Nominative nomenclature…

[ratings]

Those familiar with one end of a biology text book from another will be aware that for the purposes of covenience/brevity/secret codes (take your pick), we use a one-letter and three-letter coding system for amino acids (the building blocks of proteins).

In a paper I must have read several times over the years, entitled ‘The liveliest effusion of wit and humor‘, the author Jan Witkowski describes some of the logic behind the one-letter codes:

The single letter amino acid code was devised in 1966 by an informal group led by Richard Eck, and the derivations of the letters are, for the most part, fairly clear [1]. For amino acids with a unique first letter, that letter is used; for example, I for isoleucine, M for methionine and V for valine. For amino acids with common first letters, that letter is used for the most common amino acid – A is used for alanine rather than aspartic acid, and L for leucine rather than lysine. That leaves a set of amino acids with a more cryptic one-letter notation. F for phenylalanine (Fenyalanine) and R for arginine (Rginine) are fairly obvious but why is W the letter for tryptophan? Eck explains this by stating that ‘tryptophan’ should be pronounced ‘twyptophan’ and, hence, ‘W’ is an appropriate symbol for it. The entry has an asterisk against it, leading the reader to a footnote: ‘My collaborators insist that I take full responsibility for this – R.V.E.’ Unfortunately, this explanation was omitted from later editions and ‘W’ is now supposed to represent the double ring system in tryptophan.

1. R.V. Eck , One- and three letter amino acid abbreviations: mneumonics of the one-letter notation. In: R.V. Eck and M.O. Dayhoff, Editors, Atlas of Protein Sequence and Structure xiii, National Biomedical Research Foundation (1966).

This leaves the infamous five amino acids that most 1st year biochemistry students forget: glutamic acid (E), asparagine (N), aspartic acid (D), glutamine (Q) and lysine (K).

Asparagine, at least, contains an ‘N’; glutamic acid results from the first syllable ‘gluE’; aspartic acid is best pronounced with a US accent, ‘asparDic’ (doesn’t work with an R.P. English accent). I have heard several reasons for why glutamine ended up with Q, and lysine with K (the latter of which is because K is close to L, which was already taken up by Leucine), but none really satisfy. None the less, they’re taught by rote and each generation of biochemists (et al.) is left to find their own reasoning.

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Illiberalism in rational causes…

The blogdom of skeptics has been in uproar over the ruling of Mr Justice Eady in the libel case Simon Singh vs British Chiropractic Association (BCA). The case has already been covered extensively, by The Lay Scientist (background | verdict) and Jack-of-Kent (background | verdict).

In Simon Singh’s book, ‘Trick or treatment: alternative medicine on trial’ (review by The Times here), he systematically addresses the pseudoscience of numerous alternative healthcare measures, including Chiropractry, about whom he said:

“The British Chiropractic Association claims that their members can help treat children with colic, sleeping and feeding problems, frequent ear infections, asthma and prolonged crying, even though there is not a jot of evidence. This organisation is the respectable face of the chiropractic profession and yet it happily promotes bogus treatments.”

The ruling hinged on Simon Singh’s use of the word ‘bogus’, which means counterfeit or fake, spurious, or bad. Unfortunately, when you start thinking about it meaning ‘counterfeit’ then this infers some degree of fraudulent use, or deliberate misuse, which is how the judge chose to rule in this case. Mr Justice Eady decided (evidently prior to the hearing had commenced) that the definition would be taken as consciously and deliberately dishonest. In this case it rules in the favour of the BCA where, by the judge’s own reasoning, Simon Singh has libelled them by labelling them deliberately dishonest. It seems strange that a judge can make any objective ruling on the definition of such a word in this case; Mr Justice Eady has effectively ‘cherry-picked’ the evidence by looking at the word ‘bogus’ within a paragraph, without including the evidential support of context from the chapter as a whole.

As I have discovered through word battles myself, different people lean towards different definitions of words when multiple definitions are available. An example might be ‘tautology’, which in one vein can be a rhetorical definition of ‘using different words to say the same thing twice’, yet can also have a meaning in logic of ‘a statement that is necessarily true’. What distinguishes the uses is the context in which they are used, and this seemed to be apparent in this case.

Continue reading “Illiberalism in rational causes…”