Replied to Hey Pressto! Conference 2020 Submissions (
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Using WordPress as a Digital Commonplace Book

A personal website is more than a blog. Rather than spread my digital identity & data across social media, I keep it in one spot for (re)search & re-use. I’ll show how my site is an evolution of the Renaissance era commonplace book, digital garden, second brain, or zettelkasten.

Bookmarked National Emergency Library : Free Texts : Free Download, Borrow and Streaming (Internet Archive)
A collection of books that supports emergency remote teaching, research activities, independent scholarship, and intellectual stimulation while universities, schools, training centers, and libraries are closed.

📑 We Have Never Been Social | Kathleen Fitzpatrick

Annotated We Have Never Been Social by Kathleen FitzpatrickKathleen Fitzpatrick (Kathleen Fitzpatrick)
I imagine that the first part of this project will focus on how it got to be this way, what got missed or ignored in some of the early warnings about what was happening online and how those warnings were swamped by the hype depicting the Internet as a space of radical democratization.  
I love the brewing idea here. We definitely need this.

Some broad initial bibliography from the top of my head:

Larry Sanger (co-founder of Wikipedia)

Some useful history/timelines:

I’m curious if you’d publicly share your current blbliography/reading list?

Bookmarked Pubnet (

Pubnet® organizes the order processes between publishers and book retailers with the standard global Electronic Data Interchange (EDI). Orders are sent to Pubnet® by ERP systems on a completely automated basis and forwarded to the appropriate publishers. The key benefit of the system is its increase in efficiency: Book retailers connect to a single system and can access all of the relevant publishers, while publishers no longer need to maintain separate links with thousands of book retailers. This is particularly relevant for communications between major book retailers and smaller publishers, and smaller book retailers and publishers.

For retailers, the service is free of charge with the exception of a setup fee, while publishers pay a fixed annual fee based on their use during the previous year. Saving energy and time EDI messages supported on Pubnet® include:

Order acknowledgments
Shipping notices

Automating the sending and receiving of these documents can dramatically reduce the cost and time spent re-keying information, sending emails, dealing with faxes or sending information via the traditional post.

Our members include Internet bookstores, college stores, wholesalers, library jobbers, trade stores, international subsidiaries of publishers, exporters, elementary and high schools, book clubs and more. Pubnet® has been serving the book industry since July 1987.

👓 ‘I Want What My Male Colleague Has, and That Will Cost a Few Million Dollars’ | New York Times

Read ‘I Want What My Male Colleague Has, and That Will Cost a Few Million Dollars (
Women at the Salk Institute say they faced a culture of marginalization and hostility. The numbers from other elite scientific institutions suggest they’re not alone.
From a statistical mechanics perspective, there isn’t much of a chance that women are all grouped at the bottom of the pack without their being systematically being drug down to that position.

The thing that goes unsung in a lot of these gender inequality articles is the assured dramatic loss to science as a result. If women were given equal footing, funding, and support what great discoveries would they have otherwise have found by this point? Assuredly the world would be far better off from those unknown discoveries.

It was quoted in the title of the article, but the full quote is even more damning.

“I know a lot of men who sincerely promote gender-equality opportunities for women, but all their efforts are devoted toward younger women,” Emerson says — because it’s less costly. “But I want what my male colleague has, and that will cost a few million dollars.”

Thoughts on open notebooks, research, and social media

I remember thinking over a decade ago how valuable it would be if researchers kept open notebooks (aka digital commonplace books) like the one Kimberly Hirsh outlines in her article Dissertating in the Open: Keeping a Public Research Notebook. I’d give my right arm to have a dozen people in research areas I’m interested in doing this very thing!

The best I could hope for back in 2008, and part of why I created the @JohnsHopkins Twitter handle, was that researchers would discover Twitter and be doing the types of things that some of the Johns Hopkins professors outlined in this recent article The Promise and Peril of Academia Wading into Twitter are now finally doing. It seems sad that it has taken over a decade and this article is really only highlighting the bleeding edge of the broader academic scene now. While what they’re doing is a great start, I think they really aren’t going far enough. They aren’t doing their audiences as much service  as they could because there’s only so much that Twitter allows in terms of depth of ideas and expressiveness. It would be far better if they were doing this sort of work from their own websites and more directly interacting with their colleagues on the open web. The only value that Twitter is giving them is a veneer of reach to a broader audience, but they’re also opening themselves up to bigger attacks as is described in the article.

In addition to Kimberly’s example, another related area of potential innovation would be moving the journal clubs run by many research groups and labs online and opening them up. Want to open up science?  Then let’s really do it!  By bookmarking a variety of articles on their own websites, various members could be aggregated to contribute to a larger group, which could then use their own websites with protocols like Webmention or even simple tools like to guide and participate in larger online conversations to move science communication along at an even faster pace. Greg McVerry and I have experimented in taking some of these tools into the classroom in the past.

If you think about it, arXiv and other preprint servers are really just journal clubs writ large. The problem is that they’re only communicating in one direction by aggregating the initial content, but they’re dramatically failing their audiences in that they aren’t facilitating or aggregating any open discussion around that content. As a result, the largest portion of their true value is still locked away in the individual brains of their readers rather than as commentary or even sentence level highlights and annotations on particular pieces out in the open. Often is the time that I’ll tweet about an interesting article only to receive a (lucky) reply that the results have been debunked, yet that information is almost never disclosed in or around the journal article (especially online) where it certainly belongs. Academic publishers are not only gouging us financially by siloing their content, they’re failing us far worse than most realize.

Another idea: Can’t get a journal of negative results to publish your latest research failure? Why not post a note or article on your own website to help out future researchers? (or even demonstrate to your students that not everything always works out?)

Naturally having aggregation services like, building planets, using OPML subscriptions, or the coming wave of feed readers could make a lot of these things easier, but we’re already right on the cusp for people who are willing to take a shot for doing this type of research online on their own websites and out in the open.

Want to try out some of the above? I’m happy to help (gratis) researchers who’d like to experiment in the area to get themselves set up. Just send me a note or give me a call.

Brief thoughts on receiving read posts

I’ve been posting “read” posts/notes/links–reads, for simplicity– to my own website for a while to indicate articles and material which I’ve spent the time to read online (and oftentimes even offline). While I automatically send notifications (via webmentions or trackbacks/pingbacks) to notify the original articles, few sites know how to receive them and even less actively display them.

It’s only in the last few weeks that my site has actively begun receiving these read posts, and I have to say it’s a really lovely and heartwarming experience. While my site gets several hundreds of hits per day, and even comments, likes and other interactions, there’s just something additionally comforting in knowing that someone took the time to read some of my material and posted that fact to their own website as a reminder to themselves as well as a signal to others.

Mentally there’s a much larger value in receiving these than likes or tweets with links from Twitter, in part because there’s a larger indicator of “work” behind these signals. They’re not simply an indicator that “I saw the headline of this thing somewhere and shared it because the friction of doing so was ridiculously low”, but they represent a lot of additional time, effort, and energy and thus are a stronger and more valuable signal (both to me and hopefully to others.)

I suppose I’ll eventually need to preface that these are especially interesting to me now when I’m only getting small numbers of them from particular people who I know are deeply engaging with specific portions of my past work. I can also imagine a day when these too may become spam-like, and I (or others) are inundated with them. But for now I’ll just revel in their joyous, little warmth.

It’s interesting from my website’s administrative interface to see the path individuals are taking through my thoughts and which topics they may find interesting. I don’t think that many (any?) social media silos provide these types of views which may actually help to spark future conversations based on our shared interests.

Of course I must also admit that, as nice as these read notifications have been, they actually pale in comparison to the rest of the work that the particular sender has been doing in replicating large portions of the sorts of things I’m doing on and with my website.  I hope all of our work, experimenting, and writing is infectious and will help others out in the future.

👓 Highly Profitable Medical Journal Says Open Access Publishing Has Failed. Right. | Forbes

Read Highly Profitable Medical Journal Says Open Access Publishing Has Failed. Right. by Steven Salzberg (Forbes)
The New England Journal of Medicine just published an editorial saying open access publishing isn't necessary, because they already make most of their content free. What are they so worried about? Yours truly breaks down a few of their bogus arguments.
You’d think that a highly respected medical journal would be great and providing some back up evidence right?!
Other than following the RSS feeds of specific people’s public highlights and annotations, is there an easier way of following people on Is there a social layer or reader side I’m missing?

Who should I be following? How can I discover interesting annotators besides besides slowly and organically? Who out there is using in unique and interesting ways?

And of course, there’s also following feeds of interesting tags, but how can one find the largest and most interesting subsets? Many of the tags I’m interested in following are only being annotated and followed by me.

Is there a master list of public tags ranked in order of prevalence? Academic based tags? 

I feel like there’s far more interesting material being unearthed by this tool, just based on how I’m using it, but that the discovery portion is largely missing, or hidden away in the dark corners of Jon Udell’s web or only via API access.

I find myself wondering what’s at the bleeding edge that I’m not seeing (without following the GitHub repo on a regular basis).


👓 Scientists Have Cracked the Code on ‘Wine Legs,’ and It Could Lead to Some Cool New Glassware | Food & Wine

Read Scientists Have Cracked the Code on ‘Wine Legs,’ and It Could Lead to Some Cool New Glassware (Food & Wine)
Some people gaze at the tears of wine; other people dedicate their life to researching them.

👓 UC terminates subscriptions with world’s largest scientific publisher in push for open access to publicly funded research | University of California | Office of the President

Read UC terminates subscriptions with world’s largest scientific publisher in push for open access to publicly funded research (University of California | Office of the President)
As a leader in the global movement toward open access to publicly funded research, the University of California is taking a firm stand by deciding not to renew its subscriptions with Elsevier. Despite months of contract negotiations, Elsevier was unwilling to meet UC’s key goal: securing universal open access to UC research while containing the rapidly escalating costs associated with for-profit journals.
This is some crazy bad-ass news. Almost everyone I know in higher education tweeted this article out today.

Now if only we could get them to all go IndieWeb using a Domain of Their Own and practice academic samizdat

👓 Data Transparency and Civil Engineers | The Scholarly Kitchen

Read Data Transparency and Civil Engineers by Angela Cochran (The Scholarly Kitchen)
Civil Engineers rely partly on data provided by others to do their research. This post describes the challenges of getting, keeping, and maintaining the data.
There’s some interesting material here to think about with respect to data journalism, data retention, and sharing.

👓 Falling asleep in your genes: biology | Economist Espresso

Read Falling asleep in your genes: biology (Economist Espresso)

Humans spend around a third of their lives asleep. But the molecular and genetic mechanisms that control sleepiness are mysteries. Now researchers have shown that a gene called nemuri could be one of the main drivers. In a study on fruit flies, neuroscientists at the University of Pennsylvania found that when they suppressed the activity of this gene, the flies woke up easily and had difficulty sleeping. Conversely, when they ramped up nemuri’s activity, the flies effortlessly entered the land of nod. Intriguingly nemuri, which encodes a small protein secreted by brain cells, was also shown to help the flies fight off bacterial infections. It seems as though sleep is a crucial part of the body’s immune response to infection or illness. Anyone sceptical of the recuperative powers of a good night’s rest now has evidence their doctors and mothers were right—sleep really does help. The results were published this week in Science.

This looks like some interesting sleep research to delve into further.

👓 a post on and IndieWeb | Jack Jamieson

Read a post by Jack JamiesonJack Jamieson (
Thank you to @RyersonResearch and especially @joyceemsmith  for inviting me to talk about my research today.  I had a great time talking IndieWeb, and specifically, Bridgy. Jan 30, 2019 Lunch and Learn at Ryerson Journalism Research Centre I presented a study I’ve been working on about Bridgy, i...