847 Matching Annotations
  1. Oct 2024
    1. English composition: Eight lectures given at the Lowell Institute, New York: Charles Scribner's Sons, 1891.

      evidence of a card system/zettelkasten method in this?


      I found a copy and indeed there is evidence!

  2. Aug 2024
  3. Jul 2024
    1. for example, Vandeputte et al. (2017) measured total-community abundance using flow cytometry

      how did you measure abundance properly without noise from particulates?

    1. Adler, Mortimer J., and Charles Van Doren. How to Read a Book: The Classical Guide to Intelligent Reading. Revised and Updated edition. 1940. Reprint, Touchstone, 2011.

      Edmund Gröpl's concept map of Adler & Van Doren's How to Read a Book via https://forum.zettelkasten.de/discussion/comment/20668#Comment_20668:

  4. Jun 2024
    1. The classic account of industrialisation was David Landes’s The Unbound Prometheus (1969), which argued that economic transformation was rooted in three crucial substitutions: of ‘machines ... for human skill and effort’, of ‘inanimate for animate sources of power’, and of ‘mineral for vegetable or animal substances’ as raw materials.
    2. Despite – or perhaps because of – all this activity, Samuel only published one sole-authored book in his lifetime, Theatres of Memory (1994), an account of the popular historical imagination in late 20th-century Britain told via case studies, from Laura Ashley fabrics to the touristification of Ironbridge. Since his death from cancer in 1996, however, Samuel has been prolific. A second volume of Theatres of Memory, titled Island Stories: Unravelling Britain, came out in 1998, followed in 2006 by The Lost World of British Communism, a volume of essays combining research and recollections.

      Theatres of Memory (1994) sounds like it's taking lots of examples from a zettelkasten and tying them together.

      It's also interesting to note that he published several books posthumously. Was this accomplished in part due to his zettelkasten notes the way others like Ludwig Wittgenstein?

    1. Dr. Harry McNeill’s June 1940 assessment in Interracial Review

      Interesting commentary here on conversion of African-Americans to Catholicism as well as self-help nature of reading for improvement. Analogizes African-Americans without Catholicism to Mortimer J. Adler as a Jew.

      Possible tone of colonialism to assimilate African-Americans into Western Culture here? Though still somehow some space for movement and growth.

    2. acques Barzun, “Review of How to Read a Book, by Mortimer Adler,”Saturday Review (March 9, 1940): 6–7; Adler, Philosopher at Large, 67.

      available at: https://www.unz.com/print/SaturdayRev-1940mar09-00006/

      Barzun, Jacques. "Read, Do Not Run" Review of How to Read a Book, by Mortimer J. Adler. The Saturday Review, March 9, 1940.

    3. After publication in February 1940, How to Read a Book propelledAdler to the forefront of the Great Books Movement and into a posi-tion now referred to as a “public intellectual.”
    4. How to Read a Book providedrules for reading. The rules constituted the book’s heart: (1) readingfrom the whole to the parts, designated as the “structural or analyticreading”; (2) reading from parts to the whole, or an “interpretive orsynthetic” reading; and (3) deciding to agree or disagree, the “criticalor evaluative” reading.

      An interesting synopsis of the rules of reading from Adler's text.

    5. Hutchins compiled those ideas in a few books, most nota-bly Higher Learning in America (1936).
  5. May 2024
  6. Apr 2024
    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?

    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
  7. Mar 2024
    1. 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.

  8. Feb 2024
    1. This approach exploits the equivalence between confidence intervals and hypothesis tests, detailed in Section 12.2.
  9. 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. 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.

  10. 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. 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

  11. Nov 2023
    1. How to Read a Book. Los Angeles: KCET Los Angeles, 1975. https://www.youtube.com/watch?v=Y_rizr8bb0c.

      13 part series including:<br /> - 01:33:02 Part 8: How to read Stories - 01:46:13 Part 9: What Makes a Story Good - 01:59:24 Part 10 How to Read a Poem - Shakespeare sonnet 116, "admit" definition - Wordsworth poem about London and nature - 02:12:49 Part 11: Activating Poetry and Plays - 02:26:09 Part 12: How to Read Two Books at the Same Time - 02:39:29 Part 13: The Pyramid of Books

      2023-11-29: Since the original video was removed, one can also view the series at: https://www.youtube.com/playlist?list=PLPajsb520dyzNw9mHsZnrzi5w9N_amS7E

    1. "Obra académica de Don Pablo"

      Pablo Cabañas Díaz

      Gaceta Políticas (FCPyS – UNAM)

      2023, febrero

      Cabañas Díaz, Pablo Alejandro, Obra académica de Don Pablo, Gaceta Políticas, Facultad de Ciencias Políticas y Sociales, núm. 293, febrero de 2023, pp. 8-11.

      CV de Pablo Cabañas Díaz: https://www.politicas.unam.mx/cedulas/ordinario/profesores/prof073516.pdf

      accessed:: 2023-11-13 21:10

    1. Cut/Copy/Paste explores the relations between fragments, history, books, and media. It does so by scouting out fringe maker cultures of the seventeenth century, where archives were cut up, “hacked,” and reassembled into new media machines: the Concordance Room at Little Gidding in the 1630s and 1640s, where Mary Collett Ferrar and her family sliced apart printed Bibles and pasted the pieces back together into elaborate collages known as “Harmonies”; the domestic printing atelier of Edward Benlowes, a gentleman poet and Royalist who rode out the Civil Wars by assembling boutique books of poetry; and the nomadic collections of John Bagford, a shoemaker-turned-bookseller who foraged fragments of old manuscripts and title pages from used bookshops to assemble a material history of the book. Working across a century of upheaval, when England was reconsidering its religion and governance, each of these individuals saved the frail, fragile, frangible bits of the past and made from them new constellations of meaning. These fragmented assemblages resist familiar bibliographic and literary categories, slipping between the cracks of disciplines; later institutions like the British Library did not know how to collate or catalogue them, shuffling them between departments of print and manuscript. Yet, brought back together in this hybrid history, their scattered remains witness an emergent early modern poetics of care and curation, grounded in communities of practice. Stitching together new work in book history and media archaeology via digital methods and feminist historiography, Cut/Copy/Paste traces the lives and afterlives of these communities, from their origins in early modern print cultures to the circulation of their work as digital fragments today. In doing so, this project rediscovers the odd book histories of the seventeenth century as a media history with an ethics of material making—one that has much to teach us today.
    1. original recordings of the theorists at that 1966 structuralism conference.“For years, everyone had said ‘there’s got to be recordings of those lectures.’ Well, we finally found the recordings of those lectures. They were hidden in a cabinet behind a bookshelf behind a couch,” said Liz Mengel, associate director of collections and academic services for the Sheridan Libraries at Johns Hopkins.

      Have these been transferred? Can we get them?

  12. Oct 2023
    1. Petersen, B. K. et al. Deep symbolic regression: recovering mathematical expressions from data via risk-seeking policy gradients. In International Conference on Learning Representations (2020).

      Description: Reinforcement learning uses neural networks to generate a mathematical expression sequentially by adding mathematical symbols from a predefined vocabulary and using the learned policy to decide which notation symbol to be added next. The mathematical formula is represented as a parse tree. The learned policy takes the parse tree as input to determine what leaf node to expand and what notation (from the vocabulary) to add.

    2. Reinforcement learning uses neural networks to generate a mathematical expression sequentially by adding mathematical symbols from a predefined vocabulary and using the learned policy to decide which notation symbol to be added next140. The mathematical formula is represented as a parse tree. The learned policy takes the parse tree as input to determine what leaf node to expand and what notation (from the vocabulary) to add

      very interesting approach

    3. In chemistry, models such as simplified molecular-input line-entry system (SMILES)-VAE155 can transform SMILES strings, which are molecular notations of chemical structures in the form of a discrete series of symbols that computers can easily understand, into a differentiable latent space that can be optimized using Bayesian optimization techniques (Fig. 3c).

      This could be useful for chemistry research for robotic labs.

    4. Neural operators are guaranteed to be discretization invariant, meaning that they can work on any discretization of inputs and converge to a limit upon mesh refinement. Once neural operators are trained, they can be evaluated at any resolution without the need for re-training. In contrast, the performance of standard neural networks can degrade when data resolution during deployment changes from model training.

      Look this up: anyone familiar with this? sounds complicated but very promising for domains with a large range of resolutions (medical-imaging, wildfire-management)

    1. sRNAs that repress transcription have been engineered to create orthogonal and composable regulators that can be used to construct RNA-only transcriptional networks
  13. Sep 2023
    1. Adler, Mortimer J., and Charles Van Doren. How to Read a Book. Revised and Updated edition. 1940. Reprint, New York: Simon & Schuster, 1972.

      Progress

      • Started reading on 2021-07-28 at 1:26 PM
      • Read through chapter 6 on 2022-11-06 at 1:40 PM

      Annotation URL: urn:x-pdf:47749dd5c860ea4a9b8749ab77a009da<br /> Annotation search

  14. Aug 2023
    1. It’s called the reAct paper, and it describes another one of these prompt engineering tricks. You tell a language model that it has the ability to run tools, like a Google search, or to use a calculator. If it wants to run them, it says what it needs and then stops. Then your code runs that tool and pastes the result back into the model for it to continue processing.

      I use this approximate pattern a lot, I didn't realize it had a name and a paper! Need to check that out.

    1. Wardrip-Fruin, Noah, and Nick Montfort, eds. The New Media Reader. MIT Press, 2002. https://mitpress.mit.edu/9780262232272/the-new-media-reader/.

      Detlef Stern (@t73fde@mastodon.social) (accessed:: 2023-08-23 12:55:47)

      Eines der wunderbarsten Bücher, die ich in letzter Zeit studierte: "The New Media Reader". Sowohl inhaltlich (grundlegende Texte von 1940-1994, Borges, Bush, Turing, Nelson, Kay, Goldberg, Engelbart, ... Berners-Lee), als auch von der Liebe zum herausgeberischem Detail (papierne Links, Druckqualität, ...). Nicht nur für #pkm und #zettelkasten Fanatiker ein Muss. Man sieht gut, welchen Weg wir mit Computern noch vor uns haben. https://mitpress.mit.edu/9780262232272/the-new-media-reader/

    1. the 2009 publication of the influential text The Spirit Level by epidemiologists Richard Wilkinson and Kate Pickett
  15. Jul 2023
  16. Jun 2023
    1. Computational studies that analyzed HGT events among bacterial genomes revealed that HGT frequency positively and strongly correlates with the similarity of tRNA pools between donors and acceptors
  17. May 2023
    1. https://pressbooks.pub/illuminated/

      A booklet prepared for teachers that introduces key concepts from the Science of Learning (i.e. cognitive neuroscience). The digital booklet is the result of a European project. Its content have been compiled from continuing professional development workshops for teachers and features evidence-based teaching practices that align with our knowledge of the Science of Learning.

  18. Apr 2023
    1. Want to read: How Romantics and Victorians Organized Information by Jillian M. Hess 📚

      https://kimberlyhirsh.com/2023/04/28/want-to-read.html

      👀 How did I not see this?!?? 😍 Looks like a good follow up to Ann Blair's Too Much to Know (Yale, 2010) and the aperitif of Simon Winchester's Knowing What We Know (Harper) which just came out on Tuesday. 📚 Thanks for the recommendation Kimberly!

    1. Zhao briefly describes Cal Newport's Questions, Evidence, Conclusions (QEC) framework which she uses as a framework for quickly annotating books and then making notes from those annotations later.

      How does QEC differ from strategies in Adler/Van Doren?

  19. Mar 2023
    1. Müller, A., and A. Socin. “Heinrich Thorbecke’s Wissenschaftlicher Nachlass Und H. L. Fleischer’s Lexikalische Sammlungen.” Zeitschrift Der Deutschen Morgenländischen Gesellschaft 45, no. 3 (1891): 465–92. https://www.jstor.org/stable/43366657

      Title translation: Heinrich Thorbecke's scientific estate and HL Fleischer's lexical collections Journal of the German Oriental Society

      ... wrote a note. There are about forty smaller and larger card boxes , some of which are not classified, but this work is now being undertaken to organize the library. In all there may be about 100,000 slips of paper; Of course, each note contains only one ...

      Example of a scholar's Nachlass which contains a Zettelkasten.

      Based on this quote, there is a significant zettelkasten example here.

    1. Noteworthy for its longstanding influence is thebook “Nonparametric statistics for the behavioralsciences” by Siege

      Highly cited book from 1956!

      Siegel (1956) pointed out that traditional parametric tests should not be used with extremely small samples, because these tests have several strong assumptions underlying their use. The t-test requires that observations are drawn from a normally distributed population and the two-sample t-test requires that the two populations have the same variance. According to Siegel (1956), these assumptions cannot be tested when the sample size is small. Siegel (1957) stated that “if samples as small as 6 are used, there is no alternative to using a nonparametric statistical test unless the nature of the population distribution is known exactly” (p. 18).

    1. Recently, redox-responsive biomolecules such as phenazines have been used in several electrochemical strategies to interrogate a range of biological activities30,31 and to control gene expression in living cells32,33, where the redox status of the biomolecules could be measured or manipulated by application of electronic potentials
    1. The genre kicked off with “Maps of Time” (2004), by David Christian, and includes such practitioners as Mr. Harari, Steven Pinker, Jared Diamond and Francis Fukuyama.

      Books similar to "Guns, Germs and Steel"

  20. takingnotenow.blogspot.com takingnotenow.blogspot.com
    1. Not sure why Manfred Kuehn removed this website from Blogger, but it's sure to be chock full of interesting discussions and details on his note taking process and practice. Definitely worth delving back several years and mining his repository of articles here.

      http://takingnotenow.blogspot.com/<br /> archive: https://web.archive.org/web/20230000000000*/http://takingnotenow.blogspot.com/

  21. Feb 2023
    1. Ramsay, J. P. & Firth, N. Diverse mobilization strategies facilitate transfer of non-conjugative mobile genetic elements. Curr. Opin. Microbiol. 38, 1–9 (2017)

      Read this - to figure out, how often do plasmids with OriT but no relaxase occur?

      Context :

      Further, numerous small plasmids do not encode for relaxases and undergo transfer by exploiting the relaxosome of other conjugative elements in trans85,6

    1. Simultaneously, it showcases how little actually has changed with therise of digital platforms, where some scholars have sought to build software edifices toemulate card index systems or speak of ‘paper-based tangible interfaces’ for research(Do ̈ring and Beckhaus, 2007; Lu ̈decke, 2015).

      Döring, T. and Beckhaus, S. (2007) ‘The Card Box at Hand: Exploring the Potentials of a Paper-Based Tangible Interface for Education and Research in Art History’. Proceedings of the First International Conference on Tangible and Embedded Interaction, Baton Rouge, Louisiana, February 15-17, 2007. New York, ACM, pp. 87–90.

      Did they have a working system the way Ludeke did?

    2. (Boyd, 2013; Burke, 2014; Krajewski, 2011: 9-20, 57; Zedel-maier, 2002)

      Most of these are on my list, but doublecheck them...

    3. in 1917 he celebrated his fifty-thousandth card with an article titled ‘Siyum’, referencing the celebration upon conclud-ing study of a tractate of Talmud (Deutsch, 1917b).

      Did he write about his zettelkasten in this article?! Deutsch, G. (1917b) ‘Siyum’, American Israelite, 8 March, 15 March.


      Gotthard Deutsch celebrated his fifty thousandth card in 1917. ᔥ