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Re-formatting tables with astropy

The fact that astropy is a very powerful tool is certainly well known these days, but I would like to briefly express my admiration especially for the Table package. This package allows, among many other things, to quickly convert tables between various formats (ASCII, CSV, LaTeX, many others) and it also allows to re-format individual columns. For example, if you would like to change the number of significant digits for a specific column (“seeing”), you simply open the table and assign the usual format specifier to this column like this:

from astropy.io import ascii




The situation of researchers

Apart from research itself, I am also interested in the situation of researchers. Actually this has caught my interest since realizing sometime in the middle of the first year of my Ph.D. that competition for scientific positions is extremely high and that it is therefore crucial for science workers to join forces if we want to ensure some minimum standards.

PhDnet survey 2009During that time I actively started to participate in the Max Planck PhDnet, the association of Ph.D. candidates in the Max Planck Society, and in 2009 became their spokesperson. One of the largest projects we performed during that time was to conduct a survey among all Ph.D. candidates about their working conditions. With a ca. 50% participation rate, this was the first large and representative Ph.D. candidate survey in the Max Planck Society.


The survey report (direct link to PDF download) has been distributed (by the Max Planck Society) to all directors and we have received quite some press coverage during that time. One of the spicy findings was that there was no difference in working conditions of contract holders and stipend holders, thereby questioning the different payment modalities. It took several more years (and some dirty fights), but eventually in 2015, the Max Planck Society decided to get rid of stipends. For the full story, see the Science Careers article “Junior Max Planck researchers win reforms“.

For most researchers it comes without asking that you want to shape your own working environment towards the better. However, sometimes junior researchers have to face strict opposition when being concerned about their careers, their contracts or such. Often it is then said that (junior) researchers should “focus on their research” and not “waste their time” with political actions. This is, with all due respect, nonsense. If it’s not for us — the junior researchers — to ask for better employment contracts, career perspectives and fair treatment in applications, then who is going to lobby for us? Ah, and sometimes it is also at least indirectly suggested that only dimwits are concerned about their careers and contracts. The really excellent scientists don’t need to worry, it goes. Let me ask my friend Albert to answer this: “I consider it important, indeed urgently necessary, for intellectual workers to get together, both to protect their own economic status and also, generally speaking, to secure their influence in the political field.” (A. Einstein, 1950. Out of my later years. New York, NY: Philosophical Library.) — a quote that I read in an excellent article about why junior researchers need to unionize.

15 April 2020 – This text used to be a part of my main website, but I will make space in my navigation bar for another topic that I deem more relevant these days: the climate crisis.

METIS in 500 words

METIS is the “Mid-Infrared ELT Imager and Spectrograph” and I will explain it by dissecting the complicated name:

Mid-infrared” refers to wavelengths between 3-20 micrometers. This range is also referred to as thermal radiation because things that are at room temperature emit the most light in these wavelengths. By looking at this wavelength range we can see objects in space that are at this temperature, about 300 degrees above absolute zero. These are, for example, planets that resemble the Earth, so not those hot Jupiter-like planets (that we have known for thirty years or so), but planets that may have an earth-like atmosphere and perhaps, yes… maybe even have a form of life. There is good hope that we’ll find an Earth-like planet in orbit around our closest star: Alpha Centauri. It is so bright that we have to be very careful when we observe it with METIS, otherwise our sensitive camera will be damaged. And that is exactly the challenge: block as much light as possible from the bright star until we can find the small planet nearby.

That is certainly the most spectacular use of METIS, but it is also the most risky one. Fortunately, there are many other things we can study with METIS. In our galaxy, the Milky Way, we will also make observations of the disks around young stars and the atmospheres of old stars. And in certain other galaxies we can also make observations in the mid-infrared light. In almost every galaxy there is a super-massive black hole in the center. And when that actively accretes matter, the surrounding swirl of gas and dust gets hot and at certain places it reaches room temperature so that we can easily see it in the middle infrared.

ELT” stands for “European Extremely Large Telescope” and that is the name of the largest telescope in the world that is now under construction. It is being built by a European organisation (the European Southern Observatory or ESO) on a mountain in the Atacama desert in Chile and will be ready in the mid 2020s. With its diameter of almost 40m, the area of that telescope will be larger than the areas of all current large telescopes combined! There is no company in the world that can produce such a large mirror and so the main mirror (the one that will be almost 40m in size) consists of 798 segments, each with a diameter of about 1.45m. And they all have to be placed in such a way that the whole mirror then becomes a parabola. Almost impossible, right?

Finally, “Imager and Spectrograph” refers to what the instrument will be able to do: record pictures and spectra. With the “Imager” we can for example take a real picture of an earth-like planet and with the “Spectrograph” we can analyze the light of that planet and compare it with models of atmospheres to discover what happens on that planet.

How to set up your Mac as a shared drive for TimeMachine on macOS High Sierra

I used to use my late 2014 Mac mini at home with an external hard drive connected as a shared drive to backup several Macs using TimeMachine. This has worked well for years now, but recently the clients stopped to recognise the Mac mini as TimeMachine server. I followed these two instructions and now it works:

  1. The official Apple support post to set up your Mac as a TimeMachine server (essentially: right click on the shared drive in the Sharing preference pane and select it to serve as a TimeMachine disk). This made the disk appear again in the client’s TimeMachine preference pane, but it wouldn’t allow me to connect saying (translating from German) “You don’t have the required permissions to use this disk”. Only after following the next step, did it work.
  2. This user-contributed instruction on the Apple discussions forum (essentially: create a folder on the shared disk and share the folder rather than the whole disk)

Don’t bother with all the old tips on the web saying that you need to download the ca. 30 € Apple server software. It doesn’t support TimeMachine anymore for newer macOS versions and it is not required anyway, as you can also just make it work using the built-in sharing feature.

Astronomy as an example for an open science

When a former Max Planck colleague who now works at the Stifterverband, a public-private think-tank, called me in October and asked if I wanted to take part in a workshop about open science, I was unsure what astronomy could offer in this regard. However, when simply writing up the tools and processes many astronomers use (and take for granted), it quickly becomes clear that astronomy is very much an open science already.

In the spirit of open science, I would like to document here my preparation for the discussion section of the workshop tomorrow.

What does openness in astronomy mean?

  • Open data: access to raw data (e.g. through the ESO archive) as well as access to surveys (e.g. through VizieR) and meta-data (e.g. through Simbad). The access is available for everyone and in most cases either in near real-time or after a proprietary period of maximum 12 months (in most cases).
  • Open source: access to scripts, libraries, programming tools, codes, … that are used to analyse the raw data and derive scientific results. In the most open projects (such as astropy), even the development process is open and anyone can contribute via e.g. github. Platforms such the Astrophysics Source Code Library, on the other hand, publish the final code itself and make it searchable through standard literature search engines.
  • Open access means free and unimpeded access to consolidated scientific results as published in peer-reviewed journals. While many relevant astronomical journals, including the just recently launched Nature Astronomy, are not open access by themselves, most (all relevant?) journals now allow publishing the author’s copy on preprint servers such as on the arXiv. Most current research articles can be found on “astro-ph” (the astrophysics’ section of the arXiv). Still troublesome, however, are technical articles (e.g. about telescope or instrumentation projects), that are published in the SPIE proceedings. A google search for the fulltext of the article, including “filetype:pdf” as a further filter, often reveals the author’s copy, however. In some cases, authors can “rebel” against the copyright notice they typically have to sign in order to publish an article (see example below for one of the articles published during my Ph.D.).


Example of a modified copyright agreement granting only a non-exclusive license to the publisher and thus allowing to publish my own article on my homepage or on preprint servers.

  • Apart from open data, open source and open access, open science can also encompass outreach and communicating with the public. This can be in more traditional “teaching” ways through blogs (e.g. the German SciLogs platform on which I have blogged about my trips to Chile during my Ph.D. and later), talks, open house days etc., but in some cases it can also mean directly embedding citizens in your research project, such as demonstrated successfully by the GalaxyZoo project that involves citizens to classify galaxy morphologies, a task in which humans have so far been better than machines.
  • Open science should can also include transparent selection procedures. After all, the particular selection of proposals, job candidates, laureates etc. can shape the de-facto view of a field for a long time and therefore comes with big influence and power. This could, for example, mean to publish the criteria which will be used to select a candidate for a job and to democratically nominate committees that decide about proposals and prizes. This is partly the case in astronomy, e.g. the committees that help select proposals for the Deutsche Forschungsgemeinschaft are elected by the scientific staff themselves.
  • Last, but not least, I believe open science should also include democratic structures in universities and research institutes. Usually, in German universities, there are “Fachschaften” that have a say on the selection of professors, and the Max Planck society sponsors one of the largest Ph.D. networks in the country, the Max Planck PhDnet. On the more senior, but not yet tenured, level, however, the situation is less good. Attempts to form a postdoc network within the Max Planck Society have not been greeted with sympathy in several institutes as some directors fear to lose influence if juniors also have a say. This is, however, not specific to astronomy, but rather a general symptom of the research and higher education landscape in Germany.

Why do we promote open-ness in astronomy?

Astronomy is a highly competitive field (typically only one out of 20 astronomy Ph.D.s eventually gets a tenured research position). Open-ness in astronomy would not be supported if it weren’t also promoting competitiveness and productivity.

  • Regarding data, observatories, that run big telescopes, promote open science in order to increase the observers’ desire to quickly publish “their” data (lest others “steal” them). Top-nodge data are often publicly available from the start. The first observations with the next, biggest space telescope will be open access from day 1, as announced today. The first observations for instruments built for the European Southern Observatory ESO, are also usually publicly available from the start, e.g. these GRAVITY science verification data. Other data are usually openly accessible after a 12 month “proprietary period”. This can sometimes be in conflict with the “owners” (PIs) of the data.
  • Regarding open source, the motivation to publish tools and software code is manifold: the author(s) of the code publish it in order to promote their code (and collect citations to associated research papers), but also so that others can contribute in the development. Last but not least, publication is the best way to help others in finding bugs and errors and therefore make your own research more credible.
  • Open access is in the interest of everyone except scrupulous publishers who want to make a profit from publicly financed research. It helps to promote science and the scientific method, also in the wider society, if the basic results are openly accessible. And it helps researchers from poorer countries who cannot afford paying expensive subscription fees to Nature, Science et al.
  • Public outreach also helps everyone, but can be a burden for researchers who also have to teach / supervise students, manage projects, deal with bureaucracy and publish, publish, publish. Motivations to nevertheless indulge in public outreach reach from simple PR for your own research (in order to attract more research money or to boost one’s ego…), but can also include serious collaboration with the public (see GalaxyZoo). Often the motivation for being active in public outreach is also to promote the scientific method (e.g. the Science March initiatives) or a feeling of a moral obligation as publicly funded research should also be of benefit for the public.
  • Transparent selection procedures and democratic structures, finally, are also a win-win situation: researchers gain trust in the process and will therefore try harder to win prizes, fellowships and jobs. The academic institutions, on the other hand, win by becoming more attractive to a wider range of (international) applicants. The only downside is an increased effort of documentation / communication, but I believe the benefits well outweigh the costs.

I am interested to see the discussion tomorrow and will try to report back with a view from the other participants / fields as well!

Update 15 Nov:

What I did the last 2.5 years…

After working on GRAVITY for about three years, I continued my postdoc phase at MPE 2015/2016 with a self-funded (*) project. (*) “self-funded” is of course a very misleading term as I didn’t fund myself out of my pocket (but was rather funded by generous German tax money via the Deutsche Forschungsgemeinschaft DFG). This project is not completely finished, but my family and I moved to Leiden this year so that I could take on my current position as “calibration scientist” with E-ELT/METIS at the Sterrewacht of the University of Leiden. I hope to complete this project with the next year or two, however, with the help of a recently recruited Ph.D. student. In the meantime, the DFG has asked everyone who was funded in this “priority programme” on the interstellar medium to write a report about what they did. This was actually an interesting reflection on the last 2.5 years of research and I would like to share it here (PDF) with anyone who would like to read it.

Ph.D. project: The multi-wavelength view of the AGN – star formation relation

I am happy to announce a new position to work on a Ph.D. project at the Sterrewacht Leiden / Leiden University

The multi-wavelength view of the AGN – star formation relation

One of the long-standing questions in astrophysical research is what exactly triggers the onset of Active Galactic Nuclei (AGNs). The aim of this project is (1) to study the nuclear star formation history in a well selected sample of nearby AGNs with exquisite data (VLT/X-SHOOTER spectra) and (2) to participate or lead pioneering efforts to study gas, dust and star formation in the parsec-scale environment of nearby actively accreting super-massive black holes using the upcoming infrared interferometer MATISSE on the VLTI.

Supervisors: Dr. Leonard Burtscher, Prof. Dr. Walter Jaffe

Promoter: Prof. Dr. Bernhard Brandl

Wieso brauchen wir den Science March auch in Deutschland?

Gestern Abend war ich (als einer der Organisatoren des Münchner Science March) im Gespräch mit einem Reporter für Bayern 5 Aktuell. Er sagte mir, dass er nur einen kurzen Bericht machen wolle und daher nur Platz für eine Frage/Antwort habe: “Wieso brauchen wir den Science March auch in Deutschland?

Was er damit meinte: Dominieren etwa in Deutschland schon “fake news”? Gibt es hier Schließungen von Universitäten und werden Wissenschaftler etwa auch hierzulande gegängelt wie in Ungarn oder der Türkei? Erhalten staatliche Agenturen Maulkörbe und verbreitet sogar die Regierung “alternative facts” wie in den USA?

Zum Glück lassen sich all diese Fragen mit einem klaren Nein beantworten.

Dennoch gibt es meiner Meinung nach aber auch hierzulande Gründe, um für die Wissenschaft zu marschieren. Hier sind ein paar:

  1. auch wenn “alternative facts” in Deutschland nicht dominieren, so gibt es sie hierzulande durchaus auch in der Politik und zwar quer durch die Parteienlandschaft:
    • Mitte der 1990er Jahre hat die rot-grüne Regierung unter Gerhard Schröder den “Binnenkonsens” im Sozialgesetzbuch verankert. Demnach müssen Medikamente nicht mehr generell nach wissenschaftlichen Standards getestet werden, sondern lediglich nach den Standards, die in der jeweiligen “Therapie-Richtung” üblich sind. Das heißt im Klartext: wer ein neues (medizinisches) Medikament zulassen will, muss in aufwändigen klinischen Studien die Wirksamkeit des Medikaments nachweisen. Wer aber neue homöopathische Globuli, Bachblüten-Extrakte oder ähnliche Quacksalberei auf den Markt bringen möchte, darf sich auf seine “besondere Therapierichtung” berufen und muss lediglich nachweisen, dass das Medikament ungiftig ist. Dafür gibt es keinen vernünftigen Grund, aber insbesondere die Grünen wollten damals diverse esoterische Praktiken in den Katalog der Krankenkassen bekommen, was dann auch so geschehen ist. Bis heute zahlen viele große deutsche Krankenkassen für Mittelchen, für die nie ein Wirknachweis erbracht worden ist.
    • nach mehreren Anläufen und Rückschlägen hat die CSU dieses Jahr die Einführung einer “Infrastrukturabgabe” (vulgo “Ausländer-Maut”) durchgesetzt. Sie hat zwar explizit auch zum Ziel, ausländische PKW-Halter zur Kasse zu bitten, begründet diesen “Racheakt” aber dann doch damit, dass zusätzliche Investitionen in die Verkehrsinfrastruktur notwendig seien. Nun sind sich die meisten Experten aber einig, dass durch diese Maut viel weniger Geld in die Bundeskasse fließt als von der CSU gedacht, womöglich wird sie gar ein Zuschuss-Geschäft. Damit fällt der wesentliche Nutzen dieser Maut weg. Das, freilich, wusste man schon seit langem, hat es aber ignoriert.
    • ganz am rechten Rand des politischen Spektrums versucht die AfD auch mit der Leugnung wissenschaftlicher Erkenntnisse Stimmen zu fangen und schreibt in ihrem Parteiprogramm zum Thema Klimawandel, dass sich das Klima immer schon geändert habe, der Einfluss des Menschen nicht gesichert sei und mehr CO_2 im übrigen gut sei für das Wachstum von Pflanzen.
  2. Die Entwicklungen in der Türkei, in Ungarn, in Polen und in den Vereinigten Staaten haben auch gezeigt, wie schnell der Abbau von Demokratie und der damit verbundene Abbau freier Wissenschaft gehen kann. Es ist daher wichtig, immer wieder daran zu erinnern, wie wichtig freie Wissenschaft für unsere Demokratie und für unseren Wohlstand ist.
  3. Vor der Bundestagswahl im September sollten wir ganz konkret dazu aufrufen, die zur Wahl stehenden Parteien kritisch bezüglich ihrer Unterstützung von Wissenschaft zu beurteilen.
  4. und letztens sehe ich den Science March auch als Appell an Wissenschaftler, mehr zu tun, um die Bedeutung ihrer Wissenschaft einer breiteren Bevölkerungs-Schicht zugänglich zu machen. Wichtig ist dabei meines Erachtens nicht nur das Vermitteln von Ergebnissen, sondern auch die Diskussion der wissenschaftlichen Methode. Wir müssen stärker aufzeigen, wie rigoros Ergebnisse hinterfragt und geprüft werden und dadurch klar machen, weshalb wissenschaftliche Ergebnisse so viel belastbarer sind als Meinungen und Gefühle.

Rescue wrongly encoded e-mail attachment

Due to the long heritage of its underlying transport protocol SMTP, e-mail messages are still base64 encoded. This ensures that binary attachments (such as PDFs or zip files) are converted into the 7-bit ASCII character set [a-zA-Z0-9+/] that the SMTP protocol knows how to handle. The character `=` is used to terminate the so encoded string. The raw content of the attachment may look like this:

Content-Disposition: inline; filename="spe1618_v4_doors_20161107.pdf"
Content-Type: application/pdf; x-unix-mode=0644; 
Content-Transfer-Encoding: base64


Usually your e-mail client handles the decoding for you and all you see is a little icon, e.g. of a PDF document, which you can double-click to open the attachment. Sometimes it happens, however, that your e-mail client fails to properly decode this string and then you cannot open the attachment. In this case, simply save the long string “JVBE…FT0Y=” to a text file, say file.txt and then decode this using this shell command:

cat text.txt | base64 --decode > text.pdf

Hike to Mount Cardigan (New Hampshire, USA)

Yesterday, I hiked up Mount Cardigan, a rocky hill in Western New Hampshire, USA, together with a group of astronomers visiting the Dartmouth AGN workshop Hidden Monsters. Despite the bad weather forecast, we were lucky and didn’t get wet. Even better, we had a fantastic view from the bare-rock summit, standing in the midst of clouds passing by. Here are some impressions:

A time lapse video of a couple of astronomers crawling up the mountain:

And another one with some changing-look cloud cover:

And, finally, here is the GPS track of the hike:


Quite exhausting. Not so much the hike, but all the digital post-processing… 🙂

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