Home › Azimuth Project › › Azimuth Blog

It looks like you're new here. If you want to get involved, click one of these buttons!

- All Categories 2.4K
- Chat 505
- Study Groups 21
- Petri Nets 9
- Epidemiology 4
- Leaf Modeling 2
- Review Sections 9
- MIT 2020: Programming with Categories 51
- MIT 2020: Lectures 20
- MIT 2020: Exercises 25
- Baez ACT 2019: Online Course 339
- Baez ACT 2019: Lectures 79
- Baez ACT 2019: Exercises 149
- Baez ACT 2019: Chat 50
- UCR ACT Seminar 4
- General 75
- Azimuth Code Project 111
- Statistical methods 4
- Drafts 10
- Math Syntax Demos 15
- Wiki - Latest Changes 3
- Strategy 113
- Azimuth Project 1.1K
- - Spam 1
- News and Information 148
- Azimuth Blog 149
- - Conventions and Policies 21
- - Questions 43
- Azimuth Wiki 719

Options

Since I quit Google+ I've been trying to post more on *Azimuth*. It's had a good effect so far: a lot of smart people have reappeared, and are posting serious comments.

Here are the next scheduled posts. You can't actually see them until the dates listed.

Information geometry (part 15), 11 January 2016. Reviving a dormant series, I explain some of Blake Pollard's new paper Open Markov processes: A compositional perspective on non-equilibrium steady states in biology. Short version: they

*don't*obey the principle of minimum entropy production; they obey another minimum principle!Information geometry (part 16), 14 January 2016. Some more about Blake Pollard's new work and how it's related to Schnakenberg's work on entropy production.

Salar de Uyuni, 22 January 2016. This is about an interesting ecosystem in Bolivia. Mainly just for fun.

I would also like to post a followup to my article about the IEA underestimating renewables. They came out with a new report in August 2015, discussed here:

If any of you would like to take a look at their new report and tell me something interesting about it, that would be great!

## Comments

Many thanks for your thoughts, always stimulating! It would be of interest to see how you approach one of the canonical biochemical cycles and I recall the Citric Acid cycle is already in your sights. Maybe the urea/ornithine cycle (also discovered by Krebs) would be an 'easier' starting point?

Most if not all enzymatic reactions are stereospecific and I wonder if this needs be taken into account: not all products will be available from the reactions written as an exercise in stoichiometry - I need to think more about this.

Another network that has long interested me is the circadian network. The recent literature is extensive, but Clocks not winding down:unravelling circadian networks a Nature Mol. Biol. review by Zhang and Kay (2010) is a good entry point (paywalled - sigh!).

(Nature is infuriating in how they package the back corpus - 5 year tranches if memory serves me, unaffordable except to the wealthiest institutions). You know all this, but publishers are the scourge of the independent scholar.

`Many thanks for your thoughts, always stimulating! It would be of interest to see how you approach one of the canonical biochemical cycles and I recall the <a href="https://en.wikipedia.org/wiki/Citric_acid_cycle">Citric Acid cycle</a> is already in your sights. Maybe the <a href="https://en.wikipedia.org/wiki/Urea_cycle">urea/ornithine cycle</a> (also discovered by Krebs) would be an 'easier' starting point? Most if not all enzymatic reactions are stereospecific and I wonder if this needs be taken into account: not all products will be available from the reactions written as an exercise in stoichiometry - I need to think more about this. Another network that has long interested me is the circadian network. The recent literature is extensive, but <a href="http://www.nature.com/nrm/journal/v11/n11/full/nrm2995.html">Clocks not winding down:unravelling circadian networks</a> a Nature Mol. Biol. review by Zhang and Kay (2010) is a good entry point (paywalled - sigh!). (Nature is infuriating in how they package the back corpus - 5 year tranches if memory serves me, unaffordable except to the wealthiest institutions). You know all this, but publishers are the scourge of the independent scholar.`

Hi, Walter. A second article on glycolysis is coming up, and then I'd like to talk about the citric acid cycle. I don't know that other one. Maybe it's easier.

My real aim, ultimately, is to treat things at such a high level of abstraction that I don't focus on any details of particular molecules or chemical reactions. You can imagine, if you like, that I want to understand biochemistry not only on all possible planets, but in all possible universes.

This may sound strange, but there are some reasons for doing it. One is that I can never match biochemists for knowledge of specifics; I can only do something new by doing something different, and what I can do is hope that

someaspects of how life works involve quite abstract and general patterns thatjust happen to be implementedin certain specific ways in the life we see here on our planet.Of course I'm also fascinated by the gory specifics of what we happen to actually see.

My friend Tim Silverman, who usually tells me wonderful things about group theory (he's a programmer who has become an expert on finite simple groups), has written a really nice comment on the Azimuth blog, in which he describes glycolysis in a very nice conceptual way that still grapples with the chemical details. I like this middle ground. But I would need to know a

lotmore chemistry to understand things at this level!`Hi, Walter. A second article on glycolysis is coming up, and then I'd like to talk about the citric acid cycle. I don't know that other one. Maybe it's easier. My real aim, ultimately, is to treat things at such a high level of abstraction that I don't focus on any details of particular molecules or chemical reactions. You can imagine, if you like, that I want to understand biochemistry not only on all possible planets, but in all possible universes. This may sound strange, but there are some reasons for doing it. One is that I can never match biochemists for knowledge of specifics; I can only do something new by doing something different, and what I can do is hope that _some_ aspects of how life works involve quite abstract and general patterns that _just happen to be implemented_ in certain specific ways in the life we see here on our planet. Of course I'm also fascinated by the gory specifics of what we happen to actually see. My friend Tim Silverman, who usually tells me wonderful things about group theory (he's a programmer who has become an expert on finite simple groups), has written a [really nice comment](https://johncarlosbaez.wordpress.com/2016/01/08/glycolysis/#comment-76256) on the Azimuth blog, in which he describes glycolysis in a very nice conceptual way that still grapples with the chemical details. I like this middle ground. But I would need to know a _lot_ more chemistry to understand things at this level!`

Here are the forthcoming posts as of today. I keep juggling the schedules, so these predictions aren't extremely reliable, but the posts have already been written, so they'll definitely appear!

Glycolysis (part 2), 18 January 2016.

Salar de Uyuni, 22 January 2016. This is about an interesting ecosystem in Bolivia. Mainly just for fun.

Ken Caldeira on what to do, 26 January 2016. A huge quote from his new article about how we're in serious trouble, and a bit of analysis.

`Here are the forthcoming posts as of today. I keep juggling the schedules, so these predictions aren't extremely reliable, but the posts have already been written, so they'll definitely appear! * [Glycolysis (part 2)](https://johncarlosbaez.wordpress.com/2016/01/18/glycolysis-part-2), 18 January 2016. * [Salar de Uyuni](https://johncarlosbaez.wordpress.com/2016/01/22/salar-de-uyuni/), 22 January 2016. This is about an interesting ecosystem in Bolivia. Mainly just for fun. * [Ken Caldeira on what to do](https://johncarlosbaez.wordpress.com/2016/01/26/ken-caldeira-on-what-to-do/), 26 January 2016. A huge quote from his new article about how we're in serious trouble, and a bit of analysis.`

Since Lisa is in Sydney I've been blogging a lot, and instead of wasting (?) my time on G+, I've been building up a reserve of articles on Azimuth:

Salar de Uyuni, 22 January 2016. This is about an interesting ecosystem in Bolivia. Mainly just for fun.

Ken Caldeira on what to do, 25 January 2016. A huge quote from his new article about how we're in serious trouble, and a bit of analysis.

The internal model principle, 27 January 2016. Attempts to formalize an interesting principle: to do the best job of regulating some system, a control apparatus should include a model of that system.

Among the bone eaters, 30 January 2016. Life among the hyenas of Ethiopia. Mainly just for fun, but also some material on network theory!

`Since Lisa is in Sydney I've been blogging a lot, and instead of wasting (?) my time on G+, I've been building up a reserve of articles on Azimuth: * [Salar de Uyuni](https://johncarlosbaez.wordpress.com/2016/01/22/salar-de-uyuni/), 22 January 2016. This is about an interesting ecosystem in Bolivia. Mainly just for fun. * [Ken Caldeira on what to do](https://johncarlosbaez.wordpress.com/2016/01/25/ken-caldeira-on-what-to-do/), 25 January 2016. A huge quote from his new article about how we're in serious trouble, and a bit of analysis. * [The internal model principle](https://johncarlosbaez.wordpress.com/2016/01/27/the-internal-model-principle/), 27 January 2016. Attempts to formalize an interesting principle: to do the best job of regulating some system, a control apparatus should include a model of that system. * [Among the bone eaters](https://johncarlosbaez.wordpress.com/2016/01/30/among-the-bone-eaters/), 30 January 2016. Life among the hyenas of Ethiopia. Mainly just for fun, but also some material on network theory!`

Some of the posts I throw together are "just for fun", since it's a relaxing hobby. But I want to write some more serious posts where I summarize work on open chemical reaction networks, and especially nonequilibrium steady states of these. Blake and I are starting to write a paper on this topic.

Here are the main things I want to talk about:

• A. S. Perelson, Network thermodyamics: an overview,

Biophys J.15(1975), 667–685.• J. Schnakenberg, Network theory of microscopic and macroscopic behavior of master equation systems,

Rev. Mod. Phys.48(1976), 571-585.• Dilip Kondepudi and Ilya Prigogine,

Modern Thermodynamics: From Heat Engines to Dissipative Structures, especially Chapter 18: Nonlinear Thermodynamics, Wiley, Chichester, 1998.• Hong Qian, Open-system nonequilibrium steady state: statistical thermodynamics, fluctuations, and chemical oscillations,

The Journal of Physical Chemistry B31(2006), 15063-15074.• Matteo Polettini,

Geometric and Combinatorial Aspects of Non-Equilibrium Statistical Mechanics, Ph.D. Thesis, University of Bologna, 2012.• Matteo Polettini and Massimiliano Esposito, Irreversible thermodynamics of open chemical networks I: Emergent cycles and broken conservation laws,

J. Chem. Phys.141(2014), 024117.`Some of the posts I throw together are "just for fun", since it's a relaxing hobby. But I want to write some more serious posts where I summarize work on open chemical reaction networks, and especially nonequilibrium steady states of these. Blake and I are starting to write a paper on this topic. Here are the main things I want to talk about: • A. S. Perelson, [Network thermodyamics: an overview](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1334728/pdf/biophysj00315-0040.pdf), _Biophys J._ **15** (1975), 667–685. • J. Schnakenberg, [Network theory of microscopic and macroscopic behavior of master equation systems](http://www2.hawaii.edu/~sstill/schnakenberg1976.pdf), _Rev. Mod. Phys._ **48** (1976), 571-585. • Dilip Kondepudi and Ilya Prigogine, _Modern Thermodynamics: From Heat Engines to Dissipative Structures_, especially Chapter 18: Nonlinear Thermodynamics, Wiley, Chichester, 1998. • Hong Qian, Open-system nonequilibrium steady state: statistical thermodynamics, fluctuations, and chemical oscillations, _The Journal of Physical Chemistry B_ **31** (2006), 15063-15074. • Matteo Polettini, _[Geometric and Combinatorial Aspects of Non-Equilibrium Statistical Mechanics](http://amsdottorato.unibo.it/4305/1/polettini_matteo_tesi.pdf)_, Ph.D. Thesis, University of Bologna, 2012. • Matteo Polettini and Massimiliano Esposito, [Irreversible thermodynamics of open chemical networks I: Emergent cycles and broken conservation laws](http://arxiv.org/abs/1404.1181), _J. Chem. Phys._ **141** (2014), 024117.`

I wrote another 'fun' one blog article:

I just discovered a former student of mine, S. Jay Olson, has written some serious papers analyzing the effects of rapidly expanding cosmic civilizations!

`I wrote another 'fun' one blog article: * [Aggressively expanding civilizations](https://johncarlosbaez.wordpress.com/2016/02/01/aggressively-expanding-civilizations/), 1 February 2016. I just discovered a former student of mine, S. Jay Olson, has written some serious papers analyzing the effects of rapidly expanding cosmic civilizations!`

Here's the new schedule of blog articles. Two of my students recently came out with a paper on network theory, so I want to release a blog article about that on Monday:

Among the bone eaters, 30 January 2016. Life among the hyenas of Ethiopia. Mainly just for fun, but also some material on network theory!

Corelations in network theory, 1 February 2016. Brandon Coya and Brendan Fong's new paper.

Aggressively expanding civilizations, 5 February 2016. Jay Olson's paper on what would happen when some civilizations start expanding at relativistic speeds by converting lots of matter into radiation.

`Here's the new schedule of blog articles. Two of my students recently came out with a paper on network theory, so I want to release a blog article about that on Monday: * [Among the bone eaters](https://johncarlosbaez.wordpress.com/2016/01/30/among-the-bone-eaters/), 30 January 2016. Life among the hyenas of Ethiopia. Mainly just for fun, but also some material on network theory! * [Corelations in network theory]( https://johncarlosbaez.wordpress.com/2016/02/01/corelations-in-network-theory/), 1 February 2016. Brandon Coya and Brendan Fong's new paper. * [Aggressively expanding civilizations](https://johncarlosbaez.wordpress.com/2016/02/05/aggressively-expanding-civilizations/), 5 February 2016. Jay Olson's paper on what would happen when some civilizations start expanding at relativistic speeds by converting lots of matter into radiation.`