So, back when it all began, I wrote ‘Why I’m Not Travelling to the US‘. Over the past four years, I went to 0 conferences in the US (of course, the pandemic these last 10 months helped with that too). I went to the states 3 times during that period to work with students at Muhlenberg, Drew, and U Mass Amherst.
So, no conference/self promotion travel, limited travel to support students.
This is my first post on wordpress.com where I have to use the Gutenberg editor and man I hate it. I should probably migrate this damned thing – 14 years old! – out of wordpress. I’ve wasted a huge amount of time just trying to get things organized so I know what the hell is going on. Yeah, I can’t stand change, once I figure out how to do something the way I like it. But, on a similar theme… I’m still trying to figure out out to *take good notes*.
When I was a PhD student, I kept incredibly dense and largely useless notes. By ‘useless’ I mean – once I’d made an entry in my great big notebook, it was incredibly hard to find it again. To see which other materials it might speak to. I had several notebooks, where I’d duly copy out interesting passages and make my observations, and then shove slips of paper or post-it notes in on those pages where I thought ‘hey, this might be important and I really need to find this again’. Because I had no structure for getting into and through those notes, I’ve never used those notebooks since. Which is a waste.
Nobody ever taught me how to take notes.
When it came time to write, I’d get a big piece of paper and try to sketch out how the Big Idea I was writing about worked. I’d write down page numbers, cryptic directions to various pages in various notebooks, half-baked references, remembrances of important things I’d read, and draw circles and lines and swoops and eventually something would emerge out of that, but it was a messy, wasteful process.
What I’ve been searching for ever since was a way where I could capture the exciting ideas I was reading, the interesting thoughts I was having, in such a way that knowledge would crystallize out of the mess. With time, I’ve started to come up with a way that works on paper – a notebook with a line down the middle of the page; observations or important phrases copied on one side, with my reflection or thoughts on the other side. A citekey scribbled at the top of the page to connect to my reference manager (I’ve used all of the reference managers, it seems). An index page at the front of the notebook. Then, when it comes time to write, my Big Page is at least a little bit tidier with references to ‘orange nb p24 re bennett 32’.
There are a number of posts on this ol’ blog about taking notes, and different systems I’ve tried to cobble together to make ’em. In recent years, I’ve really become interested in the whole zettlekasten scene; the basic idea is one idea, one note. Sometimes I copy the relevant passage down, but most of the time, it’s just me riffing on something I’ve read; usually no more than three or four sentences. Then a system for indexing these so that notes can be compiled into larger overview notes or broken back down again. It doesn’t have to be digital, but of course, digital search and storage makes life easier. I’ve used everything from Notational Velocity through to plugins and mods for Sublime Text or Atom. And these all work in the sense that I’m able to pull together all of my relevant atomic notes and sometimes – if I’ve been really switched on – the compiled overview note goes into whatever I’m writing in its entirety. The note taking process is the writing process.
I really like when that happens.
Unfortunately, I find it hard to maintain the use of these different packages for zettles consistently. I think the reason for this is because, despite the ability to recombine, search, and find my atomic notes, I still can’t see the connections between things very well. But, with my most recent book project finally out of the way, and a bunch of other things finally having made their way through the publishing process, I’m ready to start again.
And boy, how the landscape has changed!
Roam, Foam, Org-roam, and Obsidian
It was a chance tweet I saw by Jonathan Reeve that sent me out on this latest note-taking odyssey, by the way:
I had to investigate. The major thing that has changed I think is the idea of ‘networked thought’ has really entered into the note taking space. And I think that’s what I’ve always missed in note taking process. The idea that if you make connections as appropriate between ideas, eventually larger structures emerge; these larger structures (network structures like shortest paths, clusters of various kinds, most-central nodes of various kinds) can give insight into the nature of your thoughts/nodes and perhaps suggest insights that you might not otherwise have spotted.
There is a wide array of editors to help you with this, all of which include network visualizations of links, backlinks, and tag structures. Some, like Roam are subscription based and keep your notes somewhere on the cloud; others like Foam or Org-Roam are open source and keep your notes locally as markdown files (though Org-Roam is built on emacs and life’s too short). Then there’s Obsidian which is not open source, but does keep your notes as separate markdown files. It has a pretty slick interface, and it will publish and host your ‘vault’ (folder of notes) as a website if you so wish (for a hosting fee, which seems pretty reasonable). If you ever read Caleb McDaniel’s ‘Open Notebook History‘ that feature will be quite interesting.*
I’ve been kicking the tires on Obsidian for the last week, and I have to say, I quite like it. I have a few community plugins installed that let me ‘refactor’ (break apart or merge together) notes as appropriate, that let me insert citations from my Zotero library (or create new notes from scratch on a given resource in my Zotero library) with links back to the original pdfs/resource, and a few cosmetic tweaks. New panes can be opened at will from a variety of places, and if you have the screen real-estate, organized however you like. I grabbed my existing folder of notes and opened it within Obsidian; I created a new index note to provide some consistent points of entry:
*I keep my notes, my ‘vault’, in a git-tracked folder, pushing online to a private git repo. I was also pushing to a public wikijs instance I host on Reclaim Cloud, but the importer broke and I can’t make it work any more. Anyway, that was probably too much – if I want to make my notes available online, I can probably just gh-pages them and that’ll serve. You can automate the process of pushing new notes to github; see this post by Bryan Jenks.
When you search for keywords or phrases or tags, the results of those searches can be turned into instant notes with wiki-style links. See that graph at top right? The green nodes are tags, the blue are notes, the red are notes that I’ve created while writing other notes that remain to be filled in.
So here’s my workflow. I have Zotero and Zotfile installed, so I can send pdfs to a folder on my ipad. On the ipad, I use pdf reader to annotate. Zotfile retrieves these and pulls them back into Zotero. I use zotero-mdnotes to push the notes to my folder (‘vault’) of notes. (If I’m reading something physical, I can just mark it up or use my paper notebooks as before, and then transfer/consolidate notes into a new note in Obsidian.)
These I can then refactor into individual atomic notes as necessary. Using BetterBibTex for Zotero, I have also exported (with constant updating) my library’s bib file (as csl json) to the vault; I can then add the cite-key to any atomic note as appropriate. I add tags as appropriate. I link to other notes as appropriate. Obsidian shows me when a given note is referenced by another or mentions another and so I can use that to guide back-linking too.
Then, I can garden. By ‘gardening’, I mean, exploring my notes and their connections and thinking about what I’m seeing. Perhaps I add new notes. Perhaps I prune or delete notes. Perhaps I add more links or tags.
I love the graph feature. But I wish I could analyze it. There is a plugin that exports your graph to Neo4j for analysis, but that’s almost too much power for what I have in mind, and besides, you need to learn the cypher query language to make sense of that kind of thing. The ‘Infranodus‘ platform might be worth exploring here, as it does network metrics and text analysis too and can ingest your notes (see for instance this post) but I didn’t feel like signing up with credit card to something I just wanted to explore a bit (Infranodus can be installed locally, but it’s a beast of a thing to configure – it depends on Neo4j! – and after wasting the better part of a day on it, I threw in the towel).
No, good ol’ gephi or cytoscape or similar is all I need. So I did a bit of digging – where does Obsidian hold all of that info? It turns out, there is a json graph in a folder called ‘ObsidianCache’ that contains the current representation of your vault and its interlinkages:
Now, I’m certain that one could write a bit of python to grab each note and its links and tags, represent as a graph, and then do a few network metrics. But I don’t know how to do that in python – yet. But I can do it with jq , and reshape the json so that I end up with note – link and note – tag pairs. Gephi doesn’t ingest json, so I use a bit of R to turn it into graphml. Hey presto, a network I can explore in Gephi! What are the most central ideas? What kinds of ‘communities’ exist? I am imagining that knowing this information would help kick start my writing, or help me detect emergent ideas I hadn’t considered yet. (Other people feed their notes in Devonthink, which does some natural language magic to find connections in your notes. That’s another of the beautiful things about keeping your notes in plain text on your own machine).
Open ‘er up in Gephi, using the multimode plugin to turn it from a network of notes to tags, to tags – tags by virtue of notes in common…
So obviously, there is some mucky data in my test vault, but interesting, eh? Incidentally, the ‘sg’ tag is for when I’ve had some inspiration that I want to come back to. And of course, maybe note to note by virtue of common tags would be a more interesting/useful view. Or perhaps, since a ‘tag’ could be considered as a kind of semantic note on its own, I just leave it notes – tags and treat it all as unimodal. Things to explore!
“Taking photographs, like drawing reconstructions, was a means by which the archaeologists could attempt to understand the object and the past and to rebuild the ruin. At Dura, photography was not a passive recording device as it is thought of in most histories of archaeology; rather, it was something that seems to have been an active means of constructing a particular past (fig. 5). Time in these photographs refers both to the practice of taking the photographs— the posing and framing—and the excavator’s construction of a time in the image; thus, they reflect a temporal breach that constructed an East in which modern peoples are equated with ancient.”
Active note taking, gardening our thoughts using these digital tools, seems to me a bit like how Baird writes about photography, perhaps. But I haven’t fully fleshed out that thought yet; perhaps its because it lets me build something new from others’ mental excavations of their own thought. Or I’m pushing the metaphor too far. Back to the garden I go!
Some useful videos
Below is a video of PhD student Courtney Applewhite describes how she uses Obsidian to study for her comps; something similar to this approach might be worth adapting.
Graham, S., Lane, A., Huffer, D. and Angourakis, A., 2020. Towards a Method for Discerning Sources of Supply within the Human Remains Trade via Patterns of Visual Dissimilarity and Computer Vision. Journal of Computer Applications in Archaeology, 3(1), pp.253–268. DOI: http://doi.org/10.5334/jcaa.59
“While traders of human remains on Instagram will give some indication, their best estimate, or repeat hearsay, regarding the geographic origin or provenance of the remains, how can we assess the veracity of these claims when we cannot physically examine the remains? A novel image analysis using convolutional neural networks in a one-shot learning architecture with a triplet loss function is used to develop a range of ‘distances’ to known ‘reference’ images for a group of skulls with known provenances and a group of images of skulls from social media posts. Comparing the two groups enables us to predict a broad geographic ‘ancestry’ for any given skull depicted, using a mixture discriminant analysis, as well as a machine-learning model, on the image dissimilarity scores. It thus seems possible to assign, in broad strokes, that a particular skull has a particular geographic ancestry. ”
The key idea: a one-shot neural network can be used to measure the web of differences in carefully selected social media images (backgrounds removed) of human skulls. patterns of similar *dissimilarities* can then be compared with osteological or forensic materials and then we can look at what vendors say about the remains. We find that the stories told are often dubious. The web of differences also seems to imply that Indigenous North American human remains are being traded, but not labelled as such. While bonetraders will be quick to point out that ‘buying human skulls is legal’ (and we’ll write more about that in due course), trading in Indigenous Human remains gets into NAGPRA territory & it’s most definitely illegal (US): https://law.cornell.edu/uscode/text/18.
I was never taught how to take notes. Periodically, I try to develop better habits. I’ll go read various blogs, forums, product pages, looking for the thing that’ll make everything come together, make my reading more effective, make my thinking so much sharper…
Some time ago I bought an ipad (‘it’ll be for research! honestly! for pdfs!’) and still my reading/note taking didn’t come together. I have Liquid Text on it and pdf viewer. Liquid Text is pretty neat… but I find its ability to pull multiple pdfs together and all of its note taking, connecting just doesn’t work for me – on an iPad. Part of the problem is that I wasn’t using it the way its designers imagined a person might use it. (Apparently, it’s now available on Microsoft devices and in that context I think it would really work for me). The other part was, well, probably a discipline thing. Or lack thereof.
PDF Viewer is a nice little app for reading pdfs, and when I tied it to Zotero with zotfile… now we’re talking! Got my notes back on my writing machine, so headway.
In the past, for various projects, I’ve tried the whole one-idea-per-card note taking system called ‘Zettelkasten‘. Combine that with an editor that does search and creation at the same time (like nvAlt), and I actually got kinda good at pulling stuff out and framing searches, finding connections between my notes. It’s a bit like ‘commonplace books‘, at least the way I’ve been using ’em. I’ve also been thinking of these in the context of open notebook science, reproducibility and that sort of thing – Caleb McDaniel put it best:
: The truth is that we often don’t realize the value of what we have until someone else sees it. By inviting others to see our work in progress, we also open new avenues of interpretation, uncover new linkages between things we would otherwise have persisted in seeing as unconnected, and create new opportunities for collaboration with fellow travelers. These things might still happen through the sharing of our notebooks after publication, but imagine how our publications might be enriched and improved if we lifted our gems to the sunlight before we decided which ones to set and which ones to discard? What new flashes in the pan might we find if we sifted through our sources in the company of others?
So how do I put these ‘zettels’ online? ‘The Archive‘ is a nice little bit of software, developed on top of nvAlt, and I like how it works. I have it saving each note as an md file into a git repository on my machine. I push these things to a github repo. Now, there are plenty of static site generators that will turn a collection of markdown into a static website, but collaboration on the underlying files is still an iffy process. I spun up a wiki.js instance on Reclaim Cloud and then figured out how to connect it to the github repo (thread here).
I am now the proud owner of a wiki that my students can edit and collaborate with me on some of my larger projects (they can just use the web interface, which is nice, no faffing about); whenever I git pull I have their research to hand in my preferred note taking app; whenever I push they get my stuff. And our research is out there in the open.
– configure storage to grab from github using https, not ssh
– spaces in file names will break the import/export
– set up a metadata template in ‘The Archive’ so that notes will render nicely there.
I started scratching out ideas for what this ‘intro to digital archaeology’ class might look like as I taught my early summer course, ‘Crafting Digital History.’ Scratches became mindmaps and random scraps of paper and orphaned text files. One thing that I found really worked well with the DH course was that it had a regular beat to it. Each week, the rhythm and routine was the same, although within that there was a lot of choice about what to do and how to approach it. I want to preserve that for the digiarch class; I also want to provide more signposts along the way, so I’m planning to seed the readings with my own annotations using hypothes.is; I also saw someone on Twitter mention that they might embed short wee videos of themselves speaking about each reading, in the reading via annotation and I thought, ‘my god, that’s brilliant’ and so I’ll give that a try too. I have the link to the tweet somewhere, just not here as I write.
Anyway, in the interests of providing more structure and more presence, I’ve also been building trailers for the course and the modules within it. Making these have helped narrow down what it is I want to do; you can’t touch on everything, so you’d better go deep rather than wide. Without further ado…
Today is the funeral of George Floyd, the man murdered by police in Minneapolis. Since his death, other instances of police brutality as the police riot have been collated in various places; one reckoning has over 400 instances (link here, kept by Greg Doucette, and just the ones that have been shared on Twitter!).
We – Andrew Reinhard and myself – wanted to honour George Floyd, and so we composed ‘Elegy for George Floyd’, a data composition built from sonifying the data in that spreadsheet and then remixing the results.
As you listen, you will hear a trumpet (police siren / police action) that waxes and wanes with the brutality of the action recorded. The reports for each incident were loaded into Voyant-Tools, where they were reorganized by the most common terms. Each word was then replaced in the report by its count; then all of the scores for each report were added up. This index value was then mapped against four octaves in D# minor, a key that invokes “…Feelings of the anxiety of the soul’s deepest distress, of brooding despair, of blackest depresssion, of the most gloomy condition of the soul. Every fear, every hesitation of the shuddering heart, breathes out of horrible D# minor. If ghosts could speak, their speech would approximate this key. ” (source). These reports are scored into the music twice – one voice in whole notes, a second voice in arpeggiated chords to reflect the sirens and chaos of the police brutality
Each city’s latitude and longitude and the cumulative report number were converted into chords and baseline.
The resulting sonification was then remixed, with an 808 bass line added. T808 runs throughout the entire song, the heartbeat of George Floyd that abruptly stops at 8:46. It contrasts with the intrusive double-bass of the police line generated in the original sonification. The crescendos of all of the data tracks reflect clashes with the police. Towards the end of the song, there are instances (and then a full minute) of tracks playing backwards, which reflects how upside-down things have become.
The remixed piece is at 90 bpm which we feel adds to the gravitas of the work; it is unsettling and sad, but yet, even now, contains beauty and hope.
How lovely, that with everything going on, that some folks found the time to try their hand at archaeological stop motion! Let’s watch some films:
Abby and Maggie Mullen write,
“We created this film because we like Vikings and we wanted to make something about the ocean. (Our team likes a lot of different archaeological sites, so we went through a lot of ideas before landing on this one!) We found that the two-minute limitation made it both easier and more challenging, because it’s difficult to communicate a complicated story in two minutes, with Legos, but that helped us narrow down our topic.
Our process started with research about different archaeological sites, and when we found two stories about different Viking ships found with GPR, we decided it could be fun to try to view the site from both above the ground and below it.
Our set designer painted our backdrops in watercolor and built the sets in Lego. We had to adjust the scale of our Lego models multiple times, which she built, to make our photography work. We weren’t 100% successful, but an 8yo’s attention span is limited and we can’t exactly run out to the store right now to get more supplies.
We used an iPhone to take the photographs. We set it up on a tripod with a remote shutter to make it easier to keep it mostly in the same place. We then transferred our photos to a MacBook Pro and put the photos into iMovie to create the stop-motion. Our “silent film” text slides were created in PowerPoint, and we used a song from the YouTube Studio free music collection for our soundtrack.”
Comments on Youtube include, “I really liked this! It was so interesting AND beautiful. Really well done. It made me want to learn more!” and “Great information! I did not know that Viking ships had been found so recently from so long ago. I greatly enjoyed the scene settings and photography. The accompanying music was excellent.”
“This video is about methodological theory in archaeology, created for SAA’s Online Archaeology Week after the cancellation of the planned Austin Public Archaeology Day at the 2020 SAA Annual Meeting. Through observing the attributes of the rim sherd (its curvature, decoration, etc.), archaeologists can make inferences about the rest of the whole, even when pieces remain missing. This is based on an in-person activity that I do at public archaeology events to help visitors understand laboratory methods and induction. I used the app Stop Motion Studio for taking the frame photos and strung them together in the Windows 10 Photos app. I drew the animated overlays frame-by-frame in Inkscape.”
To Maggie and Abby Mullen, in the ‘Story of a Site’ category
To Karen Miller, in the ‘Biography of an Object’ category
To Beth Pruitt, in the ‘Archaeological Theory’ category
Best Overall and Choix du Peuple
To be announced May 4th! Make your votes on the Choix du Peuple:
$ wget https://www.loc.gov/rr/frd/Military_Law/Military_Law_Review/pdf-files/ -A .pdf
should just download them all directly. But it doesn’t. However, you can copy the source html to a text editor, and with a bit of regex you end up with a file with just the paths directly to the pdf. Pass that file as -i urls.txt to wget, and you end up with a corpus of materials.
Anyway, the thought occurred that the ruby script that inukshuk wrote with regard to my query about adding materials to tropy notes in json (full thread here, .rb file here ) could easily be modified to produce the json from simple lists in txt.
Warning: There are many photographs of human remains in this post.
There is a literature on the online trade in human remains going back to at least Huxley and Finnegan’s 2004 piece on eBay in the Journal of Forensic Science, and since then, several academics have been active in discussing the ethical, moral, and legal dimensions of this trade, producing a steady stream of articles. At the same time, the trade was transformed by the merging of social media with marketplace and ad-driven revenue models, expanding in scope and reach. Several platforms, over the last decade, have added wording to their prohibited categories of goods that deals with human remains. Let’s walk through some of that.
I found a copy of the World Archaeological Congress 2010 Newsletter in the Internet Archive, with this one line describing a human skull seen on Etsy, and WAC’s successful request to Etsy to remove the post.
The post was not in fact removed. And can still be found online.
It sold in 2011. What’s etsy’s stance on human remains, anyway?
Etsy’s current policy on human remains. Such as it is. Human remains were added to the prohibited list in 2012.
The seller from 2010, still active, using a different skull as a prop. Still selling human remains, now points people towards her Facebook page, and since Etsy banned human remains, wants you to send private messages if you’re interested. Facebook’s good for that sort of thing, eh? Private messaging, I mean.
Facebook says no human body parts or fluids.
But here’s a Facebook store selling…. human remains.
We are not surprised, to find human remains on Facebook. After all, Facebook owns Instagram, and there are any number of posts there selling human remains. Including this one. But wait, is that an Amazon box? Does Amazon have a human remains policy?
Yes, yes they do. And it seems a bit contradictory. And unenforced.
And it is trivial to find human remains being sold on Amazon. Like this skull. Displayed sideways, since the photo was taken with the seller’s cellphone.
Since I’m on wordpress.com, you might see advertisements interspersed in this essay. It will be interesting to see which advertisements WordPress matches to this post; it might even be hard to see the difference between those ads and these screencaptures.
Ebay, 2012: ” [the policy prohibits] “humans, the human body, or any human body parts” but expressly permits “clean, articulated (jointed), non-Native American skulls and skeletons used for medical research.” (Marsh, 2012, HuffPost). Today?
It was on eBay that we all (the archaeological ‘we’) first twigged that human remains selling online was lucrative and booming. While their policy has changed over the years, the policy is now admirably lucid and succinct. Did this tighter, stronger, policy have any impact?
It is possible to find the ruins and remains of specialist eBay aggregator sites like this one in the Internet Archive. I spent quite a lot of time tracking as many of these down as I could, teasing out which posts were actually for human remains, and which ones were replicas or adjacent materials, and scraping the data, plotting it over time.
And I see three phases here. An early phase where there was a lot of money happening (remember, these values are approximate indications rather than absolute totals. They give us a sense of the trend rather than the exact dollar number); a phase where language is suddenly cagey about what precisely is being sold (the stand? or the skull? Remember the earlier wishy-washy policy of 2012?), and the volume drops; and then, from July 2016: eBay bans human remains outright. And human remains drop out of the aggregators completely. The ban – to judge from these numbers – worked. Graphs and underlying research Graham, forthcoming.
Have we accomplished anything? eBay certainly has, I think, and that’s worth thinking about. Perhaps an auction site where sales are also dependent on reputation responds better to moral suasion than the other platforms. When is it in a platform’s best interest to actually police its own policies?
Human remains are in a nebulous zone, legally. In Canada, the law to my mind seems pretty clear:
Section 182.B seems to cover it. These materials are human beings. Buying and selling humans interferes -at the very least!- with human dignity. I’m no lawyer, and I don’t think this has ever been tested in court. But: If a platform profits from a user’s breaking of the platform’s very own policies on human remains, if a platform turns a blind eye, is the platform not condoning the trade? Is this not a nudge-nudge wink-wink tacit approval of the trade? Who should want to invest in a platform that makes money from selling human beings? Should we not hold such a platform accountable?
See ACCO for more on various illicit and illegal trades happening across social media. For more on our project studying the trade in human remains, see bonetrade.github.io.
Posts referred to have also been saved to the Internet Archive.
Sometimes, I have files that are larger than github’s 100 mb. So here’s what you need to do.
brew install git-lfs brew upgrade git-lfs
Start a new git repository, and then make sure git large file storage (git lfs) is tracking the large file. For instance, I just moved a topic model visualization to a repo on github (20,000 archaeological journal articles). It has a data csv that is 135 mb. So I made a new repo on github, but didn’t initialize it on the website. Instead, after getting git-lfs installed on my machine: