Update: Installing Molden on 64bit Debian based GNU/Linux Systems

Quite some time ago, I have posted a script that attempts to install Molden. This has become a very popular post but when I read the script again recently, I felt a strong obligation to post a much cleaner way to do things. The following instructions should work for any Debian based GNU/Linux distribution. This includes Ubuntu, but – while in the past, I have been using Ubuntu myself – I cannot recommend it any longer because it does a poor job in respecting your freedom. If you like Ubuntu‘s look & feel but value your freedom, you might want to give Trisquel a try. Anyway, this is about getting Molden to work.

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A Questionable Interview on Climatic Change

Today’s afternoon, there was an interview with the Austrian limnologist Prof. em. Wilhelm Ripl in Deutschlandfunk’s “Zwischentöne” [5]. Whilst mentioning a couple of very interesting things, Ripl also said a few things that can’t be left without criticism.

Ripl was criticizing that established climatic models are making use of data which is of questionable representativity stating that it is not possible to use such data for statistic analysis and averaging because it is “non-statistical in some way”. He was also bemoaning that too much funding was spent on computer simulations which he thinks are in principle unable to represent the global climatic processes accurate. Fist of all, the climatic models used nowadays are consistent and correct as approved by measurement as shown below. At least for a time range of decades. No one can deny this.

Figure and description taken from ref. 1.

He was further criticizing that the models exclude the processes of (especially small scale) heat transfer via water vaporization and condensation. I’m not an expert on climatic modeling but a quick research on the topic lead me to NASA Earth Science’s Integrated Biosphere Simulator (IBIS) [2] which seems to implement just what Ripl felt was missing. It is an Open Source Fortran framework that allows for Dynamic Global Vegetation Modeling (DGVM). (Freely available from [3].) It is described in a well cited review article by Foley et al. (1996), [4]. Unfortunately, my university refuses to by this journal so I was left with the abstract but I’ll post an update as soon as I could manage to read the whole article.

At an other point, Ripl makes the very strange claim that giving off energy by radiation into empty space was impossible. I’m not certain if he maybe just confused his own words but taken as given, the statement is of course complete nonsense. Radiating means emitting photons, each of them having a relativistic energy of E = h c / λ. Where h is Planck’s constant, c is the speed of light and λ is the wavelength of the emitted photon. Thus the emitter looses this energy with each photon being sent to outer space. If this process was not existing, all stars (and many other things) were to explode immediately.

Last but not least, he (and the interviewer) were mentioning several times that meteorologists should not focus exclusively on carbon dioxide as the only green house gas. They don’t do so at all. But one has to be careful if listening to them. Many models do not account for each green house gas explicitly (which would mean rather unfeasible computational effort) but instead use a “virtual” green house gas measured in CO₂ equivalents. That is, if a substance, say methane, is 25 times more active as a green house gas than is CO₂ it accounts for 25 CO₂ equivalents. The factor 25 is called the Global warming potential (GWP) for methane. Determining the GWP must not only account for the green house activity but also the retention time of the gas in the atmosphere. For example, methane is removed from the atmosphere by naturally occurring processes rather quickly while SF₆ stays in the atmosphere for thousands of years. The aforementioned value of 25 for methane corresponds to an averaging timespan of 100 years. Frequently, if CO₂ is said, CO₂ equivalents are actually meant.

I do not want to compromise Prof. Ripl with this text in no way. But I believe that mistakes have to be corrected. Even (or especially) if they were made by honorable scientists.

References

[1] S. Solomon, D. Qin, M. Manning, Z. Chen, K.B. Marquis, M. ans Averyt, M. Tignor, and H.L. Miller (Eds.), IPCC Fourth Assessment Report (AR4) – Climate Change 2007: The Physical Science Basis. Cambridge University Press, 2007.
[2] NASA Earth Science, Integrated Biosphere Simulator Model (IBIS), Version 2.5. http://daac.ornl.gov/MODELS/guides/IBIS_Guide.html
[3] http://www.sage.wisc.edu/download/IBIS/ibis.html
[4] J. Foley et al., An integrated biosphere model of land surface processes, terrestrial carbon balance, and vegetation dynamics. Global Biogeochemical Cycles, 10(4):603-628, 1996.
[5] Zwischentöne – Der Limnologe Wilhelm Ripl im Gespräch mit Michael Langer. Deutschlandfunk, 2011-05-01 13:30 (CEST). http://www.dradio.de/dlf/playlist/dlf_zwischentoene/1445206/

Mr. zu Guttenberg Damages Germany’s Scientific Reputation if not Standing Down Now

Earlier this month, Prof. Andreas Fischer-Lescano (professor for municipal, european and international law at the University of Bremen) published a critical article in the magazine “Kritische Justiz” about the PhD thesis of Karl-Theodor zu Guttenberg [1] who currently serves as the minister of defense for the Federal Republic of Germany. In this article Mr. Fischer-Lescano stated and referenced, that several pieces of the thesis were likely to be not written by the author but taken from other works without proper citation. Meanwhile, a wiki project [2] was launched that attempts to analyze the work based on recommendations of Weber-Wulff und Wohnsdorf [3] and—in my humble opinion—does a serious job. Up till today the found abuse of foreign work on as many as 73 % of the pages, excluding index and appendices.

Pages with presumably plagiarized text passages in Mr. zu Guttenberg's PhD thesis. Taken from and with permission of the GuttenPlag Wiki. black: Pages with plagiarism, red: pages with plagiarism from multiple sources, white: pages without plagiarism, light-blue: index and appendix

After denying he had done any fault at the beginning, Mr. zu Guttenberg quickly had to admit that he did make significant mistakes in his work and asked the University of Bayreuth to withdraw his PhD, which did so yesterday. However, he firmly rejects to have cheated intentionally [4].

The University confirmed the work violating their scientific standards but refused to give a statement on whether or not Mr. zu Guttenberg plagiarized. The rules for dissertation of the University of Bayreuth [5] state

§ 16 Ungültigkeit der Promotionsleistungen

1. Ergibt sich vor der Aushändigung der Urkunde, daß sich der Bewerber im Promotionsverfahren einer Täuschung schuldig gemacht hat, so erklärt die Promotionskommission alle bisher erworbenen Berechtigungen für ungültig und stellt das Verfahren ein.
2. Wird die Täuschung erst nach Aushändigung der Urkunde bekannt, so kann nachträglich die Doktorprüfung für nicht bestanden erklärt werden. Die Entscheidung trifft die Promotionskommission.
3. Waren die Voraussetzungen für die Zulassung zur Promotion nicht erfüllt, ohne daß der Kandidat hierüber täuschen wollte, und wird diese Tatsache erst nach Aushändigung der Urkunde bekannt, so wird dieser Mangel durch das Bestehen der Doktorprüfung geheilt.

Number 2 and 3 are of special interest to me since they clearly distinguish between a candidate unintentionally producing poor scientific work, in which case the PhD can’t be withdrawn once the final document has been passed to the candidate and intentional fraud, which makes it possible to do so. From my point of view the university indeed would have been obligated to check if intentional plagiarism was handed in to decide whether or not to withdraw or not the PhD. The minister can’t just waive his PhD just as he can’t give it to himself. Attempting to do so means mocking on the university’s authority.

Even worse, Mr. zu Guttenberg thinks that this affair is no reason to stand down from his occupation as minister but asks the parliament to excuse this mistake due to personal exhaustion.

I’ve never been a political opponent of Mr. zu Guttenberg and I’m really convinced that he indeed served the country well as a minister and appreciated the refreshing style of politics that came with him. Even more, I’ve already made my thoughts about him eventually becoming the next chancellor. But speaking as a scientist, I urgently call him to stand down from his office. The university avoided taking a clear position on the question of plagiarism or not, which I think would have been their obligation. Nevertheless, one doesn’t accidentally copies two third of his thesis after spending seven years writing it. This is almost certainly a case of intended cheating. This is unacceptable for a states official for several reasons.

First of all, our modern societies are based on the ideals of the enlightenment and a scientific view on the world. A person who represents our state built upon these principles must pay a minimum amount of respect to them. I simply can’t trust a person who was cheating on such elementary questions any longer. Secondly, an official not only does his job but also represents the state he serves. And I do not want to be represented by a gambler just as I don’t want to be represented by someone who steals or a drives drunk. (Two examples mentioned earlier in the debate by other commentators.) And last but not least, his behavior counteracts any effort on behalf of the Federal Republic of Germany to strengthen scientific accuracy and respect of intellectual property. What should his colleagues tell Chinese officials to convince them to protect intellectual property better? What should a soldier in Germany’s army think, who is struggling hard to get a higher degree but fails? What should I tell a student whom I catch upon cheating on an exam?

Science is not the exclusive club of infallible gurus but an open society of honest hard working people making and correcting their mistakes. Being wrong is natural as can be. But being dishonest is an unjustifiable misbehavior. If zu Guttenberg’s thesis was just bad in the sense that he did poor work, it wouldn’t need a word of public comment. But his work wasn’t bad. (As far as jurists tell me these days.) It was dishonest. I never liked it when lab supervisors checking student’s reports only had an eye on their results (which unfortunately happens too often). I always encouraged my colleagues to hand in their actual results and never ever manipulate anything and often fought for that. (See a prior blog on this issue.) My results were often bad, the conclusions I drew were often wrong and perhaps my own PhD thesis will some day become a real disaster. But I do claim that I have always been honest on what I was saying which frequently was to my own and other’s disadvantage.

Withdrawing a PhD is not something that happens every now and then. It is an ultima ratio in cases of severe misbehavior. Please, Mr. zu Guttenberg, be honest enough now to admit your fault, stand down from your office and prevent further damage to the scientific community of Germany. I don’t believe that dishonesty can be justified in any way. But I do believe that people feeling truly sorry for their faults some day should and will get a second chance.

 

P.S. No matter what end this political story will take I deeply hope that it will finally convince any German university to routinely use anti-plagiarism software to double check anything handed in to them. This is state of the art and really should be used. It could prevent a lot of unpleasing things.

References

[1] http://www.kj.nomos.de/fileadmin/kj/doc/zu_guttenberg.pdf
[2] http://de.guttenplag.wikia.com/wiki/GuttenPlag_Wiki
[3] Weber-Wulff and Wohnsdorf; Strategien und Plagiatsbekämpfung. Wissenschaft & Praxis, (2) 2006, pp. 90–98
[4] Uni Bayreuth kassiert Guttenbergs Doktortitel. Financial Times Deutschland, 2011-02-23 — http://www.ftd.de/politik/deutschland/:plagiatsaffaere-uni-bayreuth-kassiert-guttenbergs-doktortitel/60016403.html
[5] Promotionsordnung für die Rechts- und Wirtschaftswissenschaftliche Fakultät der Universität Bayreuth in der Fassung der Achten Änderungssatzung Vom 10. August 2010 — http://www.uni-bayreuth.de/universitaet/leitung_und_organe/Universitaetsverwaltung/abt1/amtliche-bekanntmachungen/konsolidierteFassungen/2010/2010-058-kF.pdf

Gravitation and the Relativity of Gold

The other day I was taught about some basics of relativistic effects in chemistry. I’m not at all into relativistic quantum mechanics (yet) but I was still amused about the following statement:

In heavy atoms, the electrons approach the speed of light which makes them gain relativistic mass. This causes additional gravitational attraction between the electron and the nucleus which leads to a contraction of the electron’s orbital.

It is obvious that gravity is by far too weak to play any role on this scale. However, “obvious” is not scientific so here I’ll supply the respective calculation.

In Bohr’s picture, the electron circles around the nucleus on a stable pathway that is determined by the equilibrium of Coulomb attraction and centripetal force. The former is given by

Equation 1

where Q_e is the elementary charge, ε₀ the electric constant (vacuum permittivity), Z_eff is the effective nuclear charge “seen” by the electron and r the nucleus–electron-distance.

The gravitational force on the other hand would be given by

Equation 2

with the gravitation constant (Newtonian constant) G and the mass of the electron and the nucleus m_e and m_n respectively. Or — if the electron’s mass increases by Δm_e — an additional gravitational force of

Equation 3

emerges. Comparing this with equation 1 we find that

Equation 4

On Wikipedia (ref. 1) I found that the 1 s electron in gold (which is considered to be one of the elements with the highest relativistic effects) “travels at a speed” of 58 % c. This means its mass increases by

Equation 5

which is in agreement to the value claimed by the person mentioned above. Putting this in equation 4 we obtain

where I have used the standard atomic mass of gold of 197.0 amu (1 amu = 1.661E^-27 kg) and the effective nuclear charge for the gold 1 s electron found at [2].
Using G = 6.674E^-11m³ kg^-1 s^-2, ε₀ = 8.854E^-12 A s V^-1 m^-1, Q_e = 1.602E^-19 C and m_{e, rest} = 9.109E^-31 kg we finally get

making it absolutely clear that gravity is completely irrelevant.

On the other hand the centripetal force is given by

Equation 6

Letting this equal the Colombian force and solving for r we find

Equation 7

If we keep everything else constant but once put m_e = m_{e, rest} and once m_e = m_{e, rest} + Δm_e the two results will differ by

This is — accepting this simple but useful picture of an atom — the relativistic orbital contraction for the 1 s orbital of gold.

References

[1] Relativistic quantum chemistry. (2010-10-27). In Wikipedia, The Free Encyclopedia. Retrieved 05:27, 2010-11-14, from http://en.wikipedia.org/w/index.php?title=Relativistic_quantum_chemistry&oldid=393187449
[2] Effective nuclear charges for gold. (2010). In WebElements: the periodic table on the web. Retrieved 05:28, 2010-11-14 from http://www.webelements.com/gold/orbital_properties.html

0.000000125 are Not a Coincidence

Recently, I had to use some ab initio results for a kinetic computation. I was interested in a transition dipole moment of the molecule but none was given. However, there were some “infrared intensities” given in — crazy enougth — km mol^-1. I was rather confused about that because, by all convention, this is no unit of an intensity.

[Klippenstein:1996] gives a conversion factor that claims basically:

A = 1.25E^-7 I(in km mol^-1) ν²(in cm^-1)

where A is the Einstein coefficient for spontaneous emission.

I generally do not trust such formulas. Furthermore I think they are an unnecessary attack on healthy physical thinking. But how to do better? A colleague found a tutorial of Dunbar where he presented essentially the same formula.

Finally [Neugebauer:2002] could give me deeper insight. The values given as “infrared intensities” seem to be what Neugebauer calls integrated absorption coefficients. Using the definitions given in [Neugebauer:2002] it is a simple and straight forward exercise to calculate the Einstein coefficient as

A = I 8 π c N_A^-1 (ν/c)²

In this formula I let I be the symbol for the integrated molar absorption coefficient for the sake of continuity.

If one investigates the numerical value of 8 π c N_A^-1 he finds it to be about 1.25115E^-14. The difference of a factor of E⁷ compared with Klippenstein’s formula is explained by recalling that he is suggesting to use km and cm^-2 instead of SI units.

References

[Klippenstein:1996] Klippenstein et. al. Ion–Molecule Radiative Association Kinetics. J. Chem. Phys., 104(12), 1996.

[Neugebauer:2002] Neugebauer et. al. Raman and IR Spectra for Buckminsterfullerene. J. Comp. Chem., 23(9), 2002.