John Baez’ Applied Category Theory 2019 post uses my animation without attribution [updated]

The post, dated Oct 2, appears at John Baez Azimuth blog. Here is what I see today Oct 4th:

baez_s

UPDATE: now there is a link to the chemlambda repository, but see also the comments, there and here. The real problem is related to the attitude concerning  Open Science. Link to archived post.

This is the gif which illustrates the chemlambda github repository.

The original animation appeared for the first time in the chemlambda collection post Metabolism as failed replication. The later post (Sept 2016) contains more about this idea and useful links.

[ UPDATE: Recently, I deleted the chemlambda collection. The content of it will become public again in a new form. Meanwhile mail me for access. However, the github repo, libraries, demos and articles are public.]

The chemlambda molecule which is used is available at the chemlambda library of molecules, as tape_long_4653_2.mol . You can download the simulation itself (which was used to make the animation) from the Chemlambda collection of simulations at Figshare, the file tape_long_4653_2.js.

The last time when one of my animations was used withot attribution, the situations was quickly solved.  I explained then that the chemlambda project is an Open Science project and that correct attribution is what is fair to do.

Now, I would expect from an academic researcher more.

Anyway, again the magic of chemlambda strikes. Let me tell you what the animation is really about. Metabolism and replication are two fundamental ingredients of life. Which came first? Are these independent?  I prepared the molecule and experimented with it to show that (in the artificial toy chemistry chemlambda) metabolism and replication may be related, in the sense that metabolism may appear as failed replication.

The molecule in question is a “tape”, topologically the same as a DNA loop. On the tape there is a very small part which triggers the duplication of the tape molecule. The duplication works perfectly, there are several examples in the chemlambda collection. But this time I took a tape which duplicates without problems and I modified it in a single place. The result is a failed duplication which is spectacular in the sense that the tape molecule produces a number of disconnected graphs (i.e. other molecules), some of them are quines.

 

 

 

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4 thoughts on “John Baez’ Applied Category Theory 2019 post uses my animation without attribution [updated]”

    1. The real problem concerns the bias against Open Science (like some years ago when yo could encounter references in articles with the form “Jane Doe, preprint” instead of arXiv:1234.56789). I reproduce here a comment left at Baez’ post, after his correction which proves my point even stronger:
      “Dear John, two points:
      (1) the correct reference is to the chemlambda project page https://github.com/chorasimilarity/chemlambda-gui/blob/gh-pages/dynamic/README.md (which gives to anybody the means to reproduce the simulation), the name of the molecule or even the place where is it available https://github.com/chorasimilarity/chemlambda-gui/blob/gh-pages/dynamic/mol/tape_long_4653_2.mol and the place where the simulation used for the animation is available https://doi.org/10.6084/m9.figshare.4747390.v1
      (2) this situation shows problems of Open Science. Indeed the chemlambda project was pursued as OS on purpose. The idea is that OS satisfies greater rigorousness criteria than previously. Instead of peer review, there is the possibility of independent validation by the reader. There are other problems which are not related to the situation at hand (like where and how can be published an article like Molecular computers http://chorasimilarity.github.io/chemlambda-gui/dynamic/molecular.html or how to handle the situation when a lazy reviewer does not use the means of validation provided by the author and instead emits an impressionistic opinion, like “not interesting for this journal”, or “how is this different than _other_article?”). But in this situation is a clear bias against OS.

      Suppose that I use lemma 1.2 from yor article J. Baez, Article about blabla, Journal of Whatever 3(4) 2014. I copy-paste it and I put it in my article without any attribution. You would be completely annoyed by this and you write a note about this. As a response I add to the lemma the text (lemma by John Baez) and no reference to the article. Or suppose I use a pretty picture obtained from a real biology experiment, without exact attribution.
      The comparison is not crazy, because there is no difference between a (program, it’s execution) and a (lemma, proof). In this case the initial and final molecules are the lemma and the execution according to the chemlambda so-called “stupid” algorithm is an (automated) proof.”

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