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Forthcoming blog articles

edited January 2016

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.

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!

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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.

Comment Source: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.
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edited January 2016

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 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!

Comment Source: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! 
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edited January 2016

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!

Comment Source: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. 
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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!

Comment Source: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! 
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edited January 2016

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 B 31 (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.

Comment Source: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: &bull; 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. &bull; 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. &bull; Dilip Kondepudi and Ilya Prigogine, _Modern Thermodynamics: From Heat Engines to Dissipative Structures_, especially Chapter 18: Nonlinear Thermodynamics, Wiley, Chichester, 1998. &bull; Hong Qian, Open-system nonequilibrium steady state: statistical thermodynamics, fluctuations, and chemical oscillations, _The Journal of Physical Chemistry B_ **31** (2006), 15063-15074. &bull; 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. &bull; 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. 
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edited January 2016

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!

Comment Source: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!
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edited January 2016

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.

Comment Source: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.