, the computer is in the expression of the information gap. The model applies  also to chemlambda, molecules have a hamiltonian as well and the graph rewrites, aka chemical reactions, have a description in the information gap. That’s part of the kaleidos project 🙂

__

Hamiltonian mechanics is the mechanism of the world. Indeed, the very simple equations (here the dot means a time derivative)

govern everything. Just choose an expression for the function $H$, called hamiltonian, and then solve these equations to find the evolution in time of the system.

Quantum mechanics is in a very precise sense the same thing. The equations are the same, only the formalism is different. There is a hamiltonian which gives the evolution of the quantum system…

Well, until measurement, which is an addition to the beautiful formalism. So we can say that hamiltonian mechanics, in the quantum version, and the measurement algorithm are, together, the basis of the quantum world.

Going back to classical mechanics, the same happens. Hamiltonian mechanics can be used as is in astronomy, or when we model the behavior of a robotic arm, or other purely mechanical system. However, in real life there are behaviors which go beyond this. Among them: viscosity, plasticity, friction, damage, unilateral contact…

There is always, in almost all applications of mechanics, this extra ingredient: the system does not only have a hamiltonian, there are other quantities which govern it and which make, most of the time, the system to behave irreversibly.

Practically every  object, machine or construction made by humans needs knowledge beyond hamiltonian mechanics. Or beyond quantum mechanics. This is the realm of applied mathematics, of differential equations, of numerical simulations.

In this classical mechanics for the real world we need the hamiltonian and we also need to explain in which way the object or material we study is different from all the other objects or materials. This one is viscous, plastic, elsot-plastic, elasto-visco-plastic, there is damage, you name it, these differences are studied and they add to hamiltonian mechanics.

They should add, but practically they don’t. Instead, what happens is that the researchers interested into such studies choose to renounce at the beaustiful hamiltonian mechanics formalism and to go back to Newton and add their knowledge about irreversible behaviours there.

(There is another aspect to be considered if you think about mechanical computers. They are mostly nice thought experiments, very powerfull ideas generators. Take for example a billiard-ball computer. It can’t be described by hamiltonian mechanics alone because of the unilateral contact of the balls with the biliard and of the balls one with another. So we can study it, but we have to add to the hamiltonian mechanics formalism.)

From all this  we see that it may be interesting to study if there is any information content of the deviation from hamiltonian mechanics.

We can measure this deviation by a gap vector, defined by

and we need new equations for the gap vector $\eta$.  Very simple then, suppose we have the other ingredient we need, a likelihood function $\pi \in [0,1]$ and we add that

where $z = z(t) = (q(t), p(t))$. That is we ask that    if the system is in the state $z$ then the velocity $\dot{z}$ and the gap vector $\eta$   maximize the likelihood $\pi$ .

Still too general, how can we choose the likelihood? We may take the following condition

that is we can suppose that the algorithm max  gives a  categorical answer when applied to any of the 2nd or 3rd argument of the likelihood.

(It’s Nature’s business to embody the algorithm max…)

We define then the information content associated to the likelihood as

So now we have a principle of minimal information content of the difference from hamiltonian evolution: minimize

In arXiv:1902.04598 I explain how this extension of hamiltonian mechanics works wonderfully with viscosity, plasticity, damage and unilateral contact.

# Scientific publishers take their money from the academic managers, blame them too

Starting with “All this is an excellent ad for sci-hub, which avoids most of the serious drawbacks of publishers like Elsevier. It was interesting how that was relegated to a veiled comment at the end, “or finding access in other channels”. But basically if the mainstream publishers can’t meet the need, we do need other channels, and right now sci-hub is the only one that actually works at scale.

Then the discussion goes to “Blame the academic administrators who demand publications in top tier journals – the same ones who charge a ton for access.

Or “ in market terms the clients (researchers) manifest a strong preference for other products than those offered by the publishers. Why do they still exist? Does not make any sense, except if we recognize also that the market is perturbed

Enjoy the thread!  It shows that people think better than, you choose:  pirates who fight  only for the media corporation rights,  gold OA diggers who ask for more money than legacy publishers, etc…

UPDATE: for those who don’t know me, I’m for OA and Open Science. I do what I support. I am not for legacy publishers. I don’t believe in the artificial distinction between green OA, which is said to be for archiving, and gold OA which is said to be for publishing. I’m for arXiv and other really needed services for research communication.

# My first programs, long ago: Mumford-Shah and fracture

A long time ago, in 1995-1997, I dreamed about really fast and visual results in image segmentation by the new then Mumford-Shah functional and in fracture. It was my first programming experience. I used Fortran, bash and all kinds of tools available in linux.

There is still this trace of my page back then, here at the Wayback Machine. (I was away until 2006.) The present day web page is this.

Here is the image segmentation by the M-S functional of a bw picture of a Van Gogh painting.

And here is a typical result of  fracture propagation (although I remember having hundreds of frames available…)

The article is here.

# What’s new around Open Access and Open Science? [updated]

In the last year I was not very much interested into Open Access and Open Science. There are several reasons, I shall explain them. But before: what’s new?

My reasons were that:

• I’m a supporter of OA, but not under the banner of gold OA. You know that I have a very bad impression about the whole BOAI thing, which introduced the false distinction between gold which is publication and green which is archival. They succeeded to delay the adoption of what researchers need (i.e. basically older than BOAI inventions, like arXiv) and the recognition that the whole academic publication system is working actively against the researchers interests. Academic managers are the first to be blamed about this, because they don’t have the excuse that they work for a private entity which has to make money no matter the price. Publishers are greedy, OK, but who gives them the money?
• Practically, for the working researcher, we can now publish in any place, no matter how close or anachronically managed, because we can find anything on Sci-Hub, if we want. So there is no reason to fight for more OA than this. Except for those who make money from gold OA…
• I was very wrong with my efforts and attempts to use corporate social media for scientific communication.
• Bu still, I believe strongly in the superiority of validation over peer-review. Open Science is the future.

I was also interested in the implications for OA and OS of the new EU Copyright Directive. I expressed my concern that again it seems that nobody cares about the needs of researchers (as opposed to publishers and corporations in general) and I asked some questions which interest me and nobody else seems to ask: will the new EU Copyright Directive affect arXiv or Figshare?  The problem I see is related to automatic filters, or to real ways the researchers may use these repositories.  See for example here for a discussion.  In   Sept 2018 I filed requests for answers to arXiv and to Figshare. For me at least the answers will be very interesting and I hope them to be as bland as possible, in the sense that there is nothing to worry about.

So from my side, that’s about all, not much. I feel like except the gold OA money sucking there’s nothing new happening. Please tell me I’m very wrong and also what can I do with my research output, in 2019.

UPDATE: I submitted two days ago a comment at Julia Reda post Article 13 is back on – and it got worse, not better. About the implications for the research articles repositories, the big ones, I mean, the ones which are used millions of times by many researchers. I waited patiently, either for the appearance of the comment or for a reaction. Any reaction. For me this is a clear answer: pirates fight for the freedom of the corporation to share in its walled garden the product of a publisher. The rest is immaterial for them. They pirates not explorers.

UPDATE 2: This draft of Article 13 contains the following definition: “‘online content sharing service provider’ means a provider of an information society service whose main or one of the main purposes is to store and give the public access to a large amount of copyright protected works or other protected subject-matter uploaded by its users which it organises and promotes for profit-making purposes. Providers of services such as not-for profit online encyclopedias, not-for profit educational and scientific repositories, open source software developing and sharing platforms, electronic communication service providers as defined in Directive 2018/1972 establishing the European Communications Code, online marketplaces and business-to business cloud services and cloud services which allow users to upload content for their own use shall not be considered online content sharing service providers within the meaning of this Directive.

If this is part of the final version of Article 13 then there is nothing to worry as concerns arXiv, for example.

Maybe a separate push should be on upload filters and their legal side (who is responsible for the output of this algorithm? surely not the algorithm!), perhaps by asking for complete, reproducible, transparent information about those: source code and all the dependencies source code, reproducible behavior.