814 Matching Annotations
  1. Last 7 days
  2. Feb 2024
  3. 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.

  4. 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

  5. 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?

  6. 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
  7. 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.


      • 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

  8. 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
  9. Jul 2023
  10. 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
  11. 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.

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


      👀 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?

  13. 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"

  14. 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/

  15. 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

    1. Historically, bacterial evolution has favored two general ecological growth strategies: high reproduction rate (r-strategists or copiotrophs) or optimal resource utilization (K-strategists or oligotrophs)(Atlas and Bartha, 1997)

      Has evolution favoured these or is this an artifact of our categorization in extremes/ the parameters we are looking at? If you look at another dimension you could get more categories maybe?

    1. A Luhmann web article from 2001-06-30!

      Berzbach, Frank. “Künstliche Intelligenz aus Holz.” Online magazine. Magazin für junge Forschung, June 30, 2001. https://sciencegarden.net/kunstliche-intelligenz-aus-holz/.

      Interesting to see the stark contrast in zettelkasten method here in an article about Luhmann versus the discussions within the blogosphere, social media, and other online spaces circa 2018-2022.

      ᔥ[[Daniel Lüdecke]] in Arbeiten mit (elektronischen) Zettelkästen at 2013-08-30 (accessed:: 2023-02-10 06:15:58)

    1. Mattei, Clara E. The Capital Order: How Economists Invented Austerity and Paved the Way to Fascism. Chicago, IL: University of Chicago Press, 2022. https://press.uchicago.edu/ucp/books/book/chicago/C/bo181707138.html.

      I've always wondered why the United States never used the phrase austerity to describe political belt tightening.

    1. M. G. Marmot, G. Rose, M. Shipley, P. J. Hamilton, Employment grade and coronary heart disease in British civil servants.J. Epidemiol. Community Health32,244–249 (1978).7R. M. Sapolsky, The influence of social hierarchy on primate health.Science308, 648–652 (2005)

      Want to read with respect to https://hypothes.is/a/hFZ1mqTgEe2MHU8Jfedg_A

    2. Kawakatsu et al. (1) make an important ad-vance in the quest for this kind of understanding, pro-viding a general model for how subtle differences inindividual-level decision-making can lead to hard-to-miss consequences for society as a whole.Their work (1) reveals two distinct regimes—oneegalitarian, one hierarchical—that emerge fromshifts in individual-level judgment. These lead to sta-tistical methods that researchers can use to reverseengineer observed hierarchies, and understand howsignaling systems work when prestige and power arein play.

      M. Kawakatsu, P. S. Chodrow, N. Eikmeier, D. B. Larremore, Emergence of hierarchy in networked endorsement dynamics. Proc. Natl. Acad. Sci. U.S.A. 118, e2015188118 (2021)

      This may be of interest to Jerry Michalski et al.

    1. maths historian George Joseph’s book The Crest of the Peacock: Non-European Roots of Mathematics (1991) and the ongoing encyclopaedic series Science Across Cultures, edited by Helaine Selin
  16. Jan 2023
    1. It was Eric Williams (Capitalism and Slavery) who first developed the idea thatEuropean slave plantations in the New World were, in effect, the first factories; theidea of a “pre-racial” North Atlantic proletariat, in which these same techniques ofmechanization, surveillance, and discipline were applied to workers on ships, waselaborated by Peter Linebaugh and Marcus Rediker (The Many-Headed Hydra).

      What sort of influence did these sorts of philosophy have on educational practices of their day and how do they reflect on our current educational milieu?

    1. the use of constructed wetlands to generate cellulosic biofuel using waste nitrogen from wastewater treatment
    1. Aglavra · 1 day agoNo, but I'm currently reading A place for everything https://www.goodreads.com/book/show/51770484-a-place-for-everything , which seems to be on similar topic - evolution of information management in the past.

      Flanders, Judith. A Place For Everything: The Curious History of Alphabetical Order. Main Market edition. London: Picador, 2021.

    1. Achille Mbembe’s recent essay‘‘Decolonizing the University: New Direc-tions’’ (2016), which urges attention to thelarge and difficult intellectual questionsinvolved in the reform project.


  17. Dec 2022
    1. The work of the late Elinor Ostrom, who was awarded the Nobel Prize in Economic Sciences in 2009, points to the fallacy of this assumption. Her Nobel Prize lecture is titled “Beyond Markets and States: Polycentric Governance of Complex Economic Systems.” Ostrom’s research focused on the organization of what she called “common pool resources.” To pick a prominent example, the free-for-all dumping of carbon into the air could be considered a degradation of the common pool resource of our global atmosphere, resulting in climate change. Among her conclusions: more often than not, effective resource management solutions come from the bottom rather than the top. Ostrom also argued that “a core goal of public policy should be to facilitate the development of institutions that bring out the best in humans.”20


    1. https://borretti.me/article/unbundling-tools-for-thought

      He covers much of what I observe in the zettelkasten overreach article.

      Missing is any discussion of exactly what problem he's trying to solve other than perhaps, I want to solve them all and have a personal log of everything I've ever done.

      Perhaps worth reviewing again to pull out specifics, but I just don't have the bandwidth today.