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The open science workshop at the Stifterverband

This is a follow-up to my post 2 days ago about open-ness in astronomy, with some observations and comments from the corresponding workshop yesterday in Berlin, organized by the Stifterverband. The workshop was visited by about 30 people from all parts of society — researchers, library managers, civil servants from national and foreign science ministries, as well as people from industry (software, automotive, airport services, among others). In the spirit of open-ness the workshop adopted the “Chatham House rule” which essentially says that you may report freely about what has been said, but only if individual participants cannot be identified.

The workshop was organised in discussions within the respective sectors science, administration and industry and round-the-table discussions with everyone. As always in a workshop with such a diverse audience and broad aim (“to explore potentials and challenges from open research and innovation processes”), it is hard to give a one paragraph summary of the many topics discussed, but I will try nevertheless.

An “innovation culture” needs to admit errors

Most participants agreed that open-ness is a mindset that helps with innovative thinking, but it was also agreed that there are limits to open-ness, e.g. due to privacy (e.g. patient data in medical applications) or security (e.g. when in connection with critical infrastructure) concerns. To be able to openly discuss not just final results, but also your way there (e.g. your methods), requires some tolerance towards failure. If you cannot risk to fail, you can also not be open as you will only talk about your project after you have achieved some major success. And it also requires some trust or self-confidence that you will have another good idea in case the one you publish today is being picked up by someone else.

The measure becomes the target

In the discussion group on open-ness in science the discussion was focused on the question “how can we fix science?”. Science is becoming more and more an industrial machinery, optimised for maximum impact and citation numbers, opting for certain results (that are often boring) rather than trying out radical new experiments (that often fail). Science managers and politicians try to increase the “output” for a given level of (public) funding and need to be able to measure the output in order to report on changes. Generally the output is now seen as number of papers and number of citations each paper receives. However, focusing too intensively on these narrow indicators leads to the effect that many scientists now try to maximise their impact as measured by these numbers, rather than try to work on something bigger that does not (immediately) result in a large number of papers or citations. Think about the gravitational wave experiments which produced null-results for decades – before receiving the Nobel Prize this year. Other metrics, such as Altmetic which measures the impact of your research in society, may be helpful to get a wider view of the relevance of research projects.

Publication bias

Typically people only publish their studies if they find a result. If nothing could be measured or the result was deemed not of interest, it is not published. A participant called the so-accumulated knowledge “dark knowledge” and cited an Austrian funding agency which estimated (by looking at allocated budgets) that this “dark knowledge” grows 2-3 times as fast as published knowledge. It was agreed that also failures should be published, but it was also agreed that publishing null-results is not honoured in our current research system, or as one participant put it: “How many unsuccessful scientists do you know”?

Science as the stroke of a genius or regular work?

Underlying many discussions about how to measure success in scientists, how to evaluate scientific work (and scientists themselves!), is the question of how scientific progress is perceived. Unfortunately many people still believe science progress when some genius has a fantastic idea. This can occasionally be the case, but usually even the genius bases his or her insight on published literature which to the most part consists of hard work by hard working people, trying out new methods and slowly progressing in understanding some topic. It was felt that this work is often not properly appreciated. We concentrate too much on people who have done some fantastic new thing, rather than on the many “smaller” scientists who contributed to the success of the “genius”. This is also reflected in the current job situation, especially in Germany, where there is little room for normal working academics: You’re either a (perceived) genius and can then advance to become a professor or you’re continuously on short-term “postdoc” contracts without stability or job security.

CitizenScience

There was some uncertainty as to how best open up the scientific process to the general public. Some believed that the next big step, after simple press releases and more interactive talks / blogs / social media is a full participation of the general public via citizen science projects. Others were more cautious and thought this is just a “hype” that is only applicable to a small set of projects. Indeed in astronomy, the GalaxyZoo project mentioned also in my previous post was highly successful, but it is unclear if citizens’ help in classifying galaxies will be needed in the future given recent advances in machine learning codes.

What can science contribute to society?

Finally the question was discussed what can science contribute to the wider society? Here I’d like to describe two of the most widely discussed points:

  • Science contributes skeptical thinking. Skepticism is one of the basic traits of a good scientist and encourages everyone not to take claims for granted, but to critically ponder whether they can be true, ask for references, proof and repetition. In times of “fake news”, “climate deniers” and vaccination hoaxers, the importance of this trait cannot be overestimated. It was also stated that science needs to be healthy to encourage skepticism. If we only try to reach the maximal numbers of papers or citations, this does not necessarily help to question existing paradigms and make real progress.
  • Science may also contribute tools and best practices for open-ness, such as the distributed version-control system github, open access publication platforms, and other tools to openly share information. Note that also the world-wide web was initiated from a research environment (the CERN) and it was created in an effort to make information accessible. Nowadays, this would perhaps also be called open science…

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:

Can you see the CMB in your analog TV?

 

Planck_and_the_Cosmic_microwave_background.jpg
Anisotropies in the Cosmic Microwave Background as seen by the Planck Satellite after removing the dipole due to Earth’s rotation around the sun as well as foreground emission. Credit: ESA and the Planck Collaboration

For a public outreach talk I wanted to start with the importance of the Cosmic Microwave Background (CMB) for our understanding of the evolution of the universe. Then I remembered this anecdote that you can “see” the CMB radiation in the noise of your analog TV (if you still have one) and started wondering if that is actually true…

TV_noise
How much of the “noise” in an old analog TV is caused by the Cosmic Microwave Background? (It seems like much less than the claimed 1%)

On the web there are several sources claiming that 1% of the noise between the channels of your TV programme are CMB, but I couldn’t find any actual calculation. So I tried my own.

Since I’m not an antenna expert and couldn’t immediately find some meaningful numbers for the radiation for analog terrestrial TV, I used this to come up with an order of magnitude number:

The old analog sender on top of mount Wendelstein in Upper Bavaria radiated at 0.4 kW in channel 48 according to the Wikipedia page. Channel 48 is at about 680 MHz and has a bandwidth of about 8 Mhz. This sender was apparently only used to broadcast to Bayrischzell which is about 2 km away. The sender had a round radiation pattern, i.e. it radiated in all directions, but only in one plane. However, since the town of Bayrischzell has a finite length, the half-power beam-width cannot have been too small. I assume here an H/R of ~ 0.2, i.e. at 2 km distance the half-power beam-width should be ~ 400m (i.e. illuminating an area of 5e6 m^2 at that distance). This is of course only a crude estimate, but for an order of magnitude calculation it should be OK. The specific flux received in Bayrischzell from this sender is thus

0.4 kW / (5e6 m^2 * 8e6 Hz) = 1e-11 W(m^2 Hz) or about 1e15 Jansky (in radio astronomers’ units)

Wendelstein_Transmitter
The old radio + TV transmitter on top of mount Wendelstein in the Bavarian alps. The transmitter is the red-white painted steel structure.

OK, now let’s look at the specific flux of the CMB. This is easy, we just need to substitute proper values (2.7 K, 680 MHz) in the Planck equation and arrive at a specific flux of about 5.4e5 Jansky at the frequency used for the local TV station.

Now we need to compare this not to the signal strength estimated above, but to the estimated noise level of a typical analog TV receiver system. This is a bit tricky, but typical carrier-to-noise ratios (CNR) should be of some help. The carrier-to-noise ratio is the signal-to-noise ratio of a modulated signal. I didn’t find any recommended CNR values for terrestrial analog TV, but other CNR values for TV might give some guidance. In an article published with the Society of Cable Telecommunications Engineers, this guidance is given:

The FCC’s minimum CNR is 43 dB, which, in my opinion, is nowhere near good enough in today’s competitive environment. Indeed, most cable operators have company specs for end-of- line CNR somewhere in the mid to high 40s, typically 46 to 49 dB.

The National Association of Broadcasters Engineering Handbook (p. 1755) has a similar statement:

Noise will become apparent in pictures as the carrier-to-noise ratio (CNR) approaches 43-44 dB […]; a good design target is 48-50 dB.

So let’s assume the sender on mount Wendelstein is calibrated such that is achieves a CNR of 50 dB for the terrestrial analog broadcasting of the local TV station in nearby Bayrischzell. This means the signal is a factor 100,000 (1e5) stronger than the noise.

In this case, the noise level in the TV is about 1e10 Jy or about 200.000 times larger than the CMB signal. So, if this calculation is correct, it seems unlikely that you would be able to see the CMB signal while searching for signal with your analog terrestrial TV.

 

An analysis of astro-ph submit times

Recently I submitted another paper to astro-ph and I wanted to play the “first” game and try to get my paper on top of the daily listing. Now, it is well documented that the deadline for the daily submissions is 16.00 EST meaning that if you submit just after that deadline you’re paper is likely to appear on top of the next day’s mailing. (NB: the announcement is inverse on the web page)

But how likely do you get your paper on top if you submit right in time? For the above mentioned paper I had prepared everything before hand. This took a bit of time since arxiv.org didn’t accept a

\maketitle

after the abstract but only spewed out weird errors about lines that aren’t ending etc. So I had prepared everything, even submitted the paper and un-submitted it again.

Then, at 20.59.59 GMT and a split second I hit the submit button. It took more than three minutes for the server to handle this request. Still, I was quite amazed that the paper appeared only as #6 (#19 if counting also the cross-lists) from the bottom of the webpage (i.e. top of presumably more important mailing), despite having been registered by the server at 21.00.04 GMT. So I used my much-loved bash tools curl, awk and grep and extracted the submission times of all astro-ph submissions this year until October and found this:

submission_histogram

There is a clear spike at 20.00 UT (which is 16.00 EDT = UTC-4) and a smaller one at 21.00 UT (corresponding to 16.00 EST = UTC-5) — most of the year so far has had (Northern hemisphere) summer time. I don’t have an explanation for the smaller and wider peaks at about 9.00 and 16.00 UT. Now we can also zoom in to the region around 20 / 21:

submission_histogram_sec

We see that the peak submission time (which is when the submission is registered by the server) is at about 12 seconds after the deadline. Going back to my case — submitting right at the deadline, registered 4 seconds after the deadline (despite server only replying 3 minutes later) — we can ask: what are the chances of getting on top if you submit within 4 seconds? Over these 10 months (ca. 200 submission days), there have been 26 submissions in this timeframe, i.e. your chances of getting on top if submitting so close in time should be almost 100%. It just so turns out, however, that on the particular day when I submitted, there were five papers submitted even closer to the deadline. Tough luck. 😉 Hopefully, however, this will play less of a role in the future as more and more people read their daily astro-ph through voxcharta or similar services where the announcement order is either randomized or sorted according to your preferences.

Querying the ESO archive

As the big observatories of the world observe ever more astronomical objects, their archives become powerful research tools. Finding out whether an object has been observed with a certain instrument is just a few mouse clicks away, if the observatory has a public archive like ESO provides for all VLT instruments.

However, if you would like to perform more complex searches, the web interface may not be enough, although it has become very comfortable to use, especially with Astropython’s astroquery package.

For a research project, I recently needed to find all local AGNs ever observed with a certain instrument (SINFONI at the VLT). Since I didn’t know the target names or programmes, I got all unique observed coordinates, resolved them via Simbad (which also gives the class of an object) and then selected the AGNs among all the targets.

Since ESO unfortunately does not provide direct access to the archive database, a query like “give me all unique observed coordinates” is not possible per se. So I had to download all headers, parse the relevant information and build my own database (SQLite for the moment).

I have a script to collect the metadata, which does this:

  • query the ESO archive for all observations of a day
  • then parse the resulting html file for the unique identifiers of each dataset (“data product ID” or DPID, e.g. XSHOO.2015-04-13T04:46:11.730)
  • download the header for the given DPID
  • parse the header for relevant information and construct an SQL insert statement
  • insert all into a database

There are also scripts that

  • query the database for all programmes and search metadata (PI/CoI names, titles) for them
  • get atmospheric data for all observations (querying the ambient conditions server)
  • And there is a top-level script that calls all of these scripts in a meaningful way and that I call about once a month or when needed to update the database.

My database consists of one table for each ESO instrument that I am interested in (currently MIDI, SINFONI and X-SHOOTER), a table with programme meta data (PI/CoI names and titles), a table with atmospheric data as well as tables with basic information about calibrators and science objects that I use for matching up observations and building LaTeX tables in a scripted way. This has become quite handy over the recent years and has helped me in building the largest sample of interferometrically observed AGNs with MIDI (Burtscher et al. 2013) as well as the largest sample of local AGNs observed with SINFONI (Burtscher et al. 2015) and a follow-up paper (submitted).

In case you are interested in tables that I have already compiled and am maintaining, please contact me and I will be happy to share the database with you. It is currently about 700 MiB and I update it every month.

Apart from nice science, one can also use this database to create other plots of interest, like a map of the exposure depth of SINFONI for example:

sinfo_coverage_10deg

Interestingly, the Galactic Center (at 17:45h, -29 deg) is not the field with the deepest SINFONI integration time (“just” about 400 hours). Instead the Extended Chandra Deep Field South is the deepest SINFONI field with about 600 hours of integration time. Another field with deep coverage is the COSMOS south field (10:00h, +02 deg). About 300 hours of total integration time have been spent on this field.

 

Update 12 Jan 2016: I have now put my codes and the database online. Please see the github project page for further details on how to use these.

Two strange and funny astronomy papers

…that are actually refereed articles or made it at least to astro-ph:

  • Gates, V.; Kangaroo, E.; Roachcock, M.; Gall, W. C.: Stuperspace – a classic. If you don’t know it, read it immediately. That is, hold on a minute… First read a quantum field theory article like this to fully value the former article…
  • Douglas Scott, Ali Frolop: Down-sizing Forever. An April’s fool article on astro-ph that reaches the astonishing conclusion that “the early Universe was in fact a giant galaxy”.

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