I'm a biomedical and electrical engineer with interests in information theory, complexity, evolution, genetics, signal processing, IndieWeb, theoretical mathematics, and big history.
I'm also a talent manager-producer-publisher in the entertainment industry with expertise in representation, distribution, finance, production, content delivery, and new media.
I rarely, if ever, reblog anything here, but this particular post from John Baez’s blog Azimuth is so on-topic, that attempting to embellish it seems silly.
Entropy and Information in Biological Systems (Part 2)
John Harte, Marc Harper and I are running a workshop! Now you can apply here to attend:
Click the link, read the stuff and scroll down to “CLICK HERE” to apply. The deadline is 12 November 2014.
Financial support for travel, meals, and lodging is available for workshop attendees who need it. We will choose among the applicants and invite 10-15 of them.
The idea
Information theory and entropy methods are becoming powerful tools in biology, from the level of individual cells, to whole ecosystems, to experimental design, model-building, and the measurement of biodiversity. The aim of this investigative workshop is to synthesize different ways of applying these concepts to help systematize and unify work in biological systems. Early attempts at “grand syntheses” often misfired, but applications of information theory and entropy to specific highly focused topics in biology have been increasingly successful. In ecology, entropy maximization methods have proven successful in predicting the distribution and abundance of species. Entropy is also widely used as a measure of biodiversity. Work on the role of information in game theory has shed new light on evolution. As a population evolves, it can be seen as gaining information about its environment. The principle of maximum entropy production has emerged as a fascinating yet controversial approach to predicting the behavior of biological systems, from individual organisms to whole ecosystems. This investigative workshop will bring together top researchers from these diverse fields to share insights and methods and address some long-standing conceptual problems.
So, here are the goals of our workshop:
To study the validity of the principle of Maximum Entropy Production (MEP), which states that biological systems – and indeed all open, non-equilibrium systems – act to produce entropy at the maximum rate.
To familiarize all the participants with applications to ecology of the MaxEnt method: choosing the probabilistic hypothesis with the highest entropy subject to the constraints of our data. We will compare MaxEnt with competing approaches and examine whether MaxEnt provides a sufficient justification for the principle of MEP.
To clarify relations between known characterizations of entropy, the use of entropy as a measure of biodiversity, and the use of MaxEnt methods in ecology.
To develop the concept of evolutionary games as “learning” processes in which information is gained over time.
To study the interplay between information theory and the thermodynamics of individual cells and organelles.
If you’ve got colleagues who might be interested in this, please let them know. You can download a PDF suitable for printing and putting on a bulletin board by clicking on this:
I’ve been a proponent and user of a variety of mnemonic systems since I was about eleven years old. The two biggest and most useful in my mind are commonly known as the “method of loci” and the “major system.” The major system is also variously known as the phonetic number system, the phonetic mnemonic system, or Hergione’s mnemonic system after French mathematician and astronomer Pierre Hérigone (1580-1643) who is thought to have originated its use.
The major system generally works by converting numbers into consonant sounds and then from there into words by adding vowels under the overarching principle that images (of the words) can be remembered more easily than the numbers themselves. For instance, one could memorize one’s grocery list of a hundred items by associating each shopping item on a numbered list with the word associated with the individual number in the list. As an example, if item 22 on the list is lemons, one could translate the number 22 as “nun” within the major system and then associate or picture a nun with lemons – perhaps a nun in full habit taking a bath in lemons to make the image stick in one’s memory better. Then at the grocery store, when going down one’s list, when arriving at number 22 on the list, one automatically translates the number 22 to “nun” which will almost immediately conjure the image of a nun taking a bath in lemons which gives one the item on the list that needed to be remembered. This comes in handy particularly when one needs to be able to remember large lists of items in and out of order.
The following generalized chart, which can be found in a hoard of books and websites on the topic, is fairly canonical for the overall system:
Mnemonic for remembering the numeral and consonant relationship
0
/s/ /z/
s, z, soft c
“z” is the first letter of zero; the other letters have a similar sound
1
/t/ /d/
t, d
t & d have one downstroke and sound similar (some variant systems include “th”)
2
/n/
n
n has two downstrokes
3
/m/
m
m has three downstrokes; m looks like a “3” on its side
4
/r/
r
last letter of four; 4 and R are almost mirror images of each other
5
/l/
l
L is the Roman Numeral for 50
6
/ʃ/ /ʒ/ /tʃ/ /dʒ/
j, sh, soft g, soft “ch”
a script j has a lower loop; g is almost a 6 rotated
7
/k/ /ɡ/
k, hard c, hard g, hard “ch”, q, qu
capital K “contains” two sevens (some variant systems include “ng”)
8
/f/ /v/
f, v
script f resembles a figure-8; v sounds similar (v is a voiced f)
9
/p/ /b/
p, b
p is a mirror-image 9; b sounds similar and resembles a 9 rolled around
Unassigned
Vowel sounds, w,h,y
w and h are considered half-vowels; these can be used anywhere without changing a word’s number value
There are a variety of ways to use the major system as a code in addition to its uses in mnemonic settings. When I was a youth, I used it to write coded messages and to encrypt a variety of things for personal use. After I had originally read Dr. Bruno Furst’s series of booklets entitled You Can Remember: A Home Study Course in Memory and Concentration1, I had always wanted to spend some time creating an alternate method of writing using the method. Sadly I never made the time to do the project, but yesterday I made a very interesting discovery that, to my knowledge, doesn’t seem to have been previously noticed!
My discovery began last week when I read an article in The Atlantic by journalist Dennis Hollier entitled How to Write 225 Words Per Minute with a Pen: A Lesson in the Lost Technology of Shorthand. 2 In the article, which starts off with a mention of the Livescribe pen – one of my favorite tools, Mr. Hollier outlines the use of the Gregg System of Shorthand which was invented by John Robert Gregg in 1888. The description of the method was intriguing enough to me that I read a dozen additional general articles on shorthand on the internet and purchased a copy of Louis A. Leslie’s two volume text Gregg Shorthand: Functional Method.3
I was shocked, on page x of the front matter, just before the first page of the text, to find the following “Alphabet of Gregg Shorthand”:
Alphabet of Gregg Shorthand
Gregg Shorthand is using EXACTLY the same consonant-type breakdown of the alphabet as the major system!
Apparently I wasn’t the first to have the idea to turn the major system into a system of writing. The fact that the consonant breakdowns for the major system coincide almost directly to those for the shorthand method used by Gregg cannot be a coincidence!
The Gregg system works incredibly well precisely because the major system works so well. The biggest difference between the two systems is that Gregg utilizes a series of strokes (circles and semicircles) to indicate particular vowel sounds which allows for better differentiation of words which the major system doesn’t generally take into consideration. From an information theoretic standpoint, this is almost required to make the coding from one alphabet to the other possible, but much like ancient Hebrew, leaving out the vowels doesn’t remove that much information. Gregg, also like Hebrew, also uses dots and dashes above or below certain letters to indicate the precise sound of many of its vowels.
The upside of all of this is that the major system is incredibly easy to learn and use, and from here, learning Gregg shorthand is just a hop, skip , and a jump – heck, it’s really only just a hop because the underlying structure is so similar. Naturally as with the major system, one must commit some time to practicing it to improve on speed and accuracy, but the general learning of the system is incredibly straightforward.
Because the associations between the two systems are so similar, I wasn’t too surprised to find that some of the descriptions of why certain strokes were used for certain letters were very similar to the mnemonics for why certain letters were used for certain numbers in the major system.
From Dr. Bruno Furst’s “You Can Remember!” The mnemonic for remembering 6, 7, 8, & 9 in the major system.From Louis Leslie’s “Gregg Shorthand: Functional Method” The mnemonic for remembering the strokes for k and g.
One thing I have noticed in my studies on these topics is the occasional references to the letter combinations “NG” and “NK”. I’m curious why these are singled out in some of these systems? I have a strong suspicion that their inclusion/exclusion in various incarnations of their respective systems may be helpful in dating the evolution of these systems over time.
I’m aware that various versions of shorthand have appeared over the centuries with the first recorded having been the “Tironian Notes” of Marcus Tullius Tiro (103-4 BCE) who apparently used his system to write down the speeches of his master Cicero. I’m now much more curious at what point the concepts for shorthand and the major system crossed paths or converged? My assumption would be that it happened in the late Renaissance, but it would be nice to have the underlying references and support for such a timeline. Perhaps it was with Timothy Bright’s publication of Characterie; An Arte of Shorte, Swifte and Secrete Writing by Character (1588) 4, John Willis’s Art of Stenography (1602) 5, Edmond Willis’s An abbreviation of writing by character (1618) 6, or Thomas Shelton’s Short Writing (1626) 7? Shelton’s system was certainly very popular and well know because it was used by both Samuel Pepys and Sir Isaac Newton.
Certainly some in-depth research will tell, though if anyone has ideas, please don’t hesitate to indicate your ideas in the comments.
UPDATE on 7/6/14:
I’m adding a new chart making the correspondence between the major system and Gregg Shorthand more explicit.
A chart indicating the correspondences between the major system and Gregg Shorthand.
References
1.
Furst B. You Can Remember: A Home Study Course in Memory and Concentration. Markus-Campbell Co.; 1965.
Bright T (1550-1615). Characterie; An Arte of Shorte, Swifte and Secrete Writing by Character. 1st ed. I. Windet; reprinted by W. Holmes, Ulverstone; 1588. https://archive.org/details/characteriearteo00brig.
5.
Willis J. Art of Stenography.; 1602.
6.
Willis E. An Abbreviation of Writing by Character.; 1618.
I’ve long been a student of the humanities (and particularly the classics) and have recently begun reviewing over my very old and decrepit knowledge of Latin. It’s been two decades since I made a significant study of classical languages, and lately (as the result of conversations with friends like Dave Harris, Jim Houser, Larry Richardson, and John Kountouris) I’ve been drawn to reviewing them for reading a variety of classical texts in their original languages. Fortunately, in the intervening years, quite a lot has changed in the tools relating to pedagogy for language acquisition.
A copy of Jenny’s Latin text which I had used 20 years ago and recently acquired a new copy for the pittance of $3.25.
Internet
The biggest change in the intervening time is the spread of the internet which supplies a broad variety of related websites with not only interesting resources for things like basic reading and writing, but even audio sources apparently including listening to the nightly news in Latin. There are a variety of blogs on Latin as well as even online courseware, podcasts, pronunciation recordings, and even free textbooks. I’ve written briefly about the RapGenius platform before, but I feel compelled to mention it as a potentially powerful resource as well. (Julius Caesar, Seneca, Ovid, Cicero, et al.) There is a paucity of these sources in a general sense in comparison with other modern languages, but given the size of the niche, there is quite a lot out there, and certainly a mountain in comparison to what existed only twenty years ago.
Software
There has also been a spread of pedagogic aids like flashcard software including Anki and Mnemosyne with desktop, web-based, and even mobile-based versions making learning available in almost any situation. The psychology and learning research behind these types of technologies has really come a long way toward assisting students to best make use of their time in learning and retaining what they’ve learned in long term memory. Simple mobile applications like Duolingo exist for a variety of languages – though one doesn’t currently exist for classical Latin (yet).
Digital Humanities
The other great change is the advancement of the digital humanities which allows for a lot of interesting applications of knowledge acquisition. One particular one that I ran across this week was the Dickinson College Commentaries (DCC). Specifically a handful of scholars have compiled and documented a list of the most common core vocabulary words in Latin (and in Greek) based on their frequency of appearance in extant works. This very specific data is of interest to me in relation to my work in information theory, but it also becomes a tremendously handy tool when attempting to learn and master a language. It is a truly impressive fact that, simply by knowing that if one can memorize and master about 250 words in Latin, it will allow them to read and understand 50% of most written Latin. Further, knowledge of 1,500 Latin words will put one at the 80% level of vocabulary mastery for most texts. Mastering even a very small list of vocabulary allows one to read a large variety of texts very comfortably. I can only think about the old concept of a concordance (which was generally limited to heavily studied texts like the Bible or possibly Shakespeare) which has now been put on some serious steroids for entire cultures. Another half step and one arrives at the Google Ngram Viewer.
The best part is that one can, with very little technical knowledge, easily download the DCC Core Latin Vocabulary (itself a huge research undertaking) and upload and share it through the Anki platform, for example, to benefit a fairly large community of other scholars, learners, and teachers. With a variety of easy-to-use tools, shortly it may be even that much easier to learn a language like Latin – potentially to the point that it is no longer a dead language. For those interested, you can find my version of the shared DCC Core Latin Vocabulary for Anki online; the DCC’s Chris Francese has posted details and a version for Mnemosyne already.
[Editor’s note: Anki’s web service occasionally clears decks of cards from their servers, so if you find that the Anki link to the DCC Core Latin is not working, please leave a comment below, and we’ll re-upload the deck for shared use.]
What tools and tricks do you use for language study and pedagogy?
‘ll be the first to admit that I’m a reading junkie, but unfortunately there isn’t (yet) a 12 step program to help me. I love reading lots of different types of things across an array of platforms (books, newspapers, magazines, computer, web, phone, tablet, apps) and topics (fiction/non-fiction and especially history, biography, economics, popular science, etc.). My biggest problem and one others surely face is time.
There are so many things I want to read, and far too little time to do it in. Over the past several years, I’ve spent an almost unreasonable amount of time thinking about what I consume and (possibly more importantly) how to intelligently consume more of it. I’ve spent so much time delving into it that I’ve befriended a professor and fellow renaissance man (literally and figuratively) who gave me a personal thank you in his opening to a best-selling book entitled “The Thinking Life: How to Thrive in an Age of Distraction.”
Information Consumption
At least twice a year I look at my reading consumption and work on how to improve it, all the while trying to maintain a level of quality and usefulness in what I’m consuming and why I’m consuming it.
I continually subscribe to new and interesting sources.
I close off subscriptions to old sources that I find uninteresting, repetitive (goodbye echo chamber), and those that are (or become) generally useless.
I carefully monitor the huge volumes of junk email that end up in my inbox and trim down on the useless material that I never seem to read, so that I’ll have more time to focus on what is important.
I’ve taken up listening to audiobooks to better utilize my time in the car while commuting.
I’ve generally quit reading large swaths of social media for their general inability to uncover truly interesting sources.
I’ve used some portions of social media to find other interesting people collating and curating areas I find interesting, but which I don’t have the time to read through everything myself. Why waste my time reading hundreds of articles, when I can rely on a small handful of people to read them and filter out the best of the best for myself? Twitter lists in particular are an awesome thing.
I’ve given up on things like “listicles” or stories from internet click farm sources like BuzzFeed which can have some truly excellent linkbait-type headlines, but I always felt like I’ve completely wasted my time clicking through to them.
A New Solution
About six months ago in the mountain of tech journalism I love reading, I ran across a site launch notice about a tech start-up calledSpritzwhich promised a radically different solution for the other side of the coin relating to my reading problem: speeding the entire process up! Unfortunately, despite a few intriguing samples at the time (and some great details on the problem and their solution), they weren’t actually delivering a product.
Well, all that seems to have changed in the past few weeks. I’ve waited somewhat patiently and occasionally checked back on their progress, but following a recent mention on Charlie Rose, and some serious digging around on the broader internet, I’ve found some worthwhile tools that have sprouted out of their efforts. Most importantly, Spritz itself now has a bookmarklet that seems to deliver on their promise of improving my reading speeds for online content. With the bookmarklet installed, one can go to almost any web article, click on the bookmarklet and then sit back and just read at almost any desired speed. Their technology uses a modified version of the 1970’s technology known as Rapid Serial Visual Presentation (RSVP) to speed up your reading ability, but does so in a way that is easier to effectuate with web and mobile technologies. Essentially they present words serially in the same position on your screen with an optimized center mass so that one’s eyes stay still while reading instead of doing the typical saccaddic eye movements which occur with typical reading – and slow the process down.
Spritz for speed reading the web.
As a biomedical engineer, I feel compelled to note the interesting physiologic phenomenon that if one sits in a rotatable chair and spins with one’s eyes closed and their fingers lightly placed on their eyelids, one will feel the eye’s saccades even though one isn’t actually seeing anything.
Spritz also allows one to create an account and log in so that the service will remember your previously set reading speed. Their website does such a great job of explaining their concept, I’ll leave it to the reader to take a peek; but you may want to visit their bookmarklet page directly, as their own website didn’t seem to have a link to it initially.
As a sample of how Spritz works on the web, OysterBooks is hosting a Spritz-able version of Stephen R. Covey’s book 7 Habits of Highly Effective People.
Naturally, Spritz’s solution is not a catch-all for everything I’d like to read, but it covers an interesting subcategory that will make things useful and easier. Though trying to speed read journal articles, textbooks, and other technical literature isn’t the best idea in the world, Spritz will help me plow through more fiction and more leisurely types of magazine and online articles that are of general interest. I generally enjoy and appreciate these types of journalism and work, but just can’t always justify taking the time away from more academic pursuits to delve into them. Some will still require some further thought after-the-fact to really get their full value out of them, but at least I can cover the additional ground without wasting all the additional time to do so. I find I can easily double or triple my usual reading speed without any real loss of comprehension.
In the last week or so since installing a my several new speed reading bookmarklets, I’ve begun using them almost religiously in my daily reading regimen.
I’ll also note in passing that some studies suggest that this type of reading modality has helped those who face difficulties with dyslexia.
How to read Boffosocko faster than you though you could…
Speed Reading Competition
Naturally, since this is a great idea, there’s a bit of competition in the speed reading arena.
There are a small handful of web and app technologies which are built upon the RSVP concept:
Clayton Morris has also developed an iOS application called ReadQuick, which is based on the same concept as Spritz, but is only available via app and not on web.
Rich Jones has developed a program called OpenSpritz. His version is opensource and has an Android port for mobile.
There’s also another similar bookmarklet called Squirt which also incorporates some nice UI tweaks and some of the technology from Readability as well.
For those wishing to Spritz .pdf or .txt documents, one can upload them using Readsy which uses Spritz’s open API to allow these types of functionalities.
There are also a variety of similar free apps in the Google Play store which follow the RSVP technology model.
Those on the Amazon (or Kindle Fire/Android Platform) will appreciate the Balto App which utilizes RSVP and is not only one of the more fully functional apps in the space, but it also has the ability to unpack Kindle formatted books (i.e. deal with Amazon’s DRM) to allow speed reading Kindle books. While there is a free version, the $1.99 paid version is more than well worth the price for the additional perks.
On and off for the past couple of years, I’ve also used a web service and app called Readfa.st which is a somewhat useful, but generally painful way to improve one’s speed reading. It also has a handy bookmarklet, but just wasn’t as useful as I had always hoped it might be. It’s interesting, but not as interesting or as useful as Spritz (and other RSVP technology) in my opinion since it feels more fatiguing to read in this manner
Bookmarklet Junkie Addendum
In addition to the handful of speed reading bookmarklets I’ve mentioned above, I’ve got over 50 bookmarklets in a folder on my web browser toolbar. I easily use about a dozen on a daily basis. Bookmarklets make my internet world much prettier, nicer, and cleaner with a range of simple clever code. Many are for URL shortening, sharing content to a variety of social networks quickly, but a large number of the ones I use are for reading-related tasks which I feel compelled to include here: web clippers for Evernote and OneNote, Evernote’s Clearly, Readability, Instapaper, Pocket, Mendeley (for reading journal articles), and GoodReads.
Do you have a favorite speed reading application (or bookmarklet)?
Learning any language involves acquiring a large amount of vocabulary. For this reason, I think it is very useful for Latin and Greek students to put time and effort into systematic vocabulary study.
I’ve added a copy of the DCC Core Latin Vocabulary to the Anki platform for those interested in utilizing it there instead of on Mnemosyne. The cards can be found/downloaded at: https://ankiweb.net/shared/info/1342288910. My personal thanks to the DCC for posting and sharing the results of their research and work in this manner. This is a brilliant example of the concept of digital humanities.
