503 Matching Annotations
  1. Last 7 days
  2. May 2021
  3. Apr 2021
    1. theoretical biologist

      This field is not well recognized, but hopefully this situation will change!

    1. Once established, however, it spreads slowly. Unlike aggressive Kentucky bluegrass, which spreads by underground stems called rhizomes, perennial ryegrass is a bunch-forming grass. Like tall fescue, it naturally grows in clumps and spreads through vertical shoots known as tillers, rather than spreading by rhizomes or horizontal above-ground stems, known as stolons.
  4. Mar 2021
    1. As well as the discussion about what is really meant by a ‘domain of one’s own‘

      Societies have been inexorably been moving toward interdependence. More and more people specialize and sub-specialize into smaller fragments of the work that we do. As a result, we become more interdependent on the work of others to underpin our own. This makes the worry about renting a domain seem somewhat disingenuous, particularly when we can reasonably rely on the underlying structures to work to keep our domains in place.

      Perhaps re-framing this idea may be worthwhile. While it may seem that we own our bodies (at least in modern liberal democracies, for the moment), a large portion of our bodies are comprised of bacteria which are simultaneously both separate and a part of us and who we are. The symbiosis between people and their bacteria has been going on so long and generally so consistently we don't realize that the interdependence even exists anymore. No one walks around talking about how they're renting their bacteria.

      Eventually we'll get to a point where our interdependence on domain registrars and hosts becomes the same sort of symbiotic interdependence.

      Another useful analogy is to look at our interdependence on all the other pieces in our lives which we don't own or directly control, but which still allow us to live and exist.

      People only tend to notice the major breakdowns of these bits of our interdependence. Recently there has been a lot of political turmoil and strife in the United States because politicians have become more self-centered and focused on their own needs, wants, and desire for power that they aren't serving the majority of people. When our representatives don't do their best work at representing their constituencies, major breakdowns in our interdependence occur. We need to be able to rely on scientists to do their best work to inform politicians who we need to be able to trust to do their best work to improve our lives and the general welfare. When the breakdown happens it creates issues to the individual bodies that make up the society as well as the body of the society itself.

      Who's renting who in this scenario?

  5. Feb 2021
    1. Fredericks DN, & Relman DA (1996). Sequence-based identification of microbial pathogens: a reconsideration of Koch’s postulates. Clinical microbiology reviews, 9 (1), 18-33 PMID: 8665474

      Repostulation of Koch's rules in the era of the virueses.

  6. Jan 2021
    1. Proteins are made up of building blocks called amino acids. N501Y means that the 501st amino acid was originally an N, which stands for the amino acid asparagine, but has been changed to a Y, which stands for tyrosine.

      The takeaway: Amino acids, represented by single letters such as N or Y make up proteins which are part of the coronavirus (as well as other biology such as animals, plants, microorganisms, etc.). Mutations are written with the original amino acid letter followed by the number of the amino acid and the new amino acid letter.

      The claim: Proteins are made up of building blocks called amino acids. N501Y means that the 501st amino acid was originally an N, which stands for the amino acid asparagine, but has been changed to a Y, which stands for tyrosine.

      The evidence:

      Coronavirus is made up of greater than 20 proteins (1). The spike protein helps coronavirus attach and enter human cells which leads to infection and disease (1). The spike protein on SARS-CoV-2, the virus that causes COVID-19, is the target of many antibodies produced by the human body to fight the SARS-CoV-2 infection (2). Changes in the spike protein sequence may necessitate a change in the human immune system to produce antibodies which stop SARS-CoV-2 from infecting human cells. Changes in the amino acid sequence are written as was stated in the claim: original amino acid, number of the amino acid in the sequence, new amino acid.


      1) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7247499/

      2) https://pubmed.ncbi.nlm.nih.gov/33448402/

    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. Johnson: Earlier I interviewed you about patrilocal residence patterns and how that alters women’s sexual choices. In contrast, matrilocal societies are more likely to be egalitarian. What are the factors that lead to the differences between these two systems?Hrdy: I think in societies where women have more say, and that does tend to be in societies that are matrilocal and with matrilineal descent or where, as it is among many small scale hunter-gatherers, you have porous social boundaries and flexible residence patterns. If I had to say what kind of residence patterns our ancestors had it would have been very flexible, what Frank Marlowe calls multilocal.

      Matrilocality, matrilinearity and egailitarianism.

  7. Nov 2020
    1. “Half of what you learned in college is wrong,” my biology professor, David Lange, once said. “Problem is, we don’t know which half.”

      Very interesting that a biology professor believes that 50% of what we learn can be wrong.

    1. Schleiss says a better analogy for COVID-19 is the mumps. For more than 45 years, we’ve had a very effective vaccine for measles, mumps, and rubella (which are also RNA viruses).

      The takeaway: Even though mutations happen in all virus, vaccines still work. Current evidence about SARS-CoV-2 indicates that an effective COVID-19 vaccine can be obtained, and that it should be able to provide immunity against the virus.

      The claim: A better analogy for COVID-19 is the mumps. For more than 45 years, we’ve had a very effective vaccine for measles, mumps, and rubella (which are also RNA viruses).

      The evidence: We are all imperfect and we all make mistakes. For a virus, a mistake means the introduction of a mutation in its sequence, and RNA viruses (like the flu, mumps, measles virus, and SARS-CoV-2) have the highest error rates in nature. Mutations are indispensable for viral survival and evolution; this property is believed to benefit the viral population, allowing it to adapt and respond to different complex environments encountered during spread between hosts, within organs and tissues, and in response to the pressure of the host immune response [1]. How fast a virus is changing can be estimated by measuring its mutation rate, and then they can be classified as changing fast – high mutation rate – like HIV or Influenza, or as stable, like measles or mumps virus. SARS-CoV-2 has a mutation rate three times slower than the flu virus [2], but it's still changing faster than the mumps virus (the mutation rate of influenza is more than 10 times higher than mumps) [3]. Of course, how fast a virus can change has implications in the efficacy of treatments and vaccines, but it's not the only determinant. Even though mutations happen in all viruses, vaccines still work. A great example is the measles virus, as the antigenic composition of the vaccine (the molecules that “wake up” the immune system) used to prevent it has remained efficient since it was developed, in the 1960s, and confers protection against the 24 circulating genotypes [4]. The same is true for the mumps virus, with a vaccine that has been efficient for many decades [5]. Sequencing data suggest that coronaviruses change more slowly than most other RNA viruses, probably because of a viral ‘proofreading’ activity that corrects all the copying mistakes [6]. Taken together, all this evidence indicates that an effective COVID-19 vaccine can be obtained, and that it should be able to provide lasting immunity against the virus.

      Sources:<br> 1

      2 SARS-CoV-2 mutation rate: 1.26 x 10-3 substitutions/site/year

      3 Influenza (flu-virus) mutation rate: 3.68 x 10-3 substitutions/site/year. Mumps mutation rate: 2.98 × 10−4 substitutions/site/year




    1. Manolis Kellis: Origin of Life, Humans, Ideas, Suffering, and Happiness | Lex Fridman Podcast #123

      My summary:


      • Life = energy + self preservation
      • Neanderthals could be the reason why wolves/dogs are living closely with humans. Maybe in the past generations, dogs had no choice but to live with humans as they were scared of our power?
      • People evolved from the deep ocean (we're made in 70% of water). We're like transporting the sea with us now
      • Dolphins as mammals came back into the water
      • RNA invented proteins. Later RNA and proteins created DNA
      • Life is like any kind of self-reinforcement such as self-reinforcement of RNA molecules which lead to the evolution process
      • Europa (moon of Jupiter) already evolves some non-DNA life there. Life could exist in its under-ice ocean, perhaps in an environment similar to Earth's deep-ocean hydrothermal vents. It will be fascinating to get to know it


      • Don't focus on goals but have a path to prevent the "rat race" sort of feeling
      • Almost every Hollywood movie has a happy ending. It prepares us, humans, really poorly for the bad times in life We need to read/watch more stories with a bad ending
      • Life is about accomplishing things, not about being happy all the time
      • As a parent, don't ask your kid if he's happy but what he's struggling to achieve
      • Most likely, we live on the best planet during the best time as the most beautiful mammals
      • If you understand yourself, you won't seek self-assurance in what other people think of you
      • It's hard to get to know your true self if you live all the time in the same location/environment and have the same friends who would like to have a stable image of you
  8. Oct 2020
    1. Ideas on how to analyze and predict network behavior have been informed by concepts arising from the computational and social sciences, which are themselves increasingly concerned with understanding networks. The interesting thing about these ideas is that they work at scales ranging from the molecular to the population level.

      scale free networks perhaps?

    2. I had bookmarked this article in the form of tearing out and keeping a paper copy of it in my to read pile back in 2008. Finally getting around to reading it today. It's still an interesting introduction to the broader area which has moved forward, but not significantly enough to date the entire area.