All posts by chorasimilarity

can do anything

Euclideon Holoverse virtual reality games revealed

Congratulations! Via a comment by roy.  If there is any other news you have then you’re welcome here, as in the old days.

Bruce Dell has a way to speak, to choose colors and music which is his own. Nevertheless, to share the key speaker honor with Steve Wozniak is just great.



It rubs me a bit in the wrong direction when he says that he has the “world first new virtual lifeforms” at 7:30. Can they replicate? Do they have a metabolism? On their own, in random conditions?

If I sneeze in a Holoverse room, will they cough the next day? If they run into me, shall I dream new ideas about bruises later?


A library of chemlambda molecules

More than 400 molecules are now  available at the the github repository for chemlambda, at this link. Many of them have been used to produce the animations from the chemlambda collection at google+.

There are more than 200 animations in that collection, which attracted an average stream of 150000 views/day and more than 30000 followers. I am proud about that because the subject is rather hard and almost all posts contain original research animations.

If you want to identify the mol file (i.e. the molecule) which has been used to create a certain animation, then follow the  path:

  • click on the animation, you’ll be presented with a page where the animated gif runs
  • try to save the gif, you’ll see a name.gif
  • in another window go to the library of molecules and look for name.mol.

In most of the cases this works, but there might be rare cases where I forgot to preserve the correspondence between name.gif and name.mol.

During the time these animations have been produced, I used various versions of the scripts (all available at the repository). They should be all compatible, but it is possible that some mol files will not work as input for the scripts. If this happens, then it is because I used, mistakenly, a port variable in a bad place and then I forgot to delete the faulty version. Please excuse me for that, in case it happens (maybe, maybe 4 or 5 mol files from the about 440 are like this).

To see how to use the repository please go to the file.

It is important to understand how I made the animations.

  • you need a linux or a mac, because the scripts are in shell or awk
  • I used a mac. I went to the folder where the scripts and the mol files are (so if you copy the mol files from the library, then copy  them in the same folder as the folder called “dynamic”, before you use the scripts). In a terminal window I typed, for example “bash”. A list of all the mol files in that folder appear.
  • I type the complete name.mol and hit enter
  • then the main script does the magic and I obtain name.html
  • mind that the parameters for the computation are in the most important part, the script quiner_shuffle.awk (and is just a wrapper of this, same for all the pairs of scripts .sh and .awk)
  • I used a browser to see name.html. Important: Safari works the best, by far, then Chrome. Firefox sucks for very obscure reasons. There is a solution for making the name.html to work on Firefox as well, is to find in the quiner_shuffle.awk the line “time_val=4; ” and to modify it into something like “time_val=120; “, for example. This variable controls the speed of the javascript animation, bigger is it, slower the animation.
  • You’ll see that the d3.js animation can take, depending on the molecule (and on the number of steps given by this line “cycounter=10000;” in quiner_shuffle.awk), from minutes to hours.
  • I made a screen capture of the animation and then I sped it, for example with ffmpeg.


If you make nice stuff with it, then tell me and I’ll be glad to host your creation here and in the chemlambda collection.

Tay has been retired, Blade Runner style

It is always unexpected when fiction becomes real. Tay, the adolescent AI, survived for about 24 hrs on Twitter. She turned into something socially unacceptable. Then she has been retired. See Gizmodo story.

Almost two years ago I posted Microbes take over and then destroy the HAL 9000 prototype. I gave 9 seconds as an estimate for the chance of life of an AI in the real world, where there is no control and faced with  the “extremely dynamic medium of decentralized, artificial life based computation we all use every day“(that post suggests an artificial life, not AI version of the future internet).

Now, the story of Tay seems unbelievably close to the Blade Runner world. The genius of Philip K. Dick manifests here because  he mixes AI with synthetic life with real life.

Real people socially hacked Tay. Virtual microbes destroy HAL 9000. The common themes are: in a decentralized environment and AI vs life (real or virtual).

Not many people understand that today obsessions with security, control, privacy are all lost battles.

Which side you take: ASAPbio or Alphabet?

Times are changing fast and old time thinking dies hard and ugly. We have winners and losers.

Winners side: the #ASAPbio hashtag signals that biologists are ready to adopt the arXiv model of research communication.

“On Feb. 29, Carol Greider of Johns Hopkins University became the third Nobel Prize laureate biologist in a month to do something long considered taboo among biomedical researchers: She posted a report of her recent discoveries to a publicly accessible website, bioRxiv, before submitting it to a scholarly journal to review for “official’’ publication.” [source: NYTimes]

OK, many people are still confused about “preprints”, mainly because the fake open movement Gold OA enshrined this distinction preprint-postprint into the brains of honest researchers looking for Internet Age ways of communication. The goal was, without doubt, to throw a shade over the well known arXiv model (which used the name “eprints” before Gold OA was a thing). And to preserve for a while longer the obsolete print business (as witnessed by their immediate association with the legacy publishers against Sci-Hub). But now, with bioRxiv, there seems to be a historical shift.

Biologists are already leaders into imagining ways to share and validate big volumes of data. They are certainly aware that sharing all data, aka Open Science, is a necessary part of the scientific method.

The scientific publishing industry, a largely useless business in the Internet Age, is the only loser in this story.

Losers side: Alphabet, the mother company of Google, sells Boston Dynamics. To be clear, BD is one of those research groups who does real impact, hard research. According to Bloomberg:

“Executives at Google parent Alphabet Inc., absorbed with making sure all the various companies under its corporate umbrella have plans to generate real revenue, concluded that Boston Dynamics isn’t likely to produce a marketable product in the next few years and have put the unit up for sale, according to two people familiar with the company’s plans.”

I am sure that there are all sort of reasons for this move. Short term reasons.

Why is this important, for researchers: because it shows that it is time to seriously acknowledge that, technically:

  • we need more data and access to research data, not more filters and bottlenecks in the way of research communication
  • and research data on the Internet is a particular kind of big data. Not even very big compared with the really big data collected, archived and used today by big commercial companies. It is technically possible to manage it by those who are the most interested, the researchers. This is not a new idea. Besides arXiv, and now bioRxiv,  see for example Bjorn Brembs  calls for a modern scientifc infrastructure.
  • Big commercial companies are not reliable for that. At any point they might dump us. Social media venues for research news and discussions are great, but the infrastructure is not to be trusted when it comes to the management of research data.



Let’s discuss the 3 Sci-Hub ideas

The site has a part called “Sci-Hub ideas”. I have not seen any discussion about this in the commercial social networks, where almost everybody is a lawyer, apparently.
What if we look at these ideas, a bit more?

Screenshot from 2016-02-28 01:23:34


Further are my opinions about those:

1. Knowledge to all. I totally support this idea. That is why I always supported Green OA and not Gold OA. Open Science, which is a far more general and future oriented concept than OA, proposes the same, because the only scientific knowledge is the one which can be independently validated. This is not possible if there are walls around knowledge.

A more sensible point is the “inequality in knowledge access across the world”. This inequality has to be recognized as such and we should fight it.

2. No copyright for scientific and educational resources. It is very convenient to forget that the copyright has been a barrier for progress, several times in the past. Aviation and PC hardware are two examples. Some people understand that: “All our Patents are Belong to You”.

3. Open access. The most puzzling reaction against Sci-Hub, at least for me, was the one coming from some of the proponents of OA. I agree that Sci-Hub is not a solution for OA publishing of new articles. It is not a OA publishing model. OK. But OA itself is a very murky thing. Is OA? According to many OA advocates, it is not, is only an open repository. However, was a real solution for publishing, i.e. fast dissemination of knowledge. People used (and they use it now as well) in order to learn and communicate, via scientific articles, open and fast. There was no publishing revolution, just people using a better system than what the legacy publishers proposed. Likewise, Sci-Hub responded to a big need of many researchers, as witnessed by the fact that the site is heavily used. I think the support of Sci-Hub for OA is only lip service, what they really want to say is that they created a solution for a real problem which is not solved by OA.

SciHub and patent wars

The Wright brothers used their patents to block the building of new airplanes. The historical solution was a pool of patents, eventually. Now everybody can fly.

We all have and use PCs because the patent wars around computer hardware were lost by those who tried to limit the production of it.

Elon Musk announced in 2014 that All Our Patent Are Belong To You.

These days publishers  complain that SciHub  breaks their paywalls. They have the copyrights for the  research works which are publicly funded mostly.

This is a new version of a patent war and I believe it will end as others in the past.