How to Keep a Lab Notebook

I saw a pointer to this reddit post with the provocative title “Org mode appearing into the wild…” Naturally, I had to follow the link to see what it was about. It turns out to refer to a Science article entitled How to keep a lab notebook. It’s mostly advice to researchers in the laboratory sciences and comprises short descriptions from many researchers on various aspects of keeping a laboratory notebook.

Other than universal agreement that it’s a necessary part of doing research, there’s a significant amount of disagreement on the best way of doing things. A surprising number of researchers prefer keeping their notebooks on paper. Some of that is no doubt driven by long standing protocols involving the protection of intellectual property but some researchers said they just liked it better.

Many of the researchers preferred a digital notebook citing advantages such as searchability and backups. One even mentioned Org-mode as the ideal way of maintaining her lab notebook saying that Org makes it easy to include a scan of handwritten notes, equations, bibliographies, tables, and even code. That’s a sentiment that many Irreal readers will identify with even if they aren’t laboratory researchers.

Finally, some of the researchers used a hybrid system where they collected notes in a traditional paper notebook as they were performing their experiments but later either transcribed or scanned them into a digital notebook.

It may be that I’m just fascinated by such things but I found the article very informative and enjoyed reading about the various strategies that people used. It’s well worth a read if you have any interest in such things.

Posted in General | Tagged , , | Leave a comment

Is It Time to Get Rid of The P-Test?

Betteridge’s law tells us to answer that question with a “no” and that’s—at least partially—the right answer. “No” is the right answer because scientists and statisticians can’t agree on what should replace the p-test. It’s the wrong answer because it’s not working and an uncomfortably large part of scientific research is proving to be irreproducible, a fact that many statisticians and other scientists are attributing to an over reliance on the concept of statistical significance.

Over at Science News, Bethany Brookshire has an excellent article on what science would look like without the concept of statistical significance. Most everyone agrees that using the p-test as a binary indicator of whether or not an experiment “succeeded” is inappropriate. The problem is that they can’t decide on what to do instead. As Steven Goodman, a Stanford University medical research methodologist, puts it, Everyone knows what they’re against. Very few people know what they’re for. Some simply want to tighten the p-test criteria from .05 to .005. Others, like Aubrey Clayton, want to replace the p-test all together with Bayesian Analysis.

Statisticians seem overwhelmingly in favor of replacing the p-test as a way of deciding the worth of an experiment. Blake McShane, a statistician at Northwestern University, notes that statistics is often wrongly perceived to be a way to get rid of uncertainty but it’s really about quantifying the degree of uncertainty. Seen in that light, it’s not that the p-test is bad, it’s the notion that you can use it to eliminate uncertainty that needs to be replaced.

Take a look at Brookshire’s article. It’s interesting and provides a good summary of a serious problem.

Posted in General | Tagged | Leave a comment

Speaking of Passwords

Yesterday, I wrote about stupid password rules and why they don’t matter for banks. Serendipitously, right after I published that post I came across an old Coding Horror post on stupid password rules. It’s a long and righteous rant on the infuriating, nonsensical password rules that confuse the less technically sophisticated leading them to seek workarounds that are less secure. At the same time, they frustrate the ideal user who employs a password manager to generate the long, random passwords that are more secure than anything the rules could provide.

Atwood doesn’t subscribe to the Irreal rule that any restriction is a sign of weakness. He divides password rules into two classes: those that you tell the users about before they attempt to choose one and those you apply as a sanity check after the a password is chosen.

There’s one rule in the first class: passwords must exceed a minimum length. What that minimum length is will vary according to the application you’re protecting and the environment you’re working in. Even if passwords are salted and hashed, a stupid password like abc is still easy to discover. A long password is effectively safe from brute forcing even with an offline attack.

The rules in the second class get rid of obvious passwords that any attacker will try. They include things like the user’s login ID, the user’s email address, and perhaps any password on one of the lists of most commonly used passwords that appear every year. You can read Atwood’s post to see the exact rules in the second class.

Of course, the only sensible thing to do is to use a password manager to generate long, random passwords. At least if the site will let you.

Posted in General | Tagged | Leave a comment

Troy Hunt on Bank Passwords

Over the years, I’ve done a lot of huffing and puffing about passwords, most recently in my post on Bad Password Policies. Troy Hunt has a slightly different take on things, at least as far as banks are concerned. It seems odd that Hunt would give banks, of all institutions, a break. After all, the stakes are generally higher and banks have ridiculously lax password policies.

Hunt does agree that banks shouldn’t have these silly policies but says that they’re usually required by legacy concerns and, in any event, don’t really matter. Wait. What? How can they not matter? There’s two reasons for that. First, banks are aggressive about blocking accounts after three failed login attempts. Even if the bank has a ridiculous password policy like four digits—yes, some banks have exactly that policy—two mistakes doesn’t leave a would-be exploiter very much room.

Second, banks don’t rely just on the customer-facing security mechanisms to verify a login. They have additional mechanisms hidden from the customer. The banks, of course, rightfully won’t say what those additional mechanisms are. We’re more or less required to trust the banks that they’re effective.

Although Hunt says the policies don’t really matter, he does, as I wrote above, say that they should do better. “We’ve got old systems to interface with” shouldn’t be a perpetual excuse. After a while you have to upgrade those old systems. One of the main reasons it matters, he says, is trust. It’s pretty hard to judge the security of a site. The best method we have is, as I’m always harping, is to consider any password restrictions a sign of weak security and worse, an indication that your passwords aren’t being salted and hashed. Trust is important with any commercial interaction and especially so when dealing with banks so they shouldn’t squander it with stupid password policies.

Take a look at Hunt’s post. It’s an interesting and informative look at a little-understood aspect of banking security.

Posted in General | Tagged | Leave a comment

The New Luddites Take Off the Mask

The other day I thanked the New York Times for proving my point. Now it’s The Guardian’s turn, albeit for a different point. I’m sure that by now many of you roll your eyes and think, Reagan like, “there he goes again” every time I write about the New Luddites. A sane person would have a hard time believing such people actually exist and that Irreal isn’t just indulging itself with a long-running gag.

That’s what you’d think but you’d be wrong. These people must assuredly exist and in case you think I’m exaggerating I offer this nifty little opinion piece by Ben Tarnoff appearing in the Guardian. In it, Tarnoff declares that we must “decomputerize” and explicitly urges a new Luddism to accomplish that.

His reasons for that are the usual but he gets a bit confused. He keeps conflating surveillance and computers. To be sure computers make surveillance easier just as cars make it easier for criminals to escape after a robbery1, yet no one—at least no one serious—suggests that we go back to the horse and buggy. It apparently never occurred to him that you can have surveillance without computers and computers without surveillance. If the problem is surveillance—and it is a problem—then fight the surveillance not one of the tools used by the snoopers.

Of course, when Tarnoff isn’t confusing computers with surveillance, he’s carrying on about all the power those computers use. But as I mentioned in my post on saving the world with smartphones, electricity use has been flat (at least in the US) for the last decade. As with smartphones, the New Luddites like to go on and on about how much power some piece of technology uses but they never consider how much power its use saves. It’s not hard to think of ways that using computers saves resources (teleconferencing is an obvious example) but you have to be willing to look.

I do wish these people would repair to their farms and live off the land or whatever it is they want to do and leave the rest of us in peace. But no, they have to drag us all along. I, for one, am not interested in outdoor toilets, dirty water and typhus, 19th century medicine, famines, or a life expectancy of 50 so I’m going to remain in the modern world. With my computers.

Footnotes:

1

Indeed, cars were once decried by a judge for making it easier for criminals to escape crime scenes.

Posted in General | Tagged , , | Leave a comment

Four Org-mode Talks

The SF Emacs Meetup group has a video of one of their recent meetings featuring talks by four Org-mode users. The middle two talks, Tikhon Elvis on reveal.js and Jeff Tull on Org Babel, are elementary overviews. They’ll be useful for those unfamiliar with the two packages but probably won’t help users who already know them.

The other two talks, John Wiegley on how he uses Org-mode, and John Kitchin on how he and his group use Org-mode to publish scientific papers, will appeal to more experienced Org-mode users.

Wiegley’s talk is really about his workflow but that workflow is Org-mode-centric so he concentrates on how he uses Org-mode to manage his life. One the big takeaways from his talk is that he doesn’t spend a lot of time in the actual Org files. Rather, he depends on the Org agenda—along with some custom views—to track his days and keep on top of things. It’s a really interesting talk and best of all, his configuration is available in his GitHub repository. One trick I learned was using a UUID as the ID property as the target for links. That’s useful if, as I often do, you want to edit the header for the link (the default target). If I make a typo or otherwise want to change one of my headers, I can’t without changing every reference. Using the ID as a target instead solves that problem neatly.

Kitchin’s talk takes us through the process he uses for writing and submitting papers to scientific journals using Org mode. Irreal has covered part of that process before, especially the really excellent org-ref package but not the actual process of preparing an article for a specific journal. The journals are notoriously crabby about the exact format you have to use when submitting papers and its more than just a house style sheet. Kitchin covers how he and his group have automated most of these annoying details. He’s the expert on this stuff because, as he says, his group have published about 30 papers using Org-mode, which is more than anyone else in the world.

The videos are a little over an hour and 45 minutes so you’ll have to schedule time but they are definitely worthwhile.

UPDATE [2019-09-19 Thu 14:27]: Fixed link to video.

Posted in General | Tagged , | Leave a comment

Emacs Workout

Tony Ballantyne is an Emacs-using Science Fiction writer whom I’ve written about before. Ballantyne has an interesting device to help him remember Emacs commands: the Emacs workout. The idea is to write short summaries of Emacs features that you find useful but don’t invoke every day. That way, you can periodically go through the list to build up your Emacs muscles. Used correctly, the technique is an example of spaced repetition, which many claim to be the most efficient way of learning something. See this excellent video by Ali Abdaal for more on the idea.

You can find Ballantyne’s list at the link. It’s worth reading to pick up some new ideas as well as remind you of old ones. For instance, I didn’t know about map-query-replace-regexp. I don’t have a need for it in my workflow right now but it’s nice to know about it for the day that one pops up.

Ballantyne’s list is a useful place to start but to really take advantage of the idea, you should make your own covering the seldom needed but useful Emacs techniques that you can never remember. That way you can review them periodically and keep them fresh in your mind and muscle memory. There are all kinds of useful shortcuts that I learn but forget because I don’t need them often. I even have functions that I’ve written in my init.el that I’ve either forgotten or only vaguely remember. You can, of course, look these things up once you know they exist but that’s a serious context switch. I’m going to try Ballantyne’s method to see if I can better keep them in mind.

Posted in General | Tagged | Leave a comment

The New York Times Proves My Point

Last week, I reminded everyone that Irreal doesn’t hold journalists in high regard and that Apple, in particular, appears to bring out the worst in tech reporters. The Paper of Record must have been feeling left out because they published a column by Charlie Warzel that combines what I consider the two worst aspects of the modern web:

  1. The ascendancy of the New Luddites with their constant carping about how technology is destroying civilization and the world, and
  2. The inexorable need to drag jejune politics into every damn discussion on the Internet.

The ostensible point of the column was that Apple should stop holding its Keynote Events but it quickly devolved into the usual “we’re killing gaia” nonsense and the assertion that we have more important things, like income inequality, to worry about than new iPhones.

Being famously curmudgeonly, Irreal’s inclination is to dismiss this nonsense with words best omitted from a blog that might be read by women or children but you don’t have to depend on me to take down this silliness. Over at Daring Fireball, John Gruber delivers a long and excellent rant on how vacuous Warzel’s column really is. It’s a righteous takedown and you should definitely read it even if you aren’t an Apple user or fan.

The worst thing about Warzel’s fatuous column is that it appeared not in Joe’s Fishing and Tech Webzine but in the freaking New York Times. If you had any remaining respect for the Times, you can let it go. This column is one more example of how they’ve forfeited that respect.

Added in editing: The Macalope weighs in.

Posted in General | Tagged | Leave a comment

The Google Nest Hub Max

I don’t know about you but I couldn’t help thinking of telescreens from Nineteen Eighty-four when I read this article about Google’s always on Nest Hub Max. The similarities are striking. The camera is always watching so that it can match your face and figure out what to show you. The microphone, needless to say, is also always on.

Google is not, of course, the Thought Police but who in their right mind would grant 24 by 7 surveillance access to a company like Google that makes its money from vacuuming up every possible bit of information about you so they can sell it? I don’t care how convenient those devices are, they’re not getting into my home.

It is, I suppose, easy to dismiss those who use them as clueless folks hurting no one but themselves but devices like the Next Hub Max normalize devices like telescreens. They move the Overton window towards more surveillance and habituate us to having someone always watching. Today they’re just a voluntary way of helping you turn on the lights or whatever. We don’t want a tomorrow where they’ve morphed into mandatory telescreens in the name of “keeping us safe” and from having inappropriate thoughts.

If you care about your privacy and don’t want constant surveillance to become the norm, just say no to the Nest Hub Max and all its evil siblings.

Posted in General | Tagged , | Leave a comment

Exporting Only the Contents of An Org Subtree

Here’s a short Org-mode tip that, although quite old, I just learned about. Suppose you want to export an Org subtree but you want only the contents and not the header. This emacs-reddit question, which alerted me to the solution, gives a typical use case for such a capability.

It turns out that there are lots of ways of doing this but the easiest is to require ox-extra as explained here. Once you’ve gotten the proper packages loaded and configured, you need only add an :ignore tag to the header that you don’t want to export. This differs from using the (typical) :noexport tag in that the contents will still be exported.

Notice that the package you need to install is org-plus-contrib not ox-extra. Also note that you’ll need to have the Org repository in your list of ELPA repositories. You can do that with something like

(add-to-list 'package-archives '("org" . "https://orgmode.org/elpa/") t)

if you don’t already have it included.

I haven’t needed something like this very often but it’s nice to know how to do it when I do have the need.

Posted in General | Tagged , | Leave a comment