3,727 Matching Annotations
  1. Last 7 days
    1. 1391r primer48 as it has better coverage of the known bacterial diversity

      Figure out how much this is better by

    2. Dueholm, M. S. et al. Generation of comprehensive ecosystem-specific reference databases with species-level resolution by high-throughput full-length 16S rRNA gene sequencing and automated taxonomy assignment (AutoTax). mBio 11, e01557–20 (2020).

      why ecosystem specific databases vs general ones?

    1. Simões, Luciana G., Rita Peyroteo-Stjerna, Grégor Marchand, Carolina Bernhardsson, Amélie Vialet, Darshan Chetty, Erkin Alaçamlı, et al. “Genomic Ancestry and Social Dynamics of the Last Hunter-Gatherers of Atlantic France.” Proceedings of the National Academy of Sciences 121, no. 10 (March 5, 2024): e2310545121. https://doi.org/10.1073/pnas.2310545121.

      saw via article:<br /> Europe's last hunter-gatherers avoided inbreeding by [[Dario Radley]]

    1. if your treatments are ordered, don't compare each mean with each other mean (multiple comparisons), instead do one test for trend to ask if the outcome is linearly related with treatment number

      How do you do hypothesis testing for trends for an ordered categorical variable?

      Could you convert x to numbers (1,2,3) and run a linear regression y ~ x? or even categorical ordered variables can be linearly regressed?

  2. Apr 2024
    1. Worth, Robert F. “Clash of the Patriarchs.” The Atlantic, April 10, 2024. https://www.theatlantic.com/magazine/archive/2024/05/russia-ukraine-orthodox-christian-church-bartholomew-kirill/677837/.

      A fantastic overview of the history, recent changes and a potential schism in the Orthodox Church with respect to the Russia/Ukraine conflict.

    1. new avenues for studying ARG transfer (Karimi et al., 2015; Li et al., 2018) (Figure 2C). Microfluidic chips equipped with delayed imaging, coupled with fluorescence technology, enable real-time observation of community changes and tracking of the transfer dynamics of ARGs
    1. Great Books tend to arise in the presence of great audiences. by [[Naomi Kanakia]]

      Kanakia looks at what may have made 19th C. Russian literature great. This has potential pieces to say about how other cultures had higher than usual rates of creativity in art, literature, etc.

      What commonalities did these sorts of societies have? Were they all similar or were there broad ranges of multiple factors which genetically created these sorts of great outputs?

      Could it have been just statistical anomaly?

  3. Mar 2024
    1. Ongweso Jr., Edward. “The Miseducation of Kara Swisher: Soul-Searching with the Tech ‘Journalist.’” The Baffler, March 29, 2024. https://thebaffler.com/latest/the-miseducation-of-kara-swisher-ongweso.

      ᔥ[[Pete Brown]] in Exploding Comma

    2. Sam Harnett’s 2020 paper “Words Matter: How Tech Media Helped Write Gig Companies Into Existence” remains one of the best accounts of how swaths of the media enthusiastically generated on-demand propaganda for the tech industry, directly setting the stage for these firms to exploit, codify, and expand legal loopholes that largely exempted them from regulation as they raided their users for data and generated billions in revenue. Such intellectual acquiescence would, as Harnett writes, “pave the way for a handful of companies that represent a tiny fraction of the economy to have an outsized impact on law, mainstream corporate practices, and the way we think about work.”

      Harnett, Sam. “Words Matter: How Tech Media Helped Write Gig Companies into Existence.” SSRN Scholarly Paper. Rochester, NY, August 7, 2020. https://doi.org/10.2139/ssrn.3668606.

    1. Theindexer will want a feel, before they begin, for the concepts that willneed to be flagged, or taxonomized with subheadings. They mightskim the book – reading it in full but at a canter – before tackling itproperly with the software open. Or they may spend a while, as apreliminary, with the book’s introduction, paying attention to itschapter outline – if it has one – to gain a sense of what to look outfor. Often, having reached the end of the book, the indexer will returnto the first few chapters, going over them again now that they havegained a conceptual mapping of the work as a whole.

      It's no wonder that Mortimer J. Adler was able to write such a deep analysis of reading in How to Read a Book after having spent so much time indexing the ideas behind The Great Books of the Western World.

      Indexing requires a solid inspectional read at minimum, but will often go deeper into contexts which require at least some analytical reading. To produce the Syntopicon, one must go even further into analytical reading to provide the proper indexing of ideas so that they may be sub-categorized and used for deeper analysis for things such as comparison and contrast of those ideas.

  4. Feb 2024
    1. This approach exploits the equivalence between confidence intervals and hypothesis tests, detailed in Section 12.2.
    1. Read [[Martha S. Jones]] in A New Face for an Old Library Catalog

      Discussion on harmful content in library card catalogs and finding aids.

      The methods used to describe archive material can not only be harmful to those using them, but they also provide a useful historical record of what cataloguers may have been thinking contemporaneously as they classified and organized materials.

      This is another potentially useful set of information to have while reading into historical topics from library card catalogs compared to modern-day digital methods.

      Is anyone using version control on their catalogs?

    1. https://www.blyberg.net/darien-statements

      The Darien Statements on the Library and Librarians<br /> Written by John Blyberg, Kathryn Greenhill, and Cindi Trainor<br /> Originally published April 3, 2009

    1. Die Zettelkastenmethode. Kontrolliere dein Wissen

      by Andrey Sukhovskii (transliteration) aka Sukhovskii https://qnnnp.substack.com/p/024#%C2%A7%D0%B8%D1%81%D1%82%D0%BE%D1%87%D0%BD%D0%B8%D0%BA%D0%B8-%D0%BD%D0%B0-%D0%B8%D0%BD%D0%BE%D1%81%D1%82%D1%80%D0%B0%D0%BD%D0%BD%D1%8B%D1%85-%D1%8F%D0%B7%D1%8B%D0%BA%D0%B0%D1%85

      A fairly solid overview of lots of note taking texts, including some historical. Nothing new to me. Almost looks like he's collected everything I've mentioned in the past several years online. Originally written in Russian.

  5. Jan 2024
    1. a kanamycin resistance gene known to be expressed in both Gram-negative and Gram-positive bacteria

      aphA-3 gene from Campylobacter coli. Ref 21, 25 ~ quoted

      A 1427-bp DNA fragment containing the kanamycin resistance gene, aphA-3, of plasmid pIP1433 from Campylobacter coli was inserted into a shuttle vector. Full expression of aphA-3 was obtained in Bacillus subtilis and in Escherichia coli.

    1. Doto, Bob. “What Do We Mean When We Say ‘Bottom-Up?’” Writing by Bob Doto (blog), January 25, 2024. https://writing.bobdoto.computer/what-do-we-mean-when-we-say-bottom-up/.

    1. generally derives from variations in filtering out spurious and low-abundant sequences (e.g. Edgar, 2017; Prodan et al., 2020).

      DADA2 like ASV vs OTU?

      Applying different workflows on the same data will always demonstrate a certain level of variation among pipelines. These variations are usually most obvious in terms of the reported number of features.

    1. read [[Dan Allosso]] in Actual Books

      Sometimes a physical copy of a book gives one information not contained in digital scans. Allosso provides the example of Charles Knowlton's book The Fruits of Philosophy which touched on abortion and was published as a tiny hand-held book which would have made it easy to pass from person to person more discretely for its time period.

    1. read [[Dan Allosso]] in Peer to Peer?

      Not sure if you've seen/found it before, but as academia has been having bigger problems with granting tenure over the past 20 years, there's been a rise of discussion of alternate academia pathways, often under the term #AltAc in social media and other locations. Careers in writing in other spaces have certainly abounded here.

    1. https://betterhumans.pub/i-built-my-own-personal-productivity-system-around-a-3-x-5-index-card-147d7a8d83de

      Melange of GTD, card index, and gamification....


      Update 2024-01-04: I knew I had heard/seen this system before, but not delved into it deeply. I hadn't seen anyone either using it or refer to it by name in the wild until yesterday. All the prior mentions were people sharing the URLs as a thing rather than as something they used.

  6. tantek.com tantek.com
    Time to begin again: restarting my #100Days of #IndieWeb project for 2024, as a #100Posts of IndieWeb project, and congrats to the IndieWeb community on a fully completed 2023 IndieWeb Gift Calendar! Last year I completed 48 out of a planned 100 posts in my #100DaysOfIndieWeb project, for nearly 48 days (some days had multiple posts). Instead of resetting my goals accordingly, say down to 50, I’m going for 100 again, however, this time for 100 posts rather than 100 days, having learned that some days I find the time for multiple posts, and other days none at all. Looking back to the start of last year’s 100 Days project, it’s been one year since I encouraged everyone to own their own notes^1. Since then many have started, restarted, or expanded their personal sites to do so. Some have switched from a #Twitter account to a #Mastodon (or other #fediverse) account as a stopgap for short-form status posts. A step in the right direction, yet also an opportunity to take the leap this year to fully own their identity and posts on the web. In 2023 Twitter also broke all existing API clients (including my website). I did not feel it was worth my time to re-apply for an API key and rebuild/retest any necessary code for my semi-automatic #POSSE publishing, not knowing when they might break things again (since there was no rational reason for them to have broken things in the first place). I manually POSSEd a few posts after that, yet from the lack of interactions, either Twitter’s feed algorithm^2 isn’t showing my posts, or people have largely left or stopped using Twitter. Either way, when your friends stop seeing your posts on a silo, there’s no need to spend any time POSSEing to it. On the positive side, the IndieWeb community really came together in 2023, shining brightly even through the darker days of December. We, the IndieWeb community (and some beyond!) provided a gift (or often multiple) to the rest of community for every single day of December 2023^3, the first time we successfully filled out the whole month since the 2018 IndieWeb Challenge^4, and only the second time ever in the seven years of the IndieWeb Challenge-turned-Gift-Calendar. By going through the various gifts (more than 2 per day on average!), there are many interesting numbers and patterns we could surface. That deserves its own post however, as does a summary of the 48 posts^5 of my 2023 100 Days of IndieWeb attempt, so I’ll end this post here. Happy New Year to all, with an especially well deserved congratulations to the IndieWeb community and everyone who contributed to the 2023 Gift Calendar. Well done! Let’s see what else we can create & share on our personal sites in 2024 and continue setting a higher bar for the independent web by showing instead of telling. #ShowDontTell This is post 1 of #100PostsOfIndieWeb. #100Posts ← ✨ → 🔮 Post glossary: API https://indieweb.org/API POSSE https://indieweb.org/POSSE silo https://indieweb.org/silo ^1 https://tantek.com/2023/001/t1/own-your-notes ^2 https://indieweb.org/algorithmic_feed ^3 https://indieweb.org/2023-12-indieweb-gift-calendar ^4 https://indieweb.org/2018-12-indieweb-challenge ^5 https://tantek.com/2023/365/t2/no-large-language-model-llm-used - Tantek
    1
  7. Dec 2023
    1. what economists call rents: that is, value extracted through the ownership of a limited resource

      How does one draw the line between rent for providing a useful platform and extractive rent seeking?

      For example, does it help if the platform undergoes regular improvements, helps in information transparency with better reviewing systems, takes user feedback (both seller and customer)?

    1. https://blumm.blog/2022/12/31/dejo-de-recomendarte-cuarenta-y-dos-libros-que-no-has-leido-en-2022-pero-yo-si-una-lista-menos/

      Bernardo Munuera Montero recommends that one never recommend books to others as it's most likely a lost cause. He contends that people are far better of discovering their own reading for their own devices.

    1. https://blumm.blog/2020/12/07/202012071340-zettelkasten/

      Bernardo starts his zettelkasten

    1. https://blumm.blog/2022/07/31/el-metodo-zettelkasten-o-como-combatir-nuestra-mediocridad-cuando-leemos/

      Bernardo Munuera Montero' review of Ahren's Smart Notes

    1. Readwise Reader

      A great article on the history of reading online that might just nudge me into trying out and eventually becoming a Reader paid subscriber.

    1. What is needed is a breakaway group of nations willing to get serious about the climate emergency. Who would join it? Most of the world’s countries, potentially.
      • for: key point: alternative COP - breakaway group of nations, quote - alternative COP

      • quote

        • What is needed is a breakaway group of nations willing to get serious about the climate emergency. Who would join it? Most of the world’s countries, potentially.
      • author: Rupert Read
      • date: Dec 4, 2021

      • comment

      • suggestion
        • This could very well work. By applying social tipping point theory, a coalition of the willing could potentially accomplish a lot more than a coalition mired in friction.
        • There is enough capacity between 100 nation states willing to take far more aggressive measures than what a few petrostates of the COP convention continuously veto that it could bring about a social tipping point.
    2. “come back next year and try again”. My response is that it will be the same old thing – they’ve had 26 chances already. The planet can’t afford any more. I think the time for the Cop process is over. We just can’t keep kicking the can down the road.
      • for: quote - COP - Rupert Read, quote - COP - come back next year and try again, quote - alternative COP

      • quote

        • come back next year and try again
      • author: Rupert Read
      • date: Dec. 4, 2021

      • quote

        • We just can't keep kicking the can down the road
      • author: Rupert Read
      • date: Dec 4, 2021

      • comment

        • Well, COP28 is over and just as Rupert Read predicted above, we will
          • kick the can down the road again
          • come back next year and try again
        • It's a perpetual groundhog day, until it isn't
    1. Rupert Read has the best idea I have heard re international climate negotiations: countries that are serious should have their own conference where they collaborate on strong targets, plans, etc. Part of which should be recognising the dangers of remaining reliant on the petrostates, planning to transcend that reliance and sanctioning them
      • for: good idea - COP alternative, COP alternative - coalition of the willing, COP alternative - social tipping point, Rupert Read - alternative to COP

      • good idea: COP alternative

        • This could work based on the principle of social tipping points
        • The current COP pits the powerful incumbents of the old system delaying as long as possible rapid system change, these are the conservatives
          • This puts the liberals at distinct disadvantage from the conservatives because in a consensus reached agreement, the conservatives can veto any strong and binding language that represents rapid system change
        • In an alternative conference where the 100+ nation states are already in agreement, action in this smaller coalition OF THE WILLING, will lead to rapid action.
        • This could lead to breaking the threshold of system change via reaching the 25% social tipping point threshold
      • question: alternative COP

        • If an alternative COP was held, is the nation state the best level to approach?
        • What about a city level COP?
      • reference

    1. How Should OneRead a Book

      Woolf, Virginia. “How Should One Read a Book?” In Gateway to the Great Books: 5 Critical Essays, edited by Robert M. Hutchins, Mortimer J. Adler, and Clifton Fadiman, 2nd ed., 5–14. Gateway to the Great Books 5. 1932. Reprint, Chicago: Encyclopædia Britannica, Inc., 1990.

      Originally:<br /> “How Should One Read a Book?” from The Second Common Reader by Virginia Woolf. Harcourt, Brace & World, Inc., 1932.

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