On the good ol' practice of writing academic text with LaTeX

I heard about LaTeX for the first time around 1993, when I was working with Prof. Diana Farkas on a manuscript we published in Acta Materialia. I fed her with my text contributions, just a few, since I was then just a master of sciences student. I watched her insert my text in the tex file and compile the source to produce the manuscript. I found that strange, since I was used with a text editor from an unknown company called Microsoft which was introduced just one or two years earlier in our university (we were late).

Then I forgot about that, I wrote my master dissertation using word (and suffering from compatibility problems related to fonts when I printed the text, there was no pdf at that time) and went to Düsseldorf to work in my doctoral thesis. Nobody used LaTeX there, so I wrote my thesis in Word too. I learned how to use the program, so it was less painful to print the text. And , of course, pdf already existed at that time.

I continued working with Word when I returned to Brazil in 1998, for my post-doc at USP. All my connections worked with word, so it seemed good to keep on using the program to write my manuscripts. Then I wrote a paper with Prof. Ryoichi Kikuchi, full of equations. When I received the proofs I noticed that many equations had strange typing errors which I didn't produce in the original manuscript. This was registered in my memory, I corrected the errors returning the proofs and kept using Word.

Some time later I decided to start using LaTeX, I must confess, it was pedantry, an ideologically motivated decision (I support free software since I first read about this in the heroic 1990' s). I believed I was not able to work with a tex file, so I started with LyX. Then the late Prof. Ibrahim (Himo) Ansara came to visit us. He saw me using LyX and told me he was a LaTeX adept. I asked what he used, and he said he edited the raw tex file, because LyX introduces many useless lines in the source. I thought "Is this possible"?

With the time, I discovered he was right. There is no problem using LyX to produce a letter, but if you try to produce a manuscript to be sent to a magazine you will end up with a lot of garbage in the preamble. By the way, soon after that, I discovered what were those errors in the proofs I mentioned before: missing backslashes in a LaTeX math formula. The publisher took my word file and converted it to LaTeX! Finally I started working with the tex file and I still do it today. In the present days I select magazines for my manuscripts based on whether they accept tex files or not, I primarily choose those who accept and use the "word-colonized" magazines only in a last case scenario.

I told all this only to show that the transition from the editor which carries its ultimate usefulness in the name (it is designed to be used in an office) to LaTeX is not easy, but can be done. As I told, I was ideologically motivated and took more than 10 years to make the transition. What bothers me is that my colleagues don' t even try it.

LaTeX is the better option to produce academic texts. Its ability to produce nice quality math equations cannot be even matched by any other text editor. The fact that you can edit the tex file in the raw version (it is ascii coded!) is also an advantage. Everybody who ever needed to insert an extra line in a matrix will agree with me that this is better performed editing the tex file rather than using the infamous "equation editor" of winword. Combined with gnuplot, LaTeX produces a manuscript with a professional look which allows you to publish your own manuscripts
if you want (and now, with ResearchGate, you can). My book was entirely typeset in LaTeX, in the final form, by me. The publisher had only to send it to the printing machines.

You don' t need to be a hardcore LaTeX user, though. Today there are plentiful tools to help generate tex files (and which does not generate garbage in the preamble). I  use Kile in a linux system. There are many useful resources, like autocompletion of commands and a previewer of equations which help a lot in finding mistakes in very complex formulas. I also used the Latex Editor when I have to work in a Windows system. I'm not implying these are the best tools, they are only the ones I use.

So, if you are a scientist, give LaTeX a try. It does not hurt, and you will enjoy the result.

The worst of peer reviewing

Have you ever been submitted to the following situation?
You submit a manuscript to a given magazine, sometimes you get a direct rejection (by the editor, using arguments like "this magazine receives too many manuscripts and we cannot publish all of them") or it enters in reviewing and after one month or so, you get a very nasty review, telling your work is nonsense (not to use another more colorful substantive). Then you decide you had been humiliated enough and send the same manuscript to another magazine, sometimes with a better impact factor and after some months more you receive a nice review, perhaps pointing out some mistakes you made, but finally approving the publication. What happened, wasn't the work nonsense?
Once in a joint dinner with some academic friends I placed the following question:
-"Did you ever approved a manuscript as you received?"
I meant, without asking some correction, some change, some new experiment. Of course everybody kept still.
The two problems are linked. In an ideal world, the peer who reviews your manuscript should be perfectly impartial and just. I try to be in the reviews I write (I'm not saying I achieve this goal). In fact, reviewers are humane and are subject to psychology as anyone else. The position of power over other authors sometimes is too strong to resist. The number of manuscripts increased considerably in the last 50 years and the same happened with the number of magazines. This means less prepared editors and reviewers.
What could be done? It is not possible to overload good reviewers more than what is done now, and reviewers should be trained as well. I read a proposal once in LinkedIn, the reviewers should receive a guideline, questions to be answered about the manuscript, to help performing the task. Other important thing would be that the editors take their roles more seriously. Bad reviews should not be considered in evaluating a manuscript. This means the editor should, at least, read the reviews before forwarding to the author.

The h index

I was explaining to a.colleague how to calculate.the h index of our department, since he got surprized that an emmeritus professor of our department (who does not publish too much) appears three times in the list of the 34 most quoted papers. I explained that this is a problem of the h index (if II remember well, Hirch pointed to this in his paper): it gives too much value to old published papers, which, due to their long lives, received lots of citations. Then I got the idea of using a time-dependent h index, let us say, based on the list of papers published in a given time span (for example, the last three years). This will give a best estimate of the citation strength os a set of researchers. Of course, this time-dependent h index may be artificially inflated by the own researcher citing his own papers, thefore I suggest introducing a secondary index, which I call the citation strengrh, which is the number of citations (full) divided by the citations excluding self-citations. In my opinipn this index computes the probability that an article published by that author is cited by someone else. I would like to hear your opinion about this idea.

Two useful services

Recently I got in touch with two online services which I find most useful.
The first is the ResearcrhGate : at first sight a social network of scientists, is much more than that. It is a draft article repository and a place to post and answer technical questions which are visible worldwide. I guess it will change the way we do science, but maybe I'm exaggerating.
The second service is SciRev : have you ever had an unpleasant experience with a magazine? A manuscript which took too much to review, a badly written reviewer report? Some manuscript which was unfairly rejected? The place to post you complain is scirev. You may also access the service to see the stats of a particular magazine.
So, have fun!