GLEON Metabolism 1 - Revision history

Thomas at 16:05, 19 November 2015

2015-11-19T16:05:08Z

Thomas at 00:53, 19 November 2015

2015-11-19T00:53:53Z

Thomas at 00:47, 19 November 2015

2015-11-19T00:47:57Z

Thomas at 00:46, 19 November 2015

2015-11-19T00:46:26Z

Thomas at 23:59, 18 November 2015

2015-11-18T23:59:10Z

Thomas at 23:48, 18 November 2015

2015-11-18T23:48:35Z

Thomas at 23:44, 18 November 2015

2015-11-18T23:44:13Z

Thomas at 23:41, 18 November 2015

2015-11-18T23:41:04Z

Thomas at 16:13, 18 November 2015

2015-11-18T16:13:36Z

Thomas at 17:33, 23 September 2015

2015-09-23T17:33:10Z

@@ Line 222: / Line 222: @@
 . Results
-    a. Model testing (pseudo-calibration/validation/illustration) with respect flow, mixing, reaction (or at least demonstration of range of model behavior—we may  really validate it)
+    a. Model testing (pseudo-calibration/validation/illustration) with respect flow, mixing, reaction (or at least demonstration of range of model behavior—we may not be in a position to really validate it)
     b. Main results:  PDF inputs into models
        i. DOC conc and age versus time for lakes for our estimate DOC reaction rates PDFs—maybe an ensemble of results for several different reaction rate PDFs (assuming we aren’t be able to constrain these definitively)

@@ Line 222: / Line 222: @@
 . Results
-    a. Presentation of the DOC data (PDFs)
+    a. Model testing (pseudo-calibration/validation/illustration) with respect flow, mixing, reaction (or at least demonstration of range of model behavior—we may  really validate it)
-   b. Model testing (pseudo-calibration/validation?) with respect flow, mixing, reaction (or at least demonstration of range of model behavior—we may  really validate it)
+    b. Main results:  PDF inputs into models
-    c. Main results:  PDF inputs into models
        i. DOC conc and age versus time for lakes for our estimate DOC reaction rates PDFs—maybe an ensemble of results for several different reaction rate PDFs (assuming we aren’t be able to constrain these definitively)
        ii. Overall synthesis:  Can we say anything semi-general about DOC age distributions in the lakes?

@@ Line 175: / Line 175: @@
 Group members are feeling a little under-tasked (paraphrasing here), so Tom volunteer to start crystallizing our work plan in manuscript form.  Hopefully, this will help us to see the tasks.  Here goes nothing!
 '''Working title:'''  Carbon Sources, Pathways and Age Distributions in Lake Basins: Reactive Transport of DOC and Metabolism in Northern Temperate Lakes [first try…keep polishing as our message becomes clear]
@@ Line 227: / Line 232: @@
+--[[User:Thomas|Tom Harmon]] ([[User talk:Thomas|talk]]) 16:47, 18 November 2015 (PST)

← Older revision		Revision as of 00:46, 19 November 2015
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	While the Pint et al (2003) focuses on Allequash, Hilary has been digging up multiple theses from Mary Anderson's group which may have similar modeling results from other NLTER Lakes. Mary and Randall Hunt (USGS co-author on Pint et al) seem happy to help, which could come in handy as we begin to make decisions about some of the groundwater conditions in our modeling exercises.		While the Pint et al (2003) focuses on Allequash, Hilary has been digging up multiple theses from Mary Anderson's group which may have similar modeling results from other NLTER Lakes. Mary and Randall Hunt (USGS co-author on Pint et al) seem happy to help, which could come in handy as we begin to make decisions about some of the groundwater conditions in our modeling exercises.

−	Roxanna was able to find a couple of good-looking papers as well	+	Roxanna was able to find a couple of good-looking papers as well on the aging of organic carbon and its effect on P and R ([[Media:Aging of allochthonous OC Prod Resp boreal lakes 2009.pdf]], on the pathway of OM from streams in N Patagonia ([[Media:Tracing DOM NPatagonian Streams 2015.pdf (file)]]), and on for the NLTER lakes on the topic of DOC as an indicator of scale [[Media:DOC indicator of scale of watershed 1999.pdf (file)]].
		+
		+	Group members are feeling a little under-tasked (paraphrasing here), so Tom volunteer to start crystallizing our work plan in manuscript form. Hopefully, this will help us to see the tasks. Here goes nothing!
		+
		+	'''Working title:''' Carbon Sources, Pathways and Age Distributions in Lake Basins: Reactive Transport of DOC and Metabolism in Northern Temperate Lakes [first try…keep polishing as our message becomes clear]
		+
		+	'''Abstract.''' Understanding the response of lakes to hydrologic or land use changes in catchments is is critical to preserving ecosystems and the services they provide. Lakes provide an integrated response to flow and nutrient loading changes in catchment, and can serve as first indicators of ecosystem shifts or tipping points beyond which resource recovery is challenging. In this work we look at the sources and reactive pathways of carbon (DOC)
		+
		+	1.Introduction
		+	a. Motivation, problem statement
		+	b. DOC sources in catchments and pathways to lakes
		+	i. Definitions
		+	ii. Relevant studies—what is known about sources and pathways? General or site/region-specific findings?
		+	iii. Key questions—what portions come from various sources?
		+	c. DOC reactions
		+	i. Definitions DOC transformation, mineralization
		+	ii. Reactivity of DOC of different age/quality
		+	iii. What is known about DOC reaction rates within different pathways?
		+	iv. For transformation, is there one rate for “young” or “easy to transform” DOC, and another for “old” DOC, or is it a wide spectrum of rates? If we could lump it into two rates, what would the age cutoff be?
		+	v. If we don’t know that much about these rates, can we infer them, given sources and pathways?
		+	d. Reactive transport to Lakes
		+	i. Pathways, residence times, and reaction rates
		+	ii. We might expect that if we knew the proportions and pathways of carbon delivered via various pathways, then we can say something about the age distribution of carbon in a lake
		+	iii. And, if we can say something about the age distribution of the carbon, then can we say something in connection to carbon age about metabolism in lakes (at least lakes in which DOC is an important part of production/respiration)??
		+
		+	2. Methods
		+	a. General approach (brief paragraph)
		+	b. Age of Carbon Model(s)
		+	i. Simple model for catchment-lake systems
		+	ii. Assumptions: what’s in it, what’s not and why
		+	iii. Development of age models, and what they mean
		+	iv. Lay out the simple model equations with a diagram [FIG 1]
		+	v. Present some test cases to demonstrate type/range of output expected [FIG 2]
		+	c. Description of the Trout Lake basin (or maybe just one lake, let’s see)
		+	i. Trout Lake basin – background information, short but well-referenced
		+	ii. DOC sources and pathways here
		+	iii. If more than one lake, then describe similarities and differences of lakes (in the context of our lake-catchment model)—for instance, in and out surface flow terms are omitted for seepage lake. [TABLE 1, perhaps]
		+	d. Model parameter probability density function (PDFs)
		+	i. Where we got the data; how we grouped it and created PDFs (or similar functions)
		+	ii. DOC source concentrations
		+	iii. DOC pathways and proportion of the pathways feeding total lake inflow (what about seasonality of flows?)
		+	iv. DOC age distribution for various pathways
		+	e. Model usage—testing its output, applying it to the PDFs developed
		+
		+	3. Results
		+	a. Presentation of the DOC data (PDFs)
		+	b. Model testing (pseudo-calibration/validation?) with respect flow, mixing, reaction (or at least demonstration of range of model behavior—we may really validate it)
		+	c. Main results: PDF inputs into models
		+	i. DOC conc and age versus time for lakes for our estimate DOC reaction rates PDFs—maybe an ensemble of results for several different reaction rate PDFs (assuming we aren’t be able to constrain these definitively)
		+	ii. Overall synthesis: Can we say anything semi-general about DOC age distributions in the lakes?
		+	iii. Overall synthesis: Can we say anything about DOC age distributions and key indicators (production, metabolism)?
		+
		+	4. Discussion (nothing here so far--TH)
		+

@@ Line 164: / Line 164: @@
 '''Skype Mtg #6 (09/23/2015)'''
-'''Attendees:'''   Tom, Sam, Hilary, Kevin
+'''Attendees:'''   Tom, Sam, Hilary, Kevin, Roxanna
 '''Summary:''' Plan of reading, synthesis and coding
-We held a brief meeting today to summarize findings in the literature, recalling that we need (1) good documentation on sources, concentrations and pathways of DOC in the NLTER Lakes, and (2) supporting information on DOC quality, reaction rates, etc. from other areas (preferably with similar climate and land coverage).  Tom mentioned a couple of papers he read, including a 2003 paper on groundwater age distributions at Lake Allequash [[Media:Pint etal flowpath 2003.pdf]], and one on stream and lake water chemistry comparisons in the NLTER region [[Media:Lottig et al LTER lakes streams chem 2011.pdf]].  These stimulated some ideas about using distributions of parameters (e.g., a PDF of groundwater travel times or ages, a PDF of stream DOC concentrations, and similar). We agreed that it would strengthen our modeling approach.
+We held a brief meeting today to summarize findings in the literature, recalling that we need (1) good documentation on sources, concentrations and pathways of DOC in the NLTER Lakes, and (2) supporting information on DOC quality, reaction rates, etc. from other areas (preferably with similar climate and land coverage).  Tom mentioned a couple of papers he read, including a 2003 paper on groundwater age distributions at Lake Allequash [[Media:Pint_etal_flowpath_GWage_2003.pdf]], and one on stream and lake water chemistry comparisons in the NLTER region [[Media:Lottig et al LTER lakes streams chem 2011.pdf]].  These stimulated some ideas about using distributions of parameters (e.g., a PDF of groundwater travel times or ages, a PDF of stream DOC concentrations, and similar). We agreed that it would strengthen our modeling approach.

← Older revision		Revision as of 23:48, 18 November 2015
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	'''Summary:''' Plan of reading, synthesis and coding		'''Summary:''' Plan of reading, synthesis and coding

−	We held a brief meeting today to summarize findings in the literature, recalling that we need (1) good documentation on sources, concentrations and pathways of DOC in the NLTER Lakes, and (2) supporting information on DOC quality, reaction rates, etc. from other areas (preferably with similar climate and land coverage). Tom mentioned a couple of papers he read, including a 2003 paper on groundwater age distributions at Lake Allequash [[Media:Pint etal flowpath ~~GWage~~ 2003.pdf]]	+	We held a brief meeting today to summarize findings in the literature, recalling that we need (1) good documentation on sources, concentrations and pathways of DOC in the NLTER Lakes, and (2) supporting information on DOC quality, reaction rates, etc. from other areas (preferably with similar climate and land coverage). Tom mentioned a couple of papers he read, including a 2003 paper on groundwater age distributions at Lake Allequash [[Media:Pint etal flowpath 2003.pdf]], and one on stream and lake water chemistry comparisons in the NLTER region [[Media:Lottig et al LTER lakes streams chem 2011.pdf]]. These stimulated some ideas about using distributions of parameters (e.g., a PDF of groundwater travel times or ages, a PDF of stream DOC concentrations, and similar). We agreed that it would strengthen our modeling approach.

← Older revision		Revision as of 23:44, 18 November 2015
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	'''Summary:''' Plan of reading, synthesis and coding		'''Summary:''' Plan of reading, synthesis and coding

−	We held a brief meeting today to summarize findings in the literature, recalling that we need (1) good documentation on sources, concentrations and pathways of DOC in the NLTER Lakes, and (2) supporting information on DOC quality, reaction rates, etc. from other areas (preferably with similar climate and land coverage). Tom mentioned a couple of papers he read, including ~~Lottig et al (~~	+	We held a brief meeting today to summarize findings in the literature, recalling that we need (1) good documentation on sources, concentrations and pathways of DOC in the NLTER Lakes, and (2) supporting information on DOC quality, reaction rates, etc. from other areas (preferably with similar climate and land coverage). Tom mentioned a couple of papers he read, including a 2003 paper on groundwater age distributions at Lake Allequash [[Media:Pint etal flowpath GWage 2003.pdf]]

@@ Line 168: / Line 168: @@
 '''Summary:''' Plan of reading, synthesis and coding
+We held a brief meeting today to summarize findings in the literature, recalling that we need (1) good documentation on sources, concentrations and pathways of DOC in the NLTER Lakes, and (2) supporting information on DOC quality, reaction rates, etc. from other areas (preferably with similar climate and land coverage).  Tom mentioned a couple of papers he read, including Lottig et al (
-−

← Older revision		Revision as of 16:13, 18 November 2015
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	--[[User:Thomas\|Tom Harmon]] ([[User talk:Thomas\|talk]]) 10:33, 23 September 2015 (PDT)		--[[User:Thomas\|Tom Harmon]] ([[User talk:Thomas\|talk]]) 10:33, 23 September 2015 (PDT)

		+	----
	----		----
		+
		+	'''Skype Mtg #6 (09/23/2015)'''
		+
		+	'''Attendees:''' Tom, Sam, Hilary, Kevin
		+
		+	'''Summary:''' Plan of reading, synthesis and coding

← Older revision		Revision as of 17:33, 23 September 2015
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	--[[User:Thomas\|Tom Harmon]] ([[User talk:Thomas\|talk]]) 10:13, 23 September 2015 (PDT)		--[[User:Thomas\|Tom Harmon]] ([[User talk:Thomas\|talk]]) 10:13, 23 September 2015 (PDT)
		+
		+
		+	----
		+	----
		+
		+	'''Skype Mtg #6 (09/23/2015)'''
		+
		+	'''Attendees:''' Tom, Paul, Sam, Hilary, Roxanna
		+
		+	'''Summary:''' Recap on where we've been and where we'd like to go, and strategy for G17
		+
		+	Tom quickly reviewed progress to date, and relayed Stuart's intention to try to move forward on the "age" part of the simple catchment-lake model. Paul suggested that we get the latest R-script out to everyone soon, before G17 travel. This will give G17 folks (Tom, Paul, Hilary) a chance to re-familiarize themselves with it before the meeting.
		+
		+	Regarding G17: We decided to try to get our WG "yellow" status up in front of people. We are open to new people with clear interests in contributing, with (a) some knowledge/expertise in the DOC/DOM arena, (b) some R-skills to help maintain and flesh out the code once we are fixed on our analytical approach. Sam suggested that we might get some others hooked into the model at the meeting, and could even try to have some breakout modeling sessions. We thought it would be worth exploring, but need to see how big/new the groups are. We also thought it might be productive to have some breakout literature exploration and model parameter constraining sessions. Again, it will depend on the circumstances. Regardless, we decided to get our Dropbox in order with our own latest literature, so we can start people off in the right direction.
		+
		+	Tom will send wishlist to Hilary by this Friday (Sep 25) outlining the kind of data/information needed from the LTER lakes, beyond the big spreadsheet that Kevin put together (which has a lot). Mainly loading and hydraulic type of stuff is needed (hydrogeology data, groundwater modeling efforts, gw DOM/DOC loads, stream DOM/DOC loads, etc.).
		+
		+	--[[User:Thomas\|Tom Harmon]] ([[User talk:Thomas\|talk]]) 10:33, 23 September 2015 (PDT)
		+
		+	----
		+