Hi Gerard & Marc
My answer was my interpretation of Bernhard's original question "what
*is* the currently accepted name of the object whose description is
'structure factor amplitude' ?", and was based both on authoritative
precedent, i.e. ITC Vol. B, and on frequency of current usage, i.e.
Google hits. Carroll was making the point that in logic the name of an
object is minimally only an arbitrary string of characters (preferably
pronounceable!), like the name of a variable in a program, which
minimally need have no semantic connotations whatsoever: "a rose by any
other name would smell as sweet". The only requirement is that it must
not be ambiguous, i.e. you can't have two different objects within the
same context with the same name. For example my name 'Ian' provides no
semantic clues as to my description (except perhaps that I'm male), and
causes no problems provided no other 'Ian's enter the discussion.
However alternate names for the same object are clearly allowed
(consider names of objects in different languages).
In this case I am not offering an opinion on what I think the name
*should be*, I am merely reporting on what the name *is* (however
illogical), based on precedent and usage. However I do accept your
argument that when making up the compound name of an object, it should
as far as possible also be accurately descriptive in the way it relates
to the names of related objects, consistent with the conflicting needs
for abbreviation and lack of ambiguity. You are going much further than
me: you are answering a different question "what *should be* the
accepted name of ... ?". In this case you have clearly made a strong
argument, which I accept, for establishing an alternate name for this
particular object. However one should not create new names or change
the names of objects lightly, if misunderstandings are to be avoided.
Fortunately in this case it can be done with minimal misunderstanding on
the part of the readers of Bernhard's textbook (though others may
disagree on that point), provided it is pointed out that there is
precedent for an alternative name for the object in question, and
perhaps a reference should be made to the original authoritative
definition.
Cheers
-- Ian
> -----Original Message-----
> From: Gerard Bricogne [mailto:[log in to unmask]]
> Sent: 12 January 2009 12:09
> To: Ian Tickle
> Cc: [log in to unmask]
> Subject: Re: [ccp4bb] structure (factor) amplitude
>
> Dear Ian,
>
> My reply to this question will be less literate and less
> democratic
> than yours. In spite of the nice Alice quote, I remain in
> favour of trying
> to use compound names whose internal structure is, as much as
> possible,
> "isomorphic" to the composition of meanings they refer to
> (even though I am
> not necessarily an unconditional fanatic of OOP). Even if,
> allegedly, only
> God has a name for each object that completely specifies it
> and even gives
> it its very existence, I feel it is not unrealistic nor
> immodest to do our
> best to achieve this in our scientific language. If we
> modelled the rigour
> of scientific language on that of Lewis Carroll's, we would
> be in serious
> trouble (perhaps this is why scientists enjoy his humour so
> much: it is
> like taking off a pair of tight shoes; and it was probably
> his own escape
> from the rigours of mathematical logic).
>
> In this case, the word "factor" refers to the fact that,
> in the Darwin
> formula for an integrated intensity, there are many factors
> in a complicated
> algebraic expression, and that one of them depends on the
> internal structure
> of the crystal. The relation to Fourier theory makes it
> desirable to use as
> the basic structure-dependent quantity the complex Fourier
> coefficient of
> the electron density, so the latter then becomes known as the
> "structure
> (-dependent) factor (in the Darwin formula)". Being a complex
> number, it
> inherits as an attribute the modulus of that complex number,
> for which the
> synonym "amplitude" is used - regrettably, but possibly
> because the word
> "modulus" was already widely used, e.g. in the theory of elasticity.
>
> Therefore the expression "structure factor amplitude"
> can be parsed as
> being "the amplitude (a.k.a. modulus) of a complex number
> which is involved
> in the structure-dependent factor in the Darwin formula".
> Along with Dirk
> Kostrewa I vote for retaining the full-length expression, as
> the abbreviated
> one makes one think that a structure has an amplitude ... .
>
> Abbreviations can be great, but they can also result in
> a substantial
> loss of intelligibility. Look at the transition to "Brazilian
> spelling" in
> Portuguese, whereby "optimo" is abbreviated to "otimo". A
> non-Portuguese
> speaker (even an English-only speaker!) can understand the
> word from its
> first spelling because the Latin derivation is clear; but
> this is no longer
> the case for the abbreviated one, unless one also remembers
> what it is an
> abbreviation of. Similarly, "structure amplitude" does not
> tell you that
> there is a complex number called the structure factor, of which one is
> considering the amplitude/modulus.
>
> Sorry for this long message: as the question originated
> from Bernhard,
> who is in the process of writing a textbook, I think it is
> important that
> points of terminology like this one be given careful
> consideration and a
> satisfactory conclusion; so I hope that many other people
> will give some
> attention to this thread (even if they disagree with me!).
>
>
> With best wishes,
>
> Gerard.
>
>
> --
> On Mon, Jan 12, 2009 at 11:09:34AM -0000, Ian Tickle wrote:
> > I think there's a confusion here between the name of an
> object (what you
> > call it) and its description (i.e. its properties). The name of the
> > object is "structure amplitude" and it's description is
> "amplitude of
> > the structure factor", or if you prefer the shortened form
> "structure
> > factor amplitude". This distinction was of course carried
> to absurdity
> > in "Alice through the Looking Glass":
> >
> > "It's long." said the Knight, "but it's very, very
> beautiful. Everybody
> > that hears me sing it - either it brings tears to their
> eyes, or else -"
> > "Or else what?" said Alice, for the Knight had made a sudden pause.
> > "Or else it doesn't, you know. The name of the song is
> called 'Haddocks'
> > Eyes.'"
> > "Oh, that's the name of the song, is it?" Alice said, trying to feel
> > interested.
> > "No, you don't understand," the Knight said, looking a little vexed.
> > "That's what the name is called. The name really is 'The Aged, Aged
> > Man.'"
> > "Then I ought to have said 'That's what the song is called'?" Alice
> > corrected herself.
> > "No you oughtn't: that's another thing. The song is called 'Ways and
> > Means' but that's only what it's called, you know!"
> > "Well, what is the song then?" said Alice, who was by this time
> > completely bewildered.
> > "I was coming to that," the Knight said. "The song really
> is 'A-sitting
> > On a Gate': and the tune's my own invention."
> >
> > Cheers
> >
> > -- Ian
> >
> > > -----Original Message-----
> > > From: [log in to unmask]
> > > [mailto:[log in to unmask]] On Behalf Of Dirk Kostrewa
> > > Sent: 12 January 2009 10:52
> > > To: CCP4BB
> > > Subject: Re: [ccp4bb] structure (factor) amplitude
> > >
> > > ... despite these informations, I still prefer "structure factor
> > > amplitude", because it is the amplitude of the "structure
> factor" ...
> > >
> > > Best regards,
> > >
> > > Dirk.
> > >
> > > Am 12.01.2009 um 11:42 schrieb Ian Tickle:
> > >
> > > > I was taught 'structure amplitude' - makes perfect
> sense to me! Why
> > > > does 'structure amplitude' make any less sense than 'structure
> > > > factor'?
> > > >
> > > > It also clearly made sense to Phil Coppens, a
> crystallographer of
> > > > considerable repute, see ITC Vol. B (2nd Ed.), sect
> 1.2., p.10: 'The
> > > > Structure Factor'. To quote the introduction to the
> section: "The
> > > > 'structure factor' is the central concept in structure
> analysis by
> > > > diffraction methods. Its modulus is called the 'structure
> > > > amplitude'".
> > > >
> > > > Also I did a 'Google vote' for the two terms. 'Structure
> > > amplitude'
> > > > has
> > > > 11300 hits. 'Structure factor amplitude' has only
> 4750. So all
> > > > round I
> > > > would say that 'structure amplitude' wins by a
> considerable margin.
> > > >
> > > > Cheers
> > > >
> > > > -- Ian
> > > >
> > > >> -----Original Message-----
> > > >> From: [log in to unmask]
> > > >> [mailto:[log in to unmask]] On Behalf Of Pavel Afonine
> > > >> Sent: 11 January 2009 03:01
> > > >> To: Ethan A Merritt
> > > >> Cc: [log in to unmask]
> > > >> Subject: Re: [ccp4bb] structure (factor) amplitude
> > > >>
> > > >>
> > > >>
> > > >> On 1/10/2009 5:14 PM, Ethan A Merritt wrote:
> > > >>
> > > >> On Saturday 10 January 2009, Bernhard Rupp wrote:
> > > >>
> > > >>
> > > >> Dear All,
> > > >>
> > > >> I am getting conflicting comments on the use of
> > > >> 'structure factor amplitude'
> > > >> vs. just
> > > >> 'structure amplitude'
> > > >> for |F|.
> > > >>
> > > >>
> > > >>
> > > >> ???
> > > >> That's just... odd.
> > > >>
> > > >> |F| is the amplitude of F.
> > > >> But no way F is a "structure".
> > > >>
> > > >>
> > > >>
> > > >> I agree. If F is a structure factor then |F| is a structure
> > > >> factor amplitude. "structure amplitude" doesn't make
> much sense...
> > > >> Pavel.
> > > >
> > > >
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> --
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> ===============================================================
> * *
> * Gerard Bricogne [log in to unmask] *
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Disclaimer
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Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof.
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