958 Matching Annotations
  1. Mar 2024
  2. Feb 2024
    1. for - adjacency - microscopic biology - macroscopic ecology - multi-scale competency architecture - Michael Levin - Jonas Wickman - micro-to-macro

      paper details - title - Eco-evolutionary emergence of macroecological scaling in plankton communities - author - Jonas Wickman - Elena Litchman - date - feb 15, 2024 - publication - Science VOL. 383, NO. 6684

      reference - https://www.science.org/doi/10.1126/science.adk6901

      summary - This is a very interesting finding that links rules in the micro world to behavior in the macro. - It is relevant to Michael Levin's research on multi-scale competency architecture

      question - how would this impact the micro relations between - the microscopic world of humans - the normal macroscopic world of humans

    1. Dubbed “litigation terrorism” by Joseph Stiglitz, the Nobel prize-winning economist. ISDS is a corporate tribunal system

      for - litigation terrorism - ISDS - corporate tribunal system - Michael Levin - multi-scale competency architecture - example - adjacency - evolutionary biology - corporate law - climate crisis

      adjacency - between - corporate law - climate crisis - evolutionary biology - cultural evolution - adjacency statement - Biologist Michael Levin's multi-scale competency architecture of evolutionary biology seems to apply here - in the field of corporate law - Corporations can be viewed as one level of a social superorganism in a cultural evolution process - Governments can be viewed similiarly, but at a higher level - The ISDS is being weaponized by the same corporations destroying the global environment to combat the enactment of government laws that pose a threat to their livelihood - Hence, the ISDS has been reconfigured to protect the destroyers of the environment so that they can avoid dealing with their unacceptable externalizations - The individual existing at the lower level of the multi-scale competency architecture(the corporation) is battling to survive against the wishes of the higher level individual (the government) in the same multi-scale competency architecture

  3. Jan 2024
    1. for - multi scale competency architecture - Michael Levin - evolutionary biology - rapid whole system change - adjacency - multi scale competency architecture - rapid whole system change - stop reset go - Deep Humanity - Indyweb - Indranet - major evolutionary transition in individuality - MET - superorganism - cumulative cultural evolution of individuality

      adjacency - between - multi scale competency architecture - rapid whole system change - progress trap - stop reset go - Deep Humanity - Indyweb - Indranet - major evolutionary transition in individuality - MET - superorganism - cumulative cultural evolution of individuality - adjacency statement - The idea of multi scale competency architecture can be extended to apply to the cultural level. - in the context of humanity's current existential poly /meta/ perma crisis, - rapid whole system change - (a cultural behavioural paradigm shift) - is required within a few short years - to avoid the worst impacts of - catastrophic, - anthropogenic - climate change, which is entangled with a host of other earth system boundary violations including - biodiversity loss - fresh water scarcity - - the driver of evolution through major evolutionary transitions in individuality has given rise to the level of cultural superorganisms that include all previous levels - progress and its intended consequences of progress traps play a major role in determining the future evolutionary trajectory of our and many other species - our species is faced with a few choice permutations in this regard: - individually regulate behaviour aligned with a future within earth system boundaries - collectively regulate behaviour aligned with a future within earth system boundaries - pursue sluggish green growth / carbon transition that is effectively tinkering at the margins of rapid whole system change - BAU - currently, there doesn't appear to be any feasible permutation of any of the above choices - There is insufficient worldview alignment to create the unity at scale for report whole system change - individual incumbent state and corporate actors still cling too tightly to the old, destructive regime, - creating friction that keeps the actual rate of change below the required - Stop Reset Go, couched within the Deep Humanity praxis and operationalized through the Indyweb / Indranet individual / collective open learning system provides a multi-dimensional tool for a deep educational paradigm shift that can accelerate both individual and collective upregulation of system change

    1. for - healthy eating - Dr. William Li - nutrition - healthy food - inflammation - angiogenesis

      summary - A good interview about human health and healthy diet. William Li begins by talking about angiogenesis as a key aspect of human health - and how pathology of angiogenesis is at the root of many major diseases. - The interviewer then asks Dr. Li about the connection between another keystone disease, and angiogenesis. - Dr. Li then describes some healthy foods and good dietary practices including extra virgin olive oil.

      adjacency - between - angiogenesis - inflammation - Micheal Levine's work - evolutionary biology - adjacency statement - they all seem related, as evolutionary biology has created legacy subsystems within the human body

  4. Dec 2023
      • annotate
      • for: evolutionary biology, big history, DH, Deep Humanity, theories of consciousness, ESP project, Earth Species Project, Michael Levin, animal communication, symbiocene

      • title: The Deep History of Ourselves: The Four-Billion-Year Story of How We Got Conscious Brains

      • author: Joseph LeDoux
      • date: Jan. 2023
      • doi: 0.1080/09515089.2022.2160311

      • ABSTRACT

        • The essence of who we are depends on our brains.
        • They enable us to think, to
          • feel joy and sorrow,
          • communicate through speech,
          • reflect on the moments of our lives, and to
            • anticipate,
            • plan for, and
            • worry about our imagined futures.
        • Although some of our abilities are comparatively new, key features of our behavior have deep roots that can be traced to the beginning of life.
        • By following the story of behavior, step-by-step, over its roughly four-billion-year trajectory,
          • we come to understand both
            • how similar we are to all organisms that have ever lived, and
            • how different we are from even our closest animal relatives.
        • We care about our differences because they are ours. But differences do not make us superior; they simply make us different.
      • comment

        • good article to contribute to a narrative of the symbiocene and a shift of humanity to belonging to nature as one species, instead of dominating nature as the apex species
      • question
        • @Gyuri, Could indranet search algorithm have made the connection between this article and the symbiocene artilces in my mindplex had I not explicitly made the associations manually through my tags? It needs to be able to do this
      • Also interesting to see how this materialistic outlook of consciousness
        • which is similiar to the Earth Species Project work and Michael Levin's work on synthesizing new laboratory life forms to answer evolutionary questions about intelligence
      • relates to nonmaterial ideas about consciousness
  5. Nov 2023
    1. 19:00 people teach personality at coaching, but it fails; what scales is biology, not personality

      • see idea on how copy/pasting from someone else doesn't work
  6. Oct 2023
      • for: sensory ecology, conservation biology, adjacency, adjacency - sensory ecology - conservation biology, anthropogenic sensory pollutants

      • title: Why conservation biology can benefit from sensory ecology

      • author Davide M. Dominoni et al.
      • date: Mar. 2020
      • abstract
        • Global expansion of human activities is associated with the introduction of novel stimuli, such as
          • anthropogenic noise,
          • artificial lights and
          • chemical agents.
        • Progress in documenting the ecological effects of sensory pollutants is weakened by sparse knowledge of the mechanisms underlying these effects.
        • This severely limits our capacity to devise mitigation measures.
        • Here,we integrate knowledge of animal
          • sensory ecology,
          • physiology and
          • life history
        • to articulate three perceptual mechanisms—
          • masking,
          • distracting and
          • misleading
        • that clearly explain how and why anthropogenic sensory pollutants impact organisms.
        • We then
          • link these three mechanisms to ecological consequences and
          • discuss their implications for conservation.
        • We argue that this framework can reveal the presence of ‘sensory danger zones’, hotspots of conservation concern
          • where sensory pollutants overlap in space and time with an organism’s activity, and
          • foster development of strategic interventions to mitigate the impact of sensory pollutants.
        • Future research that applies this framework will provide critical insight to preserve the natural sensory world.
  7. Sep 2023
    1. Another feature of this vision that aligns well with Buddhist ideas is the lack of a permanent, unique, unitary Self [68]. The picture given by the evolutionary cell-biological perspective is one where a cognitive agent is seen as a self-reinforcing process (the homeostatic loop), not a thing [69,70,71].
      • for: illusory self, non-self, lack of self, organism - as process, human INTERbeCOMing, bio-buddhism, biology - buddhism
      • for: Michael Levine, developmental biology, human superorganism, multi-scale competency architecture, eukaryote multi-cellular superorganism - interlevel communication, interoception

      • definition: multi-scale competency architecture

        • a complex living organism is not simply nested structurally in terms of cells which comprise tissues, comprising organs, and bodies, and then ultimately societies. Each of these layers has certain problem-solving competencies.
      • comment

        • The HUMAN interBEcomING is a multi-level system.
        • It would be insightful to learn if there are ways our human consciousness level can communicate to each level, including the social level
      • future work
        • literature review of research on specific areas related to the level of human consciousness communicating with other levels of the superorganism
          • perhaps called "interlevel communication of multi-level superorganism
          • interoception signals?
  8. Aug 2023
    1. Capra Biosciences harnesses the superpowers of a biofilm-forming organism Marinobacter atlanticus to make fat-soluble products like retinol which is used in anti-aging face creams, and high-end industrial lubricants for electric car engines
    2. Some startups, like MicroByre, have been working to domesticate those reluctant, recalcitrant, and rebellious microbes by adapting them for use in the lab and creating genetic tools to manipulate them
  9. Jul 2023
    1. Biology used to be considered taxonomy and dissection, like listing and looking at. But now biology, modern biology, is a molecular science.

      What is modern biology... a vast and eclectic field composed of many specialized disciplines that study the structure, function, growth, distribution, evolution, or other features of living organisms.

    1. The notion of functional integration as a basis for biological identity was fully developed only in the 19th century, where it was transformed by the rise of both cell and evolutionary theory. Herbert Spencer
      • Herbert Spencer fully developed Digby's concept into the modern concept of functional integration
        • Spencer introduced the term "survival of the fittest"
        • ‘He tried to unite complex new findings about metabolism and organismic development with evolution and the seeming correspondence of organisms to their environments.
          • In The Principles of Biology (1864), Spencer wrote
            • a biological individual is one in which
            • the interdependence of the parts allows it to function and
            • respond to environmental change as a whole.
          • That is: ‘any concrete whole having a structure which enables it,
            • when placed in appropriate conditions,
        • to continuously adjust its internal relations to external relations, - so as to maintain the equilibrium of its functions.’
  10. Jun 2023
    1. Found this webpage for a 3D brain model when someone (maybe frymatic?) mentioned a region of the brain I was having trouble imagining.

  11. May 2023
  12. Apr 2023
  13. Mar 2023
    1. Review coordinated by Life Science Editors.

      Reviewed by: Dr. Helen Pickersgill, Life Science Editors

      Potential Conflicts of Interest: None

      Main point of the paper: By combining multiple stains and antibodies with ultrastructural expansion (light) microscopy in Plasmodium falciparum during the course of mitosis within red blood cells (the asexual blood stage), when it causes the symptoms of malaria, the authors identified new structural features of cell division in this important human parasite.

      Why this is interesting: Imaging the dramatic physical events that occur when cells divide tells us a lot about the biology of the process and is insightful to compare between different eukaryotes, but many organisms are too small to visualise by light microscopy, which is the most versatile imaging technique. So, they used an existing preparation technique to enlarge the parasites, a wide array of dyes and antibodies, and sampled at multiple timepoints so that more intracellular structures could be visualised and their behaviour and potential functions in cell division revealed.

      Background: Expansion microscopy (ExM) has been around since 2015 (doi: 10.1126/science.1260088) and is a fairly simple and affordable technique. It involves physically magnifying a specimen by embedding it in a polyelectrolyte gel that swells up in water enabling super-resolution imaging. It has been previously applied to Plasmodium and other Apicomplexa, but not with so many different labels across different timepoints at this important life-stage.

      Results: • They imaged 13 subcellular structures (including microtubules, microtubule organising centres, apicoplasts, Golgi and the ER) at multiple timepoints covering the entire asexual blood stage. • Among many results were the following: • They found a central role for the nuclear MTOC in coordinating mitosis and likely in establishing apical-basal polarity early during the asexual cycle. o the MTOC is tethered to the parasite plasma membrane (via cytoplasmic extensions) throughout mitosis. o the cytoplasmic extensions of the MTOC were closely associated (in numbers and positions) with several apical structures including the Golgi and the basal complex. o the MTOC is tethered to the mitochondria and apicoplast during fission and may also regulate their copy numbers. • They performed the first detailed characterization of the short-lived interpolar spindles, previously difficult to visualize, which consist of microtubules connecting duplicated MTOCs as they move to opposite sides of the cell. They found a large variation in their size, which may be how they enable the MTOCs to move without detaching from the plasma membrane. • They were able to study the biogenesis of rhoptries, which secrete proteins required for the parasite to invade host red blood cells, and discovered that: o biogenesis begins earlier than thought and that they associate with MTOCs during the remaining rounds of mitosis. o Rhoptry pairs are likely synthesized independently because over 95% are different sizes and densities.

      Remaining thoughts: • Clearly written and easy to read paper with stunning images. • Comprehensive (including descriptions of when things didn’t work), but remains largely descriptive (of course). • Could be shortened/sharpened to make it more manageable to read without losing the main messages, which are somewhat lost in the text. • A top-level, specialised paper that opens the door for more targeted studies of organelle functions during mitosis and comparisons of these functions with other (higher) eukaryotes. • By identifying key players in mitosis during the asexual blood stage it may reveal candidate therapeutic targets for treating malaria.

    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
  14. Feb 2023
    1. Review coordinated by Life Science Editors

      Reviewed by: Dr. Helen Pickersgill, Life Science Editors

      Potential Conflicts of Interest: None

      Impact Point: Transcription factors may mediate the release of specific genes in extracellular vesicles that could be taken up by other cells and directly influence their behaviour.

      Background: Extracellular vesicles (EVs) are nanoscale, membrane-bound vesicles containing proteins, nucleic acids and lipids that are released by most cell types. Originally thought of as a cell waste disposal mechanism, they have since been rebranded as a means of intercellular communication, both short and long range, (like a cellular postal service), and can, for example, modify gene expression and function in recipient cells via the transfer of specific RNAs (DOI: 10.1038/s41580-020-0251-y). One interesting function for EVs was the recent discovery that antigen presenting cells (APCs) could donate telomeres via EVs to recipient T cells and rescue them from senescence (DOI: 10.1038/s41556-022-00991-z).

      Given EVs contain a wide variety of cargos derived from the secreting cells, which have been extensively profiled (e.g., DOI: 10.1016/j.cell.2020.07.009) they are particularly interesting as sources of biomarkers for diagnosing diseases such as cancer (e.g., DOI: 10.1038/s12276-019-0219-1). We might also be able to use them as stable delivery mechanisms for controlling cell behaviour or targeting therapeutics/diagnostics.

      We know quite a bit about how RNAs and proteins are selected for secretion by EVs (mediated by the autophagy protein LC3: e.g., DOIs: 10.1080/15548627.2020.1756557; 10.1038/s41556-019-0450-y). But little is known about DNA. DNA presents a particular challenge as it is packed up into the nucleus. This is also particularly important to understand in the context of horizontal gene transfer, i.e., passing functional genes between cells.

      Main question: How does a cell ‘select’ specific DNA cargo from the nucleus and enable it to be released by EVs?

      The advance: They discover that a transcription factor (FOXM1) plays a central role in mediating DNA release in EVs.

      Results: • FOXM1 and LC3 (autophagy protein) colocalize and interact in cultured cells (coIP endogenous and exogenous, EMSA, immunostaining and identify an FOXM1-binding domain mutant). • FOXM1, LC3 and DNA colocalise in the cytoplasm in cultured cells, which increases upon starvation-induced autophagy (immunofluorescence). • FOXM1 and LC3 are found in EVs released from cultured cells (Western blot). • 15,544 DNA identified in EVs released from cultured cells (evDNA sequencing), of which 25 overlapped with DNA loci binding FOXM1 (ChIP). • FOXM1-bound nuclear DNA is transported to the cytoplasm upon induction of autophagy and is released in EVs in cultured cells (knock-in tagged chromatin with CRISPR-cas9, IF and PCR). This is dependent on FOXM1 (knock-out in cultured cells).

      Significance: Transcription factors display strong DNA binding specificity and so are ideal candidates for directing specific genes into EVs for potential transfer to recipient cells.

      Remaining questions/points: Care needs to be taken with regard to purification of EVs. Are the FOXM1-DNAs in the EVs functional in recipient cells? Is the DNA being actively ‘selected’ for an intercellular signalling purpose or is this just random degradation? Is it all FOXM1 bound DNA that has the potential to be trafficked to EVs or just a subset? Do other transcription factors have the same function or is it specific to this protein/family? Does this mechanism occur in other contexts (e.g., in vivo, under disease conditions).

    1. Review coordinated by Life Science Editors.

      Reviewed by: Dr. Angela Andersen, Life Science Editors

      Potential Conflicts of Interest: Dr. Mill has worked with Life Science Editors on other manuscripts.

      Background: Retinitis pigmentosa (RP) is a group of rare eye diseases that cause vision loss. Symptoms usually start in childhood, and most people eventually lose most of their sight. There is no cure for RP. Mutations in retinitis pigmentosa GTPase regulator (RPGR) cause RP and compromise the renewal of light-sensitive “disc” membranes (specialized cilia) at the outer segment of photoreceptors, resulting in the loss of these cells over time. Evidence suggests that disc formation is similar to the release of ectosomes (small extracellular vesicles) and that both rely on the actin cytoskeleton. Knockdown of RPGR in retinal pigmented epithelium cells showed stronger actin filaments and reduced cilia suggesting that it may regulate nascent photoreceptor disc formation by regulating actin-mediated membrane extension in the retina (Gakovic et al., Human Molecular Genetics, 2011). In addition, RPGR patient iPSC-retinal models displayed phenotypes consistent with abnormal actin regulation (Megaw et al., Nature Communications, 2017; Karam et al., J Personalized Medicine, 2022).

      Question: What function of RPGR is compromised in photoreceptors to cause RP?

      Advance: The authors generated novel Rpgr mutant mice harboring human disease-causing mutations that recapitulate human disease phenotypes: aborted membrane shedding as ectosome-like vesicles, photoreceptor death and visual loss. RPGR is located at the site of disc formation – to test if it plays a role in disc genesis, they engineered a novel reporter mouse to track outer segment turnover. Rhodopsin was tagged with the self-labelling peptide SNAP- Rhodopsin is the major protein component of outer segment discs, and so incubating RhodSNAP retinal slice cultures with SNAP fluorophores results in outer segment labelling. Perturbation of RPGR resulted in a slowed rate of disc formation, leading to shortened outer segments and increased vesicle shedding. To me, the breakthrough is in the last figure: the actin depolymerizing drug Cytochalasin D in PBS was injected intravitreally, and fixed retinas were analyzed 6 hours later by electron microscopy. Cytochalasin D treatment significantly reduced the number of shed vesicles from the base of the outer segment in Rpgr-mutant mice (they now look like wild-type).

      Significance: Nails down the disease-relevant function of RPGR and a molecular mechanism of RP in photoreceptor cells, in vivo, in mice. Pharmacological rescue not only demonstrates the importance of the mechanism to disease but also sheds light on a potential therapeutic avenue for RP.

    1. I really highly recommend Robert Hazen's _Story of Earth_ [1] if you're into this sort of stuff. Highly knowledgeable and entertaining geologist argues that the geosphere and the biosphere should really be viewed as one co-evolving system, over deep time. There are thousands of species of minerals that can only exist because of the action of life, and those minerals in turn enable new forms of life, which enable new species of mineral, and so on in a complex and ever evolving system within which we exist for only a fraction of an instant.[1] https://www.amazon.com/Story-Earth-Billion-Stardust-Living/d...

      .

  15. Jan 2023