No, only people with accounts that I have authorized can post here. The vast majority of the edits are made by me, but a small number may be made by graduate or undergraduate research assistants. Check the “history” tab on any given page to see who changed what; any changes made by “Caleb McDaniel” or “wcaleb” are attributable to me.

In that time, the notebook has seen six projects go from conception to publication, and a seventh founder on a null result (see #tribolium). Several more projects continue to unfold.

Welcome to my open lab notebook. This is the active, permanent record of my scientific research, standing in place of the traditional paper bound lab notebook. The notebook is primarily a tool for me to do science, not communicate it. I write my entries with the hope that they are intelligible to my future self; and maybe my collaborators and experts in my field. Only the occasional entry will be written for a more general audience. […] In these pages you will find not only thoughts and ideas, but references to the literature I read, the codes or manuscripts I write, derivations I scribble and graphs I create and mistakes I make.

Unless otherwise noted (i.e., on a draft manuscript), notes posted here is made available under the Creative Commons NonCommercial-Attribution-ShareAlike license. This means you are free to make use of it, change it, use it for any non-commercial purposes, as long as you acknowledge the source. Journal manuscripts under development here are often NOT covered by this Creative Commons license, because they will eventually be subject to whatever license the target journal requires. Thus, drafts are readable in their posted form, but all rights are reserved beyond viewing (and, of course, having your own ideas with respect to the material).

But by far the more important aspect of open science is an open process, and reproducible results. To that end, I have been exploring the use of wikis and blogs to record interim thinking on research topics, and this is the second iteration of an online "lab notebook" that goes beyond occasional blog posting. My first digital lab notebook was a local installation of the Instiki wiki, synchronized with Dropbox. This was useful for doing my own work wherever I happened to be, but was not truly "open" in the sense of public access. I have been migrating some of those reading notes, and topical notebooks to this current iteration, and that process is ongoing. My first "online open notebook" was hosted by Wikispaces, but I found that the lack of offline access was difficult for me, given travel and limited internet access where I live and work.

My commitment to open science began with open access, and attempts to ensure that my written output was -- to the extent possible -- available online in freely downloadable format. This is always a work in progress, because older publications are often unavailable given paywalls or commercial licenses by academic publishers. To the extent possible, I will always make versions of publications available online, and I will attempt to choose journals with permissive preprint/postprint policies. I am slowly attempting to reconstruct PDF versions of older conference papers, many of which I have only in print files, which will need to be scanned.

For many of us, the main audience of our research is our colleagues. But colleagues is about as vague and useless a term as “the public” and so when you develop a new project you should pin down (for yourself) the scholarly topics that your work will contribute to, and some examples of individuals who do related work.

“Who gets to use what I make? Who am I leaving out? How does what I make facilitate or hinder access?”

A better approach, from a pedagogical point of view, is to encourage students to explore and try things out, with the grading being focused on documenting the process rather than on the final outcome.

By manipulating the code that produces these images in both random and patterned ways, we manipulate the meaning of the image and the way in which these images communicate information to the viewer.

Digital tools and their use are not theory-free nor without theoretical implications. There is no such thing as neutral, when digital tools are employed.

Trust – we tend to trust the devices we employ (why would we use them otherwise?) but what is this trust based upon?

Information flow between agent and artefact, including one-way flow (from artefact to agent, where we simply look at the artefact to extract the information we require), two-way flow (typically where we store information on the artefact and subsequently retrieve it); reciprocal flow (a two-way flow that is incremental, additive, and cyclical, so there is a continuous information exchange); and system flow (where there are multiple agents and multiple artefacts cooperating in the exchange) (Heersmink 2012, 49-50; 2015, 583-6).

Cognitive artefacts may be seen in terms of functioning in a similar fashion to the equivalent human cognitive process. This is the basis for seeing computer reasoning as a model of the human mind

we have witnessed a move from analogue dumpy levels and tapes to digital total stations and electronic distance meters that employ built-in algorithms to capture, record and process data through a mixture of semi-automated and fully automated methods

These cognitive artefacts support us in performing tasks that otherwise at best we would have to conduct using more laborious and time-consuming methods (film photography or measured survey using tapes, for instance) or that we would not be able to undertake (we cannot physically see beneath the ground, or determine the chemical constituents of an object, for example). Furthermore, a characteristic of archaeology is the way that we adopt and apply tools and techniques developed in other domains (Schollar 1999, 8; Lull 1999, 381). Consequently, most if not all of the cognitive artefacts used in archaeology are designed outside their discipline of application, meaning we have little or no control over their development and manufacture, and hence their internal modes of operation have to be taken at face value.