Science by press release

I woke up today with the news that researchers at the University of Aveiro had, "for the first time", altered the translational apparatus of an organism. I was outraged with the news: not with the science itself, but with the mindless hype surrounding it: actually, such a modification had already been performed in 2011 in C. elegans . I first thought that the "first time evah" pitch had been added by ignorant journalists, but the hype was already present in the press release from Univ. Aveiro!
The research publicized today is good and interesting, no doubt about that, but the quest for "good press" should never come at the expense of the truth. There is no excuse for that. Every bit of "good press" achieved with hype/exageration unfairly benefits those institutions and/or researchers with no moral qualms, leaving those researchers who are honest enough to not misrepresent their results in a disadvantage.

I've always disliked "science by press release", because (all other things being equal) it disproportionately benefits those who have access to the mass media, or who can afford publicists. Hyped press releases are even worse. And this can only end when science journalists stop relying on press releases to decide what is newsworthy. Though I strongly believe that such a day will not happen in the next 5 * 10⁹ years.


Addendum: Previous reports all reassigned a STOP codon to an unnatural aminoacid. The report from Univ. Aveiro is indeed the first time that a non-STOP codon has been reassigned in an organism. This difference is unfortunately not present in the press release. I still stand by all other points on my post.

Gamess (US) frequently asked questions Part 1: SCF convergence

In spite of the very high quality of the Gamess(US) documentation, the Gamess(US) list is very often flooded with requests from new users regarding the lack of convergence of the SCF procedure. A few words of advice:

When your SCF does not converge,  you should re-run the job including a $guess guess=moread $end line, as well as the complete $VEC group present in the output PUNCH file (usually called <jobname>.dat, and present in you scratch directory).

Addendum:

Whenever you read a $VEC group from a UHF run you must assign NORB in the $GUESS group. An additional problem is that by default the $VEC group only includes the occupied orbitals, and this means that in UHF runs the $VEC group does not include equal numbers of alpha and beta orbitals (e.g., a run with 41 electrons and MULT=2) will have 21 alpha orbitals and 20 beta orbitals. Therefore, if you include

$guess guess=moread NORB=21 $end

Gamess will crash because there are not 21 beta orbitals, and if you input

$guess guess=moread NORB=20 $end

there will be another error, since there are more than 20 alpha orbitals. In these cases, you should check the number of alpha and beta orbitals. Then , copy the coefficients of the extra alpha orbitals to the end of the beta orbitals. In my example above

$guess guess=moread NORB=21 $end

will yield no problems, since the modification of the VEC group yields equal numbers of alpha and beta orbitals. There is also an option to PUNCH every orbital (occupied+virtuals) at every step. In this case, Gamess always punches a full $VEC group, making it very easy to assign NORB as one can simply inspect the output file to learn the number of orbitals. However, this yields gigantic PUNCH files, and may therefore not be feasible.

You should also experiment with changing convergers, damping, etc. Some systems are notoriously hard to converge, and may require several re-iterations of the whole process.