Phe—Val crosslink in symerythrin

The crystal structure of diiron protein symerythrin from Cyanophora paradoxa reveals a novel C—C cross-link between valine and phenylalanine residues [1].

1. Cooley, R.B., Rhoads, T.W., Arp, D.J. and Karplus, P.A. (2011) A diiron protein autogenerates a valine-phenylalanine cross-link. Science 332, 929.

Open and closed P450 2B4

The crystal structures of rabbit P450 2B4 covalently bound to the mechanism-based inactivator 4-tert-butylphenylacetylene in closed (a) and open (b) conformations have been solved [1].

(a)

(b)

1. Gay, S.C., Zhang, H., Wilderman, P.R., Roberts, A.G., Liu, T., Li, S., Lin, H.-l., Zhang, Q., Woods, V.L., Jr., Stout, C.D., Hollenberg, P.F. and Halpert, J.R. (2011) Structural analysis of mammalian cytochrome P450 2B4 covalently bound to the mechanism-based inactivator tert-butylphenylacetylene: insight into partial enzymatic activity. Biochemistry 50, 4903—4911.

Importance of being obsessive-compulsive

Never underestimate the importance of naming. For instance, I would probably never read the excellent paper by Kuhn and Wahl-Jensen [1] if not for its title. (Seriously, read it. Although the note appears in Binomina, it is relevant to scientific nomenclature and terminology in general, not just biological taxonomy.) They write:

When terms get renamed just for the sake of renaming them then outrage at nomenclature experts is justified. But it is a two-way street. Nomenclature without discourse with the scientific community working in laboratories is useless — but science without nomenclature cannot be performed, either.

Conversely, Roderic Page argues that “quite a lot” of biology can be performed without “proper” taxonomic names [2], even though his

definition of “proper” name is a little loose: anything that had two words, second one starting with a lower case letter, was treated as a proper name.

Just imagine the fury of those who are “obsessive-compulsive about terminology” on reading that! Surely not any binomial name is “proper”? However, that is beyond the point. Linnaean names are just labels. They may be preferable to NCBI tax_id codes because of aesthetic considerations but ultimately they are dispensable. We only cling to them because we believe that these labels have, as Robert M. Pirsig put it, “an intrinsic sacredness” of their own [3]:

One finds that in the Judeo-Christian culture in which the Old Testament ‘Word’ had an intrinsic sacredness of its own, men are willing to sacrifice and live by and die for words.

But what about chemistry? On the one hand, chemistry appears to be in a better position because of superiority of chemical nomenclature over, well, any other known nomenclature. The name constructed according to the rules of systematic chemical nomenclature holds the key to the structure of the entity in question. It does not mean that there could or should be only one “proper” name for one structure. For example, “tetrafluoridolead” (additive nomenclature) and “tetrafluoroplumbane” (substitutive nomenclature) correspond to the same entity, PbF₄. You don’t have to know it, because you can figure it out. Compare this with the situation in biology: there is no way to deduce that, say, Prunus dulcis and Amygdalus communis are synonyms.

On the other hand, we chemists often fall into the same trap as anyone else: we tend to believe that “proper” naming of a compound (of known structure) automatically improves our knowledge of it. But why? The terms can change. The nomenclature rules are changing. For a structure of certain complexity, the application of the same rules by different chemists (or different naming software) may result in different systematic names. Some structures as yet cannot be named by any software. So what? It is highly unlikely that a name which takes more than 100 characters will be used in any discourse. I distinctly remember thinking about it a few years ago while reading the draft of IUPAC Recommendations for rotaxane nomenclature [4]. Why not to use the (equally unpronounceable but more useful) InChI string instead?

Still, I wouldn’t dismiss the aesthetics that easily. For me, concise, clear, elegant is good; long, ambiguous, ugly is bad. And coming back to the title of [1]: “being obsessive-compulsive about terminology and nomenclature” is neither a vice nor a virtue. It is a mental condition that some people (myself included) have, for better or for worse.

1. Kuhn, J.H. and Wahl-Jensen, V. (2010) Being obsessive-compulsive about terminology and nomenclature is not a vice, but a virtue. Bionomina 1: 11—14.
2. Page, R. (2011) Dark taxa: GenBank in a post-taxonomic world.
3. Pirsig, R.M. (1974) Zen and the Art of Motorcycle Maintenance.
4. Yerin, A., Wilks, E.S., Moss, G.P. and Harada, A. (2008) Nomenclature for rotaxanes and pseudorotaxanes (IUPAC Recommendations 2008). Pure Appl. Chem. 80, 2041—2068.

Amethyst

Last Summer, we bought this crystal-growing kit in Oxfam. It contains ingredients and instructions to grow several types of crystals. Those nicknamed “quartz” and “emerald” in fact are monoammonium phosphate, NH₄H₂PO₄, while “amethyst” and “fluorite” are grown from a solution of potassium aluminium sulphate, KAl(SO₄)₂. Our latest experiment was to grow an “amethyst” crystal cluster. Timur and I prepared the solution, poured it over two stones from our garden and left to grow for a week. Here’s the result.

Chlorite dismutase

Photosynthesis is not the only dioxygen-evolving biological process. For instance, chlorite dismutase (Cld; EC 1.13.11.49) catalyses the production of O₂ from chlorite (1):

ClO2− → Cl− + O2

(1)

The reaction (1) is not really disproportionation, and NC-IUBMB made a valid point that the term “chlorite dismutase” is “misleading”. Even so, the NC-IUBMB-approved, sorry, “accepted” name “chlorite O₂-lyase” for an oxidoreductase is equally absurd; I am going to ignore it.

Chlorite dismutase from Azospira oryzae exists as a homohexamer [1] while Cld from Dechloromonas aromatica [2] and enzyme from Candidatus Nitrospira defluvii [3] are homopentamers.

The active site contains a single haem group [Fe(ppIX)] coordinated by a proximal histidine residue. Goblirsch et al. [2] propose the mechanism where the reaction of chlorite within the distal pocket of Cld generates hypochlorite (ClO⁻) and a compound I intermediate [Fe(ppIX)O] (1a). Then ClO⁻ rebounds with compound I forming the chloride and dioxygen (1b):

ClO2− + [Fe(ppIX)] → ClO− + [Fe(ppIX)O]	(1a)
ClO− + [Fe(ppIX)O] → Cl− + O2 + [Fe(ppIX)]	(1b)

1. de Geus, D.C., Thomassen, E.A.J., Hagedoorn, P.-L., Pannu, N.S., van Duijn, E. and Abrahams, J.P. (2009) Crystal structure of chlorite dismutase, a detoxifying enzyme producing molecular oxygen. J. Mol. Biol. 387, 192—206.
2. Goblirsch, B.R., Streit, B.R., DuBois, J.L. and Wilmot, C.W. (2010) Structural features promoting dioxygen production by Dechloromonas aromatica chlorite dismutase. J. Biol. Inorg. Chem. 15, 879—888.
3. Kostan, J., Sjöblom, B., Maixner, F., Mlynek, G., Furtmüller, P.G., Obinger, C., Wagner, M., Daims, H. and Djinović-Carugo, K. (2010) Structural and functional characterisation of the chlorite dismutase from the nitrite-oxidizing bacterium “Candidatus Nitrospira defluvii”: Identification of a catalytically important amino acid residue. J. Struct. Biol. 172, 331—342.

Femtosecond X-ray nanocrystallography of PSI

It is a well known fact (to those who know it well) that in order to obtain a decent diffraction pattern one has to grow a decent-size crystal first. Well, that is about to change. The PDB entry enigmatically named “femtosecond X-ray protein nanocrystallography” [1] in fact contains the structure of the photosystem I (PSI) from Thermosynechococcus elongatus solved by this new method [2]. In this work, more that 3 million diffraction patterns were collected from really small PSI crystals (from ~200  nm to 2  μm in size) illuminated by the new femtosecond X-ray laser, the Linac Coherent Light Source in Stanford. According to the authors,

We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes.

1. PDB:3PCQ
2. Chapman, H.N., Fromme, P., Barty, A. et al. (2011) Femtosecond X-ray protein nanocrystallography. Nature 470, 73—77.

P450 from Actinoplanes teichomyceticus

The crystal structure of the P450 monooxygenase from Actinoplanes teichomyceticus (CYP165D3) involved in biosynthesis of antibiotic teicoplanin has been solved [1].

1. Li, Z., Rupasinghe, S., Schuler, M. and Nair, S.K. (2011) Crystal structure of a phenol-coupling P450 monooxygenase involved in teicoplanin biosynthesis. Proteins: Structure, Function, and Bioinformatics 79, 1728—1738.

P450 monooxygenase AurH from S. thioluteus

The first crystal structures of the unique P450 monooxygenase AurH from Streptomyces thioluteus have been solved [1].

1. Zocher, G., Richter, M.E.A., Mueller, U. and Hertweck, C. (2011) Structural fine-tuning of a multifunctional cytochrome P450 monooxygenase. J. Am. Chem. Soc. 133, 2292—2302.

Natural products

Do a Google search and you’ll find all sorts of stuff claimed to be “natural products” — amazingly, some of them even are “chemical-free”! Now seriously. To quote IUPAC’s 1999 recommendations [1],

The nomenclature of natural products has suffered from much confusion.

That does not surprise me. What is surprising, however, that neither these nor the previous recommendations [2] tell us what the “natural products” are. Ditto the Gold Book. It may define terpenoids as “natural products and related compounds formally derived from isoprene units” but the natural products go without explanation. (Nor is it clear what “related compounds” are.) The very same Gold Book says that natural graphite is “a mineral found in nature”. Therefore, “natural” means “found in nature”. Right? Right. Is natural graphite a natural product? I am not sure.

Let us look in Webster then:

A chemical substance produced by a living organism; — a term used commonly in reference to chemical substances found in nature that have distinctive pharmacological effects. Such a substance is considered a natural product even if it can be prepared by total synthesis.

Is that any better? Both dioxygen and nitric oxide are produced by living organisms and have rather distinctive pharmacological effects, yet most chemists would hesitate to call them natural products. In The Concise Oxford Dictionary, the first definition of “natural” is

existing in or caused by nature; not artificial.

Of course human beings are parts of nature, but maybe this negative definition, “not artificial”, is indeed most useful?

In ChEBI, natural product (no definition so far) is an organic molecular entity (so no O₂ or NO here) and includes the following classes:

• alkaloid
• carbohydrate
• cyclitol
• heterocyclic natural product
• lipid
• peptide
• phenylpropanoid
• polyphenol

On the first glance, nothing looks particularly disturbing here. But I see a bit of a problem with ontology. First, all is a children of natural product have to be natural products. What if we have, say, (artificially) fluorinated carbohydrates? Are they still carbohydrates? If no, then the True path rule is broken. If yes, then some “unnatural” compounds will be considered natural products. I don’t mind that — perhaps that will cover “related compounds” (whatever they are) nicely.

Second, CHEBI:33243 belongs to chemical entity ontology, which is (or at least it should be) purely structure-based. The origin does not enter here. There is no such thing as intrinsic “naturalness” in a natural product molecule: natural product remains a natural product even if (artificially) prepared by total synthesis.

Natural products often are equated with secondary metabolites. This does not seem right. In ChEBI, secondary metabolite (“A metabolite that is not directly involved in the normal growth, development or reproduction of an organism” — another negative definition?) belongs to role ontology. (The role ontology sounded such a good idea at the time... no, don’t get me started.) At best, one can say some natural products have role “secondary metabolite”. Yuck.

To summarise: “natural product” appears to be a rather useless top-level term. Let us look at the sources of natural products: plants, fungi, bacteria, animals. What if, instead of saying “fungal natural product”, we say “fungi-specific compound”? In this case, we discard primary metabolites, other simple compounds found just about everywhere in the universe and are left with exactly what we want: molecules isolated from and specific for fungi.

Or are we? Antibiotics, naturally synthesised by fungi, are not naturally found in humans. But when we take them, they are naturally metabolised in our liver and eventually excreted with urine. Are these metabolites the natural products? If yes, are they fungal or animal or neither?

1. Revised Section F: Natural products and related compounds (IUPAC Recommendations 1999). Pure Appl. Chem. 71, 587—643 (1999).
2. Nomenclature of Organic Chemistry. Section F: Natural Products and Related Compounds. Recommendations 1976. Eur. J. Biochem. 86, 1—8 (1978).

It’s elementary

According to IUPAC’s Principles of Chemical Nomenclature [1],

An element (or an elementary substance) is matter, the atoms of which are alike in having the same positive charge on the nucleus (or atomic number). In certain languages, a clear distinction is made between the terms ‘element’ and ‘elementary substance’. In English, it is not customary to make such nice distinctions, and the word ‘atom’ is sometimes also used interchangeably with element or elementary substance. Particular care should be exercised in the use and comprehension of these terms. An atom is the smallest unit quantity of an element that is capable of existence, whether alone or in chemical combination with other atoms of the same or other elements.

You can’t help noticing the circular nature of these definitions: An element is matter, the atoms of which have the same atomic number; while an atom is the smallest unit quantity of an element. And what are “atoms of the same or other elements” if not just “any atoms”?

Of course it is not helpful that ‘element’ is used for either ‘elementary substance’ or ‘atom’. The ChEBI solution was to get away from ‘element’. Instead, there are either atoms or elemental molecular entities. These belong to different branches of ontology, so they should not really be confused. Or at least, that was the idea.

In ChEBI, ‘elemental’ applies to any class of molecular entities which consist of only one type of atom, be they mono- or polyatomic. For instance, elemental oxygen can be mono-, di- or triatomic. On the other hand, the oxygen atom can be part of a non-elemental molecular entity.

If there is a scope for confusion, people will get confused. Here’s a question I heard on more than one occasion: what is the difference between monoatomic oxygen and oxygen atom? After all, any form of monoatomic oxygen, viz. oxide(•1−), oxide(2−), or neutral monooxygen, can also be referred to as an ‘oxygen atom’. Ditto any of the monooxygen groups: oxido (—O⁻), oxo (=O) and oxy (‒O‒). The thing is, they belong to different universes (which, properly, should be made disjoint):

• monoatomic oxygen is a monoatomic entity is a molecular entity
• monooxygen group is a group
• oxygen atom is a atom

A group does not exist on its own: it is always a part of polyatomic entity and consists of at least one atom plus at least one bond. Monoatomic entity consists of one (and only one) atom and does exist on its own. Since we need ‘atom’ to define both groups and molecular entities, it is a good idea to keep atoms in an independent, disjoint branch.

1. Leigh, G.J., Favre, H.A. and Metanomski, W.V. Principles of Chemical Nomenclature: A Guide to IUPAC Recommendations. Blackwell Science, 1998, p. 3.

Ontology and reality

One of these days, I keep promising myself, I am going to publish something incredibly clever about chemistry, ontology and/or chemical ontology. Then again, I need some incentive to do so, and there’s none in my view. In the meantime, I am happy that somebody else has bothered to write a paper dealing with so-called “realist” approach to ontology [1].

Personally, I never cared much about the “reality” as used in context of OBO Foundry Principles [2]:

Terms in an ontology should correspond to instances in reality.

Worse still is its “corollary”:

Ontologies consist of representations of types in reality — therefore, their preferred terms should consist entirely of singular nouns.

(Why? Does “reality” really consist of singular English nouns?)

Now Lord and Stevens confirm my gut feeling that “realism” (the authors take care to clarify that “realism” in [1] stands for “realism as practiced by BFO”) applied to ontology building often results in unnecessary complexity. Everybody who ever studied physics (or English) in school would agree that expression |dr/dt| is much better definition of speed than the one provided by PATO: “A physical quality inhering in a bearer by virtue of the bearer’s rate of change of position”. To quote [1],

It makes little sense to replicate the models of physics using English instead of a more precise mathematical notation.

Alas, this is exactly what BFO (and most of OBOs) are trying to do. By going “where science has gone before” without learning the language of the science, BFO & Co. keep reinventing the square wheel.

OK, what about chemistry? Chemistry has developed its own language which makes the plain-text definitions for molecular entities redundant. The 2-D diagram (connectivity) defines the molecule of interest better than a paragraph in English. In theory, the systematic name should provide the exactly same information (and thus to be usable as a definition). However, the systematic names for even relatively small molecules often are too complicated to be widely (or ever) used.

Take the systematic name (a) for beauvericin. You are extremely unlikely to either hear it (because it is more or less unpronounceable) or see it (it takes more than one line of text, which is annoying). More importantly, there is a certain limit of molecular complexity above which the systematic names (according the existing nomenclature rules, that is) simply cannot be generated. On the other hand, the diagram (b) is both beautiful and useful.

(a)	(3S,6R,9S,12R,15S,18R)-3,9,15-tribenzyl-4,10,16-trimethyl-6,12,18-tri(propan-2-yl)-1,7,13-trioxa-4,10,16-triazacyclooctadecane-2,5,8,11,14,17-hexone
(b)

Not only are the 2-D diagrams self-defining, they provide all the information needed to build the consistent ontology for molecular entities. With a few simple rules, the ontology will build itself from scratch, I promise. But this is a topic for another post.

1. Lord, P. and Stevens, R. (2010) Adding a little reality to building ontologies for biology. PLoS ONE 5, e12258.
2. OBO Foundry Principles.

Terminology vs nomenclature

First published 8 September 2010 @ just some words

According to The Concise Oxford Dictionary,

nomenclature n. 1 a person’s or community’s system of names for things. 2 the terminology of a science etc. 3 systematic naming. 4 a catalogue or register.

terminology n. (pl. -ies) 1 the system of terms used in a particular subject. 2 the science of the proper use of terms.

I must say that these definitions do not add much clarity. Do you see any difference between “system of names for things” and “system of terms”? Moreover, the nomenclature (2) appears to be equated with the terminology. As for terminology (2), it is akin to terminology as defined by Wikipedia: “the study of terms and their use”, although I have my doubts whether there is such thing as “the science of the proper use of terms”. As was mentioned before, “logy” does not always mean “a subject of study or interest”. And what is “proper”?

On the other hand, Merriam-Webster defines terminology as

1 the technical or special terms used in a business, art, science, or special subject
2 nomenclature as a field of study

No, this does not help at all. Let us agree on the following: terminology is not nomenclature, and nomenclature is not terminology. I suggest these working definitions:

terminology: a set of terms used in a particular field.
nomenclature: a system of generating new terms for a particular field.

Completely different things. Terminology is a subset of vocabulary and, therefore, is part of the language. Nomenclature is a set of external rules. A good nomenclature system has few rules all of which should be understood and applied, preferably with reproducible results, by more than one person.

That is not to say that terminology does not depend on nomenclature or vice versa. Terms can be formed by systematic application of nomenclature rules — that’s what the nomenclature is devised for. But they also can arise by different mechanisms, just like any new words do. Often, terms are recruited from the existing lexicon and conferred new meanings. For instance, the word “residue” acquired specific meanings in fields of math, chemistry or law.

The Russian word for nomenclature, номенклатура, has an additional meaning: the bureaucratic class of Soviet Union and its descendants (as in “post-Soviet nomenklatura”).

Spoken chemistry

As I was going, for the n^th time, through the draft of the “new Blue Book”, it did strike me how much attention is paid to the appearance of a printed word. It is discussed in length what type of dash or bracket to use, which part of term has to be italicised and so on, whereas we often do not even know how to pronounce it. Which is a shame really, because I think IUPAC should take care of pronunciation (and comprehension of a spoken word) when coming with nomenclature recommendations. These are meant to improve the quality of chemical language, right? But the language where words cannot be pronounced is dead. (Think ancient Egyptian.)

Imagine we are given a task of recording an audio book on chemical nomenclature. Suddenly the names that look neat on paper become next to useless. Why? We do not pronounce parentheses (brackets, braces). We can’t pronounce sub- or superscripts. Ditto dashes, full stops and colons, which all can be parts of systematical names. Not to mention white space.

No, in olden days the pronunciation of your chemicals was taken seriously. Back in 1949, Dr. W. Bryce Orme wrote in a letter to British Medical Journal [1]:

Doctors and chemists are aware that difficulties occur in reaching consistency in the pronunciation of certain chemical terms, such as benzene and benzine, but generally it is conceded that the former should be rendered as ben'zēn and the latter ben'zin. It was, however, a shock to hear several highly qualified and distinguished chemists at a well-known pharmaceutical laboratory all referring to the radical CH₃ as mēthyl. I had the temerity to correct them and pointed out that the term was derived from the Greek μεθυ = wine + ύλη = wood. . . . Neither Dorland’s Medical Dictionary nor our old school friend, Liddell and Scott’s Lexicon, refers to any latitude in the pronunciation of methyl.

Well I never. American Chemical Society had a Nomenclature, Spelling and Pronunciation Committee, which even came up in 1934 with a list of recommended pronunciation for 437 terms [2]. Apparently, one even could order the complete report by writing to the chairman of the committee:

A charge of five cents per reprint (postage acceptable) to cover costs is made.

Sounds like a bargain, but that was quite a while ago. So far I was unable to get hold of the report. However, I found the next best thing: a list of about 400 common chemical terms that originally appeared on an audio tape prepared by Dr. M.P. Sammes and the Hong Kong Association for Science and Mathematics Education in 1988 [3]. Now, at long last, I know how to say “2-ethanoyloxybenzenecarboxylic acid”.

1. Orme, W.B. (1949) Points from letters: Pronunciation of chemical terms. Br. Med. J. 2 (4638), 1236.
2. Crane, E.J. (1934) The pronunciation of chemical words. J. Chem. Educ. 11, 454.
3. Sammes, M.P. Pronunciation of Chemical Terms.

Don’t trust your eyes

Ultramarine differs from other inorganic pigments in that it does not contain any transition metals. It is the sulfur species that confer the colour: S₃^•− (blue ultramarine), S₂^•− (yellow ultramarine) or S₄ (red ultramarine). Green ultramarine contains both S₂^•− and S₃^•− [1].

You’d think that by now they should know what the structure of ultramarine is. But no. In the Inorganic Crystal Structure Database I’ve found only two structures called “ultramarine” (ICSD 27523 and 27524), both associated with a paper from 1936 [2]. The composition of ICSD 27523 is given as Na₈Al₆Si₆O₂₄S_2.5·(H₂O)_0.6. The structure (see figure below) is an aluminosilicate cage containing sodium cations and beautiful octahedral sulfur clusters. Wait a minute. S₇ clusters? Never heard about those before.

A more recent structure of deuterated lazurite, Na_7.5Al₆Si₆O₂₄S_4.5·(D₂O)_0.5 (ICSD 63022), also featuring S₇ octahedra, provided an explanation. The authors [3] wrote that

to accommodate the indications emerging from the difference maps, the octahedral model of sulfur occupancy was modified to reproduce a more even density inside cage by adding a further sulfur to the hollow octahedral shell, with sulfur occupancies rescaled accordingly to maintain S₃ overall.

I feel relieved if slightly disappointed.

1. Landman, A.A. (2003) Aspects of solid-state chemistry of fly ash and ultramarine pigments. Doctoral Thesis, University of Pretoria.
2. Podschus, E., Hofmann, U. & Leschewski, K. (1936) Röntgenographische Strukturuntersuchung von Ultramarinblau und seinen Reaktionsprodukten. Zeitschrift für anorganische und allgemeine Chemie 228, 305—333.
3. Tarling, S.E., Barnes, P. and Klinowski, J. (1988) The structure and Si,Al distribution of the ultramarines. Acta Crystallographica B44, 128—135.

Rhodothermus marinus HiPIP at 1.0 Å

Meike Stelter and colleagues have solved the crystal structure of the reduced form of a high-potential iron–sulfur protein (HiPIP) from the thermophilic eubacterium Rhodothermus marinus.

This is the first structure of a HiPIP isolated from a nonphotosynthetic bacterium involved in an aerobic respiratory chain. The structure shows a similar environment around the cluster as the other HiPIPs from phototrophic bacteria, but reveals several features distinct from those of the other HiPIPs of phototrophic bacteria, such as a different fold of the N-terminal region of the polypeptide due to a disulfide bridge and a ten-residue-long insertion.

Popular health supplements

David McCandless and Andy Perkins have created a generative data-visualisation of scientific evidence for popular health supplements. The more Google hits, the bigger the bubble. The greater the evidence for its effectiveness (according to PubChem abstracts and The Cochrane Collaboration), the higher a bubble. The evidence ranges from “none” to “strong” (through “slight”, “conflicting”, “promising” and “good”). This visualisation generates itself from this spreadsheet. As you can see, these supplements are quite a mixed bag, e.g.

• L-lysine
• (unspecified) arginine
• selenium (in which form?)
• fish oil
• probiotics

Interestingly, of all the metals used as “health supplements”, only calcium (effective only for the specific condition of colorectal cancer) is above “worth it” line.

Hydrogen

I say, Hydrogen is a bit unusual name for a boat. But here she is, the Thames sailing barge Hydrogen (1906) in Maldon, Essex.

She circumnavigated Great Britain for Bells Whisky and became charter barge based Maldon.

This page contains some historic photographs of Hydrogen.

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.

Selenite

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.

(1)

(2)

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.

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.