Sunday, November 14, 2010

It’s elementary

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

Principles of Chemical Nomenclature: A Guide to Iupac Recommendations (IUPAC Chemical Data Series) (Bk. 2)
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.

Monday, September 13, 2010

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.

Wednesday, September 08, 2010

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”).

Tuesday, July 27, 2010

Spoken chemistry

As I was going, for the nth 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.

Tuesday, May 11, 2010

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 Na8Al6Si6O24S2.5·(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, Na7.5Al6Si6O24S4.5·(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.

Tuesday, April 06, 2010

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.

Saturday, March 20, 2010

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.

Thursday, March 18, 2010

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.

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

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.

selenite(2-)
(1)
selenite crystal
(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.

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.

Sunday, January 24, 2010

BioMetals 2010

Online registration for 7th International Biometals Symposium (BioMetals 2010) is now open. The meeting will take place in Tucson, Arizona, USA, July 25—30, 2010.

Sessions are planned on Arsenic: Toxicity and Transformation; Siderophores and Iron Transport; Interplay of Metals; Metals and Gene Regulation; Metals in Disease and Metal Transport. See the current list of invited speakers.

The conference is limited to 200 participants, so early registration is recommended.

Monday, January 18, 2010

Metals in ancient Egypt

The al of “alchemy” is an Arabic article, but what about the rest of the word? Wikipedia mentions theories favouring Egyptian, Greek or Persian origin of the root. Whatever the etymology, it looks like ancient Egyptians knew quite a lot of chemistry.

This table of Egyptian symbols for the metals (don’t think any of them is in Unicode) misses two or three metals known to ancient Egyptians. According to Hamed A. Ead,

tin was used in the manufacture of bronze, and cobalt has been detected as a coloring agent in certain specimens of glass and glaze. Neither metal occurs naturally in Egypt, and it seems probable that supplies of ore were imported from Persia.
Mercury <...> is stated to have been found in Egyptian tombs of from 1500—1600 B.C.
Perhaps not surprisingly, the terminology used in ancient Egyptian chemical literature sometimes was deliberately misleading:
The use of the trade names for the purpose of concealing the character of the substance used where secrecy seemed desirable was not unknown at that period.
The secret names as the later alchemists used extensively: “blood of the serpent”, “blood of Hephaistos”, “blood of Vesta”, “seed of the lion”, “seed of Hercules”, “bone of the phyasimian”, etc.
The term “blood of the dove” used in the papyrus, von Lippmann has identified from other sources as meaning red lead or sometimes cinnabar.

Saturday, January 09, 2010

Below minus forty

Cold snap, you say? I do remember one New Year’s Day when the temperature in the Moscow region dropped below −40°. (Celsius or Fahrenheit? In this particular case, it’s the same: −40 °C = −40 °F = 233.15 K.) On 1 January 1979, we woke up in the (late) morning only to discover that we are stuck without any tea or hot food. We couldn’t switch on the gas cooker, which was running on propane/butane mixture. Why? As explained in this useful guide,
When the temperature of the liquids falls below its current boiling point the pressure inside the canister will no longer drive vapour out.
The boiling point of butane is −0.5 °C and that of propane is −42 °C; the temperature outside was below −42 °C, and the gas canisters were outside!

My mum called for a friendly neighbour who was better equipped than us. We kids did not worry too much about a guy warming up a gas canister with a blow torch. Anyway, everything went just fine and we had a wonderful day.