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# Blog - carbon cycle box models (part 1)

I started a draft Blog - carbon cycle box models (part 1)

I think its going to be 2 or 3 posts initially for the carbon cycle and some more later.

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1.
edited December 2011

Please feel free to chime in and if you don't like the approach with Venture Cap pitch i'll remove it. also i want to do

• part 1 intro plus 1d boxes
• part 2 more boxes; redox and 2-box ocean
• part 3 nonlinear box models

and at the same time re-program the box model after each and end up with something that can be reused for other cycles.

initially i want to add support for juggling with boxes and IC's and means to create and display So that is feasible now where you add symbolic equations for the boxes. I also looked at the Sage graph_editor() - math graphs and i decided t skip that for now and instead add "save" of models and boxes between sessions.

So do you think that is a good initial approach for the Sage program?

Comment Source:Please feel free to chime in and if you don't like the approach with Venture Cap pitch i'll remove it. also i want to do * part 1 intro plus 1d boxes * part 2 more boxes; redox and 2-box ocean - part 3 nonlinear box models and at the same time re-program the box model after each and end up with something that can be reused for other cycles. initially i want to add support for juggling with boxes and IC's and means to create and display So that is feasible now where you add symbolic equations for the boxes. I also looked at the Sage graph_editor() - math graphs and i decided t skip that for now and instead add "save" of models and boxes between sessions. So do you think that is a good initial approach for the Sage program?
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2.
edited December 2011

i want to use a couple of videos in the first intro part and i tried html embed but no luck . but video ... works good :-)

Comment Source:i want to use a couple of videos in the first intro part and i tried html embed but no luck . but video ... works good :-)
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3.

...in Chrome only sofar...:--(

Comment Source:...in Chrome only sofar...:--(
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4.

Hi! Looks interesting!

I'll read it and comment this weekend!

Comment Source:Hi! Looks interesting! <img src = "http://math.ucr.edu/home/baez/emoticons/thumbsup.gif" alt = ""/> I'll read it and comment this weekend!
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5.

Just look at the structure and content and factual errors and we might hold off English until we know how many posts and what order

btw I got the video tag to work in Explorer 9 now by using alt sources for wmv and mp4 videos.

Comment Source:Just look at the structure and content and factual errors and we might hold off English until we know how many posts and what order btw I got the video tag to work in Explorer 9 now by using alt sources for wmv and mp4 videos.
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6.
edited December 2011

I can't really read English without correcting it!

One comment is that this post seems aimed at a broader audience than I usually aim for. To take one example, I would assume my readers know what 'carnivores' and 'herbivores' are, instead of explaining those terms. I guess I'm mainly aiming my blog posts at scientists or people who know science, and probably native English speakers.

What goal are you heading towards? A few box models, with differential equations and pictures of the solutions? Software that runs on the web, too?

Comment Source:I can't really read English without correcting it! One comment is that this post seems aimed at a broader audience than I usually aim for. To take one example, I would assume my readers know what 'carnivores' and 'herbivores' are, instead of explaining those terms. I guess I'm mainly aiming my blog posts at scientists or people who know science, and probably native English speakers. What goal are you heading towards? A few box models, with differential equations and pictures of the solutions? Software that runs on the web, too?
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7.
edited December 2011
Ok I think I want to write for a slightly broader audience but i might make Azimuth - wikipedia links instead because I notice it takes too long time to explain. I restructured part 1 and put more of the "how", in that section by the way.

I want to write the three first - so people get a feeling how the carbon cycle works and how it can be modeled and refined in steps and end up with the coupled DEs whichh I have started to implement in Sage and with interaction. Then after that I might write one blog post on the program and maybe get more people on board to build a more generic framework for box models of other element cycles. If you have a better idea on how to structure this and also if you have a gut feeling for this broader approach i am all ears.

But as I said on the other thread I am leaving for vacation dec 14 - jan 15 to Argentina. I will work on it there but a bit slower. It depends on where we are going.
Comment Source:Ok I think I want to write for a slightly broader audience but i might make Azimuth - wikipedia links instead because I notice it takes too long time to explain. I restructured part 1 and put more of the "how", in that section by the way. I want to write the three first - so people get a feeling how the carbon cycle works and how it can be modeled and refined in steps and end up with the coupled DEs whichh I have started to implement in Sage and with interaction. Then after that I might write one blog post on the program and maybe get more people on board to build a more generic framework for box models of other element cycles. If you have a better idea on how to structure this and also if you have a gut feeling for this broader approach i am all ears. But as I said on the other thread I am leaving for vacation dec 14 - jan 15 to Argentina. I will work on it there but a bit slower. It depends on where we are going.
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8.

I read a lot about the Isotope+geochemistry and I think might enough a blog on that. But what do you think?

Comment Source:I read a lot about the [[Isotope+geochemistry]] and I think might enough a blog on that. But what do you think?
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9.
edited September 2012

I would love a blog article on that too, Steffan! However, you — and Blake Stacey, and Cameron Smith, and others — seem to be starting more blog articles than you're finishing!

The trick is to 1) plan to write something short, 2) know ahead of time what point you're trying to make, 4) write until you make that point, 5) stop writing, 6) show it to me when it's done, 7) let me edit it a bit and put it on the blog. Ideally step 4) is done in one or two sessions, in a couple of days, while your enthusiasm is high.

Comment Source:I would love a blog article on that too, Steffan! However, you &mdash; and Blake Stacey, and Cameron Smith, and others &mdash; seem to be starting more blog articles than you're finishing! The trick is to 1) plan to write something short, 2) know ahead of time what point you're trying to make, 4) write until you make that point, 5) stop writing, 6) show it to me when it's done, 7) let me edit it a bit and put it on the blog. Ideally step 4) is done in one or two sessions, in a couple of days, while your enthusiasm is high.
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10.
edited January 2012

I will focus on the first two as originally planned . thx i will take your points seriously when I back from vacation in Buenos Aires on jan 20. Part one is almost finished btw .

Comment Source:I will focus on the first two as originally planned . thx i will take your points seriously when I back from vacation in Buenos Aires on jan 20. Part one is almost finished btw .
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11.

I feel that this is finished draft, so pls feel free to comment and tell if its to long or too short. (The second will be about two box models of lan-atm, ocean atm and a little about the nonlinear nature of the carbon cycle

Comment Source:I feel that this is finished draft, so pls feel free to comment and tell if its to long or too short. (The second will be about two box models of lan-atm, ocean atm and a little about the nonlinear nature of the carbon cycle
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12.

Okay, I'll look at it! Sorry to be taking so long. You may have noticed that Jim Stuttard is interested in getting specifications of some models for the purposes of implementing them online. Maybe these blog entries can help do that!

Comment Source:Okay, I'll look at it! Sorry to be taking so long. You may have noticed that Jim Stuttard is interested in getting specifications of some models for the purposes of implementing them online. Maybe these blog entries can help do that!
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13.

I needed to take a break from Azimuth - as you might have noticed - but now i will finish the experiments and blog posts and keep Jim in the loop while doing that.

Comment Source:I needed to take a break from Azimuth - as you might have noticed - but now i will finish the experiments and blog posts and keep Jim in the loop while doing that.
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14.

After I post Week 319 maybe your post should be the next big one I do!

Comment Source:After I post [Week 319](http://math.ucr.edu/home/baez/week319.html) maybe your post should be the next big one I do!
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15.

the problem is i cannot edit any pages anymore , (i get u are not allowed to edit, spam filtwer...) . so I have been inactive due to that. It might be that I use dynamic DNS with my ISP. can You get the admin to look at this?

Comment Source:the problem is i cannot edit any pages anymore , (i get u are not allowed to edit, spam filtwer...) . so I have been inactive due to that. It might be that I use dynamic DNS with my ISP. can You get the admin to look at this?
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16.

I just added some links to the references. I am done with part one , so if you re-read it and think it is ok you can go ahead and publish it or if you want to me to make any changes before publication .

After that I am going to need to re-design some models in Sage for the second part. I used ODE solvers which is overkill for the simple box-models and Sage has support for \ (solve_right() for solving systems like in Matlab.

Comment Source:I just added some links to the references. I am done with part one , so if you re-read it and think it is ok you can go ahead and publish it or if you want to me to make any changes before publication . After that I am going to need to re-design some models in Sage for the second part. I used ODE solvers which is overkill for the simple box-models and Sage has support for \ (solve_right() [for solving systems](http://www.sagemath.org/doc/tutorial/tour_linalg.html?highlight=solve_right ) like in Matlab.
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17.

Sorry to take so long! I'll edit and post this right very soon!

the problem is i cannot edit any pages anymore [...] You get the admin to look at this?

Are you still stuck? Whenever you have a technical problem with the wiki or this forum, you're supposed to post something in the Technical category, so Andrew Stacey will see it. He's the 'admin'.

Comment Source:Sorry to take so long! I'll edit and post this right very soon! > the problem is i cannot edit any pages anymore [...] You get the admin to look at this? Are you still stuck? Whenever you have a technical problem with the wiki or this forum, you're supposed to post something in the [Technical](http://forum.azimuthproject.org/9/) category, so Andrew Stacey will see it. He's the 'admin'.
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18.

No I am not anymore (just in case you didn't read the other thread)

Comment Source:No I am not anymore (just in case you didn't read the other thread)
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19.

Okay, good. I should really edit and post your article... sorry, I get distracted.

Comment Source:Okay, good. I should really edit and post your article... sorry, I get distracted.
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20.
edited May 2012

Staffan - here are some comments on Blog - carbon cycle box models (part 1). To save time I've made changes when we might want them. But, you might not want to make these changes. So, feel free to undo these changes.

1. for πξ. This is mysterious and confusing so I will delete it; if you want to thank someone it's better to thank them near the end and in a less cryptic way.

2. this innovative cycle - do you mean the carbon cycle? Is this a joke, calling it "innovative"? Our readers may be sort of confused by what's going on here. I'll change this to "the carbon cycle".

3. our proposal - what proposal? Is this just a joke, again? Remember, our readers don't know you so they won't be able to tell if this is a joke or a reference to something they don't know about.

4. [[carbon cycle]] - remember, the blog is not the wiki so links using [[ ]] will not work. They need to be changed to HTML links. I'll do this now... but in the future, maybe you can do it.

5. invented stem-cell usage to grow the new outer layer - I don't know what "invented stem-cell usage" means. Do you mean the trees invented stem cells? Or that they started using stem cells to grow a new outer layer? What outer layer is this? The cambium?

I've also made lots and lots of changes to make the English sound more like that of a native.

Comment Source:Staffan - here are some comments on [[Blog - carbon cycle box models (part 1)]]. To save time I've made changes when we _might_ want them. But, you might not want to make these changes. So, feel free to undo these changes. 1. for πξ. This is mysterious and confusing so I will delete it; if you want to thank someone it's better to thank them near the end and in a less cryptic way. 2. this innovative cycle - do you mean the carbon cycle? Is this a joke, calling it "innovative"? Our readers may be sort of confused by what's going on here. I'll change this to "the carbon cycle". 3. our proposal - what proposal? Is this just a joke, again? Remember, our readers don't know you so they won't be able to tell if this is a joke or a reference to something they don't know about. 4. [[carbon cycle]] - remember, the blog is not the wiki so links using [[ ]] will not work. They need to be changed to HTML links. I'll do this now... but in the future, maybe you can do it. 5. invented stem-cell usage to grow the new outer layer - I don't know what "invented stem-cell usage" means. Do you mean the trees invented stem cells? Or that they started using stem cells to grow a new outer layer? What outer layer is this? The cambium? I've also made lots and lots of changes to make the English sound more like that of a native.
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21.

Ugh, I lost all the changes I made, somehow.

Comment Source:Ugh, I lost all the changes I made, somehow.
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22.
edited May 2012

I've made a bunch of changes again, but not all. I decided the whole 'venture capitalist' story is more confusing than helpful, so I removed that... but someone else here may disagree.

One question I have is about the end. You say

I get results that correspond to this diagram

but you don't say what 'correspond' means. Are you getting the exact same results? Probably not.

Comment Source:I've made a bunch of changes again, but not all. I decided the whole 'venture capitalist' story is more confusing than helpful, so I removed that... but someone else here may disagree. One question I have is about the end. You say > I get results that correspond to this diagram but you don't say what 'correspond' means. Are you getting the exact same results? Probably not.
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23.
edited May 2012

i was on the verge to remove the whole venture cap pitch as i felt i was loosing opportunity to write more on the carbon cycle and i also thought it was a draft idea that sounded good but a tad silly which one can sense in my language. So keep your changes and also remove $\pi\chi ! (it is spanish for pidgeon chick and is a nick name i have for my wife) your 2-5 was using words from the venture capital investment pitch - on selling the idea of gaining knowledge onthe carbon cycle, so that is usual words and sentences for them. I'll read the whole thing and then answer your question on 'correspond'. Comment Source:i was on the verge to remove the whole venture cap pitch as i felt i was loosing opportunity to write more on the carbon cycle and i also thought it was a draft idea that sounded good but a tad silly which one can sense in my language. So keep your changes and also remove$\pi\chi ! (it is spanish for pidgeon chick and is a nick name i have for my wife) your 2-5 was using words from the venture capital investment pitch - on selling the idea of gaining knowledge onthe carbon cycle, so that is usual words and sentences for them. I'll read the whole thing and then answer your question on 'correspond'.
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24.

I rewrote the latter part. See if it makes sense now John.

Comment Source:I rewrote the latter part. See if it makes sense now John.
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25.

Okay, I'll reread it and maybe make some more changes. I'll explain them and see if you like them.

I'm very embarrassed at how long it's taken me to do this... I hope we can finish part 2, on the actual box models, more quickly!

Comment Source:Okay, I'll reread it and maybe make some more changes. I'll explain them and see if you like them. I'm very embarrassed at how long it's taken me to do this... I hope we can finish part 2, on the actual box models, more quickly!
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26.
edited May 2012

I made some changes, which are barely worth explaining... you can click See changes at the bottom of the page to see what I did. But I think this blog entry would be more interesting if we included more material from your page Experiments with carbon cycle box model. Do you mind if I copy some of this material into this blog entry, and polish it up into more of a story? There's good stuff here!

invented stem-cell usage to grow the new outer layer - I don't know what "invented stem-cell usage" means. Do you mean the trees invented stem cells? Or that they started using stem cells to grow a new outer layer? What outer layer is this - the cambium?

I would like to change this to make it easier to understand. If you answer the 3 questions I asked, I could do this.

Comment Source:I made some changes, which are barely worth explaining... you can click *See changes* at the bottom of the page to see what I did. But I think this blog entry would be more interesting if we included more material from your page [[Experiments with carbon cycle box model]]. Do you mind if I copy some of this material into this blog entry, and polish it up into more of a story? There's good stuff here! By the way, about this: > invented stem-cell usage to grow the new outer layer - I don't know what "invented stem-cell usage" means. Do you mean the trees invented stem cells? Or that they started using stem cells to grow a new outer layer? What outer layer is this - the cambium? I would like to change this to make it easier to understand. If you answer the 3 questions I asked, I could do this.
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27.

I'm eager to work on this blog article now...

Comment Source:I'm eager to work on this blog article now...
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28.

invented stem-cell usage to grow the new outer layer - I don't know what "invented stem-cell usage" > means. Do you mean the trees invented stem cells? Or that they started using stem cells to grow a new outer layer? What outer layer is this - the cambium?

Yes me too ! The latter it was mentioned in the Colin Tudge book but I left that in argentina for a friend. but let me double check.

Sorry but i am off a bit more right now but anyway I will be on Azimuth now when we work and publish this.

Comment Source:> invented stem-cell usage to grow the new outer layer - I don't know what "invented stem-cell usage" > means. Do you mean the trees invented stem cells? Or that they started using stem cells to grow a > new outer layer? What outer layer is this - the cambium? Yes me too ! The latter it was mentioned in the Colin Tudge book but I left that in argentina for a friend. but let me double check. Sorry but i am off a bit more right now but anyway I will be on Azimuth now when we work and publish this.
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29.
edited May 2012

Okay. I'm mainly waiting for you to say "Okay, John - add stuff from the page I wrote." I'll be glad to do that.

Or, if you prefer, you could say "Don't add stuff from that page! That should be a separate blog post!"

Comment Source:Okay. I'm mainly waiting for you to say "Okay, John - add stuff from the [page I wrote](http://www.azimuthproject.org/azimuth/show/Experiments%20with%20carbon%20cycle%20box%20model)." I'll be glad to do that. Or, if you prefer, you could say "Don't add stuff from that page! That should be a separate blog post!"
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30.

Okay John - add stuff from the page i wrote :-)

Comment Source:Okay John - add stuff from the page i wrote :-)
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31.

I have found a short and very readable introduction to the carbon cycle:

• David Archer: The Global Carbon Cycle (Princeton Primers in Climate), Princeton University Press, 1st edition, 2010

and added it to the carbon cycle Wiki page as a reference. I'll try go and read it soon, then maybe I'll be able to offer some constructive criticism :-)

Comment Source:I have found a short and very readable introduction to the carbon cycle: * David Archer: _The Global Carbon Cycle (Princeton Primers in Climate)_, Princeton University Press, 1st edition, 2010 and added it to the [[carbon cycle]] Wiki page as a reference. I'll try go and read it soon, then maybe I'll be able to offer some constructive criticism :-)
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32.

All of the Princeton Primers in Climate books (that I've seen) are good introductions.

Comment Source:All of the Princeton Primers in Climate books (that I've seen) are good introductions.
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33.

I also have

and

• Shawn J. Marshall: "The Cryosphere" which already was on Cryosphere.
Comment Source:I also have * Climate and the Oceans (added to [[Oceanography]]) and * Shawn J. Marshall: "The Cryosphere" which already was on [[Cryosphere]].
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34.

I used the Global Carbon cycle by Archer a lot when i was doing the experiments and writing the blog. They are good. For the ocean I used Broecker "The great ocean conveyor" and some articles by Sarmiento.

Comment Source:I used the Global Carbon cycle by Archer a lot when i was doing the experiments and writing the blog. They are good. For the ocean I used Broecker "The great ocean conveyor" and some articles by Sarmiento.
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35.

Okay, I will add stuff from the page Staffan wrote. Sorry this is going so absurdly slow - all my fault.

Comment Source:Okay, I will add stuff from the page Staffan wrote. Sorry this is going so absurdly slow - all my fault.
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36.

its ok for me I am also slow with the 2nd part of "the carbon cycle in a box". I have done a lot of thinking on what I want to contribute next. See the thread Staffand todo when I create it.

Comment Source:its ok for me I am also slow with the 2nd part of "the carbon cycle in a box". I have done a lot of thinking on what I want to contribute next. See the thread Staffand todo when I create it.
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37.

btw I will write the second blog post on the ocean only and try to add some other pages, while doing that. Yes John I will cross-announce this in the correct thread .

Comment Source:btw I will write the second blog post on the ocean only and try to add some other pages, while doing that. Yes John I will cross-announce this in the correct thread .
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38.

I'm glad it's okay with you that I'm going so slow, Staffan. I feel extremely guilty... there always seems to be something else I need to do first. My goal for this week is to

1) polish Blog - carbon cycle box models (part 1) and put it on the blog

and

2) finish Blog - network theory (part 19) and put it on the blog.

You see, Jacob Biamonte is visiting Singapore now, and we're turning the 'network theory' posts into a book, which means I need to write a few more posts in that series, just to finish it up.

In the next 3.5 hours I'll try to do number 2. I need to become more disciplined...

Comment Source:I'm glad it's okay with you that I'm going so slow, Staffan. I feel _extremely_ guilty... there always seems to be something else I need to do first. My goal for this week is to 1) polish [[Blog - carbon cycle box models (part 1)]] and put it on the blog and 2) finish [[Blog - network theory (part 19)]] and put it on the blog. You see, [[Jacob Biamonte]] is visiting Singapore now, and we're turning the 'network theory' posts into a book, which means I need to write a few more posts in that series, just to finish it up. In the next 3.5 hours I'll try to do number 2. I need to become more disciplined...
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39.
edited July 2012

Hi, Staffan!

I'm finally putting your article on the blog... I somehow seem to have lost the desire to add extra stuff to it... and I note it ends:

Next time I will do a survey of the results from the 2-box land and atmosphere models and also the importance to understand and manage non-linearity in the models of the carbon cycle.

But recently you wrote:

I will write about the ocean part of the carbon cycle [...]

So, should I change or eliminate the sentence where you promise to do a survey of results from 2-box land and atmosphere models, etc?

Also, how certain are you that you'll write Part 2? If you're not certain, I can call this first article 'Carbon Cycle Box Models' without labelling it 'Part 1'. Does that seem like a good idea, or a bad idea? I can always add the phrase 'Part 1' later.

Apart from these small issues, the blog article will be ready in half an hour! I'll wait for your answers to these 2 questions before I post it.

Comment Source:Hi, Staffan! I'm finally putting your article on the blog... I somehow seem to have lost the desire to add extra stuff to it... and I note it ends: > Next time I will do a survey of the results from the 2-box land and atmosphere models and also the importance to understand and manage non-linearity in the models of the carbon cycle. But recently you wrote: > I will write about the ocean part of the carbon cycle [...] **So, should I change or eliminate the sentence where you promise to do a survey of results from 2-box land and atmosphere models, etc?** Also, how certain are you that you'll write Part 2? If you're not certain, I can call this first article 'Carbon Cycle Box Models' without labelling it 'Part 1'. **Does that seem like a good idea, or a bad idea?** I can always add the phrase 'Part 1' later. Apart from these small issues, the blog article will be ready in half an hour! I'll wait for your answers to these 2 questions before I post it.
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40.

Yes chargé it to ocean john

Comment Source:Yes chargé it to ocean john
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41.

I want to do a 2nd part but it'll take time as you'd seen already, but maybe its better to announce it later as you propose.

So, should I change or eliminate the sentence where you promise to do a survey of results from 2-box land and atmosphere models, etc? refer to experiments with ocean box models instead yes and

referto my page Experiments with ocean carbon box model.

Comment Source:I want to do a 2nd part but it'll take time as you'd seen already, but maybe its better to announce it later as you propose. > So, should I change or eliminate the sentence where you promise to do a survey of results from 2-box land and atmosphere models, etc? refer to experiments with ocean box models instead yes and referto my page [[Experiments with ocean carbon box model]].
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42.

Okay, I posted it!

Congratulations, and thanks for writing it!!!

Comment Source:Okay, I posted it! * Staffan Liljgeren, [Carbon Cycle Box Model](http://johncarlosbaez.wordpress.com/2012/07/24/carbon-cycle-box-models/), _Azimuth_, 24 July 2011. <img src = "http://math.ucr.edu/home/baez/champagne.jpg" alt = ""/> Congratulations, and thanks for writing it!!!
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43.
edited July 2012

Wonderful bad i had too be on holiday still. but i'll check and try to answer ! Thx John for all Your effort ! You just gave me momentum to write blog two.

Good collaboration btw!

Comment Source:Wonderful bad i had too be on holiday still. but i'll check and try to answer ! Thx John for all Your effort ! You just gave me momentum to write blog two. Good collaboration btw!