I don’t recall though, are either of them open source, or do we need to re-build by hand?
Six years ago I received an email from a colleague in the mathematics department at UC Berkeley asking me whether he should participate in a study that involved “collecting DNA from the brigh…
This post, Gowers’, and Tao’s are all excellent reasons for a more IndieWeb philosophical approach in academic blogging (and other scientific communication). Many of the respondents/commenters have little, if any, indication of their identities or backgrounds which makes it imminently harder to judge or trust their bonafides within the discussion. Some even chose to remain anonymous and throw bombs. If each of the respondents were commenting (preferably using their real names) on their own websites and using the Webmention protocol, I suspect the discussion would have been richer and more worthwhile by an order of magnitude. Rivin at least had a linked Twitter account with an avatar, though I find it less than useful that his Twitter account is protected, a fact that makes me wonder if he’s only done so recently as a result of fallout from this incident? I do note that it at least appears his Twitter account links to his university website and vice-versa, so there’s a high likelihood that they’re at least the same person.
I’ll also note that a commenter noted that they felt that their reply had been moderated out of existence, something which Lior Pachter certainly has the ability and right to do on his own website, but which could have been mitigated had the commenter posted their reply on their own website and syndicated it to Pachter’s.
Hiding in the comments, which are generally civil and even-tempered, there’s an interesting discussion about academic publishing that could have been its own standalone post. Beyond the science involved (or not) in this entire saga, a lot of the background for the real story is one of process, so this comment was one of my favorite parts.
A senior official at Memorial Sloan Kettering Cancer Center has received millions of dollars in payments from companies that are involved in medical research.
I’m kind of shocked that major publishers like Elsevier are continually saying they add so much value to the chain of publishing they do, yet somehow, in all the major profits they (and others) are making that they don’t do these sorts of checks as a matter of course.
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Researcher posts research work to their own website (as bookmarks, reads, likes, favorites, annotations, etc.), they can post their data for others to review, they can post their ultimate publication to their own website.
The researcher’s post can webmention an aggregating website similar to the way they would pre-print their research on a server like arXiv.org. The aggregating website can then parse the original and display the title, author(s), publication date, revision date(s), abstract, and even the full paper itself. This aggregator can act as a subscription hub (with WebSub technology) to which other researchers can use to find, discover, and read the original research.
Readers of the original research can then write about, highlight, annotate, and even reply to it on their own websites to effectuate peer-review which then gets sent to the original by way of Webmention technology as well. The work of the peer-reviewers stands in the public as potential work which could be used for possible evaluation for promotion and tenure.
Readers of original research can post metadata relating to it on their own website including bookmarks, reads, likes, replies, annotations, etc. and send webmentions not only to the original but to the aggregation sites which could aggregate these responses which could also be given point values based on interaction/engagement levels (i.e. bookmarking something as “want to read” is 1 point where as indicating one has read something is 2 points, or that one has replied to something is 4 points and other publications which officially cite it provide 5 points. Such a scoring system could be used to provide a better citation measure of the overall value of of a research article in a networked world. In general, Webmention could be used to provide a two way audit-able trail for citations in general and the citation trail can be used in combination with something like the Vouch protocol to prevent gaming the system with spam.
Government institutions (like Library of Congress), universities, academic institutions, libraries, and non-profits (like the Internet Archive) can also create and maintain an archival copy of digital and/or printed copies of research for future generations. This would be necessary to guard against the death of researchers and their sites disappearing from the internet so as to provide better longevity.
Resources mentioned in the microcast
IndieWeb for Education
IndieWeb for Journalism
arXiv.org (an example pre-print server)
A Domain of One’s Own
Article on A List Apart: Webmentions: Enabling Better Communication on the Internet
Synidicating to Discovery sites
The world of scholarly communication is broken. Giant, corporate publishers with racketeering business practices and profit margins that exceed Apple’s treat life-saving research as a private commodity to be sold at exorbitant profits. Only around 25 per cent of the global corpus of research knowledge is ‘open access’, or accessible to the public for free and without subscription, which is a real impediment to resolving major problems, such as the United Nations’ Sustainable Development Goals.
So yes, more of the how to fix it piece please.
If you’ve already blogged about these in the past, then even links to those could be helpful to others using similar publishing practices in the future. Thoughts on brainstorming, best practices, pros/cons, could be highly useful as the landscape changes.
I’ve been thinking more lately about how to create a full stack IndieWeb infrastructure to replace the major portions of the academic journal ecosystem which would allow researchers to own their academic papers but still handle some of the discovery piece. Yesterday’s release of indieweb.xyz, which supports categories, reminds me that I’d had an idea a while back that something like IndieNews’ structure could be modified to create a syndication point that could act as an online journal/pre-print server infrastructure for discovery purposes.
A little birdie has told me that there’s about to be a refback renaissance to match the one currently happening with webrings.
At present I’m relying on a PESOS solution to post on another site and syndicate a copy back to my own site. I’ve used Hypothesis, in large part for their fantastic UI and as well for the data transfer portion (via RSS and even API options), to own the highlights and marginalia I’ve made on the original on Ian’s site. Since he’s syndicated a copy of his original to Medium.com, I suppose I could syndicate copies of my data there as well, but I’m saving myself the additional manual pain for the moment.
Rather than send a dozen+ webmentions to Ian, I’ve bundling everything up in one post. He’ll receive it and it would default to display as a read post though I suspect he may switch it to a reply post for display on his own site. For his own use case, as inferred from his discussion about self-publishing and peer-review within the academy, it might be more useful for him to have received the dozen webmentions. I’m half tempted to have done all the annotations as stand alone posts (much the way they were done within Hypothesis as I read) and use some sort of custom microformats mark up for the highlights and annotations (something along the lines of
u-annotation-of). At present however, I’ve got some UI concerns about doing so.
One problem is that, on my site, I’d be adding 14 different individual posts, which are all related to one particular piece of external content. Some would be standard replies while others would be highlights and the remainder annotations. Unless there’s some particular reason to do so, compiling them into one post on my site seems to be the most logical thing to do from my perspective and that of my potential readers. I’ll note that I would distinguish annotations as being similar to comments/replies, but semantically they’re meant more for my sake than for the receiving site’s sake. It might be beneficial for the receiving site to accept and display them (preferably in-line) though I could see sites defaulting to considering them vanilla mentions as a fallback. Perhaps there’s a better way of marking everything up so that my site can bundle the related details into a single post, but still allow the receiving site to log the 14 different reactions and display them appropriately? One needs to not only think about how one’s own site looks, but potentially how others might like to receive the data to display it appropriately on their sites if they’d like as well. As an example, I hope Ian edits out my annotations of his typos if he chooses to display my read post as a comment.
One might take some clues from Hypothesis which has multiple views for their highlights and marginalia. They have a standalone view for each individual highlight/annotation with its own tag structure. They’ve also got views that target highlights/annotation in situ. While looking at an original document, one can easily scroll up and down through the entire page’s highlights and annotations. One piece of functionality I do wish they would make easier is to filter out a view of just my annotations on the particular page (and give it a URL), or provide an easier way to conglomerate just my annotations. To accomplish a bit of this I’ll typically create a custom tag for a particular page so that I can use Hypothesis’ search functionality to display them all on one page with a single URL. Sadly this isn’t perfect because it could be gamed from the outside–something which might be done in a classroom setting using open annotations rather than having a particular group for annotating. I’ll also note in passing that Hypothesis provides RSS and Atom feeds in a variety of ways so that one could quickly utilize services like IFTTT.com or Zapier to save all of their personal highlights and annotations to their website. I suspect I’ll get around to documenting this in the near future for those interested in the specifics.
Another reservation is that there currently isn’t yet a simple or standard way of marking up highlights or marginalia, much less displaying them specifically within the WordPress ecosystem. As I don’t believe Ian’s site is currently as fragmentions friendly as mine, I’m using links on the date/time stamp for each highlight/annotation which uses Hypothesis’ internal functionality to open a copy of the annotated page and automatically scroll down to the fragment as mentioned before. I could potentially see people choosing to either facepile highlights and/or marginalia, wanting to display them in-line within their text, or possibly display them as standalone comments in their comments section. I could also see people wanting to be able to choose between these options based on the particular portions or potentially senders. Some of my own notes are really set up as replies, but the CSS I’m using physically adds the word “Annotation”–I’ll have to remedy this in a future version.
The other benefit of these date/time stamped Hypothesis links is that I can mark them up with the microformat
u-syndication class for the future as well. Perhaps someone might implement backfeed of comments until and unless Hypothesis implements webmentions? For fun, some of my annotations on Hypothesis also have links back to my copy as well. In any case, there are links on both copies pointing at each other, so one can switch from one to the other.
I could imagine a world in which it would be nice if I could use a service like Hypothesis as a micropub client and compose my highlights/marginalia there and micropub it to my own site, which then in turn sends webmentions to the marked up site. This could be a potential godsend to researchers/academics using Hypothesis to aggregate their research into their own personal online (potentially open) notebooks. In addition to adding bookmark functionality, I could see some of these be killer features in the Omnibear browser extension, Quill, or similar micropub clients.
I could also see a use-case for adding highlight and annotation kinds to the Post Kinds plugin for accomplishing some of this. In particular it would be nice to have a quick and easy user interface for creating these types of content (especially via bookmarklet), though again this path also relies on doing individual posts instead of a single post or potentially a collection of posts. A side benefit would be in having individual tags for each highlight or marginal note, which is something Hypothesis provides. Of course let’s not forget the quote post kind already exists, though I’ll have to think through the implications of that versus a slightly different semantic version of the two, at least in the ways I would potentially use them. I’ll note that some blogs (Colin Walker and Eddie Hinkle come to mind) have a front page that display today’s posts (or the n-most recent); perhaps I could leverage this to create a collection post of highlights and marginalia (keyed off of the original URL) to make collection posts that fit into my various streams of content. I’m also aware of a series plugin that David Shanske is using which aggregates content like this, though I’m not quite sure this is the right solution for the problem.
Eventually with some additional manual experimentation and though in doing this, I’ll get around to adding some pieces and additional functionality to the site. I’m still also interested in adding in some of the receipt/display functionalities I’ve seen from Kartik Prabhu which are also related to some of this discussion.
Is anyone else contemplating this sort of use case? I’m curious what your thoughts are. What other UI examples exist in the space? How would you like these kinds of reactions to look on your site?
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.
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:
- Florida public school teacher has a white nationalist podcast | Huffington Post
- Forida teacher says her racist podcast was satire | New York Times
personal learning network perhaps marking it up with <abbr> tags would be useful here?
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!
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
Red–Example to work through
Andrew Jordan reviews Peter Woit's Quantum Theory, Groups and Representations and finds much to admire.
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.
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
I think there is a need to develop a system to track the draft of a manuscript from the beginning to the end of the process. This will open up new possibilities to scaffold new scholars while we onboard them in the process. This will also provide new opportunities for open scholarship and open science. Finally, this will allow researchers to replicate, remix, or reproduce the (research, reflection, writing, revision, publishing) process. The answer may be in indieweb philosophies, but the main impediment may be in the people and systems that make all of this possible. I think we have an opportunity for new technological opportunities in academic publisher, but I’m not sure if culturally we’re ready. Let me explain.
I think there is a need to develop a system to track the draft of a manuscript from the beginning to the end of the process.
If you’re drafting in WordPress you can set the number of revisions of your posts to infinite so that you can keep (archive) all of your prior drafts. see: https://codex.wordpress.org/Revisions
“pre-print” versions of manuscripts
This is just another, albeit specific, form of academic samizdat.
So during my (ongoing) microformats crash course I have styled many citations. Writing an APA citation in html with proper markup take time. A lot of time when you write a lot of citations. While I would consider a canonical link back to to a piece listed or displayed on an author’s website as leg...