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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?

 

A Comment on the Academica Wordpress Theme

2 min read

In reply to: https://wordpress.org/support/topic/surprised-by-all-the-bad-reviews

I agree wholeheartedly with Adam, though I don't think I'd really seen any small issues except perhaps for an odd CSS issue in formatting an h2 tag somewhere. (Note: This comment applies to v1.2.3 of Academica as on 4/2/15, the theme publisher made a DRASTIC change to the theme, so take caution in upgrading!!)

I have created a child-theme with one or two small customizations (slightly larger headings in side widgets and some color/text size changes), but otherwise have v1.2.3 working as perfectly as it was intended to. This includes the slideshow functionality on the homepage. See BoffoSocko as an example.

For those, perhaps including Adam, wanting to get the slider to work properly:

  • Go to your WP Dashboard hover on the menu tab "appearance" and click on "customize"
  • On the "Featured Content" tab, enter a tag you want to use to feature content on the homepage of your site. (In my case, I chose "featured" and also clicked "Hide tag from displaying in post meta and tag clouds".)
  • Go to one or more posts (I think it works on up to 10 featurable posts) and tag them with the word you just used in the featured content setting (in my case "featured"
  • Next be sure to actually set a "Featured photo" for the post--930x300 pixels is the optimal photo size if I recall.
  • Now when you visit your home page, the slider should work properly and include arrows to scroll through them (these aren't as obvious on featured photos with white backgrounds).
  • Note that on individual pages, you'll still have static header image(s) which are also customizable in the "customize" section of the WP dashboard, which was mentioned in step 1.

I hope this helps.

 

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.

 

Upgrading @WithKnown on One's Own Server

3 min read

It's only been a short time since I installed my own copy of WithKnown (GitHub) and there have been a few small upgrades since that time, but I was overdue for upgrading. I'd also seen one or two errors when posting, and figured that the small bugs I was seeing would have been worked out.

When I went to upgrade earlier in the week, I figured I'd wing it since at the time there weren't any instructions for upgrading in the documentation (or at least that I'd noticed at the time.)  Somehow I got sidetracked and finally just came back to it today.  Following the general procedure for upgrading projects like Drupal and WordPress, I trundled along and found generally reasonable results until I realized that URLs weren't mapping quite properly, photos were missing, and something was a bit "off". (I had tried reinstalling my original config.ini file along with the Uploads file, but that didn't seem to work somehow.)

I went back to check the documentation, and lo-and-behold, in the intervening week,  there are now some scant upgrade instructions available which follow below: 

Upgrading Known is designed to be very simple.

  • Take a backup of your Known directory and database.
  • Overwrite your Known files except your upload directory.
  • Access your Known site homepage.

I was reticent upon visiting my homepage as I received a splash screen exactly like the original set up, and was very worried that I might manage to blow out some of the primary data and crash the whole thing. (I did remember to do a back up before starting, but who wants to deal with that if they don't have to.)

I decided to plunge ahead and proceeded like I was setting things up for the first time. I was directed to a page to enter in the database name, login, password, etc., which creates a config.ini file in the root, and was then redirected to my site, with all the links and data perfectly intact and functioning properly. 

For those who haven't done it themselves, and have the same reticence I did, I'd recommend adding a few additional steps to the process:

4. Click on the set up button

5. Enter in your database name, user name, host name and password

6. Update the path for the "Uploads" folder. (It may automatically default to the proper path name, but double check it.)

7. Hit enter and you'll be taken to your site.

Depending on what one is using for the update, I might also recommend blowing out (deleting) the original Known files in your root directory in step 2, and installing the new ones rather than simple overwriting so one isn't left with out of date files.

 

David, Congrats on officially putting your plugins up on Wordpress!

My WP skills are certainly below that of yours, but I applaud you for making the effort on behalf of the IndieWeb. I'm happy to help test/bang on your plugins and give feedback, (and If I can to delve through the code to help there too occasionally).

One thing I notice about post kinds in the 1.3.0 version is that the number of post kinds is much smaller compared to the circa 1.2.X releases. Did you deprecate them? temporarily? while you work out issues on each?

On syndication links I notice that the resultant icons (on your site as well as mine) shift over a few pixels when hovering over them - is this by design or a quirk in my (our) CSS perhaps?

Congratulations again and keep up the good work!

 

At the most basic level [book:Getting What You Came For: The Smart Student's Guide to Earning an M.A. or a Ph.D.|460669] has some relatively sound advice. If you need something entertaining my friend Adam Ruben's book [book:Surviving Your Stupid, Stupid Decision to Go to Grad School|7769479] is pretty good.

For some of the other topics you mention, start reading The Chronicle of Higher Education. Most of it is available online without a subscription, but they've got lots of current faculty writing regularly on the topics you mentioned.

Slowly you'll find a community of online professors like Robert Talbert (http://chronicle.com/blognetwork/castingoutnines/) or blogs like http://mathwithbaddrawings.com/ that can be very helpful. Then there's even folks like https://terrytao.wordpress.com/ as well.

On twitter, you might consider following some the people on this list to start: https://twitter.com/ChrisAldrich/lists/mathematicians/members
Within twitter, there are a handful of hashtags you might following/comment along with including: , , and likely a handful of others.

On the practical side, consider creating accounts on mendeley.com, academica.com, researchgate.com, etc. as a way to find people, help, material, etc. You might also consider starting yourself a blog (aka Commonplace book) to collect all your thoughts: http://stream.withknown.com/2015/why-you-should-start-a-website-as-a-college-student (Keep in mind that some platforms like WordPress allow you to keep things as "drafts" without publishing them, so they're then available everywhere you might need them.)

Finally, for graduate level math, I highly recommend spending the $100-200 for a Livescribe Pulse pen: http://www.livescribe.com.

Feel free to ping me here or via other means (http://boffosocko.com) for help/questions.

 

Perhaps it's one of the other IndieWeb modules not working properly, but I'm using Indieweb Post Kinds in a relatively out-of-the box WP setting. I find that when filling out the data for URL, Name, Author Name, Author Photo, Content/Excerpt fields, that after saving, the URL field didn't actually save any data to the database (or at least it doesn't show up when going back to edit the post). Additionally, the post itself shows the text "In Reply To" but doesn't actually display a link for which the post is actually in reply to as I would expect. Naturally the last part may be a result of the URL field being blank when going back to it after saving.

As a separate semantic issue, all of the post kinds seem to show the appropriate icon at the top of the post, and are then followed by the appropriate title "Article", "Favorite", "Liked", etc., however, if one accidentally marks a post-type and saves/publishes and then later comes back to change the mistake, the icon changes appropriately, but the following tag title stays the same as the original one that was saved and doesn't change to the updated post kind title.

https://wordpress.org/plugins/indieweb-post-kinds/