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Relative Entropy in Biological Systems by John Baez and Blake Pollard https://johncarlosbaez.wordpress.com/2015/11/27/relative-entropy-in-biological-systems/

 
 

My WordPress install just started porting in replies to replies on Facebook! @schnarfed, https://www.brid.gy/ & https://wordpress.org/plugins/indieweb/

 

@diane1859 You might add a twitter follow button to your blog, so you're easier to find: https://en.support.wordpress.com/twitter/twitter-follow-button/

 

I like what you've done with the final product and have always thought about doing something similar myself, particularly after I saw what Martin Fenner (https://plus.google.com/106537123721037364937/posts) did with his site at http://blog.martinfenner.org/ which actually allows others to make changes to it via github. Naturally, I'm also highly interested in his take on scholarly communication too, which makes me want to delve in there even more.

Another thing I've been playing around with lately has been some tools/toys at http://indiewebcamp.com primarily within WordPress (I noticed you had one at http://teaching.proftalbert.com/, so you're at least somewhat familiar) though also a bit with http://withknown.com which is a platform built specifically with education in mind (https://withknown.com/education/).

A large part of their philosophy is to own one's own data and then syndicate it out to other social media/external site, but some of their infrastructure allows one to easily make posts on one's own page which then act as replies on another's site. This is particularly interesting from the viewpoint of teaching wherein students and professors can interact with each other, but still have/own all of their individual work. (Incidentally, it also makes for using one's own site as a commonplace book of sorts, which I often find valuable.)

As an exmple, you'll notice on the post on my blog http://boffosocko.com/2015/05/21/category-theory-anyone/ got automatically syndicated to Google+ the other day. Then you replied to it within Google+ but my site sucked your comment back into the comments section on my original blog post, thereby keeping the conversation on my site and not only just on Google's.

 

I've been doing something similar myself, particularly given the number of social media outlets to which one can publish. To solve part of the problem, I've been attempting to utilize the tenets of the Indie Web (http://indiewebcamp.com/) as well as several of their projects including WordPress and WithKnown. Perhaps some of the material you'll find there will help you to hone what you're trying to accomplish in your "project." One of my favorite portions is being able to publish everything in one place and then syndicate it everywhere else that makes sense as well as to give it the broadest reach. Having a handful of sources like Twitter and Facebook feed back into the comments is pretty nice as well. I've written a tad about it at http://www.boffosocko.com as well. Perhaps you might keep your WordPress blog as a primary hub and then cross-post the appropriate material here to take advantage of your audience?

 

Replied to a post on 1-m.cc :

Just noticed via @benborges_ that @dshanske has a semantic markup plugin for @WordPress under way! https://github.com/dshanske/wp-semantics

 

First, let's unpack your question a bit. What we're really doing is taking mathematical form, function, and theory and apply it in some sort of unifying manner to unify the areas of information theory and statistical thermodynamics.

You can also ask your question in the reverse direction to apply the mathematics of information to thermodynamics as well as there should be a mathematical duality of sorts, if in fact the two are directly related.

First, let's unpack your question a bit. What we're really doing is taking mathematical form, function, and theory and apply it in some sort of unifying manner to unify the areas of information theory and statistical mechanics and thermodynamics.

You can also ask your question in the reverse direction to apply the mathematics of information to thermodynamics as well as there should be a mathematical duality of sorts, if in fact the two are directly related.

The original link between the two areas stems from a paper by E.T. Jaynes entitled "Information Theory and Statistical Mechanics" (downloadable from http://bayes.wustl.edu/etj/articles/theory.1.pdf). Since then there has been a lot of uninformed back and forth in the literature from agreement to flat out denial, primarily as a result of the multitude of areas from which a researcher can approach the topics and rarely are many/any experts in more than one of these areas. (I specifically recall an article in 2011-2012 in the esteemed journal Science from a senior researcher in information theory that flatly stated there was no link between the two fields!)

Since then, in my opinion, the best source tying the fields together mathematically is A Farewell To Entropy: Statistical Thermodynamics Based on Information by Arieh Ben-Naim [http://www.amazon.com/gp/product/9812707077/ref=as_li_tl?ie=UTF8&camp=1789&creative=390957&creativeASIN=9812707077&linkCode=as2&tag=itbio-20&linkId=WDUVNEIJG5BIO242]. In it he closely and coherently ties the two fields directly together and does a reasonable job of pointing out problems with some of the more popular misconceptions and conflicts in the literature. (For those without the physics, engineering, or math backgrounds in these subjects, I can also highly recommend Arieh Ben-Naim's forthcoming book Information, Entropy, Life and the Universe: What We Know and What We Do Not Know [http://www.amazon.com/gp/product/9814651672/ref=as_li_tl?ie=UTF8&camp=1789&creative=390957&creativeASIN=9814651672&linkCode=as2&tag=itbio-20&linkId=WKTUT4I7WDIYS5MG] which is due out at the end of May.)

As for other connections, I've not seen anything as direct, primarily as there aren't any other major concepts with the exact same name. However, because of the underlying mathematics, I strongly suspect that there are many similar 'concepts'. A few in particular, I have a feeling will come out of the more rigorous mathematical frameworks based on Lieb and Yngvason’s concptualization of thermodynamics (see Resource Convertibility (Part 1)[https://johncarlosbaez.wordpress.com/2015/04/07/resource-convertibility-part-1/] and The Entropy Principle: Thermodynamics for the Unsatisfied: Andre Thess [http://www.amazon.com/gp/product/3642133487/ref=as_li_tl?ie=UTF8&camp=1789&creative=390957&creativeASIN=3642133487&linkCode=as2&tag=itbio-20&linkId=3XLV4PT33UDZ2XLW].) Given the power of the mathematics and the more abstract nature of information theory, I suspect that thermodynamics and statistical mechanics will eventually be viewed as a sub-area or application of information theory.

Another fruitful area of conceptual similarities is slowly grown out of quantum information theory and the statistical mechanics of black holes, though there is some heavily rarified air surrounding these given the required background needed to operate with them both simultaneously.

 

Some brief thoughts for a scientific link blog for @wbialek
If you're going to invest the time to collect interesting papers for yourself, a group, or even for the broader public, take a few minutes to think about how to not only most easily collect, but to curate them, make them searchable, and thus make them useful in a longer and broader context.

Depending on your needs and interests, I'd recommend building a link blog on a free broad platform like Wordpress that will let you save the title of the article, the URL, a short synopsis, and then tag it with metadata (categories like physics, chemistry, biology, math, etc. or sub-specific tags like information theory, statistical thermodynamics, etc.), and then broadcast it to various social media sites like Twitter, Google+, and others.

Other options with similar functionality to consider are:
WithKnown https://withknown.com/
example: http://stream.boffosocko.com/
Radio3: http://radio3.io/
example:http://radio3.io/users/ChrisAldrich/
Mendeley: https://www.mendeley.com/groups/2545131/itbio-information-theory-microbiology-evolution-and-complexity/

Given the value I think I'd personally get out of you doing something like this, I'm happy to volunteer some time to build, set up, and simplify the process for you. I'm pretty sure that with a minimum of work, you could have a simple bookmarklet on your webbrowser that would easily allow you to "clip" the article you want, add any quick bits of metadata or tags, and then automatically publish it to one or more of your social media sites automatically, keeping the work to doing it well under a minute while allowing you to easily come back and search, sort, and filter later if you choose.

 

Dan, since you're primarily on WordPress, if you weren't already, you might like to be aware that most of the principles behind WithKnown stem from the indieweb movement. You can find some information specific to WordPress at https://indiewebcamp.com/Getting_Started_on_WordPress.

Most of the field of plugins specific to WordPress can be found by installing the base plugin https://wordpress.org/plugins/indieweb/installation/ which will give you a simple interface for installing the others you'll need to plug in to get functionality similar to WithKnown. Perhaps this might give you the best of both worlds?

 

I'm impressed that @cstanhope has an .html-only site: http://charles.stanho.pe/

I'll offer help to get him set up with WordPress if he wants something a bit more dynamic: http://indiewebcamp.com/Getting_Started_on_WordPress

 

Thanks for the great plugin.

One small semantic issue involving menu placement of "SI Capture Options" that's not really a bug and doesn't affect performance:

I notice that the menu option is placed under the "Plugins" menu heading in the WordPress dashboard while the majority of plugins would put this menu item under the "Settings" menu instead.

Changing it may help in terms of overall UI understanding - particularly for newer users.