Thursday, February 25, 2010

Aluminium ion clock

The scientists at the National Institute of Standards and Technology (NIST) created a new optical clock of unprecedented precision.
The clock, which is based on a single aluminium ion, could remain accurate to within one second over 3.7 billion years. The previous record was held by a clock with one mercury ion, which was good to one second in 1.7 billion years.
My, these are some mind-boggling figures.

I thought that one 27Al+ ion should not take much space. But then, they needed another “logic ion”, 25Mg+. And a vacuum chamber. And two lasers. (Not three lasers, as in earlier model which used Al+/Be+ pair, so I presume the new clock is more compact.) I couldn’t find in the preprint what are the dimensions of the whole contraption. However, the NIST press release features the photo of one of the authors, Chin-wen Chou, together with the famous clock. The caption says that
The ion is trapped inside the metal cylinder (center right).

Not exactly wristwatch size but easily fits in Big Ben.

Thursday, February 11, 2010


  1. In chemistry, selenite, [SeO3]2−, is a diconjugate base of selenous acid, H2SeO3.
  2. In mineralogy, selenite is a variety of gypsum, CaSO4·2H2O.
  3. In science fiction, e.g. in The First Men in the Moon by H. G. Wells, the native inhabitants of the Moon are referred to as “Selenites”.
All three words are derived from Σελήνη, Greek for the Moon. Ironically, only fictitious Selenites have a “real” lunar connection.

selenite crystal

Selenite (1) — not to be confused with selenate or selenide — is named similarly to other oxoanions of “ous” acids, such as sulfite or nitrite. The systematic name recommended by the Red Book is trioxidoselenate(2−). Now, Berzelius gave the element selenium its name by analogy with tellurium, which, in its turn, was named after Tellus, Latin for Earth. (Do you follow the logic?) The Mineral Information Institute gives an alternative explanation:
This is a reference to the silvery-gray color of metallic, non-crystalline selenium.
A similar line of thinking is responsible for naming of selenite (2):
From the Greek σελήυη, for “moon”, in allusion to the moon-like white reflections of the mineral or to the quality of the light transmitted by semi-pellucid gypsum slabs of cleavages used as windows.
Fine, but not as touching as this childhood belief:
When we were studying chemistry and the teacher talked about selenium, I thought that selenium was named after a Mexican pop star Selena who died during my childhood.
Speaking of Mexico: the world’s largest natural crystals, some as long as 11 meters, consist of selenite (2) and are found in Cueva de los Cristales in Chihuahua, Mexico.

Thursday, February 04, 2010

The rise and fall of the Zinc World

I like the way the journals such as Biology Direct now publish reviewers’ comments and authors’ responses together with a final version of the paper. The fact that reviewers’ names are made public ensure that reviewers are properly acknowledged as well as share some responsibility for releasing another pointless paper into the wild. The discussion is often more interesting than a paper. Take the couple of recent highly speculative articles on Zinc world and origin of life [1, 2]. Even though I myself would not recommend any of these manuscripts for publication (luckily nobody asked me), I am glad that these were eventually published, because I really enjoyed reading the reviews — and, occasionally, the authors’ responses.

Reviewer 4: Last but not least I find the last sentence of the paper rather revealing: what could the aesthetics of minerals to do with a scientific argument on the origin of life?

Author’s response: Aesthetic criteria are of great importance in scientific research <...> For example, my initial opposition to the idea of abiogenesis at the floor of the Hadean ocean, when I first heard about it, was purely aesthetic. I simply did not like the idea of the origin of life being in complete darkness.
Similarly, it could have been stated “I simply liked the idea of using a single type of metal cation to fulfill all life’s metal needs”. The authors acknowledge the need for transition metal ions for origin of life but argue that the zinc is preferred to other transition metals because it is not redox-active. (According to modern view, zinc is not a transition element at all — why to bring transition metals in the first place?) For example, both papers contain the statement that “iron, unlike zinc, is redox-active”. Wait a minute. Is it bad? Since zinc is not redox-active, it cannot be used as a redox cofactor, therefore there won’t be any oxidoreductases utilising zinc. But fear not; apparently, the authors think that NAD(P)H, FAD and FMN evolved before primitive life forms learned how to use Fe2+ ions safely.

Incidentally, the only danger of redox-active iron mentioned in these papers seems to be the “harmful hydroxyl radicals”. I would not worry much about them though because I don’t think they were the main hazard in largely anoxygenic environment. In general, conditions on Earth at the time were rather harsh. You would’t go outside without an oxygen mask and a very thick (a few inches?) layer of sunscreen. Now add, on top of that, ZnS-catalysed photosynthetic production of formaldehyde [2, equation 1]... yep, sounds a plausible enough way to kick off that life thing.

  1. Mulkidjanian, A.Y. (2009) On the origin of life in the Zinc world: 1. Photosynthesizing, porous edifices built of hydrothermally precipitated zinc sulfide as cradles of life on Earth. Biology Direct 4, 26.
  2. Mulkidjanian, A.Y. and Galperin, M.Y. (2009) On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth. Biology Direct 4, 27.