Wikimedia Meta-Wiki

Evolution and evolvability

Joined 13 May 2013

THOMAS SHAFEE
Catalytic triad
THOMAS SHAFEE
Evolution and Evolvability

ABOUT ME

I'm originally from Britain, where I studied a degree in Natural Sciences and a PhD in biochemistry, specialising in directed evolution and evolvability. I then moved to Australia and my expanded my research to bioinformatics, sequence space, convergent evolution and protein engineering. I and have additionally worked as a freelance scientific illustrator for a few popular science books and now mostly work in w:data science and research analytics. I've been active on Wikipedia since 2013[1] and now run workshops on Wikipedia editing for scientists, academics, students and doctors.[2][3][4][5][6][7][8] I also focus on facilitating collaborations between the academic and Wikipedic communities in general.[9][10][11][12][13] My main programing language is R, and I maintain the WikidataR package for reading and writing to wikidata.

MY WORK

On Wikipedia, I mainly edit articles in biochemistry and evolutionary biology. Since diagrams are key to clear science articles, I focus on adding and improving images (all my images are CC-BY licensed). I also generate interactive wikilinked diagrams and, where possible, I try to make sure that formatting I use is compatible with mobile devices. I'm also on the editorial boards of WikiJournal of Medicine and WikiJournal of Science, Wikipedia-integrated, peer-reviewed, open-access academic journals[14][15][16] and I organise the Wikipedia-integrated Topic Page format for PLOS Genetics.[17] I also edit scientific and bibliometric information on wikidata.

FEATURED/GOOD ARTICLES
CREATED

EXPANDED

2020
Open access from Class C
Defensin from start
Plant defensin from stub
Copyright policies of academic publishers from start

2015
Low-barrier h-bond from Stub
Macromolecule from Start
WikiProject Molecular and Cell Biology redesign
Substrate from Stub
Product from Stub

2014
Epistasis from Class C
Robustness from Start
θ-Defensin from Stub
Directed evolution from Start

2013
Proteases from Start
Threonine protease from Stub
TEV protease from Stub
Diffusion limited enzymes from Stub

Disclaimer: As of April 2023, I have a role as Executive Director of the WikiJournal User Group funded as part of a grant from the Wikimedia Foundation. The activities encompassed by this role are primarily off-wiki coordination tasks. All other edits performed outside of this scope are done in an unpaid, voluntary capacity.

CONTACT ME

Feel free to leave a message on my talk page or send me an email


On other sites
ORCID
GoogleScholar 
LinkedIn
AltMetric
Scholia
Github
University repository

  The Original Barnstar Thanks for your excellent article on the PA clan and many other contributions to Protein and RNA families! Alexbateman (talk) 11:15, 15 January 2014 (UTC)
  The Graphic Designer's Barnstar Awarded to Evolution and evolvability for contributing and evolvability many outstanding images to Wikipedia, including this highly informative and unique overview of gene structure. Adrian J. hunter(talk•contribs) 04:24, 10 June 2015 (UTC)
  The Science Barnstar I know how much of a pain in the ass it can be to get an article promoted to FA. It's a big accomplishment, so congrats! Seppi333 (InSert 2¢) 01:15, 13 March 2016 (UTC)
          The Special,
Original,
Tireless Contributor,
and Diligence Barnstars

Thanks for all your tireless work on the Antarctic women wikibomb. Without your help we would have managed about 10 pages I reckon. Thanks so much for guiding us through the process. You are a legend. Janstrugnell (talk) 07:06, 28 August 2016 (UTC)

T, you are our hero! Thank you for making the Antarctic women wikibomb a roaring success! Ngwilson (talk) 08:03, 28 August 2016 (UTC)

T - for all the work you did making the Wiki Bomb go with a bang - despite it being out side your area of science interest - you put up with all the dumb questions... you've made a good thing happen! WavygeEk (talk) 15:40, 28 August 2016 (UTC)

Thank you so much for helping to inspire thousands of budding young female scientists from about the world - and for teaching us more about Wikipedia than we ever thought we would know! Baeseman (talk) 08:29, 6 September 2016 (UTC)

T - your contribution to showcasing the role of women scientists in Antarctic research has been outstanding. Thank you so much for your efforts!! Shawjustine (talk) 06:47, 7 September 2016 (UTC)

  The Technical Barnstar Thanks for the improvements to the "pubmed indexed" template. Doc James (talk · contribs · email) 11:08, 6 September 2016 (UTC)
  The Medicine Barnstar Thanks for the great work that you are doing and would continue to do for medical content on Wikipedia as well as on WikiJournal of Medicine. Diptanshutalk 08:17, 1 November 2016 (UTC)
  The Original Barnstar Thanks so much for getting us all editing at Shut up and wiki fridays! Loztron (talk) 03:15, 1 June 2018 (UTC)
  The Psychology Barnstar For your invited address at the American Psychological Association and for welcoming one of those wacky psychologists to the WikiJournals enterprise!   - Mark D Worthen PsyD (talk) (I am a man. The traditional male pronouns are fine.) 23:44, 12 August 2019 (UTC)
  Science made visible Thank you for quality articles such as serpins, sharing your scientific expertise on evolution and evolvability ("experimental protein evolution"), for making it accessible by fascinating illustrations, for more accessibility by meaningful redirects, for a clear and informative user page, - T, you are an awesome wiKipedian! --Gerda Arendt (talk) 05:52, 2 April 2016 (UTC)
  Signpost Articles

1) Interviewed about WikiProject Molecular and Cell Biology on 20 May 2015
2) Article about the SCAR Antarctic Women Wikibomb on 18 Aug 2016
3) Article about biomedical content and collaborations on 6 Sept 2017
4) Article about WikiJournals 30 June 2019

  3RRR radio Interviews

1) Interviewed about Directed evolution and Wikipedia editing in general on 3RRR radio's Einstein A Go-Go show on 18 Oct 2015
2) Interviewed about the SCAR Antarctic Women Wikibomb on 3RRR radio's Parallel Lines show on 31 Aug 2016

  Wikimedia Foundation Blog post Article about incentives for academics and medical professionals to contribute to Wikipedia in the WMF blog on 18 Aug 2016
  The Cure Award Thank you for all the great work you are doing promoting Wikipedia and medicine. Best Doc James (talk · contribs · email) 07:32, 1 November 2016 (UTC)


LICENSE

    All text and images that I add to any wiki is released under a Creative Commons Attribution license (CC BY 4.0) - the only requirement for distribution/reuse/adaptation is attribution. If one of my images an image is incorrectly labelled, or if you're uncertain, feel free to message me to confirm.


TODO

Evolutionary landscape/fitness landscape - image
Evolvability - image?
Neutral mutation - causes and types
Experimental evolution
Bacteriophage experimental evolution - currently a crazy mess
Enzyme promiscuity
Mutations - expand 'beneficial mutations' and clean up 'DFE'
Defensin - requires overhaul
Cyclic peptide - expand and separate cyclic proteins section
Active site - new images
Binding site - new images
Oxyanion hole - image, chemistry, examples
Directional selection - improve image
Genome engineering - merge with genome editing?
Protein structure - evolution/conservation
Help:intro to pages - New welcome, MOS, navidation?
Protein stability - create or insert into existing article?
Hairpinin - create


REFERENCES

  1. ↑ Shafee, T (2015). "My second life as a Wikipedian". latrobe.edu.au. RED Alert, La Trobe University. Retrieved 2016-08-22. 
  2. ↑ Shafee, T (2018). "Wikipedia as an outreach platform". La Trobe Institute for Molecular Science. 
  3. ↑ Shafee, T (2016). "Wikipedia Editing for Scientists". Lorne Proteins. 
  4. ↑ Shafee, T (2016). "Wikipedia Editing for Scientists". Society for Molecular Biology and Evolution. 
  5. ↑ Shafee, T (2016). "Women in Antarctic Research Wikibomb". Scientific Committee for Antarctic Research.  (summary page)
  6. ↑ Shafee, T (2016-08-18). "Engaging diverse communities to profile women of Antarctica". The Signpost. 
  7. ↑ Savage, S; Strugnell, J; Shafee, T (31 August 2016). "Parallel Lines" (Audio interview). 3RRR radio. 
  8. ↑ Shafee, T. "Health Literacy" (in en-gb). Torque Global Health Education Program. Archived from the original on 2017-04-18. 
  9. ↑ Strugnell, J; Shafee, T; Wilson, N; Downey, R; Stevens, C; Shaw, J; Baeseman, J. "Profiles: Kudos for female Antarctic researchers". Nature 536 (7615): 148–148. doi:10.1038/536148b. 
  10. ↑ Masukume, G; Kipersztok, L; Das, D; Shafee, T; Laurent, M; Heilman, J (November 2016). "Medical journals and WP: a global health matter". The Lancet Global Health 4 (11): e791. doi:10.1016/S2214-109X(16)30254-6. 
  11. ↑ Shafee, T. "Wikipedia is already the world's 'Dr Google' – it's time for doctors and researchers to make it better". The Conversation. Retrieved 2016-10-18. 
  12. ↑ Shafee, T; Mietchen, D; Su, A (August 2017). "Academics can help shape Wikipedia". Science 357 (6351): 557–558. doi:10.1126/science.aao0462. 
  13. ↑ Shafee, T; Masukume, G; Kipersztok, L; Das, D; Häggström, M; Heilman, J (August 2017). "Evolution of Wikipedia’s medical content: past, present and future". JECH. PMID 28847845. doi:10.1136/jech-2016-208601. 
  14. ↑ Shafee, T; Das, D; Masukume, G; Häggström, M. "WikiJournal of Medicine, the first Wikipedia-integrated academic journal". WikiJournal of Medicine 4. doi:10.15347/wjm/2017.001. 
  15. ↑ Shafee, T (2018-06-01). "The aims and scope of WikiJournal of Science". WikiJournal of Science 1 (1): 1. doi:10.15347/wjs/2018.001. 
  16. ↑ Shafee, Thomas (2017). "Wikipedia-integrated publishing: a comparison of successful models". Health Inform 26 (2). doi:10.13140/RG.2.2.27470.77129. 
  17. ↑ Ann Luk (2017-04-12). "Continuing to Bridge the Journal-Wikipedia Gap: Introducing Topic Pages for PLOS Genetics". PLOS Biologue (in en-US). Retrieved 2017-05-31. 
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