Re: [CF-metadata] new standard name request for pH

[John Graybeal]

I believe this request has been pending for a long time now, with no  
comments since May 26.  Can we finalize it? (Please?)


sea_water_pH_reported_on_total_scale:
The measure of acidity of sea water, defined as the negative logarithm  
of the concentration of dissolved hydrogen
ions plus bisulfate ions in a seawater medium; it can be measured or  
calculated; when measured the scale is defined according to a series  
of buffers prepared in artificial seawater containing bisulfate.  
pH(total) = - log([H+](free) + [HSO4-]). [canonical units = moles/kg ].


John


On May 26, 2009, at 11:38 PM, Jonathan Gregory wrote:


Dear John

Thanks. I'm still happy with

 sea_water_pH_reported_on_total_scale

which is actually a phrase I found on Google.

Best wishes

Jonathan
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[CF-metadata] new standard name request for pH

[Jonathan Gregory]

Dear John

Thanks. I'm still happy with
>   sea_water_pH_reported_on_total_scale
which is actually a phrase I found on Google.

Best wishes

Jonathan
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Re: [CF-metadata] new standard name request for pH

[John Graybeal]

Hello again Jonathan and all,

On May 21, 2009, at 12:12 AM, Jonathan Gregory wrote:
each of these seems to be referring to only this  particular entity  
(sea_water_pH) as having the characteristic.

I'm sorry, I don't understand that remark.


I was just trying to say that the 'total scale' refers conceptually to  
the chemical model of the medium also, not *just* the pH. (A very fine  
hair indeed.)   So in my amateur mind it ('total_scale') does modify  
the whole bit.   (Hence I liked 'total_scale_pH_of_sea_water', because  
it doesn't preclude the understanding I express above.)


But one of my experts has returned and, presented with all the latest  
options and a few others besides, saved us from further analysis by  
preferring your earlier suggestion:

  sea_water_pH_reported_on_total_scale
as the best of the compromise options.  (Alternatively, since total  
scale only makes sense in sea water measurements of pH, you could say

  pH_reported_on_total_scale
to collocate all the pH names. But as I recall that is not a  
motivation for you, and the longer one provides better context I'd say.)


Let me know if this (sea_water_pH_reported_on_total_scale) has, or has  
not, gotten us to potential closure.  Thanks,


John




On May 21, 2009, at 12:12 AM, Jonathan Gregory wrote:


Dear John


I'll mention as a nit that they don't quite capture the
essence.  While the fundamental construct is the basic chemistry of
the system, each of these seems to be referring to only this
particular entity (sea_water_pH) as having the characteristic.


I'm sorry, I don't understand that remark.


I guess I'll just
ask how much you think the extra words add value.


All existing standard names are phrases with sufficient English glue  
so you

can work out how to parse them. For me

sea_water_pH_total_scale
is not ideal because it doesn't indicate what "total scale" refers  
to. Perhaps
your remark above indicates I still haven't understood what it  
*does* refer to,

unfortunately.

What about
total_scale_pH_of_sea_water
Would that be better? That indicate that "total scale pH" is a  
quantity
which is being measured in sea water. The "total scale" refers to  
"pH".


Cheers

Jonathan
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[CF-metadata] new standard name request for pH

[Jonathan Gregory]

Dear John

> I'll mention as a nit that they don't quite capture the  
> essence.  While the fundamental construct is the basic chemistry of  
> the system, each of these seems to be referring to only this  
> particular entity (sea_water_pH) as having the characteristic.

I'm sorry, I don't understand that remark.

> I guess I'll just  
> ask how much you think the extra words add value.

All existing standard names are phrases with sufficient English glue so you
can work out how to parse them. For me
> sea_water_pH_total_scale
is not ideal because it doesn't indicate what "total scale" refers to. Perhaps
your remark above indicates I still haven't understood what it *does* refer to,
unfortunately.

What about
total_scale_pH_of_sea_water
Would that be better? That indicate that "total scale pH" is a quantity
which is being measured in sea water. The "total scale" refers to "pH".

Cheers

Jonathan
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Re: [CF-metadata] new standard name request for pH

[John Graybeal]

Jonathan,

I could live with any of these (though my science experts are less  
keen), but I'll mention as a nit that they don't quite capture the  
essence.  While the fundamental construct is the basic chemistry of  
the system, each of these seems to be referring to only this  
particular entity (sea_water_pH) as having the characteristic. But  
since translations to the other systems are possible, I suppose I am  
way down in the weeds on that point.


Other than that, I just wish they weren't so wordy.  I guess I'll just  
ask how much you think the extra words add value.


So in order, my preferences would be

sea_water_pH_total_scale
sea_water_pH_on_total_scale
sea_water_pH_defined_by_total_scale
sea_water_pH_reported_on_total_scale
sea_water_pH_according_to_total_scale

If you can see your way clear to one of the first 2, great; otherwise  
I'll settle for the first one you and the list find agreeable.


John

On May 20, 2009, at 1:46 AM, Jonathan Gregory wrote:


Dear John

I have consulted a colleague of mine who has the same opinion as  
your pH
colleague, that there isn't a simple way to describe the scales and  
therefore
no clear alternative to using the expert terminology. I also  
learned, usefully,
that models would report on a particular pH scale, even if they do  
not simulate
all the species. Therefore I agree with your approach. Thanks for  
tolerating
the discussion, which has been useful to understand a bit better  
what we are

talking about.

As I said, I'd be happier with some explanatory linking phrase e.g.

sea_water_pH_defined_by_total_scale
sea_water_pH_according_to_total_scale
sea_water_pH_reported_on_total_scale

What do you think?

Best wishes

Jonathan
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[CF-metadata] new standard name request for pH

[Jonathan Gregory]

Dear John

I have consulted a colleague of mine who has the same opinion as your pH
colleague, that there isn't a simple way to describe the scales and therefore
no clear alternative to using the expert terminology. I also learned, usefully,
that models would report on a particular pH scale, even if they do not simulate
all the species. Therefore I agree with your approach. Thanks for tolerating
the discussion, which has been useful to understand a bit better what we are
talking about.

As I said, I'd be happier with some explanatory linking phrase e.g.

sea_water_pH_defined_by_total_scale
sea_water_pH_according_to_total_scale
sea_water_pH_reported_on_total_scale

What do you think?

Best wishes

Jonathan
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[CF-metadata] new standard name request for pH

[Jonathan Gregory]

Dear John

I agree that

> "there are several systems of sea water  
> chemistry (or its analogs) within which pH is measured or computed."   
> I would say it is the chemical systems that vary, not merely the  
> measurement technique.

could mean that the different pH scales are different geophysical quantities
and therefore need different standard names. You also say

> My non-expert impression is that the notion of pH is fairly well  
> defined, but that different chemical systems will produce different pH  
> measurements or calculated values, through no failure of the core  
> definition of pH. 

I am not an expert either, of course, but what I have read in this discussion
suggests to me that the notion of pH is actually inherently dependent on the
chemical system. These different scales are therefore *not* measuring the same
quantity, given the same sample of sea water, but somewhat similar quantities
that have distinct definitions.

I agree that it is not always possible to find a name that non-experts will
understand. For instance, atmosphere_sigma_coordinate tells a non-expert that
it is a kind of atmosphere coordinate, but if you don't know what sigma means,
you have to look at the definition. In many or most cases, however, we have
managed to find names that are somewhat more self-explanatory. That is why I
asked whether there were any more informative alternatives for "total scale"
and "sea water scale", because these terms are jargon. They have a precise
meaning, and they are used for convenience, but they are uninformative to
non-experts.

If we are to use these phrases in the standard name, I'd like to join them up
with some extra phrase to make their status clearer e.g.
sea_water_pH_defined_by_total_scale or _according_to_total_scale.

Personally, I'd still prefer an alternative if anyone knows any! I think a
workable alternative is one which would convey the meaning to an expert. That
is, it would be a phrase to which an expert would say, "Ah, you mean total
scale, of course!" The expert would probably go on to say, "Well, why didn't
you say total scale, then? It would be much clearer, and it's what is always
said." The answer to that would be that the chosen phrase would be more
informative to non-experts, if we had chosen it well. The definition would
confirm that it meant "total scale".

Best wishes

Jonathan
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Re: [CF-metadata] new standard name request for pH

[John Graybeal]

On May 12, 2009, at 1:10 AM, Jonathan Gregory wrote:


Dear Roy

I agree with what you say. But John and his colleague tell us that  
it is not possible simply to describe the difference between pH  
total scale and sea-water scale. Like you, I suggested that they  
could be described as being just [H+], or the sum of [H+] and other  
ions, but that's not right, apparently (and I am

certainly not an expert). John says

"There are several systems for measuring pH in sea water, and this  
one [total scale] best takes into account the chemistry and other  
interactions at the depths we make these observations."


Sorry, my terminology again was ambiguous.  When I wrote "there are  
several systems for measuring pH in sea water", a more precise  
phrasing would have been "there are several systems of sea water  
chemistry (or its analogs) within which pH is measured or computed."   
I would say it is the chemical systems that vary, not merely the  
measurement technique.


On May 11, 2009, at 10:29 AM, Jonathan Gregory wrote:

If the difference is so detailed and hard to summarise, it seems to  
me that it really is a matter of
technique, and not of different geophysical quantities. I would  
expect it to be possible to say, in a phrase, what the *essence* is  
of the difference between geophysical quantities, whereas that  
cannot necessarily be done for methods.


Can your "expectation of elegance" be justified by some analysis?  I  
suspect that in the case of complex systems, reduction of differences  
to a simple essence is not always feasible -- that different  
geophysical quantities may be different in complex ways.


In such cases, possibly the difference may be captured by a phrase  
that appears to be a 'specialist term', if only because the system's  
complexity is not yet broadly appreciated.  In our particular case,  
our offered phrases may be more specialist terms than reflective of  
the essence of the difference, but the latter quality also seems  
present to a degree.


On May 12, 2009, at 1:10 AM, Jonathan Gregory wrote:

Their opinion is that pH is always measuring the same geophysical  
quantity, but that it is hard to measure. In turn, that might be  
because it is hard to define just what pH really is; I have to admit  
that it is not clear to me from what I have read. If you know others  
who could help us with this, that would

be great.



My non-expert impression is that the notion of pH is fairly well  
defined, but that different chemical systems will produce different pH  
measurements or calculated values, through no failure of the core  
definition of pH. It is the need to know which system was in play when  
the measurement/calculation was made -- in order to properly interpret  
the values that are given -- that drives the naming.


In short, I concur with Roy's opinion that the quantities are  
different, and his analogies seem to the point. Apologies if my  
previous wording led you astray.


John

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Monterey Bay Aquarium Research Institute
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[CF-metadata] new standard name request for pH

[Jonathan Gregory]

Dear Roy

I agree with what you say. But John and his colleague tell us that it is not
possible simply to describe the difference between pH total scale and sea-water
scale. Like you, I suggested that they could be described as being just [H+],
or the sum of [H+] and other ions, but that's not right, apparently (and I am
certainly not an expert). John says

"There are several systems for measuring pH in sea water,
and this one [total scale] best takes into account the chemistry and other
interactions at the depths we make these observations."

Their opinion is that pH is always measuring the same geophysical quantity,
but that it is hard to measure. In turn, that might be because it is hard to
define just what pH really is; I have to admit that it is not clear to me from
what I have read. If you know others who could help us with this, that would
be great.

Best wishes

Jonathan
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Re: [CF-metadata] new standard name request for pH

[Lowry, Roy K]

Hello Jonathan/Nan,

In the case of pH I am still convinced that the quantities are different.  If 
we take an example of nitrate concentration in sea water.  We would have no 
compunction about setting up separate Standard Names for nitrate in moles/litre 
and nitrate in moles/kg.  Why is this different from [H+] in moles/litre and 
moles/kg that just happens to by convention to have a log transform applied? 
Similar arguments can be developed for the other pH scales: they are 
effectively summed concentrations of different inseperable species 
combinations. If a request came in for nitrate+nitrite concentration (nitrate 
is usually reduced to nitrite for colorometric assay and nitrite correction 
isn't always possible) wouldn't we give that a different Standard Name?

To answer Nan's point, I know that creating definitions isn't easy, but they 
provide a much better vehicle for presenting complex information than 
structured text that ideally has limited length.

Cheers, Roy.

-Original Message-
From: cf-metadata-boun...@cgd.ucar.edu 
[mailto:cf-metadata-boun...@cgd.ucar.edu] On Behalf Of Jonathan Gregory
Sent: 11 May 2009 18:30
To: cf-metadata@cgd.ucar.edu; Lowry, Roy K
Subject: [CF-metadata] new standard name request for pH

Dear Nan and Roy

I think it is a bit arbitrary whether one regards them as different quantities
or different methods of measurement, but now I am tending in the direction of
the latter because of what John last said about it. It is actually somewhere
between, because the answers are known to be systematically different with the
different methods. However, it turns out not to be possible to describe in a
phrase (even a long phrase) what the difference is. That is, if asked the
question in a seminar, the expert would say, "The quantities differ because of
various details in the way they are measured." If the difference is so
detailed and hard to summarise, it seems to me that it really is a matter of
technique, and not of different geophysical quantities. I would expect it to be
possible to say, in a phrase, what the *essence* is of the difference between
geophysical quantities, whereas that cannot necessarily be done for methods.
Consequently, I would say that if we introduce a new attribute to identify
methods of measurement, we would not expect it to be as self-explanatory as
standard names. Whereas it is reasonable to expect an average scientist to
understand what is meant by a standard name, it is not necessary or reasonable
for different measurement/calculation methods. They depend on domain expertise.
Does that sound sensible to you?

A new attribute would also be able to distinguish between cloud fraction from
cloudsat, calipso or isccp, which is the other example we've had. We've agreed
these intend to be the same geophysical quantity, but it is known or expected
that the retrievals from different instruments will not give exactly the same
answers. However, it is not possible to summarise simply what these differences
are or to give them a geophysical explanation. So this is again a matter of
methods of measurement, like pH scales, it seems to me.

A further purpose for this attribute, if we designed it generally enough, could
be to identify the raw quantities which we have discussed in another thread.
The standard name for something could be a measured voltage, for instance,
and the other attribute says what function this quantity has in a sensor. That
definitely refers to methods of measurement.

Regarding Nan's question, I think pH by all the definitions is a dimensionless
quantity. It is a logarithm, so it must be dimensionless. However, that
does imply that the quantity whose logarithm is being taken must be in certain
units, to get the right answer, numerically. That has to be recorded in the
definition of the quantity. I agree, that is awkward. There is some precedent
for this. For instance, we have some standard names which specify units of
decibels. These quantities are logarithms too, and involve a reference level,
with specified units, in their definition.

Best wishes

Jonathan
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[CF-metadata] new standard name request for pH

[Jonathan Gregory]

Dear Nan and Roy

I think it is a bit arbitrary whether one regards them as different quantities
or different methods of measurement, but now I am tending in the direction of
the latter because of what John last said about it. It is actually somewhere
between, because the answers are known to be systematically different with the
different methods. However, it turns out not to be possible to describe in a
phrase (even a long phrase) what the difference is. That is, if asked the
question in a seminar, the expert would say, "The quantities differ because of
various details in the way they are measured." If the difference is so
detailed and hard to summarise, it seems to me that it really is a matter of
technique, and not of different geophysical quantities. I would expect it to be
possible to say, in a phrase, what the *essence* is of the difference between
geophysical quantities, whereas that cannot necessarily be done for methods.
Consequently, I would say that if we introduce a new attribute to identify
methods of measurement, we would not expect it to be as self-explanatory as
standard names. Whereas it is reasonable to expect an average scientist to
understand what is meant by a standard name, it is not necessary or reasonable
for different measurement/calculation methods. They depend on domain expertise.
Does that sound sensible to you?

A new attribute would also be able to distinguish between cloud fraction from
cloudsat, calipso or isccp, which is the other example we've had. We've agreed
these intend to be the same geophysical quantity, but it is known or expected
that the retrievals from different instruments will not give exactly the same
answers. However, it is not possible to summarise simply what these differences
are or to give them a geophysical explanation. So this is again a matter of
methods of measurement, like pH scales, it seems to me.

A further purpose for this attribute, if we designed it generally enough, could
be to identify the raw quantities which we have discussed in another thread.
The standard name for something could be a measured voltage, for instance,
and the other attribute says what function this quantity has in a sensor. That
definitely refers to methods of measurement.

Regarding Nan's question, I think pH by all the definitions is a dimensionless
quantity. It is a logarithm, so it must be dimensionless. However, that
does imply that the quantity whose logarithm is being taken must be in certain
units, to get the right answer, numerically. That has to be recorded in the
definition of the quantity. I agree, that is awkward. There is some precedent
for this. For instance, we have some standard names which specify units of
decibels. These quantities are logarithms too, and involve a reference level,
with specified units, in their definition.

Best wishes

Jonathan
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Re: [CF-metadata] new standard name request for pH

[Nan Galbraith]

I think I'd have to defer to Roy and John about whether these are
really different geophysical quantities or just different scales, since
I have no experience with pH measurements (yet). 


On the other hand, Roy, it's no less daunting to provide definitions
for attributes that characterize the 5 (to date) different scales than to
define new standard names for them, if we went that route. It's just
the down side of using a standard - definitions will be required,
either way.

One question for Jonathan, and I apologize if this has already been
determined - I appreciate the time you're putting into this.

If we went with the approach that these are different ways to measure
the same quantity,  and used a single standard name, how would you
implement this to allow different units?  Would we need to use 
dimensionless
units (1) and provide the actual units in the new attribute?  That might 
make

the data fairly difficult to use and share effectively.

I don't know of any other measured parameters that are treated this way;
you mentioned cloud area fraction, but I'm not clear on how that was
implemented to allow different scales, and since "fraction" is part of the
standard name, it does seem that "1" is a more appropriate unit there than
here.  Having the actual units specified (or worse,  implied)  in another
attribute it wouldn't be anything we'd deal with in existing code. Not
that this couldn't be written, but as a programmer, I think  limiting the
number of special cases we have to deal with is generally a good thing.

Thanks - Nan


Hello Jonathan,

I don't see the different pH scales as the same geophysical quantity measured 
in different ways.  I see them more as subtley different geophysical quantities 
(activities or concentrations of different groups of species) expressed through 
a common syntax (negative log transform).

My initial reaction to an additional attribute is one of caution.  I can see 
the need but have concerns as to how it would be populated.  Plaintext doesn't 
scale and standardised sensor descriptions have kept a group of us in MMI 
pretty busy over the past year, which makes doing the same for analytical 
methods look very daunting.

Cheers, Roy.

-Original Message-
From: cf-metadata-boun...@cgd.ucar.edu 
[mailto:cf-metadata-boun...@cgd.ucar.edu] On Behalf Of Jonathan Gregory
Sent: 08 May 2009 10:29
To: cf-metadata@cgd.ucar.edu; Lowry, Roy K
Subject: [CF-metadata] new standard name request for pH

Dear John

Thanks for the helpful information and all your time, and your colleagues',
spent on this.

If the conclusion is "There are several ways of measuring pH and this is the
best one for the circumstances", as you say, it sounds to me that pH is the
geophysical quantity, and "total scale" is a measurement technique. That
means I tend to the solution of not including it in the standard name, and
deciding on another attribute to record it in. We do not define distinct
standard names for different ways of measuring the same quantity. That's a
point that came up, for instance, regarding cloud area fraction from different
satellites. But it is still important to record the information, since the
results may be systematically different. Maybe we need a new CF attribute
for this kind of purpose. What do you think, Roy, Nan and others?

Best wishes

Jonathan
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Re: [CF-metadata] new standard name request for pH

[Lowry, Roy K]

Hello Jonathan,

I don't see the different pH scales as the same geophysical quantity measured 
in different ways.  I see them more as subtley different geophysical quantities 
(activities or concentrations of different groups of species) expressed through 
a common syntax (negative log transform).

My initial reaction to an additional attribute is one of caution.  I can see 
the need but have concerns as to how it would be populated.  Plaintext doesn't 
scale and standardised sensor descriptions have kept a group of us in MMI 
pretty busy over the past year, which makes doing the same for analytical 
methods look very daunting.

Cheers, Roy.

-Original Message-
From: cf-metadata-boun...@cgd.ucar.edu 
[mailto:cf-metadata-boun...@cgd.ucar.edu] On Behalf Of Jonathan Gregory
Sent: 08 May 2009 10:29
To: cf-metadata@cgd.ucar.edu; Lowry, Roy K
Subject: [CF-metadata] new standard name request for pH

Dear John

Thanks for the helpful information and all your time, and your colleagues',
spent on this.

If the conclusion is "There are several ways of measuring pH and this is the
best one for the circumstances", as you say, it sounds to me that pH is the
geophysical quantity, and "total scale" is a measurement technique. That
means I tend to the solution of not including it in the standard name, and
deciding on another attribute to record it in. We do not define distinct
standard names for different ways of measuring the same quantity. That's a
point that came up, for instance, regarding cloud area fraction from different
satellites. But it is still important to record the information, since the
results may be systematically different. Maybe we need a new CF attribute
for this kind of purpose. What do you think, Roy, Nan and others?

Best wishes

Jonathan
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[CF-metadata] new standard name request for pH

[Jonathan Gregory]

Dear John

Thanks for the helpful information and all your time, and your colleagues',
spent on this.

If the conclusion is "There are several ways of measuring pH and this is the
best one for the circumstances", as you say, it sounds to me that pH is the
geophysical quantity, and "total scale" is a measurement technique. That
means I tend to the solution of not including it in the standard name, and
deciding on another attribute to record it in. We do not define distinct
standard names for different ways of measuring the same quantity. That's a
point that came up, for instance, regarding cloud area fraction from different
satellites. But it is still important to record the information, since the
results may be systematically different. Maybe we need a new CF attribute
for this kind of purpose. What do you think, Roy, Nan and others?

Best wishes

Jonathan
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Re: [CF-metadata] new standard name request for pH

[Lowry, Roy K]

Dear All,

I'm getting the distinct feeling that we're heading for impasse here.  I think 
it's to admit that despite our best efforts getting all the necessary 
information into the term, rather than an accompanying definition, isn't 
possible in this case.  This leaves us with John's initial suggestion of four 
Standard Names for the different scales, plus Jonathan's term for cases where 
the data creators don't know (or care about) the scale used.

How about we go with all five, capturing their meanings/chemistries in the 
definition?

I for one have learned a lot during this thread.

Cheers, Roy.

-Original Message-
From: cf-metadata-boun...@cgd.ucar.edu 
[mailto:cf-metadata-boun...@cgd.ucar.edu] On Behalf Of John Graybeal
Sent: 08 May 2009 07:54
To: CF List Metadata; Lowry, Roy K
Subject: Re: [CF-metadata] new standard name request for pH

On May 6, 2009, at 5:37 AM, Jonathan Gregory wrote:

> Dear John
>
>> He believes other terminology will be opaque
>> and ambiguous, and therefore essentially useless.
>
> Perhaps you could ask him, not what he calls
> the quantity normally, but how would he answer, in one sentence, the
> question,
> "What does that mean?", if he was giving a seminar in which he
> mentioned the
> concept of pH total scale to a scientifically literature audience
> who were not
> ocean chemists. Such people could be expected to know that pH measures
> hydrogen ion concencentration in some way, but not any more details.
> Surely it
> must be possible to say, in a phrase, what "total scale" indicates
> sufficiently
> to get across the point of it, if not the details?
>

Jonathan, all,

Yes, I have asked that question.  Short answer: No, I don't think it
is possible to say what this means in the type of phrase you are
looking for. Hence my conclusion that we may be stuck.

Having spent the last two weeks learning 'what does that mean' --
well, as much as high school chemistry allows -- I will  give you his
answer, then mine.  It may help the list to know that most folks don't
measure it directly (what we do at MBARI), especially in the deep
ocean. Instead, pH is more commonly determined as the solution to an
equation with several other measured components, and it appears to be
the entire interaction of that chemical system that is referenced by
the term, not simply a characterization of the single measurement.
(The other chemical parts of the system determine key equilibrium
constants that help specify the resulting interactions and the
conversions between scales.) That may be a reason it resists summary.

His answer: "There are several systems for measuring pH in sea water,
and this one best takes into account the chemistry and other
interactions at the depths we make these observations."  (Yes, I know
that is not sufficiently descriptive for your purposes.)  Any attempt
to get a more concrete summary immediately devolves into detailed
explanations of chemistry; our previous attempts at summary concepts
appeared to be unsatisfactory on their face. We have since asked 2 of
the leading experts in the field, with nearly identical results. (They
offered a second reference[1] in support, and another set of
explanatory detail, below -- note its final summary.) If there were
any readily acceptable answer I think we would have found it.

My answer, attempting to be more concrete: "Ocean chemists have
developed several regimes in which they perform their observations and
state their results; this regime best derives the activity of hydrate
ions taking into account temperature, pressure, high salinity
(especially), and a wide range of pressures in situ." Any more precise
summary of the context would require at least a few more sentences. To
synthesize all those nouns into a meaningful and sufficiently specific
phrase really would give you a Standard Paragraph.

So. There we are.  Sorry I can not be more obliging, I really have
tried but this one defies easy answers.

The good news is, I will be off the list for the next week while on
vacation. So you have plenty of time to consider or ignore these
matters. :->

Thanks for all your help considering this matter.

John

[1] Pure Appl. Chem., Vol. 74, No. 11, pp. 2169-2200, 2002.
INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY -- MEASUREMENT OF
pH.   DEFINITION, STANDARDS, AND PROCEDURES (IUPAC Recommendations 2002)

== Expert Recommendation on Naming 

The definitions are:

(A)   pH(total) =  - log  ([H+]total / k0)  =  - log ( [H+]free (1 +
ST/K(HSO4-)) / k0)

(B)   pH(sws)  = - log ([H+]sws / k0)  =  - log ( [H+]free (1 + ST /
K(HSO4-) + FT/K(HF)) / k0)

(C)   pH(IUPAC) = operational pH calibrated using IUPAC primary
standard buffers

NOTES:
1.  Any measured pH value needs to also identify the temperature (&
pressure) at which it was measured.

Re: [CF-metadata] new standard name request for pH

[John Graybeal]

On May 6, 2009, at 5:37 AM, Jonathan Gregory wrote:


Dear John


He believes other terminology will be opaque
and ambiguous, and therefore essentially useless.


Perhaps you could ask him, not what he calls
the quantity normally, but how would he answer, in one sentence, the  
question,
"What does that mean?", if he was giving a seminar in which he  
mentioned the
concept of pH total scale to a scientifically literature audience  
who were not

ocean chemists. Such people could be expected to know that pH measures
hydrogen ion concencentration in some way, but not any more details.  
Surely it
must be possible to say, in a phrase, what "total scale" indicates  
sufficiently

to get across the point of it, if not the details?



Jonathan, all,

Yes, I have asked that question.  Short answer: No, I don't think it  
is possible to say what this means in the type of phrase you are  
looking for. Hence my conclusion that we may be stuck.


Having spent the last two weeks learning 'what does that mean' --  
well, as much as high school chemistry allows -- I will  give you his  
answer, then mine.  It may help the list to know that most folks don't  
measure it directly (what we do at MBARI), especially in the deep  
ocean. Instead, pH is more commonly determined as the solution to an  
equation with several other measured components, and it appears to be  
the entire interaction of that chemical system that is referenced by  
the term, not simply a characterization of the single measurement.  
(The other chemical parts of the system determine key equilibrium  
constants that help specify the resulting interactions and the  
conversions between scales.) That may be a reason it resists summary.


His answer: "There are several systems for measuring pH in sea water,  
and this one best takes into account the chemistry and other  
interactions at the depths we make these observations."  (Yes, I know  
that is not sufficiently descriptive for your purposes.)  Any attempt  
to get a more concrete summary immediately devolves into detailed  
explanations of chemistry; our previous attempts at summary concepts  
appeared to be unsatisfactory on their face. We have since asked 2 of  
the leading experts in the field, with nearly identical results. (They  
offered a second reference[1] in support, and another set of  
explanatory detail, below -- note its final summary.) If there were  
any readily acceptable answer I think we would have found it.


My answer, attempting to be more concrete: "Ocean chemists have  
developed several regimes in which they perform their observations and  
state their results; this regime best derives the activity of hydrate  
ions taking into account temperature, pressure, high salinity  
(especially), and a wide range of pressures in situ." Any more precise  
summary of the context would require at least a few more sentences. To  
synthesize all those nouns into a meaningful and sufficiently specific  
phrase really would give you a Standard Paragraph.


So. There we are.  Sorry I can not be more obliging, I really have  
tried but this one defies easy answers.


The good news is, I will be off the list for the next week while on  
vacation. So you have plenty of time to consider or ignore these  
matters. :->


Thanks for all your help considering this matter.

John

[1] Pure Appl. Chem., Vol. 74, No. 11, pp. 2169–2200, 2002.  
INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY -- MEASUREMENT OF  
pH.   DEFINITION, STANDARDS, AND PROCEDURES (IUPAC Recommendations 2002)


== Expert Recommendation on Naming 

The definitions are:

(A)   pH(total) =  - log  ([H+]total / k0)  =  - log ( [H+]free (1 +  
ST/K(HSO4-)) / k0)


(B)   pH(sws)  = - log ([H+]sws / k0)  =  - log ( [H+]free (1 + ST /  
K(HSO4-) + FT/K(HF)) / k0)


(C)   pH(IUPAC) = operational pH calibrated using IUPAC primary  
standard buffers


NOTES:
1.  Any measured pH value needs to also identify the temperature (&  
pressure) at which it was measured.


2. Although pH is a dimensionless quantity, the concentrations in (A)  
and (B) are specified in moles per kilogram of solution. That is k0  
has the value of 1 mol/kg-soln.
For (C), conventionally 10^-pH is thought of as a single ion activity  
for hydrogen ion with associated concentration units of mol/kg-H2O,  
though this is essentially meaningless for sea water.


3. ST = total concentration of sulfate ion in seawater - f(salinity)
FT = total concentration of fluoride ion in seawater - f(salinity)
K(HSO4) = dissociation constant for HSO4 in seawater - free H+  
scale; f(salinity, temperature)
K(HF) = dissociation constant for HF in seawater - free H+ scale;  
f(salinity, temperature)


4. Values of pH(SWS) or pH (total) ultimately are not calculated from  
the definitions (A) and (B) but are calibrated relative to hydrogen  
ion concentration values assigned to Tris/Tris-H+ buffers in synthetic  
seawater using a Harned cell. These

Re: [CF-metadata] new standard name request for pH

[John Graybeal]

I didn't mean to suggest we not create a standard name for it, I just  
suggested it not be a part of this proposal. What I didn't like about  
the original name is that it implies NBS scale is appropriate for sea  
water, whereas the documentation I had suggested that was not the case  
(and my impression was that the errors could be bigger than 0.1, but  
I'm talking out of my hat there).  So another name might be more  
suited -- or this might be your preference.  If you want that name I  
won't stand in your way!


You know, an analogous name for some of this is  
'sea_surface_temperature'.  I know that's a favorite of yours Roy!   
The argument (I think you've made this point very effectively in  
presentations?) is "What do we do with this? We don't know what the  
values mean!"  So a number of more precise terms were defined (though  
I don't know that the original is precluded, or even discouraged?).  I  
think 'sea_water_pH' is an excellent analog.


John

On May 7, 2009, at 5:14 AM, Lowry, Roy K wrote:


Hi John,

Your suggestion that we disallow storage of NBS scale pH in CF by  
not creating a Standard Name for it worries me.  We have significant  
quantities of NBS-scale pH in BODC (from estuarine systems and the  
days before ocean chemists discovered the kilogram) that we may wish  
to put into CF in the future.  Whilst conversion based on  
approximation to free_scale is possible in some (but not all) cases  
(need additional data), it's something I'd rather not do.  I would  
much rather label precisely and leave any manipulations up to the  
user who is aware of the proposed usage and what is fit for that  
purpose.


My attraction to Jonathan's simple 'pH_in sea_water' is that it  
gives us a way of handling data in CF where 0.1 pH units don't  
matter.  We have one dataset monitoring waters off a chrome plating  
plant where pH varies between 2 and 6. At the same time I am acutely  
aware of the effects errors of that magnitude have on deep ocean  
carbon budget calculations.


Cheers, Roy.

-Original Message-
From: cf-metadata-boun...@cgd.ucar.edu [mailto:cf-metadata-boun...@cgd.ucar.edu 
] On Behalf Of John Graybeal

Sent: 02 May 2009 01:28
To: CF Metadata List; Lowry, Roy K
Subject: Re: [CF-metadata] new standard name request for pH

Hi everyone,

Thanks very much for considering and responding to the pH terms
proposal.  To respond, I spent considerable time being educated by our
in-house pH expert, even reading pages myself from the referenced book
[1], and reviewed this email with him. So I claim this email
represents a high level of expertise in this scientific field. I
apologize for the length, but it seemed necessary to present
justifying details.

To recap, the original proposal as revised was for 4 names related to
pH:
A)  sea_water_pH_NBS_scale  (moles/liter)
B)  sea_water_pH_free_scale (moles/kg)
C)  sea_water_pH_total_scale  (moles/kg)<-- the one we care about
D)  sea_water_pH_seawater_scale  (moles/kg)

Through this thread we have had several suggestions for replacements
[5], most recently arriving at
a) pH_of_sea_water_defined_by_moles_of_hydrogen_ion_per_unit_mass
b) pH_of_sea_water_defined_by_mole_concentration_of_hydrogen_ion
c)
mole_concentration_of_H_and_HSO4_per_unit_mass_in_sea_water_expressed_as_pH
d) mole_concentration_of_H_and_HSO4_and_HF_per_unit_mass
in_sea_water_expressed_as_pH
e) (added) pH_of_sea_water

I believe the focus of these responses was on the concentration of the
solution, but this mis-states the actual chemical definition of this
particular concept. (Unfortunately we incorrectly presented this in
the original definitions for B, C, and D.)  In the reference[1]  it is
made clear that:
(a) pH is strongly affected by abundance of hydrogen (actually
hydrate) ions, but is not defined by their quantity; it is determined
according to the *activity* of those ions, and this is not a linear
relationship (though it is close to 1 in some regimes)[2].   We will
change the proposed definitions to replace 'concentration' with
'activity'; my apologies for this error.
(b) The use of the NBS scale is not recommended for sea water[3], as
errors will be induced (up to at least 0.1 units in situ); in this
light we propose to simply withdraw [A] from consideration, especially
as we don't need it.
(c) There are significant differences in the values obtained for these
different quantitiies, up to .12 units; thus to say just
'pH_of_sea_water' is to have a very loose concern about the accurate
meaning of the so-labelled pH values[4]. For comparison, measurements
are often made, and needed, at the level of 0.0005 units.
(d) All 3 of {B, C, D} above are in regular use, but (C) is the most
promising for the common reference[4].

Additionally, the units are expressed as noted above by common
convention (see for example UCUM uni

Re: [CF-metadata] new standard name request for pH

[Lowry, Roy K]

Hi John,

Your suggestion that we disallow storage of NBS scale pH in CF by not creating 
a Standard Name for it worries me.  We have significant quantities of NBS-scale 
pH in BODC (from estuarine systems and the days before ocean chemists 
discovered the kilogram) that we may wish to put into CF in the future.  Whilst 
conversion based on approximation to free_scale is possible in some (but not 
all) cases (need additional data), it's something I'd rather not do.  I would 
much rather label precisely and leave any manipulations up to the user who is 
aware of the proposed usage and what is fit for that purpose.

My attraction to Jonathan's simple 'pH_in sea_water' is that it gives us a way 
of handling data in CF where 0.1 pH units don't matter.  We have one dataset 
monitoring waters off a chrome plating plant where pH varies between 2 and 6. 
At the same time I am acutely aware of the effects errors of that magnitude 
have on deep ocean carbon budget calculations.

Cheers, Roy.

-Original Message-
From: cf-metadata-boun...@cgd.ucar.edu 
[mailto:cf-metadata-boun...@cgd.ucar.edu] On Behalf Of John Graybeal
Sent: 02 May 2009 01:28
To: CF Metadata List; Lowry, Roy K
Subject: Re: [CF-metadata] new standard name request for pH

Hi everyone,

Thanks very much for considering and responding to the pH terms
proposal.  To respond, I spent considerable time being educated by our
in-house pH expert, even reading pages myself from the referenced book
[1], and reviewed this email with him. So I claim this email
represents a high level of expertise in this scientific field. I
apologize for the length, but it seemed necessary to present
justifying details.

To recap, the original proposal as revised was for 4 names related to
pH:
A)  sea_water_pH_NBS_scale  (moles/liter)
B)  sea_water_pH_free_scale (moles/kg)
C)  sea_water_pH_total_scale  (moles/kg)<-- the one we care about
D)  sea_water_pH_seawater_scale  (moles/kg)

Through this thread we have had several suggestions for replacements
[5], most recently arriving at
a) pH_of_sea_water_defined_by_moles_of_hydrogen_ion_per_unit_mass
b) pH_of_sea_water_defined_by_mole_concentration_of_hydrogen_ion
c)
mole_concentration_of_H_and_HSO4_per_unit_mass_in_sea_water_expressed_as_pH
d) mole_concentration_of_H_and_HSO4_and_HF_per_unit_mass
in_sea_water_expressed_as_pH
e) (added) pH_of_sea_water

I believe the focus of these responses was on the concentration of the
solution, but this mis-states the actual chemical definition of this
particular concept. (Unfortunately we incorrectly presented this in
the original definitions for B, C, and D.)  In the reference[1]  it is
made clear that:
(a) pH is strongly affected by abundance of hydrogen (actually
hydrate) ions, but is not defined by their quantity; it is determined
according to the *activity* of those ions, and this is not a linear
relationship (though it is close to 1 in some regimes)[2].   We will
change the proposed definitions to replace 'concentration' with
'activity'; my apologies for this error.
(b) The use of the NBS scale is not recommended for sea water[3], as
errors will be induced (up to at least 0.1 units in situ); in this
light we propose to simply withdraw [A] from consideration, especially
as we don't need it.
(c) There are significant differences in the values obtained for these
different quantitiies, up to .12 units; thus to say just
'pH_of_sea_water' is to have a very loose concern about the accurate
meaning of the so-labelled pH values[4]. For comparison, measurements
are often made, and needed, at the level of 0.0005 units.
(d) All 3 of {B, C, D} above are in regular use, but (C) is the most
promising for the common reference[4].

Additionally, the units are expressed as noted above by common
convention (see for example UCUM units section on pH [5]), in order to
make certain conversions handy for the enlightened.  Yet the second
sentence of the following statement does not hold true for pH, given
the depths at which these measurements are being made:

On Apr 30, 2009, at 9:22 AM, Jonathan Gregory wrote:
> Boussinesq models (most ocean climate models are Boussinesq) treat
> density
> as constant 1000 kg m-3 except in the computation of pressure
> gradients, where
> it matters to the dynamics. Therefore in dealing with concentrations
> of
> tracers, per kg and per litre are identical and to choose one or the
> other
> would be arbitrary and hence unhelpful for data exchange.

We therefore do not believe a substitution of moles/liter or moles/
m**3 is appropriate for the canonical moles/kg, as this would force
most practitioners to convert their data before naming it with this
name. [7] Obviously if there is a set of practitioners that are
working with seawater pH using a different canonical unit, that would
be another matter to consider; we think it is unlikely that any
observationalists are doing so.

[CF-metadata] new standard name request for pH

[Jonathan Gregory]

Dear John

As Philip says, if we adopt a standard name that does not say "total scale"
in it, we should certainly say that in the definition.

> In your option (1) (sea_water_pH universally), it isn't clear to me  
> what other attribute would indicate the scale difference.

No, I don't know either. This would be part of whatever solution is adopted
for recording information about how things are measured, as we have discussed
in other threads.

> In case (2) (different geophysical quantities), we may be a little  
> stuck. I quote from my own ocean chemist: "as an ocean chemist, I know  
> EXACTLY what is meant by sea_water_pH_total_scale, and so do all the  
> other ocean chemists."

Yes, fair enough. As I said, my questioning it does not imply that he doesn't
know his subject! That is not the point.

> He believes other terminology will be opaque  
> and ambiguous, and therefore essentially useless.

Perhaps you could ask him, not what he calls
the quantity normally, but how would he answer, in one sentence, the question,
"What does that mean?", if he was giving a seminar in which he mentioned the
concept of pH total scale to a scientifically literature audience who were not
ocean chemists. Such people could be expected to know that pH measures
hydrogen ion concencentration in some way, but not any more details. Surely it
must be possible to say, in a phrase, what "total scale" indicates sufficiently
to get across the point of it, if not the details?

Best wishes

Jonathan
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Re: [CF-metadata] new standard name request for pH

[Philip J. Cameronsmith1]

Hi,

For option (2), would it satisfy both the CF and ocean chemistry 
communities to have the more descriptive standard name as Jonathan 
suggests, and then put in the comments that 'This quantity is known as the 
"total scale" for pH in the ocean chemistry community'?   (and similarly 
for the other pH quantities)


Best wishes,

 Philip


On Mon, 4 May 2009, John Graybeal wrote:


Jonathan,

No worries, I think we are zeroing in on the key points now. Though I don't 
yet know how ocean chemists will feel about the end results!  But I 
appreciate the thorough analysis brought to the issue.


In your option (1) (sea_water_pH universally), it isn't clear to me what 
other attribute would indicate the scale difference. I had understood that if 
the standard name and units were the same, CF users would assume the data 
could be exchanged, from a numerical standpoint anyway. If that is true, or 
if the specific attribute where this scale information must be entered, and 
the controlled vocabulary to use, is not specified, option (1) does not seem 
attractive. The likely outcome would be the attribute is unspecified or 
ambiguous, rendering the associated values useless to many potential users of 
the data.


In case (2) (different geophysical quantities), we may be a little stuck. I 
quote from my own ocean chemist: "as an ocean chemist, I know EXACTLY what is 
meant by sea_water_pH_total_scale, and so do all the other ocean chemists." 
He believes other terminology will be opaque and ambiguous, and therefore 
essentially useless.  As I understand the situation, the entire system of 
related chemistry in sea water is considered different depending on which 
scale is in use, so it is a pervasive concept in this domain, not simply an 
obscure name for this one measurement.


Since I am unable to personally verify this last assertion with all those 
other ocean chemists, and you might not want to take my word for it anyway, 
it may be that you would like to verify this perspective with other experts 
in the domain? (I can provide some names offline if you would like to do 
that.)  I think the reason to consider doing so in this case is that if there 
is indeed some ambiguity in the name you choose, then it may apply equally 
well in the future to a different scale, and this would be problematic.


If, after such a discussion, or regardless of that point, you choose a name 
that seems more appropriate to you, we can always create our preferred name 
in another vocabulary and map it to yours. (Eventually I am sure the CF 
convention will support this technique in an embedded way. :->)  So all is 
not lost, so long as the definition makes clear that the name you choose 
refers precisely to sea water pH total scale.  Such an approach seems 
sufficiently usable to me, and we can bear the brunt of name translation for 
our cadre of ocean chemists.


John


On May 2, 2009, at 5:53 AM, Jonathan Gregory wrote:


Dear John

Thanks for your thoughtful email. I follow the argument but in the end I do
not (yet) agree with the conclusion, that sea_water_pH_total_scale should 
be a
standard name. I am sorry if you find that exasperating. As in previous 
such
discussions, it is not because I am suggesting that you or your pH expert 
are
mistaken about what terms are normally used and what they mean. My 
difficulty
is that "total scale" is not informative to a general scientific 
readership,

which CF standard names are designed to be.

I've had a look at Zeebe and Wolf-Gladrow. Thanks for that reference.
Wikipedia summarises similar ideas. I also looked at a IUPAC document on 
the

subject. It seems that problem of definition arises because pH is actually
impossible to measure, as defined! Hence the true value is somewhat 
unknowable.

These different scales represent different methods of measurement and
estimation. I think we could take two views about that:

* The different pH scales are actually trying to measure the same 
geophysical
quantity. In that case the standard name should just be sea_water_pH. Then 
the

scale is an aspect of the method of measurement, and should be recorded in
some other attribute. This is somewhat related to the other thread, about
quantities relating to the techniques of measurement.

* The different pH scales are different geophysical quantities. In that 
case

they need distinct standard names, and it ought to be possible to indicate
in some non-jargon way what the difference refers to, even though it 
couldn't
be fully described in the name, so we still need a definition. Following 
this
route, the total scale could be called 
sea_water_pH_including_bisulfate_ions,

for instance. (A side-issue is a question of whether to call them bisulfate
or the IUPAC name of hydrogen_sulfate.)

pH is a dimensionless quantity. It has no units. It's the logarithm of
a number which does have units, so the units of that quantity need to be
specified in the definition.


Yet the second
sentence of the fol

Re: [CF-metadata] new standard name request for pH

[John Graybeal]

Jonathan,

No worries, I think we are zeroing in on the key points now. Though I  
don't yet know how ocean chemists will feel about the end results!   
But I appreciate the thorough analysis brought to the issue.


In your option (1) (sea_water_pH universally), it isn't clear to me  
what other attribute would indicate the scale difference. I had  
understood that if the standard name and units were the same, CF users  
would assume the data could be exchanged, from a numerical standpoint  
anyway. If that is true, or if the specific attribute where this scale  
information must be entered, and the controlled vocabulary to use, is  
not specified, option (1) does not seem attractive. The likely outcome  
would be the attribute is unspecified or ambiguous, rendering the  
associated values useless to many potential users of the data.


In case (2) (different geophysical quantities), we may be a little  
stuck. I quote from my own ocean chemist: "as an ocean chemist, I know  
EXACTLY what is meant by sea_water_pH_total_scale, and so do all the  
other ocean chemists." He believes other terminology will be opaque  
and ambiguous, and therefore essentially useless.  As I understand the  
situation, the entire system of related chemistry in sea water is  
considered different depending on which scale is in use, so it is a  
pervasive concept in this domain, not simply an obscure name for this  
one measurement.


Since I am unable to personally verify this last assertion with all  
those other ocean chemists, and you might not want to take my word for  
it anyway, it may be that you would like to verify this perspective  
with other experts in the domain? (I can provide some names offline if  
you would like to do that.)  I think the reason to consider doing so  
in this case is that if there is indeed some ambiguity in the name you  
choose, then it may apply equally well in the future to a different  
scale, and this would be problematic.


If, after such a discussion, or regardless of that point, you choose a  
name that seems more appropriate to you, we can always create our  
preferred name in another vocabulary and map it to yours. (Eventually  
I am sure the CF convention will support this technique in an embedded  
way. :->)  So all is not lost, so long as the definition makes clear  
that the name you choose refers precisely to sea water pH total  
scale.  Such an approach seems sufficiently usable to me, and we can  
bear the brunt of name translation for our cadre of ocean chemists.


John


On May 2, 2009, at 5:53 AM, Jonathan Gregory wrote:


Dear John

Thanks for your thoughtful email. I follow the argument but in the  
end I do
not (yet) agree with the conclusion, that sea_water_pH_total_scale  
should be a
standard name. I am sorry if you find that exasperating. As in  
previous such
discussions, it is not because I am suggesting that you or your pH  
expert are
mistaken about what terms are normally used and what they mean. My  
difficulty
is that "total scale" is not informative to a general scientific  
readership,

which CF standard names are designed to be.

I've had a look at Zeebe and Wolf-Gladrow. Thanks for that reference.
Wikipedia summarises similar ideas. I also looked at a IUPAC  
document on the
subject. It seems that problem of definition arises because pH is  
actually
impossible to measure, as defined! Hence the true value is somewhat  
unknowable.

These different scales represent different methods of measurement and
estimation. I think we could take two views about that:

* The different pH scales are actually trying to measure the same  
geophysical
quantity. In that case the standard name should just be  
sea_water_pH. Then the
scale is an aspect of the method of measurement, and should be  
recorded in
some other attribute. This is somewhat related to the other thread,  
about

quantities relating to the techniques of measurement.

* The different pH scales are different geophysical quantities. In  
that case
they need distinct standard names, and it ought to be possible to  
indicate
in some non-jargon way what the difference refers to, even though it  
couldn't
be fully described in the name, so we still need a definition.  
Following this
route, the total scale could be called  
sea_water_pH_including_bisulfate_ions,
for instance. (A side-issue is a question of whether to call them  
bisulfate

or the IUPAC name of hydrogen_sulfate.)

pH is a dimensionless quantity. It has no units. It's the logarithm of
a number which does have units, so the units of that quantity need  
to be

specified in the definition.


Yet the second
sentence of the following statement does not hold true for pH, given
the depths at which these measurements are being made:

On Apr 30, 2009, at 9:22 AM, Jonathan Gregory wrote:

Boussinesq models (most ocean climate models are Boussinesq) treat
density
as constant 1000 kg m-3 except in the computation of pressure
gradients, where
it matters to the 

[CF-metadata] new standard name request for pH

[Jonathan Gregory]

Dear John

Thanks for your thoughtful email. I follow the argument but in the end I do
not (yet) agree with the conclusion, that sea_water_pH_total_scale should be a
standard name. I am sorry if you find that exasperating. As in previous such
discussions, it is not because I am suggesting that you or your pH expert are
mistaken about what terms are normally used and what they mean. My difficulty
is that "total scale" is not informative to a general scientific readership,
which CF standard names are designed to be.

I've had a look at Zeebe and Wolf-Gladrow. Thanks for that reference.
Wikipedia summarises similar ideas. I also looked at a IUPAC document on the
subject. It seems that problem of definition arises because pH is actually
impossible to measure, as defined! Hence the true value is somewhat unknowable.
These different scales represent different methods of measurement and
estimation. I think we could take two views about that:

* The different pH scales are actually trying to measure the same geophysical
quantity. In that case the standard name should just be sea_water_pH. Then the
scale is an aspect of the method of measurement, and should be recorded in
some other attribute. This is somewhat related to the other thread, about 
quantities relating to the techniques of measurement.

* The different pH scales are different geophysical quantities. In that case
they need distinct standard names, and it ought to be possible to indicate
in some non-jargon way what the difference refers to, even though it couldn't
be fully described in the name, so we still need a definition. Following this
route, the total scale could be called sea_water_pH_including_bisulfate_ions,
for instance. (A side-issue is a question of whether to call them bisulfate
or the IUPAC name of hydrogen_sulfate.)

pH is a dimensionless quantity. It has no units. It's the logarithm of
a number which does have units, so the units of that quantity need to be
specified in the definition.

> Yet the second  
> sentence of the following statement does not hold true for pH, given  
> the depths at which these measurements are being made:
> 
> On Apr 30, 2009, at 9:22 AM, Jonathan Gregory wrote:
> >Boussinesq models (most ocean climate models are Boussinesq) treat  
> >density
> >as constant 1000 kg m-3 except in the computation of pressure  
> >gradients, where
> >it matters to the dynamics. Therefore in dealing with concentrations  
> >of
> >tracers, per kg and per litre are identical and to choose one or the  
> >other
> >would be arbitrary and hence unhelpful for data exchange.

Actually this is a digression now, since all the quantities concerned are
logs of mol per kg. However, I maintain the above is a correct statement about
ocean *models*. I did not say it's a correct statement about nature! It is
not, as you point out. However, Boussinesq models are only approximate. In
such models, that distinction could not be made. No-one has yet requested
pH for an ocean model, but I expect it will come up sometime.

Best wishes

Jonathan
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Re: [CF-metadata] new standard name request for pH

[John Graybeal]

Hi everyone,

Thanks very much for considering and responding to the pH terms  
proposal.  To respond, I spent considerable time being educated by our  
in-house pH expert, even reading pages myself from the referenced book  
[1], and reviewed this email with him. So I claim this email  
represents a high level of expertise in this scientific field. I  
apologize for the length, but it seemed necessary to present  
justifying details.


To recap, the original proposal as revised was for 4 names related to  
pH:

A)  sea_water_pH_NBS_scale  (moles/liter)
B)  sea_water_pH_free_scale (moles/kg)
C)  sea_water_pH_total_scale  (moles/kg)<-- the one we care about
D)  sea_water_pH_seawater_scale  (moles/kg)

Through this thread we have had several suggestions for replacements  
[5], most recently arriving at

a) pH_of_sea_water_defined_by_moles_of_hydrogen_ion_per_unit_mass
b) pH_of_sea_water_defined_by_mole_concentration_of_hydrogen_ion
c)  
mole_concentration_of_H_and_HSO4_per_unit_mass_in_sea_water_expressed_as_pH
d) mole_concentration_of_H_and_HSO4_and_HF_per_unit_mass  
in_sea_water_expressed_as_pH

e) (added) pH_of_sea_water

I believe the focus of these responses was on the concentration of the  
solution, but this mis-states the actual chemical definition of this  
particular concept. (Unfortunately we incorrectly presented this in  
the original definitions for B, C, and D.)  In the reference[1]  it is  
made clear that:
(a) pH is strongly affected by abundance of hydrogen (actually  
hydrate) ions, but is not defined by their quantity; it is determined  
according to the *activity* of those ions, and this is not a linear  
relationship (though it is close to 1 in some regimes)[2].   We will  
change the proposed definitions to replace 'concentration' with  
'activity'; my apologies for this error.
(b) The use of the NBS scale is not recommended for sea water[3], as  
errors will be induced (up to at least 0.1 units in situ); in this  
light we propose to simply withdraw [A] from consideration, especially  
as we don't need it.
(c) There are significant differences in the values obtained for these  
different quantitiies, up to .12 units; thus to say just  
'pH_of_sea_water' is to have a very loose concern about the accurate  
meaning of the so-labelled pH values[4]. For comparison, measurements  
are often made, and needed, at the level of 0.0005 units.
(d) All 3 of {B, C, D} above are in regular use, but (C) is the most  
promising for the common reference[4].


Additionally, the units are expressed as noted above by common  
convention (see for example UCUM units section on pH [5]), in order to  
make certain conversions handy for the enlightened.  Yet the second  
sentence of the following statement does not hold true for pH, given  
the depths at which these measurements are being made:


On Apr 30, 2009, at 9:22 AM, Jonathan Gregory wrote:
Boussinesq models (most ocean climate models are Boussinesq) treat  
density
as constant 1000 kg m-3 except in the computation of pressure  
gradients, where
it matters to the dynamics. Therefore in dealing with concentrations  
of
tracers, per kg and per litre are identical and to choose one or the  
other

would be arbitrary and hence unhelpful for data exchange.


We therefore do not believe a substitution of moles/liter or moles/ 
m**3 is appropriate for the canonical moles/kg, as this would force  
most practitioners to convert their data before naming it with this  
name. [7] Obviously if there is a set of practitioners that are  
working with seawater pH using a different canonical unit, that would  
be another matter to consider; we think it is unlikely that any  
observationalists are doing so.


So, in summary, the longer, explicit terms being proposed are so  
approximate (for the reasons described above) as to be inaccurate to  
the scientists that use this data. Indeed, they would not use these  
terms. Therefore we re-propose the original terms (B), (C), and (D),  
or alternatively simply (C), as these represent the common and most  
descriptive usage.


John


[1] Zeebe & Wolf-Gladrow (2001). CO2 in Seawater: Equilibrium, Kinetics,
Isotopes. Published by Elsevier as part of their oceanographic series.

[2] Ibid, p 54 ff.  The exact quote was helpful to me, so I provide it  
here: "In high school we all learned that pH is the negative common  
logarithm of the concentration of hydrogen ions. ... Things are a bit  
more complicated for several reasons... The symbol H+ represents  
hydrate complexes rather than the concentration of free hydrogen  
ions In a refined theory one should use activity (an 'effective'  
concentration...) instead of concentration"  It goes on to explain  
the derivation of the various scales, in case that is of interest.


[3] Ibid, p 55

[4] Ibid, p 59

[5] Section 45 in http://aurora.regenstrief.org/~ucum/ucum.html#section-Other-Legacy-Units 
 (which unfortunately does not agree with the cited reference [1]  
ab

Re: [CF-metadata] new standard name request for pH

[Lowry, Roy K]

Hi Again,

Like it or not the oceanograpghic domain is using:

mass of solute per volume of solvent
mass of solute per unit mass of solvent
moles of solute per unit volume of solvent
moles of solute per unit mass of solute
volume of solute per unit mass of solvent
volume of solute per unit volume of solvent

depending on community within the domain.  Following my understanding of CF 
each of these needs to be addressed by the Standard Name system through a 
consistent syntax.  What we need to do is establish a convention for this, 
which is what I see Jonathan's efforts addressing.  Any advances on his 
conventions obviously need consideration.

Cheers, Roy.

From: Christiane Textor [christiane.tex...@lsce.ipsl.fr]
Sent: 30 April 2009 20:41
To: Lowry, Roy K; Lowry, Roy K
Cc: cf-metadata@cgd.ucar.edu
Subject: Re: [CF-metadata] new standard name request for pH

Hi Roy,

Concerning my question 4) I am sorry for not having more carefully read
previous postings.

You write about concentration per mass. However, I think this is not
correct as concentration is generally related to volume in CF as far as
I know, see my 5) below. There is mass_concentration and
mole_concentration, but both is per unit volume.

I have checked old postings and I have found that this has been
previously discussed:
 From godin at mbari.org  Wed Jan  3 17:09:34 2007
Date: Wed Jan  3 17:11:17 2007
Subject: [CF-metadata] Proposed standard names for biological model outputs

In text books mole/mass is referred to as molality, but this is not a
commonly used expression. Anyway, I think if we use concentration in
different ways than previously defined, this will lead to confusion.

Best regards,
Christiane

Lowry, Roy K a écrit :
> Hi Christiane,
>
> Please check out the previous postings.  There are in fact 3 pH
> scales covering pH based on a concentration per kg: one based on H+,
> a second on H+ and bisulphate and a third on H+, bisulphate and HF.
> We did consider having 4 Standard names but I was arguing for just 2
> based on H+ alone to try and match the level of specialism covered
> with other areas.
>
> The negative log transform between the appropriate concentration term
> and 'pH' has always been taken as read by all involved in the
> discussion, but maybe we should be more explicit when it comes to
> term definitions.
>
> Oceanographers are moving towards expressing chemical data in the
> dimension moles/kg rather than moles/litre.  We need a standardised
> convention to distinguish these as they have different canonical
> units and therefore need different Standard Names.  I think the
> approach Jonathan is taking is the most sensible way to do this
> without large scale deprecation of existing names.  We must always
> remember to include definitions and to read them: they are the key to
> eliminating confusion.
>
> Cheers, Roy.
>
>  From:
> cf-metadata-boun...@cgd.ucar.edu [cf-metadata-boun...@cgd.ucar.edu]
> On Behalf Of Christiane Textor [christiane.tex...@lsce.ipsl.fr] Sent:
> 30 April 2009 17:13 To: Lowry, Roy K; Jonathan Gregory Cc:
> cf-metadata@cgd.ucar.edu Subject: Re: [CF-metadata] new standard name
> request for pH
>
> Dear all,
>
> I am not an expert ocean acidification at all, but there are some
> general questions I have concerning these names for the pH of sea
> water:
>
> 1) large scale medium Why not use sea_water (or ocean_) as a prefix
> as we have agreed on?
>
> 2) definded_by For the atmospheric chemistry names we have used
> expressed_as, why not use this here as well?
>
> 3) definition of pH  (-log(H+))
>
> As far as I know the pH is defined as the negative logarithm of the
> concentration of H+ (or whatever else), this is missing in the
> suggested names. I would suggest to use expressed_as instead of
> defined_by to circumvent this problem.
>
> 4) definition of pH (N.B.S or free)
>
> I have checked the different definitions of the pH in sea water and
> it seems to me that the NBS and the free pH do not all refer to the
> concentration of H+ alone but consider also other ions, please see
> http://en.wikipedia.org/wiki?title=Talk:Ocean_acidification#cite_note-zeebe-0
>  (rather bad page, but still..)
>
> Am I confused?
>
> 5) concentration For the atmospheric chemistry names we have
> mass_concentration and mole_concentration which is mass or mole per
> volume. This means that concentration always means per unit volume,
> and not per unit mass. If you say now concentration per unit mass,
> this is confusing.
>
> Best regards, Christiane
>
>
>
>
> ___ CF-metadata mailing
> list CF-metadata@cgd.ucar.edu
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Re: [CF-metadata] new standard name request for pH

[Christiane Textor]

Hi Roy,

Concerning my question 4) I am sorry for not having more carefully read 
previous postings.


You write about concentration per mass. However, I think this is not 
correct as concentration is generally related to volume in CF as far as 
I know, see my 5) below. There is mass_concentration and 
mole_concentration, but both is per unit volume.


I have checked old postings and I have found that this has been 
previously discussed:

From godin at mbari.org  Wed Jan  3 17:09:34 2007
Date: Wed Jan  3 17:11:17 2007
Subject: [CF-metadata] Proposed standard names for biological model outputs

In text books mole/mass is referred to as molality, but this is not a 
commonly used expression. Anyway, I think if we use concentration in 
different ways than previously defined, this will lead to confusion.


Best regards,
Christiane

Lowry, Roy K a écrit :

Hi Christiane,

Please check out the previous postings.  There are in fact 3 pH
scales covering pH based on a concentration per kg: one based on H+,
a second on H+ and bisulphate and a third on H+, bisulphate and HF.
We did consider having 4 Standard names but I was arguing for just 2
based on H+ alone to try and match the level of specialism covered
with other areas.

The negative log transform between the appropriate concentration term
and 'pH' has always been taken as read by all involved in the
discussion, but maybe we should be more explicit when it comes to
term definitions.

Oceanographers are moving towards expressing chemical data in the
dimension moles/kg rather than moles/litre.  We need a standardised
convention to distinguish these as they have different canonical
units and therefore need different Standard Names.  I think the
approach Jonathan is taking is the most sensible way to do this
without large scale deprecation of existing names.  We must always
remember to include definitions and to read them: they are the key to
eliminating confusion.

Cheers, Roy.

 From:
cf-metadata-boun...@cgd.ucar.edu [cf-metadata-boun...@cgd.ucar.edu]
On Behalf Of Christiane Textor [christiane.tex...@lsce.ipsl.fr] Sent:
30 April 2009 17:13 To: Lowry, Roy K; Jonathan Gregory Cc:
cf-metadata@cgd.ucar.edu Subject: Re: [CF-metadata] new standard name
request for pH

Dear all,

I am not an expert ocean acidification at all, but there are some 
general questions I have concerning these names for the pH of sea

water:

1) large scale medium Why not use sea_water (or ocean_) as a prefix
as we have agreed on?

2) definded_by For the atmospheric chemistry names we have used
expressed_as, why not use this here as well?

3) definition of pH  (-log(H+))

As far as I know the pH is defined as the negative logarithm of the 
concentration of H+ (or whatever else), this is missing in the

suggested names. I would suggest to use expressed_as instead of
defined_by to circumvent this problem.

4) definition of pH (N.B.S or free)

I have checked the different definitions of the pH in sea water and
it seems to me that the NBS and the free pH do not all refer to the 
concentration of H+ alone but consider also other ions, please see 
http://en.wikipedia.org/wiki?title=Talk:Ocean_acidification#cite_note-zeebe-0

 (rather bad page, but still..)

Am I confused?

5) concentration For the atmospheric chemistry names we have
mass_concentration and mole_concentration which is mass or mole per
volume. This means that concentration always means per unit volume,
and not per unit mass. If you say now concentration per unit mass,
this is confusing.

Best regards, Christiane




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list CF-metadata@cgd.ucar.edu 
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--
==
Christiane Textor
Laboratoire des Sciences du Climat et de l'Environnement
Unite Mixte de Recherche CEA-CNRS-UVSQ

LSCE/IPSL laboratoire CEA/CNRS/UVSQ
Saclay, Orme des Merisiers,
Bat. 701, Piece 3b, Point Courrier 129
F-91191 Gif-sur-Yvette Cedex
FRANCE

mailto: christiane.tex...@lsce.ipsl.fr
Tel ++33 1 69 08 34 07 Fax ++33 1 69 08 77 16

GEOmon scientific coordinator http://www.geomon.eu
==


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Re: [CF-metadata] new standard name request for pH

[Lowry, Roy K]

Hi Christiane,

Please check out the previous postings.  There are in fact 3 pH scales covering 
pH based on a concentration per kg: one based on H+, a second on H+ and 
bisulphate and a third on H+, bisulphate and HF.  We did consider having 4 
Standard names but I was arguing for just 2 based on H+ alone to try and match 
the level of specialism covered with other areas.

The negative log transform between the appropriate concentration term and 'pH' 
has always been taken as read by all involved in the discussion, but maybe we 
should be more explicit when it comes to term definitions.

Oceanographers are moving towards expressing chemical data in the dimension 
moles/kg rather than moles/litre.  We need a standardised convention to 
distinguish these as they have different canonical units and therefore need 
different Standard Names.  I think the approach Jonathan is taking is the most 
sensible way to do this without large scale deprecation of existing names.  We 
must always remember to include definitions and to read them: they are the key 
to eliminating confusion.

Cheers, Roy.


From: cf-metadata-boun...@cgd.ucar.edu [cf-metadata-boun...@cgd.ucar.edu] On 
Behalf Of Christiane Textor [christiane.tex...@lsce.ipsl.fr]
Sent: 30 April 2009 17:13
To: Lowry, Roy K; Jonathan Gregory
Cc: cf-metadata@cgd.ucar.edu
Subject: Re: [CF-metadata] new standard name request for pH

Dear all,

I am not an expert ocean acidification at all, but there are some
general questions I have concerning these names for the pH of sea water:

1) large scale medium
Why not use sea_water (or ocean_) as a prefix as we have agreed on?

2) definded_by
For the atmospheric chemistry names we have used expressed_as, why not
use this here as well?

3) definition of pH  (-log(H+))

As far as I know the pH is defined as the negative logarithm of the
concentration of H+ (or whatever else), this is missing in the suggested
names. I would suggest to use expressed_as instead of defined_by to
circumvent this problem.

4) definition of pH (N.B.S or free)

I have checked the different definitions of the pH in sea water and it
seems to me that the NBS and the free pH do not all refer to the
concentration of H+ alone but consider also other ions, please see
http://en.wikipedia.org/wiki?title=Talk:Ocean_acidification#cite_note-zeebe-0
(rather bad page, but still..)

Am I confused?

5) concentration
For the atmospheric chemistry names we have mass_concentration and
mole_concentration which is mass or mole per volume. This means that
concentration always means per unit volume, and not per unit mass.
If you say now concentration per unit mass, this is confusing.

Best regards,
Christiane




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[CF-metadata] new standard name request for pH

[Jonathan Gregory]

Dear John

>  - The vague term violates the concept of consistent units, doesn't  it

I don't think so. pH is dimensionless. However, because it is dimensionless,
the exact definition has to state the unit of mass or volume being used, to
get the right numbers.

Boussinesq models (most ocean climate models are Boussinesq) treat density
as constant 1000 kg m-3 except in the computation of pressure gradients, where
it matters to the dynamics. Therefore in dealing with concentrations of
tracers, per kg and per litre are identical and to choose one or the other
would be arbitrary and hence unhelpful for data exchange.

>  - The interest in making things clear to the chemist seems to be at  
> the cost of making things straightforward to the people who work with  
> sea water pH.

This is an issue similar to many we have had before. CF stdnames are intended
to be interdisciplinary. The use of a longer, explicit term in standard names
does not imply that there is anything wrong with the usual terminology. It
is simply intended to make things clearer to non-experts. I believe this
approach is a strength of CF standard names. What is confusing, perhaps, is
that we call them "names", which might suggest we should stick to the most
familiar terms. We use familiar terms whenever we can, but often with added
precision.

Best wishes

Jonathan
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Re: [CF-metadata] new standard name request for pH

[Christiane Textor]

Dear all,

I am not an expert ocean acidification at all, but there are some 
general questions I have concerning these names for the pH of sea water:


1) large scale medium
Why not use sea_water (or ocean_) as a prefix as we have agreed on?

2) definded_by
For the atmospheric chemistry names we have used expressed_as, why not 
use this here as well?


3) definition of pH  (-log(H+))

As far as I know the pH is defined as the negative logarithm of the 
concentration of H+ (or whatever else), this is missing in the suggested 
names. I would suggest to use expressed_as instead of defined_by to 
circumvent this problem.


4) definition of pH (N.B.S or free)

I have checked the different definitions of the pH in sea water and it 
seems to me that the NBS and the free pH do not all refer to the 
concentration of H+ alone but consider also other ions, please see 
http://en.wikipedia.org/wiki?title=Talk:Ocean_acidification#cite_note-zeebe-0

(rather bad page, but still..)

Am I confused?

5) concentration
For the atmospheric chemistry names we have mass_concentration and 
mole_concentration which is mass or mole per volume. This means that 
concentration always means per unit volume, and not per unit mass.

If you say now concentration per unit mass, this is confusing.

Best regards,
Christiane




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Re: [CF-metadata] new standard name request for pH

[John Graybeal]

There are a few issues from the perspective of my pH experts, we will  
put together a more detailed reply shortly.  But two quick thoughts  
until we can prepare that:
 - The vague term violates the concept of consistent units, doesn't  
it? pH_of_sea_water units require conversion depending on which  
measurement technique they mean.  I think a model that is so generic  
perhaps is not really doing pH_of_sea_water, since the differences are  
fundamental.  (But I am not the expert)
 - The interest in making things clear to the chemist seems to be at  
the cost of making things straightforward to the people who work with  
sea water pH.  Given the prevalence of these terms in the broader  
(e.g., Wikipedia) community, I'm not sure translating to chemistry is  
a necessary step.


We will provide additional details shortly.

John


On Apr 30, 2009, at 7:50 AM, Lowry, Roy K wrote:


Thanks Jonathan,

Yes, OK.

I guessed why you wanted the vaguer term!

Cheers, Roy.

-Original Message-
From: cf-metadata-boun...@cgd.ucar.edu [mailto:cf-metadata-boun...@cgd.ucar.edu 
] On Behalf Of Jonathan Gregory

Sent: 30 April 2009 15:43
To: cf-metadata@cgd.ucar.edu; Lowry, Roy K
Subject: [CF-metadata] new standard name request for pH

Dear Roy

Thanks for clarification.

pH_of_sea_water_defined_by_mole_concentration_of_hydrogen_ion_per_unit_mass 
 (free scale)
pH_of_sea_water_defined_by_mole_concentration_of_hydrogen_ion_per_unit_volume 
 (NBS)


In other standard names, "mole concentration" means mol m-3. So the  
second

should be


pH_of_sea_water_defined_by_mole_concentration_of_hydrogen_ion (NBS)


In existing names, we say "moles per unit mass" for mol kg-1. So the  
first is


pH_of_sea_water_defined_by_moles_of_hydrogen_ion_per_unit_mass  
(free scale)


OK?

My main argument for plain pH_of_sea_water is that in many ocean  
models these

two quantities would be identical.

Cheers

Jonathan
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John

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John Graybeal   <mailto:grayb...@mbari.org>  -- 831-775-1956
Monterey Bay Aquarium Research Institute
Marine Metadata Interoperability Project: http://marinemetadata.org

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Re: [CF-metadata] new standard name request for pH

[Lowry, Roy K]

Thanks Jonathan,

Yes, OK.

I guessed why you wanted the vaguer term!

Cheers, Roy.

-Original Message-
From: cf-metadata-boun...@cgd.ucar.edu 
[mailto:cf-metadata-boun...@cgd.ucar.edu] On Behalf Of Jonathan Gregory
Sent: 30 April 2009 15:43
To: cf-metadata@cgd.ucar.edu; Lowry, Roy K
Subject: [CF-metadata] new standard name request for pH

Dear Roy

Thanks for clarification.

> pH_of_sea_water_defined_by_mole_concentration_of_hydrogen_ion_per_unit_mass 
> (free scale)
> pH_of_sea_water_defined_by_mole_concentration_of_hydrogen_ion_per_unit_volume 
> (NBS)

In other standard names, "mole concentration" means mol m-3. So the second
should be

> pH_of_sea_water_defined_by_mole_concentration_of_hydrogen_ion (NBS)

In existing names, we say "moles per unit mass" for mol kg-1. So the first is

> pH_of_sea_water_defined_by_moles_of_hydrogen_ion_per_unit_mass (free scale)

OK?

My main argument for plain pH_of_sea_water is that in many ocean models these
two quantities would be identical.

Cheers

Jonathan
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[CF-metadata] new standard name request for pH

[Jonathan Gregory]

Dear Roy

Thanks for clarification.

> pH_of_sea_water_defined_by_mole_concentration_of_hydrogen_ion_per_unit_mass 
> (free scale)
> pH_of_sea_water_defined_by_mole_concentration_of_hydrogen_ion_per_unit_volume 
> (NBS)

In other standard names, "mole concentration" means mol m-3. So the second
should be

> pH_of_sea_water_defined_by_mole_concentration_of_hydrogen_ion (NBS)

In existing names, we say "moles per unit mass" for mol kg-1. So the first is

> pH_of_sea_water_defined_by_moles_of_hydrogen_ion_per_unit_mass (free scale)

OK?

My main argument for plain pH_of_sea_water is that in many ocean models these
two quantities would be identical.

Cheers

Jonathan
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Re: [CF-metadata] new standard name request for pH

[Lowry, Roy K]

Hi Jonathan,

Not quite the correct interpretation.  Both NBS and free scale are based on the 
number of moles of hydrogen ions.  The difference is that NBS referes to the 
number of moles in a litre of water whereas free scale refers to the number of 
moles in a kilogram of water.  So following your logic we should really have:

pH_of_sea_water_defined_by_mole_concentration_of_hydrogen_ion_per_unit_mass 
(free scale)
pH_of_sea_water_defined_by_mole_concentration_of_hydrogen_ion_per_unit_volume 
(NBS)

This certainly fulfils my 'does what is says on the tin' criterion!

Having the Standard Name 'pH_of_sea_water' defined as 'pH defined on any scale: 
past, present or future' appeals to the pragmatic side of my nature but others, 
particularly carbonate system chemists, might see it as inviting bad practice.  
With me pragmatism wins, so I'd give your suggestion a tentative 'yes' vote but 
would be prepared to back down if there were strong objections from elsewhere 
in the CF community.

Cheers, Roy.


-Original Message-
From: cf-metadata-boun...@cgd.ucar.edu 
[mailto:cf-metadata-boun...@cgd.ucar.edu] On Behalf Of Jonathan Gregory
Sent: 30 April 2009 15:16
To: cf-metadata@cgd.ucar.edu; Lowry, Roy K
Subject: [CF-metadata] new standard name request for pH

Dear Roy

> The two pH variants I knew of before I prodded John for information were NBS, 
> which is based on hydrogen ion concentration per unit volume (moles/litre), 
> and free scale based on hydrogen ion concentration per unit mass (moles/kg).

Ah, I see.

> pH_per_unit_mass_in_sea_water for free scale
> pH_per_unit_volume_in_sea_water for NBS

They're not really pH per unit something, but H per unit something expressed
as pH, aren't they. What about

pH_of_sea_water_defined_by_mass_concentration_of_hydrogen_ion
pH_of_sea_water_defined_by_mole_concentration_of_hydrogen_ion

and just

pH_of_sea_water

for applications which don't want to be precise.

Cheers

Jonathan
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[CF-metadata] new standard name request for pH

[Jonathan Gregory]

Dear Roy

> The two pH variants I knew of before I prodded John for information were NBS, 
> which is based on hydrogen ion concentration per unit volume (moles/litre), 
> and free scale based on hydrogen ion concentration per unit mass (moles/kg).

Ah, I see.

> pH_per_unit_mass_in_sea_water for free scale
> pH_per_unit_volume_in_sea_water for NBS

They're not really pH per unit something, but H per unit something expressed
as pH, aren't they. What about

pH_of_sea_water_defined_by_mass_concentration_of_hydrogen_ion
pH_of_sea_water_defined_by_mole_concentration_of_hydrogen_ion

and just

pH_of_sea_water

for applications which don't want to be precise.

Cheers

Jonathan
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Re: [CF-metadata] new standard name request for pH

[Lowry, Roy K]

Dear Jonathan,

The two pH variants I knew of before I prodded John for information were NBS, 
which is based on hydrogen ion concentration per unit volume (moles/litre), and 
free scale based on hydrogen ion concentration per unit mass (moles/kg).  Both 
of these are what I would consider to be 'pure' pH based solely on the 
abundance of hydrogen ions. So, what to call them? Could we go with:

pH_per_unit_mass_in_sea_water for free scale
pH_per_unit_volume_in_sea_water for NBS

This follows the precedent set by Standard Names such as 
'moles_of_silicate_per_unit_mass_in_sea_water'

As for the other two variants I agree with Jonanthan that they need to have 
more explicit naming, maybe along the lines of:

mole_concentration_of_H_and_HSO4_per_unit_mass_in_sea_water_expressed_as_pH
mole_concentration_of_H_and_HSO4_and_HF_per_unit_mass 
in_sea_water_expressed_as_pH

These are more 'Standard Essays' than 'Standard Names' but they tell somebody 
with my level of chemistry instantly what's going on whereas 
'pH_seawater_scale' would have me searching out references.

Another question I would ask now that I've been educated by John's input is 
whether for the purposes of CF we need all four or could we just have the first 
two?

Cheers, Roy.

-Original Message-
From: cf-metadata-boun...@cgd.ucar.edu 
[mailto:cf-metadata-boun...@cgd.ucar.edu] On Behalf Of Jonathan Gregory
Sent: 28 April 2009 08:32
To: cf-metadata@cgd.ucar.edu; Lowry, Roy K
Subject: [CF-metadata] new standard name request for pH

Dear John

There is a large backlog of standard name proposals at present, which Alison
is working through.

>From an inexpert point of view, I believed that pH always measured hydrogen ion
concentration, what you call "free scale". It's interesting to learn that it's
more complicated than that. Nonetheless, it might be useful to have a
standard name of sea_water_pH, for cases where users do not wish to be precise,
for instance for model data that does not represent the complex chemistry of
sea water, so that these distinctions cannot be drawn.

For the more specific applications, I would propose that we introduce names
as they are required, as usual. You require "total scale" at present.

I have a difficulty with "free scale", "total scale" and "seawater scale", that
these terms, while no doubt well-known to experts, do not convey information
to non-experts about what the distinction is. I would suggest that it would be
more helpful to have names that indicate that the pH measures H+ only, H+ and
HSO4-, or H+ HSO4- and HF, respectively, as your definitions indicate.

Best wishes

Jonathan
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[CF-metadata] new standard name request for pH

[Jonathan Gregory]

Dear John

There is a large backlog of standard name proposals at present, which Alison
is working through.

>From an inexpert point of view, I believed that pH always measured hydrogen ion
concentration, what you call "free scale". It's interesting to learn that it's
more complicated than that. Nonetheless, it might be useful to have a
standard name of sea_water_pH, for cases where users do not wish to be precise,
for instance for model data that does not represent the complex chemistry of
sea water, so that these distinctions cannot be drawn.

For the more specific applications, I would propose that we introduce names
as they are required, as usual. You require "total scale" at present.

I have a difficulty with "free scale", "total scale" and "seawater scale", that
these terms, while no doubt well-known to experts, do not convey information
to non-experts about what the distinction is. I would suggest that it would be
more helpful to have names that indicate that the pH measures H+ only, H+ and
HSO4-, or H+ HSO4- and HF, respectively, as your definitions indicate.

Best wishes

Jonathan
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Re: [CF-metadata] new standard name request for pH

[John Graybeal]

As near as I can tell, it has been a month since the last  
communication to the list on this proposal (for pH names).  Is there  
an appropriate next step to take at this point?


John

--
Subject:Re: [CF-metadata] new standard name request for pH

Date:   March 25, 2009 11:05:22 AM PDT

Per Roy's keen suggestion, here are some definitions for the 4 terms
for pH, provided by my scientific expert. A reference for those  
interested is [1].


sea_water_pH_NBS_scale: the measure of acidity of sea water, defined as
the negative logarithm of the activity of dissolved hydrogen ions; it
can be measured or calculated; when measured, the scale is defined
according to standard solutions from the National Institute of Standards
and Technology (formerly NBS).  This scale is acceptable for freshwater
pH measurements, but because of the large difference in ionic strength
between seawater and these buffers which significantly changes the  
liquid

junction potentials, it is generally not recommended that seawater pH be
measured on this scale. [canonical units = moles/liter]

sea_water_pH_free_scale: the measure of acidity of sea water, defined as
the negative logarithm of the concentration of dissolved hydrogen ions
in a seawater medium; it can be measured or calculated; when measured
the scale is defined according to a series of buffers prepared in
artificial seawater. pH(free) = - log[H+](free). [canonical units =  
moles/kg ].


sea_water_pH_total_scale: the measure of acidity of sea water, defined
as the negative logarithm of the concentration of dissolved hydrogen
ions plus bisulfate ions in a seawater medium; it can be measured or
calculated; when measured the scale is defined according to a series of
buffers prepared in artificial seawater containing bisulfate.
pH(total) = - log([H+](free) + [HSO4-]). [canonical units = moles/kg ].

sea_water_pH_seawater_scale: the measure of acidity of sea water,
defined as the negative logarithm of the concentration of dissolved
hydrogen ions plus bisulfate ions plus hydrogen fluoride in a seawater
medium; it can be measured or calculated; when measured the scale is
defined according to a series of buffers prepared in seawater
containing both sulfate and fluoride ions.
pH(sws) = - log([H+](free) + [HSO4-] + [HF]). [canonical units = moles/ 
kg ].


John

[1] Zeebe & Wolf-Gladrow (2001). CO2 in Seawater: Equilibrium, Kinetics,
Isotopes. Published by Elsevier as part of their oceanographic series.


On Mar 11, 2009, at 6:18 AM, Roy Lowry wrote:


Hi John,

How about a nice concise definition to store with the standard name?

Might it also be useful to capture the expertise you have behind  
this proposal and create a full set of pH standard names, embracing  
the scales you mention (that are new to me) and the version widely  
used outside the carbonate system community based on moles of  
hydrogen ion per litre?


Cheers, Roy.


John Graybeal  03/09/09 8:12 PM >>>

In the ocean we are measuring pH, and I have not found a term for pH
in the standard names. We therefore propose for our particular
measurement

  sea_water_pH_total_scale

Two notes:  First, about the scale.  The total_scale refers to one of
the 3 scales with which pH is measured in sea water:  total scale, sea
water scale, and free scale (these all represent chemical activity,
with units in moles/kg). Although many of these have the same units
(moles/kg), the actual value will be different (in non-trivial ways)
in the different scales.  As the value in total_scale will not be
immediately convertible to a value in free scale they are measurements
with different meanings and can be easily confused.  It was not
obvious to me how this should be indicated other than by the standard
name.

Second, pH has the H capitalized, reflecting common usage. I couldn't
see any rule against this but I wanted to point it out, just in case.

John

--
John Graybeal  -- 831-775-1956  -- Monterey Bay Aquarium Research
Institute


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John Graybeal   <mailto:grayb...@mbari.org>  -- 831-775-1956
Monterey Bay Aquarium Research Institute
Marine Metadata Interoperability Project: http://marinemetadata.org

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Re: [CF-metadata] new standard name request for pH

[John Graybeal]

Per Roy's keen suggestion, here are some definitions for the 4 terms
for pH, provided by my scientific expert. A reference for those  
interested is [1].


sea_water_pH_NBS_scale: the measure of acidity of sea water, defined as
the negative logarithm of the activity of dissolved hydrogen ions; it
can be measured or calculated; when measured, the scale is defined
according to standard solutions from the National Institute of Standards
and Technology (formerly NBS).  This scale is acceptable for freshwater
pH measurements, but because of the large difference in ionic strength
between seawater and these buffers which significantly changes the  
liquid

junction potentials, it is generally not recommended that seawater pH be
measured on this scale. [canonical units = moles/liter]

sea_water_pH_free_scale: the measure of acidity of sea water, defined as
the negative logarithm of the concentration of dissolved hydrogen ions
in a seawater medium; it can be measured or calculated; when measured
the scale is defined according to a series of buffers prepared in
artificial seawater. pH(free) = - log[H+](free). [canonical units =  
moles/kg ].


sea_water_pH_total_scale: the measure of acidity of sea water, defined
as the negative logarithm of the concentration of dissolved hydrogen
ions plus bisulfate ions in a seawater medium; it can be measured or
calculated; when measured the scale is defined according to a series of
buffers prepared in artificial seawater containing bisulfate.
pH(total) = - log([H+](free) + [HSO4-]). [canonical units = moles/kg ].

sea_water_pH_seawater_scale: the measure of acidity of sea water,
defined as the negative logarithm of the concentration of dissolved
hydrogen ions plus bisulfate ions plus hydrogen fluoride in a seawater
medium; it can be measured or calculated; when measured the scale is
defined according to a series of buffers prepared in seawater
containing both sulfate and fluoride ions.
pH(sws) = - log([H+](free) + [HSO4-] + [HF]). [canonical units = moles/ 
kg ].


John

[1] Zeebe & Wolf-Gladrow (2001). CO2 in Seawater: Equilibrium, Kinetics,
Isotopes. Published by Elsevier as part of their oceanographic series.


On Mar 11, 2009, at 6:18 AM, Roy Lowry wrote:


Hi John,

How about a nice concise definition to store with the standard name?

Might it also be useful to capture the expertise you have behind  
this proposal and create a full set of pH standard names, embracing  
the scales you mention (that are new to me) and the version widely  
used outside the carbonate system community based on moles of  
hydrogen ion per litre?


Cheers, Roy.


John Graybeal  03/09/09 8:12 PM >>>

In the ocean we are measuring pH, and I have not found a term for pH
in the standard names. We therefore propose for our particular
measurement

   sea_water_pH_total_scale

Two notes:  First, about the scale.  The total_scale refers to one of
the 3 scales with which pH is measured in sea water:  total scale, sea
water scale, and free scale (these all represent chemical activity,
with units in moles/kg). Although many of these have the same units
(moles/kg), the actual value will be different (in non-trivial ways)
in the different scales.  As the value in total_scale will not be
immediately convertible to a value in free scale they are measurements
with different meanings and can be easily confused.  It was not
obvious to me how this should be indicated other than by the standard
name.

Second, pH has the H capitalized, reflecting common usage. I couldn't
see any rule against this but I wanted to point it out, just in case.

John

--
John Graybeal  -- 831-775-1956  -- Monterey Bay Aquarium Research
Institute


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Monterey Bay Aquarium Research Institute
Marine Metadata Interoperability Project: http://marinemetadata.org

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Re: [CF-metadata] new standard name request for pH

[Roy Lowry]

Hi John,

How about a nice concise definition to store with the standard name?  

Might it also be useful to capture the expertise you have behind this proposal 
and create a full set of pH standard names, embracing the scales you mention 
(that are new to me) and the version widely used outside the carbonate system 
community based on moles of hydrogen ion per litre?

Cheers, Roy.

>>> John Graybeal  03/09/09 8:12 PM >>>
In the ocean we are measuring pH, and I have not found a term for pH
in the standard names. We therefore propose for our particular  
measurement

sea_water_pH_total_scale

Two notes:  First, about the scale.  The total_scale refers to one of  
the 3 scales with which pH is measured in sea water:  total scale, sea  
water scale, and free scale (these all represent chemical activity,  
with units in moles/kg). Although many of these have the same units  
(moles/kg), the actual value will be different (in non-trivial ways)  
in the different scales.  As the value in total_scale will not be  
immediately convertible to a value in free scale they are measurements  
with different meanings and can be easily confused.  It was not  
obvious to me how this should be indicated other than by the standard  
name.

Second, pH has the H capitalized, reflecting common usage. I couldn't  
see any rule against this but I wanted to point it out, just in case.

John

--
John Graybeal  -- 831-775-1956  -- Monterey Bay Aquarium Research  
Institute


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[CF-metadata] new standard name request for pH

[John Graybeal]

In the ocean we are measuring pH, and I have not found a term for pH
in the standard names. We therefore propose for our particular  
measurement


   sea_water_pH_total_scale

Two notes:  First, about the scale.  The total_scale refers to one of  
the 3 scales with which pH is measured in sea water:  total scale, sea  
water scale, and free scale (these all represent chemical activity,  
with units in moles/kg). Although many of these have the same units  
(moles/kg), the actual value will be different (in non-trivial ways)  
in the different scales.  As the value in total_scale will not be  
immediately convertible to a value in free scale they are measurements  
with different meanings and can be easily confused.  It was not  
obvious to me how this should be indicated other than by the standard  
name.


Second, pH has the H capitalized, reflecting common usage. I couldn't  
see any rule against this but I wanted to point it out, just in case.


John

--
John Graybeal  -- 831-775-1956  -- Monterey Bay Aquarium Research  
Institute



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