Wondering what a modern, digital version would be? Imagine a repo could work for the time-stamping and not deleting mistakes (immutable record). Images, annotations (i.e. 'Circle rogue points') seem much harder.
"In late 1987, Robert Malone performed a landmark experiment. He mixed strands of messenger RNA with droplets of fat, to create a kind of molecular stew. Human cells bathed in this genetic gumbo absorbed the mRNA, and began producing proteins from it.
Realizing that this discovery might have far-reaching potential in medicine, Malone, a graduate student at the Salk Institute for Biological Studies in La Jolla, California, later jotted down some notes, which he signed and dated. If cells could create proteins from mRNA delivered into them, he wrote on 11 January 1988, it might be possible to “treat RNA as a drug”. Another member of the Salk lab signed the notes, too, for posterity. Later that year, Malone’s experiments showed that frog embryos absorbed such mRNA. It was the first time anyone had used fatty droplets to ease mRNA’s passage into a living organism."
I've become a big fan of the Center for Open Science's Open Science Framework: https://osf.io/
It isn't really a thing in my field, but it enables pre-registered studies, and it has some really lovely integrations with github, cloud storage, etc.
I know scientists who still use paper notebooks. They are quite common in chemistry and other "wet lab" sciences, where it's actually hard to narrate at the keyboard while also wearing rubber gloves and writing with one hand while holding something with the other. I'm sure there's also a mental discipline about it, that might help them think.
When I was a science student, my notebooks were a disaster, and I paid the price by having to repeat work when I couldn't figure out what the hell I did. Writing was always awkward and painful for me.
Today, I use Jupyter notebooks. They are not a strict timeline type of narrative, but have the benefit that I can see if they are complete before taking a break by doing a "restart kernel and run all cells." And they are suited to the kind of work I do, lots of data and computation. And they are at least crudely searchable.
For my work I don't need time-stamping or an immutable record. I need to be able to figure out what I did, hours or years later.