Tag Archives: Open Science

How to use the chemlambda collection of simulations

The chemlambda_casting folder (1GB) of simulations is now available on Figshare [1].

How to use the chemlambda collection of simulations? Here’s an example. The synthesis from a tape video [2] is reproduced here with a cheap animated gif. The movie records the simulation file 3_tape_long_5346.html which is available for download at [1].

That simple.

If you want to run it in your computer then all you have to do is to download 3_tape_long_5346.html from [1], download from the same place d3.min.js and jquery.min.js (which are there for your convenience). Put the js libs in the same folder as the html file. Open the html file with a browser, strongly recommend Safari or Chrome (not Firefox which blocks with these d3.js animations, for reasons related to d3). In case your computer has problems with the simulation (I used a macbook pro with safari) then slow it like this: edit the html file (with any editor) and look for the line starting with

return 3000 + (4*(step+(Math.random()*

and replace the “4” by “150”, it should be enough.

Here is a longer explanation. The best would be to read carefully the README [4].
“Advanced”: If you want to make another simulation for the same molecule then follow the steps.

1. The molecule used is 3_tape_long_5346.mol which is available at the library of chemlambda molecules [3].

2. So download the content of the gh-pages branch of the chemlambda repository at github [4] as explained in that link.

3. then follow the steps explained there and you’ll get a shiny new 3_tape_long_5346.html which of course may be different in details than the initial one (it depends on the script used, if you use the random rewrites scripts then of course the order of rewrites may be different).

[1] The Chemlambda collection of simulations
https://doi.org/10.6084/m9.figshare.4747390.v1

[2] Synthesis from a tape
https://plus.google.com/+MariusBuliga/posts/Kv5EUz4Mdyp

[3] The library of chemlambda molecules
https://github.com/chorasimilarity/chemlambda-gui/tree/gh-pages/dynamic/mol

[4] Chemlambda repository (readme) https://github.com/chorasimilarity/chemlambda-gui/blob/gh-pages/dynamic/README.md

The chemlambda collection is a social hack, here’s why

 

People from data deprived places turn to available sources for scientific information. They have the impression that Social Media may be useful for this. Reality is that it is not, by design.

But we can socially hack the Social Media for the benefit of Open Science.

Social Media is not fit for Open Science by design. They are Big Data gatherers, therefore they are interested not in the content per se, but in the metadata. The huge quantity of metadata they suck from the users tells them about the instantaneous interests and social links or preferences. That is why cat pics are everywhere: the awww moment is data poor but metadata rich.

Open Science has as aim to share scientific data and rigorous validation means. For free! Therefore Open Science is data rich. It is also, by design, metadata poor, because at least if a piece of research is not yet popular, there is not much interaction (useful for example to advertisers or to tech companies or govenrnments) to be encoded in
metadata.

The public impression is that science is hard and many times boring. There are however many people interested in science, like for example smart kids or creative people living in data deprived places. There are so many people with access to the Social Media so that, in principle, even the most seemingly boring science project may gather the attentions of tens of thousands of them. If well done!

Such science projects may never see the light of the media attention because classical media works with big numbers and very low level content. Classical media has still to adapt to the new realities of the Net. One of them is that the Net people are in such a great number that there is no need to adapt a message for a majority of people which is not, generically, interested in science.

Likewise, Social Media is by design driven by big numbers (of metadata, this time). They couldn’t care less about the content provided that it generates big data exhaust (Zuboff, Big other: surveillance capitalism and the prospects of an information civilization).

They can be tricked!

This was the purpose of the chemlambda collection: beautiful animations, data rich content hidden behind for those interested. My previous attempts to use classical channels for Open Science gave only very limited results. Indeed, the same is true for a smart kid or a creative person from Africa.

If you are not born in the right place, studied at the right university and made the right friends then your ideas will not spread through the classical channels, unless your
ideas are useful to a privileged team. You, smart kid or creative person from Africa, will never advance your ideas to the world unless they are useful first not to you, but to privileged people from far away places. If this happens, the best you can expect is to be an useful servant for them.

So, with these ideas and experiences, I tried to socially hack the Big Data gatherers. I presented short animations (under 10s) obtained from real scientific simulations. I chose them among those which are visually appealing. Each of them can be reproduced and researched by anybody interested via a GitHub repository.

It worked. The Algorithmic Gods from Google decided to make chemlambda a featured collection. I had more than 50 000 followers and more than 50 millions views of these scientific, original simulations.

To compare, another collection, dedicated to censorship on social media, had no views!

I shall make, acording to my access to data, which is limited, an analysis of people who saw the collection.

It seems to me that there were far more women that men. Probably the algorithms used the prior that women, stupid as they are, are more interested in pictures than text. Great, let’s hack this stupid prior and turn it into a chance to help Women access to science 🙂

There were far more people from Asia and Africa than from the West. Because, of course, they are stupid and don’t speak the language (English), but they can look at the pictures. Great, let’s turn this snobbery into an advantage, because they are the main public which could benefit from Open Science.
The amazing (for me) popularity of this experiment showed that there is something more to dig in this direction!
Science can be made interesting and remain rigorous too.

Science and art are not as different as they look, in particular for this project the visual arts.

And the chemlambda project is very interesting, of course, because it a take on life at molecular level done by a mathematician. The biologists need this, not only mathematical tools, but also mathematical minds. Biologists, as the Social Media companies, sit on heaps of Big Data.

Finally, there is the following question I’d like to ask.
Scientific data is, in bits, a tiny proportion of the Big Data gathered everyday. Is tiny, ridiculously tiny.

Question: where to put it freely, so that it stays free and is treated properly, I mean as visible and easy to access as a cat pic? Would it be so hard to dedicate something like 1/10 000 of the servers used for Big Data in order to keep Open Science alive? In order to not let it rot along with older cat pics?

Open peer review is something others should do, Open science is something you could do

This post follows Peer review is not independent validation, where it is argued that independent validation is one of the pillars of the scientific method. Peer review is only a part of the editorial process. Of course that peer review is better than nothing, but it is only a social form of validation, much less rigorous than what the scientific method asks.

If the author follows the path of Open science, then the reader has the means to perform an independent validation. This is great news, here is why.

It is much easier to do Open science than to change the legacy publishing system.

Many interesting alternatives to the legacy publishing have been proposed already. There is green OA, there is gold OA (gold is for $), there is arXiv.org. There are many other versions, but the main problem is that research articles are not considered really serious unless they are peer reviewed. Legacy publishing provides this, it is actually the only service they provide. People are used to review for established journals and any alternative publishing system has to be able to compete with that.

So, if you want to make an OA platform, it’s not serious unless you find a way to make other people to peer review the articles. This is hard!

People are slowly understanding that peer review is not what we should aim for. We are so used with the idea that peer review is that great thing which is part of the scientific method. It is not! Independent validation is the thing, peer review is an old, unscientific way (very useful, but not useful enough to allow research finding to pass the validation filter).

The alternative, which is Open science, is that the authors of research findings make open all the data, procedures, programs, etc, everything they have. In this way, any other group of researchers, anybody else willing to try can validate those research findings.

The comparison is striking. The reviewers of the legacy publishing system don’t have magical powers, they just read the article, they browse the data provided by the very limited article format and they make an opinion about the credibility of the research findings. In the legacy system, the reviewer does not have the means to validate the article.

In conclusion, it is much simpler to do Open science than to invent a way to convince people to review your legacy articles. It is enough to make open your data, your programs, etc. It is something that you, the author can do.

You don’t have to wait for the others to do a review for you. Release your data, that’s all.

Peer review is not independent validation

People tend to associate peer review with science. As an example, even today there are still many scientists who believe that an arXiv.org article is not a true article, unless it has been peer reviewed. They can’t trust the article, without reading it first, unless it passed the peer review, as a part of the publishing process.

Just because a researcher puts a latex file in the arXiv.org (I continue with the example), it does not mean that the content of the file has been independently validated, as the scientific method demands.

The part which slips from the attention is that peer review is not independent validation.

Which means that a peer reviewed article is not necessarily one which passes the scientific method filter.

This simple observation is, to me, the key for understanding why so many research results communicated in peer reviewed articles can not be reproduced, or validated, independently. The scale of this peer reviewed article rot is amazing. And well known!

Peer review is a part of the publishing process. By itself, it is only a social validation. Here is why: the reviewers don’t try to validate the results from the article because they don’t have the means to do it in the first place. They do have access only to a story told by the authors. All the reviewers can do is to read the article and to express an opinion about it’s credibility, based on the reviewers experience, competence (and biases).

From the point of view of legacy publishers, peer review makes sense. It is the equivalent of the criteria used by a journalist in order to decide to publish something or not. Not more!

That is why it is very important for science to pass from peer review to validation. This is possible only in an Open Science frame. Once more (in this Open(x) fight) the medical science editors lead. From “Journal Editors To Researchers: Show Everyone Your Clinical Data” by Harlan Krumholz, a quote:

“[…] last Wednesday, the editors of the leading medical journals around the world made a proposal that could change medical science forever. They said that researchers would have to publicly share the data gathered in their clinical studies as a condition of publishing the results in the journals. This idea is now out for public comment.

As it stands now, medical scientists can publish their findings without ever making available the data upon which their conclusions were based.

Only some of the top journals, such as The BMJ, have tried to make data sharing a condition of publication. But authors who didn’t want to comply could just go elsewhere.”

This is much more than simply saying “peer review is bad” (because is not, only that it is not a part of the scientific method, it is a part of the habits of publishers). It is a right step towards Open Science. I repeat here my opinion about OS, in the shortest way I can:

There are 2 parts involved in a research communication:   A (author, creator, the one which has something to disseminate) and R (reader). The legacy publishing process introduces a   B (reviewer).  A puts something in a public place, B expresses a public opinion about this and R uses B’s opinion as a proxy for the value of A’s thing, in order to decide if A’s thing is worthy of R’s attention or not.  Open Access is about the direct interaction of A with R, Open Peer-Review is about transparent interaction of A with B, as seen by R and Validation (as I see it) is improving the format of A’s communication so that R could make a better decision than the social one of counting on B’s opinion.

That’s it! The reader is king and the author should provide everything to the reader, for the reader to be able to independently validate the work. This is the scientific method at work.

 

Excellent: The Journal of Brief Ideas

Here is another new initiative: The Journal of Brief Ideas.

There are interesting reactions to this:

OK, what is this, in just a few words?

From the About page of the journal:

The Journal of Brief Ideas is a research journal, composed entirely of ‘brief ideas’. The goal here is to provide a place for short ideas to be described – in 200 words or less – for these ideas to be archived (courtesy of Zenodo), searchable and citable.
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I submitted the following: Build a molecular computer.
A visualisation for the Ackermann function here:

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In my opinion this is part of the exploration of new ways of communicate, do collaborative work and explore in the research world.
The article format is obsolete, even if put in digital form. More is needed, one of the ideas it to eventually arrive to run the article in the browser.
It is very encouraging to see that in only few days two excellent, different initiatives concerning new ways, new meanings of publication appeared, the Journal of Brief Ideas and PeerJ/paper-now.
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This new journal recalls me the proposal  of a Journal of very short papers.
The idea behind JVSP was to use the legacy format for journals in order to peer-review articles from OA repositories, like arXiv.
After writing that article I got replies, resulting in an update which I reproduce here:
”   Helger Lipmaa  points to the journal “Tiny ToCS“.  However, the real purpose of JVSP  is not to be brief, but to create a “subversive”, but with rigorous and solid results old-school like journal for promoting free open access.Another journal could be “The RXI Journal of Mathematics” which is as rigorous as any journal, only it asks to have at least 3 occurences of the string ‘rxi’ in the text.David Roberts discusses about fitting a paper into a refereed tweet. It is an interesting idea, some statements are too long, but some of them not. On the top of my head, here is one: “A Connected Lie Group Equals the Square of the Exponential Image, Michael Wüstner, Journal of Lie Theory. Volume 13 (2003) 307–309 Proof: http://emis.math.ca/journals/JLT/vol.13_no.1/wuestla2e.pdf “,  here is another which satisfies also the requirements of JVPS  “W is a monad, David Roberts, Theorem: W:sGrp(S)->sS lifts to a monad. Proof:http://arxiv.org/abs/1204.4886 “, which will  appeared in the New York Journal of Mathematics,   in  an open access journal.” [my comment: in a 10 pages long form which obsoletes arXiv:1204.4886] Interesting that the Twitter idea appears also.
But this is not about Twitter, nor about peer-reviews. It is a NEW idea.
The Journal of Brief Ideas makes the excellent proposal to attach DOI to ideas, in a short format (up to 200 words), but with enough place for using the power of the Net.
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Can’t resist to point also to the Journal of Uncalled Advices, will it appear some day?
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