Education and publishing giant Pearson is drawing criticism after using its software to experiment on over 9,000 math and computer science students across the country. In a paper presented Wednesday at the American Association of Educational Research, Pearson researchers revealed that they tested the effects of encouraging messages on students that used the MyLab Programming educational software during 2017's spring semester.
I noticed a few days ago that professor and writer John Naughton not only has his own website but that he’s posting both his own content to it as well as (excerpted) content he’s writing for other journalistic outlets, lately in his case for The Guardian. This is awesome for so many reasons. The primary reason is that I can follow him via his own site and get not only his personally posted content, which informs his longer pieces, but I don’t need to follow him in multiple locations to get the “firehose” of everything he’s writing and thinking about. While The Guardian and The Observer are great, perhaps I don’t want to filter through multiple hundreds of articles to find his particular content or potentially risk missing it? What if he was writing for 5 or more other outlets? Then I’d need to delve in deeper still and carry a multitude of subscriptions and their attendant notifications to get something that should rightly emanate from one location–him! While he may not be posting his status updates or Tweets to his own website first–as I do–I’m at least able to get the best and richest of his content in one place. Additionally, the way he’s got things set up, The Guardian and others are still getting the clicks (for advertising sake) while I still get the simple notifications I’d like to have so I’m not missing what he writes.
His site certainly provides an interesting example of either POSSE or PESOS in the wild, particularly from an IndieWeb for Journalism or even an IndieWeb for Education perspective. I suspect his article posts occur on the particular outlet first and he’s excerpting them with a link to that “original”. (Example: A post on his site with a link to a copy on The Guardian.) I’m not sure whether he’s (ideally) physically archiving the full post there on his site (and hiding it privately as both a personal and professional portfolio of sorts) or if they’re all there on the respective pages, but just hidden behind the “read more” button he’s providing. I will note that his WordPress install is giving a rel=”canonical“ link to itself rather than the version at The Guardian, which also has a rel=”canonical” link on it. I’m curious to take a look at how Google indexes and ranks the two pages as a result.
In any case, this is a generally brilliant set up for any researcher, professor, journalist, or other stripe of writer for providing online content, particularly when they may be writing for a multitude of outlets.
I’ll also note that I appreciate the ways in which it seems he’s using his website almost as a commonplace book. This provides further depth into his ideas and thoughts to see what sources are informing and underlying his other writing.
Alas, if only the rest of the world used the web this way…
The scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated privately in letters, ephemerally in lectures, or all at once in books. There was no public forum for incremental advances. By making room for reports of single experiments or minor technical advances, journals made the chaos of science accretive. Scientists from that point forward became like the social insects: They made their progress steadily, as a buzzing mass.
The earliest papers were in some ways more readable than papers are today. They were less specialized, more direct, shorter, and far less formal. Calculus had only just been invented. Entire data sets could fit in a table on a single page. What little “computation” contributed to the results was done by hand and could be verified in the same way.
Not quite the cutting edge stuff I would have liked, but generally an interesting overview of relatively new technology and UI set ups like Mathematica and Jupyter.
Issuing badges to credit authors for their work on academic papers https://badges.mozillascience.org/
Exploring the use of digital badges for crediting contributors to scholarly papers for their work
As the research environment becomes more digital, we want to test how we can use this medium to help bring transparency and credit for individuals in the publication process.
@mrkrndvs I've really been interested in the collection/curation I see from you &
@chrisaldrich - I'm in the process of figuring out how to build up a WordPress site to serve as the "commonplace book" on the WordPress site, keep it simple, and have it pump into my weekly newsletter. Any links/guidance/plugins on how to make this happen is definitely appreciated.
I want to keep this as simple/lightweight as possible. :)
My favorite piece of the puzzle is using the Post Kinds Plugin for WordPress which has some useful browser bookmarklets for quickly saving what I read, bookmark, and interact with online. Having the ability to add categories, tags, and other behind-the-scenes metadata also helps a lot.
You can then turn around and add all this to a newsletter at your leisure.
Happy to share more, but this should be a good start.
TLDR: I wrote a Twitter bot to tweet the most interesting bioRxiv preprints. Follow it to stay up to date about the most recent preprints which received a lot of attention. The past few months have…
There’s so much great material out there to read and not nearly enough time. The question becomes: “How to best organize it all, so you can read even more?”
I just came across a tweet from Michael Nielsen about the topic, which is far deeper than even a few tweets could do justice to, so I thought I’d sketch out a few basic ideas about how I’ve been approaching it over the last decade or so. Ideally I’d like to circle back around to this and better document more of the individual aspects or maybe even make a short video, but for now this will hopefully suffice to add to the conversation Michael has started.
Lots of good insights in the responses. One thing stands out: this is a real pain point for many, & I don’t think anyone feels like they’ve nailed it (or how they organize information in general). It’d be great to have more ideas added to the thread! https://t.co/6KfhO5aVU3
How do people organize their reading? Perennially frustrated by this. I want one system that lets me trivially add books, papers, webpages, etc, re-organize very easily, search & filter. What works for you?
Keep in mind that this is an evolving system which I still haven’t completely perfected (and may never), but to a great extent it works relatively well and I still easily have the ability to modify and improve it.
Overall Structure
The first piece of the overarching puzzle is to have a general structure for finding, collecting, triaging, and then processing all of the data. I’ve essentially built a simple funnel system for collecting all the basic data in the quickest manner possible. With the basics down, I can later skim through various portions to pick out the things I think are the most valuable and move them along to the next step. Ultimately I end up reading the best pieces on which I make copious notes and highlights. I’m still slowly trying to perfect the system for best keeping all this additional data as well.
Since I’ve seen so many apps and websites come and go over the years and lost lots of data to them, I far prefer to use my own personal website for doing a lot of the basic collection, particularly for online material. Toward this end, I use a variety of web services, RSS feeds, and bookmarklets to quickly accumulate the important pieces into my personal website which I use like a modern day commonplace book.
Collecting
In general, I’ve been using the Inoreader feed reader to track a large variety of RSS feeds from various clearinghouse sources (including things like ProQuest custom searches) down to individual researcher’s blogs as a means of quickly pulling in large amounts of research material. It’s one of the more flexible readers out there with a huge number of useful features including the ability to subscribe to OPML files, which many readers don’t support.
As a simple example arXiv.org has an RSS feed for the topic of “information theory” at http://arxiv.org/rss/math.IT which I subscribe to. I can quickly browse through the feed and based on titles and/or abstracts, I can quickly “star” the items I find most interesting within the reader. I have a custom recipe set up for the IFTTT.com service that pulls in all these starred articles and creates new posts for them on my WordPress blog. To these posts I can add a variety of metadata including top level categories and lower level tags in addition to other additional metadata I’m interested in.
I also have similar incoming funnel entry points via many other web services as well. So on platforms like Twitter, I also have similar workflows that allow me to use services like IFTTT.com or Zapier to push the URLs easily to my website. I can quickly “like” a tweet and a background process will suck that tweet and any URLs within it into my system for future processing. This type of workflow extends to a variety of sites where I might consume potential material I want to read and process. (Think academic social services like Mendeley, Academia.com, Diigo, or even less academic ones like Twitter, LinkedIn, etc.) Many of these services often have storage ability and also have simple browser bookmarklets that allow me to add material to them. So with a quick click, it’s saved to the service and then automatically ported into my website almost without friction.
My WordPress-based site uses the Post Kinds Plugin which takes incoming website URLs and does a very solid job of parsing those pages to extract much of the primary metadata I’d like to have without requiring a lot of work. For well structured web pages, it’ll pull in the page title, authors, date published, date updated, synopsis of the page, categories and tags, and other bits of data automatically. All these fields are also editable and searchable. Further, the plugin allows me to configure simple browser bookmarklets so that with a simple click on a web page, I can pull its URL and associated metadata into my website almost instantaneously. I can then add a note or two about what made me interested in the piece and save it for later.
Note here, that I’m usually more interested in saving material for later as quickly as I possibly can. In this part of the process, I’m rarely ever interested in reading anything immediately. I’m most interested in finding it, collecting it for later, and moving on to the next thing. This is also highly useful for things I find during my busy day that I can’t immediately find time for at the moment.
At regular intervals during the week I’ll sit down for an hour or two to triage all the papers and material I’ve been sucking into my website. This typically involves reading through lots of abstracts in a bit more detail to better figure out what I want to read now and what I’d like to read at a later date. I can delete out the irrelevant material if I choose, or I can add follow up dates to custom fields for later reminders.
Slowly but surely I’m funneling down a tremendous amount of potential material into a smaller, more manageable amount that I’m truly interested in reading on a more in-depth basis.
Document storage
Calibre with GoodReads sync
Even for things I’ve winnowed down, there is still a relatively large amount of material, much of it I’ll want to save and personally archive. For a lot of this function I rely on the free multi-platform desktop application Calibre. It’s essentially an iTunes-like interface, but it’s built specifically for e-books and other documents.
Within it I maintain a small handful of libraries. One for personal e-books, one for research related textbooks/e-books, and another for journal articles. It has a very solid interface and is extremely flexible in terms of configuration and customization. You can create a large number of custom libraries and create your own searchable and sort-able fields with a huge variety of metadata. It often does a reasonable job of importing e-books, .pdf files, and other digital media and parsing out their meta data which prevents one from needing to do some of that work manually. With some well maintained metadata, one can very quickly search and sort a huge amount of documents as well as quickly prioritize them for action. Additionally, the system does a pretty solid job of converting files from one format to another, so that things like converting an .epub file into a .mobi format for Kindle are automatic.
Calibre stores the physical documents either in local computer storage, or even better, in the cloud using any of a variety of services including Dropbox, OneDrive, etc. so that one can keep one’s documents in the cloud and view them from a variety of locations (home, work, travel, tablet, etc.)
I’ve been a very heavy user of GoodReads.com for years to bookmark and organize my physical and e-book library and anti-libraries. Calibre has an exceptional plugin for GoodReads that syncs data across the two. This (and a few other plugins) are exceptionally good at pulling in missing metadata to minimize the amount that must be done via hand, which can be tedious.
Within Calibre I can manage my physical books, e-books, journal articles, and a huge variety of other document related forms and formats. I can also use it to further triage and order the things I intend to read and order them to the nth degree. My current Calibre libraries have over 10,000 documents in them including over 2,500 textbooks as well as records of most of my 1,000+ physical books. Calibre can also be used to add document data that one would like to ultimately acquire the actual documents, but currently don’t have access to.
BibTeX and reference management
In addition to everything else Calibre also has some well customized pieces for dovetailing all its metadata as a reference management system. It’ll allow one to export data in a variety of formats for document publishing and reference management including BibTex formats amongst many others.
Reading, Annotations, Highlights
Once I’ve winnowed down the material I’m interested in it’s time to start actually reading. I’ll often use Calibre to directly send my documents to my Kindle or other e-reading device, but one can also read them on one’s desktop with a variety of readers, or even from within Calibre itself. With a click or two, I can automatically email documents to my Kindle and Calibre will also auto-format them appropriately before doing so.
Typically I’ll send them to my Kindle which allows me a variety of easy methods for adding highlights and marginalia. Sometimes I’ll read .pdf files via desktop and use Adobe to add highlights and marginalia as well. When I’m done with a .pdf file, I’ll just resave it (with all the additions) back into my Calibre library.
Exporting highlights/marginalia to my website
For Kindle related documents, once I’m finished, I’ll use direct text file export or tools like clippings.io to export my highlights and marginalia for a particular text into simple HTML and import it into my website system along with all my other data. I’ve briefly written about some of this before, though I ought to better document it. All of this then becomes very easily searchable and sort-able for future potential use as well.
Here’s an example of some public notes, highlights, and other marginalia I’ve posted in the past.
Synthesis
Eventually, over time, I’ve built up a huge amount of research related data in my personal online commonplace book that is highly searchable and sortable! I also have the option to make these posts and pages public, private, or even password protected. I can create accounts on my site for collaborators to use and view private material that isn’t publicly available. I can also share posts via social media and use standards like webmention and tools like brid.gy so that comments and interactions with these pieces on platforms like Facebook, Twitter, Google+, and others is imported back to the relevant portions of my site as comments. (I’m doing it with this post, so feel free to try it out yourself by commenting on one of the syndicated copies.)
Now when I’m ready to begin writing something about what I’ve read, I’ve got all the relevant pieces, notes, and metadata in one centralized location on my website. Synthesis becomes much easier. I can even have open drafts of things as I’m reading and begin laying things out there directly if I choose. Because it’s all stored online, it’s imminently available from almost anywhere I can connect to the web. As an example, I used a few portions of this workflow to actually write this post.
Continued work
Naturally, not all of this is static and it continues to improve and evolve over time. In particular, I’m doing continued work on my personal website so that I’m able to own as much of the workflow and data there. Ideally I’d love to have all of the Calibre related piece on my website as well.
Earlier this week I even had conversations about creating new post types on my website related to things that I want to read to potentially better display and document them explicitly. When I can I try to document some of these pieces either here on my own website or on various places on the IndieWeb wiki. In fact, the IndieWeb for Education page might be a good place to start browsing for those interested.
One of the added benefits of having a lot of this data on my own website is that it not only serves as my research/data platform, but it also has the traditional ability to serve as a publishing and distribution platform!
Currently, I’m doing most of my research related work in private or draft form on the back end of my website, so it’s not always publicly available, though I often think I should make more of it public for the value of the aggregation nature it has as well as the benefit it might provide to improving scientific communication. Just think, if you were interested in some of the obscure topics I am and you could have a pre-curated RSS feed of all the things I’ve filtered through piped into your own system… now multiply this across hundreds of thousands of other scientists? Michael Nielsen posts some useful things to his Twitter feed and his website, but what I wouldn’t give to see far more of who and what he’s following, bookmarking, and actually reading? While many might find these minutiae tedious, I guarantee that people in his associated fields would find some serious value in it.
I’ve tried hundreds of other apps and tools over the years, but more often than not, they only cover a small fraction of the necessary moving pieces within a much larger moving apparatus that a working researcher and writer requires. This often means that one is often using dozens of specialized tools upon which there’s a huge duplication of data efforts. It also presumes these tools will be around for more than a few years and allow easy import/export of one’s hard fought for data and time invested in using them.
If you’re aware of something interesting in this space that might be useful, I’m happy to take a look at it. Even if I might not use the service itself, perhaps it’s got a piece of functionality that I can recreate into my own site and workflow somehow?
If you’d like help in building and fleshing out a system similar to the one I’ve outlined above, I’m happy to help do that too.
Brian Wansink won fame, funding, and influence for his science-backed advice on healthy eating. Now, emails show how the Cornell professor and his colleagues have hacked and massaged low-quality data into headline-friendly studies to “go virally big time.”
This article is painful to read and has some serious implications for both science in general and the issue of repeat-ability. I suspect that this is an easily caught flagrant case and that it probably only scratches the surface. The increased competition in research and the academy is sure to create more cases of this in the future.
We really need people to begin publishing their negative results and doing a better job on understanding and practicing statistics. Science is already not “believed” by far too many in the United States, we really don’t need bad actors like this eroding the solid foundations we’ve otherwise built.
Scientists solve problems; that’s their job. But which problems are promising topics of research? This is the question I set out to answer in Lost in Math at least concerning the foundations of physics.
A first, rough, classification of research problems can be made using Thomas Kuhn’s cycle of scientific theories. Kuhn’s cycle consists of a phase of “normal science” followed by “crisis” leading to a paradigm change, after which a new phase of “normal science” begins. This grossly oversimplifies reality, but it will be good enough for what follows.
A nice little article on a question many of us should be asking ourselves more often. This one has some additional nice overview of bits of physics in addition, but circling back around to the original question is always very valuable.
Fragmention is a portmanteau word made up of fragment and mention (or even Webmention), but in more technical terms, it’s a simple way of creating a URL that not only targets a particular page on the internet, but allows you to target a specific sub-section of that page whether it’s a photo, paragraph, a few words, or even specific HTML elements like <div> or <span> on such a page. In short, it’s like a permalink to content within a web page instead of just the page itself.
Back in December Aaron Davis had made a quote card for one of his posts that included a quote from one of my posts. While I don’t think he pinged (or webmentioned) it within his own post, I ran across it in his Twitter feed and he cross-posted it to his Flickr account where he credited where the underlying photo and quote came from along with their relevant URLs.
Fragmentions could have not only let him link to the source page of the quote, it would have let him directly target the section or the paragraph where the quote originated or–even more directly–the actual line of the quote.
They both obviously point to the same specific page, and their beginnings are identical. The second one has a # followed by the words “I’m not looking” with some code for blank spaces and an apostrophe. Clicking on the fragmention URL will take you to the root page which then triggers a snippet of JavaScript on my site that causes the closest container with the text following the hash to be highlighted in a bright yellow color. The browser also automatically scrolls down to the location of the highlight.
This can be a very useful thing, particularly on pages with huge amounts of text. I use it quite often in my own posts to direct people to particular sub-parts of my website to better highlight the pieces I think they’ll find useful.
It can be even more useful for academics and researchers who want to highlight or even bookmark specific passages of text online. Those with experience on the Medium.com platform will also notice how useful highlighting can be, but having a specific permalink structure for it goes a step further.
I will note however, that it’s been rare, if ever, that anyone besides myself has used this functionality on my site. Why? We’ll look at that in just a moment.
Extending fragmentions for easier usability.
Recently as a result of multiple conversations with Aaron Davis (on and between our websites via webmention with syndication to Twitter), I’ve been thinking more about notes, highlights, and annotations on the web. He wrote a post which discusses “Page Bookmarks” which are an interesting way of manually adding anchors on web pages to allow for targeting specific portions of web pages. This can make it easy for the user to click on links on a page to let them scroll up and down specific pages. Sadly, these are very painful to create and use both for a site owner and even more so for the outside public which has absolutely no control over them whatsoever.
His post reminded me immediately of fragmentions. It also reminded me that there was a second bit of user interface related to fragmentions that I’d always meant to also add to my site, but somehow never got around to connecting: a “fragmentioner” to make it more obvious that you could use fragmentions on my site.
In short, how could a user know that my website even supports fragmentions? How could I make it easier for them to create a fragmention from my site to share out with others? Fortunately for me, our IndieWeb friend Kartik Prabhu had already wired up the details for his own personal website and released the code and some pointers for others who were interested in setting it up themselves. It’s freely available on Github and includes some reasonable details for installation.
So with a small bit of tweaking and one or two refinements, I got the code up and running and voilà! I now have a natural UI for highlighting things.
How?
When a user naturally selects a portion of my page with their mouse–the way they might if they were going to cut and paste the text, a simple interface pops up with instructions to click it for a link. Kartik’s JavaScript automatically converts the highlight into the proper format and changes the page’s URL to include the appropriate fragmention URL for that snippet of the page. A cut and paste allows the reader to put that highlighted piece’s URL anywhere she likes.
Highlighting text pulls up some simple user interface for creating a fragmention to the highlighted text.
The future
What else would be nice?
I can’t help but think that it would be fantastic if the WordPress Fragmention plugin added the UI piece for highlight and sharing text via an automatically generated link.
Perhaps in the future one could allow a highlight and click interaction not only get the link, but to get a copy of both the highlighted text and the link to the URL. I’ve seen this behavior on some very socially savvy news websites. This would certainly make a common practice of cutting and pasting content much easier to do while also cleverly including a reference link.
The tough part of this functionality is that it’s only available on websites that specifically enable it. While not too difficult, it would be far nicer to have native browser support for both fragmention creation and use. This would mean that I don’t need to include the JavaScript on my website to do the scrolling or highlighting and I wouldn’t need any JavaScript on my site to enable the highlighting to provide the specific code for the custom URL. How nice would it be if this were an open web standard and supported by major browsers without the need for work at the website level?
Medium-like highlighting and comments suddenly become a little easier for websites to support. With some additional code, it’s only a hop, skip, and a jump to dovetail this fragmention functionality with the W3C Webmentions spec to allow inline marginalia on posts. One can create a fragmention targeting text on a website and write a reply to it. With some UI built out, by sending a webmention to the site, it could pick up the comment and display it as a marginal note at that particular spot instead of as a traditional comment below the post where it might otherwise loose the context of being associated at the related point in the main text. In fact our friend Kartik Prabhu has done just this on his website. Here’s an example of it in his post announcing the feature.
Example of inline marginalia on Kartik Prabhu’s website “Parallel Transport”.
You’ll notice that small quotation bubbles appear at various points in the text indicating marginalia. By clicking on them, the bubble turns green and the page expands to show the comment at that location. One could easily imagine CSS that allows the marginalia to actually display in the margin of the page for wider screens.
How could you imagine using fragmentions? What would you do with them? Feel free to add your thoughts below or own your site and send me a webmention.
Sci-Hub, often referred to as the "Pirate Bay of Science," lost three of its domain names this week. The suspensions are likely the result of the lost court case against the American Chemical Society. Despite the setback, Sci-Hub remains resilient, pointing out that there are other ways to access the site including its own custom DNS servers.
I knew at a pretty early stage in my life — my freshman year of college, to be exact — that I wanted to become a research mathematician. I have degrees from fancy research universities…
If you write clearly, then your readers may understand your mathematics and conclude that it isn't profound. Worse, a referee may find your errors. Here are some tips for avoiding these awful possibilities.
I want to come back and read this referenced article by Milne. The comments on this are pretty interesting as well.
Rolling out to Medium users over the coming week will be a new, more satisfying way for readers to give feedback to writers. We call it “Claps.” It’s no longer simply whether you like, or don’t like, something. Now you can give variable levels of applause to a story. Maybe clap once, or maybe 10 or 20 times. You’re in control and can clap to your heart’s desire.
Yet another way to “like” a post….
This reminds me a lot of Path’s pivot to stickers. We all know how relevant it has made them since.
And all this just after Netflix, the company that has probably done more research on ranking than any other, has gone from a multi-star intent to a thumbs up/thumbs down in the past month.
Most of the measurements social media and other companies are really trying to make are signal to noise ratios as well as creating some semblance of dynamic range. A simple thumbs up creates almost no dynamic range compared to thumbs up/nothing/thumbs-down. Major platforms drive enough traffic that the SNR all comes out in the wash. Without the negative intent (dis-like, thumbs down, etc.) we’re missing out on some important data. It’s almost reminiscent to the science community only publishing their positive results and not the negative results. As a result scientific research is losing a tremendous amount of value.
We need to be more careful what we’re doing and why…
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