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The article mentions, but doesn't elaborate, on the purpose of the notebook as a legal document. This was much more important when notebooks could be used to sh

The article mentions, but doesn't elaborate, on the purpose of the notebook as a legal document. This was much more important when notebooks could be used to show priority in patent disputes, but only if well kept. My parents were both research scientists. Where my dad worked, the company patent lawyer read and critiqued your notebooks, and maintained the discipline. Many of those rules became unnecessary when the US patent system joined the rest of the world by adopting "first to file" priority. Rules such as: Always writing in pen, and crossing things with a single strike-through. Notebooks are still a great way to preserve the little details of "what the hell was I thinking?" A colleague told me a good notebook prevents you from having to repeat a study because you can't figure out what you did the first time. There are still industries that require legally defensible record management -- you'll know if you're in that boat. If not, you can DIY whatever method works for you. The success metric is if you actually use it. On paper, I write in pencil because I'm more concerned about readability than a precise narrative. On the computer, Jupyter, just because nothing else really lets me document "thinking in code."

doctorpangloss 3y ago
To your specific point, the legal issues are so idiosyncratic. You can’t write an article about them. You can’t tease out the difference between “this is a best practice everyone should follow” and “the patent lawyer is selling the holistic social experience of compliance,” which is the non-trial attorney’s primary product. It’s the same energy as DocuSign: when your biggest competitor is a pen, you know all the bullshit they peddle about timestamps and tracking and custody is just that, bullshit. It really comes down to, what is your role? Are you making discoveries or working for people who do? Both are very worthy. In my experience, the PIs - and their subordinates who become PIs - they aren’t thinking very hard about lab notebooks and their tactics vary widely. No best practices. However they are focused on maximizing the amount of serendipity they can have per unit time, which tends to devalue how you’re documenting stuff for patent lawyers. Does Benchling have a manifesto about why you should care about lab notebooks? No. It has a ton of little reactive opinions that are relevant to its sales pipeline. But nothing like “Agile, except for life sciences” which incorporates their software. It’s everything to all people, like most life science software. I know people receive huge grants on promising discoveries in life sciences, and some of their labs have Benchling licenses and don’t use them. The people first authoring the papers use lab notebooks of course, but see this as a small part of their process.
- analog31 3y ago
  I just looked up Benchling. My first impression is that it's enterprise software. You're not expected to just buy a license and start using it, and being the first user at your site won't gain you much over what you're using right now. Where I think software like that gains its use is when you have multiple people working on similar research or processes, and trying to manage that kind of research and the data that it generates. At the extreme, I see job openings like this: Wanted, quality control chemist for third shift... On the other hand, I work in a "small lab" setting. I'm often the only person working on a project. No two of my projects resemble one another, though there are themes that progress through my work, and tools that I re-use and share. My choice of a notebook system, if you can grace it with such a description, is almost solely for my own benefit.
j0k3r_85 3y ago
Have you tried quarto markdown? It’s similar to rmarkdown but language agnostic and allows me to think in code in a way that can easily be added to notebooks. To work with them in notebook fashion I can work through one file a day and save the rendered pages in a folder.
- crispyambulance 3y ago
  Quarto, I think, is definitely a step in the right direction. It allows for publication quality rendering into pdf, and various html flavors including Confluence. You can write fluently in it, mix-in actual running code, and you've got options for sophisticated graphics, tables and mathematics. I do hope the Quarto project makes it and survives. It's a cut above the other notebook solutions like jupyter.
  - ac50hz 3y ago
    I’ve been heading in this direction, and Quarto continues to be the end point, on the road from pandoc.
  - eternauta3k 3y ago
    What's the advantage of Quarto over Jupyter? I looked at Quarto and rejected it because I couldn't find a way for a single cell to programatically generate interleaved markdown and plots (I can do this with Jupyter).
    - crispyambulance 3y ago
      Not sure what you mean as there is no notion of "cell" in Quarto. Instead, everything is markdown and you can interleave codeblocks (or inline code statements) anywhere you like to generate plots/tables, etc. I haven't had a need to generate markdown programmatically, though I imagine there's probably at least a "hard way" to do that. FWIW, quarto is still in its early stages. The quarto devs on github are very nice and responsive to questions if you ever look into again.
- chaxor 3y ago
DarkSucker 3y ago
> Notebooks are still a great way to preserve the little details of "what the hell was I thinking?" Here here. WWIT (what was I thinking) is so valuable. I'm spending much more time now writing notes that provide context in addition to a bare description of what I did. I hate it when I look at old notes, have a million questions, and curse myself for not writing more. Also, thank you for making the point about the US patent system. I recall somewhere around 1990, where people silently didn't bother to issue notebooks for me to record ideas (i.e. inventions) in favor of electronic disclosure forms.
- ac50hz 3y ago
  Record keeping, for better or worse, is essential. Memories fade. Ink fades but rarely corrupts.
  - Aerbil313 3y ago
    I grew up with the stories of real people (students and scholars of the past times) being able to memorize things by just hearing or reading them once. Seems a forgotten thing in the modern world.
    - melagonster 3y ago
      there are a lot of book teach you writing note later and give client deep impression.
    - malfist 3y ago
      Because it's a myth. Photographic memory isn't real. Check out the wikipage on eidetic memory. People that claimed it in the past were not telling the full truth. There are only a few examples of savants being able to recall specific things after one showing, but it's terribly narrow. Like being able to draw a horse you saw, but not human faces. https://en.wikipedia.org/wiki/Eidetic_memory https://en.wikipedia.org/wiki/Eidetic_memory
arminiusreturns 3y ago
I honed my lab notebook taking during my time working under a brilliant geneticist, (I actually used raw yaml before I got into emacs org-mode) and really enjoyed the daily detail... and then when I got more into the startup world I kept getting "don't write that down because it's then discoverable!" but in shaded language from the in house counsels... and it was very off-putting. I ended up CYA'ing at some of those by sending slack/etc messages to myself of things like that. Let's just say I much prefer working with scientist heavy companies and teams.

doctorpangloss 3y ago

To your specific point, the legal issues are so idiosyncratic. You can’t write an article about them. You can’t tease out the difference between “this is a best practice everyone should follow” and “the patent lawyer is selling the holistic social experience of compliance,” which is the non-trial attorney’s primary product. It’s the same energy as DocuSign: when your biggest competitor is a pen, you know all the bullshit they peddle about timestamps and tracking and custody is just that, bullshit. It really comes down to, what is your role? Are you making discoveries or working for people who do? Both are very worthy. In my experience, the PIs - and their subordinates who become PIs - they aren’t thinking very hard about lab notebooks and their tactics vary widely. No best practices. However they are focused on maximizing the amount of serendipity they can have per unit time, which tends to devalue how you’re documenting stuff for patent lawyers. Does Benchling have a manifesto about why you should care about lab notebooks? No. It has a ton of little reactive opinions that are relevant to its sales pipeline. But nothing like “Agile, except for life sciences” which incorporates their software. It’s everything to all people, like most life science software. I know people receive huge grants on promising discoveries in life sciences, and some of their labs have Benchling licenses and don’t use them. The people first authoring the papers use lab notebooks of course, but see this as a small part of their process.

analog31 3y ago
I just looked up Benchling. My first impression is that it's enterprise software. You're not expected to just buy a license and start using it, and being the first user at your site won't gain you much over what you're using right now. Where I think software like that gains its use is when you have multiple people working on similar research or processes, and trying to manage that kind of research and the data that it generates. At the extreme, I see job openings like this: Wanted, quality control chemist for third shift... On the other hand, I work in a "small lab" setting. I'm often the only person working on a project. No two of my projects resemble one another, though there are themes that progress through my work, and tools that I re-use and share. My choice of a notebook system, if you can grace it with such a description, is almost solely for my own benefit.

j0k3r_85 3y ago

Have you tried quarto markdown? It’s similar to rmarkdown but language agnostic and allows me to think in code in a way that can easily be added to notebooks. To work with them in notebook fashion I can work through one file a day and save the rendered pages in a folder.

crispyambulance 3y ago
Quarto, I think, is definitely a step in the right direction. It allows for publication quality rendering into pdf, and various html flavors including Confluence. You can write fluently in it, mix-in actual running code, and you've got options for sophisticated graphics, tables and mathematics. I do hope the Quarto project makes it and survives. It's a cut above the other notebook solutions like jupyter.
- ac50hz 3y ago
  I’ve been heading in this direction, and Quarto continues to be the end point, on the road from pandoc.
- eternauta3k 3y ago
  What's the advantage of Quarto over Jupyter? I looked at Quarto and rejected it because I couldn't find a way for a single cell to programatically generate interleaved markdown and plots (I can do this with Jupyter).
  - crispyambulance 3y ago
    Not sure what you mean as there is no notion of "cell" in Quarto. Instead, everything is markdown and you can interleave codeblocks (or inline code statements) anywhere you like to generate plots/tables, etc. I haven't had a need to generate markdown programmatically, though I imagine there's probably at least a "hard way" to do that. FWIW, quarto is still in its early stages. The quarto devs on github are very nice and responsive to questions if you ever look into again.
chaxor 3y ago

DarkSucker 3y ago

> Notebooks are still a great way to preserve the little details of "what the hell was I thinking?" Here here. WWIT (what was I thinking) is so valuable. I'm spending much more time now writing notes that provide context in addition to a bare description of what I did. I hate it when I look at old notes, have a million questions, and curse myself for not writing more. Also, thank you for making the point about the US patent system. I recall somewhere around 1990, where people silently didn't bother to issue notebooks for me to record ideas (i.e. inventions) in favor of electronic disclosure forms.

ac50hz 3y ago
Record keeping, for better or worse, is essential. Memories fade. Ink fades but rarely corrupts.
- Aerbil313 3y ago
  I grew up with the stories of real people (students and scholars of the past times) being able to memorize things by just hearing or reading them once. Seems a forgotten thing in the modern world.
  - melagonster 3y ago
    there are a lot of book teach you writing note later and give client deep impression.
  - malfist 3y ago
    Because it's a myth. Photographic memory isn't real. Check out the wikipage on eidetic memory. People that claimed it in the past were not telling the full truth. There are only a few examples of savants being able to recall specific things after one showing, but it's terribly narrow. Like being able to draw a horse you saw, but not human faces. https://en.wikipedia.org/wiki/Eidetic_memory https://en.wikipedia.org/wiki/Eidetic_memory

arminiusreturns 3y ago

I honed my lab notebook taking during my time working under a brilliant geneticist, (I actually used raw yaml before I got into emacs org-mode) and really enjoyed the daily detail... and then when I got more into the startup world I kept getting "don't write that down because it's then discoverable!" but in shaded language from the in house counsels... and it was very off-putting. I ended up CYA'ing at some of those by sending slack/etc messages to myself of things like that. Let's just say I much prefer working with scientist heavy companies and teams.