Using OSX Shortcuts to copy Perplexity.ai responses to markdown apps (Bear, Quarto)

productivity
artificial intelligence
Published

June 20, 2024

“I … am rarely happier than when spending an entire day programming my computer to perform automatically a task that would otherwise take me a good ten seconds to do by hand.”

Douglas Adams, Last Chance to See

I am trying to get into the habit of reading stuff in Bear app, so that I have a record of the stuff that I read and I can highlight things as I read them, so I can then use progressive summation to make the most of the time I spend reading. So I need easy methods to get content into Bear. This little essay is about getting content from Perplexity.ai into Bear.

Modifying the clipboard with the OSX Shortcuts app

Perplexity.ai is pretty good for learning new scientific concepts. It provides references for all it’s assertions, making it more reliable (or at least easier to fact-check) than responses from ChatGPT. If you copy a response from Perplexity.ai, it is in Markdown format (hurray!), but uses a non-standard format for footnotes (boo!), which works neither in Bear (my note taking app of choice), nor Quarto (which I use to maintain this website). I want the methods I use to copy and paste stuff to be as easy as possible, so I decided to create a OSX Shortcut to make the necessary adjustments to the Perplexity output. Here it is:

Lessons learned

What have I learned from this? The Shortcuts app is annoying and has a lot of idiosyncrasies that make it frustrating to use. It would be better to be able to write a python or Javascript script to do this type of thing. Actually, that’s a really nice idea. Now I have to do that.

Results

If you are wondering what the results of a Perplexity search looks like rendered from Markdown format, here is an example:

I understand that some bacteria and fungi can create proteins that help water to freeze, and so can cause frost damage to plants which they can exploit. Can you tell me more about this?

Yes, certain bacteria and fungi produce proteins that facilitate the formation of ice at relatively high sub-zero temperatures, which can lead to frost damage in plants. This phenomenon is known as biological ice nucleation. Here is a detailed explanation of how these microorganisms contribute to frost damage and their broader implications:

Ice-Nucleating Bacteria and Fungi

Mechanism of Ice Nucleation

  • Ice-Nucleating Proteins (INPs): These proteins are produced by certain bacteria and fungi and have the ability to catalyze the formation of ice crystals at temperatures just below the freezing point of water. The most well-known ice-nucleating bacterium is Pseudomonas syringae, which uses specialized proteins to control the molecular structure and energy transfer in interfacial water, thereby inducing ice formation1.
  • Role in Frost Damage: When these ice-nucleating microorganisms colonize plant surfaces, they can induce ice formation at higher temperatures than would occur naturally. This ice formation can cause physical damage to plant tissues, leading to frost injury. The bacteria benefit from this damage as it allows them to access plant nutrients more easily2.

Environmental and Agricultural Impact

  • Agricultural Damage: The presence of ice-nucleating bacteria on crops can lead to significant frost damage, which is a major concern for agriculture. This damage can reduce crop yields and quality, leading to economic losses for farmers3.
  • Atmospheric Processes: Ice-nucleating bacteria and fungi also play a role in atmospheric processes. They can influence cloud formation and precipitation by acting as nuclei for ice crystal formation in clouds. This can affect weather patterns and the water cycle45.

Examples of Ice-Nucleating Microorganisms

  • Bacteria: Besides Pseudomonas syringae, other bacteria such as Pseudomonas fluorescens and Erwinia herbicola are also known to have ice-nucleating activity. These bacteria produce ice-nucleating proteins that are often associated with the outer membrane of the cell6.
  • Fungi: Certain fungi, such as species from the genera Fusarium and Mortierella, also produce ice-nucleating proteins. These fungal proteins differ from bacterial INPs in some basic characteristics but serve a similar function in promoting ice formation78.

Mitigation Strategies

  • Biological Control: One approach to mitigate frost damage is to reduce the population of ice-nucleating bacteria on plant surfaces. This can be achieved through the use of bactericides, antagonistic bacteria, or cultural control strategies that limit the conditions favorable for the growth of these microorganisms9.
  • Genetic Engineering: Another strategy involves the use of antifreeze proteins (AFPs) from other organisms, such as fish or insects, to protect plants from frost damage. Transgenic plants expressing these AFPs have been developed to enhance their frost tolerance10.

Research and Applications

  • Artificial Snow Production: Ice-nucleating bacteria are used in the production of artificial snow for recreational purposes. Their ability to induce ice formation at higher temperatures makes them useful for creating snow in conditions where natural snow formation is not possible11.
  • Biomimetic Materials: The principles of biological ice nucleation are also being applied in the development of biomimetic materials for controlled interfacial freezing, which has potential applications in various industries12.

In summary, ice-nucleating bacteria and fungi play a significant role in both environmental processes and agricultural challenges. Understanding their mechanisms and impacts can help in developing strategies to mitigate frost damage and harness their properties for beneficial applications.

Footnotes

  1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4846457/↩︎

  2. https://pubmed.ncbi.nlm.nih.gov/36122194/↩︎

  3. https://pubmed.ncbi.nlm.nih.gov/36122194/↩︎

  4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4846457/↩︎

  5. https://www.semanticscholar.org/paper/0abcc5d1939e89387ef906fc2674177185158738↩︎

  6. https://pubmed.ncbi.nlm.nih.gov/36122194/↩︎

  7. https://www.semanticscholar.org/paper/3b475926fb2bdbbe119c50b11783748db95e7b97↩︎

  8. https://www.semanticscholar.org/paper/59e4ee323c39f15e1fbf4d3c2d6a63ed1577fa47↩︎

  9. https://pubmed.ncbi.nlm.nih.gov/36122194/↩︎

  10. https://www.semanticscholar.org/paper/0a5c954a1052a6e7737ab1da81c939dc3ffa45cd↩︎

  11. https://pubmed.ncbi.nlm.nih.gov/36122194/↩︎

  12. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4846457/↩︎