[Coral-List] coral calcifiction paper

[Richard Dunne]

Thank you Travis - that is helpful to know but is still insufficient 
information to judge that the data you collected was reliable enough to 
be used in your analyses.

Seven years ago I wrote a post (10 Sep 2017) to Coral List on the 
subject of submersible light sensors - in that case it was a PAR sensor 
produced by Odyssey (a NZ company). The full post is at the bottom of 
this post.

Particularly relevant here to the use of any of these 'cheap' light 
sensors is this extract from what I wrote:

    "use requires caution, proper calibration and a sufficient
    assessment of errors in relation to the data being examined. It
    behoves on authors to include these details in any publication,
    otherwise we should remain sceptical of the data quality".

So of course I am disappointed to see none of this in your paper and 
what you say in your post below makes us none the wiser. HOBO produce 
two light sensors (the MX2202 and the UA002) both of which have quite 
different characteristics but you do not even tell us which type you 
used. They are both called HOBO Pendant.

Some key questions that need to be answered include:
1. What type of light loggers were used and what were their spectral 
responses and limitations (as acknowledged by the manufacturer)
2. How were they calibrated for PAR (or cross-calibrated between and 
within sites at the very least for 'intensity') - you say you used 4 at 
each site and averaged them. Why? What where the errors between each 4?
3. How often were they cleaned to prevent the build up of biofouling 
from degrading their response? Could the effect of biofouling be 
detected from a step change in readings before and after cleaning?
4. Was there any sensor drift and how often were any recalibrations 
performed?

Since I wrote my post in 2010 there has been a paper published (Long et 
al 2012 Limnology & Oceanography Methods 10:416-424) which looks at both 
the Odyssey Logger and the HOBO Pendant type UA002. It is encouraging 
that the authors concluded that "simple light intensity loggers can be 
used to estimate PAR as accurately reliably as scalar PAR sensors". 
(Note however that for measuring calcification in small massive corals 
it is the 2 phi light field that is likely to be of interest not the 4 
phi). They describe the HOBO UA002 as requiring calibration and having 
limited factory specifications. For the HOBO they showed that in air 
calibrations did not hold good underwater - separate calibration is 
needed (this will be partly due to what is called the 'immersion 
effect') and that different underwater environments also impacted the 
calibration coefficients including that a HOBO calibration in deep water 
did not hold good for shallower water.  They concluded that "trustworthy 
PAR measurements can only be estimated if a careful sensor calibration 
is performed" and that calibrations "cannot be generalized to all sites 
....  and conditions ... for example, care must be taken when using a 
calibration from a deeper site, from sites with different albedos, and 
from sites with different water clarities and light-scattering properties".

Solar radiation and its accurate measurement in coral studies requires a 
detailed understanding, adequate instrumentation (which unfortunately is 
not cheap), and caution if pitfalls are to be avoided.

Richard Dunne

MY 10 SEP 2017 POST:

ODYSSEY PAR LOGGERS
Three years ago there were a few posts about low cost submersible PAR 
(Photosynthetically Active Radiation) loggers. One, the Odyssey 
Photosynthetic Irradiance Logger manufactured by Dataflow Systems of New 
Zealand was mentioned and recommended by a reader.

The Odyssey is sold as a low cost (approx US dollars 220) 2 phi PAR 
sensor for use in air or underwater. Because it is self contained and 
waterproof to 20m and can be deployed for extended periods, it is 
attractive for use in scientific studies. Since 2004 its has been used 
in at least 14 published studies.

I recently had the opportunity to calibrate 3 of these Odyssey PAR 
loggers using a LiCor 192 PAR sensor and a Macam PAR sensor. Coral 
Listers might find my observations informative.

THE ODYSSEY AS A PAR SENSOR
Although it is sold by Dataflow Systems as a PAR sensor, the Odyssey 
produces its output as a milliVolt signal which is integrated over a 
user selected time period. The shortest sampling interval is 10 secs. It 
is not capable of recording instantaneous values. The logger is not 
‘calibrated’ when supplied. In order to convert the milliVolt signal 
into PAR units (micromole/ sq m/ sec) the user must calibrate it against 
another PAR sensor. Typically this might be done against a LiCor 192. 
Calibration against a 4 phi sensor such as a LiCor 193 is not 
appropriate because the geometry and response is different. There is 
also no information available as to the immersion effect correction 
required when the Odyssey is used underwater. This requires a 
calibration to be run in both air and in water.

None of this information is easily available to the potential purchaser 
since the company’s website contains minimal information.

Of the 14 scientific publications, 9 made no mention of calibration, and 
the remaining 4 did not say whether the calibration was in air or water. 
None contained any details of the magnitude of calibration errors, and 
therefore the errors in the data presented.

WHAT DID THE CALIBRATIONS SHOW?
IN AIR
Firstly, the measurement errors for the Odyssey were very large at low 
sun angles. Although I was unable to conduct a detailed examination of 
the cosine response, this result suggested that the cosine errors are 
much larger than for the LiCor 192 or Macam. These latter instruments 
have errors better than 5% out to 75 degrees when used in air. 
Underwater, the cosine errors are about double the air values.

In their handbook, Dataflow state that “The sensor features a cosine 
response and is based on a design evaluated by the University of Western 
Australia. The design was published by the Freshwater Biological 
Association in the UK as a simple and inexpensive equal energy response 
photosynthetic irradiance sensor….” I was unable to find any details of 
either study, and the company did not respond to my requests for the 
information. In these circumstances the detailed cosine errors remain 
unknown, but indications are that readings taken when sun angles are 
lower than 20 degrees result in measurement errors in excess of 10%, 
rising to 24% at 13 degrees, and considerably higher thereafter. This 
makes the sensor generally unreliable for use during winter months at 
high latitudes, and for data collected during the first and last 1.5 hrs 
of each day in the tropics.

Excluding data from sun angles below 20 degrees, the Odyssey error was 
approximately ± 4.5% from about 100 – 2500 micromoles/sq m/sec (95% 
prediction interval ± 25%). This is about double the comparable error 
using the LiCor 192 sensors.

UNDERWATER
Because of the geometry of the underwater calibration setup, cosine 
errors could not be examined. For the range 200 – 2000 micromoles/ sq 
m/sec errors were of the order of ± 8 to 9% (95% prediction interval ± 
25%). Again, the errors in the LiCor 192 sensors were about half this.

A computation of the Immersion Effect Correction for the Odyssey gave 
values of between 1.54 and 1.76 depending on the sensor. This indicates 
that between 54% and 76% of light is reflected back out of the sensor 
when it is used underwater. This is unusually large for a 2 phi sensor 
design. The comparable LiCor 192 has a correction of 1.32.

COMPANY CALIBRATION RECOMMENDATIONS
Dataflow produce an Excel spreadsheet for customers giving an ‘example’ 
calibration of an Odyssey. Worryingly, this is incorrect since not only 
does it regress the Odyssey and calibrating sensor the wrong way round, 
but it also uses only the slope and ignores any offset. As a result a 
customer using the ‘Dataflow method’ will obtain a calibration where the 
Odyssey systematically over-reads the true irradiance by about 2% at 
1500 micromoles/ sq m/ sec, rising to 5% at 500 micromoles, and above 
15% below 100 micromoles. Despite drawing this to Dataflow’s attention 
they remain in denial and continue to inform customers of their 
incorrect calibration method.

SPECTRAL RESPONSE
When a PAR sensor is used underwater there are additional errors which 
arise because the spectral response of a given sensor cannot be tailored 
to the ideal quantum response. Each sensor manufacturer uses their own 
combination of filter glasses to achieve the best response possible and 
normally makes details of the spectral response available to customers. 
For both the LiCor 192 and the Macam sensors the respective responses 
keep additional errors to within about 5%. This error is in addition to 
the calibration errors above, resulting in a systematic shift in the 
readings depending on the water depth and water type (clear oceanic or 
turbid).

No spectral response is available for the Odyssey and Dataflow did not 
respond to a request for this information. It is not possible therefore 
to estimate the additional errors for the Odyssey logger.

IS THE ODYSSEY A RESEARCH GRADE INSTRUMENT?
Certainly it is not of a comparable quality to other established PAR 
sensors such as those sold by LiCor or Macam. Even when used 
appropriately its errors are x2 greater compared to these instruments. 
At low irradiances and when the sun is low in the sky, the errors 
associated with the Odyssey rise somewhat alarmingly. However, LiCor and 
Macam sensors are about x10 more expensive and additionally are ‘wired’ 
sensors which can only be deployed by a user above the sea surface. 
Dataflow must therefore be commended for having produced a true 
submersible sensor in the Odyssey. What is regrettable is their failure 
to release relevant information about the sensor, or to respond to 
information requests. Neither of these things are to be expected from a 
responsible manufacturer of scientific instrumentation.

The Odyssey PAR logger has a useful role to play in underwater 
scientific research but its use requires caution, proper calibration and 
a sufficient assessment of errors in relation to the data being 
examined. It behoves on authors to include these details in any 
publication, otherwise we should remain sceptical of the data quality.

Finally, if any Coral Lister has access to an optical bench and the time 
to examine the spectral and cosine response then we would also be much 
wiser. Better still if Dataflow were to do this and also offer customers 
an optional pre-purchase calibration service.

On 13/11/2017 23:38, Travis Courtney wrote:
> Hello all,
>
> To clarify the recent response in regards to the light measurements in
> "Environmental controls on modern scleractinian coral and reef-scale
> calcification," all light measurements were made by onset HOBO loggers
> (lux) secured on the benthos at each reef site facing perpendicular to the
> water surface. Maximum calcification rates (max in August to November)
> lagged maximum benthic irradiance measurements (max lux in mid-June) by a
> few months. The complexity of such time lags with respect to the Structural
> Equation Modeling are discussed in the manuscript.
>
> Best,
> Travis Courtney
>
> On Mon, Nov 13, 2017 at 9:00 AM,<coral-list-request at coral.aoml.noaa.gov>
> wrote:
>
>> ---------- Forwarded message ----------
>> From: Richard Dunne<RichardPDunne at aol.com>
>> To:coral-list at coral.aoml.noaa.gov
>> Cc:
>> Bcc:
>> Date: Sun, 12 Nov 2017 13:54:01 +0000
>> Subject: Re: [Coral-List] coral calcifiction paper
>> For measurement of solar radiation the authors chose sensors which record
>> units of lux (a measure of human visual perception of brightness).  As far
>> as I can tell these measurements were above water, presumably on a
>> horizontal surface (they don't say), although if this was a buoy moving
>> with wave motion then this would produce added variability in the readings.
>> They then use this as one of their environmental inputs to their Structural
>> Equation Modelling.
>>
>> Lux cannot be converted to units of PAR (photosynthetically active
>> radiation) or irradiance unless you also know the spectral composition of
>> the light at the time of measurement. As regards photobiology and coral
>> calcification, measurements in lux are thus pretty meaningless. Worse still
>> the fact that underwater both the spectral power distribution and
>> irradiance will have varied with depth and changes in water quality, the
>> net effect is not encouraging if you are using this to see if there is a
>> relationship between calcification and solar radiation.
>>
>> The authors found that "the lack of correlation with light ......   are
>> inconsistent with anticipated results". Quelle suprise! Rubbish in -
>> rubbish out.
>>
>> Richard P Dunne
>>
>> On 10/11/2017 23:17, Douglas Fenner wrote:
>>
>>> Environmental controls on modern scleractinian coral and reef-scale
>>> calcification.  Scientific Reports
>>>
>>> http://advances.sciencemag.org/content/3/11/e1701356?utm_cam
>>> paign=toc_advances_2017-11-10&et_rid=17045989&et_cid=1656609
>>>
>>> Open-access
>>> Abstract
>>>
>>> Modern reef-building corals sustain a wide range of ecosystem services
>>> because of their ability to build calcium carbonate reef systems. The
>>> influence of environmental variables on coral calcification rates has been
>>> extensively studied, but our understanding of their relative importance is
>>> limited by the absence of in situ observations and the ability to decouple
>>> the interactions between different properties. We show that temperature is
>>> the primary driver of coral colony (*Porites astreoides* and *Diploria
>>> labyrinthiformis*) and reef-scale calcification rates over a 2-year
>>> monitoring period from the Bermuda coral reef. On the basis of multimodel
>>> climate simulations (Coupled Model Intercomparison Project Phase 5) and
>>> assuming sufficient coral nutrition, our results suggest that *P.
>>> astreoides* and *D. labyrinthiformis* coral calcification rates in Bermuda
>>> could increase throughout the 21st century as a result of gradual warming
>>> predicted under a minimum CO2 emissions pathway [representative
>>> concentration pathway (RCP) 2.6] with positive 21st-century calcification
>>> rates potentially maintained under a reduced CO2 emissions pathway (RCP
>>> 4.5). These results highlight the potential benefits of rapid reductions
>>> in
>>> global anthropogenic CO2 emissions for 21st-century Bermuda coral reefs
>>> and
>>> the ecosystem services they provide.
>>>
>>> Cheers,  Doug
>>>
>>>
>>