'Ecological differentiation is the necessary condition for coexistence'
December 3, 2014 4:13 PM Subscribe
The Ecological Society of America will mark its 100th anniversary in 2015, and to celebrate, the ESA is asking people to weigh in with their ideas about the biggest ecological innovations over the past century. Brian McGill at Dynamic Ecology presents a thoughtful summary of the most important concepts and methods over 100 years of ecological research, and many other ecologists are weighing in as well.
McGill shares his thoughts on a great many concepts in his piece, from old standbys like ecological succession, food webs, competitive exclusion and niches, and ecophysiology to newer ideas such as macroecology, spatial ecology, and facilitation & mutualism dynamics. He also includes influential methods, including remote sensing, population abundance modeling with differential equations, phylogenetics, and use of stable isotopes.
Some ecologists are giving short answers on twitter (#ESA100), while others are writing long-form pieces:
McGill shares his thoughts on a great many concepts in his piece, from old standbys like ecological succession, food webs, competitive exclusion and niches, and ecophysiology to newer ideas such as macroecology, spatial ecology, and facilitation & mutualism dynamics. He also includes influential methods, including remote sensing, population abundance modeling with differential equations, phylogenetics, and use of stable isotopes.
Some ecologists are giving short answers on twitter (#ESA100), while others are writing long-form pieces:
- Small Pond Science: Amy Parachnowitsch and Terry McGlynn suggest a number of ideas, including the measurement of natural selection, the concept of pseudoreplication, systems ecology, biological field stations, women's suffrage, the Keeling curve, remote sensing, and the development of the modern tenure and PhD system.
- The EEB and Flow's Marc Cadotte and Caroline Tucker examine how statistical methods have advanced the field of ecology, from p-values and hypothesis testing to spatial statistics and Bayesian methods.
- Christopher Buddle at SciLog's Expiscor approaches the question by thinking about what we expect modern students to know about ecology, from K-12 through university, and comes to the conclusion that food pyramids or chains (now more commonly known as trophic webs) have had the most lasting impact on ecological education.
- Some ideas from twitter include Schindler's experimental lakes (from @pnis_co), ecological stoichiometry and coupled biogeochemical cycles (from @jillbaron4), and urban ecology (@temptalker).
With respect to methods, one tool I was surprised to see left out of the responses so far is GIS, which is a very powerful tool with all the "double-edged sword" that entails; it enables some incredible analysis but can also give people an inflated sense of the accuracy and precision of their conclusions, and can too easily mask underlying problems with the data or with scale mismatches. The other tool I was surprised not to see mentioned is R, which is a free statistical package used by the vast majority of ecologists and which has enabled ecologists to use increasingly sophisticated statistical methods without having to get secondary degrees in statistics (though again, this has positives and negatives - some would likely argue that this has caused more harm than good).
I'll add that the subset of ecologists who are outspoken on the internet tends to be more concerned with theoretical ecology, so ecologists who work on more applied questions tend to be underrepresented in the responses so far.
posted by dialetheia at 4:38 PM on December 3, 2014 [5 favorites]
I'll add that the subset of ecologists who are outspoken on the internet tends to be more concerned with theoretical ecology, so ecologists who work on more applied questions tend to be underrepresented in the responses so far.
posted by dialetheia at 4:38 PM on December 3, 2014 [5 favorites]
The other tool I was surprised not to see mentioned is R, which is a free statistical package used by the vast majority of ecologists and which has enabled ecologists to use increasingly sophisticated statistical methods without having to get secondary degrees in statistics
I'm often surprised to see how prevalent R is in ecology compared to other sciences. I'm fundamentally an ecologist, and no-one I work with uses anything else but R now. It's just the default. However, my research is interdisciplinary, and I work at times with atmospheric physicists and epidemiologists, and am frequently quite shocked to learn they're often still using things like SAS or SPSS, and putting graphs for publications together in Excel. Why? Why?
posted by Jimbob at 4:48 PM on December 3, 2014 [3 favorites]
I'm often surprised to see how prevalent R is in ecology compared to other sciences. I'm fundamentally an ecologist, and no-one I work with uses anything else but R now. It's just the default. However, my research is interdisciplinary, and I work at times with atmospheric physicists and epidemiologists, and am frequently quite shocked to learn they're often still using things like SAS or SPSS, and putting graphs for publications together in Excel. Why? Why?
posted by Jimbob at 4:48 PM on December 3, 2014 [3 favorites]
I know a handful of ecologists that do their analyses in R, but still make figures in Excel because ggplot2 is too frustrating. ¯\_(ツ)_/¯
I do everything in R (self-taught - I was the last graduate cohort in this department to take biometry in its pure theory form instead of the current R-based course). My advisor has spent years trying to get me to use SAS instead, but it's not going to happen.
posted by pemberkins at 5:07 PM on December 3, 2014 [1 favorite]
I do everything in R (self-taught - I was the last graduate cohort in this department to take biometry in its pure theory form instead of the current R-based course). My advisor has spent years trying to get me to use SAS instead, but it's not going to happen.
posted by pemberkins at 5:07 PM on December 3, 2014 [1 favorite]
Great post! I haven't read Dynamic Ecology's latest but they're a pretty thoughtful group so I'm looking forward to their post and especially the comments.
And yes, dialetheia, GIS is a huge missing tool.
posted by hydrobatidae at 5:21 PM on December 3, 2014 [2 favorites]
And yes, dialetheia, GIS is a huge missing tool.
posted by hydrobatidae at 5:21 PM on December 3, 2014 [2 favorites]
Computer modeling has changed so much in ecology I think it has to be the "most" important thing. I'm typing this while I run a complex bio-physical model on a cheap pos Dell and it'll be done before I am.
Followed by computers allowing you to do non parametric statistical analysis in a reasonable amount of time. I agree R is a very useful language but statistical packages like Primer have made many analysis possible that simply weren't 30 years ago. (And still fucking aren't in SPSS no matter how many times you "normalize" your data! /endrant)
posted by fshgrl at 5:52 PM on December 3, 2014 [1 favorite]
Followed by computers allowing you to do non parametric statistical analysis in a reasonable amount of time. I agree R is a very useful language but statistical packages like Primer have made many analysis possible that simply weren't 30 years ago. (And still fucking aren't in SPSS no matter how many times you "normalize" your data! /endrant)
posted by fshgrl at 5:52 PM on December 3, 2014 [1 favorite]
Oops, actually it crashed. Let's try that again without browsing the internet!
posted by fshgrl at 5:56 PM on December 3, 2014 [2 favorites]
posted by fshgrl at 5:56 PM on December 3, 2014 [2 favorites]
Oops, actually it crashed.
I don't do modeling myself, but that's the constant soundtrack from colleagues who do, usually in the last fifteen minutes of an 11-hour run.
I agree with the suggestion above about GIS, but agree even more with the caveats that it allows people to accidentally or deliberately hide and/or create data problems and inconsistencies.
Even more than the technical and conceptual tools, at least at my applied end of the world, the regulatory regimes (based on things like the ESA, Clean Water Act, etc) are probably the most powerful ecological innovations we have managed to put together in this country. They are huge and getting more intense every year. A lot of that is purely for the good (mostly in preventing the most egregious of bad projects), but it also ends up structuring how ecological work is done, what is possible and what is not, and what the timelines for implementation are, and sometimes it pushes the work in ways that feel increasingly divorced from the interesting and important theoretical work.
posted by Dip Flash at 6:42 PM on December 3, 2014 [2 favorites]
I don't do modeling myself, but that's the constant soundtrack from colleagues who do, usually in the last fifteen minutes of an 11-hour run.
I agree with the suggestion above about GIS, but agree even more with the caveats that it allows people to accidentally or deliberately hide and/or create data problems and inconsistencies.
Even more than the technical and conceptual tools, at least at my applied end of the world, the regulatory regimes (based on things like the ESA, Clean Water Act, etc) are probably the most powerful ecological innovations we have managed to put together in this country. They are huge and getting more intense every year. A lot of that is purely for the good (mostly in preventing the most egregious of bad projects), but it also ends up structuring how ecological work is done, what is possible and what is not, and what the timelines for implementation are, and sometimes it pushes the work in ways that feel increasingly divorced from the interesting and important theoretical work.
posted by Dip Flash at 6:42 PM on December 3, 2014 [2 favorites]
Great posts, both dialetheia's and Brian's. It's a tough question because I feel like ecology barely existed as a discipline 100 years ago, so almost ANY concept we have is applicable, aside from the prerequisite Darwin "entangled bank" quote. A nice companion piece would summarize the state of the field in 1914!
posted by Ian Scuffling at 7:20 PM on December 3, 2014 [3 favorites]
posted by Ian Scuffling at 7:20 PM on December 3, 2014 [3 favorites]
Building off the suggestion of the Keeling Curve, I will make a broader case for the humble data logger. Most of my dissertation involved probes recording data in streams every 10 minutes for 2 years. My foreparents spent 24 hours camping by a single stream doing hourly titrations to get a single daily estimate of stream metabolism, while I have 1000+ metabolism estimates calculated from 100,000+ datapoints, requiring nothing more than biweekly battery changes and maintenance. It's amazing how much more we can know about the world when data collection is automated and rapid and amazing.
And we can put those loggers in places that would be impossible to sample at any frequency by hand, like above the canopy on eddy covariance towers or on remote buoys. Or we can just have them providing useful real-time hydrologic data that serves the public as well as scientists.
posted by hydropsyche at 4:08 AM on December 4, 2014 [3 favorites]
And we can put those loggers in places that would be impossible to sample at any frequency by hand, like above the canopy on eddy covariance towers or on remote buoys. Or we can just have them providing useful real-time hydrologic data that serves the public as well as scientists.
posted by hydropsyche at 4:08 AM on December 4, 2014 [3 favorites]
> Stable Isotopes – I’ve never personally used this technique, but the ability to quantify
> the ratio of different isotopes of an element (say oxygen 16 and 18) in small samples has
> revolutionized what we can measure. (-- from the fpp)
Man, I've done that by the long ton, as manager* of the Stable Isotope/Soil Biology lab at the UGa Institute of Ecology (now the Odum School of Ecology, named after founder Eugene Odum.) If you're interested in energetics (taking "energy" as meaning "nutrients") you're asking where it comes from, what forms it takes, what transformations it undergoes, how it's partitioned and channeled within your system of interest, and where does it all end up (if it stays in the system long term) or go (if it exits.) For soil, plant, and water samples the huge practical insight was that pretty much any kind of anlysis your state soil/plant lab is doing for farmers and gardeners, any kind of analysis your state water lab is doing for water treatment facilities or for pollution abatement, is worth learning and applying to samples from wild ecosystems.
This works in the other direction also in all but a few cases, of which stable isotope work is one. Not too many gardeners crying out to know their garden's C12/C13 ratios. Where stable isotopes are especially good for ecologists is pathway tracing. Take "before" samples from everything in sight in your system, run all the samples through your mass spectrometer, and record what all the unmodified C12/C13 ratios are. Then release some C13-tagged nutrient into the system, let it percolate, re-sample, fire up your mass spec for another run. Output, comparing before and after, is how much of your spiked tracer substance went hither and how much went yon for (depending on your study's funding, heh) quite a large number of hithers and yons. Step 3,profit publication!
* "manager" = for that particular lab, everything: sample prep (stable isotope samples for soils and plants take a lot of prep, and the samples come in by the hundreds), reagent prep, the sample analysis itself. Also equipment maintenance, grant proposal writing, annual budgeting, glassware washing, floor sweeping.
> A lot of [current regulatory regimes] is purely for the good (mostly in preventing the
> most egregious of bad projects), but it also ends up structuring how ecological work is done,
> what is possible and what is not
Lots of the tracer work using C13 could also be done with radioactive C14 as the tracer. C14 has lots of practical advantages as a technique. It's much easier to detect in your samples, and a scintillation counter (even a top end one capable of really churning out the sample readings) is a HELL of a lot cheaper than a mass spec. But when you're deciding which to use in your project a big consideration is just how incredibly heavily regulated academic work with radionuclides is. (The laws for industrial use are different and a great deal less strict. Why am I not surprised?) Still and all, it doesn't really look good for self-proclaimed ecologists to go throwing radioactive substances around in the environment. I'm for tightening up reglation on industry (BWAHAHAHAHA) rather than easing up on academics.
> Followed by computers allowing you to do non parametric statistical analysis in a reasonable
> amount of time.
My boss at UGa told me that when he was a grad student the single factor that absolutely determined how big your brilliant new study was going to be was how much time and grunt work with pencil and paper you were prepared to put into the statistical analysis.
> The other tool I was surprised not to see mentioned is R
How about BASIC? The first ecological computer model I ever beat my head against until I understood it was published in Byte (June 1981) in the article "Mathematical Modeling: A BASIC Program to Simulate Real-World Systems" by Randy Hicks, now full professor at U. Minn., then a graduate student at UGa working at the Marine Institute on Sapelo Island. This was long before I ever worked at UGa, being then just a microcomputer hobbyist, and the article was vastly heavier than anything I had ever encountered before (Star Trek simulations etc.) in the hobbyist press.
My purpose is to demonstrate how useful microcom-
puters can be in mathematical simulations. I will intro-
duce you to modeling the behavior of a system by de-
scribing it mathematically with a system of time-invari-
ant linear differential equations. I will show how to solve
systems of differential equations by two separate numeri-
cal methods. As a framework for the simulation tasks, I
will use a simple model as an example for you to follow: a
hydrologic model of the forested uplands surrounding
Okefenokee swamp in Georiga.
It was written for a machine called a Compucolor, a long-vanished brand of the 8 bit generation, one of which the Marine Institute happened to own. Much later when I actually did work for UGa I found this exact same Compucolor in storage at the Institute of Ecology, which has close ties to the Marine Institute. Nope, would not boot.
By utter chance I just located a full copy of this ancient Byte online, courtesy of an outfit called americanradiohistory.com. Article starts on p.74 and has complete program code--in Compucolor basic. Warning, 36 MB pdf file, if for any reason you want the code you're in for some retyping, just as you wouda been if you had gotten the June 1981 Byte on paper. Archive.org has the full text of that issue but the code listing is garbled and worthless, don't bother.
The pdf, OTOH, is absolutely worth a look, both for the wonderful 1981 computer gear ads and for some other remarkable articles. There's "CP/M: A Family of 8- and 16-bit Operating Systems" by Gary Kildall starting on p.216, and on p.392 an article called "The Impossible Dream: Computing e to 116,000 places with a Personal Computer" by some dude named Stephen Wozniak.
posted by jfuller at 6:31 AM on December 4, 2014 [4 favorites]
> the ratio of different isotopes of an element (say oxygen 16 and 18) in small samples has
> revolutionized what we can measure. (-- from the fpp)
Man, I've done that by the long ton, as manager* of the Stable Isotope/Soil Biology lab at the UGa Institute of Ecology (now the Odum School of Ecology, named after founder Eugene Odum.) If you're interested in energetics (taking "energy" as meaning "nutrients") you're asking where it comes from, what forms it takes, what transformations it undergoes, how it's partitioned and channeled within your system of interest, and where does it all end up (if it stays in the system long term) or go (if it exits.) For soil, plant, and water samples the huge practical insight was that pretty much any kind of anlysis your state soil/plant lab is doing for farmers and gardeners, any kind of analysis your state water lab is doing for water treatment facilities or for pollution abatement, is worth learning and applying to samples from wild ecosystems.
This works in the other direction also in all but a few cases, of which stable isotope work is one. Not too many gardeners crying out to know their garden's C12/C13 ratios. Where stable isotopes are especially good for ecologists is pathway tracing. Take "before" samples from everything in sight in your system, run all the samples through your mass spectrometer, and record what all the unmodified C12/C13 ratios are. Then release some C13-tagged nutrient into the system, let it percolate, re-sample, fire up your mass spec for another run. Output, comparing before and after, is how much of your spiked tracer substance went hither and how much went yon for (depending on your study's funding, heh) quite a large number of hithers and yons. Step 3,
* "manager" = for that particular lab, everything: sample prep (stable isotope samples for soils and plants take a lot of prep, and the samples come in by the hundreds), reagent prep, the sample analysis itself. Also equipment maintenance, grant proposal writing, annual budgeting, glassware washing, floor sweeping.
> A lot of [current regulatory regimes] is purely for the good (mostly in preventing the
> most egregious of bad projects), but it also ends up structuring how ecological work is done,
> what is possible and what is not
Lots of the tracer work using C13 could also be done with radioactive C14 as the tracer. C14 has lots of practical advantages as a technique. It's much easier to detect in your samples, and a scintillation counter (even a top end one capable of really churning out the sample readings) is a HELL of a lot cheaper than a mass spec. But when you're deciding which to use in your project a big consideration is just how incredibly heavily regulated academic work with radionuclides is. (The laws for industrial use are different and a great deal less strict. Why am I not surprised?) Still and all, it doesn't really look good for self-proclaimed ecologists to go throwing radioactive substances around in the environment. I'm for tightening up reglation on industry (BWAHAHAHAHA) rather than easing up on academics.
> Followed by computers allowing you to do non parametric statistical analysis in a reasonable
> amount of time.
My boss at UGa told me that when he was a grad student the single factor that absolutely determined how big your brilliant new study was going to be was how much time and grunt work with pencil and paper you were prepared to put into the statistical analysis.
> The other tool I was surprised not to see mentioned is R
How about BASIC? The first ecological computer model I ever beat my head against until I understood it was published in Byte (June 1981) in the article "Mathematical Modeling: A BASIC Program to Simulate Real-World Systems" by Randy Hicks, now full professor at U. Minn., then a graduate student at UGa working at the Marine Institute on Sapelo Island. This was long before I ever worked at UGa, being then just a microcomputer hobbyist, and the article was vastly heavier than anything I had ever encountered before (Star Trek simulations etc.) in the hobbyist press.
My purpose is to demonstrate how useful microcom-
puters can be in mathematical simulations. I will intro-
duce you to modeling the behavior of a system by de-
scribing it mathematically with a system of time-invari-
ant linear differential equations. I will show how to solve
systems of differential equations by two separate numeri-
cal methods. As a framework for the simulation tasks, I
will use a simple model as an example for you to follow: a
hydrologic model of the forested uplands surrounding
Okefenokee swamp in Georiga.
It was written for a machine called a Compucolor, a long-vanished brand of the 8 bit generation, one of which the Marine Institute happened to own. Much later when I actually did work for UGa I found this exact same Compucolor in storage at the Institute of Ecology, which has close ties to the Marine Institute. Nope, would not boot.
By utter chance I just located a full copy of this ancient Byte online, courtesy of an outfit called americanradiohistory.com. Article starts on p.74 and has complete program code--in Compucolor basic. Warning, 36 MB pdf file, if for any reason you want the code you're in for some retyping, just as you wouda been if you had gotten the June 1981 Byte on paper. Archive.org has the full text of that issue but the code listing is garbled and worthless, don't bother.
The pdf, OTOH, is absolutely worth a look, both for the wonderful 1981 computer gear ads and for some other remarkable articles. There's "CP/M: A Family of 8- and 16-bit Operating Systems" by Gary Kildall starting on p.216, and on p.392 an article called "The Impossible Dream: Computing e to 116,000 places with a Personal Computer" by some dude named Stephen Wozniak.
posted by jfuller at 6:31 AM on December 4, 2014 [4 favorites]
Or we can just have them providing useful real-time hydrologic data that serves the public as well as scientists.
The USGS stream gages have been my BFF for a good portion of my dissertation, and it breaks my heart a little more every time I go back to that page and see new sites added to the list of those that have been discontinued because there is no funding to maintain them.
posted by pemberkins at 7:49 AM on December 4, 2014 [2 favorites]
The USGS stream gages have been my BFF for a good portion of my dissertation, and it breaks my heart a little more every time I go back to that page and see new sites added to the list of those that have been discontinued because there is no funding to maintain them.
posted by pemberkins at 7:49 AM on December 4, 2014 [2 favorites]
The USGS stream gages have been my BFF for a good portion of my dissertation, and it breaks my heart a little more every time I go back to that page and see new sites added to the list of those that have been discontinued because there is no funding to maintain them.
It's especially frustrating as cities and agencies are being forced to try and understand critical things like how climate change will impact flood control infrastructure and public safety; this continued defunding of basic public science is incredibly short sighted and will cost far more in the long run.
posted by Dip Flash at 8:00 AM on December 4, 2014 [2 favorites]
It's especially frustrating as cities and agencies are being forced to try and understand critical things like how climate change will impact flood control infrastructure and public safety; this continued defunding of basic public science is incredibly short sighted and will cost far more in the long run.
posted by Dip Flash at 8:00 AM on December 4, 2014 [2 favorites]
Yeah, the vast amount of data that's out there certainly drives my ecological research. Remote sensing, as a whole, has enabled us to look at the earth and its dynamics in ways unimaginable before.
posted by Jimbob at 6:11 PM on December 4, 2014 [1 favorite]
posted by Jimbob at 6:11 PM on December 4, 2014 [1 favorite]
Wow! There are a lot more ecologists on mefi than I thought! Yay! This pleases me.
(I am not surprised, however, that we all use R.)
(and I'm assuming everyone has hopped on board to using the wesanderson package when plotting whenever possible...)
posted by redbeard at 5:24 AM on December 5, 2014 [2 favorites]
(I am not surprised, however, that we all use R.)
(and I'm assuming everyone has hopped on board to using the wesanderson package when plotting whenever possible...)
posted by redbeard at 5:24 AM on December 5, 2014 [2 favorites]
Oh dear. Why was I not aware of the wesanderson package until now? I am a fan of colorbrewer (and frequently just write my own color palettes because I am neurotic about figures), but this package has totally escaped my notice.
Please expect my talk/poster/whatever at ESA100 to be fully WesAnderson-ed.
posted by pemberkins at 7:48 AM on December 5, 2014 [2 favorites]
Please expect my talk/poster/whatever at ESA100 to be fully WesAnderson-ed.
posted by pemberkins at 7:48 AM on December 5, 2014 [2 favorites]
Having since shared that package with another student in my department, I quote:
"oh my god I love them I think I am going to have to use it for my dissertation !!!!!!!!!!!!!!!"
So, thank you from my entire department to you!
posted by pemberkins at 7:57 AM on December 5, 2014 [3 favorites]
"oh my god I love them I think I am going to have to use it for my dissertation !!!!!!!!!!!!!!!"
So, thank you from my entire department to you!
posted by pemberkins at 7:57 AM on December 5, 2014 [3 favorites]
Author of the wesanderson package here. Thanks for the kind words! Please tweet (@_inundata) or memail me a link if you use it in a paper! I'll include you in the list of publications. Cheers!
posted by special-k at 4:34 PM on December 5, 2014 [6 favorites]
posted by special-k at 4:34 PM on December 5, 2014 [6 favorites]
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My own nomination would be the application of chaos theory to population dynamics in real world systems.
posted by Chocolate Pickle at 4:31 PM on December 3, 2014 [3 favorites]