Tag Archives: personal

500: a year review at chorasimilarity, first half

Personal post triggered by the coincidence of the year’s end and a round number of posts here: 500.

I started this year with high hopes about the project described in the article GLC actors, artificial chemical connectomes, topological issues and knots. Louis Kauffman wrote in the introduction some unbelievably nice words about graphic lambda calculus:

Even more generally, the movement between graphs and algebra is part of the larger picture of the relationship of logical and mathematical formalisms with networks and systems that was begun by Claude Shannon in his ground-breaking discovery of the relationship of Boolean algebra and switching networks.

We believe that our graphical formulation of lambda calculus is on a par with these discoveries of Shannon. We hope that the broad impact of this proposal will be a world-wide change in the actual practice of distributed computing. Implemented successfully, this proposal has a potential impact on a par with the internet itself.

But in June we got news that the project “Secure Distributed Computing with Graphic Lambda Calculus” will not be funded by NSF, see my comments in this post.  We got good reactions, from the reviewers, on the theoretical side (i.e. what is described in the GLC actors article), but fair critics on the IT part of the project. Another mistake was the branding of the project as oriented towards security.

I should have follow my initial plan, namely to start from the writing of simple tools, programs, which should also have some fun side, ideally, but which at least would allow to start the exploration of the formalism in much more detail than the what pen and papers allows. Instead of that, as concerns this project, there has been a waste of time from Jan to Jun, waiting for one puny source of funding before doing any programming work.

I parallel, a better trend appeared, one which I have not dreamed about two years ago: artificial life. During the summer of 2013 I thought it is worthy to try to get rid of a weakness of the graphic lambda calculus, namely that is has one global graph rewrite, called GLOBAL FAN-OUT. That’s why I wrote the Chemical concrete machine article, describing a purely local graph rewrite formalism which later was renamed  chemlambda. That was great, I even made an icon for it:

chemlambda4

which is made by two lambda symbols, one being up side down, to suggest that writing linear conventions are obsolete. The lambdas are  arranged into a DNA like double spiral, to suggest connections with life. (Of course that means I entered in the alife field, but everything about that was so fresh for me. Later I learned about Alchemy and other approaches, mixing either lambda calculus with alife, or rewriting systems with alife, but not both, and surely not the way is done in chemlambda, as abundantly documented in this blog)

Several (personal as well) novelties related to the article. One was that the article appeared on figshare too, not only on arXiv. This relates with another subject which I follow, namely what means of dissemination of research to use, seen that publishing academic articles is no longer enough, unless you want your work to be used only as a kind of fertilizer for future data mining projects.

More about this later.

The initial purpose of chemlambda was to be aimed at biologists, chemists, somewhere there, but apparently, with almost certainly, if a guy does computing then he will not do chemistry, or if he does chemistry then he has no idea about lambda calculus. I’m mean, there are exceptions, like to be part of an already existing team which do both, which I’m not. Anyway, so initially I hoped for interactons with biochemists (I still do, looking for that rare bird who would dare to lower himself to talk with a geometer from a non dominant country, motivated purely by the research content, and who would have the trivial idea to use his chemistry notions for something which is not in the scope of already existing projects).

With Louis Kauffman, we set out to write a kind of continuation of the GLC actors article, this time concentrated on chemlambda, as seen from our personal interests. The idea was to participate at the biggest event in the field, the ALIFE 14 conference. Which we did: Chemlambda, universality and self-multiplication.

Putting together the failure of the NSF project and the turn towards alife, is only natural that I set to write more explanations about the formalism, like this series  of 7  expository posts on chemlambda described with the help of g-patterns:

This was a bridge towards starting to write programs, that’s for later.

In parallel with other stuff, which I’ll explain in the second half.

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Where’s the ship? (lots of questions part II)

I explain in Lots of questions, part I how Plato and Brazil made me want to switch from math to biology.  Eventually it seems I ended in fundamentals of computing, but there is this strange phenomenon. I can’t figure it how it works, or why, or even if is widespread or rare. I think is widespread, but I don’t have clear evidence about it other than the old saying that people don’t change.

So Plato+Rio gives geometry+biology gives artificial chemistry+distributed computing.

Obvious.

I don’t get how this functions.

Makes no sense.

Now I have a hint that we are the computation,  we execute ourselves during our lifetime, our brains are just part of the seed, part of the program. We don’t really have billions of neurons and cells, everything is just the state of a computation.  Part of the seed is our genetic inheritance, other part of the seed is our geographical and more largely cultural inheritance. We are not separated from the external medium, there is no external medium, exactly like there is no me and the Net, only many actors interacting asynchonously and locally according to some protocols. In the case of real life the protocols are casted in   real molecules, at a finer scale only emerging phenomena of a much faster and wider computation going on, of a geometrical nature. But the principle is scale independent, that is how we manage space (perception and interaction) in our brains.

So we don’t change.

Take this blog, I make from time to time some counts. For the last 3 months gives this. There are 491 posts on chorasimilarity. In the last week 78 of them have been read, last month 219, last quarter 331. This series makes no sense unlese there are very long range relations between the posts, relations which are perceived by enough readers of this blog.

Oh, great!

Two mysteries. The first is that I have no idea why exactly there long time correlations arrive in my writing. The second mystery is why do you perceive them too.

So there is this strange phenomenon, which I can’t explain.

I remark though that there has to be something starts the new computation cycle, the new turn of spiral, the new chamber of the snail shell.

It is stimulation.

Last time was Plato and Rio.

I feel that I lack something in order to tell you more and for me to learn more in the absence of enough external stimuli.

I know I can build really new and also classical stuff, but I loose interest in time without stimuli. That is why I change every few years what I do. It is not rewarding for me to see that after I left a field somebody picks an idea and makes it stronger, it is not rewarding to see that I was right when nobody believed.  Maybe I just have a nose for good ideas which float in the air and I detect them before many others, but I don’t have the right spce and culture position to make them grow really big. You know, just an explorer who comes back home after a lonely expedition and tells you about blue seas and wide skies with strange constellations. Yeah, OK creep. But then, after some years the trend is to go to bath in those blue seas. And where is the creep? Just coming home, telling about that new jungle and the road from there to the clouds.

Stimulation. Trust. New worlds await. Need my ship, now.

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Lots of questions, part I

There is a button for “publish”. So what?

I started this open notebook  with the goal to disseminate some of my work and ideas.  There are always many subjects to write about, this open notebook has almost 500 posts. Lately the rhythm of about a post every 3 days slowed down to a post a week.  I have not run out of ideas, or opinions. It is only that I don’t get anything in return.

I explain what I mean by getting something in return. I don’t believe that one should expect a compensation for the time and energy converted into a post. There are always a million posts to read.  There is not a lot of time to read them. It is costly in brain time to understand them, and probably, from the point of view of the reader, the result of this investment does not worth the effort.

So it’s completely unreasonable to think that my posts should have any treatment out of the usual.

Then, what can be the motivation to have an open notebook, instead of just a notebook? Besides vanity, there is not much.

But vanity was not my motivation, although it feels very good to have a site like this one. Here is why:   from the hits I can see that people read old posts as frequently as new posts. You have to agree that this is highly unusual for a blog. So, incidentally,  perhaps this is not a blog, doh.

I put vanity aside and I am now closer to the real motivations for maintaining this open notebook.

Say you have a new idea, product, anything which behaves like a happy virus who’s looking for hosts to multiply. This is pretty much the problem of any creator: to find hosts.  OK, what is available for a creator who is not a behemoth selling sugar solutions or other BRILLIANT really simple viruses like phones, political ideas, contents for lazy thinking trolls and stuff like this?

What if I don’t want to sell ideas, but instead I want to find those rare people with similar interests?

I don’t want to entertain anybody, instead that’s a small fishing net in the big sea.

OK, this was the initial idea. That compared to the regular ways, meaning writing academic articles, going to conferences, etc, there might be more chances to talk with interesting people if I go fishing in the high seas, so to say.

These are my expectations. That I might find interesting people to work with, based on common passions, and to avoid the big latency of the academic world, so that we can do really fast really good things now.

I know that it helps a lot to write simple. To dilute the message. To appeal to authority, popularity, etc.

But I expect that there is a small number of you guys who really think as fast as I do. And then reply to me, simultaneously to Marius.Buliga@imar.ro and Marius.Buliga@gmail.com .

Now that my expectations are explained, let’s look at the results. I have to put things in context a bit.

This site was called initially lifeinrio@wordpress.com . I wanted to start a blog about how is it to live in Rio with wife and two small kids. Not a bad subject, but I have not found the time for that side project, because I was just in the middle of an epiphany. I wanted to switch fields, I wanted to move from pure and applied mathematics to somewhere as close as possible to biology and neuroscience. But mind you that I wanted also to bring with me the math. Not to make a show of it, but to use the state of mind of a mathematician in these great emerging fields. So, instead of writing about my everyday life experiences, I started to write to everybody I found on the Net who was not (apparently) averse to mathematics and who was also somebody in neuroscience. You can imagine that my choices were not very well informed, because these fields were so far from what I knew before. Nevertheless I have found out interesting people, telling them about why I want to switch. Yes, why? Because of the following  reasons: (1) I am passionate about making models of reality, (2) I’m really good at finding unexpected points of view, (3) I learn very fast, (4) I understood that pure or applied math needs a challenge beyond the Cold War ones (i.e. theories of everything, rocket science, engineering).  OK, I’ll stop here with the list, but there were about 100 more reasons, among them being to understand what space is from the point of the view of a brain.

I got fast into pretty weird stuff. I started to read philosophy, getting hooked by Plato. Not in the way the usual american thinker does. They believe that they are platonic but they are empiricists, which is exactly the poor (brain) version of platonism. I shall stop giving kicks to empiricists, because they have advanced science in many ways in the last century.  Anyway empiricism looks more and more like black magic these days. Btw, have you read anything by Plato? If you do, then try to go to the source. Look for several sources,  you are not a good reader of ancient Greek.  Take your time, compare versions, spell the originals (so to say), discover the usual phenomenon that more something is appreciated, more shit inside.

Wow, so here is it a mathematician who wants to move to biology, and he uses Plato as a vehicle. That’s perhaps remarkabl…y stupid to do, Marius. What happened, have you ran out of the capacity to do math? Are you out in the field where people go when they can’t stand no more the beauty and hardness of mathematics? Everybody knows, since that guy who wrote with Ramanujan and later, after R was dead, told us that mathematics is for young people. (And probably white wealthy ones.)

No, what happened was that the air of Rio gave me the guts I have lost during the education process. Plato’s Timaeus spoke to me in nontrivial ways, in particular. I have understood that I am really on the side of geometers, not on the side of language people. And that there is more chance to understand brains if we try to model what the language people assume it works by itself, the low level, non rational processes of the brain. Those who need no names, no language, those highly parallel ones. For those, I discovered, there was no math to apply.  You may say that for example vision is one of the most studied subjects and that really there is a lot of maths already used for that. But if you say so then you are wrong.  There is no model of vision up to now, which explains how biological vision works without falling into the internal or external homunculus fallacies. If you look to computer vision, you know, you can do anything with computers, provided you have enough of them and enough time. There is a huge gap between computer vision and biological vision, a fundamental one.

OK, when I returned home to Bucharest I thought what if I reuse the lifeinrio.wordpress.com and transform it into chorasimilarity.worpress.com? This word chorasimilarity is made of “chora”, which is the feminine version of “choros”, which means place or space. Plato invented the “chora” as a term he used in his writings. “Similarity” was because of my background in math: I was playing with “emergent algebras”, which I invented previously of going on the biology tangent. In fact these emergent algebras made me think first that it is needed a new math, and that maybe they are relevant for biological vision.

I stop a bit to point to the post Scale is a place in the brain, which is about research on grid cells and place cells (research which just got a Nobel in medicine in 2014).

Emergent algebras are about similarity. They make visible that behind is hidden an abstract graph rewrite system. Which in turn can be made concrete by transforming it into chemistry. An artificial chemistry.  But also, perhaps, a real one. Or, the brain is most of it chemistry. Do you see how everything gets in place?  Chora is just chemistry in the brain. Being universal, it is not surprising that we distilled, us humans, a notion of space from that.

There is a lot of infrastructure to build in order to link all these in a coherent way.

Varia: updates and preparations

Yesterday I found a bug in one of the programs for the chemlambda visualiser, namely an  unexpected functioning of the priority choice part when applied to a particular mol file (graph).

Today I took it methodically and found two bugs which create that behaviour. One was that the priority choice was not covering all the possibilities in a correct way, the other was a pure programming bug.

So I corrected everything and checked that on the examples from the gallery it works as expected, and also I checked it on many other examples which I have and it works well.

Of course, only to check a program on examples means nothing without a proof that the algorithm works well. I have done that, now the priority choice is indeed well implemented.

What is funny is that by trying to correct the priority choice part I have found the other stupid bug.

OK, so now all the new tar files are marked with 06_10_2014.

And anyway, as everything is open here, you may compare the versions and arrive to your own conclusions.

Mind that in a sense there is still a bug in the main_viral from the “play” archive:  it may happen that at some point the json file which is seen with look.html may be empty. This happens because in the “play” algorithm the loops are erased, and it is possible that a molecule reduces to a collection of loops, hence an empty json file eventually.

No problem with that, by using the “add_new” tar you have an algorithm which does not remove the loops (and also has the FOE node and its new moves). This one works perfectly now.

On a different subject: the artificialagora.wordpress.com  will launch soon. I don’t know yet if chorasimilarity and artificialagora will coexist, or if artificialagora will be the luxury version of chorasimilarity (hope not).

But soon enough we’ll see this.

Chorasimilarity site is still read in a strange way for a blog, because old posts receive comparable hits with new ones. Not all posts are good, for example posts as this one, where I indulge into telling about updates and preparations.

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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
http://marciovm.com/i-want-a-github-of-science
“- 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?

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The price of publishing with arXiv

This is a very personal post. It is emotionally triggered by looking at this old question  Downsides of using the arXiv and by reading the recent The coming Calculus MOOC Revolution and the end of math research.

What I think? That a more realistic reason for a possible end (read: shrinking) of math research comes from  thinking  that there are any downsides of using the arXiv. That there are any downsides of using an open peer review system. It comes from those who are moderately in favour of open research until they participate into a committee or until it comes to protecting their own little church from strange ideas.

And from others, an army of good but not especially creative researchers, a high mediocracy (high because selected, however) who will probably sink research for a time, because on the long term a lot of mediocre research results add to noise. But on the short term, this is a very good business: write many mediocre, correct articles, hide them behind a paywall and influence the research policy to favour the number (and not the content) of those.

What I think  is that will happen exactly like it happened with the academic painters, a while ago.

You know that I’m right.

Now, because the net is not subtle enough, in order to show you that indeed, these people are right from a social point of view, to say that there is a price for not behaving as they expect, indulge me to explain what was the price which I paid for using the arXiv as the principal means of publication.

The advantage: I had a lot of fun. I wrote articles which contain more than one idea, or which use more than one field of research. I wrote articles on subjects which genuinely interest me, or articles which contain more questions than answers. I wrote articles which were not especially designed to solve problems, but to open ones. I changed fields, once about 3-4 years.

The price: I was told that I don’t have enough published articles. I lost a lot of cites, either because the citation was incorrectly done, or because the databases (like ISI) don’t count well those (not that I care, really). Because I change fields (for those who know me, it’s clear that I don’t do this randomly, but because there are connections between fields) I seem to come from nowhere and go nowhere. Socially, and professionally, is very bad for the career to do what I did. Most of the articles I sent for publication (to legacy publishers) have spent incredible amounts of time there and most of the refusals were of the type “seems OK but maybe another journal” or “is OK but our journal …”. I am incredibly (i.e. the null hypothesis statistically incredible) unlucky to publish in legacy journals.

But, let me stress this, I survived. And I still have lots of ideas, better than before, and I’m using dissemination tools (like this blog) and I am still having a lot of fun.

So, it’s your choice: recall why you have started to do research, what dreams you had. I don’t believe you that you dreamed, as a kid, to write a lot of ISI papers about a lot of arcane problems of others, in order to attract grant financing from bureaucrats who count what is your social influence.

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