Thanks Alison,
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.
Cheers, Roy.
-----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: 26 March 2010 14:35
To: cf-metadata at cgd.ucar.edu; John.Dunne at noaa.gov
Cc: chris.d.jones at metoffice.gov.uk; pierre.friedlingstein at lsce.ipsl.fr; James.Orr at lsce.ipsl.fr; ernst.maier-reimer at zmaw.de; doutriaux1 at llnl.gov
Subject: Re: [CF-metadata] CMIP5 ocean biogeochemistry standard names
Dear Roy,
>
> Some (ended up quite a lot) comments. Any discussion of this lot
could
> well descend into chaos. Could I suggest that responses are made
> separately to each of the 11 numbered comments so we end up with 11
> threads that individually stand some chance of closure.
>
If possible, I would prefer not to create a large number of separate
threads as that can sometimes make it difficult to follow complete
conversations when looking back through the mailing list archives.
Names can be accepted as they are agreed which will allow them to be
added to the standard name table, even if others are still under
discussion. Regarding your specific comments, I have tried to address
each one in turn.
>
> (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.
>
> (2)
>
'mole_concentration_of_miscellaneous_phytoplankton_expressed_as_carbon_
> in_sea_water' is a very imprecise term that I think needs specifying
> more precisely. Once the definition is tightened up finding a better
> phrase for the Standard Name should be possible. Likewise for
>
'mole_concentration_of_miscellaneous_zooplankton_expressed_as_carbon_in
> _sea_water', '
>
mass_concentration_of_miscellaneous_phytoplankton_expressed_as_chloroph
> yll_in_sea_water', .
>
My understanding of "miscellaneous" is that it means all the other
phytoplankton that are not mentioned in the names for specific
categories such as diatoms, diazatrophs, picophytoplankton, etc. In
that sense it is intended to allow a looser definition than some of the
other names. I think that
diatoms + diazotrophs + calcareous phytoplankton + picophytoplankton +
miscellaneous phytoplankton = total phytoplankton.
This information will certainly be included in the definitions of all
the relevant names. However, if we can come up with a more meaningful
collective noun than "miscellaneous" then I'd welcome suggestions.
>
> (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 way
that 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.
>
> (4) There are a number of standard names for elemental concentrations
> in the particulate phase where the long names are very familiar to me,
> but the Standard Names seem counter-intuitive, such as '
>
mole_concentration_of_particulate_organic_matter_expressed_as_nitrogen_
> in_sea_water' for the parameter commonly known as particulate organic
> nitrogen or more usually PON. I guess what is bugging me is that the
> standard name describes the primary quantity as the suspended
> particulate material (SPM) concentration, whereas in fact the chemical
> composition of the SPM is of at least equal importance.
I think the main reason for arriving at this particular wording was to
be consistent with existing standard names. We use
particulate_organic_matter in quite a number of existing atmosphere
names. The "expressed_as_species" construction and its position within
the standard name was also something that we arrived at after lengthy
discussion with the atmospheric chemists. I think that we should try,
as far as is practicable, to keep the wording and construction of
standard names consistent between the different components of the
climate system. I don't think the order of the wording is intended to
imply that the particulate state is more or less important than the name
of the chemical species.
>
> (5) I have much deeper rooted problems with '
>
tendency_of_mole_concentration_of_organic_carbon_in_sea_water_due_to_ne
> t_primary_production' for primary production. In a nutshell, the
> process of primary production involves the transition of primarily
> inorganic carbon in the dissolved phase into organic carbon in the
> particulate phase (in the form of plant cells). The standard name
> gives no indication that the organic carbon quantity change is in the
> particulate phase. At the very least I think we need
>
'tendency_of_mole_concentration_of_particulate_organic_carbon_in_sea_wa
> ter_due_to_net_primary_production', which with the existing syntax
form
> would in fact become '
>
tendency_of_mole_concentration_of_particulate_organic_matter_expressed_
> as_carbon_in_sea_water_due_to_net_primary_production'. Ditto for new
> production, biogenic iron production and biogenic silica production,
> but this doesn't apply to calcite and aragonite which are be
definition
> part of the particulate phase being crystalline forma of calcium
> carbonate. Also affects primary production by phytoplankton groups
such
> as diatoms (lines 53-57 of the spreadsheet).
Thank you for clarifying the production process. Personally, I would be
happy with the addition of the word "particulate", as you suggest.
>
> (6) I now see,
> 'sinking_mole_flux_of_particulate_organic_carbon_in_sea_water', which
> if for consistency with the POC standard name would need to be
> 'sinking_mole_flux_of_
> particulate_organic_matter_expressed_as_carbon_in_sea_water'.
> Personally, I much prefer 'particulate_organic_carbon'.
I see your point. Having argued for consistency of naming conventions
above, I would actually tend to favour
sinking_mole_flux_of_particulate_organic_matter_expressed_as_carbon_in_s
ea_water.
>
> (7)
>
'tendency_of_mole_concentration_of_dissolved_iron_in_sea_water_due_to_s
> cavenging_by_particles' should be '
>
tendency_of_mole_concentration_of_dissolved_iron_in_sea_water_due_to_sc
> avenging_by_inorganic_particles'. 'particles' could easily be taken
to
> include plankton. Similarly for '
>
tendency_of_mole_concentration_of_dissolved_iron_in_sea_water_due_to_di
> ssolution_from_particles'.
That sounds fine to me.
>
> (8) When we come to integrated primary production the standard name
> syntax becomes ' net_primary_mole_productivity_of_carbon' instead of
>
'net_tendency_of_mole_concentration_of_particulate_organic_carbon_in_se
> a_water_due_to_net_primary_production' (which in itself needs
revising:
> see above). I'm not sure how comfortable biogeochemists would be with
> the use of 'net' to signify depth integration. 'net' tends to have
> other meanings such as the result of competing processes like
> photosynthesis and respiration in oxygen budgets. I would much prefer
> 'depth_integrated'.
I think "net" refers to the productivity (i.e. net productivity = gross
productivity minus destruction) rather than to the vertical integration.
The vertical integration is implied by the fact that the units of this
quantity are mol m-2 s-1, rather than mol m-3 s-1 for 3-D tendencies.
In fact, Jonathan's idea was to reserve the term "productivity"
specifically to mean this type of vertically integrated quantity (as in
the atmosphere names gross_primary_productivity_of_carbon and
net_primary_productivity_of_carbon) and use "production" for the 3-D
quantities. The definition of the name needs to make this clear. If we
wanted to make the vertical integration part of the name itself the
correct syntax would be
integral_wrt_depth_of_tendency_of_mole_concentration_of_particulate_orga
nic_carbon_in_sea_water_due_to_net_primary_production. Would that be
better?
>
> (9) When we come to
> 'tendency_of_ocean_mole_content_of_iron_due_to_biological_production',
> there is no indication at all that the quantity is depth integrated.
> Ditto for lines 75-78, 86, 95-106.
The term "content" is well established in standard names to mean a
vertically integrated quantity, for example, there are many
"atmosphere_content" names with precisely this interpretation. This is
really just a convention that has been adopted within CF but it is one
that has been used pretty much from the inception of standard names, I
believe.
>
> (10)
'surface_downward_mass_flux_of_carbon_dioxide_expressed_as_carbon'
> doesn't indicate to me the that it's a flux from atmosphere to water
> body that's involved. It could equally well be a chemical flux
between
> two layers of the atmosphere, or is 'surface' explicitly defined as
the
> ocean/atmosphere interface?
The definition of "surface" in standard names is "the surface called
"surface" means the lower boundary of the atmosphere" which in this case
does indeed mean the atmosphere interface with the sea surface, although
it could also mean the interface with dry land, land-ice, sea-ice, etc.,
depending on the quantity being described. If we were talking about a
layer interface within a medium then we would need to adopt some new
terminology to describe it.
>
> (11) Rows 95-106 refer to the rate of change of depth integrated
values
> in the upper 100m of the water column, but the standard name gives no
> indication that it's depth integrated (see above) or that the region
of
> interest is confined to the top 100m. I can appreciate the quandry
> here that standard names shouldn't indicate spatial coverage, but
might
> it be possible to argue that the top 100m of the water column
> approximates to a layer (euphotic zone?) of the ocean that should be
> treated in the same way as layers of the atmosphere?
As in point (9), the use of the term "content" and the units of mol m-2
s-1 indicate that the quantities are vertical integrals. In practice,
variables containing these quantities would also need to have vertical
coordinate bounds to specify the limits of integration and this fact can
be indicated in the definitions of the names.
Thanks very much for taking the time to look through all these names and
for posting your comments. I think that with a small number of
adjustments these names are generally in pretty good shape.
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 Mar 26 2010 - 09:59:29 GMT
