According to Oxford English Dictionary, “compound” (in chemistry) is
a substance formed from two or more elements chemically united in fixed proportions. |
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I quite like this definition. There are four statements in it:
Humans were consuming, growing and trading (in this order) the psychoactive plants and derived substances since time immemorial. Most governments tried (and failed) to control and restrict them. Without these plants, not only pharmacology as we know it would not exist, but the whole human history would be completely different. Surely Guía de las plantas psicoactivas by Dr. Josep Lluís Berdonces i Serra [1], published by Ediciones Invisibles (I am not joking) is not the first and not the last book dealing with this topic. Why would we need another one? That’s exactly the question Jonathan Ott, the author of classic Pharmacotheon [2], asks (and answers) in the preface, which also mentions such classics as Plants of the Gods [3] and The Encyclopedia of Psychoactive Plants [4]. As for me, I just saw this beautifully illustrated book on display in the library and felt compelled to borrow it. It is written in a lively, easy-to-read Spanish. For such a relatively slim volume (333 pages including appendices and index), it’s surprisingly informative. I learned that...
It also contains a short chapter on psychoactive fungi and another one on pharmacology of principal active compounds, including (o joy!) their structural formulae. Perhaps inevitably, there are some omissions (which I hope will be addressed in the subsequent editions). For example, Guía dedicates enough space to coffee and kola, but where is tea? To fix that oversight, we’ve published our own short guide to psychoactive plants illustrated by Tamara Kulikova.
In Dr Ott’s view, this book “viene a expandir nuestros horizontes” (came to expand our horizons) — without the necessary consumption of its protagonists. With a cup of tea, maybe.
From The Information: A History, A Theory, A Flood by James Gleick:
It was once thought that a perfect language should have an exact one-to-one correspondence between words and their meanings. There should be no ambiguity, no vagueness, no confusion. Our earthly Babel is a falling off from the lost speech of Eden: a catastrophe and a punishment. “I imagine,” writes the novelist Dexter Palmer, “that the entries of the dictionary that lies on the desk in God’s study must have one-to-one correspondences between the words and their definitions, so that when God sends directives to his angels, they are completely free from ambiguity. Each sentence that He speaks or writes must be perfect, and therefore a miracle.” We know better now. With or without God, there is no perfect language.
Leibniz thought that if natural language could not be perfect, at least the calculus could: a language of symbols rigorously assigned. “All human thoughts might be entirely resolvable into a small number of thoughts considered as primitive.” These could then be combined and dissected mechanically, as it were. “Once this had been done, whoever uses such characters would either never make an error, or, at least, would have the possibility of immediately recognizing his mistakes, by using the simplest of tests.” Gödel ended that dream.
On the contrary, the idea of perfection is contrary to the nature of language. Information theory has helped us understand that — or, if you are a pessimist, forced us to understand it.
In astrology they are called ‘terrestrial’ or ‘subterranean planets’, because of the analogous correspondences between the planets and the metals. For this reason astrologers consider that there are only seven metals (influenced by the same number of spheres), which does not mean that mankind during the astrobiological period did not recognize more. As Piobb has pointed out, some engineers have noted that the seven planetary metals make up a series which is applicable to the system of the twelve polygons. But, apart from the theory of correspondences, the metals symbolize cosmic energy in solidified form and, in consequence, the libido. On this basis, Jung has asserted that the base metals are the desires and the lusts of the flesh. Extracting the quintessence from these metals, or transmuting them into higher metals, is equivalent to setting creative energy free from the fetters of the sense world, a process identical with what esoteric tradition and astrology regard as liberation from the ‘planetary influences’. The metals can be grouped within a progressive ‘series’ in which each metal displays its hierarchical superiority over the one preceding it, with gold as the culminating point of the progression. This is why, in certain rites, the neophyte is required to divest himself of his ‘metals’ — coins, keys, trinkets — because they are symbolic of his habits, prejudices and characteristics, etc. We, for our part, however, are inclined to believe that in each particular pairing of planet with metal (as Mars with iron) there is an essential element of the ambitendent, in that its positive quality tends one way and its negative defect tends the other. Molten metal is an alchemic symbol expressing the coniunctio oppositorum (the conjunction of fire and water), related to mercury, Mercury and Plato’s primordial, androgynous being. And at the same time, the solid or ‘closed’ properties of matter emphasize its symbolism as a liberator — hence the connexion with Hermes the psychopomp <...> . The correspondences between the planets and the metals, from inferior to superior, are: Saturn — lead, Jupiter — tin, Mars — iron, Venus — copper, Mercury — mercury, Moon — silver, Sun — gold.
From Architecture of First Societies: A Global Perspective by Mark Jarzombek:
Known scientifically as hematite, ochre is a reddish iron-containing rock that was used as a coloring substance made by grinding the stone into a powder that when mixed with fat or water formed a paste. Homo erectus had already begun to work with ochre, thus securing it as a key, nonfunctional element in human life.
Ochre was a great universal of all First Societies. The Blackfeet of the American Plains referred to it as nitsisaan or “real paint” and profusely daubed it on their ceremonial garments. Its color was thought to represent the sun and the energy that permeates all things, making a person rubbed with it appear holy and powerful. Its redness and brilliance signaled supernatural potency overlapping with a range of cosmological concepts revolving around rain, fertility, hunting, and death. The nineteen-century painter George Catlin painted the Sioux worshipping at a red boulder in the open grasslands of the Great Plains.
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| George Catlin, Sioux Worshiping at the Red Boulders, 1837—1839 |
Ceremonial uses of ochre still exist today, such as among the Maasai in Kenya during certain initiation rituals, by Amazon tribes and by Aboriginal people in Australia.
The !Kung, who live in the Kalahari desert of Botswana and who are among the oldest of the surviving First Society people in the world, use the pigment in rituals dealing with a woman’s first menstruation. A female initiate, on emergence from seclusion, would present the women of her kin group with lumps of ochre for decorating their faces and cloaks and also for adorning the young men to protect them when out hunting.
This volume, edited by Lucia Banci, is probably the first real book on metallomics. The table of contents looks very promising, and judging from those bits that I am able to access, I’d love to say that is is a great book... But honestly I can’t. The days when I could persuade the library to purchase (for me) a book, however expensive, are long gone. At the Springer website, eBook is priced at €142.79 and hardcover costs €181.85. You can buy them slightly cheaper from Amazon ($175.82 and $227.05, respectively.)
The book is dedicated to Ivano Bertini, who sadly passed away last year. I was lucky enough to meet the man himself on a few occasions. Ivano was a formidable scientist and one of the most colourful figures of bioinorganic chemistry and structural biology.
It’s been a while since I read a science/technology book from back to back. And was it worth it? Definitely.
The book is about collaboration and is a collaboration. Ironically, the best-written chapters almost invariably are those by single authors. Which confirms my own theory that writing (including scientific writing) is not exactly collaborative activity. The contributions by Robert Porter Lynch [1], Robin W. Spencer [2], Victor J. Hruby [3], Edward D. Zanders [4], Brian Pratt [5] and Keith T. Taylor [6] are especially worth noting — I wish the whole book was written at the level of these chapters. Then again, collaboration is always a compromise. The material presented here is diverse and heterogeneous — what did you expect?
I am sure there are people who do all sorts of stuff using their smartphones, including scientific database browsing and chemical structure drawing [7]. This latter activity does not strike me as especially productive or convenient. (Also, makes me glad that the use of mobile phones while driving is outlawed in most of Europe.) In my view, for the purposes of computer graphics bigger is better: if I had a choice, I’d go for HIPerWall (25,600 × 8000 pixels) or, better still, HIPerSpace (35,840 × 8000 pixels) display walls [8]. Then I could draw some really large (in many senses) molecules.
As much as I enjoy reading the real (hardcopy) book, it could be nice to see it online, preferably in open access. For instance, Chapter 25 [9] has 196 references, all of them are URLs, and some of them are rather long ones. I’d love to be able to click on them rather than type!
Will the wikis, virtual communities and cloud computing replace the behemoth pharma companies and NCBI? A man can dream. Ekins et al. write [10]:
As a result of the recent recession there is a lot of drug discovery and development talent available now due to company lay-offs. If the software or other tools to enable this workforce to be productive and collaborate were available and they participated in the existing scientific collaboration networks, then there may be potential for enormous breakthroughs.
I wish I could share the authors’ optimism. Yes there is potential, but it is highly unlikely that unemployed researchers are in the mood to collaborate. In case you wonder why: being unemployed is a full-time occupation, which leaves preciously little spare time. I rather inclined to agree with Robin W. Spencer [2]:
Especially for cutting-edge scientific challenges, the participants you need are probably well paid and not particularly enthused by another tee shirt, coffee cup, or $100 voucher.
More quotes from this book can be found here.
I use this opportunity to lament the decline of old-fashioned copy editing [11]. I get used to the lack of any such luxury in open access publications: if the paper is accepted, the publisher tends to keep all your typos intact. But when you buy a book from John Wiley & Sons for a hundred something bucks, you’d expect some editorial intervention. (To be honest, I did not buy it. I can’t afford buying books at such prices anyway.) The major and minor irritations include:
Now for “crowdsourcing”: I find the term not only ugly but offensive. As a scientist (once a scientist, always a scientist), I am open to collaboration. Also, as a scientist, I detest being part of a crowd. Period.
Don’t get me wrong: it is a good book. I wouldn’t hesitate to recommend it to any decent scientific library. But it could have been a great book.
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.
According to IUPAC’s Principles of Chemical Nomenclature [1],
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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). |
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):
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.
Two chemistry-related quotes from Dr. Strangelove:
You’ve obviously never heard of cobalt chlorium G. It has a radioactive half-life of 93 years.
Have you ever heard of a thing called fluoridation of water?
In contrast to fictitious “cobalt chlorium G”, water fluoridation is real. So is opposition to it. To quote the recent Australian study, “water fluoridation appears to be a low-risk, high-outrage controversy”. Luckily, the communist threat is no longer mentioned — or so I thought until I came across a recent publication quoting a Californian mum who wondered whether the dentist was “one of those socialists trying to poison us with fluoride”. From The Fluoride Wars: How a Modest Public Health Measure Became America’s Longest Running Political Melodrama:
It seemed such simple act at the time <in 1945>. A tap was turned, and water that had been chlorinated for many years without much fuss now carried a second chemical supplement to help keep us healthy. Soon, the taps would be turned in city after city across the nation. For most, it was another blessing bestowed on us by modern medical science. But for some, it was one chemical too many.
The Gold Book and the Silver Book (currently under revision) are two of the so-called colour books. Which kind of implies that gold and silver are colours. Not that IUPAC ran out of ‘real’ colours — e.g. they still could have chosen pink or yellow or black. For long time I thought that the reason behind naming the Gold Book ‘Gold Book’ was its (intended) role as a gold standard for chemical terminology. I was wrong. It was named in honour of Victor Gold (1922—1985), the British chemist who was the first author and compiler of the book. No such story with the Silver Book, I am afraid.
One of problems with the Gold Book (as opposed to other colour books) is that it deals with ‘general’ chemical nomenclature. Therefore, when it comes to terms which are different meanings in different fields of chemistry, the Gold Book gives more than one definition. Which one should be used? Take ligands. The definition 1 (coordination chemistry) is short and nice, while the definition 2 (biochemistry) is long and horrible. At least it mentions that in bioinorganic chemistry, one should be careful which definition to use.
In case of sulfides, there are three different meaning. Sulfides 1 (organic chemistry) is the replacement term for obsolete but less ambiguous ‘thioethers’, while sulfides 2 (inorganic chemistry) are “salts or other derivatives of hydrogen sulfide”. I am happy with salts but not with the “other derivatives”. Is sulfenic acid (IUPAC name ‘sulfanol’) a sulfide? As for sulfides 3, the definition goes “a term used in additive nomenclature”. Excellent.
Similarly, there is a consistency problem with related terms that are derived from different IUPAC recommendations. The entry for dipolar bond (1994) says:
The term is preferred to the obsolescent synonyms ‘coordinate link’, ‘coordinate covalence’, ‘dative bond’, ‘semipolar bond’.
And yet the more recent entry for dative bond (1999) does not mention that the term is obsolete. It is even states that
In spite of the analogy of dative bonds with covalent bonds, in that both types imply sharing a common electron pair between two vicinal atoms, the former are distinguished by their significant polarity, lesser strength, and greater length.
A textbook example of dative bond is the one in ammonium. Of course, all the N—H bonds are exactly the same, even if you choose to represent one of them with an arrow.
“Metalloproteomics” is a relatively new and not that widely known term. Today (20 October 2009), PubMed search produces only 13 hits. (The search for “metallomics” gives only twice as many hits.) The earliest use of the term is by Alfredo Sanz-Medel and by Scott et al. — incidentally, both papers were published online 23 December 2004.
Metalloproteomics by Eugene Permyakov (Wiley-Interscience, 2009) gives us a definition of the term:
Metalloproteomics is a proteomics of metal-binding proteins.
That’s easy, right? But wait. Check out the table of contents. It looks to me like another bioinorganic chemistry book, and a rather pricey one. It mostly deals with metalloproteins, but there are also Chapter 15, Interactions of metal cations with nucleic acids, and Chapter 16, “Nonphysiologic” metals. Nothing here is specifically proteomic or metallomic. I suppose that Chapter 3, Experimental methods used for studies of the binding of metal cations could be of some relevance to metalloproteomics. Then again, maybe not: how come that mass spectrometry, the most obvious proteomics technique, is not mentioned at all? And why metal cations only? Some metalloproteins contain vanadate. Maybe I am jumping to conclusions here (without even reading the book!), but this title is simply misleading.
Here’s a short fragment of Accident by Agatha Christie.
Evans paid no attention, but went on. ‘You interrupted me just now. After Marsh’s test, Merrowdene heated a substance in a test tube, the metallic residue he dissolved in water and then precipitated it by adding silver nitrate. That was a test for chlorates. A neat, unassuming little test. But I chanced to read these words in a book that stood open on the table. “H2SO4 decomposes chlorates with evolution of Cl2O4. If heated, violent explosions occur, the mixture ought therefore to be kept cool and only very small quantities used.”’
What book was that? Googling gave me The Elements of Chemical Arithmetic with a Short System of Elementary Qualitative Analysis by J. Milnor Coit, Ph.D., published in 1886. On page 80, section 103, I’ve found the original description (shortened in Agatha Christie’s version):
H2SO4 decomposes chlorates with evolution of Cl2O4, a greenish-yellow gas having a powerful odor. If heated, violent explosions occur; the mixture ought therefore to be kept cold, and only very small quantities should be used.
The full text of this, apparently, still very useful book is copyright-free.
We’ve got this wonderful, profusely illustrated book bought for the office, called Molecules That Changed the World, by K. C. Nicolaou and T. Montagnon. I’d say some of the molecules mentioned there (like LSD) change not so much the world per se but our perception of the world. Still, I’d recommend every chemistry or chemistry-related department/lab to have this book.
On p. 42, it quotes Sir Robert Robinson’s wise words on the value of basic research (from his Nobel Lecture):
The synthesis of brazilin would have no industrial value; its biological importance is problematical, but it is worth while to attempt it for the sufficient reason that we have no idea how to accomplish the task. There is a close analogy between organic chemistry in its relation to biochemistry and pure mathematics in its relation to physics. In both disciplines it is in the course of attack of the most difficult problems, without consideration of eventual applications, that new fundamental knowledge is most certainly garnered.
