[CF-metadata] Silicate vs. dissolved inorganic silicon

John Dunne - NOAA Federal john.dunne at noaa.gov
Mon Mar 27 12:11:40 MDT 2017


and the push started even earlier than that, e.g.:

Goering, J.J., Nelson, D.M. and Carter, J.A., 1973. Silicic acid uptake by
natural populations of marine phytoplankton. In *Deep Sea Research and
Oceanographic Abstracts* (Vol. 20, No. 9, pp. 777-789).

Brzezinski was also a big proponent in the 1990s.

On Mon, Mar 27, 2017 at 7:23 AM, James Orr <James.Orr at lsce.ipsl.fr> wrote:

> Hi Roy,
>
> There has been a trend as you suggest, although it started a few decades
> ago, e.g., "silicic acid" is used instead of "silicate" in the following:
>
> Gordon, L. I., Jennings Jr, J. C., Ross, A. A., & Krest, J. M. (1993). A
> suggested protocol for continuous flow automated analysis of seawater
> nutrients (phosphate, nitrate, nitrite and silicic acid) in the WOCE
> Hydrographic Program and the Joint Global Ocean Fluxes Study. WOCE
> Operations Manual, Part, 3(3), 91-1.
>
> Knap, A. H., Michaels, A., Close, A. R., Ducklow, H., & Dickson, A. G.
> (1996). Protocols for the joint global ocean flux study (JGOFS) core
> measurements.
>
> For our purposes though, both terms can be used synonymously.  To avoid
> confusion, would you agree to the following 2nd correction to the CF
> Standard Name List:
>
> (2) '"Dissolved inorganic silicon" means the sum of all dissolved silicon
> in solution (including silicic acid and its first dissociated anion
> SiO(OH)3-)'
> i.e., for the definition of mole_concentration_of_dissolve
> d_inorganic_silicon_in_sea_water
>
> I've just now replaced 'silicate' with 'its first dissociated anion
> SiO(OH)3-' to keep the more general sense of silicate intact. For
> simplicity, we may want to remove the chemical formula after the word
> 'anion'.
>
> Your thoughts?
>
> Jim
>
> On Mon, 27 Mar 2017, Lowry, Roy K. wrote:
>
>
>> Many thanks James,
>>
>>
>> I like it. I had visions of tens of thousands of files needing to be
>> edited - we're bringing in semantically
>> aware compliance checkers that require action if deprecated terms are
>> used.
>>
>>
>> Interesting, in 36 years I have never heard an oceanographer refer to
>> silicic acid - it's always been
>> 'silicate' referring to the measurement made by the standard colorometric
>> analytical technique.
>>
>>
>> Out of curiosity I'll sound out my own organisation (UK National
>> Oceanography Centre) on the usage of DIP and
>> DISi to see if there is any change in the viewpoint in the younger
>> oceanographers.
>>
>>
>> Cheers, Roy.
>>
>> ____________________________________________________________
>> _________________________________________________
>>
>> From: James Orr <James.Orr at lsce.ipsl.fr>
>> Sent: 25 March 2017 14:21
>> To: Lowry, Roy K.
>> Cc: John Dunne - NOAA Federal; <martin.juckes at stfc.ac.uk>; Alison
>> Pamment; cf-metadata at cgd.ucar.edu
>> Subject: Re: [CF-metadata] Silicate vs. dissolved inorganic silicon
>> Hi Roy,
>>
>> I understand your concern and would agree that it would be fine to keep
>> the standard names but to explain what we mean by them in the
>> definitions.
>>
>> So in response to Martin's questions, I would suggest the following
>> corrections in the CF Standard Name List:
>>
>> (1) '"Dissolved inorganic phosphorus" means the sum of all dissolved
>> inorganic phosphorus in solution (including phosphate, hydrogen
>> phosphate, dihydrogen phosphate, and phosphoric acid)' for the
>> definition of
>> mole_concentration_of_dissolved_inorganic_phosphorus_in_sea_water, and
>>
>> (2) '"Dissolved inorganic silicon" means the sum of all dissolved
>> silicon in solution (including silicic acid and silicate)' for the
>> definition of
>> mole_concentration_of_dissolved_inorganic_silicon_in_sea_water
>>
>> By the way, although many oceanographers refer only to silicate as you
>> mention, many others refer only to silicic acid.  In both cases though
>> what is meant is the sum of both.
>>
>> Best regards,
>>
>> Jim
>>
>> On Fri, 24 Mar 2017, Lowry, Roy K. wrote:
>>
>> >
>> > Dear All,
>> >
>> >
>> > That would make no sense at all for the observational oceanographic
>> community who have referred to silicate
>> > and phosphate for decades because all the various types of phosphate
>> and silicate react to the standard
>> > colorometric reagents in exactly the same way. Replacing terminology in
>> common usage with more pedantic
>> > synonyms can only result in confusion.
>> >
>> >
>> > So, the situation we have is that we have a technically precise
>> Standard Names and Standard Names that
>> > reflect terminology in common usage.  One solution might be to leave
>> all four Standard Names in place but
>> to
>> > clarify the definitions. In our server the pairs could be mapped as
>> synonyms if Alison requests it.
>> >
>> >
>> > Cheers, Roy.
>> >
>> >
>> > Please note that I partially retired on 01/11/2015. I am now only
>> working 7.5 hours a week and can only
>> > guarantee e-mail response on Wednesdays, my day in the office. All
>> vocabulary queries should be sent to
>> > enquiries at bodc.ac.uk. Please also use this e-mail if your requirement
>> is urgent.
>> >
>> >
>> >
>> >___________________________________________________________
>> _________________________________________________
>> _
>> > From: John Dunne - NOAA Federal <john.dunne at noaa.gov>
>> > Sent: 24 March 2017 17:14
>> > To: <martin.juckes at stfc.ac.uk>
>> > Cc: James Orr; Lowry, Roy K.; Alison Pamment; cf-metadata at cgd.ucar.edu
>> > Subject: Re: [CF-metadata] Silicate vs. dissolved inorganic silicon
>> > Is the plan also to demote the "silicate" and "phosphate" names?  That
>> would seem to make sense to me,
>> > consistent with Jim's points.
>> >
>> > On Fri, Mar 24, 2017 at 12:13 PM, <martin.juckes at stfc.ac.uk> wrote:
>> >       Dear Jim,
>> >
>> >       thanks. I think that means that we need a corrections to the
>> statements, from the CF Standard
>> >       Name list, that:
>> >
>> >       (1) '"Dissolved inorganic phosphorus" means phosphate ions in
>> solution' in the CF Standard Name
>> >       definition for mole_concentration_of_dissolve
>> d_inorganic_phosphorus_in_sea_water, and
>> >       (2) '"Dissolved inorganic silicon" means silicate ions in
>> solution' in the definition of
>> >       mole_concentration_of_dissolved_inorganic_silicon_in_sea_water
>> >
>> >       regards,
>> >       Martin
>> >       ________________________________________
>> >       From: James Orr [James.Orr at lsce.ipsl.fr]
>> >       Sent: 24 March 2017 15:46
>> >       To: Lowry, Roy K.
>> >       Cc: Juckes, Martin (STFC,RAL,RALSP); cf-metadata at cgd.ucar.edu
>> >       Subject: Re: [CF-metadata] Silicate vs. dissolved inorganic
>> silicon
>> >
>> >       Dissolved inorganic phosphorus in seawater takes several forms,
>> with
>> >       phosphate (P043-) being only one of them. Furthermore, PO43- is
>> not
>> >       even the most abundant form at normal seawater pH. Rather it is
>> HPO42-
>> >       (hydrogen phosphate). Oceanographers do often refer to phosphate
>> but
>> >       what they really taking about is total dissolved inorganic
>> phosphorus
>> >       (the sum of all inorganic forms).
>> >
>> >       The seawater system for dissolved inorganic silicon is simpler
>> because
>> >       we only need to consider two forms: silicic acid (Si(OH)4) and
>> silicate
>> >       (SiO(OH)3-). The former is more abundant than the latter in
>> seawater.
>> >
>> >       It is best then to refer to
>> >       - total dissolved inorganic phosphorus rather than phosphate and
>> >       - total dissolved inorganic silicon rather than silicate.
>> >
>> >       For more insight see the last figure in the OMIP-BGC protocols
>> paper
>> >       in the CMIP6 special issue at
>> >
>> >       http://www.geosci-model-dev-discuss.net/gmd-2016-155/
>> GMDD - Biogeochemical protocols and diagnostics for the ...
>> www.geosci-model-dev-discuss.net
>> Biogeochemical protocols and diagnostics for the CMIP6 Ocean Model
>> Intercomparison Project (OMIP)
>>
>>
>> >
>> >       Cheers,
>> >
>> >       Jim
>> >
>> >       On Fri, 24 Mar 2017, Lowry, Roy K. wrote:
>> >
>> >       > Dear All,
>> >       >
>> >       >
>> >       > If one makes the assumption that all the silicon and phosphorus
>> atoms not associated with
>> >       organic ligands are
>> >       > in a single chemical form associated with oxygen in solution
>> then what Martin says is correct.
>> >       In my
>> >       > experience I have never known anybody challenge this assumption
>> and I cannot think of any other
>> >       anions
>> >       > incorporating P and Si. Consequently, I would agree that whilst
>> there is a theoretical semantic
>> >       difference
>> >       > between the members of each Standard Name pair I would agree
>> that this could be ignored and
>> >       they could be
>> >       > considered synonyms.
>> >       >
>> >       >
>> >       > Note, this only holds true as these are MOLE concentrations.
>> The MASS concentration of
>> >       inorganic phosphorus
>> >       > is very different from the MASS concentration of phosphate as
>> the oxygen atoms have mass.
>> >       >
>> >       >
>> >       > If the decision is taken to take action on this then I would
>> recommend that the
>> >       'inorganic_silicon' and
>> >       > 'inorganic_phosphorus' names be than ones to be converted to
>> aliases. This is based on common
>> >       terminology
>> >       > usage in the oceanographic community.
>> >       >
>> >       >
>> >       > Cheers, Roy.
>> >       >
>> >       >
>> >       > Please note that I partially retired on 01/11/2015. I am now
>> only working 7.5 hours a week and
>> >       can only
>> >       > guarantee e-mail response on Wednesdays, my day in the office.
>> All vocabulary queries should be
>> >       sent to
>> >       > enquiries at bodc.ac.uk. Please also use this e-mail if your
>> requirement is urgent.
>> >       >
>> >       >
>> >       >
>> >      >____________________________________________________
>> _______________________________________________________
>> _
>> >       _
>> >       > From: CF-metadata <cf-metadata-bounces at cgd.ucar.edu> on behalf
>> of martin.juckes at stfc.ac.uk
>> >       > <martin.juckes at stfc.ac.uk>
>> >       > Sent: 24 March 2017 08:48
>> >       > To: cf-metadata at cgd.ucar.edu
>> >       > Subject: [CF-metadata] Silicate vs. dissolved inorganic silicon
>> >       > Hello Alison, others,
>> >       >
>> >       > the standard name list includes both
>> >       > (1) mole_concentration_of_dissolved_inorganic_silicon_in_sea_water
>> and (2)
>> >       > mole_concentration_of_silicate_in_sea_water
>> >       >
>> >       > The definition of the first says that "dissolved inorganic
>> silicon" means silicate ions in
>> >       solution. Both
>> >       > have units of "mol m-3". It looks to me as though they are
>> describing the same thing. If this
>> >       is true, should
>> >       > one be demoted to the alias of the other? If they are
>> different, what is the difference?
>> >       >
>> >       > The same question applies to mole_concentration_of_dissolve
>> d_inorganic_phosphorus_in_sea_water
>> >       and
>> >       > mole_concentration_of_phosphate_in_sea_water.
>> >       >
>> >       > regards,
>> >       > Martin
>> >       >
>> >       > _______________________________________________
>> >       > CF-metadata mailing list
>> >       > CF-metadata at cgd.ucar.edu
>> >       > http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
>> CF-metadata Info Page - mailman.cgd.ucar.edu Mailing Lists
>> mailman.cgd.ucar.edu
>> This is an unmoderated list for discussions about interpretation,
>> clarification, and proposals for extensions
>> or change to the CF conventions.
>>
>>
>> >       > CF-metadata Info Page - mailman.cgd.ucar.edu Mailing Lists
>> >       > mailman.cgd.ucar.edu
>> >       > This is an unmoderated list for discussions about
>> interpretation, clarification, and proposals
>> >       for extensions
>> >       > or change to the CF conventions.
>> >       >
>> >       >
>> >      >____________________________________________________
>> _______________________________________________________
>> _
>> >       _
>> >       > This message (and any attachments) is for the recipient only.
>> NERC is subject to the Freedom of
>> >       Information
>> >       > Act 2000 and the contents of this email and any reply you make
>> may be disclosed by NERC unless
>> >       it is exempt
>> >       > from release under the Act. Any material supplied to NERC may
>> be stored in an electronic
>> >       records management
>> >       > system.
>> >       >
>> >      >____________________________________________________
>> _______________________________________________________
>> _
>> >       _
>> >       >
>> >       >
>> >
>> >       --
>> >       LSCE/IPSL, Laboratoire des Sciences du Climat et de
>> l'Environnement
>> >       CEA-CNRS-UVSQ
>> >
>> >       LSCE/IPSL, CEA Saclay http://www.ipsl.jussieu.fr/~jomce
>> >       Bat. 712 - Orme mailto: James.Orr at lsce.ipsl.fr
>> >       Point courrier 132
>> >       F-91191 Gif-sur-Yvette Cedex Phone: (33) (0)1 69 08 39 73
>> >       FRANCE Fax: (33) (0)1 69 08 30 73
>> >       _______________________________________________
>> >       CF-metadata mailing list
>> >       CF-metadata at cgd.ucar.edu
>> >       http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
>> CF-metadata Info Page - mailman.cgd.ucar.edu Mailing Lists
>> mailman.cgd.ucar.edu
>> This is an unmoderated list for discussions about interpretation,
>> clarification, and proposals for extensions
>> or change to the CF conventions.
>>
>>
>> >
>> >
>> >___________________________________________________________
>> _________________________________________________
>> _
>> > This message (and any attachments) is for the recipient only. NERC is
>> subject to the Freedom of Information
>> > Act 2000 and the contents of this email and any reply you make may be
>> disclosed by NERC unless it is exempt
>> > from release under the Act. Any material supplied to NERC may be stored
>> in an electronic records management
>> > system.
>> >
>> >___________________________________________________________
>> _________________________________________________
>> _
>> >
>> >
>>
>> --
>> LSCE/IPSL, Laboratoire des Sciences du Climat et de l'Environnement
>> CEA-CNRS-UVSQ
>>
>> LSCE/IPSL, CEA Saclay           http://www.ipsl.jussieu.fr/~jomce
>> Bat. 712 - Orme                 mailto:  James.Orr at lsce.ipsl.fr
>> Point courrier 132
>> F-91191 Gif-sur-Yvette Cedex    Phone:   (33) (0)1 69 08 39 73
>> FRANCE                          Fax:     (33) (0)1 69 08 30 73
>>
>> ____________________________________________________________
>> _________________________________________________
>> This message (and any attachments) is for the recipient only. NERC is
>> subject to the Freedom of Information
>> Act 2000 and the contents of this email and any reply you make may be
>> disclosed by NERC unless it is exempt
>> from release under the Act. Any material supplied to NERC may be stored
>> in an electronic records management
>> system.
>>
>> ____________________________________________________________
>> _________________________________________________
>>
>>
>>
> --
> LSCE/IPSL, Laboratoire des Sciences du Climat et de l'Environnement
> CEA-CNRS-UVSQ
>
> LSCE/IPSL, CEA Saclay           http://www.ipsl.jussieu.fr/~jomce
> Bat. 712 - Orme                 mailto:  James.Orr at lsce.ipsl.fr
> Point courrier 132
> F-91191 Gif-sur-Yvette Cedex    Phone:   (33) (0)1 69 08 39 73
> FRANCE                          Fax:     (33) (0)1 69 08 30 73
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.cgd.ucar.edu/pipermail/cf-metadata/attachments/20170327/fdb2998f/attachment-0001.html>


More information about the CF-metadata mailing list