Replied to a tweet by Dr LJ Dr LJ (Twitter)

The @unpaywall has a pretty useful web extension for many of these cases: https://unpaywall.org/

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 Hypothes.is 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 indieweb.xyz, 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.

👓 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

The bookmarking service CiteULike is shutting down on March 30, 2019 after a 15 year run. While some may turn to yet-another-silo or walled garden I highly recommend going IndieWeb and owning all of your own bookmarks on your own website.

I’ve been doing this for several years now and it gives me a lot more control over how much meta data I can add, change, or modify as I see fit. Let me know if I can help you do something similar.

Following Julia Strand

Followed Julia Strand (juliastrand.com)

Julia Strand is an Assistant Professor of Psychology at Carleton College.  She holds a B.A. in Psychology & English from Tufts University, an M.A. and PhD. from Washington University in St. Louis, program Brain, Behavior, & Cognition, and completed a postdoctoral fellowship in the Laboratory of Sensory Neuroscience and Neuroengineering, Department of Biomedical Engineering at Washington University in St. Louis.

She teaches courses including Introduction to Psychology, the Psychology of Spoken Words, Sensation & Perception, and Perceptual & Cognitive Expertise. Her research focuses on how humans are able to turn sensory information about speech into meaningful representations. Topics of research include how cognitive abilities influence language perception, what traits of words promote easy recognition, how word recognition abilities change with age, and how visual information (seeing the talker) influences language processing.

Julia Strand

❤️ Protohedgehog tweet

Liked a tweet by Jon TennantJon Tennant (Twitter)

The IndieWeb and Academic Research and Publishing
A microcast with an outline for disrupting academic publishing

#openscience #scholcomm #scicomm #libchat #higherED

https://boffosocko.com/2018/07/28/the-indieweb-and-academic-research-and-publishing/

👓 Interviewing my digital domains | W. Ian O’Byrne

Read Interviewing my digital domains by W. Ian O'ByrneW. Ian O'Byrne (W. Ian O'Bryne)

Alan Levine recently posted a series of questions to help others think through some of thoughts and motivations as we develop and maintain a domain of our own.

I’ve written a lot about this in the past, and I’ll try to include some links to content/posts as I respond to the prompts. This is a bit long as I get into the weeds, so consider yourself warned.

And now…let’s get to it…

Highlights, Quotes, & Marginalia

Having a domain is important to me as I research, develop, and teach.

example of a domain as thinking out loud or thought spaces
blogging as thinking


This should be a space where you can create the identity that you want to have. You can write yourself into existence.

I like this sentiment. Had René Descartes been born a bit later might he have said “Blogeō, ergo sum”?


Most of this work is focused on collaboration, transparency, and working/thinking in the open.


The plan is to use the site to share surveys, interviews, and researcher notes.

Note to self: I need to keep documenting examples of these open labs, open notebooks, etc. in the open science area.


teachers hid their Facebook accounts for fear of being fired.

The sound of this to me know reminds me of the type of suppression of thought that might have occurred in the middle ages. Of course open thought and discussion is important for teachers the same way it is for every other person. However there are a few potential counterexamples where open discussion of truly abhorrent ideas can run afoul of community mores. Case in point:


PLN

personal learning network perhaps marking it up with <abbr> tags would be useful here?


luck

lucky


.A

space


I feel like this culture in academia may be changing.


academia is built on the premise (IMHO) of getting a good idea, parlaying that into a job and tenure, and waiting for death. I’ve had a lot of colleagues and acquaintances ask why I would bother blogging. Ask why I share all of this content online. Ask why I’m not afraid that someone is going to steal my ideas.

Though all too true, this is just a painful statement for me. The entirety of our modern world is contingent upon the creation of ideas, their improvement and evolution, and their spreading. In an academic world where attribution of ideas is paramount, why wouldn’t one publish quickly and immediately on one’s own site (or anywhere else they might for that matter keeping in mind that it’s almost trivially easy to self-publish it on one’s own website nearly instantaneously)?
Early areas of science were held back by the need to communicate by handwriting letters as the primary means of communication. Books eventually came, but the research involved and even the printing process could take decades. Now the primary means of science communication is via large (often corporate owned) journals, but even this process may take a year or more of research and then a year or more to publish and get the idea out. Why not write the ideas up and put them out on your own website and collect more immediate collaborators? Funding is already in such a sorry state that generally, even an idea alone, will not get the ball rolling.
I’m reminded of the gospel song “This little light of mine” whose popular lyrics include:
“Hide it under a bushel? No! / I’m gonna let it shine” and
“Don’t let Satan blow it out, / I’m gonna let it shine”
I’m starting to worry that academia in conjunction with large corporate publishing interests are acting the role of Satan in the song which could easily be applied to ideas as well as to my little light.


Senior colleagues indicate that I should not have to balance out publishing in “traditional, peer-reviewed publications” as well as open, online spaces.

Do your colleagues who read your work, annotate it, and comment on it not count as peer-review? Am I wasting my time by annotating all of this? 🙂 (I don’t think so…)


or at least they pretend

I don’t think we’re pretending. I know I’m not!


PDF form

Let me know when you’re done and we’ll see about helping you distribute it in .epub and .mobi formats as e-books as well.


This is due to a natural human reaction to “Google” someone before we meet them for the first time. Before we show up to teach a class, take a class, interview for a job, go on a date…we’ve been reviewed online. Other people use the trail of breadcrumbs that we’ve left behind to make judgements about us. The question/challenge is that this trail of breadcrumbs is usually incomplete, and locked up in various silos. You may have bits of your identity in Facebook or Twitter, while you have other parts locked up in Instagram, Snapchat, or LinkedIn. What do these incomplete pieces say about you? Furthermore, are they getting the entire picture of you when they uncover certain details? Can they look back to see what else you’re interested in? Can they see how you think all of these interests fit together…or they seeing the tail end of a feverish bout of sharing cat pics?

I can’t help but think that doing this is a form of cultural anthropology being practiced contemporaneously. Which is more likely: someone a 100 years from now delving into my life via my personal website that aggregated everything or scholars attempting to piece it all back together from hundreds of other sites? Even with advanced AI techniques, I think the former is far more likely.
Of course I also think about what @Undine is posting about cats on Twitter or perhaps following #marginaliamonday and cats, and they’re at least taking things to a whole new level of scholarship.


Guide to highlight colors

Yellow–general highlights and highlights which don’t fit under another category below
Orange–Vocabulary word; interesting and/or rare word
Green–Reference to read
Blue–Interesting Quote
Gray–Typography Problem
Red–Example to work through

📺 Open science: Michael Nielsen at TEDxWaterloo | YouTube

Watched Open science: Michael Nielsen at TEDxWaterloo by Michael NielsenMichael Nielsen from YouTube

Michael Nielsen is one of the pioneers of quantum computation. Together with Ike Chuang of MIT, he wrote the standard text in the field, a text which is now one of the twenty most highly cited physics books of all time. He is the author of more than fifty scientific papers, including invited contributions to Nature and Scientific American. His research contributions include involvement in one of the first quantum teleportation experiments, named as one of Science Magazine's Top Ten Breakthroughs of the Year for 1998. Michael was a Fulbright Scholar at the University of New Mexico, and has worked at Los Alamos National Laboratory, as the Richard Chace Tolman Prize Fellow at Caltech, as Foundation Professor of Quantum Information Science at the University of Queensland, and as a Senior Faculty Member at the Perimeter Institute for Theoretical Physics. Michael left academia to write a book about open science, and the radical change that online tools are causing in the way scientific discoveries are made.

Sadly this area of science hasn’t opened up as much as it likely should have in the intervening years. More scientists need to be a growing part of the IndieWeb movement and owning their own data, their content, and, yes, even their own publishing platforms. With even simple content management systems like WordPress researchers can actively practice academic samizdat to a much greater extent and take a lot of the centralized power away from the major journal and textbook publishing enterprises.

I can easily see open web technology like the Webmention spec opening up online scientific communication and citations drastically even to the point of quickly replacing tools like Altmetric. If major publishing wants something to do perhaps they could work on the archiving and aggregation portions?

What if one could publish a research paper or journal article on one’s own (or one’s lab’s) website? It could receive data via webmention about others who are bookmarking it, reading it, highlighting and annotating it. It could also accept webmention replies as part of a greater peer-review process–the equivalent of the researcher hosting their own pre-print server as well as their own personal journal and open lab notebook.

We need to help empower scientists to be the center of their own writing and publishing. For those interested, this might be a useful starting point: https://indieweb.org/Indieweb_for_Education

 

 

Reply to Open Science notebooks | Ryan Barrett

Replied to a post by Ryan BarrettRyan Barrett (snarfed.org)
Notebooks like Jupyter and Observable are great for research, data science, and really any interactive computing or documentation. I want to start using them for ops/SRE projects too. Thomas Kluyver‘s bash_kernel works, but has lots of rough edges. Anyone have any other ideas?

I’ve been watching that space for a few years. Apparently you saw the same article push them into the broader mainstream consciousness. I would mention Mathematica, but you’re certainly aware of it. There are a few other math-related platforms I’ve used, but I suspect they’re not within the realm you’re looking for.

I’ve seen one or two much smaller projects along the lines of bash_kernel, but they’re either in incredibly rough shape or have very limited scopes or very niche uses. There’s a reasonably interesting list of open science related resources on GitHub, but it’s a tad old and some of the projects on it have merged or changed drastically since it was started. Foster has some interesting material and resources on open science if you care to dig through it. One day I’ll delve into the Open Science Framework to see if they’ve got anything I haven’t seen before too.

I keep meaning to document people who are using their own websites for pieces of this type of thing , but most are doing it in a hybrid fashion. Carl Boettiger is certainly a good example[1][2] and may be aware of some additional resources including one he helps manage.

🔖 Open: The Philosophy and Practices that are Revolutionizing Education and Science from Rajiv Jhangiani, Robert Biswas-Diener (eds.)

Bookmarked Open: The Philosophy and Practices that are Revolutionizing Education and Science by Rajiv Jhangiani, Robert Biswas-Diener (eds.) (Ubiquity Press)

Affordable education. Transparent science. Accessible scholarship.

These ideals are slowly becoming a reality thanks to the open education, open science, and open access movements. Running separate—if parallel—courses, they all share a philosophy of equity, progress, and justice. This book shares the stories, motives, insights, and practical tips from global leaders in the open movement.

It’s not just the book about which there’s so much to find interesting, but the website that’s serving it is well designed, crafted, and very forward thinking in what it is doing.