After mulling it over, I'd suggest restricting the picoplankton
definition to <2, and having a separate definition for nanoplankton, if
necessary. I think there is at least one model that has explicit
nanoplankton, but not mine, so I'm not sure if it's necessary.
----- Original Message -----
From: "Lowry, Roy K" <rkl at bodc.ac.uk>
Date: Friday, April 23, 2010 9:14 am
Subject: RE: [CF-metadata] CMIP5 ocean biogeochemistry standard names
> Hi Alison,
>
> John's response got buried in my 'todo' pile. His 'flexible'
> definition almost works for me, but I would prefer to take 2um (the
> definition of field taxonomists) as the default, giving a
> definition like:
>
> 'Picophytoplankton are the smallest size class of phytoplankton
> with a maximum size of 2um for observational data and some models.
> Other models may specify the upper limit elsewhere in the range 2-5
> um, in which case the actual upper limit used should be specified.'
>
> Whether this specification should be done through the long name or
> a scalar co-ordinate variable as John suggests is something I'm not
> sure about. Anybody any preferences?
>
> Cheers, Roy.
>
>
> -----Original Message-----
> From: alison.pamment at stfc.ac.uk [mailto:alison.pamment at stfc.ac.uk]
> Sent: 23 April 2010 13:39
> To: cf-metadata at cgd.ucar.edu; Lowry, Roy K; John.Dunne at noaa.gov;
> taylor13 at llnl.govCc: chris.d.jones at metoffice.gov.uk;
> pierre.friedlingstein at lsce.ipsl.fr; doutriaux1 at llnl.gov;
> James.Orr at lsce.ipsl.fr; ernst.maier-reimer at zmaw.de
> Subject: RE: [CF-metadata] CMIP5 ocean biogeochemistry standard names
>
> Dear John and Roy,
>
> Apart from the iron flux name which was discussed and agreed in the
> 'HAMOCC variablen' thread, there have been no further comments
> during the last three weeks on the ocean biogeochemistry names.
> There is one outstanding question regarding the definition and
> naming of the picophytoplankton quantities:
>
> >
> > > > > (1) I don't understand what the definition of
> picophytoplankton> > > (carbon
> > > > > concentration from the picophytoplankton (<2 um; < 5um)
> component
> > > > > alone) means Does it mean cells between 2 and 5 um in
> size, in
> > > > which> case it should be expressed as 2-5um, or does it mean
> > > > something else?
> > > > >
> > > >
> > > > I agree that this definition doesn't make sense as it stands -
> I'll
> > > > check with John Dunne.
> > >
> > > The wishy-washiness of this definition was intended to account for
> > the
> > > fact that some groups make their distinction of smallest
> > phytoplankton
> > > class at the <2um size, while others do it at the <5um size. I
> agree
> > > that it would be better to have a single cut off for clarity.
> > Perhaps
> > > we should use the '2um' designation to be consistent with the
> > > traditional definition of 'picoplankton' (where nanoplankton is
> the> 2-5
> > > umclass), and leave the individual participants to determine
> whether
> > > they think their definition is consistent with this designation.
> >
> > >From the CF point of view, adopting a single cut off of <2um for
> > picophytoplankton would certainly be clear. However, will this
> cause
> > problems for modelling groups with different cut off sizes? I.e.
> will
> > it make intercomparison between models difficult? As an
> alternative,
> > we could write the definitions to cope with the vagueness, for
> > example:
> > "Picophytoplankton are the smallest class of phytoplankton. The
> maximum
> > size of picophytoplankton is in the range 2-5 um and may vary
> between
> > models. A scalar coordinate variable should be used to specify
> the
> > maximum size of picophytoplankton included in the data variable."
> >
> > This would then require the different modelling groups to specify
> the
> > threshold they used, but would allow them all to write their data
> with
> > the same standard name. (We could even give the coordinate
> variable a
> > standard name such as 'plankton_size_threshold'). Would that be a
> > suitable solution? Or do you still prefer to stick with the
> single cut
> > off?
>
> I am hoping that John will advise on which is the best approach to
> take with these names as I think we are close to being able to
> accept them.
> I have temporarily removed these particular names from the attached
> spreadsheet.
> The remaining names, including those modified in response to Roy's
> comments are now accepted for inclusion in the standard name table
> and are listed in the attached spreadsheet. To summarize, the
> modifications relative to the original proposals are as follows:
> Row 13: correction to typo in 'concentration'
> Rows 37-38: 'organic_carbon' changed to
> 'particulate_organic_matter_expressed_as_carbon'
> Row 42: 'particulate_organic_carbon' changed to
> 'particulate_organic_matter_expressed_as_carbon'Rows 51-54:
> 'organic_carbon' changed to
> 'particulate_organic_matter_expressed_as_carbon'
> Rows 61-62: 'particles' changed to 'inorganic_particles'
>
> I should also say that the clarifications to the definitions that
> have been suggested by both Roy and John during the discussion of
> these names will be included when the names are added to the table.
>
> Best wishes,
> Alison
>
> ------
> Alison Pamment Tel: +44 1235 778065
> NCAS/British Atmospheric Data Centre Fax: +44 1235 446314
> Rutherford Appleton Laboratory Email:
> alison.pamment at stfc.ac.ukChilton, Didcot, OX11 0QX, U.K.
>
>
> > -----Original Message-----
> > From: cf-metadata-bounces at cgd.ucar.edu [mailto:cf-metadata-
> > bounces at cgd.ucar.edu] On Behalf Of alison.pamment at stfc.ac.uk
> > Sent: 01 April 2010 13:28
> > To: cf-metadata at cgd.ucar.edu; rkl at bodc.ac.uk; John.Dunne at noaa.gov
> > Cc: chris.d.jones at metoffice.gov.uk;
> pierre.friedlingstein at lsce.ipsl.fr;
> > doutriaux1 at llnl.gov; James.Orr at lsce.ipsl.fr;
> ernst.maier-reimer at zmaw.de
> > Subject: Re: [CF-metadata] CMIP5 ocean biogeochemistry standard
> names>
> > Dear Roy and John,
> >
> > Roy wrote:
> >
> > > The one point I think you have possibly misunderstood is the one
> > about
> > > 'miscellaneous'. It's not the word, so much as the possibility of
> > the
> > > concept having meaning that changes with time that worries me.
> This
> > > can be addressed through the definition by a statement that
> > > 'miscellaneous means phytoplankton that are not diatoms,
> diazotrophs,
> > > calcareous phytoplankton or picophytoplankton'. I did briefly
> > consider
> > > the phrase
> 'phytoplankton_not_diatom_diazotroph_calcareous_pico' in
> > the
> > > standard name, but then thought better of it.
> > >
> >
> > Yes, I see now. I agree that the definitions should contain a
> > statement such as the one you suggest. Thanks for not suggesting
> the
> > other version of the name :)
> >
> > John wrote:
> >
> > > > > (1) I don't understand what the definition of
> picophytoplankton> > > (carbon
> > > > > concentration from the picophytoplankton (<2 um; < 5um)
> component
> > > > > alone) means Does it mean cells between 2 and 5 um in
> size, in
> > > > which> case it should be expressed as 2-5um, or does it mean
> > > > something else?
> > > > >
> > > >
> > > > I agree that this definition doesn't make sense as it stands -
> I'll
> > > > check with John Dunne.
> > >
> > > The wishy-washiness of this definition was intended to account for
> > the
> > > fact that some groups make their distinction of smallest
> > phytoplankton
> > > class at the <2um size, while others do it at the <5um size. I
> agree
> > > that it would be better to have a single cut off for clarity.
> > Perhaps
> > > we should use the '2um' designation to be consistent with the
> > > traditional definition of 'picoplankton' (where nanoplankton is
> the> 2-5
> > > umclass), and leave the individual participants to determine
> whether
> > > they think their definition is consistent with this designation.
> >
> > >From the CF point of view, adopting a single cut off of <2um for
> > picophytoplankton would certainly be clear. However, will this
> cause
> > problems for modelling groups with different cut off sizes? I.e.
> will
> > it make intercomparison between models difficult? As an
> alternative,
> > we could write the definitions to cope with the vagueness, for
> > example:
> > "Picophytoplankton are the smallest class of phytoplankton. The
> maximum
> > size of picophytoplankton is in the range 2-5 um and may vary
> between
> > models. A scalar coordinate variable should be used to specify
> the
> > maximum size of picophytoplankton included in the data variable."
> >
> > This would then require the different modelling groups to specify
> the
> > threshold they used, but would allow them all to write their data
> with
> > the same standard name. (We could even give the coordinate
> variable a
> > standard name such as 'plankton_size_threshold'). Would that be a
> > suitable solution? Or do you still prefer to stick with the
> single cut
> > off?
> >
> > John wrote:
> >
> > > > > (3) 'mole_concenration_of_dissolved_iron_in_sea_water'.
> Besides> > the
> > > > > typo (concentration), does this refer to iron in all oxidation
> > > > states> (Fe2+/Fe3+) and chemical environments. If so,
> calling it
> > > > 'total iron'
> > > > > might be better.
> > > >
> > > > Thanks for pointing out the typo - I'll correct it. I think
> > whenever
> > > > the word "total" has come up in standard names proposals in the
> > past
> > > > that we have tried to avoid using it. Indeed, there are no
> > standard
> > > > names that use the term. I think "iron" essentially should
> be
> > > > understood to mean "total iron" and if we want more specific
> names> > for
> > > > Fe2+, etc, we should introduce terms such as "divalent iron" in
> the
> > > > waythat we have done for elemental and divalent mercury in
> the
> > > > atmosphere.Having said all that, I think it would be helpful
> if
> > > > John could clarify the definition.
> > >
> > > In the geochemical literature, 'total' iron refers to the sum of
> iron
> > > associated with the particulate organic, particulate inorganic,
> > > dissolved organic and dissolved inorganic components (both Fe2+
> and> > Fe3+). As we treat phytoplankton iron and particulate
> detrital iron
> > > separately from dissolved, 'total' does not equal 'dissolved'.
> As
> > > most, if not all, of the models do not distinguish between Fe2+
> and
> > > Fe3+,
> I
> > > think we could simply add a note in the definition to the effect
> that
> > > 'dissolved' is intended to represent both Fe2+ and Fe3+.
> >
> > Agreed. I'll add a sentence to the definitions.
> >
> > Best wishes,
> > Alison
> >
> > ------
> > Alison Pamment Tel: +44 1235 778065
> > NCAS/British Atmospheric Data Centre Fax: +44 1235 446314
> > Rutherford Appleton Laboratory Email:
> > alison.pamment at stfc.ac.uk
> > Chilton, Didcot, OX11 0QX, U.K.
> >
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Received on Fri Apr 23 2010 - 18:02:01 BST
