[CF-metadata] Silicate vs. dissolved inorganic silicon

Lowry, Roy K. rkl at bodc.ac.uk
Tue Mar 28 02:25:58 MDT 2017


Hmm,


Just noticed the Knap et al reference that should have been on my radar as I was JGOFS DMTT chair at the time! I guess I'll just have to plead senior moment!


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: 27 March 2017 19:11
To: James Orr
Cc: Lowry, Roy K.; <martin.juckes at stfc.ac.uk>; Alison Pamment; cf-metadata at cgd.ucar.edu
Subject: Re: [CF-metadata] Silicate vs. dissolved inorganic silicon

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<mailto: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_dissolved_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<mailto: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<mailto:martin.juckes at stfc.ac.uk>>; Alison Pamment; cf-metadata at cgd.ucar.edu<mailto: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<mailto: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<mailto:john.dunne at noaa.gov>>
> Sent: 24 March 2017 17:14
> To: <martin.juckes at stfc.ac.uk<mailto:martin.juckes at stfc.ac.uk>>
> Cc: James Orr; Lowry, Roy K.; Alison Pamment; cf-metadata at cgd.ucar.edu<mailto: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<mailto: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_dissolved_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<mailto: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<mailto: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<http://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<mailto: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<mailto:cf-metadata-bounces at cgd.ucar.edu>> on behalf of martin.juckes at stfc.ac.uk<mailto:martin.juckes at stfc.ac.uk>
>       > <martin.juckes at stfc.ac.uk<mailto:martin.juckes at stfc.ac.uk>>
>       > Sent: 24 March 2017 08:48
>       > To: cf-metadata at cgd.ucar.edu<mailto: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_dissolved_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<mailto:CF-metadata at cgd.ucar.edu>
>       > http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
CF-metadata Info Page - mailman.cgd.ucar.edu<http://mailman.cgd.ucar.edu> Mailing Lists
mailman.cgd.ucar.edu<http://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<http://mailman.cgd.ucar.edu> Mailing Lists
>       > mailman.cgd.ucar.edu<http://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<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<mailto:CF-metadata at cgd.ucar.edu>
>       http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
CF-metadata Info Page - mailman.cgd.ucar.edu<http://mailman.cgd.ucar.edu> Mailing Lists
mailman.cgd.ucar.edu<http://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<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<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.
________________________________
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.cgd.ucar.edu/pipermail/cf-metadata/attachments/20170328/4b791255/attachment-0001.html>


More information about the CF-metadata mailing list