Chris Aldrich Blog: BoffoSocko.com

🔖 Emerging Frontiers of Neuroengineering: A Network Science of Brain Connectivity

Bookmarked Emerging Frontiers of Neuroengineering: A Network Science of Brain Connectivity (arxiv.org)

Neuroengineering is faced with unique challenges in repairing or replacing complex neural systems that are composed of many interacting parts. These interactions form intricate patterns over large spatiotemporal scales, and produce emergent behaviors that are difficult to predict from individual elements. Network science provides a particularly appropriate framework in which to study and intervene in such systems, by treating neural elements (cells, volumes) as nodes in a graph and neural interactions (synapses, white matter tracts) as edges in that graph. Here, we review the emerging discipline of network neuroscience, which uses and develops tools from graph theory to better understand and manipulate neural systems, from micro- to macroscales. We present examples of how human brain imaging data is being modeled with network analysis and underscore potential pitfalls. We then highlight current computational and theoretical frontiers, and emphasize their utility in informing diagnosis and monitoring, brain-machine interfaces, and brain stimulation. A flexible and rapidly evolving enterprise, network neuroscience provides a set of powerful approaches and fundamental insights critical to the neuroengineer's toolkit.

17 pages, 6 figures. Manuscript accepted to the journal Annual Review of Biomedical Engineering [1]

References

[1]

D. Bassett S., A. Khambhati N., and S. Grafton T., “Emerging Frontiers of Neuroengineering: A Network Science of Brain Connectivity,” arXiv, 23-Dec-2016. [Online]. Available: https://arxiv.org/abs/1612.08059. [Accessed: 03-Jan-2017]

🔖 A Physical Basis for the Second Law of Thermodynamics: Quantum Nonunitarity

Bookmarked A Physical Basis for the Second Law of Thermodynamics: Quantum Nonunitarity (arxiv.org)

It is argued that if the non-unitary measurement transition, as codified by Von Neumann, is a real physical process, then the "probability assumption" needed to derive the Second Law of Thermodynamics naturally enters at that point. The existence of a real, indeterministic physical process underlying the measurement transition would therefore provide an ontological basis for Boltzmann's Stosszahlansatz and thereby explain the unidirectional increase of entropy against a backdrop of otherwise time-reversible laws. It is noted that the Transactional Interpretation (TI) of quantum mechanics provides such a physical account of the non-unitary measurement transition, and TI is brought to bear in finding a physically complete, non-ad hoc grounding for the Second Law.

Download .pdf copy

🔖 100 years after Smoluchowski: stochastic processes in cell biology

Bookmarked 100 years after Smoluchowski: stochastic processes in cell biology (arxiv.org)

100 years after Smoluchowski introduces his approach to stochastic processes, they are now at the basis of mathematical and physical modeling in cellular biology: they are used for example to analyse and to extract features from large number (tens of thousands) of single molecular trajectories or to study the diffusive motion of molecules, proteins or receptors. Stochastic modeling is a new step in large data analysis that serves extracting cell biology concepts. We review here the Smoluchowski's approach to stochastic processes and provide several applications for coarse-graining diffusion, studying polymer models for understanding nuclear organization and finally, we discuss the stochastic jump dynamics of telomeres across cell division and stochastic gene regulation.

65 pages, J. Phys A 2016 [1]

References

[1]

D. Holcman and Z. Schuss, “100 years after Smoluchowski: stochastic processes in cell biology,” arXiv, 26-Dec-2016. [Online]. Available: https://arxiv.org/abs/1612.08381. [Accessed: 03-Jan-2017]

Reply to Manton Reece: This morning I launched the Kickstarter project for Micro.blog. Really happy with the response. Thank you, everyone!

Replied to Manton Reece (manton.org)

This morning I launched the Kickstarter project for Micro.blog. Really happy with the response. Thank you, everyone!

Manton, I’ve been following your blog and your indieweb efforts for creating a microblogging platform for a while. I’m excited to see your Kickstarter effort doing so well this afternoon!

As a fellow IndieWeb proponent, and since I know how much work such an undertaking can be, I’m happy to help you with the e-book and physical book portions of your project on a voluntary basis if you’d like. I’ve got a small publishing company set up to handle the machinery of such an effort as well as being able to provide services that go above and beyond the usual low-level services most self-publishing services might provide. Let me know if/how I can help.

1200 Free Online Courses from Top Universities | Open Culture

Bookmarked 1200 Free Online Courses from Top Universities (openculture.com)

Download 1200 free online courses from the world's top universities -- Stanford, Yale, MIT, & more. Over 30,000 hours of free audio & video lectures.

Don Katz’s letter about Ralph Ellison’s influence

Read Don Katz's letter about Ralph Ellison's influence by Don Katz (audible.com)

Dear Listener,During the winter of 1971 I was a freshman at NYU, and I read two books that changed me. The first was Faulkner’s The Sound and the Fury—a book I read in a single afternoon-to-dawn sitting. The second was Invisible Man, an astonishingly artful and complex work of literature written by a man I heard was actually teaching a course at NYU the next semester.

Over the next three years, after Ralph Ellison allowed me into a small seminar focused on the American vernacular, and a year after that, when he took me on as a tutee every Wednesday afternoon until I graduated, one of the greatest of all American writers taught me how to read. Ralph also helped me gain the courage and occasional insight to write, and I went on to make a living as a writer for 20 years after that. Ralph encouraged me and spoke up for me publicly until he died in 1994.

I learned from Ralph Ellison that Americans worked to create an identity from a synthesis of divergent cultures. We created a distinctive way of talking and telling stories, which led to the distinctive voice in the way we wrote. I understood from Ralph that the American experience derived from the process of a nation constantly making and remaking itself, a place that needed to create its own myths and art and even its own sounds because we had to. While Ralph Ellison taught me that Americans needed to create our own archetypes and myths, he also conveyed that in a nation creating itself without kings, a new order was created based on the color of people’s skin.

Because of Ralph I always heard the sound of what I read and what I wrote. Well-composed words sound like music to me, and after being a writer for 20 years, this led directly to an idea that became Audible.com and our 20-years of applying new technologies to the celebration and elevation of the unbridled power of the well-spoken word.

A few feet from my cube is the Ralph Ellison room, and the following is what I wrote about Ralph for the glass wall I see every day: Ralph Ellison’s understanding of the power of the oral tradition and his ability to hear the music in well-wrought arrangements of spoken words informed the vision and mission of Audible from the beginning. Ellison was the teacher and mentor of Audible’s founder. According to Ellison, the way the early American vernacular embraced storytelling around campfires, the braggadocio of our salesmanship, and the sound of our lamenting in the fields became the distinctive voice that defined American novels and our singularly “conscious and conscientious” culture, a culture that created itself “out of whatever it found useful.” Ellison loved the melodies in language and he told stories in a voice that sounded like a coal car coming out of a mine. He loved enormous cigars, jazz, and ideas. In many ways Audible exists to honor his legacy.

Don’t let anyone ever tell you that great teachers can’t direct the course and meaning of a life.

Don Katz

CEO, Founder of Audible

Watch a Needle Ride Through LP Record Grooves Under an Electron Microscope | Open Culture

Read Watch a Needle Ride Through LP Record Grooves Under an Electron Microscope (openculture.com)

Last year, we highlighted a 1956 video from RCA Victor which demonstrated how vinyl records were made back in the good old days. If you have 23 free minutes, you can get a pretty good look at the production process — the live audio recording, the making of a master disc, the production of a mold, the eventual mass production of vinyl records, etc.

Almost 60 years later, vinyl is making a comeback. So why not let Ben Krasnow, a hardware engineer at Google X, give us a much more modern perspective on the LP? Above, watch Krasnow’s stop motion animation, made with an electron microscope, which shows us a phonograph needle riding through grooves on an LP. Much of the 9-minute video offers a fairly technical primer on what went into making this stop motion clip in the first place. So if you want to get to the action, fast forward to the 4:20 mark.

If you hang with Krasnow’s video, you can also see him take some microscopic looks at other media formats — CD-ROMs, early forms of DVDs, and more.

via Devour

PressForward as an IndieWeb WordPress-based RSS Feed Reader & Pocket/Instapaper Replacement

As many know, for the past 6 months or so, I’ve been slowly improving some of the IndieWeb tools and workflow I use to own what I’m reading both online and in physical print as well as status updates indicating those things. [1][2][3]

Since just before IndieWebCamp LA, I’ve been working on better ways to own the articles I’ve been reading and syndicate/share them out to other social platforms. The concept initially started out as a simple linkblog idea and has continually been growing, particularly with influence from my attendance of the Dodging the Memory Hole 2016: Saving Online News conference at UCLA in October. Around that same time, it was announced that Pinterest was purchasing Instapaper and they were shutting down some of Instapaper’s development and functionality. I’ve been primarily using Pocket for several years now and have desperately wanted to bring that functionality into my own site. I had also been looking at the self-hostable Wallabag alternative which is under heavy active development, but since most of my site is built on WordPress, I really preferred having a solution that integrated better into that as a workflow.

Enter PressForward

I’ve been looking closely at PressForward for the past week and change as a self-contained replacement for third party services like Pocket and Instapaper. I’ve been looking around for this type of self-hosted functionality for a while.

PressForward was originally intended for journalists and news organizations to aggregate new content, add it to their newsroom workflow, and then use it to publish new content. From what I can see it’s also got a nice following in academia as a tool for aggregating content for researchers focused on a particular area.

It only took a minute or two of looking at PressForward to realize that it had another off-label use case: as a spectacular replacement for read-later type apps!

In an IndieWeb fashion, this fantastic WordPress plugin allows me to easily own private bookmarks of things I’d like to read (PressForward calles these “Nominations” in keeping with its original use case). I can then later read them on my own website (with Mercury f.k.a Readability functionality built in), add commentary, and publish them as a read post. [Note: To my knowledge the creators of PressForward are unaware of the IndieWeb concept or philosophies.]

After some playing around for a bit and contemplating several variations, configurations, and options, I thought I’d share some thoughts about it for others considering using it in such an off-label manner. Hopefully these may also spur the developers to open up their initial concept to a broader audience as it seems very well designed and logically laid out.

Examples

The developers obviously know the value of dogfooding as at least two of them are using it in a Pocket-like fashion (as they many not have other direct use-cases).

Pros

PressForward includes a beautiful, full built-in RSS Feed Reader!

This feature alone is enough to recommend using it even without any other feature. I’ve tried Orbit Reader and WhisperFollow (among others) which are both interesting in their own rights but are somewhat limited and have relatively clunky interfaces. The best part of WhisperFollow’s premise is that it has webactions built in, but I suspect these could easily be added onto PressForward.

In fact, not just hours before I’d discovered PressFoward, I’d made this comment on the WordPress Reader Refresh post announcing the refresh of WordPress.com’s own (separate) reader:

Some nice visual changes in this iteration. Makes it one of the most visually pretty feed readers out there now while still maintaining a relatively light weight.

I still wish there were more functionality pieces built into it like the indie-reader Woodwind.xyz or even Feedly. While WordPress in some sense is more creator oriented than consumption oriented, I still think that not having a more closely integrated reader built into it is still a drawback to the overall WordPress platform.

Additionally,

It’s IndieWeb and POSSE friendly
It does automatic link forwarding in a flexible/responsible manner with canonical URLs
Allows for proper attributions for the original author and content source/news outlet
Keeps lots of metadata for analyzing reading behavior
Taggable and categorizable
Allows for comments/commenting
Could be used for creating a linkblog on steroids
Archives the original article on the day it was read.
Is searchable
Could be used for collaboration and curation
Has Mercury (formerly known as Readability) integrated for a cleaner reading interface
Has a pre-configured browser bookmarklet
Is open source and incredibly well documented
One can count clicks to ones’ own site as the referer while still pushing the reader to the original
Along with other plugins like JetPack’s Publicize or Social Networks Auto-Poster, one can automatically share their reads to Twitter, Facebook, or other social media silos. In this case, you own the link, but the original publisher also gets the traffic.

Cons

No clear path for nominating articles on mobile.

This can be a dealbreaker for some, so I’ve outlined a pretty quick and simple solution below.

No direct statistics

Statistics for gauging ones’ reading aren’t built in directly (yet?), but some scripts are available. [4][5][6]

No larger data aggregation

Services like Pocket are able to aggregate the data of thousands of users to recommend and reveal articles I might also like. Sadly this self-hosted concept makes it difficult (or impossible) do have this type of functionality. However, I usually have far too much good stuff to read anyway, so maybe this isn’t such a loss.

Suggested Improvements

Adding the ability to do webactions directly from the “Nominated” screen would be fantastic, particularly for the RSS reader portion.

Default to an unread view of the current “All Content” page. I find that I have to filter the view every time I visit the page to make it usable. I suspect this would be a better default for most newsrooms too.

It would be nice to have a pre-configured archive template page in a simple linkblog format that filters posts that were nominated/drafted/published via the Plugin. This will prevent users from needing to create one that’s compatible with their current theme. Something with a date read, Title linked to the original, Author, and Source attribution could be useful for many users.

A PressForward Nomination “Bookmarklet” for Mobile

One of the big issues I came up against immediately with PressForward is ease of use on mobile. A lot of the content I read is on mobile, so being able to bookmark (nominate) articles via mobile or apps like Nuzzel or Twitter is very important. I suspect this may also be the case for many of their current user base.

Earlier this year I came across a great little Android mobile app called URL Forwarder which can be used to share things with the ubiquitous mobile sharing icons. Essentially one can use it to share the URL of the mobile page one is on to a mobile Nomination form within PressForward.

I’d suspect that there’s also a similar app for iOS, but I haven’t checked. If not available, URL Forwarder is open source on Github and could potentially be ported. There’s also a similar Android app called Bookmarklet Free which could be used instead of URL Forwarder.

PressForward’s built in bookmarklet kindly has a pre-configured URL for creating nominations, so it’s a simple case of configuring it. These details follow below for those interested.

Configuring URL Forwarder for PressForward

Open URL Forwarder
Click the “+” icon to create a filter.
Give the filter a name, “Nominate This” is a reasonable suggestion. (See photo below.)
Use the following entry for the “Filter URL” replacing example.com with your site’s domain name: http://example.com/wp-content/plugins/pressforward/includes/nomthis/nominate-this.php?u=@url
Leave the “Replaceable text” as “@url”
Finish by clicking on the checkmark in the top right corner.

Simple right?

Configuring URL Forwarder

Sharing from a web page to URL Forwarder

Choose “Nominate” to share to PressForward

Nominating a post via mobile

With the configuration above set up, do the following:

On the mobile page one wants to nominate, click the ubiquitous “share this” mobile icon (or share via a pull down menu, depending on your mobile browser or other app.)
Choose to share through URL Forwarder
Click on the “Nominate” option just created above.
Change/modify any data within your website administrative interface and either nominate or post as a draft. (This part is the same as one would experience using the desktop bookmarklet.)

What’s next?

Given the data intensity of both the feed reader and what portends to be years of article data, I’m left with the question of hosting it within my primary site or putting it on a subdomain?

I desperately want to keep it on the main site, but perhaps hosting it on a subdomain, similar to how both Aram Zucker-Scharff and James Digioia do it may be better advised?

I’ve also run across an issue with the automatic redirect which needs some troubleshooting as well. Hopefully this will be cleared up quickly and we’ll be off to the races.

References

[1]

C. Aldrich, “A New Reading Post-type for Bookmarking and Reading Workflow,” BoffoSocko | Musings of a Modern Day Cyberneticist, 22-Aug-2016. [Online]. Available: http://boffosocko.com/2016/08/22/a-new-reading-post-type-for-bookmarking-and-reading-workflow/. [Accessed: 31-Dec-2016]

[2]

C. Aldrich, “Owning my Online Reading Status Updates,” BoffoSocko | Musings of a Modern Day Cyberneticist, 20-Nov-2016. [Online]. Available: http://boffosocko.com/2016/11/20/owning-my-online-reading-status-updates/. [Accessed: 31-Dec-2016]

[3]

C. Aldrich, “Notes, Highlights, and Marginalia from E-books to Online,” BoffoSocko | Musings of a Modern Day Cyberneticist, 24-Oct-2016. [Online]. Available: http://boffosocko.com/2016/10/24/notes-highlights-and-marginalia/. [Accessed: 31-Dec-2016]

[4]

A. Zucker-Scharff, “Personal Statistics from 3 Months of Internet Reading,” Medium, 05-Sep-2015. [Online]. Available: https://medium.com/@aramzs/3-month-internet-reading-stats-f41fa15d63f0#.dez80up7y. [Accessed: 31-Dec-2016]

[5]

A. Zucker-Scharff, “Test functions based on PF stats for collecting data,” Gist. [Online]. Available: https://gist.github.com/AramZS/d10fe64dc33fc9ffc2d8. [Accessed: 31-Dec-2016]

[6]

A. Zucker-Scharff, “PressForward/pf_stats,” GitHub. [Online]. Available: https://github.com/PressForward/pf_stats. [Accessed: 31-Dec-2016]

The Real Theme of Charlotte’s Web

E.B. White’s backstory

Elwyn Brooks “E. B.” White (July 11, 1899 – October 1, 1985) was an acclaimed American writer who contributed to The New Yorker magazine and co-authored the quintessential English language style guide The Elements of Style, which is commonly known as “Strunk & White” ostensibly making him the writer’s writer.

He is probably best known by most as the author of children’s books Stuart Little (1945), Charlotte’s Web (1952), and The Trumpet of the Swan (1970).

While re-reading Charlotte’s Web and then watching the movie version of Charlotte’s Web (Paramount, 2006) while thinking about the struggling writer in White (and all of us really), I’ve found a completely different theme in the piece as an adult that I certainly didn’t consider as a child when I viewed it simply as a maudlin, coming-of-age, commentary on the cycle of life.

An Alternate Theme

One can think of the characters Charlotte, the heroine spider, and Templeton, the despicable rat, as the two polar opposite personalities of almost any (good) writer. Charlotte represents the fastidious, creative, thinking, and erudite writer that writers aspire to be–which White espouses in The Elements of Style.

The rat was swollen to twice his normal size, Charlotte's Web, page 147 illustration, 1952, GM Williams — The rat was swollen to twice his normal size, Charlotte’s Web, page 147 illustration, 1952, GM Williams

Templeton is a grubbing, greedy, and not-so-discerning writer who takes almost any word to get the story written so he can feast on his next meal of left-over slop.

Wilbur, the runt Spring pig desperately wanting to live to see the first snow, represents the nascent story. It too starts out stunted and scrawny, and it’s not really quite clear that it will live long enough to get published.

Wilbur summersaults like any developing story

The writers struggle represented by Charlottes Web — The writer’s struggle represented by Charlotte’s Web

And so the struggle begins between the “Templeton” in the writer, and the “Charlotte” that the writer wants to become.

Charlotte represents care, devotion, creation, and even life (she not only desperately tries to creatively save Wilbur’s life, but dies to give birth to hundreds), while Templeton is a scavenger, doing the least he can to get by and generally taking advantage of others. Charlotte is crafting art while Templeton represents the writer churning out dreck in hopes of making a buck.

Alas, once the written work emerges to finally see its first “Spring”, one finds that Charlotte has died the death we knew was coming, while Templeton remains–as selfish and dreadful as before–ready to gorge himself once more.

There’s also the bleak and looming fact that Charlotte is now gone and only the vague hope that one of her few progeny will survive to live up to even a fraction of her good name. (Will my next book be as good as the first??)

The Writer takes on the Editor

The other two voices a writer often hears in her head are those represented by the characters of Fern, the doe-eyed youngster, and John Arable, the pragmatic farmer whose sir name is literally defined as “suitable for farming”, but not too coincidentally similar to parable, but without the ‘p.’ The sensible farmer (editor) says kill the runt pig (read: story) before you fall in love with it, while Fern (the creative writer) advocates to let it live a while longer–naively perhaps–wanting to know what results.

Dont Kill Wilbur! John Arable fights with his daughter Fern over an axe as he intends to kill the runt Wilbur. — A visualization of the struggle between the creative author and the sensible and pragmatic editor.

Who will you be?

So as you work on your own writing process, who will you be? Templeton, Charlotte, Fern, or John Arable? Whichever you choose for the moment, remember that all of them are ultimately necessary for the best story seeing the proverbial Spring.

Though your story may not win the “blue ribbon at the fair”, the fact that it has a life that extends the winter is a special prize all on its own to the team that created it.

On Why E.B. White Actually Wrote Charlotte’s Web

I haven’t told why I wrote the book, but I haven’t told you why I sneeze, either. A book is a sneeze.

E.B. White, author (September 29, 1952)
in a letter to his editor Ursula Nordstrom of Harper & Row, who asked him why he wrote Charlotte’s Web

Now that I’ve sketched out the argument, I suspect that most writers will now know, as I do, why E.B. White wrote Charlotte’s Web.

References

References

Enter PressForward

Examples

Pros

PressForward includes a beautiful, full built-in RSS Feed Reader!

Cons

No clear path for nominating articles on mobile.

No direct statistics

No larger data aggregation

Suggested Improvements

A PressForward Nomination “Bookmarklet” for Mobile

Configuring URL Forwarder for PressForward

Nominating a post via mobile

What’s next?

References

E.B. White’s backstory

An Alternate Theme

The Writer takes on the Editor

Who will you be?

On Why E.B. White Actually Wrote Charlotte’s Web

–Achoo!