Tag Archives: open notebooks

Open notebook science for everyone, done by everyone

I am deeply impressed by the post:

Jean Claude Bradley Memorial Symposium; July 14th; let’s take Open Notebook Science to everyone

Here are some quotes:

Jean-Claude Bradley was one of the most influential open scientists of our time. He was an innovator in all that he did, from Open Education to bleeding edge Open Science; in 2006, he coined the phrase Open Notebook Science. His loss is felt deeply by friends and colleagues around the world.

“Science, and science communication is in crisis. We need bold, simple visions to take us out of this, and Open Notebook Science (ONS) does exactly that. It:

  • is inclusive. Anyone can be involved at any level. You don’t have to be an academic.
  • is honest. Everything that is done is Open, so there is no fraud, no misrepresentation.
  • is immediate. The science is available as it happens. Publication is not an operation, but an attitude of mind
  • is preserved. ONS ensures that the record, and the full record, persists.
  • is repeatable or falsifiable. The full details of what was done are there so the experiment can be challenged or repeated at any time
  • is inexpensive. We waste 100 Billion USD / year of science through bad practice so we save that immediately. But also we get rid of paywalls, lawyers, opportunity costs, nineteenth century publishing practices, etc.”

Every word is true!

This is the future of the research communication. Or at least the beginning of it. ONS has open, perpetual peer review as a subset.

Personal notes.  Look at the left upper corner of this page, it reads:

chorasimilarity | computing with space | open notebook.

Yay! the time  is coming!  the weirdos who write on arXiv, now figshare,  who use open notebooks, all  as a replacement for legacy publication,   will soon be mainstream 🙂

Now, seriously, let’s put some gamification into it, so those who ask “what IS a notebook?”  can play too. They ARE the future. Hope that soon the Game of Research and Review, aka playing  MMORPG  games at the knowledge frontier, will emerge.

There are obvious reasons for that:

  • the smartphone freeds us from staying in one physical place while we surf the virtual world
  • which has as an effect that we rediscover that physical space is important for our interactions, see  Ingress
  • gamification of human activities is replacing the industrial era habits, (pyramidal, static organizations, uniformization, identification of humans with their functions (worker, consumer, customer, student) and with their physical location (this or that country, city, students in the benchs, professors at the chair, payment for working hours ans for staying at the counter, legacy publishing).

See also Notes for “Internet of Things not Internet of Objects”.





Bitcoin, figshare, dropbox, open peer-review and hyperbolic discounting

Thinking out loud about the subject  of models of OA publication

  1. which are also open peer-review friendly,
  2. which work in the real world,
  3. which offer an advantage to the researchers using them,
  4. which have  small costs for the initiators.

PeerJ  is such an example, I want to understand why does it work and find a way to emulate it’s success, as quickly as possible.

You may wonder what difference is between 2 (works in real world) and  3(gives advantage to the user). If it gives an advantage to the user than it should work in real life, right? I don’t think so, because the behaviour of real people is far from being rational .

A hypothesis for achieving 2 is to exploit hyperbolic discounting.  I believe that one of the reasons PeerJ works is not only that it is cheaper than PLOS, but it also exploits this human behaviour.

It motivates the users to  review and to submit and it also finances the site (buys the cloud time, etc).

How much of the problem 4 can be solved by using the trickle of money which comes from exploiting hyperbolic discounting? Some experiments can be made.

What else? Let’s see, there is more which intrigues me:

  • the excellent figshare   of Mark Hahnel. It’s a  free repository,  which provides a DOI and collects some citation and use data.
  • there is a possibility to make blogs on dropbox. I have to understand well, but it seems that Scriptogr.am offers this service, which is an interesting thing in many ways. For example can one use a dropbox blog for sharing the articles, making it easy to collect reactions to them (as comments), in parallel with using figshare for getting a DOI for the article and for depositing versions of the article?
  • tools like git.macropus.org/twitter-viewer  for collecting twitter reactions to the articles (and possibly write other tools like this one)
  •  what is a review good for? a service which an open review could bring to the user is to connect the user with other people interested in the same thing. Thus, by collecting “social mentions” of the article, the author of the article might contact the interested people.
  • finally, and coming back to the money subject (and hyperbolic discounting), if you think, there is some resemblance in the references of an article and the block chains of bitcoin.  Could this be used?

I agree that these are very vague ideas, but it looks like there may be several sweet spots in this 4 dim space

  • (behavioral pricing , citing as  block chain)
  • (stable links like DOI , free repository)
  • (editor independent blog as open article)
  • (APIs for collecting social mentions as reviews)


An experiment in open writing and open peer-review

I shall try the following experiment in open writing/open peer-review which uses only available soft and tools.

No technical  knowledge is needed to do this.

No new platform is needed for this.

The idea is the following. I take an article (written by me) and I copy-paste it as text + figures in a publicly shared google document with comments allowed.

On top of the document I mention the source (where is the article from) , then I add a CC-BY licence.

This is all. If anybody wishes to comment the article, it can be done precisely, by pointing to the controversial paragraphs.

In the comments are allowed links, of course, therefore there is no limit to the quantity of data which can be put in such a comment.

There could be comment replies.

In conclusion, this is a very cheap way to do both a (limited) way of open writing and to allow open peer-review.

For the moment I started not with articles directly, but with edited content from this open notebook.  I made until now two “archives”

Even better would be to make a copy of the doc and put it in the figshare, to get a DOI. Then you stick the DOI  link in the doc.

Public shared chemlambda archive

Let’s try this experiment.  I prepared and shared publicly the

Chemlambda archive

which is an all-in-one document about the building of chemlambda (or the chemical concrete machine), from the vague beginnings to the moment when the work on Distributed GLC started.

The sources are from this open notebook.

I hope it makes an interesting reading, but what I hope more is that you shall comment on it and

  • help to make it better
  • identify new ideas which have potential
  • improve the presentation
  • ask questions!


Quick reaction on spnetwork part 4

Triggered by the spnetwork 4 post by Christopher Lee, hosted at John Baez’ Azimuth.

Only a very brief reaction, written from a beach, will come back later to it.

I am intrigued by this:

Think about it: that’s what search engines do all the time—a search engine pulls material out of all the worlds’ walled gardens, and gives it a new life by unifying it based on what it’s about. All selectedpapers.net does is act as a search engine that indexes content by what paper and what topics it’s about, and who wrote it.

There seems to be a huge potential here.

OK, I am thinking about it and I’m having the usual conversation with the regular naysayer, who tells me that in order to switch to the spnetwork, ot to ANY alternative of the actual publishing system, you need to have an incentive for that. What’s wrong with the actual system, besides the double monopoly (monopoly and monopsony, hence a banana republic situation) of greedy publishers hand in hand with managers in academia? Not much (with the condition that you pay the publisher with OTHER PEOPLE MONEY). The researcher writes an article, which is peer-reviewed, everything is verified and working nicely, why change that?

The regular naysayer tells me that the real problem is the huge number of articles. Which one to read and which not? Which one to check to the bones, even if already peer-reviewed? The answer is this: is statistically better to read the articles appeared in good journals.

Any system aiming to improve  the old one should solve this problem of picking articles from the huge pile which is produced every day.

Apparently, the name, “Selected Papers Network”, suggests that Lee’s project tries to solve this. But now here he comes with a really interesting and different idea!

Forget the incentive, let’s think about articles. The truth is that even if there are many articles, too many to read, there are very few readers of an article  chosen at random. As authors, we all want our articles to be read. As readers, we long for fewer, more interconnected articles.

There are too many articles either because the article is written for ISI points, or because there are too many articles writers, or even because the article is not touching the readers who might do something with it, because they read other articles or, rarely, because they are not yet born (sorry, but I can’t stop to mention again the comparison of what is happening now in research publishing with the impressionists revolution, so why not accept that there are already articles which don’t have yet readers, like, say, Van Gogh paintings during his lifetime).

Or, an article, as it is written today, with the manifold stupid conventions which are reppelant now, but have reasons in the past, is a very bad vector of information. There are a lot of articles, each trying to get a bit og brain time, on it’s own, without trying to collaborate with others. In this respect, I believe this is a far consequence of  the cartesian method, which I think is obsolete in some respects, because it is  “designed as a technique for understanding performed by one mind in isolation, severely handicapped by the bad capacity of communication with other isolated minds. It was a very efficient technique, which is now challenged by two effects of its material outcomes:

  • better communication channels provided by the www,
  • mechanical, or should I say digital, applications of the method which largely surpass the capacity of understanding of one human mind, as witnessed for example by the first computer aided mathematical proofs, or for another example by the fact that we can numerically model physical phenomena, without understanding rigorously why the method works.”

As far as I understand the new idea of Christopher Lee, the tagging system proposed by spnetwork could be a part of a solution for the problem of having too may articles not communicating one with another (by grouping them).

Another part of the solution could be using other vehicles than articles for communicating science, I am thinking  about open notebooks. There are not too many open notebooks, but they have the following advantages over articles:

  • more honesty, be it about negative results, apparent dead ends, more clear background data and real motivations for research,
  • more lively, welcoming discussions, than the dry and often hidden peer-review
  • naturally interactive.

Articles are like movies, open notebooks are more like games.

Therefore, to conclude, it seems to me that Christopher Lee’s federated ecosystem could have more chances if it allows open notebooks (besides articles, which are still necessary) to join the party.