commonmeta-ruby 3.3.15 → 3.3.17

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Files changed (39) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile.lock +1 -1
  3. data/lib/commonmeta/readers/json_feed_reader.rb +8 -8
  4. data/lib/commonmeta/utils.rb +14 -0
  5. data/lib/commonmeta/version.rb +1 -1
  6. data/spec/cli_spec.rb +2 -2
  7. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/json_feed_by_blog.yml +189 -1704
  8. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/json_feed_unregistered.yml +54 -1969
  9. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/by_blog_id.yml +210 -518
  10. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/not_indexed_posts.yml +6 -1450
  11. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/unregistered_posts.yml +54 -8
  12. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/blog_post_with_non-url_id.yml +18 -88
  13. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/blogger_post.yml +11 -50
  14. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_author_name_suffix.yml +64 -173
  15. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_doi.yml +13 -75
  16. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_institutional_author.yml +15 -11
  17. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_organizational_author.yml +15 -46
  18. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_without_doi.yml +17 -155
  19. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/jekyll_post.yml +14 -45
  20. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/jekyll_post_with_anonymous_author.yml +13 -16
  21. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/substack_post_with_broken_reference.yml +938 -1865
  22. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/syldavia_gazette_post_with_references.yml +128 -267
  23. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/upstream_post_with_references.yml +570 -1279
  24. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post.yml +12 -119
  25. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post_with_many_references.yml +4095 -5759
  26. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post_with_references.yml +24 -220
  27. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post_with_tracking_code_on_url.yml +13 -12
  28. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_anonymous_author.yml +13 -16
  29. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_doi.yml +12 -119
  30. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_organizational_author.yml +15 -46
  31. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_upstream_blog.yml +13 -201
  32. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_with_references.yml +104 -813
  33. data/spec/readers/json_feed_reader_spec.rb +22 -24
  34. data/spec/utils_spec.rb +40 -0
  35. data/spec/writers/crossref_xml_writer_spec.rb +4 -4
  36. metadata +2 -5
  37. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/blog_post.yml +0 -360
  38. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/blog_post_uuid.yml +0 -980
  39. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed_unregistered/blog_post_uuid.yml +0 -49
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- presentations today at MTE14, and the papers that go with them\",\"summary\":\"BIG
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- day today. The 14th Symposium on Mesozoic Terrestrial Ecosystems and Biota
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- (MTE14) is taking place in Salt Lake City this week. Normally I’d be there
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- in a heartbeat, but my son is graduating from high school next week and I’m
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- far too busy to get away. Still, I’m an author on one poster and two talks
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- that are running today, along with the three associated short papers that
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- are published in the conference volume in The Anatomical Record.  I will be
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- blogging about these things, and shortly,...\",\"date_published\":\"2023-06-09T13:02:26Z\",\"date_modified\":\"2023-06-09T13:02:26Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":null,\"name\":\"Matt
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- Wedel\"}],\"image\":null,\"content_html\":\"\\n<p><a href=\\\"https://svpow.files.wordpress.com/2023/06/ripple-rock-in-the-oklahoma-morrison.jpg\\\"><img
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- data-orig-file=\\\"https://svpow.files.wordpress.com/2023/06/ripple-rock-in-the-oklahoma-morrison.jpg\\\"
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- 768w\\\" sizes=\\\"(max-width: 480px) 100vw, 480px\\\" /></a></p>\\n<p>BIG
71
- day today. The 14th Symposium on Mesozoic Terrestrial Ecosystems and Biota
72
- (MTE14) is taking place in Salt Lake City this week. Normally I&#8217;d be
73
- there in a heartbeat, but my son is graduating from high school next week
74
- and I&#8217;m far too busy to get away. Still, I&#8217;m an author on one
75
- poster and two talks that are running today, along with the three associated
76
- short papers that are published in the conference volume in The Anatomical
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- Record. </p>\\n<p>I will be blogging about these things, and shortly, but
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- for now here are Wedel-related presentations and links to the papers, in chronological
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- order. (The whole conference volume is available <a href=\\\"https://anatomypubs.onlinelibrary.wiley.com/doi/full/10.1002/ar.25219\\\">here</a>,
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- I just extracted the papers I&#8217;m on as separate PDFs to post in the links
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- below.)</p>\\n<p>1. Wedel and Atterholt on expanded neurocentral joints in
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- sauropods &#8212; Jessie is presenting our poster, which should be up for
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- most of the day. Citation and link to paper:</p>\\n<p style=\\\"padding-left:
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- 40px\\\"><a href=\\\"https://sauroposeidon.files.wordpress.com/2010/04/wedel-and-atterholt-2023-expanded-neurocentral-joints-in-sauropods.pdf\\\">Wedel,
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- M.J., and Atterholt, J. 2023. Expanded neurocentral joints in the vertebrae
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- of sauropod dinosaurs. In Hunt-Foster, R.K., Kirkland, J.I., and Loewen, M.A.
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- (eds), 14th Symposium on Mesozoic Terrestrial Ecosystems and Biota. The Anatomical
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- Record 306(S1):256-257.</a></p>\\n<p>2. Curtice et al. on the first material
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- of <em>Haplocanthosaurus</em> from Dry Mesa &#8212; I believe Brian Curtice
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- and Colin Boisvert are tag-teaming this talk at 2:00 pm MDT. </p>\\n<p style=\\\"padding-left:
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- 40px\\\"><a href=\\\"https://sauroposeidon.files.wordpress.com/2010/04/curtice-et-al-2023-haplocanthosaurus-from-dry-mesa.pdf\\\">Curtice,
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- B., Wedel, M.J., Wilhite, D.R., and Boisvert, C. 2023. New material of <em>Haplocanthosaurus</em>
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- (Hatcher 1903) from the Dry Mesa Dinosaur Quarry and a comment on sauropod
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- diversity. In Hunt-Foster, R.K., Kirkland, J.I., and Loewen, M.A. (eds), 14th
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- Symposium on Mesozoic Terrestrial Ecosystems and Biota. The Anatomical Record
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- 306(S1):79-81.</a></p>\\n<p>3. Weil et al. on Morrison microvertebrates from
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- the Oklahoma panhandle &#8212; Anne Weil is giving this talk at 2:15 pm MDT.</p>\\n<p
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- style=\\\"padding-left: 40px\\\"><a href=\\\"https://sauroposeidon.files.wordpress.com/2010/04/weil-et-al-2023-oklahoma-morrison-microvertebrates.pdf\\\">Weil,
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- A., Hall, L., and Wedel, M.J. 2023. Microvertebrate expansion of known fauna
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- of the Morrison Formation of Oklahoma will enable more meaningful comparisons
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- with other regions. In Hunt-Foster, R.K., Kirkland, J.I., and Loewen, M.A.
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- (eds), 14th Symposium on Mesozoic Terrestrial Ecosystems and Biota. The Anatomical
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- Record 306(S1):257-258.</a></p>\\n<p>Stand by for more info on all this stuff.
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- And if you&#8217;re attending MTE14, go catch these presentations and say
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- hi to all these excellent human beings!</p>\\n\",\"tags\":[\"#MTE14\",\"conferences\",\"navel
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- on the disturbing plausibility of ChatGPT\",\"summary\":\"Prompted by a post
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- on Mastodon (which, like all Mastodon posts, I can no longer find), I asked
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- ChatGPT to tell me about my own papers. The response started out well but
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- quickly got much worse. I will indent my comments on its response. Q. What
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- are some articles written by Michael P. Taylor? A. Michael P. Taylor is a
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- vertebrate paleontologist and open science advocate. He has written numerous
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- articles and papers on topics such as the taxonomy and systematics of sauropod
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- dinosaurs, open access...\",\"date_published\":\"2023-04-12T22:40:38Z\",\"date_modified\":\"2023-04-12T22:40:38Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":null,\"name\":\"Mike
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- Taylor\"}],\"image\":null,\"content_html\":\"<p>Prompted by a post on Mastodon
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- (which, like all Mastodon posts, I can no longer find), <a href=\\\"https://chat.openai.com/chat/e3febb81-8cf4-47c5-bf2b-49dade1f6518\\\">I
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- asked ChatGPT to tell me about my own papers</a>. The response started out
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- well but quickly got much worse. I will indent my comments on its response.</p>\\n<hr
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- />\\n<p><strong>Q. What are some articles written by Michael P. Taylor?</strong></p>\\n<p>A.
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- Michael P. Taylor is a vertebrate paleontologist and open science advocate.
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- He has written numerous articles and papers on topics such as the taxonomy
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- and systematics of sauropod dinosaurs, open access publishing, and scholarly
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- communication.</p>\\n<blockquote><p>So far, so good. In general, LLMs seem
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- to be good at synthesizing overviews. It&#8217;s specific facts that trip
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- them up.</p></blockquote>\\n<p>Here are a few examples of his articles:</p>\\n<p>Taylor,
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- M. P. (2009). A re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria,
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- Sauropoda) and its generic separation from Giraffatitan brancai (Janensch
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- 1914) (Dinosauria, Sauropoda). Journal of Vertebrate Paleontology, 29(3),
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- 787-806.</p>\\n<blockquote><p>The first one gives is pretty good. The only
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- mistake is that it&#8217;s oddly appended &#8220;(Dinosauria, Sauropoda)&#8221;
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- to the end of the article title. The journal, volume, issue and page-numbers
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- are all correct.</p></blockquote>\\n<p>Taylor, M. P. (2011). Sauropod dinosaur
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- research: a historical review. In A. W. A. Kellner, & D. A. S. Silva (Eds.),
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- Vertebrate paleontology and sedimentology of the Jurassic-Cretaceous boundary
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- in the northern and central parts of the Lusitanian Basin, Portugal (pp. 11-43).
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- Sociedade de Geologia de Portugal.</p>\\n<blockquote><p>I did write a book-chapter
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- titled &#8220;Sauropod dinosaur research: a historical review&#8221;. But
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- it came out in 2010, not 2011. And it ran from pages 361–386, not 11-43. And
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- it was in <em>Dinosaurs and Other Extinct Saurians: a Historical Perspective</em>,
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- not <em>Vertebrate paleontology and sedimentology of the Jurassic-Cretaceous
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- boundary in the northern and central parts of the Lusitanian Basin, Portugal</em>
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- (which doesn&#8217;t exist). Which was edited by Richard T. J. Moody, Eric
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- Buffetaut, Darren Naish and David M. Martill, not A. W. A. Kellner & D. A.
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- S. Silva. And published by the Geological Society of London, not Sociedade
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- de Geologia de Portugal.</p></blockquote>\\n<p>Taylor, M. P., & Wedel, M.
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- J. (2018). Why sauropods had long necks; and why giraffes have short necks.
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- PeerJ Preprints, 6, e27537v1.</p>\\n<blockquote><p>I and Matt did co-write
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- a paper with a similar title in <em>PeerJ</em>. But it&#8217;s Why sauropods
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- had long necks; and why giraffes have short necks, not the other way around.
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- And it came out in 2013, not 2018. And it was in <em>PeerJ</em> proper, not
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- <em>PeerJ Preprints</em>.</p></blockquote>\\n<p>Taylor, M. P. (2020). The
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- open-access wars: How to free science from academic paywalls. Wired.</p>\\n<blockquote><p>I
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- never wrote any such paper. <a href=\\\"https://www.vox.com/the-highlight/2019/6/3/18271538/open-access-elsevier-california-sci-hub-academic-paywalls\\\">There <em>is</em>
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- an article out there</a> whose HTML title is the one given here, though the
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- visible title is completely different: &#8220;The war to free science&#8221;.
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- It&#8217;s in <em>Vox</em>, not <em>Wired;</em> it came out in 2019, not 2020.
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- And it&#8217;s by Brian Resnick and Julia Belluz.</p></blockquote>\\n<p>Taylor,
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- M. P., & Knope, M. L. (2021). The future of scholarly publishing is in our
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- hands. The Conversation.</p>\\n<blockquote><p>As far as I recall, I never
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- wrote anything for <em>The Conversation</em>. There seems to be no article
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- named &#8220;The future of scholarly publishing is in our hands&#8221;. And
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- I have never met or corresponded with, far less co-authored with, anyone with
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- the surname Knope.</p></blockquote>\\n<hr />\\n<p>All in all, a pretty horrible
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- performance — but, and this is the scary part, one that even someone pretty
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- familiar with my work could very easily have swallowed.</p>\\n<p>I made a
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- very similar point a few months ago in <a href=\\\"https://svpow.com/2023/01/15/these-new-artificial-intelligence-programs-dont-know-what-theyre-talking-about/\\\">These
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- new “artificial intelligence” programs don’t know what they’re talking about.</a>
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- If the responses were obviously wrong, there wouldn&#8217;t be too much of
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- a problem here. But this is close enough to fool most people most of the time.</p>\\n<p>As
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- more and more of what we read is likely to be written by LLMs in the next
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- years, I am concerned that we&#8217;re going to be dealing with an awful lot
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- of this kind of thing. The ability to pan gold out of the stream of lies is
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- going to become really important.</p>\\n\",\"tags\":[\"Just Plain Wrong\",\"rants\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"dkvra02\",\"blog\":{\"id\":\"dkvra02\",\"title\":\"Sauropod
177
- Vertebra Picture of the Week\",\"description\":\"SV-POW! ... All sauropod
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- vertebrae, except when we&#039;re talking about Open Access\",\"language\":\"en\",\"favicon\":null,\"feed_url\":\"https://svpow.com/feed/atom/\",\"home_page_url\":\"https://svpow.com\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T14:28:02+00:00\",\"indexed_at\":\"2023-02-01\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"WordPress
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- a sitemap with Quarto\",\"summary\":\"Sitemaps are an easy way to list all
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- pages that a search engine should crawl and index. Quarto supports the standard,
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- Quarto will automatically produce a sitemap if the website’s URL is given
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- as site-url property: website: title: tarleb site-url: 'https://tarleb.com'
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- must be put in quotes. You’ll find the sitemap.xml file in your _site...\",\"date_published\":\"2022-08-24T00:00:00Z\",\"date_modified\":null,\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":null,\"name\":\"Albert
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- yaml\\\"><span id=\\\"cb1-1\\\"><span class=\\\"fu\\\" style=\\\"color: #4758AB;\\\">website</span><span
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- class=\\\"kw\\\" style=\\\"color: #003B4F;\\\">:</span></span>\\n<span id=\\\"cb1-2\\\"><span
196
- class=\\\"at\\\" style=\\\"color: #657422;\\\"> </span><span class=\\\"fu\\\"
197
- style=\\\"color: #4758AB;\\\">title</span><span class=\\\"kw\\\" style=\\\"color:
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- #003B4F;\\\">:</span><span class=\\\"at\\\" style=\\\"color: #657422;\\\">
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- tarleb</span></span>\\n<span id=\\\"cb1-3\\\"><span class=\\\"at\\\" style=\\\"color:
200
- #657422;\\\"> </span><span class=\\\"fu\\\" style=\\\"color: #4758AB;\\\">site-url</span><span
201
- class=\\\"kw\\\" style=\\\"color: #003B4F;\\\">:</span><span class=\\\"at\\\"
202
- style=\\\"color: #657422;\\\"> </span><span class=\\\"st\\\" style=\\\"color:
203
- #20794D;\\\">'https://tarleb.com'</span></span>\\n<span id=\\\"cb1-4\\\"><span
204
- class=\\\"at\\\" style=\\\"color: #657422;\\\"> </span><span class=\\\"fu\\\"
205
- style=\\\"color: #4758AB;\\\">site-path</span><span class=\\\"kw\\\" style=\\\"color:
206
- #003B4F;\\\">:</span><span class=\\\"at\\\" style=\\\"color: #657422;\\\">
207
- </span><span class=\\\"st\\\" style=\\\"color: #20794D;\\\">'/'</span></span></code></pre></div>\\n<p>The
208
- URL will contain a colon <code>:</code>, which is why the YAML value must
209
- be put in quotes.</p>\\n<p>You’ll find the <code>sitemap.xml</code> file in
210
- your <code>_site</code> folder after re-rendering your pages with <code>quarto
211
- render</code>.</p>\\n\\n\\n\\n \",\"tags\":[\"quarto\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"7gyq558\",\"blog\":{\"id\":\"7gyq558\",\"title\":\"tarleb\",\"description\":\"tarleb's
212
- blog\",\"language\":\"en\",\"favicon\":null,\"feed_url\":\"https://tarleb.com/index.xml\",\"home_page_url\":\"https://tarleb.com/index.html\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T16:58:43+00:00\",\"indexed_at\":\"2023-04-20\",\"feed_format\":\"application/rss+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"Quarto
213
- 1.2.475\",\"category\":\"Engineering and Technology\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-03-24T00:00:00+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":false,\"authors\":null}},{\"id\":\"https://doi.org/10.59350/btxxm-sr025\",\"uuid\":\"6eb9a4e0-b8b4-4867-bcf0-5e6e0b84c9df\",\"url\":\"http://gigasciencejournal.com/blog/indexed-in-pubmed/\",\"title\":\"GigaByte
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- now indexed in PubMed and PubMed Central (PMC)\",\"summary\":\"GigaScience
215
- Press is pleased to announce GigaByte journal is now indexed in PubMed and
216
- PubMed Central (PMC) databases run by the US National Library of Medicine.
217
- PubMed being a searchable database of biomedical citations and abstracts,
218
- and PMC being a free digital archive of the full-text of Open Access articles.
219
- While both increase the discoverability of our published papers, our now automatic
220
- inclusion into PMC is also necessary for many researchers to meet their research
221
- funders policies...\",\"date_published\":\"2023-02-28T12:10:05Z\",\"date_modified\":\"2023-02-28T12:10:06Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":\"http://orcid.org/0000-0001-6444-1436\",\"name\":\"Scott
222
- Edmunds\"}],\"image\":null,\"content_html\":\"\\n<figure class=\\\"wp-block-image
223
- size-large is-resized\\\"><img decoding=\\\"async\\\" loading=\\\"lazy\\\"
224
- src=\\\"http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/1-1024x1024.png\\\"
225
- alt=\\\"indexed in pubmed\\\" class=\\\"wp-image-4831\\\" width=\\\"768\\\"
226
- height=\\\"768\\\" srcset=\\\"http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/1-1024x1024.png
227
- 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/1-300x300.png
228
- 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/1-150x150.png
229
- 150w, http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/1-768x768.png
230
- 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/1-1536x1536.png
231
- 1536w, http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/1.png
232
- 1620w\\\" sizes=\\\"(max-width: 768px) 100vw, 768px\\\" /></figure>\\n\\n\\n\\n<p></p>\\n\\n\\n\\n<p>GigaScience
233
- Press is pleased to announce <em>GigaByte</em> journal is now indexed in PubMed
234
- and <a href=\\\"https://www.ncbi.nlm.nih.gov/pmc/journals/4281/\\\">PubMed
235
- Central (PMC)</a> databases run by the US National Library of Medicine. PubMed
236
- being a searchable database of biomedical citations and abstracts, and PMC
237
- being a free digital archive of the full-text of Open Access articles. While
238
- both increase the discoverability of our published papers, our now automatic
239
- inclusion into PMC is also necessary for many researchers to meet their research
240
- funders policies and mandates on Open Access. As Open Access advocates, now
241
- this has been added to our publication workflow our authors do not need to
242
- worry about depositing their publications themselves. We <a href=\\\"https://clockss.org/clockss-announces-the-support-of-additional-libraries-and-publishers-2/\\\">use
243
- CLOCKSS</a> for the long-term digital preservation of our scholarly content,
244
- and archiving in PMC also provides an additional level of protection and survival
245
- of preserved digital content.</p>\\n\\n\\n\\n<p>PubMed and PMC join googlescholar,
246
- <a href=\\\"https://scholar.cnki.net/home/search?region=db&val=SQHE&resType=Journal\\\">CNKI</a>,
247
- <a href=\\\"https://jgateplus.com/home/j-gate/\\\">JGate</a> and the <a href=\\\"https://doaj.org/toc/2709-4715\\\">Directory
248
- of Open Access Journals (DOAJ)</a> as indexes to discover and browse our content.
249
- Our partners at River Valley Technologies have worked hard to produce the
250
- highest quality XML for our human and machine readers (see our <a href=\\\"https://gigabytejournal.com/text-and-data-mining\\\">text
251
- and data mining portal</a>), and this has made the process of indexing easier.
252
- PMC, <a href=\\\"https://doaj.org/toc/2709-4715\\\">DOAJ</a> and JGate using
253
- converted versions of our XML to mirror our Open Access content. The DOAJ
254
- awarding us their seal for journals that demonstrate best practice in open
255
- access publishing, and CrossRef giving us a near-100% score in their <a href=\\\"https://www.crossref.org/members/prep/23445\\\">Participation
256
- Reports</a> for the richness of our metadata (only being let down on the funding
257
- categories as our <a href=\\\"https://gigabytejournal.com/open-access-and-apc\\\">cost-effective
258
- APCs</a> and waivers mean we publish quite a lot of number of papers without
259
- external funding).</p>\\n\\n\\n\\n<p></p>\\n\\n\\n\\n<figure class=\\\"wp-block-image
260
- size-large is-resized\\\"><img decoding=\\\"async\\\" loading=\\\"lazy\\\"
261
- src=\\\"http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/Screenshot-2023-02-28-at-5.57.33-PM-1024x972.png\\\"
262
- alt=\\\"indexing in PubMed\\\" class=\\\"wp-image-4833\\\" width=\\\"768\\\"
263
- height=\\\"729\\\" srcset=\\\"http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/Screenshot-2023-02-28-at-5.57.33-PM-1024x972.png
264
- 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/Screenshot-2023-02-28-at-5.57.33-PM-300x285.png
265
- 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/Screenshot-2023-02-28-at-5.57.33-PM-768x729.png
266
- 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/Screenshot-2023-02-28-at-5.57.33-PM.png
267
- 1342w\\\" sizes=\\\"(max-width: 768px) 100vw, 768px\\\" /></figure>\\n\\n\\n\\n<p></p>\\n\\n\\n\\n<p>Not
268
- only is our XML rich with this metadata, but we’ve been using it to capture
269
- <a href=\\\"http://gigasciencejournal.com/blog/how-to-publish-multilingual-articles/\\\">multilingual
270
- versions of our content</a>, and this also displays in the PMC versions of
271
- our papers (see our recent English/Spanish/Ukrainian paper in <em><a href=\\\"https://doi.org/10.46471/gigabyte.73\\\">GigaByte</a></em>
272
- and <a href=\\\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9693923/\\\">PMC</a>).
273
- Further increasing the accessibility and global reach of our papers.</p>\\n\\n\\n\\n<figure
274
- class=\\\"wp-block-image size-large is-resized\\\"><img decoding=\\\"async\\\"
275
- loading=\\\"lazy\\\" src=\\\"http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/Screenshot-2023-02-28-at-5.47.47-PM-1024x704.png\\\"
276
- alt=\\\"\\\" class=\\\"wp-image-4834\\\" width=\\\"768\\\" height=\\\"528\\\"
277
- srcset=\\\"http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/Screenshot-2023-02-28-at-5.47.47-PM-1024x704.png
278
- 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/Screenshot-2023-02-28-at-5.47.47-PM-300x206.png
279
- 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/Screenshot-2023-02-28-at-5.47.47-PM-768x528.png
280
- 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/Screenshot-2023-02-28-at-5.47.47-PM-1536x1056.png
281
- 1536w, http://gigasciencejournal.com/blog/wp-content/uploads/2023/02/Screenshot-2023-02-28-at-5.47.47-PM.png
282
- 1644w\\\" sizes=\\\"(max-width: 768px) 100vw, 768px\\\" /></figure>\\n\\n\\n\\n<p></p>\\n\\n\\n\\n<p>Now
283
- we have sufficient quantity and quality of publishing data for many other
284
- indexes we are continuing the process of submitting to these databases, so
285
- watch this space for updates on how that process goes.</p>\\n<p>The post <a
286
- rel=\\\"nofollow\\\" href=\\\"http://gigasciencejournal.com/blog/indexed-in-pubmed/\\\">GigaByte
287
- now indexed in PubMed and PubMed Central (PMC)</a> appeared first on <a rel=\\\"nofollow\\\"
288
- href=\\\"http://gigasciencejournal.com/blog\\\">GigaBlog</a>.</p>\\n\",\"tags\":[\"Open
289
- Access\",\"GigaByte\",\"Indexing\",\"open access\",\"pubmed\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"3ffcd46\",\"blog\":{\"id\":\"3ffcd46\",\"title\":\"GigaBlog\",\"description\":\"Data
290
- driven blogging from the GigaScience editors\",\"language\":\"en\",\"favicon\":null,\"feed_url\":\"http://gigasciencejournal.com/blog/feed/atom/\",\"home_page_url\":\"http://gigasciencejournal.com/blog\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T13:42:00+00:00\",\"indexed_at\":\"2023-02-05\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"WordPress
291
- 6.2.2\",\"category\":\"Natural Sciences\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-05-24T20:01:37+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.53731/ejtg5cm-mtt292s\",\"uuid\":\"4eb9ac30-9edc-4830-b2ad-25183fb1548a\",\"url\":\"https://syldavia-gazette.org/data-sharing-challenger-expedition-research-software/\",\"title\":\"Data
292
- Sharing, Challenger Expedition, Research Software, Adornment, Prostate Cancer\",\"summary\":\"Ten
293
- (not so) simple rules for clinical trial data-sharingThe authors propose 10
294
- (not so) simple rules for researchers wishing to share data, aligned on the
295
- clinical trial lifecycle.The Challenger Expedition - 1872Report of a BBC Radio
296
- episode about the 1872 four-year-long Challenger expedition to investigate
297
- the oceans of the earth.Defining the roles of research softwareWorkshop report
298
- that tries to define the various roles of research software.This 2,300-Year-Old
299
- Mummy Has a Heart (and...\",\"date_published\":\"2023-03-15T20:37:00Z\",\"date_modified\":\"2023-04-13T12:34:10Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":\"https://orcid.org/0000-0003-1419-2405\",\"name\":\"Martin
300
- Fenner\"}],\"image\":\"https://digitalpress.fra1.cdn.digitaloceanspaces.com/gtpg506/2023/04/journal.pcbi.1010879.g001.png\",\"content_html\":\"
301
- <h3 id=\\\"ten-not-so-simple-rules-for-clinical-trial-data-sharing\\\"><a
302
- href=\\\"https://doi.org/10.1371/journal.pcbi.1010879?ref=syldavia-gazette.org\\\">Ten
303
- (not so) simple rules for clinical trial data-sharing</a></h3><p>The authors
304
- propose 10 (not so) simple rules for researchers wishing to share data, aligned
305
- on the clinical trial lifecycle.</p><h3 id=\\\"the-challenger-expedition1872\\\"><a
306
- href=\\\"https://world.hey.com/ian.mulvany/the-challenger-expedition-1872-e067bad9?ref=syldavia-gazette.org\\\">The
307
- Challenger Expedition - 1872</a></h3><p>Report of a BBC Radio episode about
308
- the 1872 four-year-long Challenger expedition to investigate the oceans of
309
- the earth.</p><h3 id=\\\"defining-the-roles-of-research-software\\\"><a href=\\\"https://doi.org/10.54900/9akm9y5-5ject5y?ref=syldavia-gazette.org\\\">Defining
310
- the roles of research software</a></h3><p>Workshop report that tries to define
311
- the various roles of research software.</p><h3 id=\\\"this-2300-year-old-mummy-has-a-heart-and-tongue-of-gold\\\"><a
312
- href=\\\"https://www.discovermagazine.com/the-sciences/this-2-300-year-old-mummy-has-a-heart-and-tongue-of-gold?ref=syldavia-gazette.org\\\">This
313
- 2,300-Year-Old Mummy Has a Heart (and Tongue) of Gold</a></h3><p>To acquire
314
- additional insight into the practice of adornment in ancient Egypt, three
315
- researchers recently \\\"digitally unwrapped\\\" the mummified body of a wealthy
316
- teenage boy from 2,300 years ago.</p><h3 id=\\\"prostate-cancer-treatments-can-be-avoided-or-delayed-in-many-cases-huge-study-finds\\\"><a
317
- href=\\\"https://www.livescience.com/prostate-cancer-treatments-can-be-avoided-or-delayed-in-many-cases-huge-study-finds?ref=syldavia-gazette.org\\\">Prostate
318
- cancer treatments can be avoided or delayed in many cases, huge study finds</a></h3><p>Fifteen-year
319
- outcomes after monitoring, surgery, or radiotherapy for localized prostate
320
- cancer. Prostate cancer–specific mortality was low regardless of the treatment
321
- assigned.</p><hr><h3 id=\\\"references\\\">References</h3><ol><li>Pellen C,
322
- Louarn AL, Spurrier-Bernard G, et al. Ten (not so) simple rules for clinical
323
- trial data-sharing. <em>PLOS Computational Biology</em>. 2023;19(3):e1010879.
324
- doi:<a href=\\\"https://doi.org/10.1371/journal.pcbi.1010879?ref=syldavia-gazette.org\\\">10.1371/journal.pcbi.1010879</a></li><li>The
325
- Challenger Expedition - 1872. Accessed March 28, 2023. <a href=\\\"https://world.hey.com/ian.mulvany/the-challenger-expedition-1872-e067bad9?ref=syldavia-gazette.org\\\">https://world.hey.com/ian.mulvany/the-challenger-expedition-1872-e067bad9</a></li><li>Nieuwpoort
326
- R van, Katz DS. Defining the roles of research software. <em>Upstream</em>.
327
- Published online March 14, 2023. doi:<a href=\\\"https://doi.org/10.54900/9akm9y5-5ject5y?ref=syldavia-gazette.org\\\">10.54900/9akm9y5-5ject5y</a></li><li>This
328
- 2,300-Year-Old Mummy Has a Heart (and Tongue) of Gold. Discover Magazine.
329
- Accessed March 28, 2023. <a href=\\\"https://www.discovermagazine.com/the-sciences/this-2-300-year-old-mummy-has-a-heart-and-tongue-of-gold?ref=syldavia-gazette.org\\\">https://www.discovermagazine.com/the-sciences/this-2-300-year-old-mummy-has-a-heart-and-tongue-of-gold</a></li><li>Prostate
330
- cancer treatments can be avoided or delayed in many cases, huge study finds
331
- | Live Science. Accessed March 28, 2023. <a href=\\\"https://www.livescience.com/prostate-cancer-treatments-can-be-avoided-or-delayed-in-many-cases-huge-study-finds?ref=syldavia-gazette.org\\\">https://www.livescience.com/prostate-cancer-treatments-can-be-avoided-or-delayed-in-many-cases-huge-study-finds</a></li></ol>
332
- \",\"tags\":[],\"language\":\"en\",\"references\":[{\"doi\":\"https://doi.org/10.1371/journal.pcbi.1010879\",\"key\":\"ref1\"},{\"key\":\"ref2\",\"url\":\"https://world.hey.com/ian.mulvany/the-challenger-expedition-1872-e067bad9\"},{\"doi\":\"https://doi.org/10.54900/9akm9y5-5ject5y\",\"key\":\"ref3\"},{\"key\":\"ref4\",\"url\":\"https://discovermagazine.com/the-sciences/this-2-300-year-old-mummy-has-a-heart-and-tongue-of-gold\"},{\"key\":\"ref5\",\"url\":\"https://livescience.com/prostate-cancer-treatments-can-be-avoided-or-delayed-in-many-cases-huge-study-finds\"}],\"blog_id\":\"f4wdg32\",\"blog\":{\"id\":\"f4wdg32\",\"title\":\"Syldavia
333
- Gazette\",\"description\":\"The Syldavia Gazette is a weekly newsletter that
334
- highlights interesting science stories from around the web.\",\"language\":\"en\",\"favicon\":\"https://syldavia-gazette.org/favicon.png\",\"feed_url\":\"https://syldavia-gazette.org/atom/\",\"home_page_url\":\"https://syldavia-gazette.org\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T16:54:04+00:00\",\"indexed_at\":\"2023-02-01\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"Ghost
335
- 5.40\",\"category\":\"Humanities\",\"prefix\":\"10.53731\",\"modified_at\":\"2023-03-15T20:37:00+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":false,\"authors\":null}},{\"id\":\"https://doi.org/10.59350/ymc6x-rx659\",\"uuid\":\"0807f515-f31d-4e2c-9e6f-78c3a9668b9d\",\"url\":\"https://iphylo.blogspot.com/2022/09/dna-barcoding-as-intergenerational.html\",\"title\":\"DNA
336
- barcoding as intergenerational transfer of taxonomic knowledge\",\"summary\":\"I
337
- tweeted about this but want to bookmark it for later as well. The paper “A
338
- molecular-based identification resource for the arthropods of Finland” doi:10.1111/1755-0998.13510
339
- contains the following: …the annotated barcode records assembled by FinBOL
340
- participants represent a tremendous intergenerational transfer of taxonomic
341
- knowledge … the time contributed by current taxonomists in identifying and
342
- contributing voucher specimens represents a great gift to future generations
343
- who will benefit...\",\"date_published\":\"2022-09-14T10:12:00Z\",\"date_modified\":\"2022-09-29T13:57:30Z\",\"date_indexed\":\"1909-06-16T11:02:21+00:00\",\"authors\":[{\"url\":null,\"name\":\"Roderic
344
- Page\"}],\"image\":null,\"content_html\":\"<p>I <a href=\\\"https://twitter.com/rdmpage/status/1569738844416638981?s=21&amp;t=9OVXuoUEwZtQt-Ldzlutfw\\\">tweeted
345
- about this</a> but want to bookmark it for later as well. The paper “A molecular-based
346
- identification resource for the arthropods of Finland” <a href=\\\"https://doi.org/10.1111/1755-0998.13510\\\">doi:10.1111/1755-0998.13510</a>
347
- contains the following:</p>\\n<blockquote>\\n<p>…the annotated barcode records
348
- assembled by FinBOL participants represent a tremendous <mark>intergenerational
349
- transfer of taxonomic knowledge</mark> … the time contributed by current taxonomists
350
- in identifying and contributing voucher specimens represents a great gift
351
- to future generations who will benefit from their expertise when they are
352
- no longer able to process new material.</p>\\n</blockquote>\\n<p>I think this
353
- is a very clever way to characterise the project. In an age of machine learning
354
- this may be commonest way to share knowledge , namely as expert-labelled training
355
- data used to build tools for others. Of course, this means the expertise itself
356
- may be lost, which has implications for updating the models if the data isn’t
357
- complete. But it speaks to Charles Godfrey’s theme of <a href=\\\"https://biostor.org/reference/250587\\\">“Taxonomy
358
- as information science”</a>.</p>\\n<p>Note that the knowledge is also transformed
359
- in the sense that the underlying expertise of interpreting morphology, ecology,
360
- behaviour, genomics, and the past literature is not what is being passed on.
361
- Instead it is probabilities that a DNA sequence belongs to a particular taxon.</p>\\n<p>This
362
- feels is different to, say iNaturalist, where there is a machine learning
363
- model to identify images. In that case, the model is built on something the
364
- community itself has created, and continues to create. Yes, the underlying
365
- idea is that same: “experts” have labelled the data, a model is trained, the
366
- model is used. But the benefits of the <a href=\\\"https://www.inaturalist.org\\\">iNaturalist</a>
367
- model are immediately applicable to the people whose data built the model.
368
- In the case of barcoding, because the technology itself is still not in the
369
- hands of many (relative to, say, digital imaging), the benefits are perhaps
370
- less tangible. Obviously researchers working with environmental DNA will find
371
- it very useful, but broader impact may await the arrival of citizen science
372
- DNA barcoding.</p>\\n<p>The other consideration is whether the barcoding helps
373
- taxonomists. Is it to be used to help prioritise future work (“we are getting
374
- lots of unknown sequences in these taxa, lets do some taxonomy there”), or
375
- is it simply capturing the knowledge of a generation that won’t be replaced:</p>\\n<blockquote>\\n<p>The
376
- need to capture such knowledge is essential because there are, for example,
377
- no young Finnish taxonomists who can critically identify species in many key
378
- groups of ar- thropods (e.g., aphids, chewing lice, chalcid wasps, gall midges,
379
- most mite lineages).</p>\\n</blockquote>\\n<p>The cycle of collect data, test
380
- and refine model, collect more data, rinse and repeat that happens with iNaturalist
381
- creates a feedback loop. It’s not clear that a similar cycle exists for DNA
382
- barcoding.</p>\\n<blockquote>\\n<p>Written with <a href=\\\"https://stackedit.io/\\\">StackEdit</a>.</p>\\n</blockquote>\",\"tags\":[],\"language\":\"en\",\"references\":[],\"blog_id\":\"tyfqw20\",\"blog\":{\"id\":\"tyfqw20\",\"title\":\"iPhylo\",\"description\":\"Rants,
383
- raves (and occasionally considered opinions) on phyloinformatics, taxonomy,
384
- and biodiversity informatics. For more ranty and less considered opinions,
385
- see my <a href=\\\"https://twitter.com/rdmpage\\\">Twitter feed</a>.<br>ISSN
386
- 2051-8188. Written content on this site is licensed under a <a href=\\\"https://creativecommons.org/licenses/by/4.0/\\\">Creative
387
- Commons Attribution 4.0 International license</a>.\",\"language\":\"en\",\"favicon\":null,\"feed_url\":\"https://iphylo.blogspot.com/feeds/posts/default\",\"home_page_url\":\"https://iphylo.blogspot.com/\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T08:03:14+00:00\",\"indexed_at\":\"2023-02-06\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"Blogger
388
- 7.00\",\"category\":\"Natural Sciences\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-05-31T17:26:00+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.59350/e7b4h-2eh30\",\"uuid\":\"eeb9b865-9fbf-4a15-b156-5363b81060ae\",\"url\":\"https://larsgw.blogspot.com/2018/08/citationjs-showing-blogger-posts-on.html\",\"title\":\"Citation.js:
389
- Showing Blogger Posts on a Different Site\",\"summary\":\"Citation.js: Showing
390
- Blogger Posts on a Different Site I made a small client for Blogger that
391
- takes a tag and transforms it into its own little blog: citation.js.org/blog/?post=542….
392
- No metadata though, as it’s all client-side. — Lars Willighagen (@larswillighagen)
393
- \ August 6, 2018 I made a Material-themed page showing Citation.js blog posts
394
- from Blogger. It supports pagination, tags, search and linking individual
395
- posts. Since it’s a single, static page I can’t support meta and link...\",\"date_published\":\"2018-08-22T19:36:00Z\",\"date_modified\":\"2023-03-30T20:48:33Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":null,\"name\":\"Lars
396
- Willighagen\"}],\"image\":null,\"content_html\":\"<!DOCTYPE html>\\n<html>\\n\\n<head>\\n
397
- \ <meta charset=\\\"utf-8\\\">\\n <meta name=\\\"viewport\\\" content=\\\"width=device-width,
398
- initial-scale=1.0\\\">\\n <title>Citation.js: Showing Blogger Posts on a
399
- Different Site</title>\\n <link rel=\\\"stylesheet\\\" href=\\\"https://stackedit.io/style.css\\\"
400
- />\\n</head>\\n\\n<body class=\\\"stackedit\\\">\\n <div class=\\\"stackedit__html\\\"><blockquote>\\n<p>I
401
- made a small client for Blogger that takes a tag and transforms it into its
402
- own little blog: <a href=\\\"https://t.co/CYoveVJIOE\\\">citation.js.org/blog/?post=542…</a>.
403
- No metadata though, as it’s all client-side.<br>\\n— Lars Willighagen (@larswillighagen)
404
- \ <a href=\\\"https://twitter.com/larswillighagen/status/1026536137958072320?ref_src=twsrc%5Etfw\\\">August
405
- 6, 2018</a></p>\\n</blockquote>\\n<p>I made a <a href=\\\"https://getmdl.io\\\">Material-themed</a>
406
- page showing Citation.js blog posts from Blogger. It supports pagination,
407
- tags, search and linking individual posts. Since it’s a single, static page
408
- I can’t support <code>meta</code> and <code>link</code> tags for metadata,
409
- that would require JavaScript which indexers don’t run.</p>\\n<p>The great
410
- thing about the Blogger API is that you can generate feeds for single tags,
411
- like Citation.js for example, and search for tags and general queries within
412
- that tag. That’s what makes all this possible. The URL scheme is very simple:</p>\\n<pre
413
- class=\\\" language-bash\\\"><code class=\\\"prism language-bash\\\"><span
414
- class=\\\"token comment\\\"># Tag feed</span>\\nhttps://<span class=\\\"token
415
- variable\\\">$BLOG</span>.blogspot.com/feeds/posts/default/-/<span class=\\\"token
416
- variable\\\">$TAG</span>\\n\\n<span class=\\\"token comment\\\"># Tag-in-tag
417
- feed</span>\\nhttps://<span class=\\\"token variable\\\">$BLOG</span>.blogspot.com/feeds/posts/default/-/<span
418
- class=\\\"token variable\\\">$TAG</span>/<span class=\\\"token variable\\\">$OTHER_TAG</span>\\n\\n<span
419
- class=\\\"token comment\\\"># Search-in-tag feed</span>\\n<span class=\\\"token
420
- comment\\\"># Note: don't copy this, there's a ZWS before ?q= for syntax highlighting</span>\\nhttps://<span
421
- class=\\\"token variable\\\">$BLOG</span>.blogspot.com/feeds/posts/default/-/<span
422
- class=\\\"token variable\\\">$TAG</span>​?q<span class=\\\"token operator\\\">=</span><span
423
- class=\\\"token variable\\\">$QUERY</span>\\n\\n<span class=\\\"token comment\\\">#
424
- Post</span>\\nhttps://<span class=\\\"token variable\\\">$BLOG</span>.blogspot.com/feeds/posts/default/<span
425
- class=\\\"token variable\\\">$POST</span>\\n</code></pre>\\n<p>Pagination
426
- and response formats complicate things a little, and are dealt with in the
427
- code below.</p>\\n<p>Apart from the Material theme, it only uses vanilla JavaScript
428
- to generate the pages. The search bar doesn’t even use JavaScript at all,
429
- just good ol’ <code>form</code> semantics. The JavaScript it does use is fairly
430
- simple. First, the query is parsed and an API URL is generated.</p>\\n<pre
431
- class=\\\" language-js\\\"><code class=\\\"prism language-js\\\">window<span
432
- class=\\\"token punctuation\\\">.</span><span class=\\\"token function-variable
433
- function\\\">onload</span> <span class=\\\"token operator\\\">=</span> <span
434
- class=\\\"token keyword\\\">function</span> <span class=\\\"token punctuation\\\">(</span><span
435
- class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>\\n
436
- \ <span class=\\\"token keyword\\\">var</span> params <span class=\\\"token
437
- operator\\\">=</span> <span class=\\\"token punctuation\\\">{</span><span
438
- class=\\\"token punctuation\\\">}</span>\\n \\n location<span class=\\\"token
439
- punctuation\\\">.</span>search<span class=\\\"token punctuation\\\">.</span><span
440
- class=\\\"token function\\\">slice</span><span class=\\\"token punctuation\\\">(</span><span
441
- class=\\\"token number\\\">1</span><span class=\\\"token punctuation\\\">)</span><span
442
- class=\\\"token punctuation\\\">.</span><span class=\\\"token function\\\">split</span><span
443
- class=\\\"token punctuation\\\">(</span><span class=\\\"token string\\\">'&amp;'</span><span
444
- class=\\\"token punctuation\\\">)</span><span class=\\\"token punctuation\\\">.</span><span
445
- class=\\\"token function\\\">map</span><span class=\\\"token punctuation\\\">(</span><span
446
- class=\\\"token keyword\\\">function</span> <span class=\\\"token punctuation\\\">(</span>pair<span
447
- class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>\\n
448
- \ pair <span class=\\\"token operator\\\">=</span> pair<span class=\\\"token
449
- punctuation\\\">.</span><span class=\\\"token function\\\">split</span><span
450
- class=\\\"token punctuation\\\">(</span><span class=\\\"token string\\\">'='</span><span
451
- class=\\\"token punctuation\\\">)</span>\\n params<span class=\\\"token
452
- punctuation\\\">[</span>pair<span class=\\\"token punctuation\\\">[</span><span
453
- class=\\\"token number\\\">0</span><span class=\\\"token punctuation\\\">]</span><span
454
- class=\\\"token punctuation\\\">]</span> <span class=\\\"token operator\\\">=</span>
455
- pair<span class=\\\"token punctuation\\\">[</span><span class=\\\"token number\\\">1</span><span
456
- class=\\\"token punctuation\\\">]</span>\\n <span class=\\\"token punctuation\\\">}</span><span
457
- class=\\\"token punctuation\\\">)</span>\\n\\n <span class=\\\"token keyword\\\">var</span>
458
- url\\n\\n <span class=\\\"token keyword\\\">if</span> <span class=\\\"token
459
- punctuation\\\">(</span>params<span class=\\\"token punctuation\\\">.</span>post<span
460
- class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>\\n
461
- \ url <span class=\\\"token operator\\\">=</span> <span class=\\\"token
462
- string\\\">'https://larsgw.blogspot.com/feeds/posts/default/'</span> <span
463
- class=\\\"token operator\\\">+</span> params<span class=\\\"token punctuation\\\">.</span>post
464
- <span class=\\\"token operator\\\">+</span> <span class=\\\"token string\\\">'?alt=json-in-script&amp;callback=cb'</span>\\n
465
- \ <span class=\\\"token punctuation\\\">}</span> <span class=\\\"token keyword\\\">else</span>
466
- <span class=\\\"token keyword\\\">if</span> <span class=\\\"token punctuation\\\">(</span>params<span
467
- class=\\\"token punctuation\\\">.</span>tag<span class=\\\"token punctuation\\\">)</span>
468
- <span class=\\\"token punctuation\\\">{</span>\\n url <span class=\\\"token
469
- operator\\\">=</span> <span class=\\\"token string\\\">'https://larsgw.blogspot.com/feeds/posts/default/-/Citation.js/'</span>
470
- <span class=\\\"token operator\\\">+</span> params<span class=\\\"token punctuation\\\">.</span>tag
471
- <span class=\\\"token operator\\\">+</span> <span class=\\\"token string\\\">'?alt=json-in-script&amp;callback=cb'</span>\\n
472
- \ <span class=\\\"token punctuation\\\">}</span> <span class=\\\"token keyword\\\">else</span>
473
- <span class=\\\"token keyword\\\">if</span> <span class=\\\"token punctuation\\\">(</span>params<span
474
- class=\\\"token punctuation\\\">.</span>query<span class=\\\"token punctuation\\\">)</span>
475
- <span class=\\\"token punctuation\\\">{</span>\\n url <span class=\\\"token
476
- operator\\\">=</span> <span class=\\\"token string\\\">'https://larsgw.blogspot.com/feeds/posts/default/-/Citation.js/?q='</span>
477
- <span class=\\\"token operator\\\">+</span> params<span class=\\\"token punctuation\\\">.</span>query
478
- <span class=\\\"token operator\\\">+</span> <span class=\\\"token string\\\">'&amp;alt=json-in-script&amp;callback=cb'</span>\\n
479
- \ <span class=\\\"token punctuation\\\">}</span> <span class=\\\"token keyword\\\">else</span>
480
- <span class=\\\"token punctuation\\\">{</span>\\n url <span class=\\\"token
481
- operator\\\">=</span> <span class=\\\"token string\\\">'https://larsgw.blogspot.com/feeds/posts/default/-/Citation.js?alt=json-in-script&amp;callback=cb'</span>\\n
482
- \ <span class=\\\"token punctuation\\\">}</span>\\n\\n <span class=\\\"token
483
- keyword\\\">var</span> startIndex <span class=\\\"token operator\\\">=</span>
484
- location<span class=\\\"token punctuation\\\">.</span>href<span class=\\\"token
485
- punctuation\\\">.</span><span class=\\\"token function\\\">match</span><span
486
- class=\\\"token punctuation\\\">(</span><span class=\\\"token regex\\\">/start-index=(\\\\d+)/</span><span
487
- class=\\\"token punctuation\\\">)</span>\\n <span class=\\\"token keyword\\\">if</span>
488
- <span class=\\\"token punctuation\\\">(</span>startIndex<span class=\\\"token
489
- punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>\\n
490
- \ url <span class=\\\"token operator\\\">+=</span> <span class=\\\"token
491
- string\\\">'&amp;'</span> <span class=\\\"token operator\\\">+</span> startIndex<span
492
- class=\\\"token punctuation\\\">[</span><span class=\\\"token number\\\">0</span><span
493
- class=\\\"token punctuation\\\">]</span>\\n <span class=\\\"token punctuation\\\">}</span>\\n\\n
494
- \ <span class=\\\"token function\\\">load</span><span class=\\\"token punctuation\\\">(</span>url<span
495
- class=\\\"token punctuation\\\">)</span>\\n<span class=\\\"token punctuation\\\">}</span>\\n</code></pre>\\n<p>Since
496
- the only JSON API for Blogger is JSON-in-script, we append a script element
497
- loading the resource. This then calls the callback, <code>cb</code>.</p>\\n<pre
498
- class=\\\" language-js\\\"><code class=\\\"prism language-js\\\"><span class=\\\"token
499
- keyword\\\">function</span> <span class=\\\"token function\\\">cb</span> <span
500
- class=\\\"token punctuation\\\">(</span>data<span class=\\\"token punctuation\\\">)</span>
501
- <span class=\\\"token punctuation\\\">{</span>\\n content<span class=\\\"token
502
- punctuation\\\">.</span>innerHTML <span class=\\\"token operator\\\">=</span>
503
- data<span class=\\\"token punctuation\\\">.</span>feed <span class=\\\"token
504
- operator\\\">?</span> templates<span class=\\\"token punctuation\\\">.</span><span
505
- class=\\\"token function\\\">feed</span><span class=\\\"token punctuation\\\">(</span>data<span
506
- class=\\\"token punctuation\\\">.</span>feed<span class=\\\"token punctuation\\\">.</span>entry<span
507
- class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">:</span>
508
- templates<span class=\\\"token punctuation\\\">.</span><span class=\\\"token
509
- function\\\">feedItem</span><span class=\\\"token punctuation\\\">(</span>data<span
510
- class=\\\"token punctuation\\\">.</span>entry<span class=\\\"token punctuation\\\">)</span>\\n\\n
511
- \ <span class=\\\"token comment\\\">// pagination</span>\\n <span class=\\\"token
512
- keyword\\\">if</span> <span class=\\\"token punctuation\\\">(</span>data<span
513
- class=\\\"token punctuation\\\">.</span>feed<span class=\\\"token punctuation\\\">)</span>
514
- <span class=\\\"token punctuation\\\">{</span>\\n <span class=\\\"token
515
- keyword\\\">var</span> href <span class=\\\"token operator\\\">=</span> location<span
516
- class=\\\"token punctuation\\\">.</span>href\\n <span class=\\\"token keyword\\\">var</span>
517
- hasIndex <span class=\\\"token operator\\\">=</span> href<span class=\\\"token
518
- punctuation\\\">.</span><span class=\\\"token function\\\">indexOf</span><span
519
- class=\\\"token punctuation\\\">(</span><span class=\\\"token string\\\">'start-index'</span><span
520
- class=\\\"token punctuation\\\">)</span> <span class=\\\"token operator\\\">&gt;</span>
521
- <span class=\\\"token operator\\\">-</span><span class=\\\"token number\\\">1</span>\\n
522
- \ <span class=\\\"token keyword\\\">var</span> hasParams <span class=\\\"token
523
- operator\\\">=</span> href<span class=\\\"token punctuation\\\">.</span><span
524
- class=\\\"token function\\\">indexOf</span><span class=\\\"token punctuation\\\">(</span><span
525
- class=\\\"token string\\\">'?'</span><span class=\\\"token punctuation\\\">)</span>
526
- <span class=\\\"token operator\\\">&gt;</span> <span class=\\\"token operator\\\">-</span><span
527
- class=\\\"token number\\\">1</span>\\n <span class=\\\"token keyword\\\">var</span>
528
- indexPattern <span class=\\\"token operator\\\">=</span> <span class=\\\"token
529
- regex\\\">/start-index=(\\\\d+)/</span>\\n\\n <span class=\\\"token keyword\\\">var</span>
530
- prev <span class=\\\"token operator\\\">=</span> <span class=\\\"token function\\\">find</span><span
531
- class=\\\"token punctuation\\\">(</span>data<span class=\\\"token punctuation\\\">.</span>feed<span
532
- class=\\\"token punctuation\\\">.</span>link<span class=\\\"token punctuation\\\">,</span>
533
- <span class=\\\"token keyword\\\">function</span> <span class=\\\"token punctuation\\\">(</span>link<span
534
- class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>
535
- <span class=\\\"token keyword\\\">return</span> link<span class=\\\"token
536
- punctuation\\\">.</span>rel <span class=\\\"token operator\\\">===</span>
537
- <span class=\\\"token string\\\">'previous'</span> <span class=\\\"token punctuation\\\">}</span><span
538
- class=\\\"token punctuation\\\">)</span>\\n <span class=\\\"token keyword\\\">if</span>
539
- <span class=\\\"token punctuation\\\">(</span>prev<span class=\\\"token punctuation\\\">)</span>
540
- <span class=\\\"token punctuation\\\">{</span>\\n prev <span class=\\\"token
541
- operator\\\">=</span> <span class=\\\"token string\\\">'start-index='</span>
542
- <span class=\\\"token operator\\\">+</span> prev<span class=\\\"token punctuation\\\">.</span>href<span
543
- class=\\\"token punctuation\\\">.</span><span class=\\\"token function\\\">match</span><span
544
- class=\\\"token punctuation\\\">(</span>indexPattern<span class=\\\"token
545
- punctuation\\\">)</span><span class=\\\"token punctuation\\\">[</span><span
546
- class=\\\"token number\\\">1</span><span class=\\\"token punctuation\\\">]</span>\\n
547
- \ <span class=\\\"token keyword\\\">var</span> url <span class=\\\"token
548
- operator\\\">=</span> hasIndex <span class=\\\"token operator\\\">?</span>
549
- href<span class=\\\"token punctuation\\\">.</span><span class=\\\"token function\\\">replace</span><span
550
- class=\\\"token punctuation\\\">(</span>indexPattern<span class=\\\"token
551
- punctuation\\\">,</span> prev<span class=\\\"token punctuation\\\">)</span>
552
- <span class=\\\"token punctuation\\\">:</span> href <span class=\\\"token
553
- operator\\\">+</span> <span class=\\\"token punctuation\\\">(</span>hasParams
554
- <span class=\\\"token operator\\\">?</span> <span class=\\\"token string\\\">'?'</span>
555
- <span class=\\\"token punctuation\\\">:</span> <span class=\\\"token string\\\">''</span><span
556
- class=\\\"token punctuation\\\">)</span> <span class=\\\"token operator\\\">+</span>
557
- prev\\n paginatePrev<span class=\\\"token punctuation\\\">.</span><span
558
- class=\\\"token function\\\">setAttribute</span><span class=\\\"token punctuation\\\">(</span><span
559
- class=\\\"token string\\\">'href'</span><span class=\\\"token punctuation\\\">,</span>
560
- url<span class=\\\"token punctuation\\\">)</span>\\n <span class=\\\"token
561
- punctuation\\\">}</span>\\n\\n <span class=\\\"token keyword\\\">var</span>
562
- next <span class=\\\"token operator\\\">=</span> <span class=\\\"token function\\\">find</span><span
563
- class=\\\"token punctuation\\\">(</span>data<span class=\\\"token punctuation\\\">.</span>feed<span
564
- class=\\\"token punctuation\\\">.</span>link<span class=\\\"token punctuation\\\">,</span>
565
- <span class=\\\"token keyword\\\">function</span> <span class=\\\"token punctuation\\\">(</span>link<span
566
- class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>
567
- <span class=\\\"token keyword\\\">return</span> link<span class=\\\"token
568
- punctuation\\\">.</span>rel <span class=\\\"token operator\\\">===</span>
569
- <span class=\\\"token string\\\">'next'</span> <span class=\\\"token punctuation\\\">}</span><span
570
- class=\\\"token punctuation\\\">)</span>\\n <span class=\\\"token keyword\\\">if</span>
571
- <span class=\\\"token punctuation\\\">(</span>next<span class=\\\"token punctuation\\\">)</span>
572
- <span class=\\\"token punctuation\\\">{</span>\\n next <span class=\\\"token
573
- operator\\\">=</span> <span class=\\\"token string\\\">'start-index='</span>
574
- <span class=\\\"token operator\\\">+</span> next<span class=\\\"token punctuation\\\">.</span>href<span
575
- class=\\\"token punctuation\\\">.</span><span class=\\\"token function\\\">match</span><span
576
- class=\\\"token punctuation\\\">(</span>indexPattern<span class=\\\"token
577
- punctuation\\\">)</span><span class=\\\"token punctuation\\\">[</span><span
578
- class=\\\"token number\\\">1</span><span class=\\\"token punctuation\\\">]</span>\\n
579
- \ <span class=\\\"token keyword\\\">var</span> url <span class=\\\"token
580
- operator\\\">=</span> hasIndex <span class=\\\"token operator\\\">?</span>
581
- href<span class=\\\"token punctuation\\\">.</span><span class=\\\"token function\\\">replace</span><span
582
- class=\\\"token punctuation\\\">(</span>indexPattern<span class=\\\"token
583
- punctuation\\\">,</span> next<span class=\\\"token punctuation\\\">)</span>
584
- <span class=\\\"token punctuation\\\">:</span> href <span class=\\\"token
585
- operator\\\">+</span> <span class=\\\"token punctuation\\\">(</span>hasParams
586
- <span class=\\\"token operator\\\">?</span> <span class=\\\"token string\\\">'&amp;'</span>
587
- <span class=\\\"token punctuation\\\">:</span> <span class=\\\"token string\\\">'?'</span><span
588
- class=\\\"token punctuation\\\">)</span> <span class=\\\"token operator\\\">+</span>
589
- next\\n paginateNext<span class=\\\"token punctuation\\\">.</span><span
590
- class=\\\"token function\\\">setAttribute</span><span class=\\\"token punctuation\\\">(</span><span
591
- class=\\\"token string\\\">'href'</span><span class=\\\"token punctuation\\\">,</span>
592
- url<span class=\\\"token punctuation\\\">)</span>\\n <span class=\\\"token
593
- punctuation\\\">}</span>\\n <span class=\\\"token punctuation\\\">}</span>\\n<span
594
- class=\\\"token punctuation\\\">}</span>\\n\\n<span class=\\\"token keyword\\\">function</span>
595
- <span class=\\\"token function\\\">load</span> <span class=\\\"token punctuation\\\">(</span>url<span
596
- class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>\\n
597
- \ loader<span class=\\\"token punctuation\\\">.</span><span class=\\\"token
598
- function\\\">setAttribute</span><span class=\\\"token punctuation\\\">(</span><span
599
- class=\\\"token string\\\">'src'</span><span class=\\\"token punctuation\\\">,</span>
600
- url<span class=\\\"token punctuation\\\">)</span>\\n<span class=\\\"token
601
- punctuation\\\">}</span>\\n</code></pre>\\n<p>The callback then uses simple
602
- templates, which are just JS functions taking in the API response and outputting
603
- HTML to show the results on the page. Then, it figures out the pagination.
604
- Below is an example template. It extracts the post id to make links and does
605
- some preprocessing, removing stackedit metadata and styling and lowering each
606
- heading two levels. Then, it puts together the HTML with some additional util
607
- functions and subtemplates.</p>\\n<pre class=\\\" language-js\\\"><code class=\\\"prism
608
- \ language-js\\\"> feedItem<span class=\\\"token punctuation\\\">:</span>
609
- <span class=\\\"token keyword\\\">function</span> <span class=\\\"token punctuation\\\">(</span>item<span
610
- class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>\\n
611
- \ <span class=\\\"token keyword\\\">var</span> id <span class=\\\"token
612
- operator\\\">=</span> item<span class=\\\"token punctuation\\\">.</span>id<span
613
- class=\\\"token punctuation\\\">.</span>$t<span class=\\\"token punctuation\\\">.</span><span
614
- class=\\\"token function\\\">replace</span><span class=\\\"token punctuation\\\">(</span><span
615
- class=\\\"token regex\\\">/^.*\\\\.post-(\\\\d+)$/</span><span class=\\\"token
616
- punctuation\\\">,</span> <span class=\\\"token string\\\">'$1'</span><span
617
- class=\\\"token punctuation\\\">)</span>\\n <span class=\\\"token keyword\\\">var</span>
618
- content <span class=\\\"token operator\\\">=</span> item<span class=\\\"token
619
- punctuation\\\">.</span>content<span class=\\\"token punctuation\\\">.</span>$t\\n
620
- \ <span class=\\\"token punctuation\\\">.</span><span class=\\\"token
621
- function\\\">replace</span><span class=\\\"token punctuation\\\">(</span><span
622
- class=\\\"token regex\\\">/^[\\\\s\\\\S]*&lt;div class=\\\"stackedit__html\\\"&gt;([\\\\s\\\\S]*)&lt;\\\\/div&gt;[\\\\s\\\\S]*$/</span><span
623
- class=\\\"token punctuation\\\">,</span> <span class=\\\"token string\\\">'$1'</span><span
624
- class=\\\"token punctuation\\\">)</span>\\n <span class=\\\"token punctuation\\\">.</span><span
625
- class=\\\"token function\\\">replace</span><span class=\\\"token punctuation\\\">(</span><span
626
- class=\\\"token regex\\\">/&lt;(\\\\/?)h([1-6])/g</span><span class=\\\"token
627
- punctuation\\\">,</span> <span class=\\\"token keyword\\\">function</span>
628
- <span class=\\\"token punctuation\\\">(</span>match<span class=\\\"token punctuation\\\">,</span>
629
- slash<span class=\\\"token punctuation\\\">,</span> level<span class=\\\"token
630
- punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>\\n
631
- \ <span class=\\\"token keyword\\\">if</span> <span class=\\\"token
632
- punctuation\\\">(</span><span class=\\\"token operator\\\">+</span>level <span
633
- class=\\\"token operator\\\">&gt;</span> <span class=\\\"token number\\\">4</span><span
634
- class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>\\n
635
- \ <span class=\\\"token keyword\\\">return</span> <span class=\\\"token
636
- string\\\">'&lt;'</span> <span class=\\\"token operator\\\">+</span> slash
637
- <span class=\\\"token operator\\\">+</span> <span class=\\\"token string\\\">'b'</span>\\n
638
- \ <span class=\\\"token punctuation\\\">}</span> <span class=\\\"token
639
- keyword\\\">else</span> <span class=\\\"token punctuation\\\">{</span>\\n
640
- \ <span class=\\\"token keyword\\\">return</span> <span class=\\\"token
641
- string\\\">'&lt;'</span> <span class=\\\"token operator\\\">+</span> slash
642
- <span class=\\\"token operator\\\">+</span> <span class=\\\"token string\\\">'h'</span>
643
- <span class=\\\"token operator\\\">+</span> <span class=\\\"token punctuation\\\">(</span><span
644
- class=\\\"token operator\\\">+</span>level <span class=\\\"token operator\\\">+</span>
645
- <span class=\\\"token number\\\">2</span><span class=\\\"token punctuation\\\">)</span>\\n
646
- \ <span class=\\\"token punctuation\\\">}</span>\\n <span class=\\\"token
647
- punctuation\\\">}</span><span class=\\\"token punctuation\\\">)</span>\\n\\n
648
- \ <span class=\\\"token keyword\\\">return</span> <span class=\\\"token
649
- string\\\">'&lt;div class=\\\"mdl-card mdl-shadow--2dp mdl-cell mdl-cell--12-col\\\"&gt;'</span>
650
- <span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token
651
- string\\\">'&lt;div class=\\\"mdl-card__title\\\"&gt;'</span> <span class=\\\"token
652
- operator\\\">+</span>\\n <span class=\\\"token string\\\">'&lt;h2 class=\\\"mdl-card__title-text\\\"&gt;'</span>
653
- <span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token
654
- string\\\">'&lt;a href=\\\"?post='</span> <span class=\\\"token operator\\\">+</span>
655
- id <span class=\\\"token operator\\\">+</span> <span class=\\\"token string\\\">'\\\"&gt;'</span>
656
- <span class=\\\"token operator\\\">+</span> item<span class=\\\"token punctuation\\\">.</span>title<span
657
- class=\\\"token punctuation\\\">.</span>$t <span class=\\\"token operator\\\">+</span>
658
- <span class=\\\"token string\\\">'&lt;/a&gt;'</span> <span class=\\\"token
659
- operator\\\">+</span>\\n <span class=\\\"token string\\\">'&lt;/h2&gt;'</span>
660
- <span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token
661
- string\\\">'&lt;/div&gt;'</span> <span class=\\\"token operator\\\">+</span>\\n
662
- \ <span class=\\\"token string\\\">'&lt;div class=\\\"mdl-card__supporting-text
663
- mdl-card--border\\\"&gt;'</span> <span class=\\\"token operator\\\">+</span>\\n
664
- \ <span class=\\\"token string\\\">'&lt;p&gt;'</span> <span class=\\\"token
665
- operator\\\">+</span>\\n <span class=\\\"token string\\\">'&lt;span&gt;&lt;i
666
- class=\\\"material-icons\\\"&gt;edit&lt;/i&gt; '</span> <span class=\\\"token
667
- operator\\\">+</span>\\n templates<span class=\\\"token punctuation\\\">.</span><span
668
- class=\\\"token function\\\">author</span><span class=\\\"token punctuation\\\">(</span>item<span
669
- class=\\\"token punctuation\\\">.</span>author<span class=\\\"token punctuation\\\">[</span><span
670
- class=\\\"token number\\\">0</span><span class=\\\"token punctuation\\\">]</span><span
671
- class=\\\"token punctuation\\\">)</span> <span class=\\\"token operator\\\">+</span>\\n
672
- \ <span class=\\\"token string\\\">'&lt;/span&gt;'</span> <span class=\\\"token
673
- operator\\\">+</span>\\n <span class=\\\"token string\\\">'&lt;span&gt;&lt;i
674
- class=\\\"material-icons\\\"&gt;access_time&lt;/i&gt; '</span> <span class=\\\"token
675
- operator\\\">+</span>\\n <span class=\\\"token function\\\">formatDate</span><span
676
- class=\\\"token punctuation\\\">(</span>item<span class=\\\"token punctuation\\\">.</span>updated<span
677
- class=\\\"token punctuation\\\">.</span>$t<span class=\\\"token punctuation\\\">)</span>
678
- <span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token
679
- string\\\">'&lt;/span&gt;'</span> <span class=\\\"token operator\\\">+</span>\\n
680
- \ <span class=\\\"token string\\\">'&lt;span&gt;&lt;i class=\\\"material-icons\\\"&gt;link&lt;/i&gt;
681
- &lt;a href=\\\"'</span> <span class=\\\"token operator\\\">+</span>\\n <span
682
- class=\\\"token function\\\">canonical</span><span class=\\\"token punctuation\\\">(</span>item<span
683
- class=\\\"token punctuation\\\">.</span>link<span class=\\\"token punctuation\\\">)</span>
684
- <span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token
685
- string\\\">'\\\"&gt;Original post&lt;/a&gt;&lt;/span&gt;'</span> <span class=\\\"token
686
- operator\\\">+</span>\\n <span class=\\\"token string\\\">'&lt;/p&gt;'</span>
687
- <span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token
688
- string\\\">'&lt;p&gt;'</span> <span class=\\\"token operator\\\">+</span>\\n
689
- \ <span class=\\\"token string\\\">'&lt;span&gt;&lt;i class=\\\"material-icons\\\"&gt;bookmark&lt;/i&gt;
690
- '</span> <span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token
691
- function\\\">map</span><span class=\\\"token punctuation\\\">(</span>item<span
692
- class=\\\"token punctuation\\\">.</span>category<span class=\\\"token punctuation\\\">,</span>
693
- templates<span class=\\\"token punctuation\\\">.</span>tag<span class=\\\"token
694
- punctuation\\\">)</span><span class=\\\"token punctuation\\\">.</span><span
695
- class=\\\"token function\\\">join</span><span class=\\\"token punctuation\\\">(</span><span
696
- class=\\\"token string\\\">' '</span><span class=\\\"token punctuation\\\">)</span>
697
- <span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token
698
- string\\\">'&lt;/span&gt;'</span> <span class=\\\"token operator\\\">+</span>\\n
699
- \ <span class=\\\"token string\\\">'&lt;/p&gt;'</span> <span class=\\\"token
700
- operator\\\">+</span>\\n <span class=\\\"token string\\\">'&lt;/div&gt;'</span>
701
- <span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token
702
- string\\\">'&lt;div class=\\\"mdl-card__supporting-text\\\"&gt;'</span> <span
703
- class=\\\"token operator\\\">+</span>\\n content <span class=\\\"token
704
- operator\\\">+</span>\\n <span class=\\\"token string\\\">'&lt;/div&gt;'</span>
705
- <span class=\\\"token operator\\\">+</span>\\n <span class=\\\"token string\\\">'&lt;/div&gt;'</span>\\n
706
- \ <span class=\\\"token punctuation\\\">}</span><span class=\\\"token punctuation\\\">,</span>\\n</code></pre>\\n<p>The
707
- full source is available at <a href=\\\"https://github.com/citation-js/site/blob/master/static/js/blog.js\\\">here</a>,
708
- and the page can be viewed <a href=\\\"https://citation.js.org/blog/\\\">here</a>.</p>\\n<p><img
709
- src=\\\"https://lh3.googleusercontent.com/Qd8EXpblQui1CSErr_BU1Os9Ykk-ximWT_hcTxGhtJBwY6JoM7jSxt7FlAwOSkAs57G4nZ64ccAtMg=s2000\\\"
710
- alt=\\\"Blog screenshot\\\"><br>\\n<em>Blog screenshot</em></p>\\n</div>\\n</body>\\n\\n</html>\",\"tags\":[\"Citation.js\",\"programming\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"y55kq35\",\"blog\":{\"id\":\"y55kq35\",\"title\":\"Syntaxus
711
- baccata\",\"description\":\"Thoughts about bibliographic metadata, programming,
712
- statistics, taxonomy, and biology.\",\"language\":\"en\",\"favicon\":\"https://blogger.googleusercontent.com/img/a/AVvXsEjHdUshBRlHAgurlZYYubJ9yfTRkteSS8hwgor7bpsdHNByrUXglmpVcCS2McVehJLgWZPyr61hB2Nq8iXql2-0qLFfZZHWdMn8wuKGz5UO1vZXWQkRKn_4EelUV6NneQW6fN1wlggv7skzUBri-T7bJZnlzXkKj6FjF8p0wLDR8DXwO7oN8QSwcN9-=s64\",\"feed_url\":\"https://larsgw.blogspot.com/feeds/posts/default\",\"home_page_url\":\"https://larsgw.blogspot.com/\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T16:56:38+00:00\",\"indexed_at\":\"2023-01-08\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"Blogger
713
- 7.00\",\"category\":\"Engineering and Technology\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-05-08T11:05:00+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.53731/m9fs5-nap05\",\"uuid\":\"fb7abef9-d035-47a0-bc31-b5b1240cac19\",\"url\":\"https://blog.front-matter.io/posts/starting-to-register-dois-for-all-blog-posts-included-in-the-rogue-scholar/\",\"title\":\"Starting
714
- to register DOIs for all blog posts included in the Rogue Scholar\",\"summary\":\"The
715
- Rogue Scholar archive of scholarly blogs has grown to 34 blogs with about
716
- 420 blog posts. In order to implement DOI registration for these blog posts,
717
- I needed two things:Content and metadata, ideally without requiring blogs
718
- to implement anything special.A way to track the DOIs that have been registeredInitial
719
- work on DOI registration for blog posts focussed on exposing the relevant
720
- metadata on the blog landing page, using schema.org and/or HTML meta tags.
721
- While this approach worked well...\",\"date_published\":\"2023-06-05T13:18:24Z\",\"date_modified\":\"2023-06-05T13:18:24Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":\"https://orcid.org/0000-0003-1419-2405\",\"name\":\"Martin
722
- Fenner\"}],\"image\":\"https://blog.front-matter.io/content/images/2023/06/Bildschirmfoto-2023-06-05-um-14.58.49-1.png\",\"content_html\":\"
723
- <p><img src=\\\"https://blog.front-matter.io/content/images/2023/06/Bildschirmfoto-2023-06-05-um-14.58.49-1.png\\\"></p><p>The
724
- <a href=\\\"https://rogue-scholar.org/\\\">Rogue Scholar</a> archive of scholarly
725
- blogs has grown to 34 blogs with about 420 blog posts. In order to implement
726
- DOI registration for these blog posts, I needed two things:</p><ul><li>Content
727
- and metadata, ideally without requiring blogs to implement anything special.</li><li>A
728
- way to track the DOIs that have been registered</li></ul><p>Initial work on
729
- DOI registration for blog posts focussed on exposing the relevant metadata
730
- on the blog landing page, using schema.org and/or HTML meta tags. While this
731
- approach worked well for this and similar blogs, it was too complicated and
732
- didn't scale well for the large and diverse number of blogs the Rogue Scholar
733
- aims to cover. </p><p>Therefore I implemented a different workflow taking
734
- advantage of the fact that all blogs come with RSS feeds that include content
735
- and metadata. More work was needed because there are different formats for
736
- these feeds (multiple flavors of RSS, as well as <a href=\\\"https://en.wikipedia.org/wiki/Atom_(web_standard)\\\">Atom</a>,
737
- and the newer <a href=\\\"https://www.jsonfeed.org/\\\">JSON Feed</a>). Luckily,
738
-  libraries in multiple programming languages exist to simplify the parsing
739
- of the various RSS Feed formats (I use the Javascript library <a href=\\\"https://www.npmjs.com/package/@extractus/feed-extractor\\\">feed-extractor</a>).</p><p>The
740
- main challenge with metadata for blog posts – and with DOI metadata more general
741
- – is author names. They might not be natural names (for example <strong>mfenner</strong>
742
- instead of <strong>Martin Fenner</strong>), might be names for organizations
743
- and not people, the blogging platform might not support multiple authors,
744
- and some work is required to include the ORCID author identifier (or ROR institutional.
745
- identifier). The Atom format supports an <strong>author URL</strong>, which
746
- can hold the ORCID ID (or ROR ID), and Wordpress can be enhanced with the
747
- popular <a href=\\\"https://wordpress.org/plugins/co-authors-plus/\\\">Co-Authors
748
- Plus</a> plugin to support multiple authors. </p><p>The other challenge with
749
- DOI registration is keeping track of the content that has already been registered,
750
- and for this I launched a database, with one record for each post. I need
751
- the database also to enable full-text search across all blog posts, something
752
- I will implement in the coming weeks. </p><p>Will all the required pieces
753
- coming together, I was finally able to start DOI registrations yesterday.
754
- You will easily detect blog posts with a DOI on the Rogue Scholar website
755
- (there is a DOI icon next to the title, and the underlying link to the blog
756
- post is a DOI):</p><figure class=\\\"kg-card kg-image-card\\\"><img src=\\\"https://blog.front-matter.io/content/images/2023/06/Bildschirmfoto-2023-06-05-um-14.58.49.png\\\"
757
- class=\\\"kg-image\\\" alt loading=\\\"lazy\\\" width=\\\"2000\\\" height=\\\"1046\\\"
758
- srcset=\\\"https://blog.front-matter.io/content/images/size/w600/2023/06/Bildschirmfoto-2023-06-05-um-14.58.49.png
759
- 600w, https://blog.front-matter.io/content/images/size/w1000/2023/06/Bildschirmfoto-2023-06-05-um-14.58.49.png
760
- 1000w, https://blog.front-matter.io/content/images/size/w1600/2023/06/Bildschirmfoto-2023-06-05-um-14.58.49.png
761
- 1600w, https://blog.front-matter.io/content/images/size/w2400/2023/06/Bildschirmfoto-2023-06-05-um-14.58.49.png
762
- 2400w\\\" sizes=\\\"(min-width: 720px) 720px\\\"></figure><p>The process of
763
- DOI registration for all included blog posts should be concluded by the end
764
- of the month. There is more work needed to resolve issues with some author
765
- names, and DOI registration can be further automated (I am currently using
766
- GitHub Actions and a cronjob). </p><p>What also needs more work is getting
767
- the DOIs displayed on the blogs (the DOIs resolve to the blog post and not
768
- the Rogue Scholar archive). This is probably straightforward when using a
769
- static site generator, but requires more work when a database is involved
770
- (e.g. Wordpress). For Ghost blogs like this one, I found the <strong>canonical_url</strong>
771
- field to be a good place to store the DOI.</p> \",\"tags\":[\"Feature\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"f0m0e38\",\"blog\":{\"id\":\"f0m0e38\",\"title\":\"Front
772
- Matter\",\"description\":\"The Front Matter Blog covers the intersection of
773
- science and technology since 2007.\",\"language\":\"en\",\"favicon\":\"https://blog.front-matter.io/favicon.png\",\"feed_url\":\"https://blog.front-matter.io/atom/\",\"home_page_url\":\"https://blog.front-matter.io\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T07:20:33+00:00\",\"indexed_at\":\"2023-01-02\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"Ghost
774
- 5.52\",\"category\":\"Engineering and Technology\",\"prefix\":\"10.53731\",\"modified_at\":\"2023-06-05T13:18:24+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.53731/z9v2s-bh329\",\"uuid\":\"2a6fb006-ecb2-45d0-9d73-ca8a0e7f559e\",\"url\":\"https://blog.front-matter.io/posts/rogue-scholar-open-for-business/\",\"title\":\"The
775
- Rogue Scholar is now open for business\",\"summary\":\"The Rogue Scholar science
776
- blog archive launched with limited functionality on April 3rd. Interested
777
- science blogs can go to the sign-up page, provide some basic information via
778
- the sign-up form, and then will be added to the Rogue Scholar archive within
779
- two business days. To be included in the service, your blog needs to:be about
780
- science or scholarship and written in English or German (more languages will
781
- follow later, reach out to me if you can help),make the full-text content
782
- available via...\",\"date_published\":\"2023-04-04T08:43:36Z\",\"date_modified\":\"2023-04-04T09:31:14Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":\"https://orcid.org/0000-0003-1419-2405\",\"name\":\"Martin
783
- Fenner\"}],\"image\":\"https://images.unsplash.com/photo-1575663620136-5ebbfcc2c597?crop&#x3D;entropy&cs&#x3D;tinysrgb&fit&#x3D;max&fm&#x3D;jpg&ixid&#x3D;MnwxMTc3M3wwfDF8c2VhcmNofDR8fG9wZW4lMjBmb3IlMjBidXNpbmVzc3xlbnwwfHx8fDE2ODA1OTI3NTU&ixlib&#x3D;rb-4.0.3&q&#x3D;80&w&#x3D;2000\",\"content_html\":\"
784
- <p><img src=\\\"https://images.unsplash.com/photo-1575663620136-5ebbfcc2c597?crop&#x3D;entropy&cs&#x3D;tinysrgb&fit&#x3D;max&fm&#x3D;jpg&ixid&#x3D;MnwxMTc3M3wwfDF8c2VhcmNofDR8fG9wZW4lMjBmb3IlMjBidXNpbmVzc3xlbnwwfHx8fDE2ODA1OTI3NTU&ixlib&#x3D;rb-4.0.3&q&#x3D;80&w&#x3D;2000\\\"></p><p>The
785
- <a href=\\\"https://rogue-scholar.org/\\\">Rogue Scholar</a> science blog
786
- archive launched with limited functionality on April 3rd. Interested science
787
- blogs can go to the sign-up page, provide some basic information via the <a
788
- href=\\\"https://jvinjjenjik.typeform.com/to/uxgAsHPl\\\">sign-up form</a>,
789
- and then will be added to the Rogue Scholar archive within two business days.
790
- </p><p>To be included in the service, your blog needs to:</p><ul><li>be about
791
- science or scholarship and written in English or German (more languages will
792
- follow later, reach out to me if you can help),</li><li>make the full-text
793
- content available via RSS feed and distributed under the terms of the Creative
794
- Commons Attribution license (<a href=\\\"https://creativecommons.org/licenses/by/4.0/legalcode\\\">CC-BY</a>).</li></ul><p>Blogs
795
- that have signed up for the service (more than twenty so far) are listed in
796
- the <a href=\\\"https://rogue-scholar.org/blogs\\\">Rogue Scholar catalog
797
- of science blogs</a> that <a href=\\\"https://doi.org/10.53731/n7vvs-h6995\\\">launched
798
- last week</a>. And since yesterday summaries of the latest fifteen blog posts
799
- of each blog are also available.</p><figure class=\\\"kg-card kg-image-card
800
- kg-card-hascaption\\\"><img src=\\\"https://blog.front-matter.io/content/images/2023/04/Bildschirmfoto-2023-04-04-um-10.12.58.png\\\"
801
- class=\\\"kg-image\\\" alt loading=\\\"lazy\\\" width=\\\"1882\\\" height=\\\"1428\\\"
802
- srcset=\\\"https://blog.front-matter.io/content/images/size/w600/2023/04/Bildschirmfoto-2023-04-04-um-10.12.58.png
803
- 600w, https://blog.front-matter.io/content/images/size/w1000/2023/04/Bildschirmfoto-2023-04-04-um-10.12.58.png
804
- 1000w, https://blog.front-matter.io/content/images/size/w1600/2023/04/Bildschirmfoto-2023-04-04-um-10.12.58.png
805
- 1600w, https://blog.front-matter.io/content/images/2023/04/Bildschirmfoto-2023-04-04-um-10.12.58.png
806
- 1882w\\\" sizes=\\\"(min-width: 720px) 720px\\\"><figcaption><a href=\\\"https://rogue-scholar.org/blogs/pm0p222\\\">Blog
807
- posts displayed at the Rogue Scholar</a></figcaption></figure><p>These summaries
808
- (precisely the information you get in the RSS feed) serve two purposes:</p><ul><li>for
809
- readers: learn more about that particular science blog. Reading the full-text
810
- post or other blog posts is only one click away</li><li>for blog authors and
811
- Rogue Scholar staff: tweak the blog and/or Rogue Scholar if there are issues
812
- with archiving. </li></ul><p>The screenshot highlights several considerations
813
- when using the RSS Feed to archive a science blog in the Rogue Scholar:</p><ul><li>optional
814
- but desired metadata, e.g logo, description, and language for blogs or description,
815
- tags, and feature image for blog posts</li><li>handling authors, including
816
- full names instead of usernames, multiple authors, and author identifiers
817
- (ORCID)</li><li>handling DOIs, including exposing them in the RSS feed, and
818
- making sure no DOI exists for the post yet</li></ul><p>The Rogue Scholar is
819
- now open for business, and I hope the limited functionality (or <a href=\\\"https://www.zentao.pm/blog/mvp-minimum-viable-product-965.html\\\">minimum
820
- viable product</a>) launched this week makes it an attractive service for
821
- blog readers and authors to try out. The next big milestone is the launch
822
- of the full-text index for searching and archiving, and that is planned to
823
- happen within the next three months. Followed by DOI registration for blog
824
- posts.</p> \",\"tags\":[\"News\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"f0m0e38\",\"blog\":{\"id\":\"f0m0e38\",\"title\":\"Front
825
- Matter\",\"description\":\"The Front Matter Blog covers the intersection of
826
- science and technology since 2007.\",\"language\":\"en\",\"favicon\":\"https://blog.front-matter.io/favicon.png\",\"feed_url\":\"https://blog.front-matter.io/atom/\",\"home_page_url\":\"https://blog.front-matter.io\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T07:20:33+00:00\",\"indexed_at\":\"2023-01-02\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"Ghost
827
- 5.52\",\"category\":\"Engineering and Technology\",\"prefix\":\"10.53731\",\"modified_at\":\"2023-06-05T13:18:24+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.59350/d3dc0-7an69\",\"uuid\":\"545c177f-cea5-4b79-b554-3ccae9c789d7\",\"url\":\"https://iphylo.blogspot.com/2021/10/reflections-on-macroscope-tool-for-21st.html\",\"title\":\"Reflections
828
- on \\\"The Macroscope\\\" - a tool for the 21st Century?\",\"summary\":\"This
829
- is a guest post by Tony Rees. It would be difficult to encounter a scientist,
830
- or anyone interested in science, who is not familiar with the microscope,
831
- a tool for making objects visible that are otherwise too small to be properly
832
- seen by the unaided eye, or to reveal otherwise invisible fine detail in larger
833
- objects. A select few with a particular interest in microscopy may also have
834
- encountered the Wild-Leica \\\"Macroscope\\\", a specialised type of benchtop
835
- microscope optimised for...\",\"date_published\":\"2021-10-07T12:38:00Z\",\"date_modified\":\"2021-10-08T10:26:22Z\",\"date_indexed\":\"1909-06-16T10:02:25+00:00\",\"authors\":[{\"url\":null,\"name\":\"Roderic
836
- Page\"}],\"image\":null,\"content_html\":\"<p><img src=\\\"https://lh3.googleusercontent.com/-A99btr6ERMs/Vl1Wvjp2OtI/AAAAAAAAEFI/7bKdRjNG5w0/ytNkVT2U.jpg?imgmax=800\\\"
837
- alt=\\\"YtNkVT2U\\\" title=\\\"ytNkVT2U.jpg\\\" border=\\\"0\\\" width=\\\"128\\\"
838
- height=\\\"128\\\" style=\\\"float:right;\\\" /> This is a guest post by <a
839
- href=\\\"https://about.me/TonyRees\\\">Tony Rees</a>.</p>\\n\\n<p>It would
840
- be difficult to encounter a scientist, or anyone interested in science, who
841
- is not familiar with the microscope, a tool for making objects visible that
842
- are otherwise too small to be properly seen by the unaided eye, or to reveal
843
- otherwise invisible fine detail in larger objects. A select few with a particular
844
- interest in microscopy may also have encountered the Wild-Leica \\\"Macroscope\\\",
845
- a specialised type of benchtop microscope optimised for low-power macro-photography.
846
- However in this overview I discuss the \\\"Macroscope\\\" in a different sense,
847
- which is that of the antithesis to the microscope: namely a method for visualizing
848
- subjects too large to be encompassed by a single field of vision, such as
849
- the Earth or some subset of its phenomena (the biosphere, for example), or
850
- conceptually, the universe.</p>\\n\\n<p><div class=\\\"separator\\\" style=\\\"clear:
851
- both;\\\"><a href=\\\"https://1.bp.blogspot.com/-xXxH9aJn1tY/YV7vnKGQWPI/AAAAAAAAgyQ/7CSJJ663Ry4IXtav54nLcLiI0kda5_L7ACLcBGAsYHQ/s500/2020045672.jpg\\\"
852
- style=\\\"display: block; padding: 1em 0; text-align: center; clear: right;
853
- float: right;\\\"><img alt=\\\"\\\" border=\\\"0\\\" height=\\\"320\\\" data-original-height=\\\"500\\\"
854
- data-original-width=\\\"303\\\" src=\\\"https://1.bp.blogspot.com/-xXxH9aJn1tY/YV7vnKGQWPI/AAAAAAAAgyQ/7CSJJ663Ry4IXtav54nLcLiI0kda5_L7ACLcBGAsYHQ/s320/2020045672.jpg\\\"/></a></div>My
855
- introduction to the term was via addresses given by Jesse Ausubel in the formative
856
- years of the 2001-2010 <a href=\\\"http://www.coml.org\\\">Census of Marine
857
- Life</a>, for which he was a key proponent. In Ausubel's view, the Census
858
- would perform the function of a macroscope, permitting a view of everything
859
- that lives in the global ocean (or at least, that subset which could realistically
860
- be sampled in the time frame available) as opposed to more limited subsets
861
- available via previous data collection efforts. My view (which could, of course,
862
- be wrong) was that his thinking had been informed by a work entitled \\\"Le
863
- macroscope, vers une vision globale\\\" published in 1975 by the French thinker
864
- Joël de Rosnay, who had expressed such a concept as being globally applicable
865
- in many fields, including the physical and natural worlds but also extending
866
- to human society, the growth of cities, and more. Yet again, some ecologists
867
- may also have encountered the term, sometimes in the guise of \\\"Odum's macroscope\\\",
868
- as an approach for obtaining \\\"big picture\\\" analyses of macroecological
869
- processes suitable for mathematical modelling, typically by elimination of
870
- fine detail so that only the larger patterns remain, as initially advocated
871
- by Howard T. Odum in his 1971 book \\\"Environment, Power, and Society\\\".</p>\\n\\n<p>From
872
- the standpoint of the 21st century, it seems that we are closer to achieving
873
- a \\\"macroscope\\\" (or possibly, multiple such tools) than ever before,
874
- based on the availability of existing and continuing new data streams, improved
875
- technology for data assembly and storage, and advanced ways to query and combine
876
- these large streams of data to produce new visualizations, data products,
877
- and analytical findings. I devote the remainder of this article to examples
878
- where either particular workers have employed \\\"macroscope\\\" terminology
879
- to describe their activities, or where potentially equivalent actions are
880
- taking place without the explicit \\\"macroscope\\\" association, but are
881
- equally worthy of consideration. To save space here, references cited here
882
- (most or all) can be found via a Wikipedia article entitled \\\"<a href=\\\"https://en.wikipedia.org/wiki/Macroscope_(science_concept)\\\">Macroscope
883
- (science concept)</a>\\\" that I authored on the subject around a year ago,
884
- and have continued to add to on occasion as new thoughts or information come
885
- to hand (see <a href=\\\"https://en.wikipedia.org/w/index.php?title=Macroscope_(science_concept)&offset=&limit=500&action=history\\\">edit
886
- history for the article</a>).</p>\\n\\n<p>First, one can ask, what constitutes
887
- a macroscope, in the present context? In the Wikipedia article I point to
888
- a book \\\"Big Data - Related Technologies, Challenges and Future Prospects\\\"
889
- by Chen <em>et al.</em> (2014) (<a href=\\\"https://doi.org/10.1007/978-3-319-06245-7\\\">doi:10.1007/978-3-319-06245-7</a>),
890
- in which the \\\"value chain of big data\\\" is characterised as divisible
891
- into four phases, namely data generation, data acquisition (aka data assembly),
892
- data storage, and data analysis. To my mind, data generation (which others
893
- may term acquisition, differently from the usage by Chen <em>et al.</em>)
894
- is obviously the first step, but does not in itself constitute the macroscope,
895
- except in rare cases - such as Landsat imagery, perhaps - where on its own,
896
- a single co-ordinated data stream is sufficient to meet the need for a particular
897
- type of \\\"global view\\\". A variant of this might be a coordinated data
898
- collection program - such as that of the ten year Census of Marine Life -
899
- which might produce the data required for the desired global view; but again,
900
- in reality, such data are collected in a series of discrete chunks, in many
901
- and often disparate data formats, and must be \\\"wrangled\\\" into a more
902
- coherent whole before any meaningful \\\"macroscope\\\" functionality becomes
903
- available.</p>\\n\\n<p>Here we come to what, in my view, constitutes the heart
904
- of the \\\"macroscope\\\": an intelligently organized (i.e. indexable and
905
- searchable), coherent data store or repository (where \\\"data\\\" may include
906
- imagery and other non numeric data forms, but much else besides). Taking the
907
- Census of Marine Life example, the data repository for that project's data
908
- (plus other available sources as inputs) is the <a href=\\\"https://obis.org\\\">Ocean
909
- Biodiversity Information System</a> or OBIS (previously the Ocean Biogeographic
910
- Information System), which according to this view forms the \\\"macroscope\\\"
911
- for which the Census data is a feed. (For non habitat-specific biodiversity
912
- data, <a href=\\\"https://www.gbif.org\\\">GBIF</a> is an equivalent, and
913
- more extensive, operation). Other planetary scale \\\"macroscopes\\\", by
914
- this definition (which may or may not have an explicit geographic, i.e. spatial,
915
- component) would include inventories of biological taxa such as the <a href=\\\"https://www.catalogueoflife.org\\\">Catalogue
916
- of Life</a> and so on, all the way back to the pioneering compendia published
917
- by Linnaeus in the eighteenth century; while for cartography and topographic
918
- imagery, the current \\\"blockbuster\\\" of <a href=\\\"http://earth.google.com\\\">Google
919
- Earth</a> and its predecessors also come well into public consciousness.</p>\\n\\n<p>In
920
- the view of some workers and/or operations, both of these phases are precursors
921
- to the real \\\"work\\\" of the macroscope which is to reveal previously unseen
922
- portions of the \\\"big picture\\\" by means either of the availability of
923
- large, synoptic datasets, or fusion between different data streams to produce
924
- novel insights. Companies such as IBM and Microsoft have used phraseology
925
- such as:</p>\\n\\n<blockquote>By 2022 we will use machine-learning algorithms
926
- and software to help us organize information about the physical world, helping
927
- bring the vast and complex data gathered by billions of devices within the
928
- range of our vision and understanding. We call this a \\\"macroscope\\\" –
929
- but unlike the microscope to see the very small, or the telescope that can
930
- see far away, it is a system of software and algorithms to bring all of Earth's
931
- complex data together to analyze it by space and time for meaning.\\\" (IBM)</blockquote>\\n\\n<blockquote>As
932
- the Earth becomes increasingly instrumented with low-cost, high-bandwidth
933
- sensors, we will gain a better understanding of our environment via a virtual,
934
- distributed whole-Earth \\\"macroscope\\\"... Massive-scale data analytics
935
- will enable real-time tracking of disease and targeted responses to potential
936
- pandemics. Our virtual \\\"macroscope\\\" can now be used on ourselves, as
937
- well as on our planet.\\\" (Microsoft) (references available via the Wikipedia
938
- article cited above).</blockquote>\\n\\n<p>Whether or not the analytical capabilities
939
- described here are viewed as being an integral part of the \\\"macroscope\\\"
940
- concept, or are maybe an add-on, is ultimately a question of semantics and
941
- perhaps, personal opinion. Continuing the Census of Marine Life/OBIS example,
942
- OBIS offers some (arguably rather basic) visualization and summary tools,
943
- but also makes its data available for download to users wishing to analyse
944
- it further according to their own particular interests; using OBIS data in
945
- this manner, Mark Costello et al. in 2017 were able to demarcate a finite
946
- number of data-supported marine biogeographic realms for the first time (Costello
947
- et al. 2017: Nature Communications. 8: 1057. <a href=\\\"https://doi.org/10.1038/s41467-017-01121-2\\\">doi:10.1038/s41467-017-01121-2</a>),
948
- a project which I was able to assist in a small way in an advisory capacity.
949
- In a case such as this, perhaps the final function of the macroscope, namely
950
- data visualization and analysis, was outsourced to the authors' own research
951
- institution. Similarly at an earlier phase, \\\"data aggregation\\\" can also
952
- be virtual rather than actual, i.e. avoiding using a single physical system
953
- to hold all the data, enabled by open web mapping standards WMS (web map service)
954
- and WFS (web feature service) to access a set of distributed data stores,
955
- e.g. as implemented on the portal for the <a href=\\\"https://portal.aodn.org.au/\\\">Australian
956
- Ocean Data Network</a>.</p>\\n\\n<p>So, as we pass through the third decade
957
- of the twenty first century, what developments await us in the \\\"macroscope\\\"
958
- area\\\"? In the biodiversity space, one can reasonably presume that the existing
959
- \\\"macroscopic\\\" data assembly projects such as OBIS and GBIF will continue,
960
- and hopefully slowly fill current gaps in their coverage - although in the
961
- marine area, strategic new data collection exercises may be required (Census
962
- 2020, or 2025, anyone?), while (again hopefully), the Catalogue of Life will
963
- continue its progress towards a \\\"complete\\\" species inventory for the
964
- biosphere. The Landsat project, with imagery dating back to 1972, continues
965
- with the launch of its latest satellite Landsat 9 just this year (21 September
966
- 2021) with a planned mission duration for the next 5 years, so the \\\"macroscope\\\"
967
- functionality of that project seems set to continue for the medium term at
968
- least. Meanwhile the ongoing development of sensor networks, both on land
969
- and in the ocean, offers an exciting new method of \\\"instrumenting the earth\\\"
970
- to obtain much more real time data than has ever been available in the past,
971
- offering scope for many more, use case-specific \\\"macroscopes\\\" to be
972
- constructed that can fuse (e.g.) satellite imagery with much more that is
973
- happening at a local level.</p>\\n\\n<p>So, the \\\"macroscope\\\" concept
974
- appears to be alive and well, even though the nomenclature can change from
975
- time to time (IBM's \\\"Macroscope\\\", foreshadowed in 2017, became the \\\"IBM
976
- Pairs Geoscope\\\" on implementation, and is now simply the \\\"Geospatial
977
- Analytics component within the IBM Environmental Intelligence Suite\\\" according
978
- to available IBM publicity materials). In reality this illustrates a new dichotomy:
979
- even if \\\"everyone\\\" in principle has access to huge quantities of publicly
980
- available data, maybe only a few well funded entities now have the computational
981
- ability to make sense of it, and can charge clients a good fee for their services...</p>\\n\\n<p>I
982
- present this account partly to give a brief picture of \\\"macroscope\\\"
983
- concepts today and in the past, for those who may be interested, and partly
984
- to present a few personal views which would be out of scope in a \\\"neutral
985
- point of view\\\" article such as is required on Wikipedia; also to see if
986
- readers of this blog would like to contribute further to discussion of any
987
- of the concepts traversed herein.</p>\",\"tags\":[\"guest post\",\"macroscope\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"tyfqw20\",\"blog\":{\"id\":\"tyfqw20\",\"title\":\"iPhylo\",\"description\":\"Rants,
988
- raves (and occasionally considered opinions) on phyloinformatics, taxonomy,
989
- and biodiversity informatics. For more ranty and less considered opinions,
990
- see my <a href=\\\"https://twitter.com/rdmpage\\\">Twitter feed</a>.<br>ISSN
991
- 2051-8188. Written content on this site is licensed under a <a href=\\\"https://creativecommons.org/licenses/by/4.0/\\\">Creative
992
- Commons Attribution 4.0 International license</a>.\",\"language\":\"en\",\"favicon\":null,\"feed_url\":\"https://iphylo.blogspot.com/feeds/posts/default\",\"home_page_url\":\"https://iphylo.blogspot.com/\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T08:03:14+00:00\",\"indexed_at\":\"2023-02-06\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"Blogger
993
- 7.00\",\"category\":\"Natural Sciences\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-05-31T17:26:00+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.59350/k4bck-1me51\",\"uuid\":\"57878bca-6994-4e35-8350-4140326a7b28\",\"url\":\"https://larsgw.blogspot.com/2019/07/citationjs-ris-rework-pt-1.html\",\"title\":\"Citation.js:
994
- RIS Rework Pt. 1\",\"summary\":\"Citation.js: RIS Rework Pt. 1 So a while
995
- ago I was looking around for the RIS specification again. I had not found
996
- it earlier, only a reference implementation from Zotero, a surprisingly complete
997
- list of tags and types on Wikipedia and some examples from various websites
998
- and programs exporting RIS files. They did not seem to go together well, however.
999
- There were some slight differences in tags here and there, and a bunch of
1000
- useful tags listed by Wikipedia were labelled “degenerate” in...\",\"date_published\":\"2019-07-30T21:16:00Z\",\"date_modified\":\"2023-03-30T20:47:44Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":null,\"name\":\"Lars
1001
- Willighagen\"}],\"image\":null,\"content_html\":\"<!DOCTYPE html>\\n<html>\\n\\n<head>\\n
1002
- \ <meta charset=\\\"utf-8\\\">\\n <meta name=\\\"viewport\\\" content=\\\"width=device-width,
1003
- initial-scale=1.0\\\">\\n <title>Citation.js: RIS Rework Pt. 1</title>\\n
1004
- \ <link rel=\\\"stylesheet\\\" href=\\\"https://stackedit.io/style.css\\\"
1005
- />\\n</head>\\n\\n<body class=\\\"stackedit\\\">\\n <div class=\\\"stackedit__html\\\"><p>So
1006
- a while ago I was looking around for the RIS specification again. I had not
1007
- found it earlier, only a reference implementation from Zotero, a surprisingly
1008
- complete list of tags and types on Wikipedia and some examples from various
1009
- websites and programs exporting RIS files. They did not seem to go together
1010
- well, however. There were some slight differences in tags here and there,
1011
- and a bunch of useful tags listed by Wikipedia were labelled “degenerate”
1012
- in the Zotero codebase, and only used for imports — implying some sort of
1013
- problem.</p>\\n<p>What could be going on? Well, I checked out the references
1014
- on the Wikipedia page again, to see if there really was no official specification
1015
- or some other more reliable source where it got its information from. And,
1016
- suddenly, there <em>was</em> an actual source this time. I do not know how
1017
- I missed it earlier, but there was a page (<a href=\\\"https://web.archive.org/web/20120526103719/http://refman.com/support/risformat_intro.asp\\\">archived</a>)
1018
- that linked to a zip file containing a PDF file with general specifications
1019
- and an Excel file with sheets with property lists for all different types.</p>\\n<p>That
1020
- sounded useful, so I spent <em>waaayy</em> to much time automating <a href=\\\"https://github.com/citation-js/ris-mappings\\\">a
1021
- script</a> to turn those sheets — with a bunch of user input — into usable
1022
- mappings for Citation.js. I just finished that today, apart from some… questionable
1023
- mappings, but I wanted to at least test the final script with an example.
1024
- As for the results, well, see for yourself. <a href=\\\"https://en.wikipedia.org/wiki/RIS_(file_format)#Example_multi-record_format\\\">The
1025
- example</a>, from the Wikipedia page (CC-BY-SA 3.0 Unported) was</p>\\n<pre><code>TY
1026
- \ - JOUR\\nT1 - On computable numbers, with an application to the Entscheidungsproblem\\nA1
1027
- \ - Turing, Alan Mathison\\nJO - Proc. of London Mathematical Society\\nVL
1028
- \ - 47\\nIS - 1\\nSP - 230\\nEP - 265\\nY1 - 1937\\nER -\\n</code></pre>\\n<p>and
1029
- my results were</p>\\n<pre class=\\\" language-js\\\"><code class=\\\"prism
1030
- \ language-js\\\"><span class=\\\"token punctuation\\\">{</span> issue<span
1031
- class=\\\"token punctuation\\\">:</span> <span class=\\\"token number\\\">1</span><span
1032
- class=\\\"token punctuation\\\">,</span> page<span class=\\\"token punctuation\\\">:</span>
1033
- <span class=\\\"token number\\\">230</span><span class=\\\"token punctuation\\\">,</span>
1034
- type<span class=\\\"token punctuation\\\">:</span> <span class=\\\"token string\\\">'article-journal'</span><span
1035
- class=\\\"token punctuation\\\">,</span> volume<span class=\\\"token punctuation\\\">:</span>
1036
- <span class=\\\"token number\\\">47</span> <span class=\\\"token punctuation\\\">}</span>\\n</code></pre>\\n<p>That
1037
- looked really weird and disappointing. Again, what could possibly be going
1038
- on here? The example on Wikipedia is using <code>T1</code>, <code>A1</code>,
1039
- <code>JO</code> and <code>Y1</code> while the specs say to use <code>TI</code>,
1040
- <code>AU</code>, <code>T2</code> and <code>PY</code> here. Where are these
1041
- differences coming from?</p>\\n<p>After some digging around on Wikipedia I
1042
- found <a href=\\\"https://en.wikipedia.org/wiki/Talk:RIS_(file_format)#Versions_of_the_specification\\\">a
1043
- comment</a> saying that there are in fact two specifications: one from 2011
1044
- and one from before. The archived spec I checked out was from 2012 (as linked
1045
- by Wikipedia!), while they use the version from before 2011; which luckily
1046
- is <a href=\\\"https://web.archive.org/web/20110930172154/http://www.refman.com/support/risformat_intro.asp\\\">still
1047
- available</a>. To be continued.</p>\\n</div>\\n</body>\\n\\n</html>\",\"tags\":[\"bibliography\",\"Citation.js\",\"programming\",\"RIS\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"y55kq35\",\"blog\":{\"id\":\"y55kq35\",\"title\":\"Syntaxus
1048
- baccata\",\"description\":\"Thoughts about bibliographic metadata, programming,
1049
- statistics, taxonomy, and biology.\",\"language\":\"en\",\"favicon\":\"https://blogger.googleusercontent.com/img/a/AVvXsEjHdUshBRlHAgurlZYYubJ9yfTRkteSS8hwgor7bpsdHNByrUXglmpVcCS2McVehJLgWZPyr61hB2Nq8iXql2-0qLFfZZHWdMn8wuKGz5UO1vZXWQkRKn_4EelUV6NneQW6fN1wlggv7skzUBri-T7bJZnlzXkKj6FjF8p0wLDR8DXwO7oN8QSwcN9-=s64\",\"feed_url\":\"https://larsgw.blogspot.com/feeds/posts/default\",\"home_page_url\":\"https://larsgw.blogspot.com/\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T16:56:38+00:00\",\"indexed_at\":\"2023-01-08\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"Blogger
1050
- 7.00\",\"category\":\"Engineering and Technology\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-05-08T11:05:00+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.59350/det4g-prf93\",\"uuid\":\"d1c551e3-7371-4683-99d8-a9a62e11d2ae\",\"url\":\"https://larsgw.blogspot.com/2021/03/github-pages-404-redirection.html\",\"title\":\"GitHub
1051
- pages 404 redirection\",\"summary\":\"Recently I moved the Citation.js API
1052
- documentation from /api to /api/0.3, to put the new documentation on /api/0.5.
1053
- I fixed all the links to the documentation, but I still got a issue request
1054
- regarding a 404 error after just a few days. All in all, I had to redirect
1055
- pages from /api/* to /api/0.3/* while all these pages are hosted as static
1056
- files on GitHub Pages. There are three ways I found to do this: I make otherwise
1057
- empty HTML files in /api/* that redirect to /api/0.3/* via JavaScript or...\",\"date_published\":\"2021-03-26T13:08:00Z\",\"date_modified\":\"2023-03-30T20:46:06Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":null,\"name\":\"Lars
1058
- Willighagen\"}],\"image\":null,\"content_html\":\"<p>Recently I moved the
1059
- <a href=\\\"https://citation.js.org\\\">Citation.js</a> API documentation
1060
- from <code>/api</code> to <code>/api/0.3</code>, to put the new documentation
1061
- on <code>/api/0.5</code>. I fixed all the links to the documentation, but
1062
- I still got a issue request regarding a 404 error after just a few days. All
1063
- in all, I had to redirect pages from <code>/api/*</code> to <code>/api/0.3/*</code>
1064
- while all these pages are hosted as static files on GitHub Pages.</p>\\n<p>There
1065
- are three ways I found to do this:</p>\\n<ol>\\n<li>I make otherwise empty
1066
- HTML files in <code>/api/*</code> that redirect to <code>/api/0.3/*</code>
1067
- via JavaScript or a <code>&lt;meta&gt;</code> tag.</li>\\n<li>I make use of
1068
- <a href=\\\"https://github.com/jekyll/jekyll-redirect-from\\\"><code>jekyll-redirect-from</code></a>.
1069
- This is equivalent to option 1, I think.</li>\\n</ol>\\n<p>Option 1 seemed
1070
- like a hassle and I do not use Jekyll so option 2 seemed out of the question
1071
- as well. However, we still have option 3 to consider:</p>\\n<ol start=\\\"3\\\">\\n<li>I
1072
- add a <code>404.html</code> to the repository which gets served automatically
1073
- on a 404. It then redirects to <code>/api/0.3/*</code> with JavaScript, and
1074
- gives guidance on how to find the new URL manually if JavaScript is disabled.</li>\\n</ol>\\n<p><code>404.html</code>
1075
- is just a normal 404 page with 4 lines of JavaScript:</p>\\n<pre class=\\\"
1076
- language-js\\\"><code class=\\\"prism language-js\\\"><span class=\\\"token
1077
- keyword\\\">var</span> docsPattern <span class=\\\"token operator\\\">=</span>
1078
- <span class=\\\"token regex\\\">/(\\\\/api)(\\\\/(?!0.[35]\\\\/)|$)/</span>
1079
- \ \\n \\n<span class=\\\"token keyword\\\">if</span> <span class=\\\"token
1080
- punctuation\\\">(</span>docsPattern<span class=\\\"token punctuation\\\">.</span><span
1081
- class=\\\"token function\\\">test</span><span class=\\\"token punctuation\\\">(</span>location<span
1082
- class=\\\"token punctuation\\\">.</span>pathname<span class=\\\"token punctuation\\\">)</span><span
1083
- class=\\\"token punctuation\\\">)</span> <span class=\\\"token punctuation\\\">{</span>
1084
- \ \\n location<span class=\\\"token punctuation\\\">.</span>pathname <span
1085
- class=\\\"token operator\\\">=</span> location<span class=\\\"token punctuation\\\">.</span>pathname<span
1086
- class=\\\"token punctuation\\\">.</span><span class=\\\"token function\\\">replace</span><span
1087
- class=\\\"token punctuation\\\">(</span>docsPattern<span class=\\\"token punctuation\\\">,</span>
1088
- <span class=\\\"token string\\\">'$1/0.3$2'</span><span class=\\\"token punctuation\\\">)</span>
1089
- \ \\n<span class=\\\"token punctuation\\\">}</span>\\n</code></pre>\\n<p>Breaking
1090
- down the RegExp pattern:</p>\\n<ul>\\n<li><code>(\\\\/api)</code> matches
1091
- “/api” in the URL</li>\\n<li><code>(\\\\/(?!0.[35]\\\\/)|$)</code> matches
1092
- one of two things, immediately after “/api”\\n<ul>\\n<li>Either <code>$</code>,
1093
- the end of the string (like “<a href=\\\"https://citation.js.org/api\\\">https://citation.js.org/api</a>”
1094
- without the trailing slash)</li>\\n<li>Or <code>\\\\/(?!0.[35]\\\\/)</code>,
1095
- which matches a forward slash (\\\"/api/\\\") followed by anything except
1096
- “0.3” or “0.5”. This is to avoid matching things like “/apical/” or “/api/0.3/does-not-exist”.</li>\\n</ul>\\n</li>\\n</ul>\\n<p>This
1097
- is not the neatest solution but I like it conceptually. It shows a bit of
1098
- potential for Single-Page Applications as well: you can serve the same HTML+JavaScript
1099
- for every possible path without having to rely on URLs like <code>https://example.org/#/path/page</code>.
1100
- The problem is that you still get the 404 HTTP status (as you should), so
1101
- if a browser or search crawler decides to care you have a problem.</p>\\n<p>Try
1102
- it out now: <a href=\\\"https://citation.js.org/api/\\\">https://citation.js.org/api/</a></p>\\n<p><img
1103
- src=\\\"https://1.bp.blogspot.com/-srnQgvIYR1c/YF3aOogA3AI/AAAAAAAAuro/gVpFdn1m-Gk4JBh9Nsrw6Gd_bR-QKApEACLcBGAsYHQ/s0/citation.js.org_api_0.3_test.png\\\"
1104
- alt=\\\"The new &quot;Page not Found&quot; page in the same style as the homepage.\\\"></p>\",\"tags\":[\"Citation.js\",\"programming\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"y55kq35\",\"blog\":{\"id\":\"y55kq35\",\"title\":\"Syntaxus
1105
- baccata\",\"description\":\"Thoughts about bibliographic metadata, programming,
1106
- statistics, taxonomy, and biology.\",\"language\":\"en\",\"favicon\":\"https://blogger.googleusercontent.com/img/a/AVvXsEjHdUshBRlHAgurlZYYubJ9yfTRkteSS8hwgor7bpsdHNByrUXglmpVcCS2McVehJLgWZPyr61hB2Nq8iXql2-0qLFfZZHWdMn8wuKGz5UO1vZXWQkRKn_4EelUV6NneQW6fN1wlggv7skzUBri-T7bJZnlzXkKj6FjF8p0wLDR8DXwO7oN8QSwcN9-=s64\",\"feed_url\":\"https://larsgw.blogspot.com/feeds/posts/default\",\"home_page_url\":\"https://larsgw.blogspot.com/\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T16:56:38+00:00\",\"indexed_at\":\"2023-01-08\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"Blogger
1107
- 7.00\",\"category\":\"Engineering and Technology\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-05-08T11:05:00+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.59350/7dz35-q5185\",\"uuid\":\"d2b5f8f3-dde5-4944-a4e1-f9776c86b38b\",\"url\":\"http://sfmatheson.blogspot.com/2023/06/design-without-designer-explaining-and.html\",\"title\":\"Design
1108
- without a designer: explaining and answering some questions\",\"summary\":\"I've
1109
- been writing and thinking about design in biology since I started Quintessence
1110
- of Dust. I want to write and think about it a lot more, so in my last post
1111
- I introduced my view of the concept and pointed ahead to this post, which
1112
- consists of edited excerpts from some conversations at a discussion forum
1113
- at the Peaceful Science site. You will find links to those conversations in
1114
- the previous post. I have removed people's names and lightly edited for clarity.
1115
- Other people’s words are indented;...\",\"date_published\":\"2023-06-06T20:22:00Z\",\"date_modified\":\"2023-06-07T20:44:58Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":null,\"name\":\"Stephen
1116
- Matheson\"}],\"image\":null,\"content_html\":\"I've been writing and thinking
1117
- about design in biology since I started <i>Quintessence of Dust</i>. I want
1118
- to write and think about it a lot more, so <a href=\\\"https://sfmatheson.blogspot.com/2023/06/design-without-designer-british.html\\\"
1119
- target=\\\"_blank\\\">in my last post</a> I introduced my view of the concept
1120
- and pointed ahead to this post, which consists of edited excerpts from some
1121
- conversations at a discussion forum at the Peaceful Science site. You will
1122
- find links to those conversations in the <a href=\\\"https://sfmatheson.blogspot.com/2023/06/design-without-designer-british.html\\\"
1123
- target=\\\"_blank\\\">previous post</a>. I have removed people's names and
1124
- lightly edited for clarity. Other people’s words are indented; the rest are
1125
- mine.<div><hr /><br /><div><div><blockquote>I would like to understand better
1126
- how you think about it because it seems quite different from the way I normally
1127
- think about it. I would really like learn more about how you see it and expand
1128
- my understanding of \\\"design\\\".</blockquote></div><div>This is a potentially
1129
- big interesting deep conversation that is worthy of a dedicated thread with
1130
- some clear goals. Someday I’ll propose that, since I believe that we can improve
1131
- the quality and tone of conversations about biological design by getting at
1132
- least some unbelievers to agree that design in biology is an interesting and
1133
- worthy question that need not and should not have inherent religious overtones.</div><div><br
1134
- /></div><div>I guess my first question for you as you compare your conception
1135
- of 'design' to mine is this: do you think design is something that is <i>done</i>
1136
- (by a designer) or do you think it is something that <i>exists</i> and can
1137
- be detected by humans? Obviously both can be true, but as long as a person
1138
- believes that 'design' necessitates a 'designer', then they won’t see design
1139
- the way I do. Because my view is that design exists whether or not it is linked
1140
- to a designer. To me, it is axiomatic that a mindless process can generate
1141
- design, not only because we have seen it happen but because there is no good
1142
- argument to the contrary. It is instructive, IMO, that the \\\"argument\\\"
1143
- offered to the contrary is something like \\\"all of our examples of design
1144
- can be traced back to a mind.\\\" This is not even an argument.</div><div><br
1145
- /></div><div>But what do we mean by 'design'? Here I think we can look at
1146
- some of the definitions and conceptions offered by the ID movement. I think
1147
- Behe’s \\\"purposeful arrangement of parts\\\" is a nice start, because it
1148
- captures something that we all detect when we consider (for example) a molecular
1149
- machine. Was a bacterial flagellum designed by a designer? I don’t know. Does
1150
- a bacterial flagellum evince design? To me, the answer is obviously yes. <span><a
1151
- name='more'></a></span>So, I disagree with many fellow unbelievers (materialists
1152
- for the most part) who use phrases like \\\"apparent design\\\" or words like
1153
- 'designoid' to describe the biological world. My view is that design is design.
1154
- If I see it, I should call it design. This doesn’t imply a designer. That
1155
- simply doesn’t follow.</div><div><blockquote>How do you manage the distinction
1156
- between design as a \\\"process of making\\\" vs. \\\"plan or schematic\\\"
1157
- vs. \\\"product of a designing process\\\"?</blockquote></div><div>I don’t
1158
- manage that. Those are all conceptions of design, but they’re not what we
1159
- see when we look at ATP synthase or a flagellum. I think those things are
1160
- all distractions away from what I (personally) care about, especially since
1161
- they all assume the presence of a designer.</div><div><blockquote>Is that
1162
- last one even rightly called design?</blockquote></div><div>Sure, why not?
1163
- Anyone who believes otherwise would have to claim that the sentence \\\"I
1164
- see design in this thing\\\" is linguistically incorrect. I can respect that,
1165
- but then it ends the conversation.</div><div><blockquote>So you are trying
1166
- to legitimize one understanding of design in its own right, separate from
1167
- other definitions.</blockquote></div><div>Yes, though I think the work of
1168
- \\\"legitimizing\\\" this understanding is already done. To reject this use
1169
- of the word/concept is defensible in principle, but there’s nothing revolutionary
1170
- about saying \\\"design is detectable without knowledge of a designer.\\\"</div><div><blockquote>Seems
1171
- like the same thing would have to be done with the term \\\"purpose.\\\"</blockquote></div><div>Maybe.
1172
- [shrug]</div><div><blockquote>I don’t think science recognizes design without
1173
- a model of a designer. So this would be pretty revolutionary.</blockquote></div><div>Science
1174
- has never spoken on this, since it can’t do that. But scientists have. Here
1175
- are just a few examples from places I know well.</div><div><a href=\\\"https://www.cell.com/molecular-cell/fulltext/S1097-2765(13)00004-X\\\"
1176
- target=\\\"_blank\\\">Design Principles of Regulatory Networks: Searching
1177
- for the Molecular Algorithms of the Cell</a></div><div><a href=\\\"https://www.cell.com/cell/fulltext/S0092-8674(20)30277-4\\\"
1178
- target=\\\"_blank\\\">Defining the Design Principles of Skin Epidermis Postnatal
1179
- Growth</a></div><div><a href=\\\"https://www.cell.com/cell-reports/fulltext/S2211-1247(18)30188-8\\\"
1180
- target=\\\"_blank\\\">Quantitative Operating Principles of Yeast Metabolism
1181
- during Adaptation to Heat Stress</a></div><div><blockquote>I tend towards
1182
- notion of \\\"appearance of design,\\\" and trying to make sense of what defines
1183
- that appearance. That is, I think, closely aligned with what you are after.</blockquote></div><div>I
1184
- don’t see that as closely aligned, because I don’t assume that design requires
1185
- a designer. \\\"Appearance of design\\\" downgrades ATP synthase to an \\\"appearance\\\"
1186
- of something I consider obvious. I understand why people do this, and especially
1187
- why naturalism leads people to do it (that infamous quote about a \\\"divine
1188
- foot in the door\\\") but I’m with Dan Dennett here. The biological world
1189
- is overflowing with design. Calling it \\\"apparent\\\" just encourages the
1190
- madness of attempting to find the \\\"real\\\" design that isn’t just \\\"apparent\\\"
1191
- design. Does this give some kind of comfort to ID creationists and their propaganda
1192
- machines? Maybe, but that just means that they didn’t read to the end of the
1193
- sentence: \\\"…without a designer.\\\"</div><div><br /></div><div>But here’s
1194
- the thought experiment. Suppose I sit down at my supercomputer to predict
1195
- ways to build a much better version of enzyme Z; let’s even say that my enzyme
1196
- has a new substrate specificity and is orders of magnitude more stable than
1197
- enzyme Z. I synthesize the gene and insert it into bacteria. Does this enzyme
1198
- evince design? Or only apparent design? Is there any way to tell the difference,
1199
- without knowing that I designed the new enzyme on my supercomputer? Are we
1200
- going to actually say, \\\"well I can’t tell whether this is design or apparent
1201
- design until I investigate supercomputer user patterns?\\\"</div><div><br
1202
- /></div><div>Just a couple of quick thoughts at this point.</div><div style=\\\"text-align:
1203
- left;\\\">\U0001F335In a universe that includes one or more omnipotent gods,
1204
- it is impossible to argue persuasively that <i>anything</i> came about without
1205
- a designer, for the straightforward reason that such beings can make anything
1206
- they want, and make it look any way they want.<br />\U0001F332To me, the fundamental
1207
- first question is not \\\"can we have design without a designer?\\\" but \\\"does
1208
- design detection imply knowledge or assumptions about possible designers?\\\"
1209
- I am saying an emphatic ‘no’ to that question, but one can coherently circumscribe
1210
- ‘design’ to essentially require the answer to be ‘yes.’ I think that creates
1211
- problems, which I’ve mentioned above, but it’s coherent and defensible to
1212
- limit ‘design’ in that way. I will grant that once you answer ‘no’ to the
1213
- fundamental question then it’s hard (maybe impossible) to answer ‘no’ to the
1214
- first question.</div><div><blockquote>What would you suggest as terminology
1215
- for the two cases?</blockquote></div><div>I don’t need any new words and I
1216
- don’t share the premise of \\\"design implies a designer\\\" with you. I have
1217
- tried to document the fact that design is a pretty integrated concept in biology,
1218
- such that many biologists talk about design and design principles with no
1219
- worry that they will be misunderstood. I’m afraid I don’t see how the concept
1220
- of design without a designer is either hard to grasp (conceptually) or hard
1221
- to understand (linguistically).</div><div><br /></div><div>People have tried
1222
- words like 'designoid' and phrases like 'apparent design.' The subtitle of
1223
- Dawkins’ <i>The Blind Watchmaker</i> is \\\"Why the Evidence of Evolution
1224
- Reveals a Universe without Design.\\\" I’m well aware that many believers
1225
- and unbelievers alike are stuck with the word 'design' linked to 'designer'.
1226
- I have seen only one argument for this approach so far, which is the dictionary.
1227
- Maybe there are other things going on. But here is Dennett (from <a href=\\\"https://www.edge.org/conversation/the-false-allure-of-group-selection#dd\\\"
1228
- target=\\\"_blank\\\">this piece</a>) on one reason why it might not be a
1229
- good idea to refuse to give ATP synthase the honor of showing design:</div><div><br
1230
- /></div><div><blockquote>The second misplaced emphasis is Pinker’s phrase&nbsp;
1231
- 'the illusion of design in the natural world.\\\" Richard Dawkins, in a similar
1232
- vein, says \\\"the illusion of design conjured by Darwinian natural selection
1233
- is so breathtakingly powerful\\\" in <i>The Ancestors’ Tale</i> (p 457), and
1234
- elsewhere proposes to speak of \\\"designoid\\\" features of the natural world
1235
- (eg., <i>Climbing Mount Improbable</i>, p 4). I disagree with this policy,
1236
- which can backfire badly. I recently overheard a conversation among some young
1237
- people in a bar about the marvels of the nano-machinery discovered inside
1238
- all cells. \\\"When you see all those fantastic little robots working away,
1239
- how can you possibly believe in evolution!\\\" one exclaimed, and another
1240
- nodded wisely. Somehow these folks had gotten the impression that evolutionary
1241
- biologists thought that the intricacies and ingenuities of life’s processes
1242
- weren’t all that wonderful. These evolution-doubters were not rednecks; they
1243
- were Harvard Medical students! They hugely underestimated the power of natural
1244
- selection because they had been told by evolutionary biologists, again and
1245
- again, that there is no actual design in nature, only the appearance of design.
1246
- This episode strongly suggested to me that one of the themes that has been
1247
- gaining ground in \\\"common knowledge\\\" is that evolutionary biologists
1248
- are reluctant to \\\"admit\\\" or \\\"acknowledge\\\" the manifest design
1249
- in nature. I recommend instead the expository policy of calling nature’s marvels
1250
- design, as real as any design in the universe, but just not the products of
1251
- an intelligent designer.</blockquote></div><div>You can read how Dennett describes
1252
- design <a href=\\\"https://books.google.com/books?id=PEp8DAAAQBAJ&amp;lpg=PP1&amp;pg=PT46#v=onepage&amp;q&amp;f=false\\\"
1253
- target=\\\"_blank\\\">here</a>, in his recent cool book <i>From Bacteria to
1254
- Bach and Back</i>.</div><div><br /></div><div>Biology shows design. I don’t
1255
- think that’s confusing or unclear, and I think it’s a mistake to make distinctions
1256
- based on old dictionaries. YMMV.</div><div><br /></div></div></div>\",\"tags\":[\"Design\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"5764g49\",\"blog\":{\"id\":\"5764g49\",\"title\":\"Quintessence
1257
- of Dust\",\"description\":\"<i>Quintessence of Dust</i> explores science,
1258
- society, and human nature, focusing on genetics, development, evolution, neuroscience,
1259
- systems biology, and topics related to scientific literacy. I occasionally
1260
- discuss intelligent design, creationism, science denial, and other political/social
1261
- influences on scientific literacy. Additional topics: philosophy, baseball,
1262
- scientific culture, and Shakespeare. My main theme is <b><u>scientific explanation</u></b>.\",\"language\":\"en\",\"favicon\":null,\"feed_url\":\"http://sfmatheson.blogspot.com/feeds/posts/default\",\"home_page_url\":\"http://sfmatheson.blogspot.com/\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T14:21:27+00:00\",\"indexed_at\":\"2023-04-18\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"Blogger
1263
- 7.00\",\"category\":\"Social Sciences\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-06-06T20:22:00+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.59350/stsb5-45v78\",\"uuid\":\"5fc2c7d7-082a-4994-aa33-d94d1e474c4c\",\"url\":\"https://jabberwocky.weecology.org/2020/04/27/supporting-and-managing-academic-labs-during-a-pandemic-some-thoughts/\",\"title\":\"Supporting
1264
- and managing academic labs during a pandemic, some thoughts\",\"summary\":\"Adjust
1265
- expectations, be flexible, support your groups Research will be different
1266
- from normal for a while and even in the best cases it will also be slower.
1267
- The shift to working remotely will limit the kinds of work we can do and everyone
1268
- doing research is experiencing a dramatic disturbance to their lives. This
1269
- means the people in our labs will need flexibility and support. Talk to your
1270
- lab members to understand their needs: Recognize that these needs will be
1271
- different for different people....\",\"date_published\":\"2020-04-27T13:19:27Z\",\"date_modified\":\"2020-04-27T13:19:27Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":\"https://orcid.org/0000-0001-6728-7745\",\"name\":\"Ethan
1272
- White\"}],\"image\":null,\"content_html\":\"<h2>Adjust expectations, be flexible,
1273
- support your groups</h2>\\n<p>Research will be different from normal for a
1274
- while and even in the best cases it will also be slower. The shift to working
1275
- remotely will limit the kinds of work we can do and everyone doing research
1276
- is experiencing a dramatic disturbance to their lives. This means the people
1277
- in our labs will need flexibility and support.</p>\\n<p><b>Talk to your lab
1278
- members to understand their needs: </b>Recognize that these needs will be
1279
- different for different people. Many will have new responsibilities and stresses
1280
- that preclude working normally, but some may use work as a coping mechanism.</p>\\n<p><b>Make
1281
- it clear that moving more slowly and delaying things is expected and 100%
1282
- OK.</b> Push back project timelines, understand that some folks will make
1283
- little to no progress for a while, consider delaying stressful graduate activities
1284
- like qualifying exams.</p>\\n<p><b>Provide financial reassurance:</b> If true,
1285
- ensure your team that their current funding won’t be cut. If possible, offer
1286
- extensions on funding. This will help alleviate stress and uncertainty.</p>\\n<p><b>Recognize
1287
- power dynamics when offering flexibility:</b> Make sure that team members
1288
- are comfortable opting-out of &#8220;optional&#8221; choices and don&#8217;t
1289
- feel pressured to be productive, to work on-campus, or work at certain times.</p>\\n<p><b>Provide
1290
- access to university resources:</b> Inform group members about university
1291
- programs related to mental health, expanded sick leave, and other forms of
1292
- support for well being.</p>\\n<p><b>Give your team the resources they need
1293
- to work from home:  </b>Encourage your group to move things from campus that
1294
- they need to work at home including computers, books, and chairs. Universities
1295
- typically allow this for remote work (there may be a form to fill out). If
1296
- possible, purchase additional supplies needed for remote work (e.g., headsets).</p>\\n<h2>Adopt
1297
- & adapt tools and approaches for managing remote teams</h2>\\n<p>Remote management
1298
- recommendations focus on good communication, breaking projects into manageable
1299
- pieces, keeping everyone on the same page with clear next steps, and tracking
1300
- progress. This will make your group more efficient and inclusive when working
1301
- remotely.</p>\\n<p><b>Use video conferencing to replace in-person interactions:</b>
1302
- Do this for any regular meetings you have (e.g., one-on-one meetings, lab
1303
- group meetings) and also informal interactions (like popping into an advisors
1304
- office or chatting science with labmates). Communicate your availability and
1305
- how to set up meetings.</p>\\n<p><b>Use a group-based discussion tool (e.g.,
1306
- Slack or Microsoft Teams) : </b>This supports asking questions and working
1307
- on group projects and facilitates interactions among lab members with different
1308
- work hours (important for those with responsibilities like child care). It
1309
- can also provide an outlet for social interactions. Text does lose subtle
1310
- social cues so video or audio is still best for delicate conversations. Check
1311
- out the getting started documentation for <a href=\\\"https://slack.com/help/categories/360000049043-Getting-started\\\">Slack</a>
1312
- or <a href=\\\"https://docs.microsoft.com/en-us/MicrosoftTeams/get-started-with-teams-quick-start\\\">Microsoft
1313
- Teams</a>.</p>\\n<p><b>Read up on managing remote teams:</b> There are some
1314
- unique skills to remote management, but there is lots of information on how
1315
- to do this including: <a href=\\\"https://www.askamanager.org/2016/10/how-to-overcome-your-worries-about-letting-people-work-remotely.html\\\">How
1316
- to overcome your worries about letting people work remotely</a>, <a href=\\\"https://www.askamanager.org/2015/05/how-to-oversee-a-remote-teams-work.html\\\">How
1317
- to oversee a remote team&#8217;s work</a>, <a href=\\\"https://doi.org/10.7287/peerj.preprints.27907v1\\\">Ten
1318
- simple rules for a successful remote postdoc</a>.</p>\\n<p><b>Use project
1319
- management and collaboration tools: </b>These tools help you use good remote
1320
- management practices. Most labs will benefit from a tool for writing and a
1321
- tool for project management. Labs that write code (including for analyzing
1322
- data) will also benefit from a code collaboration platform. Check out getting
1323
- started guides for <a href=\\\"https://www.howtogeek.com/420971/the-beginners-guide-to-google-docs/\\\">Google
1324
- Docs (for writing)</a> and <a href=\\\"https://trello.com/guide/trello-101\\\">Trello
1325
- (for project management)</a>. Learning version control for managing code is
1326
- a bigger commitment, but the <a href=\\\"http://swcarpentry.github.io/git-novice/\\\">Software
1327
- Carpentry lessons</a> are a good starting point.</p>\\n<h3>Help identify research
1328
- that can be done remotely, but understand the limits</h3>\\n<p>It’s important
1329
- to prioritize the safety of your team over research. This may mean changing
1330
- your research plans to support social distancing and reduce or eliminate travel.</p>\\n<p><b>Focus
1331
- on analyzing and writing up existing data and ideas: </b>This is the easiest
1332
- adjustment because it minimizes shifts in research area and need for new skills.
1333
- Existing data isn’t just what a specific student has already collected, but
1334
- can include previous data collection from your lab.</p>\\n<p><b>Synthesize
1335
- existing knowledge: </b>Writing reviews lets your team use their expertise
1336
- to synthesize existing knowledge.</p>\\n<p><b>Conduct research on open data:</b>
1337
- There are increasingly large amounts of openly available data in many fields.
1338
- There may be data that can be used to address questions similar to those you
1339
- are studying using field or lab based approaches.</p>\\n<p><b>Collaborate
1340
- when extending into new research areas: </b>Computational research, working
1341
- with large datasets, systematic reviews and metaanalyses all take expertise.
1342
- To pivot into new methods or topics consider finding someone with the associated
1343
- expertise to collaborate with. There may well be experts on your students&#8217;
1344
- committees or in your department or university.</p>\\n<p><b>Develop new skills/expertise
1345
- to expand your groups&#8217; research horizons:</b> Instead of jumping into
1346
- a new project requiring new skills support your team taking this time to learn
1347
- new skills (e.g., computing methods or statistical approaches) or develop
1348
- new expertise (reading up on new areas of the literature) to serve as the
1349
- foundation for future research.</p>\\n<p><i>Initially prepared for the UF/IFAS
1350
- Faculty Forum: Living, Working, and Adapting to the New Normal of COVID-19.
1351
- Led by </i><a href=\\\"https://twitter.com/ethanwhite\\\"><i>Ethan White (@ethanwhite)</i></a><i>
1352
- (who is responsible for anything bad) with contributions from </i><a href=\\\"https://twitter.com/skmorgane\\\"><i>SK
1353
- Morgan Ernest (@skmorgane)</i></a><i>, </i><a href=\\\"https://twitter.com/Hao_and_Y\\\"><i>Hao
1354
- Ye (@Hao_and_Y)</i></a><i>, </i><a href=\\\"https://twitter.com/brandonscooper\\\"><i>Brandon
1355
- S. Cooper (@brandonscooper)</i></a><i>, </i><a href=\\\"https://twitter.com/JJ_Emerson\\\"><i>JJ
1356
- Emerson (@JJ_Emerson)</i></a><i>, </i><a href=\\\"https://twitter.com/katyhuff\\\"><i>Katy
1357
- Huff (@katyhuff)</i></a><i>, </i><a href=\\\"https://twitter.com/ryneches\\\"><i>Russell
1358
- Neches (@ryneches)</i></a><i>, </i><a href=\\\"https://twitter.com/RallidaeRule\\\"><i>Auriel
1359
- Fournier (@RallidaeRule)</i></a><i>, </i><a href=\\\"https://twitter.com/TrashBirdEcol\\\"><i>Jessica
1360
- Burnett (@TrashBirdEcol)</i></a><i>, </i><a href=\\\"https://twitter.com/mlrethlefsen\\\"><i>Melissa
1361
- Rethlefsen (@mlrethlefsen)</i></a><i>, </i><a href=\\\"https://twitter.com/LeafyEricScott\\\"><i>Eric
1362
- Scott (@LeafyEricScott)</i></a><i>, </i><a href=\\\"https://twitter.com/KatheMathBio\\\"><i>Kathe
1363
- Todd-Brown (@KatheMathBio)</i></a><i>, </i><a href=\\\"https://twitter.com/itatiVCS\\\"><i>itati
1364
- en casa (@itatiVCS)</i></a><i>, </i><a href=\\\"https://twitter.com/ashiklom711\\\"><i>Alexey
1365
- Shiklomanov (@ashiklom711)</i></a><i> (who are responsible for anything awesome).
1366
- A lot of the thinking in &#8220;Adopt & adapt tools and approaches for managing
1367
- remote teams&#8221; was influenced by &#8220;<a href=\\\"https://doi.org/10.7287/peerj.preprints.27907v1\\\">Ten
1368
- simple rules for a successful remote postdoc</a>&#8221; by <a href=\\\"https://twitter.com/KRBurgio\\\">Kevin
1369
- Burgio</a>, <a href=\\\"https://twitter.com/CaitlinInMaine\\\">Caitlin McDonough
1370
- MacKenzie</a>, <a href=\\\"https://twitter.com/PetrelStation\\\">Stephanie
1371
- Borrelle</a>, <a href=\\\"https://twitter.com/skmorgane\\\">Morgan Ernest</a>,
1372
- <a href=\\\"https://twitter.com/JacquelynGill\\\">Jacquelyn Gill</a>, <a href=\\\"https://twitter.com/kurtingeman\\\">Kurt
1373
- Ingeman</a>, <a href=\\\"https://twitter.com/tefferfish\\\">Amy Teffer</a>,
1374
- and me.<br />\\n</i></p>\\n\",\"tags\":[\"science\"],\"language\":\"en\",\"references\":[],\"blog_id\":\"h56tk29\",\"blog\":{\"id\":\"h56tk29\",\"title\":\"Jabberwocky
1375
- Ecology\",\"description\":\"Ethan White and Morgan Ernest&#039;s blog for
1376
- discussing issues and ideas related to ecology and academia.\",\"language\":\"en\",\"favicon\":\"https://secure.gravatar.com/blavatar/805953466a80fcabef50a73dfb96d52b?s=96&#038;d=https%3A%2F%2Fs0.wp.com%2Fi%2Fbuttonw-com.png\",\"feed_url\":\"https://jabberwocky.weecology.org/feed/atom/\",\"home_page_url\":\"https://jabberwocky.weecology.org\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T13:55:58+00:00\",\"indexed_at\":\"2023-01-04\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"WordPress
1377
- (.com)\",\"category\":\"Natural Sciences\",\"prefix\":\"10.59350\",\"modified_at\":\"2023-03-13T12:16:00+00:00\",\"version\":\"https://jsonfeed.org/version/1.1\",\"backlog\":true,\"authors\":null}},{\"id\":\"https://doi.org/10.53731/fearkb7-7wz03w9\",\"uuid\":\"7291350e-4828-429a-a188-5bf77c96efda\",\"url\":\"https://syldavia-gazette.org/planetary-defense-healthy-food-slime/\",\"title\":\"Planetary
1378
- Defense, Healthy Food, Slime, Software Citation, Parthenon Marbles\",\"summary\":\"The
1379
- Era of Planetary Defense Has BegunIn their textbook Modern Principles of Economics,
1380
- Tyler and Tabarrok use asteroid defense as an example of a public good.Food
1381
- fight: FDA is redefining ‘healthy’ and food industry is pushing backLess saturated
1382
- fat, less sodium, less added sugar; manufacturers say almost no packaged foods
1383
- would qualify under the agency’s new rules.From Ghostbusters to H.P. Lovecraft:
1384
- A Cultural History of SlimeA short cultural history of slime.Advancing Software
1385
- Citation...\",\"date_published\":\"2023-03-08T21:30:00Z\",\"date_modified\":\"2023-04-13T13:58:33Z\",\"date_indexed\":\"1970-01-01T00:00:00+00:00\",\"authors\":[{\"url\":\"https://orcid.org/0000-0003-1419-2405\",\"name\":\"Martin
1386
- Fenner\"}],\"image\":\"https://digitalpress.fra1.cdn.digitaloceanspaces.com/gtpg506/2023/04/Elgin_Marbles_east_pediment.jpg\",\"content_html\":\"
1387
- <h3 id=\\\"the-era-of-planetary-defense-has-begun\\\"><a href=\\\"https://marginalrevolution.com/marginalrevolution/2023/03/the-era-of-planetary-defense-has-begun.html?ref=syldavia-gazette.org\\\">The
1388
- Era of Planetary Defense Has Begun</a></h3><p>In their textbook <em>Modern
1389
- Principles of Economics</em>, Tyler and Tabarrok use asteroid defense as an
1390
- example of a public good.</p><h3 id=\\\"food-fight-fda-is-redefining-%E2%80%98healthy%E2%80%99-and-food-industry-is-pushing-back\\\"><a
1391
- href=\\\"https://www.washingtonpost.com/business/2023/03/05/fda-healthy-food-sugar/?ref=syldavia-gazette.org\\\">Food
1392
- fight: FDA is redefining ‘healthy’ and food industry is pushing back</a></h3><p>Less
1393
- saturated fat, less sodium, less added sugar; manufacturers say almost no
1394
- packaged foods would qualify under the agency’s new rules.</p><h3 id=\\\"from-ghostbusters-to-hp-lovecraft-a-cultural-history-of-slime\\\"><a
1395
- href=\\\"https://lithub.com/from-ghostbusters-to-h-p-lovecraft-a-cultural-history-of-slime/?ref=syldavia-gazette.org\\\">From
1396
- Ghostbusters to H.P. Lovecraft: A Cultural History of Slime</a></h3><p>A short
1397
- cultural history of slime.</p><h3 id=\\\"advancing-software-citation-implementation-software-citation-workshop-2022\\\"><a
1398
- href=\\\"https://doi.org/10.48550/arXiv.2302.07500?ref=syldavia-gazette.org\\\">Advancing
1399
- Software Citation Implementation (Software Citation Workshop 2022)</a></h3><p>This
1400
- report outlines a series of collaborative discussions that brought together
1401
- an international group of stakeholders and experts. </p><h3 id=\\\"the-strange-journey-of-the-parthenon-marbles-to-the-british-museum\\\"><a
1402
- href=\\\"https://aeon.co/videos/the-strange-journey-of-the-parthenon-marbles-to-the-british-museum?ref=syldavia-gazette.org\\\">The
1403
- strange journey of the Parthenon Marbles to the British Museum</a></h3><p>Short
1404
- video telling the story of how the Parthenon Marbles were moved from Athens
1405
- to London 200 years ago.</p><hr><h3 id=\\\"references\\\">References</h3><ol><li>Tabarrok
1406
- A. The Era of Planetary Defense Has Begun. Marginal REVOLUTION. Published
1407
- March 8, 2023. Accessed March 28, 2023. <a href=\\\"https://marginalrevolution.com/marginalrevolution/2023/03/the-era-of-planetary-defense-has-begun.html?ref=syldavia-gazette.org\\\">https://marginalrevolution.com/marginalrevolution/2023/03/the-era-of-planetary-defense-has-begun.html</a></li><li>Reiley
1408
- L. Food fight: FDA is redefining ‘healthy’ and food industry is pushing back.
1409
- <em>Washington Post</em>. <a href=\\\"https://www.washingtonpost.com/business/2023/03/05/fda-healthy-food-sugar/?ref=syldavia-gazette.org\\\">https://www.washingtonpost.com/business/2023/03/05/fda-healthy-food-sugar/</a>.
1410
- Published March 6, 2023. Accessed March 28, 2023.</li><li>From Ghostbusters
1411
- to H.P. Lovecraft: A Cultural History of Slime ‹ Literary Hub. Accessed March
1412
- 28, 2023. <a href=\\\"https://lithub.com/from-ghostbusters-to-h-p-lovecraft-a-cultural-history-of-slime/?ref=syldavia-gazette.org\\\">https://lithub.com/from-ghostbusters-to-h-p-lovecraft-a-cultural-history-of-slime/</a></li><li>Bouquin
1413
- D, Trisovic A, Bertuch O, Colón-Marrero E. Advancing Software Citation Implementation
1414
- (Software Citation Workshop 2022). Published online February 15, 2023. doi:<a
1415
- href=\\\"https://doi.org/10.48550/arXiv.2302.07500?ref=syldavia-gazette.org\\\">10.48550/arXiv.2302.07500</a></li><li>The
1416
- strange journey of the Parthenon Marbles to the British Museum | Aeon Videos.
1417
- Aeon. Accessed March 28, 2023. <a href=\\\"https://aeon.co/videos/the-strange-journey-of-the-parthenon-marbles-to-the-british-museum?ref=syldavia-gazette.org\\\">https://aeon.co/videos/the-strange-journey-of-the-parthenon-marbles-to-the-british-museum</a></li></ol>
1418
- \",\"tags\":[],\"language\":\"en\",\"references\":[{\"key\":\"ref1\",\"url\":\"https://marginalrevolution.com/marginalrevolution/2023/03/the-era-of-planetary-defense-has-begun.html\"},{\"key\":\"ref2\",\"url\":\"https://washingtonpost.com/business/2023/03/05/fda-healthy-food-sugar\"},{\"key\":\"ref3\",\"url\":\"https://lithub.com/from-ghostbusters-to-h-p-lovecraft-a-cultural-history-of-slime\"},{\"doi\":\"https://doi.org/10.48550/arxiv.2302.07500\",\"key\":\"ref4\"},{\"key\":\"ref5\",\"url\":\"https://aeon.co/videos/the-strange-journey-of-the-parthenon-marbles-to-the-british-museum\"}],\"blog_id\":\"f4wdg32\",\"blog\":{\"id\":\"f4wdg32\",\"title\":\"Syldavia
1419
- Gazette\",\"description\":\"The Syldavia Gazette is a weekly newsletter that
1420
- highlights interesting science stories from around the web.\",\"language\":\"en\",\"favicon\":\"https://syldavia-gazette.org/favicon.png\",\"feed_url\":\"https://syldavia-gazette.org/atom/\",\"home_page_url\":\"https://syldavia-gazette.org\",\"user_id\":\"8498eaf6-8c58-4b58-bc15-27eda292b1aa\",\"created_at\":\"2023-05-31T16:54:04+00:00\",\"indexed_at\":\"2023-02-01\",\"feed_format\":\"application/atom+xml\",\"license\":\"https://creativecommons.org/licenses/by/4.0/legalcode\",\"generator\":\"Ghost
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1468
- registry of research data repositories launched","summary":"Earlier this week
1469
- re3data.org – the Registry of Research Data Repositories – officially launched.
1470
- The registry is nicely described in a preprint also published this week.re3data.org
1471
- offers researchers, funding organizations, libraries and publishers and overview
1472
- of the heterogeneous research data repository landscape. Information icons
1473
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1474
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1475
- know...","date_published":"2013-06-01T00:00:00+00:00","date_modified":"2023-06-29T18:04:53+00:00","date_indexed":"2023-06-28T18:13:09+00:00","authors":[{"url":"https://orcid.org/0000-0003-1419-2405","name":"Martin
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1480
- cancer risk following computed tomography scans","summary":"Two papers (this
1481
- and this) and an editorial in the latest issue of Archives of Internal Medicine
1482
- examine the cancer risks associated with the use of computed tomography (CT)
1483
- examinations.1Ionizing radiation increases the risk for developing cancer.
1484
- There is direct evidence from atomic bomb survivors in Japan in 1945 and from
1485
- nuclear accidents such as the one in Chernobyl in 1986. There are no studies
1486
- directly demonstrating an increased cancer risk from the diagnostic use of
1487
- X-rays (either...","date_published":"2009-12-20T00:00:00+00:00","date_modified":"2023-06-29T17:49:57+00:00","date_indexed":"2023-06-28T18:13:09+00:00","authors":[{"url":"https://orcid.org/0000-0003-1419-2405","name":"Martin
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