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It's long been known how to fix soil; see for example from 1987: "Towards Holistic Agriculture: A Scientific Approach" by R.W. Widdowson: https://www.elsevier.c

It's long been known how to fix soil; see for example from 1987: "Towards Holistic Agriculture: A Scientific Approach" by R.W. Widdowson: https://www.elsevier.com/books/towards-holistic-agriculture/widdowson/978-0-08-034211-5 https://www.elsevier.com/books/towards-holistic-agriculture/... Or from 1911: https://permaculturenews.org/files/farmers_of_forty_centuries.pdf https://permaculturenews.org/files/farmers_of_forty_centurie... More: http://soilandhealth.org/ http://soilandhealth.org/ Adding rock dust works wonders too: https://remineralize.org/ https://remineralize.org/ My wife and I wrote a FOSS garden simulator in the 1990s (a six+ person-year labor of love) to help people understand some of this: http://www.kurtz-fernhout.com/summary_gwi.html http://www.kurtz-fernhout.com/summary_gwi.html I got the idea while working as the Program Administrator on summer for the NOFA-NJ Organic Farm Certification Program in the later 1980s, but it took many years (including more education in grad school in biology) to make the software. See especially from the help system of that software on how conventional agriculture destroys the soil: http://www.gardenwithinsight.com/help100/00000385.htm http://www.gardenwithinsight.com/help100/00000385.htm "In the soil, tiny charged particles called micelles usually have many areas of negative charge (called sites) on their surfaces. Positively charged ions (cations) are drawn to these negative charge sites and stick to the clay particles (are adsorbed). In most soils, 99% of soil cations can be found attached to micelles (clay particles and organic matter) and 1% can be found in solution. Mineral cations in the soil (mainly Ca2+, Mg2+, K+ and Na+) maintain an equilibrium between adsorption to the negative sites and solution in the soil water. This equilibrium produces exchanges -- when one cation detaches from a site (leaving it free), another cation attaches to it. Therefore the negatively charged sites are called cation exchange sites. The number of these sites per unit weight of dry soil is called the cation exchange capacity, or the capacity of the soil to hold cations. Because any cations loose in the soil solution are vulnerable to leaching as water flows out of the soil, a high cation exchange capacity is always desirable. Cation exchange sites act as a sort of mineral buffer for the soil, storing minerals important to plant and animal growth for long periods of time. The attraction of cations to cation exchange sites is strongest for H+ ions (which make the soil acidic) and for polyvalent ions such as Ca2+ and Al3+. The weakest attraction is for monovalent ions such as K+. When ammonium nitrate fertilizers are added to the soil, the ammonium ions (NH4+) are strongly attracted to cation exchange sites because of their high valence (4). The ammonium ions displace many other cations which are then leached out of the soil and lost to plants. Some of the ammonium ions are converted to nitrate during nitrification (by aerobic soil bacteria); the process produces excess H+ ions which acidify the soil (causing earthworms and other soil organisms to die or desert the area). (For an excellent description of cation exchange capacity, see Widdowson's Towards Holistic Agriculture: A Scientific Approach.)" That's a big reason why organic agriculture which focuses on building up organic matter in the soil (which increases cation exchange capacity) is better for soil health (and human health too, as the plants are better fed). That's reflected in the article when it describes two lumps of soil put on wire mesh that behave differently -- one falling apart as dust (from lack of organic matter and so not much CEC) and one clumped together (more organic matter and CEC). Wish I had time to bring that Delphi app to the web as a JavaScript app... And improve it further. I don't know the exact numbers to completely quantify this, but I suspect poor farming practices on the US prairies that have reduced (in some places) six feet of topsoil to six inches of top soil have released a vast amount of carbon from lost organic matter into the air and contributed to climate change.

roel_v 9y ago
Does your model support root nodule nitrogen fixation? I've been looking for simulation software to estimate optimal levels of nitrogen fixers, but I didn't find any comprehensive models that included this. I didn't look at your model for it though; although I did come across it several years earlier when I was looking for plant growth simulations for another reason. In what way(s) does it diverge from EPIC? EPIC & APEX are (widely) applied for policy evaluation purposes (how much sense that makes is another matter, but let's just accept reality for now); is your model robust enough for such things, I mean comparable to EPIC? And does it still run on Windows 10? I tried to install it but got some error that it failed writing to a registry key, and then I didn't look any further.
- pdfernhout 9y ago
  Most of the model source code is derived from EPIC (and a bit from SPUR which was about rangelands, weather, and plant competition). The EPIC conversion involved a person-year of painstaking work going through EPIC and creating sensible names for the cryptic FORTRAN variables (which were also sometimes reused multiple times with different meanings) and short function names as the code was rewritten into C++ and then later Delphi. My wife -- who I met via the PhD program in Ecology and Evolution I went to to try to learn enough to write the simulator -- did most of that translation. It's been twenty years, so I could not answer detailed questions about it of the top of my head without digging into the code (and maybe not even then). But the core parts of the soil percolation model should be very close to EPIC's code and data. The source code for the soil models references the EPIC equations and the related scientific literature. The simulator was written under earlier versions of windows (Win 3.1 and 95), and from around WinXP and later it seems the code that updates the registry causes an error. Not sure how to easily work around that. You can download the source here: http://www.kurtz-fernhout.com/GardenSimulatorSourceCirca1997InDelphi.zip http://www.kurtz-fernhout.com/GardenSimulatorSourceCirca1997... Or, I just put it up on GitHub right now for you: :-) https://github.com/pdfernhout/GardenSimulatorSourceCirca1997InDelphi https://github.com/pdfernhout/GardenSimulatorSourceCirca1997... Here is the file you would want to focus on first, and it does mention nitrogen fixation and nodules, but you'd have to make your own decision about how useful that was to you as a reference: https://github.com/pdfernhout/GardenSimulatorSourceCirca1997InDelphi/blob/master/ueq.pas https://github.com/pdfernhout/GardenSimulatorSourceCirca1997... Here are the lines to look first inside that file: https://github.com/pdfernhout/GardenSimulatorSourceCirca1997InDelphi/blob/master/ueq.pas#L4741-L4764 https://github.com/pdfernhout/GardenSimulatorSourceCirca1997... Remember that a lot of EPIC is empirically derived functions and values from US soils in certain climates -- so it may not be totally applicable elsewhere, even if it is a place to start. And here is a 100 page programmer's manual: http://www.kurtz-fernhout.com/progmanlong.htm http://www.kurtz-fernhout.com/progmanlong.htm I put our PlantStudio and StoryHarp code up on GitHub (which share some common code with the garden simulator) and have been meaning to someday put the garden simulator code there. I spent a couple of months about a decade ago porting part of the code base to Java and also Python which involved writing a Delphi parser and translation tool, but the result is not a finished work. But the converted code for the garden simulator is not on GitHub (yet). You can see some of the converted plant drawing code here though: https://github.com/pdfernhout/PlantStudio https://github.com/pdfernhout/PlantStudio I had wanted to help develop self-replicating space habitats and helping people grow their own food better seemed like a good first step towards that which both had short-term on-Earth benefits plus long-term benefits for space settlement. We did this all on our own money from consulting and also credit cards. When they were maxed out (~US$100K) we took unrelated programming jobs at IBM Research and elsewhere to pay it all back on-time with interest -- it took many years to get back to zero -- and we never got a chance to do that much more with the simulator... Our (at first shareware) PlantStudio software was a spinoff for breeding virtual plants which got substantial interest from 3D modellers -- but even there, we did not have time to keep improving it since we were both working full-time the at IBM. PlantStudio was mainly my wife's project in response to user feedback from the Garden Simulator that people liked playing with the plant design part of it. We eventually made that free and then open source. http://www.kurtz-fernhout.com/PlantStudio/userssay.htm http://www.kurtz-fernhout.com/PlantStudio/userssay.htm And then we had a kid: :-) http://www.kurtz-fernhout.com/historyandfuture.html http://www.kurtz-fernhout.com/historyandfuture.html After that effort on our own, I'd get a bit annoyed I got when I'd watch NASA and other places give big grants to people who then made proprietary software with it. That motivated me to write essays like this back around 2001: http://pdfernhout.net/on-funding-digital-public-works.html http://pdfernhout.net/on-funding-digital-public-works.html "As a software developer and content creator, I find it continually frustrating to visit web sites of projects funded directly or indirectly by government agencies or foundations, only to discover I can't easily improve on those projects because of licensing restrictions both on redistribution and on making derived works of their content and software. ..." But I can give kudos at the USDA ARS BRC and the EPIC team for developing their code in-house and putting it in the public domain. The EPIC developers (but not administrators) were annoyed a bit themselves at our own plan originally to make proprietary software from their models, which was another factor in our making that garden simulator effort FOSS. Our hope had been to keep improving those models and getting more people involved in that process online with a 2.0 version of the software as a shared modelling environment. But our few small efforts to find funding to continue in that direction were not productive. I guess we were just better software developers than sales people. :-) Plus we have learned a lot since then about a more incremental development style. http://gardenwithinsight.com/nsfprop.htm http://gardenwithinsight.com/nsfprop.htm Anyway, I can hope that using that Garden Simulator software as an initial reference point can help a next generation of soil scientists and free software developers create even better software for research, education, and applications from bringing soil anywhere back to life. :-)

roel_v 9y ago

Does your model support root nodule nitrogen fixation? I've been looking for simulation software to estimate optimal levels of nitrogen fixers, but I didn't find any comprehensive models that included this. I didn't look at your model for it though; although I did come across it several years earlier when I was looking for plant growth simulations for another reason. In what way(s) does it diverge from EPIC? EPIC & APEX are (widely) applied for policy evaluation purposes (how much sense that makes is another matter, but let's just accept reality for now); is your model robust enough for such things, I mean comparable to EPIC? And does it still run on Windows 10? I tried to install it but got some error that it failed writing to a registry key, and then I didn't look any further.

pdfernhout 9y ago
Most of the model source code is derived from EPIC (and a bit from SPUR which was about rangelands, weather, and plant competition). The EPIC conversion involved a person-year of painstaking work going through EPIC and creating sensible names for the cryptic FORTRAN variables (which were also sometimes reused multiple times with different meanings) and short function names as the code was rewritten into C++ and then later Delphi. My wife -- who I met via the PhD program in Ecology and Evolution I went to to try to learn enough to write the simulator -- did most of that translation. It's been twenty years, so I could not answer detailed questions about it of the top of my head without digging into the code (and maybe not even then). But the core parts of the soil percolation model should be very close to EPIC's code and data. The source code for the soil models references the EPIC equations and the related scientific literature. The simulator was written under earlier versions of windows (Win 3.1 and 95), and from around WinXP and later it seems the code that updates the registry causes an error. Not sure how to easily work around that. You can download the source here: http://www.kurtz-fernhout.com/GardenSimulatorSourceCirca1997InDelphi.zip http://www.kurtz-fernhout.com/GardenSimulatorSourceCirca1997... Or, I just put it up on GitHub right now for you: :-) https://github.com/pdfernhout/GardenSimulatorSourceCirca1997InDelphi https://github.com/pdfernhout/GardenSimulatorSourceCirca1997... Here is the file you would want to focus on first, and it does mention nitrogen fixation and nodules, but you'd have to make your own decision about how useful that was to you as a reference: https://github.com/pdfernhout/GardenSimulatorSourceCirca1997InDelphi/blob/master/ueq.pas https://github.com/pdfernhout/GardenSimulatorSourceCirca1997... Here are the lines to look first inside that file: https://github.com/pdfernhout/GardenSimulatorSourceCirca1997InDelphi/blob/master/ueq.pas#L4741-L4764 https://github.com/pdfernhout/GardenSimulatorSourceCirca1997... Remember that a lot of EPIC is empirically derived functions and values from US soils in certain climates -- so it may not be totally applicable elsewhere, even if it is a place to start. And here is a 100 page programmer's manual: http://www.kurtz-fernhout.com/progmanlong.htm http://www.kurtz-fernhout.com/progmanlong.htm I put our PlantStudio and StoryHarp code up on GitHub (which share some common code with the garden simulator) and have been meaning to someday put the garden simulator code there. I spent a couple of months about a decade ago porting part of the code base to Java and also Python which involved writing a Delphi parser and translation tool, but the result is not a finished work. But the converted code for the garden simulator is not on GitHub (yet). You can see some of the converted plant drawing code here though: https://github.com/pdfernhout/PlantStudio https://github.com/pdfernhout/PlantStudio I had wanted to help develop self-replicating space habitats and helping people grow their own food better seemed like a good first step towards that which both had short-term on-Earth benefits plus long-term benefits for space settlement. We did this all on our own money from consulting and also credit cards. When they were maxed out (~US$100K) we took unrelated programming jobs at IBM Research and elsewhere to pay it all back on-time with interest -- it took many years to get back to zero -- and we never got a chance to do that much more with the simulator... Our (at first shareware) PlantStudio software was a spinoff for breeding virtual plants which got substantial interest from 3D modellers -- but even there, we did not have time to keep improving it since we were both working full-time the at IBM. PlantStudio was mainly my wife's project in response to user feedback from the Garden Simulator that people liked playing with the plant design part of it. We eventually made that free and then open source. http://www.kurtz-fernhout.com/PlantStudio/userssay.htm http://www.kurtz-fernhout.com/PlantStudio/userssay.htm And then we had a kid: :-) http://www.kurtz-fernhout.com/historyandfuture.html http://www.kurtz-fernhout.com/historyandfuture.html After that effort on our own, I'd get a bit annoyed I got when I'd watch NASA and other places give big grants to people who then made proprietary software with it. That motivated me to write essays like this back around 2001: http://pdfernhout.net/on-funding-digital-public-works.html http://pdfernhout.net/on-funding-digital-public-works.html "As a software developer and content creator, I find it continually frustrating to visit web sites of projects funded directly or indirectly by government agencies or foundations, only to discover I can't easily improve on those projects because of licensing restrictions both on redistribution and on making derived works of their content and software. ..." But I can give kudos at the USDA ARS BRC and the EPIC team for developing their code in-house and putting it in the public domain. The EPIC developers (but not administrators) were annoyed a bit themselves at our own plan originally to make proprietary software from their models, which was another factor in our making that garden simulator effort FOSS. Our hope had been to keep improving those models and getting more people involved in that process online with a 2.0 version of the software as a shared modelling environment. But our few small efforts to find funding to continue in that direction were not productive. I guess we were just better software developers than sales people. :-) Plus we have learned a lot since then about a more incremental development style. http://gardenwithinsight.com/nsfprop.htm http://gardenwithinsight.com/nsfprop.htm Anyway, I can hope that using that Garden Simulator software as an initial reference point can help a next generation of soil scientists and free software developers create even better software for research, education, and applications from bringing soil anywhere back to life. :-)