A quantum of science

In physics we do things and afterwards worry about whether they worked

Category Archives: General

The Open Science Unjournal

I haven’t been posting for a while – I do apologize. I have been quite busy but I do have quite a few drafts that need to be finished and posted and I intend to do that as soon as I can.

For now, however, I would like to heartily support the Open Science unjournal. It is an initiative to rid scientific publishing of some of its biggest problems, such as the commercialisation (fees), loss of copyright by the author etc. I would urge anyone to whom this is relevant to become involved, it really IS something that needs to be enocuraged. I don’t think I can do any better at explaining the details than Jan Jensen in his post on Molecular Modelling Basics, so I am reblogging his post below:

What is an unjournal?
An unjournal is to journals what an unconference is to conferences.  To define what an unjournal is, take the first 2 sentences in the wikipedia entry on unconferences and substitute a few words:  “An unjournal is a facilitated, participant-driven journal centered on a theme or purpose. The term “unjournal” has been applied, or self-applied, to a wide range of publications that try to avoid one or more aspects of a conventional publishing, such as loss of copyright, high fees, [list your favorite pet-publishing-peeve here].”

Here are some frequently asked questions (FAQs) about Open Science:

How do I publish in Open Science?
The usual way is to deposit your manuscript on openscienceunjournal.org.  Once you have completed the submission process the paper is given a time and date stamp and the paper is published and open for review (see next question).  While there is a recommended template available for the paper, there is no fixed formatIt is possible to upload all your raw data or link to the data if it is hosted elsewhere.  Experience has shown that this tends to increase the scores (see below) of your papers significantly.

You can also choose to publish the paper on any of the unjournal sites whose contents are linked to openscienceunjournal.org.  These sites are often run by established publishers and offer more user-friendly interfaces, but may require a fee and may ask you to give up your copyright (though the content is open access by definition).

Is Open Science peer reviewed?
For a publication in an unjournal such as Open Science the question should be: is my article in Open Science peer reviewed?  That is in large part up to you.  The paper is open for online, non-anonymous, and completely transparent review and you have 2 months in which you can change the content of the article in response to the comments.  After the 2 month period you cannot change the content, but you can of course respond to new comments online.  For very serious criticisms you may want published a new Open Science article to respond.

It is up to you to solicit reviews, though any published author of a peer-reviewed paper (defined below) can review your paper during the 2 months review process.  Based on our experience only well-written and well-presented articles on scientifically interesting questions get reviewed.

An Open Science article is neither rejected nor accepted at the end of the review process.  Instead it receives an initial score (see next FAQ).  Obviously, any paper that does not generate a single review (or is reviewed but gets an initial score of 0) is not considered peer reviewed.

What is the impact factor of Open Science?
For a publication in an unjournal such as Open Science the question should be: what is the impact factor of my article in Open Science?  During the 2 months review process each reviewer gives the paper a score between 5 (good) and 0 (bad).  This score can be adjusted by the reviewers based on the changes you make within the first 2 months, after that it is fixed. The initial score for your paper is the average of all reviewers final scores.

If the paper is cited it receives an additional score (called the current score).  The score is determined by the number of citations, and if the citing paper is published in Open Science, the score is weighted by the initial and current score of that paper.  The authors of that paper can also choose to indicate how important your paper was to theirs.  If high scoring papers cite your paper in a positive manner, the current score of your paper increases. Self-citations are not included.

Why should I review for Open Science?
The work you put into reviewing is now documented for all to see.  Have you contributed greatly to science by identifying Open Science papers with high current scores?  Do the reviews you submit carry more weight with the author and other reviewers as a result?  Some sites now list Open Science reviewers with particularly high impact as a kind of editorial board for the journal.

How should I cite an Open Science paper?
One suggestion is: Author(s), Title, Open Science, date of submission, initial/current score.  If you publish in Open Science using the suggested template, the current score is updated automatically.

Why should I publish in Open Science?
There are many reasons:
(1) You retain the copyright and anyone can see the paper.
(2) Your paper is accessible upon submission. (Don’t rush to publish though: you only have 2 months to get a good initial score).
(3) The impact of your paper is evident in the citation, but disconnected from the conventional impact factor of the journal you managed to get it in to.  The initial score of your paper can help the paper off to a good start, but your truly important papers will ultimately be identified by its current score.
(4) You choose the publishing format you like.  What’s your pleasure? machine readable? interactive figures? link to raw data?
(5) Your paper is a living document: comments or questions continue to roll in on important papers and you can update links to your papers (related articles, a new data format) as you see fit.
(6) If you write a good paper, you will get more reviews (i.e. more suggestions and input) but the rantings of a single idiot reviewer will not prevent publication.  Isn’t this the place to publish daring and ground-breaking work?

So what brought this on?
The blogosphere: Egon Willighagen’s latest post got me thinking about this particular idea, but the general problems it is trying to address was brought to my attention by many other blogs such as Michael Nielsen‘s The Future of Science and Is Scientific Publishing About to be Disrupted? posts; most posts by Peter Murray-Rust; Henry Rzepa‘s long fight to include interactive figures in conventional journals; Mat Todd‘s excitement for an unconference and the discussion it generated at Derek Lowe’s blog.  Why can’t we have this in a journal?

Is the Open Science unjournal a good idea?
The blogosphere will decide: no comments on, and no re-blogging of, this post will mean this idea dies a quiet death (by receiving an initial and current score of 0).  But if you get enough smart people fired up about an important idea that can be solved by IT, good things can happen.

Carbon is this year’s theme: Nobel Prize in Chemistry

Congratulations to Richard F. Heck, Ei-iechi Negishi and Akira Suzuki who were awarded this year’s Nobel Prize in Chemistry for “palladium catalysed cross couplings in organic synthesis”. It is a very well deserved prize: one of today’s articles mentioned that about 25% of all reactions in pharmaceutics uses the methods developed by the three professors, and with that in mind it is a surprise that they they did not receive the award earlier.

As has already been pointed out elsewhere, carbon seems to be the theme of this year’s Nobel Prizes, in science at least, given the graphene Physics Prize (see the post below) and today’s prize on carbon bonding. It is a testimony, I think, to the growing important of the emerging interdisciplinary field of Materials Science 🙂

For those interested in learning more about Heck, Negishi and Suzuki’s work, I would point to the Swedish Academy’s Scientific Background document for the prize (the link is directly to a reasonably-sized pdf file). If you are interested in theoretical approaches to the problem, I would suggest that you visit this article by Ross H. McKenzie who has found a study of the problem using DFT.

Nobel Prize in Physics 2010

Congratulations to Andre Geim and Konstantin Novoselov who received today’s Nobel Prize in Physics for their work on graphene.

Graphene, as some of you will no doubt know, has been a “hot” research topic since 2004 with an astonishing number of potential applications; however, how much of this potential is actually realized is to be seen, as Joerg Heber argues in his post Great, the physics Nobel prize for graphene! Now don’t overhype it… .

For those wishing to find out more, I recommend the post on Backreaction which contains some excellent links.

Finally, I would also like to congratulate the exceptionally well deserved yesterday’s Nobel Prize in Medicine laureate, Robert Edwards.

QuantumFIRE alpha

QuantumFIRE alpha is a research project that invites the public to donate computing power for scientific research in Quantum Foundations and Solid State Physics. The initiative comes from Cambridge University research groups I believe (though I may be wrong on this one!). It is easy to participate: you just download and run a free program on your computer – see here.

Needless to say, I encourage everyone to take part in this initiative, if you can. I certainly will.


Ginzburg’s important problems in Physics

In 1900, David Hilbert published his list of 24 problems that he believed would be part of the development of mathematics in 20th century – and so they were! The closest we come to a 21st century analogue of these are the Clay Institute Millenium Prizes, and Steve Smale’s problems (though these have not, sadly, become as widely known as the others). Certainly anyone involved in mathematics research is aware of most, if not all of these problems.

Until today, the only physics counterpart to these that I was aware of was Wikipedia’s List of unsolved problems in physics – which is reasonably comprehensive and has drawn my attention to some interesting unexplained phenomena in CMP (ever heard of sonoluminescence?). However, just now I’ve come across a list by a Russian physicist Vitaly L. Ginzburg. It’s a list of thirty problems that Ginzburg thinks every physicist should know about.

As far as I know, the list first appeared in his 2003 Nobel Lecture. The paper may be found here, but I’ll reproduce the list below anyway:

  1. Controlled nuclear fusion
  2. High-temperature and room temperature superconductivity.
  3. Metallic hydroge. Other exotic substances.
  4. Two-dimensional electron liquid (the anomalous Hall effect and other effects).
  5. Some questions of solid-state physics (heterostructures in semiconductors, quantum wells and dots, metal-dielectric transitions, charge- and spind-density waves, mesoscopics).
  6. Second-order and related phase transitions. Some examples of such transtitions. Cooling, in particular laser cooling, to superlow temperatures. Bose-Einstein condensation in gases.
  7. Surface physics. Clusters.
  8. Liquid crystals. Ferroelectrics. Ferrotorics.
  9. Fullerenes. Nanotubes.
  10. The bahaviour of matter in superstrong magnetic fields.
  11. Nonlinear physics. Turbulence. Solitons. Chaos. Strange attractors.
  12. X-ray lasers, gamma-ray lasers, superhigh-power lasers.
  13. Superheavy elements. Exotic nuclei.
  14. Mass specturm. Quars and gluons. Quantum chromodynamics. Quark-gluon plasma.
  15. Unified theory of weak and electromagnetic interactions.W^{\pm}  and Z^0 bosons. Leptons.
  16. Standard model. Grand unification. Superunification. Proton decay. Neutrino mass. Magnetic monopoles.
  17. Fundamental length. Particle interaction at high and superhigh energies. Colliders.
  18. Non-conservation of CP invariance.
  19. Nonliear phenomena in vacuum and in superstrong magnetic fields. Phase transitions in a vacuum.
  20. Strings. M-theory.
  21. Experimental verification of the general theory of relativity. [You might like to take a look at this.]
  22. Gravitational wanes and their detection.
  23. The cosmological problem. Inflation. The \Lambda term and quintessence. Relationship between cosmologyand high-energy physics.
  24. Neutron starts and pulsars. Supernova stars.
  25. Black holes. Cosmic strings (?).
  26. Quasars and galactic nuclei. Formation of galaxies.
  27. The problem of dark matter (hidden mass) and its detection.
  28. The origin of superhigh-energy cosmic rays.
  29. Gamma-ray bursts. Hypernovae.
  30. Neutrino physics and astronomy. Neutrino oscillations.

Ginzburg also says that:

It should be added that three “great problems” of modern physics are also to be included in the “physics minimum,” included in the sense that they should be singled out in some way and specially discussed, and their development should be reviewed. This is discussed at some length in the book About Science, Myself, and Others (Ginzburg, 2003). The “great problems” are, first, the increase in entropy, time irreversibility, and the “time arrow.” Second is the problem of interpretation of nonrelativistic quantum mechanics and the possibility of learning something new even in the field of its applicability. I personally doubt this possibility but believe that one’s eyes should remain open. And third is the question of the emergence of life, i.e., the feasibility of explaining the origin of life and thought on the basis of physics alone. On the face of it, how could it be otherwise? But until the questions are elucidated, one cannot be quite sure of anything. I think that the problem of the origin of life will unreservedly be solved only after “life in a test-tube” is created. Until then, this will be an open question.

Ginzburg sadly passed away on November 8th, 2009. Among his achievements are a partially phenomenological theory of superconductivity, the Ginzburg-Landau theory, developed with Landau in 1950; the theory of electromagnetic wave propagation in plasmas (for example, in the ionosphere); and a theory of the origin of cosmic radiation. He was beyond a doubt a great physicst, and maybe one day his list will be counted among his greatest achievements. It might steer the progress of physics in the coming years -we’ll see.

Finally this last quote from Ginzburg’s paper:

One more concluding remark. In the past century, and even nowadays, one could encounter the opinion that in physics nearly everything had been done. There allegedly are only dim “cloudlets” in the sky or theory, which will soon be eliminated to give rise to the “theory of everything.” I consider these views as some kind of blindness. The entire history of physics, as well as the state of present-day physics and, in particular, astrophysics, testifies to the opposite. In my view we are facing a boundless sea of unresolved problems.
It only remains for me to envy the younger members of the audience, who will witness a great many new, important, and interesting things.

LaTeX2WP

I’ve come across this piece of software by Luca Trevisan which makes it possible to convert LaTeX documents to put them up on wordpress painlessly, without going through the rigmarole of using JavaScript. It is available at http://lucatrevisan.wordpress.com/latex-to-wordpress/download/. It’ll make the more technical posts a lot easier to write, for sure.

Nicola Cabibbo

I would like to pay tribute to the great physicist, Nicola Cabibbo who died on Monday at the age of 75.

Nicola Cabibbo

He was mainly known for his work on weak interactions. He explained why the transitions between up and down quarks, electrons and electron neutrinos, muons and muon neutrinos had similar quantum amplitudes by postulating weak universality. He also explained why transitions with a change in strangeness had about a quarter the amplitude of those with no change in strangeness through the mixing angle (also called Cabibbo angle).