propagating changes; comment on "Time To Rethink Retractions And Corrections?"

A comment on Amending Published Articles: Time To Rethink Retractions And Corrections? (doi: 10.1101/118356) which asks for making it easier and less of a matter of guilt to change published articles.

Update: Leonid Schneider from forbetterscience notes that there’s a whole dungeon of misconduct which might be facilitated by “living papers”. We need investigate problems in depth before changing established processes. Scientific communication is a complex process. Publication is an important part of it.

Firstoff: The underlying problem which makes it so hard to differenciate between honest errors and fraud is that publications are kind of a currency in science.

arctic unraveling

Report: Arctic Is Unraveling, discusses assessment Snow, Water, Ice and Permafrost, notes the article rising tide — sounds more like Hansen was right.

Thanks for all the fish

AGU publications published "The world's biggest gamble", a short commentary on how to go on with climate change.

I am hard pressed not to become sarcastic. Not because the commentary is wrong. It’s spot on. But because we, as a species, are …

I’ll stop speaking my mind for now. Let’s hope that hope wins against frustration and our children don’t have to pay too dearly for the idiocy of my generation and the generation before.

Oh well, Happy Halloween and enjoy Samhain.

Conversion factor from ppmv CO₂ to Gt C

I just spent half an hour on finding the references for this, so I can spend 5 minutes providing it for others on the web.

conversion factor footnote

IPCC bibtex entries

I repeatedly stumbled over needing bibtex entries for the IPCC reports. So I guess, others might stumble over that, too. Here I share my bibtex entries for some parts of the IPCC reports.1

IPCC 1990 WG1 (physical science basis)

  title = {Climate Change 1990 The Science of Climate Change},
  publisher = {The Intergovernmental Panel on Climate Change},
  year = {1996},
  editor = {J.T. Houghton and G.J. Jenkins and J.J. Ephraums},
  author = {IPCC Working Group I}

  1. In IPCC 2013 WG1 they finally provide bibtex in their zip of references, but without item headers — you can’t use these directly. 

Information challenges for scientific publishing

On 2015-08-27, Researchers from the Reproducibility Project: Psychology reported that in 100 reproduction studies, only “47% of original effect sizes were in the 95% confidence interval of the replication effect size” (RPP SCIENCE 2015, an overview of the results is available in Scientific American; in german from DLF Forschung Aktuell).

I take this worrying result as cue to describe current challenges to scientific publishing and measures to address them — including reproduction experiments, and what to do if they contest previously published and referenced work.


PDF (to print)

Org (source)

Scientific publishing has come a long way since its beginning, and its principles have allowed it to scale up from a few hundred active scientists worldwide to conferences with tens of thousands of people for a given topic. But in the last few years it hit its limits. It becomes harder each year to keep up with the amount of new papers being published and even scientists from similar fields repeatedly reinvent the same methods. To scale further and to continue to connect the scientific community, it must adapt to make it easier to get an understanding of the current state of science and keep up to date with new findings.

To grow from these challenges, scientific publishing needs to


For or about scientific work.

Surface Area of regions on an ellipsoid Earth


PDF (to print)

Org (source)

Data (netCDF4)

Calculating the area of arbitrary regions on the Earth approximated as an ellipsoid. I needed this for conversion between the output of different models.

It’s calculated in Emacs Lisp, which showed me that for somewhat complex mathematical tasks Lisp syntax isn’t only unproblematic, but actually helps avoiding mistakes. And full unicode support is great for implementing algorithms with ω, λ and φ.


Ambition the Film: This is where magic happens

I just watched the short film Ambition from ESA, and I still have tears in my eyes.

The film is awesome.

timezones of tccon stations

Timezones of most active TCCON stations in UTC+x (without daylight saving time (DST). Because I needed it and could not find a simple list quickly.

anmyondo: +9,
ascension: 0,
bialystok: +1,
bremen: +1,
caltech: -8,
darwin: 9, # Timezones2008 says 9 1/2???

Easily converting ris-citations to bibtex with emacs and bibutils

The problem

Nature only gives me ris-formatted citations, but I use bibtex.

Also ris is far from human readable.

The background

ris can be reformatted to bibtext, but doing that manually disturbs my workflow when getting references while taking note about a paper in emacs.

I tend to search online for references, often just using google scholar, so when I find a ris reference, the first data I get for the ris-citation is a link.

The solution

Track your scientific scripts with Mercurial

If you want to publish your scientific scripts, as Nick Barnes advises in Nature, you can very easily do so with Mercurial.

All my stuff (not just code), excempting only huge datasets, is in a Mercurial source repository.1

Whenever I change something and it does anything new, I commit the files with a simple commit (even if it’s only “it compiles!”).

  1. Mercurial is free software for versiontracking: 

The scientific method in a dent/tweet (140 characters)

science in a dent:

(1) Form a theory. (2) design an experiment to test the theory. (3) do it. (4) Adjust the theory, if needed → (2)

→ written in GNU social.

Please feel free to use it!

If that’s to brief:

the scientific method, explained very basically and simply.


*That’s not faith. It’s theory.

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