remove biological temperature?

[teixeirak]

Based on a recent email thread with NEON folks (copied below), it sounds like biological temperature is not what we were thinking/ hoping. I knew that the sensors were aimed fairly randomly, but I didn't realize that they point down (at an angle). We're waiting on further info, but my suspicion/ default assumption is that this is not giving us any kind of meaningful vertical profile of leaf temperature. I suggest we drop it.

@mcgregorian1, what do you think? If you agree, let's go ahead and remove that panel. We could always restore it in case we get evidence contrary to my suspicion, but unless we can get a definitive answer quickly, I'd rather just remove it.

Thank you!

It looks like this diagram gives some more accurate height data, so we’ll update our figure accordingly.

Is that 32.9 m boom level with the tallest trees in the surrounding area, or a bit above? I suspect that that upper sensor is more likely seeing underneath the canopy than above, but the only way to know is to look at it. The next time you’re on the tower, would you mind looking at where that sensor is pointing, and if possible taking a photo?  This will determine whether it makes sense to include that particular panel in this publication, and how to interpret. (The paper looks at how trees of different heights respond to drought, and the goal of this figure is to characterize what kind of environmental conditions are being experienced by the trees at different heights.)

Many thanks,

Krista

Kristina J. Anderson-Teixeira
Ecologist, Leader of ForestGEO Ecosystems & Climate Program
Smithsonian Institution
Smithsonian Conservation Biology Institute
1500 Remount Rd. MRC 5535; Front Royal, VA 22630 USA
1-540-635-6546 | teixeirak@si.edu
CTFS-ForestGEO Ecosystems & Climate Program 
Lab Website

From: John Schnebelen <jschnebelen@battelleecology.org>
Date: Thursday, September 19, 2019 at 10:53 AM
To: "Teixeira, Kristina A." <TeixeiraK@si.edu>, Jim Coloso <jcoloso@battelleecology.org>
Cc: Ian McGregor <mcgregorian93@gmail.com>
Subject: RE: Interpreting biological temperature data from SCBI NEON tower

I believe you are correct. Maybe this will help too. I’ve attached 2 pages from our tower As-Built that includes the height of measurement level 4 (as well as all the others), which would be the last level to contain an IR Biological Temperature Sensor. That’s 32.9 meters. Page 3 shows the height of each measurement level on the tower, including the top, and page 4 (using Detail C because it will be identical for all levels with that instrument configuration) showing the actual layout of everything on that radiation boom. I don’t think page 4 has any really useful information, but it does a visual of the sensor configuration, with that IR Temp sensor being the one angled down at the end of the drawn boom.

It's good see some tower data in use though! Obviously it didn’t show what you expected, but, how far off was it to your predictions?

John

From: Teixeira, Kristina A. <TeixeiraK@si.edu> 
Sent: Thursday, September 19, 2019 10:26 AM
To: John Schnebelen <jschnebelen@battelleecology.org>; Jim Coloso <jcoloso@battelleecology.org>
Cc: Ian McGregor <mcgregorian93@gmail.com>
Subject: Re: Interpreting biological temperature data from SCBI NEON tower

Hi John & Jim,

Thanks, this is helpful. 

My understanding, then, would be that its integrating whatever it sees over a 44° field of view (i.e., approximately everything between straight down and horizontal out from the tower). Is this correct? Is the the top censor (at 40m) above the top of the canopy? Within the ForestGEO plot, 40m would be above ~99% of the trees, but whether you’re seeing the top of the canopy or down through it probably depends on the arrangement of trees neighboring the tower.

The attached figure shows the biological temperature profile that Ian extracted from these data (panels a-d are NEON data). As you’ll see, there’s no vertical trend in monthly mean minima and maxima of biological temperature during the peak growing season months. I was a little surprised not to see higher temperatures at the top of the canopy, but I’m not sure that we’d expect them.

Many thanks,

Krista

Kristina J. Anderson-Teixeira
Ecologist, Leader of ForestGEO Ecosystems & Climate Program
Smithsonian Institution
Smithsonian Conservation Biology Institute
1500 Remount Rd. MRC 5535; Front Royal, VA 22630 USA
1-540-635-6546 | teixeirak@si.edu
CTFS-ForestGEO Ecosystems & Climate Program 
Lab Website

From: John Schnebelen <jschnebelen@battelleecology.org>
Date: Thursday, September 19, 2019 at 8:07 AM
To: Jim Coloso <jcoloso@battelleecology.org>, "Teixeira, Kristina A." <TeixeiraK@si.edu>
Cc: Ian McGregor <mcgregorian93@gmail.com>
Subject: RE: Interpreting biological temperature data from SCBI NEON tower

The Apogee SI-111 is an infrared radiometer made by Apogee Instruments that measures IR radiation in the 8 – 14 µm range.; Since IR radiation is a function of temperature, it measures the surface temperature of the plant canopy and the ground at which it is aimed by comparing the difference in IR temperature of the target with its own ambient temperature.; A white radiation shield insulates the sensor from rapid temperature changes, and allows ambient air to flow between the radiation shield and the sensor body to ensure that the sensor body is always at ambient temperature.; With a 44° total field of view (22° half-angle), it is normally mounted on the lowest profile boom of the tower or on a ground arbor to limit the area measured, and is mounted at 22° from vertical. In the case of our towers, we have one mounted on all but the top 2 levels.

Hope This Helps,

John Schnebelen
Sr.  Ecologist  – Instrumentation
Domain 2, Mid-Atlantic
National Ecological Observatory Network
Office: 540-692-1900 | Mobile: 9124330483
jschnebelen@BattelleEcology.org

NEON – Smithsonian Conservation Biology Institute
1500 Remount Road
Building 90 MRC 5560
Front Royal, VA 22630
http://www.battelle.org/neon 

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From: Jim Coloso <jcoloso@battelleecology.org> 
Sent: Thursday, September 19, 2019 7:59 AM
To: Teixeira, Kristina A. <TeixeiraK@si.edu>
Cc: Ian McGregor <mcgregorian93@gmail.com>; John Schnebelen <jschnebelen@battelleecology.org>
Subject: RE: Interpreting biological temperature data from SCBI NEON tower

Hi Kristina,

The sensors are not pointing at any one thing.  They are on most of the tower levels and are pointed at a specific angle downward from that level.  I don’t know off hand what their field of view is, but it is not a single point.  Thus, they are measuring from many leaves, stems, branches, etc.  I’m copying John, our tower technician, as he would know more about this than I do. 

Jim

From: Teixeira, Kristina A. <TeixeiraK@si.edu> 
Sent: Wednesday, September 18, 2019 8:48 PM
To: Jim Coloso <jcoloso@battelleecology.org>
Cc: Ian McGregor <mcgregorian93@gmail.com>
Subject: Interpreting biological temperature data from SCBI NEON tower

Dear Jim,

You’re probably not the right person to ask this, but could you please pass this along as appropriate?

Along with my recent intern Ian McGregor, we’re writing up a paper that uses NEON’s biological temperature data from the tower.  My understanding is that these sensors are pointed somewhat randomly at the vegetation. I’m hoping to learn what they’re sensing at SCBI (e.g., leaves, stems).

Many thanks,

Krista

[mcgregorian1]

Hm. Copying from the NEON site, biotemp specifically gives us: "Infrared Biological Temperature (i.e., surface temperature) is available as one- and thirty-minute averages of 1 Hz observations. Biological temperature can be used in conjunction with other measurements to draw conclusions on topics such as plant respiration, evapotranspiration rates, and stomatal conductance."

I guess the argument to keep it is that it's a different measurement of temperature , but since we're only using temperature in general as an overall view of height profiles of the environment, as opposed to specifically using this data within our model, I think it's ok to drop it

[teixeirak]

A further developments from NEON:

John took pictures of the upper boom of the height profile, which I loaded here. It is clear that the boom is above the canopy and seeing at least some upper canopy leaves.

I therefore think it is justified to include it, but I'm not sure how valuable it is. We don't know what portion of the field of vision is occupied by leaves, which is our main interest. I think we may get more interesting results if we look at the 75th or 90th percentile of maximum daily temperatures during the month (rather than the mean).

Thinking of this, I think there are a few things we could do to improve the vertical profiles figure. I'll open a new issue.

I'll leave it up to you as to whether you want to include biological temperature.

[mcgregorian1]

Yep I saw those pictures. I've never seen biotemp used in papers unless it was used for specific model parameters, so I agree with you; I'm not sure what we'd be able to point to as a reason for keeping it in other than using available NEON data.

I will look up some better definitions and usage of biotemp in order to understand it more, so I can make a better-informed decision about keeping or removing it

[mcgregorian1]

I think I'm going to drop biotemp, because really the only reason to keep it would be if that was a variable in our models, otherwise leaving it in would simply be a way of including irrelevant data.

I'm going to put the legend for the three plots within the first box (with windspeed)

[mcgregorian1]

I'd like to put a hold on my previous comment after seeing #58. Let's decide the fate of this issue based on what the graphs look like from 58

[mcgregorian1]

As in #58 we have decided to drop biological temperature.