#occupy_scientific_journals

The main aim of this post is to propose a peer-review system on the ArXiv. We need a revolution in the scientific publication scheme.

1.- What is wrong?

Today I needed a scientific article for my research. My institution is not subscribed to the journal, but the publisher said “No problem, dude, just pay $33 and you can read the paper”. Seriously!?

Scientific publishing is a peculiar business model. Authors make no money from publication. Neither do referees. The typesetting of the articles is usually done by the authors themselves. Yet, the alleged cost per article is around $1.000-$10.000… Seriously!?

Work in fundamental science is usually paid by governmental funds, through taxes. And, even when the money comes from private hands, still their aim is to create knowledge and make it publicly available. But, as of now, the general public does not have free access to the results of the research they fund. Even professional scientists have frequent problems to obtain articles they need, thus making their research more difficult. This problem is getting worse with the economic crisis, and has always been a major issue in developing countries.

If authors do not make any money, why do they publish? For want of reputation and dissemination of their work. Funding agencies need some quality measurements in order to make decisions about which project to support. The accepted system, worldwide, is the number of publications and citations, and the prestige of the journals in which you publish. Journals are ranked by the JCR (journal citations report) index, which is itself… another private company (Thomson Reuters), which charges enormous amounts of money to universities and research institutes to pay for a faulty database.

Of course, some publishers are better than others. IOP and the DPG started New Journal of Physics, which is open. The problem is that publishing there is quite expensive. Other open journals can be found here.

2.- What do we want?

We want a cheap and open publication scheme. Most of the work is already done already by us.

We want a fair reputation system, which rewards high quality research, to serve as a guide for government agencies to direct their funding. And also as an internal guide to the relevant literature (too much to read, otherwise!)

3.- Ideas

The most promising point of departure is the ArXiv. It is free and open. It costs its maintainers (a board of worldwide research institutions) around $10 per article. Why not creating a peer-review system on the ArXiv? If authors so desire, they might ask for a “peer-review stamp” on their preprint. It wouldn’t be so difficult. A similar idea was already put forward by John Baez.

The peer-review process, as it stands today, is both too slow and too fast. It’s too slow because it takes months for a regular submission to see the light. By then, it is very often well known by the community, who had access to it through the ArXiv or otherwise. And it is also too fast because the referee process is not good enough to assess whether a paper will have impact or not. It takes time to know. So, why not making two “peer-review” processes? A quick-and-dirty one when the paper appears in the ArXiv. A second one, more detailed, after a few years, to evaluate its real importance.

Another nice idea would be to create an open discussion forum for each paper, where people might be able to make comments and ask questions. In the stack-exchange community style, reputation might be awarded for making questions and providing answers which the community approve. Of course, the forums need not be attached to papers only. The concept of paper as the “unit of research” may become outdated in such a structure. Papers were the natural medium for the exchange of information when the dead-tree technology was dominant… but, just like the mechanical loom, animal traction and congressmen, may be overthrown by history.

Qubism

Scientists tend to be very visual people. We love to understand through pictures. About one year ago, we had one of those ideas which remind you why it’s so fun to be a theoretical physicist… Simple and deep. The idea was about how to represent quantum many-body wavefunctions in pictures. Speaking very coarsely, the high complexity of the wavefunction maps into fractality of the final image.

So, more slowly. As you know, bit can take only two values: 0 and 1. A qubit is a quantum bit, which can be in any linear combination of 0 and 1, like Schrödinger’s cat, which we denote by and . In other terms: a qubit is represented by two complex numbers: . If you have two qubits, the basic states are four: 00, 01, 10 and 11, so we get

If you add one qubit, the number of parameters doubles. For N qubits, you need parameters in order to specify completely the state! The task of representing those values in a picture in a meaningful way seems hopeless… Our idea is to start with a square and divide it in four quadrants. Each quadrant will be filled with a color associated with the corresponding parameter.

What if we get a second pair of qubits? Then we move to “level-2″: we split each quadrant into four parts, again, and label them according to the values of the new qubits. We can go as deeply as we want. The thermodynamical limit corresponds to the continuum limit.

The full description of the algorithm is in this paper from arXiv, and we have launched a webpage to publish the source code to generate the qubistic images. So, the rest of this blog entry will be just a collection of pictures with some random comments…

This is the ground state of the Heisenberg hamiltonian for qubits. It is an antiferromagnetic system, which favours neighbouring qubits to be opposite (0-1 or 1-0). The main diagonal structures are linked to what we call a spin liquid.

These four pics correspond to the so-called half-filling Dicke states: systems in which half the qubits are 0 and the other half 1… but you do not know which are which! The four pics show the sequence as you increase the number of qubits: 8, 10, 12 and 14.

This one is the AKLT state for N=10 qu-trits (each can be in three states: -1, 0 or 1). It has some nice hidden order, known as the Haldane phase. The order shows itself quite nicely in its self-similarity.

This one is the Ising model in a transverse field undergoing a quantum phase transition… but the careful reader must have realized that it is not fitting in a square any more! Indeed, it is plotted using a different technique, mapping into triangles. Cute, ein?

But I have not mentioned its most amazing properties. The mysterious quantum entanglement can be visualized from the figures. This property of quantum systems is a strong form of correlation, much stronger than any classical system might achieve.

So, if you want to learn more, browse the paper or visit this webpage, although it is still under construction…

With warm acknowledgments to my coauthors: Piotr Midgał, Maciej Lewenstein (ICFO), Miguel I. Berganza and Germán Sierra (IFT), and also to Silvia N. Santalla and Daniel Peralta.

Neutrino jokes (and more)

To be honest, I do not expect much from all this neutrino fuss. I bet that, when the dust settles down, c will remain majestic in her velocity throne and forgive magnanimously our misgivings. Why? OK, first, because superluminal neutrinos would produce a vast amount of electron-positron pairs in their way (see this paper by Cohen and Glashow), which has never been observed.  But, more importantly, because, as Alvaro de Rújula once said, “You must bet so that losing becomes the most intersting option”. That’s what xkcd said, using different words:

But, in any case, the best offspin from this story are few nice neutrino jokes that have come to stay among us:

MY ALL-TIME TOP SIX NEUTRINO JOKES

• A neutrino. “Who’s there?” Knock-knock!
• The bar-tender: “We don’t serve tachyons in here”. A neutrino comes into a bar.
• A neutrino and a photon come into a bar. For the next 60 nanoseconds, the neutrino complains about how dark it is.
• What does a neutrino do in an optical fiber? Honk the photons!
• A neutrino boyfriend: interacts weakly, goes through you without you noticing and ends before you even started.
• To reach the other side. Why did the neutrino cross the road?

And, profiting from the physics-jokes-revival, here you have two other physics jokes I didn’t know:

- Researchers from INFN have found traces of the elusive Berluschino, the supersymmetric partner of Berlusconi. As opposed to the original, it’s tall, honest and believes in democracy. Unfortunately, it is extremely short-lived in the current Italian political environment.

- Schrödinger’s cat comes into a bar. And doesn’t.

BONUS. I just invented three out of all those jokes. Can you tell which?

Hey, what’s that!?

Hey, long time without posting. Hope this will change drastically in the near future. In the meantime… can anybody tell me what’s that!? :)

Mάθησις, Mathesis

Today I would like to make a proposal: Mathesis, a dependency road map for science.

Consider that you’re a student or researcher in science trying to learn a new topic. This topic is explained in a paper, or a book, but it is not accessible to you because there are some pre-requisites that you’ve not covered. Of course, the bibliography of the paper or book can help you, but normally they are not so useful. How to trace it back to the point where you should start reading? And what if you need to take it at several different starting points, converging in the paper that you need?

Precisely because of that, we scientists write books and review articles. But textbooks are linear structures, while knowledge is not. A textbook takes you from point A to B, along a certain excursion path. But, more likely than not, only part of it is relevant to your needs. Hopefully, you can reach your desired knowledge by linking paths taken from different books or papers.

This is the very ambitious target of mathesis: a dependency tree for learning science. This means, to create a graph whose nodes are (small) pieces of knowledge, and whose links are the dependency relations among them. Thus, if you want to learn X, then you proceed to find the node for X. Its outcoming arrows denote on which pieces of knowledge it depends. Then you can trace them back, until you find which nodes correspond to your current knowledge and proceed from them backwards.

Each node need not contain a full explanation of the topic. That would imply to build a full encyclopaedia of science, which is a meta-ambitious target. No, it should  contain some good bibliography, taking into account the dependency structure. Of course, it is much better if this bibliography is free.

This idea resembles a lot the debian repository dependency network, and an attempt to implement it for knowledge has already been done.

So, this is a call for collaboration. We need:

• Examples. You can try to create the dependency tree for your favourite result. Or the dependency tree in order to understand one of your papers.
• A standard format for the nodes. They should contain, at least, a brief description, and a list of the nodes on which it depends. The nodes might be weighted, with a low number meaning that only the general idea is required and 1 that the topic should be mastered. And, of course, some bibliography.
• A nice visualization tool, in order to view parts of the total tree which are relevant to you. Maybe, in java.

This stems from an idea that I had long back, in 2004. I created project Euler, in Spanish, with the full text of my classes of maths in high school, with a dependency tree associated. And I still like the logo I prepared at that time… :)

P.S.: And out of the topic… guess some nice properties of the logo figure? ;)

Rough is beautiful (sometimes)

No posts for three weeks… you know, we’ve been revolting in Spain, and there are times in which one has to care for politics. But physics is a jealous lover… :)

So, we have published a paper on kinetic roughening. What does it mean? OK, imagine that, while your mind is roaming through some the intricacies of a physics problem, the corner of your napkin falls into your coffee cup. You see how the liquid climbs up, and the interface which separates the dry and wet parts of the napkin becomes rough. Other examples: surface gowth, biological growth (also tumors), ice growing on your window, a forest fire propagating… Rough interfaces appear in many different contexts.

We have developed a model for those phenomena, and simulated it on a computer. Basically, the interface at any point is a curve. It grows always in the normal direction, and the growth rate is random. The growth, also, is faster in the concavities, and slower in the convex regions. After a while, the interfaces develop fractal morphology. I will show you a couple of videos, one in which the interface starts out flat, and another one in which it starts as a circle. The first looks more like the flames of hell, the second more like a tumor.

The fractal properties of those interfaces are very interesting… but also a bit hard to explain, so I promise to come back to them in a (near) future.

The work has been done with Silvia Santalla and Rodolfo Cuerno, from Universidad Carlos III de Madrid. Silvia has presented it at FisEs’11, in Barcelona, a couple of hours ago, so I got permission at last to upload the videos… ;) The paper is published in JSTAT and the ArXiv (free to read).

Who needs doors, when I can tunnel?

Tunneling is one of the mysterious features of quantum mechanics, but there is a very nice way to visualize it. There is a simulation method in order to obtain the ground state of quantum systems, called path integral Monte Carlo. It is based, as its name suggests, on Feynman’s path integral approach to quantum mechanics, but I will not go deeper in that… The idea is the following: a particle becomes a set of many, many copies, beads or replicas. Which one is the real particle? All of them, and none. Then, link them all, each one to the next, with a spring whose natural length is zero, and with a spring constant which increases with the mass. Now, put all the system in a “fake temperature”, which depends on … and that’s all! Simulate that, just using Monte Carlo, and the equilibrium distribution that you obtain is the ground state of the quantum system.

In the simulation, the potential is represented with the background colors: blue is low, orange is high. So, you see the potential consists of many minima, the central one is deeper. In fact, the energy of the particle is not enough to jump over the barriers… but it does not matter now. The “ring polymer” can jump, even if a classical particle can’t. The height of the barrier is not a huge problem if it is thin, because in that case the “spring” can stretch, and make one of the beads jump over it! That’s the tunneling, indeed.

So, what you’re observing in that video is the quantum cloud. In fact, each ring polymer represents a possible history for the particle, returning to the initial point.  Each bead corresponds to the position of the particle at a certain instant, and the energy in the springs corresponds to… the kinetic energy, which will not be zero because of the uncertainty principle.

If you need more explanations (I would!), read qfluct…

Let me count the ways…

Alice was so bored, waiting for a message from Bob, that she started to play with the five white rabbits she had got from the Queen of Hearts. She tried to figure out in how many ways she could split her rabbits in groups, like 5 = 4+1 = 3+2 = 3+1+1 = 2+2+1 = 2+1+1+1 = 1+1+1+1+1, so, for 5 rabbits, 7 ways.

She decided to count the partitions in which no group contained more than 3 rabbits… in our example, there are 5. And then, she counted the partitions with no more than 3 groups. Amazingly, although the groups were not the same, the two numbers coincided, also 5.

Alice wondered… She wonders all the time (why?). Is that a coincidence?

One plus one plus one plus one...

Quantum dreams

Quantum mechanics, the dreams stuff is made of… (David Moser)

A quantum particle, prisoner in a square box of infinite walls, starts out with minimal energy, which grows and grows, slowly… although, no matter how much energy it gathers, no matter it grows quadratically… it will never escape…

You can also see it as the vibrational modes of a square drum. It looks continuous because I interpolated between them for a smoother visualization…

π=80

A few unrelated questions around π…

• Why is it true that  π=80?
• Why on Earth did we define π as we did, instead of giving a nice symbol to 2π? Life would be much easier… So many less factors 2 in our books… A quadrant would be just  π/4, not the nonsensical π/2… Can you see any notational advantage? Read this for more info.
• Do you recognize this sequence: 3, 7, 15, 1, 292, 1, 1, 1, 2, 1, 3, 1, 14, 2, 1, 1, 2, 2, 2, 2, …?
• Why should I have posted this yesterday?

OK, let’s keep it short. And thanks to S.N. Santalla…

Update (March 17) My birthday date appears at position 45,260,128 of π, not counting the initial 3. When was I born? ;) Hint. (Via Pepe Aranda) Moreover: possession of all digits of π makes you infringe all known copyright laws… Do you know why?