I still remember in the 1980’s how impressed we physicists were when we discovered Tex. The program was written by Donald Knuth. The macro package Tex is so good and complete that all new developments are mere front ends and user interfaces to Tex, of which Latex and AmsTex packages are the most popular. Newer distributions deal with newer hardware, new fonts and better font management, and pdf creation, but the fundament is still Tex.

Those scientists, like chemists and biologists, that use an occasional mathematical formula can do without Tex. All kinds of handy add-ins allow incorporating math formula’s in standard office documents. However, if your paper has many math formula’s the Tex-way is the only solution. In the rest I will limit myself to LaTex.

Office document or (La)Tex
Creating a pdf file
Additional requirements
Bookmark generation with MS Word
Save to PDF
Show your tree
Skip numbered entries
Different numbering of the same level
Thinning your pdf file
Fast web view
Bookmarks with Latex
Example pdf files
Recap

Adobe has blessed the digital world with a document format that is really platform independent. I am referring to the pdf (”portable document format“). As a result the leading format for scientific articles is the pdf file. Scientific journal editors require from prospective authors that they submit their manuscript as a pdf document. More and more grant organizations also request proposals to be sent in as a pdf file.


Office document or (La)Tex
The pdf standard has many advantages. Its major disadvantage is its limited editing possibility. As a result authors have to keep at least two files of a manuscript in sync: the “source” manuscript and the pdf version. Additional graphic material is either embedded in the source or is kept as separate files. The most popular formatter for generating the source is Microsoft’s Word, or a comparable office document formatter. Another source approach is to use a simple ascii file, containing script language directives that are to be interpreted or compiled. Of the latter class the Tex, LaTex, AmsTex family is the most popular. For some fortunate reason the Tex-family has escaped the fate of almost any open-source project: multiple distributions, bad documentation, incompatible versions, and a Windows-hostile developers community.

A week ago I went to an international conference where I had to give a presentation. I was confronted with an unpleasant surprise when I wanted to deliver my presentation.

Glass surface
The conference was held in an expensive hotel in Majorca (Spain). The rooms had a fast Internet connection. Only when I checked out I discovered I had to pay for the connection. There was a luxurious desk in the room, unfortunately covered by a nicely looking glass plate. As could be expected my optical mouse did not work on the glass plate. I always bring a cordless optical mouse for a number of reasons: I prefer a mouse over a touch pad and I use the mouse during my presentation. My improvised solution was a that I slid a sheet of paper under the glass plate.

Conference room
The presenters were supposed to put their laptop on a reading desk present in the conference room. Against my principle I did not check this out before my talk. When it was my turn I discovered that the nicely styled reading desk had two bad properties: (i) the laptop had to be put in there in an almost vertical position and (ii) it was fully made out of transparent perspex.

Some time ago I described my first steps in setting up a research group at a UK university. After one year it is time to evaluate some of the developments made so far. In general, I am quite happy with the progress. Certainly it has not been a very high-flying year scientifically. However, when you can forget for a moment the pressure to deliver, running your own little research group is actually very much fun. I will point out some aspects which have been particularly important this year.

Bringing in money
The first thing is to break the negative spiral resulting from insufficient research budgets. Without ’seedcorn’ money, it will be difficult to do research and therefore to attract more funding. There are some opportunities for getting this kind of funding especially for new academics. This year I have been successful in getting money from the Royal Society (£15,000, Research Grant) and from the EPSRC (£125,000, First Grant), mainly for equipment. To give an impression of the success rate, 2 out of 7 First Grant proposals were funded in this panel. So even in this special round for starting academics, 72% did not get the money needed to start up their first research project. It cannot be underestimated how crucial these small amounts of money are for taking off during the first years. Also not unimportant is the fact that bringing in money turns out to be one of your most important deliverables which will be highly evaluated by your university, most of times above publications or teaching.

The career path in the academic world is tough. After a demanding undergraduate period, you will enter graduate school and another period of at least four years of hard work lies ahead. After acquiring your PhD you will have to work as a postdoc for a number of years.

In all those years other people tell you what to do or what to study. Your own input, as far as research subject goes, is marginal. For the majority of young scientists the final goal is to become a principal Investigator themselves, or at least to work in a group where their influence on the research direction is substantial.

When you have almost finished your PhD or just started your postdoc period, the future of being a group leader seems far away. You have other problems on your mind. Nevertheless there is question that you should ask yourself over and over again. The earlier you start with considering this question the better. Here is the question:

What research subject would you choose, and what equipment would you buy if you would get five million dollars?

I haven’t written much for this blog for a while now. The reason is that I had some serious lecturing duties this semester, which runs for 12 weeks until next week. If you are an academic in a university, you almost certainly have to do a fair bit of teaching. So I thought it might be appropriate to give you a flavour of what that means in practice (just in case you were considering an academic career yourself).

Obi-Wan Klaasnobi

This semester, I teach an introductory astronomy course for first-year students from all over the university although most of these students are from physics and chemistry. The middle third of it (about planets), I have taught for the past 10 years. This year, I took over the first and third parts as well. On the face of it, it does not sound like a lot: two unique lectures a week (repeated once) for total of 24 lectures (48 including the repeats). However, this does not mean that I just spend 48 hours teaching this course.

Depending on your discipline you write your scientific papers with either MS Word or you prepare them with a more professional text formatter like LaTeX.

Besides scientific papers scientist produce all kinds of other documents. I often notice that those MS-Word prepared documents have an ugly ragged right side, or have a repugnant flood of white space. With a little more effort it is possible to produce text, even with MS Word, with a professional look. Two aspects are important: hyphenation and justification.

Hy-phen-ation
When I look at the documents the Dutch ministeries produce, I must come to the conclusion that hyphenation is either never heard off or it is forbidden. In the Dutch language a complication is that in a sequence of nouns the nouns are combined into one word. So the Dutch language has a number of very long words, like “regeringsvoornemen” or “onafhankelijksverklaringstekst”. Using long words in a text without hyphenation makes the text ugly and unclear.

Experimental observations always are coming with uncertainties. Any measurement is an estimate of the real value, if indeed such an objective value exist.

The uncertainty in the magnitude of a measured quantity is more important as the value itself. Many readers will find this remark alarming. The determination of the “error bars” is considered a dull, redundant exercise. Especially when the reported observable quantity has a surprising value that reporting it without the associated uncertainty will certainly get the authors the attention of the media, or get their manuscript accepted in Nature or Science.

The problem with a reported observable without an uncertainty is that people, including the reporting scientists, will draw conclusions from these observations that are in no way corroborated by that experiment.

Social networks are everywhere. Personally I like Facebook to keep track of old friends and add new ones. These friends are mostly of nonscientific background. Until recently I had never realized the importance of social networks in science. When you do your PhD and perhaps some postdoc projects here and there, it is hard to think about what it takes to become a successful scientist other than doing brilliant science. Although scientific skills are undoubtedly important, I believe that one of the key ingredients which can make or break a scientific career is a good network of friends.

Successful scientists are driven by curiosity and by ego. Lay people find it disappointing when told that egos of individual scientists play a  crucial role in the progress of science. But the same people complain that their country has produced too few Nobel prize winners.

First discovery claims and disputes have always been part of science, from Newton to Montaigner (Nobel prize medicine 2008). Big ego’s and accompanying priority claims will always be part of science.

Example 1
Today I read an amusing story by Herman de Lang in the Dutch magazine Tijdschrift voor Natuurkunde (September 2009) about Millikan, the physicist who was the first to determine the charge of the electron. Robert Millikan had such a big ego that people at Caltech, where Millikan was president,  had defined the unit of vanity as the “Kan”. But to classify people on the vanity scale it was easier to use the milliKan.