22 January, 2009

Things I don't like in Mathematica. Part II: A writing tool.

Here is what I think about writing in Mathematica. For quite a long time I thought that Mathematica can be used for nothing else but calculations. Later I came across a post of Terry Tao "Write professionally", where (among other good things) he states:

"The standard format for mathematical papers is TeX, AMS-TeX, LaTeX, or AMS-LaTeX; other formats such as Word or Mathematica can cause technical difficulties (and will ultimately need to be converted to a TeX format), and so should be avoided."

The first thing I thought was "No way, I do not believe that somebody uses Mathematica for writing papers." I know a few experimentalists who submit articles in .doc format and are happy with it, due to lack of equations. But, as far as I know, using something but TeX is considered as kind of "mauvais ton" in math community (please tell me if I'm not right).

This post is not really about some disadvantages of Mathematica interface. But such useless options of notebook formatting as e.g. "Journal Article", "Preprint", "Report", "Book" and "Monograph" can inculcate a bad taste of writing papers in students, who may postpone learning TeX. 

Nevertheless, as mentioned by Philip, Mathematica notebooks can be used to write up some daily results with the following data analysis. For a final draft it is better to use something else, though.

19 January, 2009

Things I don't like in Mathematica. Part I: License.

In my daily work I use Mathematica, and I like it very much. About 7-8 years ago, during first years of university, we were mainly using Maple for analytical derivations. Mathematica was considered to be better for numerics, since it was impossible for Maple to do them more or less fast. But nowadays (on my opinion), Mathematica is the best instrument to work with analytical stuff.

However, it is absolutely useless to write about "what I like", so I better describe things which I don't like, and which I hope will be changed soon. First I thought that it will be a little post with a list of disadvantages, but it looks like there is no way to make it short. So, there will be a few posts, and here is the first part - about the license.

In our relatively small and, in general, experimental institute we have about 20 online Mathematica licenses. In other words, twenty people can connect the server and perform calculations in the same time. 

One of my roommates was doing quite extensive computations, often lasting several days. Sometimes his calculations were stopped during the night, because Mathematica suddenly decided to check the online license, and simply interrupted the ongoing evaluation before doing this. 

Why are guys from Wolfram so agitated about the copyright? I guess I know the reason. For instance, in Russia one can buy a DVD with the last versions of Mathematica, Matlab, Mathcad, Origin Pro and other stuff (of total cost more than 10k Euro) for about 5 (yes, five) Euro. And people usually do. Furthermore, the illegal software is widely used for teaching in high schools and universities even nowadays. Hopefully, in Germany this is not the case.

Piracy is a problem. But do you really think that interrupting computations is the best way to attract new users?

The described above was actually the reason for my boss to buy me two home-licenses. But even activating home licenses is usually a pain in the neck, as mentioned in comment of BiophysicsMonkey to Chad's post, and I agree with it. Even updating licenses on both of my computers once a year is some kind of a problem I have to waste my time on, not to mention if you have a lot of machines as Chad does.

I'm completely ignorant in commercial software development, but I do not believe that there is no easier way to preserve the copyright.

18 January, 2009

16 January, 2009

Nature Chemistry

Today I found a little advertising brochure from Nature in my mailbox. It is about a new journal, Nature Chemistry, starting this year (a first issue will appear mid-March). I hope that apart from biochemical articles there will be a bit of usual chemistry in there...

Some photos from Zürich

(Ensuring security)

(Free entrance for everybody? No.)

Took it from here (Russian).

I wonder whether this applies to students, postdocs ad guest scientists as well...

11 January, 2009

Links for 11.01.09

1) The Fine Line Between Plagiarism and Necessary Repetition by Chad Orzel.

2) Next generation search engines could rank sites by “talent” - in the physics arXiv blog.

3) Think atheist - a social network for those who has no shame being an atheist.

4) A Staged Scene in a Gaza Hospital? - a CNN video of a twelve year old boy, dying in the hospital, with remarks of a specialist. The (most likely) fake video, was later withdrew from the CNN website with no further comments.

10 January, 2009

The greatest math problem ever

This is a problem, which can be easily solved by children before entering elementary school. If you want to give it a try, please forget everything you have ever studied. Here it comes:

8809 = 6
7111 = 0
2172 = 0
6666 = 4
1111 = 0
3213 = 0
7662 = 2
9312 = 1
0000 = 4
2222 = 0
3333 = 0
5555 = 0
8193 = 3
8096 = 5
7777 = 0
9999 = 4
7756 = 1
6855 = 3
9881 = 5
5531 = 0

2581 = ?

I took it from here (Russian)

What to do with deleted sections?

When we write an article, we almost always have to omit some material, which has a lot of work behind it. There may be some restrictions to the article length, as in the case of letters to the editor. Also, a referee may ask to shorten appendices and skip insignificant details. An he/she will be right - a short paper is most likely to be read.

So, one usually has a choice: on the one hand an article should describe new and interesting results, without technical stuff interesting for 5% of readers or less. On the other hand, It might be a good idea to keep all the relevant material in the same place. This may be useful for further work of authors, or also for somebody else, who wants to learn from the paper or to work out something similar.

Recently there was a post by "How many deleted sections do you write?", where Daniel Lemire proposes a good idea what to do with deleted pages. Daniel suggests to put them in the article's supplementary material, with a reference in the article. In such a way, one can expect the article to be easily read with an access to all necessary details.

Another way might be to keep all the omitted material in the arXiv preprint, and cite it in the forthcoming paper.

Why one needs peer review?

A few days ago Michael Nielsen published an excellent post "Three myths about scientific peer review". Briefly, in the nonscientific (and sometimes in the scientific) community it is usually supposed that:

i) Peer review system was used since very long time ago. Actually, it was not. For instance, Albert Einstein, while living in Germany, was not used to "independent referees" - in such journals as Zeitschrift für Physik the decision "whether to publish a paper or not" was always made by editors. And, as far as I know, before WWII this journal was considered as much better place to publish than Physical Review. After moving to the US, Einstein had withdrew one of his contributions from the Physical Review, because he "has not authorized the editor to show it to specialists before it is printed". I wrote a little post about this story before.

ii) It is reliable, in other words "it nearly always picks up errors, is a very accurate gauge of quality, and rarely suppresses innovation". Of course, no one can predict the future, and say which piece of work will be a "citation classic" in ten years. Furthermore, there is probably no way to discuss the reliability of peer review since we simply don't know how many revolutionary papers were never published (or were, but in some obscure journals) due to negative referee reports.


iii) It can show what is right and what is wrong in science. This is also not true, because it is impossible to check all math in the manusript, redo computations, not to mention repeating experimental results.

The post of Michael was followed by interesting comments of Daniel Lemire, "The purpose of peer review", induced by another comment of Peter Turney to Michael's post: "I’m sympathetic to much of what you’re saying, but, on the other hand, I know that peer review has immensely improved many of my own papers."

Being nothing but graduate student, I absolutely agree with Daniel and Peter: at least two from three papers, written during the first year of my PhD, were substantially improved after referee's comments. Apart from submitting  the papers, we have always sent preprints to some good friends from our field - always getting positive feedback (some of them may be the referees in the same time, but this we don't know).

In my opinion, the fact of peer review doesn't mean that the article is reliable, correct or "interesting to a wide community of scientists" (as it should be e.g. for Nature and Phys. Rev. Lett.). But, the review process is some kind of necessary (but not the sufficient!) condition for paper to be read and cited in the long-time future. After publication the scientific community will make it clear, whether such a condition was actually sufficient - there will be a lot of readers  and time for it, much more than two referees having three weeks to submit a report.

Of course, no one can read all journals in his field, even if the field is small enough. Let alone that articles show what was done about one year ago, but not now. Almost no one is actually reading journals - conferences and arXive give a perfect taste of what is going on. But if we come across an arXive preprint dated back to 2007 without any journal reference - this looks strange, doesn't it?

And last, but not least, it seems that reviewing good papers is an excellent way to learn how to write good papers.

04 January, 2009

25 amazing people celebrated by Google

I came across a collection of Google pictures designated to scientists' and artists' birthdays. Here is the one for Louis Braille:
I wonder whether anyone has a collection of all Google pictures...