As part of my PhD thesis I studied an emerging field of bacterial adaptive immunity, known as CRISPR. At the time I was interested in tracking this type of immune system in bacterial communities to track co-evolution between bacteria and their viruses. For anyone interested and brave enough, here is a link to my thesis. After I finished up writing, submitting, and ultimately obtaining my PhD I realised that large portions of the literature review section would never be published in a scientific journal. I came to the realisation that if this summary of CRISPR (of which I was very proud of) would ever be read I needed it to be published in an “alternative” way.
That way was Wikipedia and one of my very first blog posts summarized my method for turning my literature review into a Wikipedia article. Perhaps my biggest motivation for contributing to the Wikipedia page was how out of date the page was. My literature review from my thesis had dozens of references and was many pages long yet much of this new information wasn’t in Wikipedia at all.
Towards the very end of my PhD the research community began studying CRISPR for gene editing which has resulted in amazing (and controversial) advances in science using this technique. While CRISPR research exploded I went off on a different research direction and eventually left academic research for a position in the biotechnology industry. Despite not being directly involved with CRISPR research anymore I still maintain two pieces of software, minced and crass, that are designed to detect CRISPR arrays in either genomes or metagenomes; and recently I got interested in how the CRISPR page on Wikipedia had changed since I made my contributions.
Not surprisingly the number of contributions has increased drastically from 2014 onwards as CRISPR gene editing got significantly more press coverage. But what did surprise me was Wikipedia’s inbuilt page statistics showing I’m the second highest author in terms of characters contributed. It’s been years since I contributed so my assumption was that most of what I wrote would have been edited away. Seeing my name so prominent really filled me with pride as this contribution is likely my most read piece of scientific literature I’ve ever made. Digging into the history of the article’s revisions it became clear that my name is still so high on the list due to the organic nature of Wikipedia article growth. I could see in the history section that large parts of the CRISPR page had been split off into the separate CRISPR gene editing page, which is itself a huge page; and the large cas9 page, which details the primary enzyme used in CRISPR gene editing. Intuitively this makes sense, people contribute small amounts to a page that already exists until someone decides that much of that information is better suited under a different title.
Some elements for my original contribution are still present including the table of signature CRISPR genes and a summary figure of the different types of CRISPR systems. Both of these elements are sorely out of date. I was disappointed to see that the table in particular hadn’t been updated as many of the rows still contained descriptions stating “function unknown”. Surely with the increased interest in CRISPR all of the proteins would have some more information about them.
Thankfully this assumption was true, much research on CRISPR has taken place but the information has yet to be disseminated back to Wikipedia. A quick literature search on Pubmed showed amazing research on many of the different cas genes. This let me change a few “function unknown” rows in the table and let me create a few new enzyme stubs on Wikipedia for cas2, cas3, and cas4. I hope that the additional pages will spurn either myself or others to add information. Right after I created the cas3 page another user added in some more information within a day!
Looking back at this has kindled my own interest in CRISPR again. A short summary of the information I found and integrated into Wikipedia while writing this blog post…
Is an endonuclease that works with cas1 and cas2 to generate spacer sequences. It looks for PAM sequences and processes the spacer before insertion into the CRISPR array.
These are essential for generating crispr-RNAs (crRNAs) which are used to target foreign DNA.
Binds to the 5’-end of the CRISPR RNA and promotes the oligomerization of other cas proteins creating the interference complex that destroys foreign DNA/RNA
