Accessing Research You Already Paid For

A long standing source of frustration in the research community has been the locking of research papers behind paywalls. It’s easy to see how detrimental this is to the scientific research enterprise. After all, the purpose of publishing papers is to share the research results among the greater scientific community.

For all of my adult life—and probably longer, maybe even forever—the research behind these papers have been paid for by the government. In modern times, that means you and me. So here’s the consequence: we pay for the research but can’t read the results of that research unless we want to pay substantial fees to the publishers of the associated papers.

You can easily see the problem from the publishers point of view. It’s an existential threat. If the papers were made available without charge, why would anyone (or more specifically, any institution) pay thousands of dollars a year for access to the journals? The journals argue that they do provide added value. They perform curation, editing, and perhaps most importantly, peer revue of the papers.

But here’s the thing. Except for some in-house copy editors, they don’t pay anything for those efforts. They’re all considered necessary public service on the part of academics. So all of that “added value” can be and is provided for open access, on-line journals. Really, the only reason that paid, dead tree journals continue to exist is academic tradition. The journals have always played a huge role in tenure and promotion decisions in academia and many can’t imagine any other way of doing business.

Regardless, for research funded by the US National Institutes of Health, at least, the journal monopoly is coming to an end. Effective July 1, 2025, the results of all NIH supported research will be available without charge. This is a slight acceleration of the previous policy that required public availability by December 31, 2025, but it serves as notice that this long standing rip off of the public will no longer be tolerated.

Of course, research not funded by the government—if there is any—is not affected but it’s hard to imagine there’s enough of it to make it worthwhile to keep charging for it. Maybe the journals will find a way to reconfigure their business model or maybe they’ll simply go out of business. Either way, we’ll be better off. These days, it’s easy to publish on line and for those who want curated papers, there are already open access sites providing that service.

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🥩 Red Meet Friday: Parenthesis: Get Over It Already

As you almost certainly know, we here at Irreal have little patience for those constantly whining about parentheses in Lisp. They seem to us like little kids complaining to Mom that “it’s not fair”. Apparently, we’re not the only ones. Joe Marshal, who I’ve mentioned before, is an old time Lisper—so old timey that he worked on the firmware for one of the actual Lisp machines—who also doesn’t have a lot of patience for the whining.

He settled on a unique solution. He asked his AI client, Gemini, to write a rant for him. I have to admit, as much as I dismiss the current AI craze as voodoo, the rant was probably better than I could have written. If you, too, are tired of the jejune whimpering from the ignorati, take a look at Marshall’s post for some well earned relief.

Maybe we can enlist an army of these AIs to beat the whiners into submission or at least into complaining about something else. The Illuminati maybe.

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Journelly!

Hooray. Journelly, which I think of as an iOS front end for Emacs’ Org mode, has been officially released. For those of you who have been waiting for an official release to try it out, your time has come.

I’ve been using this app everyday for the last month and even though I was working with a beta, it has been rock solid. I really, really like this app and recommend that everyone try it out. It’s $14.99 but let me assure you that it’s worth every penny.

One of the things that I haven’t mentioned in my posts about it is that there’s seamless syncing of your data. No third party apps or difficult configuration. You simply specify that you want to sync your data to iCloud and it’s instantly available to Org mode on your Mac and the rest of your iOS devices. Exactly what we expect, but seldom get from apps that interface between iOS and Emacs. Ramírez says that exporting to Markdown is on his todo list so even if you aren’t—for some reason—an Org mode user, he’s got you covered.

This is the first app that I’ve bought for a long time but I’m happy to spend the money. Journelly has become an important part of my workflow.

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Preventing Minor Modes From Appearing On The Mode Line

The Emacs mode line contains a wealth of information, much of which I depend on daily. Some of that information is what the major mode is and what minor modes are active. Again, that’s often useful information. Still, there are plenty of minor modes that I don’t care about, either because they’re always enabled or because they simply don’t matter to my workflow.

For a long time, the standard way of dealing with that was the diminish command that would prevent a given minor mode from appearing on the mode line. The problem was that it sometimes didn’t work and, at least in my experience, every update of a package would reset the diminish function to off for that mode.

Relief is finally—or at least will be—here. Coming in Emacs 31 is mode-line-collapse-minor-modes. The idea is that you will list in a single variable those minor modes you don’t want to appear on the mode line or, optionally, those you do. By default those modes excluded are represented by a single ... on the mode line. You can click on that to see a list of the hidden modes.

As I’ve said before, I usually have two side-by-side windows in a single Emacs frame. That means that there’s not a lot of room on my mode line so getting rid of less important information is essential to me. Diminish has worked reasonably well for that but I’ll be glad to have a simpler way of handling the problem. Emacs 31 is still sometime away but it’s something to look forward to.

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Scrim Released

A couple of weeks ago, I wrote about Charles Choi’s Scrim beta. Scrim is an app that makes the Org Protocol work in macOS. The problem, as Choi explains is that Org Protocol depends on calling emacsclient to deliver the messages to Emacs. Unfortunately, this became impossible when Apple started sandboxing applications for security reasons.

Choi is a huge fan of Org Protocol so he he wrote Scrim to act as a native macOS client for Emacs server. That gets around the sandboxing and allows Org Protocol to work on macOS. Scrim is now available on the on the App store by itself or as a bundle with the related app Captee that allows sharing links from other applications via the share menu.

I’ve tried using Org Protocol before but could never get it to work. Now I understand why. If you too have tried and failed to get Org Protocol working, you can get Scrim and Captee for $7.99. That’s a very reasonable price and since the two apps scratch one of Choi’s itches, it’s very likely that they’ll be maintained on an ongoing basis.

Take a look at Choi’s announcement to see if Scrim might be helpful to you.

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JTR’s Month With Journelly

It’s been about a month since JTR (over at TAONAW) and I started using Journelly. Although it’s still in beta—but approaching its release date—I’ve nevertheless come to rely on it for my memo book. It’s smooth integration with Org mode and Emacs makes it a natural iOS front end for Org and a perfect fit for my memo book. Keeping its file in Org format and syncing it to my Mac make it really easy to integrate it into my Emacs workflow.

JTR has a post reporting on his own experience with using Journelly over the last month. Like me, he’s settled into using Journelly as part of his day-to-day work and depends on it even though it’s still beta software. As I discussed the last time I wrote about JTR and his use of Journelly, he uses it as a staging area for his other Org files. That appears to be working well for him and he’s been refining his workflow as he gains experience with the app.

One of his major concerns is dealing with the photos that he adds to the entries. He likes to tweak them in various ways such as reducing their resolution and sometimes even editing the photo itself. Happily, I don’t have those problems. I suppose it might happen that I need to work on a photo for some reason or another but I can do that from the comfort of my Mac.
If you’re dealing with the Journelly photos a lot, you might want to read about how JTR deals with the fact that Journelly names them with unique IDs that give no clue as to what the photo is of. The TL;DR is that he uses Dired thumbnails to see what each picture is about. The photos are kept in a separate file so it’s easy to display the thumbnails in Dired.

As I’ve said before, Journelly can adapt itself to a variety of workflows so it’s worth your while to read about as many of them as you can. Take a look at JTR’s post to see one of those workflows.

Update [2025-04-29 Tue 13:06]: In a subsequent post JTR writes a bit more about how he handles pictures in Journelly.

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Digital Life Update

It’s been a while since my last post on living the digital life. For those of you just joining the conversation, I’m several years in on trying to live a digital life, by which I mean giving up pens and paper, recording all my records electronically, and enacting all my business digitally. My touchstone for how I know when I’ve achieved this is to be able to leave home with nothing but my iPhone. That means, among other things, no credit cards, no driver’s license, and no house or car keys. Other than my license and car keys, I’m pretty much there. Who knows, maybe Florida will get its act together before I die and I’ll be able to stop carrying a paper license.

In the meantime, the technical world has been moving on and cell phones are no longer the only feasible way staying connected remotely. Devices like the iWatch can now do much of what we previously relied on smart phones for. When the iWatch was first announced, it depended on an associated iPhone for most of its capabilities.

That’s no longer the case. The iWatch and its Android brethren now operate independently and can form the basis of our remote digital lifeline. It’s possible, as this article suggests, that modern e-watches can do most of what we’ve been depending on smart phones for.

After more than 20 years of not wearing watch—I had an iPhone that told me the time and much more; why would I need a watch—I recently got an iWatch to help track my health. I was surprised at how flexible it is. I can use it in place of credit cards, can control my Smart Home functions with it (including unlocking my door), can track my appointments, can receive and respond to texts, and can even make and answer phone calls.

That raises the question of whether the iWatch will replace my iPhone as my go to remote device. I don’t think so. I use the iWatch if in my phone is in my pocket and it’s easier to just use my iWatch but I mostly depend on my iPhone and keep it with me all the time. But who knows? Maybe we really will wear our digital interface on our wrists. What are you guys doing?

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Sorting String In A Line

Charles Choi has posted a tip mostly, he says, as a reminder to his future self. It’s about how to sort strings on a single Emacs line. At first blush that may not seem all that useful but a moment’s thought will bring to mind all sorts of situations where it’s just what you need.

The secret sauce is sort-regexp-fields, which actually sorts a region whether or not it’s on a single line. When called interactively, you will need to supply two regexes. The first is used to identify the record and the second to identify the key of that record.

If you specify a match field in the record regex, you can use a match number (\n) for the key regex. If the key is the whole field, you can use \&.

Choi has an example that shows how to sort quote-delimited strings on a single line and the documentation has an example of sorting lines by the first word that starts with f. The documentation example shows how powerful the method really is.

In any event, this post is partially a reminder to future me and you should bookmark Choi’s post to remind yourself how to do it. It’s another one of those things that you don’t need very often but when you do, you’ll be really glad to have a reminder of how to do it.

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Keeping Org Files Sorted

Christian Tietze has an informative post that tells us how to keep an Org file sorted. Your first question should be, “What do you mean by sorted?” Your second question should be, “What does ‘keep sorted’ mean?”

Tietze answers both these questions. The answer to the second question is easier. By “keep sorted” he means that after adding an entry to the file, it will automatically be inserted into its proper “sorted” place without the user having to do anything special.

The answer to the first question is “it depends”. Not very helpful, I know. The precise answer is “whatever sorting order you can describe with org-sort-entries.” Take a look at its documentation to see how many possibilities that entails. You can also provide your own comparison and data extraction functions so the practical answer is “just about any order you desire.”

There is, of course, a bit of configuration that you have to do to have all this take place. Tietze’s post explains how to set things up. The org-sort-entries function is so flexible that it will cover most cases out of the box but there is, as I said, an escape hatch for special needs.

This is another example of how much flexibility is built into Emacs and Org. Most users probably don’t need and aren’t even aware of the functionality that Tietze writes about but it’s there for those who do need it.

As I and others keep telling you, it’s not an editor, it’s a Lisp instance with built in editing commands. You can make just about anything you need happen, usually pretty easily.

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Emacs Time Stamps

The Emacs Cat has a post on an Emacs feature that I use but had mostly forgotten about. It concerns the Emacs time stamp that lets you record in a file when it was last modified. I use it at the top of my init.el to record when it was last changed.

It’s pretty simple to use. You just add a Time-stamp: string somewhere in the first few lines of the file, do a tiny bit of Emacs configuration, and Emacs will add a time stamp whenever the file is saved. My impression is that it’s mostly used in init.el files but it can be used in any file that you edit with Emacs. The Cat’s post give some examples of using it with an Elisp file, an Org file, and a C++ file.

Usually you have to have the Time-stamp: as part of a comment but in some cases, as shown in the Org file, it can be part of the actual file data. Almost everything is configurable. You can specify how many lines from the top of the file to look for the Time-stamp, and you can specify what the time stamp itself with look like.

Take a look at the Cat’s post or the documentation for the details

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