Tag Archives: open access

How I hit a wall when I used the open access and open source practices when applying for a job

UPDATE 11.10.2015. What happened since the beginning of the “contest”? Nothing. My guess is that they are going to follow the exact literary sense of their announcement. It is a classic sign of cronyism. They write 3 times that they are going to judge according to the file submitted (the activity of the candidate as it looks from the file), but they don’t give other criteria than the ones from an old law. In my case I satisfy these criteria, of course, but later on they write about “candidates considered eligible”, which literary means candidates that an anonymous board considers they are eligible and not simply eligible according to the mentioned criteria.

Conclusion: this is not news, is dog bites man.

I may be wrong. But in the case I’m right then the main subject (namely what happens in a real situation with open access practices in case of a job opening) looks like a frivolous, alien complaint.

The split between:
– a healthy, imaginative, looking to the future community of individuals and
– a kafkian old world of bureaucratic cronies
is growing bigger here in my country.


UPDATE 14.10.2015: Suppositions confirmed. The results have been announced today, only verbally, the rest is shrouded in mystery. Absolutely no surprise. Indeed, faced with the reality of local management, my comments about open access and open source practices are like talking about a TV show to cavemen.

Not news.

There is a statement I want to make, for those who read this and have only access to info about Romanians from the media, which is, sadly, almost entirely negative.

It would be misleading to judge the local mathematicians (or other creative people, say) from these sources. There is nothing wrong with many Romanian people. On the contrary, these practices which show textbook signs of corruption are typical for the managers of state institutions from this country. They are to be blamed. What you see in the media is the effect of the usual handshake between bad leadership and poverty.

Which sadly manifest everywhere in the state institutions of Romania, in ways far beyond the ridicule.

So next time when you shall interact with one such manager, don’t forget who they are and what they are really doing.

I am not going to pursue a crusade against corruption in Romania, because I have better things to do. Maybe I’m wrong and what is missing is more people doing exactly this. But the effects of corrupt practices is that the state institution becomes weaker and weaker. So, by psycho historic reasons 🙂 there is no need for a fight with dying institutions.

Let’s look to the future, let’s do interesting stuff!


This is real: there are job openings at the Institute of Mathematics of the Romanian academy, announced by the pdf file


The announce is in Romanian but you may notice that they refer to a law from 2003, which asks for a CV, research memoire, list of publications and ten documents, from kindergarden to PhD. On paper.

That is only the ridicule of bureaucracy, but the real problems were somewhere else.

There is no mention of criteria of selection, members of the committee, but in the announcement is written 3 times that every candidate’s work will be considered only as it appears from looking at the file submitted.

They also ask that the scientific, say, part of the submission to be sent by email to two addresses which you can grasp from the announcement.

So I did all the work and I hit a wall when I submitted by email.

I sent them the following links:

– my homepage which has all the info needed (including links to all relevant work)

– link to my arxiv articles
because all my published articles and all my cited articles, published or not) are available at arXiv

– link to the chemlambda repository for the programming, demos, etc part

I was satisfied because I finished this, when I got a message from DanTimotin@imar.ro telling me that I have to send them, as attachment, the pdf files of at least 5 relevant articles.

In the paper file I put 20+ of these articles (selected from 60+), but they wanted also the pdf files.

I don’t have the pdfs of many legacy published articles because they are useless for open access, you can’t distribute them publicly.
Moreover I keep the relevant work I do as open as possible.

Finally, how could I send the content of the github repository? Or the demos?

So I replied by protesting about the artificial difference he makes between a link and the content available at that link and I sent a selection of 20 articles with links to their arXiv version.

He replied by a message where he announced that if I want my submission to be considered then I have to send 5 pdfs attached.

I visited physically Dan Timotin to talk and to understand why a link is different from the content available to that link.

He told me that these are the rules.

He told that he is going to send the pdfs to the members of the committees and it might happen that they don’t have access to the net when they look for the work of the candidate.

He told me that they can’t be sure that the arXiv version is the same as the published version.

He has nothing to say about the programming/demo/animations part.

He told that nobody will read the paper file.

I asked if he is OK if I make public this weird practice and he agreed to that.

Going back to my office, I arrived to find 9 pdfs of the published articles. In many other cases my institute does not have a subscription to journals where my articles appeared, so I don’t think that is fair to be asked to buy back my work, only because of the whims of one person.

Therefore I sent to Dan Timotin a last message where I attached these 9 pdfs, I explained that I can’t access the others, but I firmly demand that all the links sent previously to be sent to the (mysterious, anonymous, net deprived, and lacking public criteria) committee, otherwise I would consider this an abuse.

I wrote that I regret this useless discussion provoked by the lack of transparency and by the hiding behind an old law, which should not stop a committee of mathematicians to judge the work of a candidate as it is, and not as it appears by an abuse of filtering.

After a couple of hours he replied that he will send the files and the links to the members of the committee.

I have to believe his word.

That is what happens, in practice, with open access and open science, at least in some places.

What could be done?

Should I wait for the last bureaucrat to stop supporting passively the publishing industry, by actively opposing open access practices?

Should I wait for all politicians to pass fake PhDs under the supervision of a very complacent local Academia?

Should I feel ashamed of being abused?

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

The title probably needs parsing:





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.


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.”


“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/


One of the first articles with means for complete validation by reproducibility

I have not stressed enough this aspect. The article

M. Buliga, Molecular computers

is one of the first articles which comes with complete means of validation by reproducibility.

This means that along with the content of the article, which contains animations and links to demonstrations, comes a github repository with the scripts which can be used to validate (or invalidate, of course) this work.

I can’t show you here how the article looks like, but I can show you a gif created from this  video of a demonstration which appears also in the article (however, with simpler settings, in order to not punish too much the browser).


This is a chemical like computation of the Ackermann(2,2) function.

In itself, is intended to show that if autonomous computing molecules can be created by the means proposed in the article, then impressive feats can be achieved.

This is part of the discussion about peer review and the need to pass to a more evolved way of communicating science.There are several efforts in this direction, like for example PeerJ’s paper-now commented in this post. See also the post Fascinating: micropublications, hypothes.is for more!

Presently one of the most important pieces of this is the peer review, which is the social practice consisting in declarations of one, two, four, etc anonymous professionals that they have checked the work and they consider it valid.

Instead, an ideal should be the article which runs in the browser, i.e. one which comes with means which would allow anybody to validate it up to external resources, like the works by other authors.

(For example, if I write in my article that “According to the work [1]   A is true. Here we prove that B follows from A.” then I should provide means to validate the proof that A implies B, but it would be unrealistical to be ask me to provide means to validate A.)

This is explained in more detail in Reproducibility vs peer review.

Therefore, if you care about evolving the form of the scientific article, then you have a concrete, short example of what can be done in this direction.

Mind that I am stubborn enough to cling to this form of publication, not because I am afraid to submit these beautiful ideas to legacy journals, but because I want to promote new ways of sharing research by using the best content I can make.


The shortest Open Access and New Forms of Publication question


then wtf is the article good for?

UPDATE: at figshare, they think about that.  Great!

UPDATE 2: for no particular reason, here is an accompanying short video done with the program

UPDATE 3:  See “Publish your computer code: it is good enough” by Nick Barnes, Nature 467, 753 (2010) | doi:10.1038/467753a

“I accept that the necessary and inevitable change I call for cannot be made by scientists alone. Governments, agencies and funding bodies have all called for transparency. To make it happen, they have to be prepared to make the necessary policy changes, and to pay for training, workshops and initiatives. But the most important change must come in the attitude of scientists. If you are still hesitant about releasing your code, then ask yourself this question: does it perform the algorithm you describe in your paper? If it does, your audience will accept it, and maybe feel happier with its own efforts to write programs. If not, well, you should fix that anyway.”


Gold OA with CC licence, Green OA without and a lesson from the dispute between Amazon and Hachette

Further are some data along with my speculations, which may be or may be not accurate, due to my limited understanding.

Hey, everybody has a limited understanding, here is mine!

TL;DR> The crux of the matter is in this part of  any recent CC 4.0 licence: in Section 2/Scope/a. Licence grant/5.

  • “5. Downstream recipients.
    1. Offer from the Licensor – Licensed Material. Every recipient of the Licensed Material automatically receives an offer from the Licensor to exercise the Licensed Rights under the terms and conditions of this Public License.
    2. No downstream restrictions. You may not offer or impose any additional or different terms or conditions on, or apply any Effective Technological Measures to, the Licensed Material if doing so restricts exercise of the Licensed Rights by any recipient of the Licensed Material.”


The new trend in academic publishing is:

  • offer a CC licence for Gold OA (i.e. after the publisher has money in the pocket from the author)
  • or  offer a non-CC licence for Green OA, which does not give the protection of the boldfaced text from the CC licences.

It matters very much because that is what happens in the dispute between Amazon and Hachette, namely Hachette has the copyright of books but Amazon puts downstream restrictions!

Conclusion: never forget about Doctorow’s first law and always ask for a CC licence from any publisher!

Doctorow’s first law:

“Any time someone puts a lock on something that belongs to you, and won’t give you the key, you can be sure that the lock isn’t there for your benefit.”

This is from the very clear explanation about the Amazon and Hachette dispute by Cory Doctorow in Locus.


Evidence now.

I made this post on G+, asking for info. I collect here the stuff:

  • In the Open letter to the AAAS about Science Advances, (new OA journal): “The default choice of a non-commercial licence (CC BY-NC) places unnecessary restrictions on reuse and does not meet the standards set out by the Budapest Open Access Initiative. Many large funders, including Research Councils UK and the Wellcome Trust, do not recognise this as an open license. The adoption of CC BY-NC as the default license means that many researchers will be unable to submit to Science Advances if they are to conform to their funder mandates unless they pay for the upgrade to CC BY. “
  • The Royal Society launches a new journal “Royal Society Open Science”. On the site of the new journal, in the section about licence to publish: they offer a licence different than CC, where they write: “4. If You decide to make the Definitive Published Version of the Article open access, this will be under a Creative Commons BY licence* [i.e. CC-BY-4.0],  You shall pay to Us the relevant fee and We shall make the Article so available from the later of the date of receipt of the relevant fee or the date of first publication of the Article.” They put  downstream restrictions for those who don’t pay them in part 6.
  • the STM new model licences, read by yourself (thanks Richard Poynder for mentioning these).

Other things:

  • the new journals of Cambridge University Press Forum of Mathematics Pi and Sigma offer only Gold OA with CC-BY-3.0, so there is no term of comparison with Green OA. (Have found this by downloading an article, nothing clear which is easy to find on their pages)
  • the new AMS journals are Gold OA, the subscription journals are Green OA.
  • the (greatest of all sites for a math or physics researcher) arXiv offers the choice between a CC-BY licence or a generic one. This is fair, because the choice is completely free left to the author.


UPDATE 16.09.2014: See the post AAAS vies for the title the  “Darth Vadar of publishing” by  longpd. “They  claim to support open access.  They redefine it to be a pay for publishing charge (APC)  of $3,000 USD and that restricts the subsequent use of the information in the article preventing commercial reuses such as publication on some educational blogs, incorporation into educational material, as well the use of this information by small to medium enterprises. If you really meant open access, the way the rest of world defines it, you’ll have to pay a surcharge of an additional $1,000.  But it gets worse.”



Github laudatio: negative Coase cost

This is a record of a mind changing experience I had with Github, one which will manifest in the months to come. (Well, it’s time to move on, to move further, new experiences await, I like to do this…)

Here is not more than what is in this ephemeral google+ post, but is enough to get the idea.

And it’s controversial, although obvious.

“I  just got hooked by github.io . Has everything, is a dream came true. Publishing? arXiv? pfff…. I know, everybody knows this already, let me enjoy the thought, for the moment. Then it will be some action.

Continuing with github and publishing, this is a worthy subject (although I believe that practically github already dwarfed legacy publishing, academia and arXiv). Here is an excerpt from a post from 2011
“- Publishing is central to Academia, but its publishing system is outclassed by what Open Source software developers have in GitHub- GitHub’s success is not just about openness, but also a prestige economy that rewards valuable content producers with credit and attention

-Open Science efforts like arXiv and PLoS ONE should follow GitHub’s lead and embrace the social web”

I am aware about the many efforts about publishing via github, I only wonder if that’s not like putting a horse in front of a rocket.

On the other side, there is so much to do, now that I feel I’ve seen rock solid proof that academia, publishing and all that jazz is walking dead, with the last drops of arterial blood splatting around from the headless body. ”

Negative Coase cost?