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Biomedical and Electrical Engineer with interests in information theory, evolution, genetics, abstract mathematics, microbiology, big history, IndieWeb, mnemonics, and the entertainment industry including: finance, distribution, representation

boffosocko.com

chrisaldrich

chrisaldrich

+13107510548

chris@boffosocko.com

stream.boffosocko.com

www.boffosockobooks.com

chrisaldrich

mastodon.social/@chrisaldrich

micro.blog/chrisaldrich

 

@hypothes_is @CarlosGoller @mbiotech Carlos, thanks for sharing your experience this morning. Based on some of your comments in (live and in chat), if you've not come across it, you and *especially your students* may appreciate Sönke Ahrens' book "How to Take Smart Notes: One Simple Technique to Boost Writing, Learning and Thinking - for Students, Academics and Nonfiction Book Writers". The techniques there can readily be implemented with Hypothesis in much the way you mentioned your students are already naturally doing for their own research. The book may help encourage them to extend their practice (in addition to a built in, but broadly unsung happiness/fun/quality of life component, which is always welcome in my book). There's also some research cited in it about how the ideas relate to learning research as well for those in the pedagogy related spaces.

https://www.amazon.com/How-Take-Smart-Notes-Nonfiction/dp/B09HSSFCPR/

I'm curious to hear what you, students, and others think about these ideas, particularly after using them for a while.

 

@chuckfrey Primarily for note taking (90%) to feed both a WordPress site and an Obsidian database presently, but also for some social annotation (10%) with respect to things I see via https://annotations.lindylearn.io/new/ or individuals' feeds

My Obsidian store serves variously as a zettelkasten, commonplace book, and wiki simultaneously though each of these are discretely fragmented. Of course I could do most of the work via Hypothesis really without any other tools at all, presuming that the data would always be there.

Large swaths of Hypothes.is use is hiding within LMSs or is geared more toward social annotation in classrooms. I'm more interested in people using that content for their future selves or their creative endeavors.

You can find my publicly available material here: https://hypothes.is/users/chrisaldrich

 

In fact, it's become quite a lot of data lately, sometimes up to 50 items a day. I'll have to add you to my list of people to follow on @hypothes_is
https://boffosocko.com/2019/11/07/following-people-on-hypothesis/

 

Against the Rules: Referees, Journalism, and Politics

2 min read

If correct, the hypothesis by Michael Lewis in Against the Rules could have some profound implications into how we view politics and particularly the current President of the United States and why we need accurate, fair, and objective journalism. Trump's fame is making him cry foul more than is necessary, particularly amidst accusations of wrongdoing. In the episode Ref, You Suck! one can see a clear analogy between the NBA and the current political hellscape.

"...he [referring to Larry Byrd, but this could easily be applied to Donald J. Trump] played with certain assumptions about the rules and how they applied to him..."
"The NBA has set out to ref the game more objectively, more accurately, more fairly. This has enraged the stars and their coaches. You want to know why? The more objectivity there is, the less power they have. Objective refs eliminate some of their privilege. The stars can't get the calls anymore just because they're stars, or anyway, not as often. Lebron James and Kevin Durant and Stef Curry and Clay Thompson, they'll all survive better refs because they're actually just better than everyone else, they don't need unfairness to win. [...]
I think American life just now has at least one thing in common with basketball. The authority of its referees is under attack. And when you have a weak referee you have a big problem. Because a weak referee is a referee who can be bought or intimidated or just simply ignored. A situation goes from being more or less well referred to more or less not. Then one day you wake up in a world that seems not just unfair but actually sort of rigged. That is, it is incapable of becoming fair because the people who benefit from the unfairness have the power to preserve it. Boom!"

tagged:

 

@MorrisPelzel @hypothes_is In some sense, but this is much more decentralized, lightweight, and I own and control it rather than farming it out to a 3rd party. Hypothesis also doesn't (yet?) send webmentions or notifications to my site when it's been marked up either.

 

@mrkrndvs Ultimately you could have more text than the original, so there's really no limit to the text beyond what your system will allow. I've not tried annotating .pdfs, but I suspect you could do it similarly to how I've done books via Kindle which let's me export/import data (example: http://boffosocko.com/2012/06/17/big-history/#Highlights,+Quotes). Having all the data on my own site (even if it's private) allows me much easier search via categories, tags, etc. as well. Typically for books I'm using fair use guidelines, though I'm often respectful and keep lots of my data viewable only to me, so copyright isn't a huge concern generally. For book length pieces, the Amazon Kindle will typically limit you to a percentage of the book to prevent copyright issues from the start. I don't think I've ever run up against their limit. Part of the process is to get enough to excerpt the thought to be able to find it later via search and reference it. I can always refer back to the original if necessary.

For more substantive annotations I try to add them slightly off to the side in a different font/size, but you'll also notice that some of the blue highlights also have "hidden" annotations if you hover over them with your mouse. Things can be a bit crowded with the additional highlights added by Hypothesis (and other people), though I can choose to disable them if I want for my personal work. Hopefully it's relatively obvious based on what's on the page which parts are the original text and which are my additions. When excerpting articles like Watters', the canonical URL on the page points to the original, so all the SEO and links ultimately redound to the original.

 
 

Replied to a post on github.com :

Settings UI/UX feature requests: Ability to globally auto-set post publicly/post to self · Issue · hypothesis/h https://github.com/hypothesis/h/issues/4229

Perhaps it exists already and I'm not seeing it, but most of what I highlight and annotate, I typically prefer if it were automatically published freely and in the open. Currently it appears that highlights default to "only me" after they're highlighted. Annotations appear to default to public initially as they're being written, but when re-entering the text without manually hitting publish, they then are posted automatically to "only me".

This may be a reasonable default, but it means spending more time with the interface while I'm reading/working and thereby taking me out of the flow of my work.

Unfortunately, there is no default setting for forcing my highlights and annotations to be public, which means when I'm done reading that I have to go into the UI and manually do three button presses to make this happen for EVERY post. Click to edit, click the setting arrow, and finally click to publish. UGH!

In addition to allowing a master setting toggle for public/private at the main account level which would alleviate a large portion of my issue, I'd also recommend that rather than a drop down menu with two options that there just be a simple toggle to switch between public/private on each post so the user can accomplish in one click (or fingerpress on touchscreens) what currently takes two. Admittedly it's also controlling a "publish" function simultaneously, but I think that each post could have a public/private toggle and a separate "publish" button without cluttering up the UI too much.

 

@jasongreen, it looks like you know @krisshaffer, but have you run across his Hypothes.is Aggregator for WordPress? http://kris.shaffermusic.com/2016/08/hypothesis-aggregator/

 

Replied to a post on github.com :

Potential future features · Issue #2 · kshaffer/hypothesis_aggregator https://github.com/kshaffer/hypothesis_aggregator/issues/2

This plugin is spectacular by the way... Here are some thoughts on future development:

It would be great if the displayed text output from the shortcode included a permalink to the original annotation on Hypothesis. As a UI suggestion, perhaps you could place it after the title of the annotated page thusly:
URL WRAPPED TITLE | < a href="permalinkhere">#</a>

Being able to circumscribe dates for displayed annotations could be useful, particularly in cases where one wants to highlight only a handful of annotations from a particular user with a particular tag but specific ones within certain time parameters. Additionally pages with embeds could, over time, require importing huge numbers of annotations which may not be ideal, or the context may change with significant future annotations that aren't relevant to what could be a static post that's trying to highlight just a few particular annotations. Time parameters could also prevent future possible spam on unwatched embeds with only "tag" parameters that could be targeted by bad actors.

 

From an indieweb perspective, it's probably far easier, more productive, and better interface hypothes.is both accepted the webmention protocol as well as sending webmentions. This way one could post their comments (highlights may be slightly tougher) directly to their Known (or other site) and the webmention protocol could handle the posting to hypothes.is. Similarly when one annotates a page, hypothes.is could webmention the page, so the post author/site admin would be aware that the page was marked up.

 

Replied to a post on hyp.is :

On the topic of extrapolating where some of this is going, there's also a pending UI issue amongst competing annotation platforms. They're going to need to watch where they put their overlays for annotating/highlighting or they aren't going to work together well. Not to mention other social media plugins that have similar popups for highlighting and sharing.
http://boffosocko.com/wp-content/uploads/2016/04/NewsGenius-vs-Hypothesis.png

 

An Annotated Domain of One’s Own

2 min read

Jeremy, Congratulations on having your own domain! I was poking around Hypothes.is today and was excited to see that you'd moved over from Genius.

I'm impressed that you specifically mention the IndieWebCamp philosophy, which I've also been using for the past couple of years myself.  If you need some help in IndieWeb-ifying your WordPress install, I'd be happy to help, though it's now much, much easier to do than it was even a year ago. Shortly, I'm hoping to finish up a post about the IndieWeb and academia/educational related sites, which might also be helpful, though I'm not sure when that's actually going to be finished.

I'd love nothing more than to have Hypothesis be able to have webmention support so that when people annotate my own pages or reference them across the web, the system would automatically send me a notification of that fact. Are there any coders at Hypothes.is who are also part of the IndieWeb movement who might consider doing this? Is there a way to help suggest this into Hypothes.is's roadmap?

Finally, as a side-note, to help beautify your web presence a bit, you might notice that your photo doesn't show up in the author position in your 2016 theme on single posts.  To fix this, you can (create and) use your WordPress.com username/password to create an account on their sister site Gravatar.com. Uploading your preferred photo on Gravatar and linking it to an email will help to automatically populate your photo in both your site and other wordpress sites across the web. To make it work on your site, just go to your user profile in your wordpress install and use the same email address in your user profile as your gravatar account and the system will port your picture across automatically. If necessary, you can use multiple photos and multiple linked email addresses in your gravatar account to vary your photos.

Congratulations again!

 
 

My reply to ‘Novel, amazing, innovative’: positive words on the rise in science papers | Nature News & Comment
http://www.nature.com/news/novel-amazing-innovative-positive-words-on-the-rise-in-science-papers-1.19024

I can readily posit a potential and very strong motivation for the uptick in the appearance of these words, and particularly for the word "novel", which the paper and this article fail to see.

Beginning in the early 90's, and certainly starting before that time, there has been an intensified interest for both research institutions and researchers writing papers for them to monetize their research outside the halls of the academy. (Particularly with decreased funding for faculty and intensified competition for research dollars - many research faculty either self-fund their salaries or rely heavily on 3rd party income.) Toward this end, individual researchers began more aggressively pursuing patents for their research work and at the institutional level, colleges and universities began very actively pursuing technology transfer to the point of opening up full offices and hiring large numbers of staff to better leverage the return of creating patents and pursuing sales and licensing deals for the resulting research work. The US Patent Office, in making a determination of whether or not to grant patents, (and even moreso when the underlying documents are published scientific research articles) uses words like "novel" and "innovative" as an indicator of their worthiness. Without a patent, it's incredibly difficult to protect the intellectual property contained within a published and public work. Other words like "amazing" which are also cited in the paper are geared (in a business sales sense) more toward potential corporate financial investors who may consider purchasing or licensing the resulting work of a research paper. What corporate bean counter wants to invest in a dull-sounding research paper title which is quite likely one of the only parts of the document they're likely to comprehend? Yet throw in some "excitement words" and you may have a sale!

When one looks at employment contracts of the professoriate (post-docs, graduate students, and the like), which presumably comprises the majority of those publishing papers with these words, one will see that professors prior to the 90's have contracts that don't mention intellectual property rights resulting from their efforts, or which grant them the lion's share. Current contracts after that period will almost necessarily keep either all or most of these types of revenue streams in the institution's pockets rather than the researchers themselves. I'd be willing to bet that this tide began turning in the mid-1970s and has certainly been overwhelming since the mid-90s.

It is these severe economic taskmasters which are almost assuredly the cause of the rise of these buzzwords in research papers, and most particularly in their titles. One need only ask themselves, which university wants to be the next proverbial "Stanford" to not have a piece of revenue from the intellectual property of a proverbial "Page rank" algorithm? Or in biomedical research, to not take a hefty cut out of a drug which could potentially cure cancer or HIV/AIDS? Take a gander at what something as simple as a HELA cell, which was taken and cultured without any notice to Henrietta Lacks, has become from an industrial perspective. If they can avoid it, academia certainly won't let multi-million (or billion) dollar enterprises spring up (again) without them receiving a piece of the pie.

Naturally, there are other factors compounding the issues at hand, particularly when one looks at negative research findings, which are sadly rarely ever published, particularly in an era of big data when what we know isn't true will surely help assist in defining the boundaries of what we do know and what could potentially be determined at that boundary. (Much the way that white space in photographs or in printed pages helps to define an image as much if not more so than the darker portions of the image.) Negative words are likely more difficult to get published as it may reflect poorly on researchers who are reliant on continued future funding and may see their sources disappear when they're not producing groundbreaking work. My hypothesis, however, is that it's more likely a direct economic impact based on technology transfer than it is the increased competitive landscape in academic research.