More on Productivity
Leonardo Castorina
3 years ago
How to Use Obsidian to Boost Research Productivity
Tools for managing your PhD projects, reading lists, notes, and inspiration.
As a researcher, you have to know everything. But knowledge is useless if it cannot be accessed quickly. An easy-to-use method of archiving information makes taking notes effortless and enjoyable.
As a PhD student in Artificial Intelligence, I use Obsidian (https://obsidian.md) to manage my knowledge.
The article has three parts:
- What is a note, how to organize notes, tags, folders, and links? This section is tool-agnostic, so you can use most of these ideas with any note-taking app.
- Instructions for using Obsidian, managing notes, reading lists, and useful plugins. This section demonstrates how I use Obsidian, my preferred knowledge management tool.
- Workflows: How to use Zotero to take notes from papers, manage multiple projects' notes, create MOCs with Dataview, and more. This section explains how to use Obsidian to solve common scientific problems and manage/maintain your knowledge effectively.
This list is not perfect or complete, but it is my current solution to problems I've encountered during my PhD. Please leave additional comments or contact me if you have any feedback. I'll try to update this article.
Throughout the article, I'll refer to your digital library as your "Obsidian Vault" or "Zettelkasten".
Other useful resources are listed at the end of the article.
1. Philosophy: Taking and organizing notes
Carl Sagan: “To make an apple pie from scratch, you must first create the universe.”
Before diving into Obsidian, let's establish a Personal Knowledge Management System and a Zettelkasten. You can skip to Section 2 if you already know these terms.
Niklas Luhmann, a prolific sociologist who wrote 400 papers and 70 books, inspired this section and much of Zettelkasten. Zettelkasten means “slip box” (or library in this article). His Zettlekasten had around 90000 physical notes, which can be found here.
There are now many tools available to help with this process. Obsidian's website has a good introduction section: https://publish.obsidian.md/hub/
Notes
We'll start with "What is a note?" Although it may seem trivial, the answer depends on the topic or your note-taking style. The idea is that a note is as “atomic” (i.e. You should read the note and get the idea right away.
The resolution of your notes depends on their detail. Deep Learning, for example, could be a general description of Neural Networks, with a few notes on the various architectures (eg. Recurrent Neural Networks, Convolutional Neural Networks etc..).
Limiting length and detail is a good rule of thumb. If you need more detail in a specific section of this note, break it up into smaller notes. Deep Learning now has three notes:
- Deep Learning
- Recurrent Neural Networks
- Convolutional Neural Networks
Repeat this step as needed until you achieve the desired granularity. You might want to put these notes in a “Neural Networks” folder because they are all about the same thing. But there's a better way:
#Tags and [[Links]] over /Folders/
The main issue with folders is that they are not flexible and assume that all notes in the folder belong to a single category. This makes it difficult to make connections between topics.
Deep Learning has been used to predict protein structure (AlphaFold) and classify images (ImageNet). Imagine a folder structure like this:
- /Proteins/
- Protein Folding
- /Deep Learning/
- /Proteins/
Your notes about Protein Folding and Convolutional Neural Networks will be separate, and you won't be able to find them in the same folder.
This can be solved in several ways. The most common one is to use tags rather than folders. A note can be grouped with multiple topics this way. Obsidian tags can also be nested (have subtags).
You can also link two notes together. You can build your “Knowledge Graph” in Obsidian and other note-taking apps like Obsidian.
My Knowledge Graph. Green: Biology, Red: Machine Learning, Yellow: Autoencoders, Blue: Graphs, Brown: Tags.
My Knowledge Graph and the note “Backrpropagation” and its links.
Backpropagation note and all its links
Why use Folders?
Folders help organize your vault as it grows. The main suggestion is to have few folders that "weakly" collect groups of notes or better yet, notes from different sources.
Among my Zettelkasten folders are:
My Zettelkasten's 5 folders
They usually gather data from various sources:
MOC: Map of Contents for the Zettelkasten.
Projects: Contains one note for each side-project of my PhD where I log my progress and ideas. Notes are linked to these.
Bio and ML: These two are the main content of my Zettelkasten and could theoretically be combined.
Papers: All my scientific paper notes go here. A bibliography links the notes. Zotero .bib file
Books: I make a note for each book I read, which I then split into multiple notes.
Keeping images separate from other files can help keep your main folders clean.
I will elaborate on these in the Workflow Section.
My general recommendation is to use tags and links instead of folders.
Maps of Content (MOC)
Making Tables of Contents is a good solution (MOCs).
These are notes that "signposts" your Zettelkasten library, directing you to the right type of notes. It can link to other notes based on common tags. This is usually done with a title, then your notes related to that title. As an example:
An example of a Machine Learning MOC generated with Dataview.
As shown above, my Machine Learning MOC begins with the basics. Then it's on to Variational Auto-Encoders. Not only does this save time, but it also saves scrolling through the tag search section.
So I keep MOCs at the top of my library so I can quickly find information and see my library. These MOCs are generated automatically using an Obsidian Plugin called Dataview (https://github.com/blacksmithgu/obsidian-dataview).
Ideally, MOCs could be expanded to include more information about the notes, their status, and what's left to do. In the absence of this, Dataview does a fantastic job at creating a good structure for your notes.
In the absence of this, Dataview does a fantastic job at creating a good structure for your notes.
2. Tools: Knowing Obsidian
Obsidian is my preferred tool because it is free, all notes are stored in Markdown format, and each panel can be dragged and dropped. You can get it here: https://obsidian.md/
Obsidian interface.
Obsidian is highly customizable, so here is my preferred interface:
The theme is customized from https://github.com/colineckert/obsidian-things
Alternatively, each panel can be collapsed, moved, or removed as desired. To open a panel later, click on the vertical "..." (bottom left of the note panel).
My interface is organized as follows:
How my Obsidian Interface is organized.
Folders/Search:
This is where I keep all relevant folders. I usually use the MOC note to navigate, but sometimes I use the search button to find a note.
Tags:
I use nested tags and look into each one to find specific notes to link.
cMenu:
Easy-to-use menu plugin cMenu (https://github.com/chetachiezikeuzor/cMenu-Plugin)
Global Graph:
The global graph shows all your notes (linked and unlinked). Linked notes will appear closer together. Zoom in to read each note's title. It's a bit overwhelming at first, but as your library grows, you get used to the positions and start thinking of new connections between notes.
Local Graph:
Your current note will be shown in relation to other linked notes in your library. When needed, you can quickly jump to another link and back to the current note.
Links:
Finally, an outline panel and the plugin Obsidian Power Search (https://github.com/aviral-batra/obsidian-power-search) allow me to search my vault by highlighting text.
Start using the tool and worry about panel positioning later. I encourage you to find the best use-case for your library.
Plugins
An additional benefit of using Obsidian is the large plugin library. I use several (Calendar, Citations, Dataview, Templater, Admonition):
Obsidian Calendar Plugin: https://github.com/liamcain
It organizes your notes on a calendar. This is ideal for meeting notes or keeping a journal.
Calendar addon from hans/obsidian-citation-plugin
Obsidian Citation Plugin: https://github.com/hans/
Allows you to cite papers from a.bib file. You can also customize your notes (eg. Title, Authors, Abstract etc..)
Plugin citation from hans/obsidian-citation-plugin
Obsidian Dataview: https://github.com/blacksmithgu/
A powerful plugin that allows you to query your library as a database and generate content automatically. See the MOC section for an example.
Allows you to create notes with specific templates like dates, tags, and headings.
Templater. Obsidian Admonition: https://github.com/valentine195/obsidian-admonition
Blocks allow you to organize your notes.
Plugin warning. Obsidian Admonition (valentine195)
There are many more, but this list should get you started.
3. Workflows: Cool stuff
Here are a few of my workflows for using obsidian for scientific research. This is a list of resources I've found useful for my use-cases. I'll outline and describe them briefly so you can skim them quickly.
3.1 Using Templates to Structure Notes
3.2 Free Note Syncing (Laptop, Phone, Tablet)
3.3 Zotero/Mendeley/JabRef -> Obsidian — Managing Reading Lists
3.4 Projects and Lab Books
3.5 Private Encrypted Diary
3.1 Using Templates to Structure Notes
Plugins: Templater and Dataview (optional).
To take effective notes, you must first make adding new notes as easy as possible. Templates can save you time and give your notes a consistent structure. As an example:
An example of a note using a template.
### [[YOUR MOC]]
# Note Title of your note
**Tags**::
**Links**::
The top line links to your knowledge base's Map of Content (MOC) (see previous sections). After the title, I add tags (and a link between the note and the tag) and links to related notes.
To quickly identify all notes that need to be expanded, I add the tag “#todo”. In the “TODO:” section, I list the tasks within the note.
The rest are notes on the topic.
Templater can help you create these templates. For new books, I use the following template:
### [[Books MOC]]
# Title
**Author**::
**Date::
**Tags::
**Links::
A book template example.
Using a simple query, I can hook Dataview to it.
dataview
table author as Author, date as “Date Finished”, tags as “Tags”, grade as “Grade”
from “4. Books”
SORT grade DESCENDING
using Dataview to query templates.
3.2 Free Note Syncing (Laptop, Phone, Tablet)
No plugins used.
One of my favorite features of Obsidian is the library's self-contained and portable format. Your folder contains everything (plugins included).
Ordinary folders and documents are available as well. There is also a “.obsidian” folder. This contains all your plugins and settings, so you can use it on other devices.
So you can use Google Drive, iCloud, or Dropbox for free as long as you sync your folder (note: your folder should be in your Cloud Folder).
For my iOS and macOS work, I prefer iCloud. You can also use the paid service Obsidian Sync.
3.3 Obsidian — Managing Reading Lists and Notes in Zotero/Mendeley/JabRef
Plugins: Quotes (required).
3.3 Zotero/Mendeley/JabRef -> Obsidian — Taking Notes and Managing Reading Lists of Scientific Papers
My preferred reference manager is Zotero, but this workflow should work with any reference manager that produces a .bib file. This file is exported to my cloud folder so I can access it from any platform.
My Zotero library is tagged as follows:
My reference manager's tags
For readings, I usually search for the tags “!!!” and “To-Read” and select a paper. Annotate the paper next (either on PDF using GoodNotes or on physical paper).
Then I make a paper page using a template in the Citations plugin settings:
An example of my citations template.
Create a new note, open the command list with CMD/CTRL + P, and find the Citations “Insert literature note content in the current pane” to see this lovely view.
Citation generated by the article https://doi.org/10.1101/2022.01.24.22269144
You can then convert your notes to digital. I found that transcribing helped me retain information better.
3.4 Projects and Lab Books
Plugins: Tweaker (required).
PhD students offering advice on thesis writing are common (read as regret). I started asking them what they would have done differently or earlier.
“Deep stuff Leo,” one person said. So my main issue is basic organization, losing track of my tasks and the reasons for them.
As a result, I'd go on other experiments that didn't make sense, and have to reverse engineer my logic for thesis writing. - PhD student now wise Postdoc
Time management requires planning. Keeping track of multiple projects and lab books is difficult during a PhD. How I deal with it:
- One folder for all my projects
- One file for each project
I use a template to create each project
### [[Projects MOC]]
# <% tp.file.title %>
**Tags**::
**Links**::
**URL**::
**Project Description**::## Notes:
### <% tp.file.last_modified_date(“dddd Do MMMM YYYY”) %>
#### Done:
#### TODO:
#### Notes
You can insert a template into a new note with CMD + P and looking for the Templater option.
I then keep adding new days with another template:
### <% tp.file.last_modified_date("dddd Do MMMM YYYY") %>
#### Done:
#### TODO:
#### Notes:
This way you can keep adding days to your project and update with reasonings and things you still have to do and have done. An example below:
Example of project note with timestamped notes.
3.5 Private Encrypted Diary
This is one of my favorite Obsidian uses.
Mini Diary's interface has long frustrated me. After the author archived the project, I looked for a replacement. I had two demands:
- It had to be private, and nobody had to be able to read the entries.
- Cloud syncing was required for editing on multiple devices.
Then I learned about encrypting the Obsidian folder. Then decrypt and open the folder with Obsidian. Sync the folder as usual.
Use CryptoMator (https://cryptomator.org/). Create an encrypted folder in Cryptomator for your Obsidian vault, set a password, and let it do the rest.
If you need a step-by-step video guide, here it is:
Conclusion
So, I hope this was helpful!
In the first section of the article, we discussed notes and note-taking techniques. We discussed when to use tags and links over folders and when to break up larger notes.
Then we learned about Obsidian, its interface, and some useful plugins like Citations for citing papers and Templater for creating note templates.
Finally, we discussed workflows and how to use Zotero to take notes from scientific papers, as well as managing Lab Books and Private Encrypted Diaries.
Thanks for reading and commenting :)
Read original post here
The woman
3 years ago
I received a $2k bribe to replace another developer in an interview
I can't believe they’d even think it works!
Developers are usually interviewed before being hired, right? Every organization wants candidates who meet their needs. But they also want to avoid fraud.
There are cheaters in every field. Only two come to mind for the hiring process:
Lying on a resume.
Cheating on an online test.
Recently, I observed another one. One of my coworkers invited me to replace another developer during an online interview! I was astonished, but it’s not new.
The specifics
My ex-colleague recently texted me. No one from your former office will ever approach you after a year unless they need something.
Which was the case. My coworker said his wife needed help as a programmer. I was glad someone asked for my help, but I'm still a junior programmer.
Then he informed me his wife was selected for a fantastic job interview. He said he could help her with the online test, but he needed someone to help with the online interview.
Okay, I guess. Preparing for an online interview is beneficial. But then he said she didn't need to be ready. She needed someone to take her place.
I told him it wouldn't work. Every remote online interview I've ever seen required an open camera.
What followed surprised me. She'd ask to turn off the camera, he said.
I asked why.
He told me if an applicant is unwell, the interviewer may consider an off-camera interview. His wife will say she's sick and prefers no camera.
The plan left me speechless. I declined politely. He insisted and promised $2k if she got the job.
I felt insulted and told him if he persisted, I'd inform his office. I was furious. Later, I apologized and told him to stop.
I'm not sure what they did after that
I'm not sure if they found someone or listened to me. They probably didn't. How would she do the job if she even got it?
It's an internship, he said. With great pay, though. What should an intern do?
I suggested she do the interview alone. Even if she failed, she'd gain confidence and valuable experience.
Conclusion
Many interviewees cheat. My profession is vital to me, thus I'd rather improve my abilities and apply honestly. It's part of my identity.
Am I truthful? Most professionals are not. They fabricate their CVs. Often.
When you support interview cheating, you encourage more cheating! When someone cheats, another qualified candidate may not obtain the job.
One day, that could be you or me.
Jari Roomer
3 years ago
5 ways to never run out of article ideas
“Perfectionism is the enemy of the idea muscle. " — James Altucher
Writer's block is a typical explanation for low output. Success requires productivity.
In four years of writing, I've never had writer's block. And you shouldn't care.
You'll never run out of content ideas if you follow a few tactics. No, I'm not overpromising.
Take Note of Ideas
Brains are strange machines. Blank when it's time to write. Idiot. Nothing. We get the best article ideas when we're away from our workstation.
In the shower
Driving
In our dreams
Walking
During dull chats
Meditating
In the gym
No accident. The best ideas come in the shower, in nature, or while exercising.
(Your workstation is the worst place for creativity.)
The brain has time and space to link 'dots' of information during rest. It's eureka! New idea.
If you're serious about writing, capture thoughts as they come.
Immediately write down a new thought. Capture it. Don't miss it. Your future self will thank you.
As a writer, entrepreneur, or creative, letting ideas slide is bad.
I recommend using Evernote, Notion, or your device's basic note-taking tool to capture article ideas.
It doesn't matter whatever app you use as long as you collect article ideas.
When you practice 'idea-capturing' enough, you'll have an unending list of article ideas when writer's block hits.
High-Quality Content
More books, films, Medium pieces, and Youtube videos I consume, the more I'm inspired to write.
What you eat shapes who you are.
Celebrity gossip and fear-mongering news won't help your writing. It won't help you write regularly.
Instead, read expert-written books. Watch documentaries to improve your worldview. Follow amazing people online.
Develop your 'idea muscle' Daily creativity takes practice. The more you exercise your 'idea muscles,' the easier it is to generate article ideas.
I've trained my 'concept muscle' using James Altucher's exercise.
Write 10 ideas daily.
Write ten book ideas every day if you're an author. Write down 10 business ideas per day if you're an entrepreneur. Write down 10 investing ideas per day.
Write 10 article ideas per day. You become a content machine.
It doesn't state you need ten amazing ideas. You don't need 10 ideas. Ten ideas, regardless of quality.
Like at the gym, reps are what matter. With each article idea, you gain creativity. Writer's block is no match for this workout.
Quit Perfectionism
Perfectionism is bad for writers. You'll have bad articles. You'll have bad ideas. OK. It's creative.
Writing success requires prolificacy. You can't have 'perfect' articles.
“Perfectionism is the enemy of the idea muscle. Perfectionism is your brain trying to protect you from harm.” — James Altucher
Vincent van Gogh painted 900 pieces. The Starry Night is the most famous.
Thomas Edison invented 1093 things, but not all were as important as the lightbulb or the first movie camera.
Mozart composed nearly 600 compositions, but only Serenade No13 became popular.
Always do your best. Perfectionism shouldn't stop you from working. Write! Publicize. Make. Even if imperfect.
Write Your Story
Living an interesting life gives you plenty to write about. If you travel a lot, share your stories or lessons learned.
Describe your business's successes and shortcomings.
Share your experiences with difficulties or addictions.
More experiences equal more writing material.
If you stay indoors, perusing social media, you won't be inspired to write.
Have fun. Travel. Strive. Build a business. Be bold. Live a life worth writing about, and you won't run out of material.
You might also like
Ray Dalio
3 years ago
The latest “bubble indicator” readings.
As you know, I like to turn my intuition into decision rules (principles) that can be back-tested and automated to create a portfolio of alpha bets. I use one for bubbles. Having seen many bubbles in my 50+ years of investing, I described what makes a bubble and how to identify them in markets—not just stocks.
A bubble market has a high degree of the following:
- High prices compared to traditional values (e.g., by taking the present value of their cash flows for the duration of the asset and comparing it with their interest rates).
- Conditons incompatible with long-term growth (e.g., extrapolating past revenue and earnings growth rates late in the cycle).
- Many new and inexperienced buyers were drawn in by the perceived hot market.
- Broad bullish sentiment.
- Debt financing a large portion of purchases.
- Lots of forward and speculative purchases to profit from price rises (e.g., inventories that are more than needed, contracted forward purchases, etc.).
I use these criteria to assess all markets for bubbles. I have periodically shown you these for stocks and the stock market.
What Was Shown in January Versus Now
I will first describe the picture in words, then show it in charts, and compare it to the last update in January.
As of January, the bubble indicator showed that a) the US equity market was in a moderate bubble, but not an extreme one (ie., 70 percent of way toward the highest bubble, which occurred in the late 1990s and late 1920s), and b) the emerging tech companies (ie. As well, the unprecedented flood of liquidity post-COVID financed other bubbly behavior (e.g. SPACs, IPO boom, big pickup in options activity), making things bubbly. I showed which stocks were in bubbles and created an index of those stocks, which I call “bubble stocks.”
Those bubble stocks have popped. They fell by a third last year, while the S&P 500 remained flat. In light of these and other market developments, it is not necessarily true that now is a good time to buy emerging tech stocks.
The fact that they aren't at a bubble extreme doesn't mean they are safe or that it's a good time to get long. Our metrics still show that US stocks are overvalued. Once popped, bubbles tend to overcorrect to the downside rather than settle at “normal” prices.
The following charts paint the picture. The first shows the US equity market bubble gauge/indicator going back to 1900, currently at the 40% percentile. The charts also zoom in on the gauge in recent years, as well as the late 1920s and late 1990s bubbles (during both of these cases the gauge reached 100 percent ).
The chart below depicts the average bubble gauge for the most bubbly companies in 2020. Those readings are down significantly.
The charts below compare the performance of a basket of emerging tech bubble stocks to the S&P 500. Prices have fallen noticeably, giving up most of their post-COVID gains.
The following charts show the price action of the bubble slice today and in the 1920s and 1990s. These charts show the same market dynamics and two key indicators. These are just two examples of how a lot of debt financing stock ownership coupled with a tightening typically leads to a bubble popping.
Everything driving the bubbles in this market segment is classic—the same drivers that drove the 1920s bubble and the 1990s bubble. For instance, in the last couple months, it was how tightening can act to prick the bubble. Review this case study of the 1920s stock bubble (starting on page 49) from my book Principles for Navigating Big Debt Crises to grasp these dynamics.
The following charts show the components of the US stock market bubble gauge. Since this is a proprietary indicator, I will only show you some of the sub-aggregate readings and some indicators.
Each of these six influences is measured using a number of stats. This is how I approach the stock market. These gauges are combined into aggregate indices by security and then for the market as a whole. The table below shows the current readings of these US equity market indicators. It compares current conditions for US equities to historical conditions. These readings suggest that we’re out of a bubble.
1. How High Are Prices Relatively?
This price gauge for US equities is currently around the 50th percentile.
2. Is price reduction unsustainable?
This measure calculates the earnings growth rate required to outperform bonds. This is calculated by adding up the readings of individual securities. This indicator is currently near the 60th percentile for the overall market, higher than some of our other readings. Profit growth discounted in stocks remains high.
Even more so in the US software sector. Analysts' earnings growth expectations for this sector have slowed, but remain high historically. P/Es have reversed COVID gains but remain high historical.
3. How many new buyers (i.e., non-existing buyers) entered the market?
Expansion of new entrants is often indicative of a bubble. According to historical accounts, this was true in the 1990s equity bubble and the 1929 bubble (though our data for this and other gauges doesn't go back that far). A flood of new retail investors into popular stocks, which by other measures appeared to be in a bubble, pushed this gauge above the 90% mark in 2020. The pace of retail activity in the markets has recently slowed to pre-COVID levels.
4. How Broadly Bullish Is Sentiment?
The more people who have invested, the less resources they have to keep investing, and the more likely they are to sell. Market sentiment is now significantly negative.
5. Are Purchases Being Financed by High Leverage?
Leveraged purchases weaken the buying foundation and expose it to forced selling in a downturn. The leverage gauge, which considers option positions as a form of leverage, is now around the 50% mark.
6. To What Extent Have Buyers Made Exceptionally Extended Forward Purchases?
Looking at future purchases can help assess whether expectations have become overly optimistic. This indicator is particularly useful in commodity and real estate markets, where forward purchases are most obvious. In the equity markets, I look at indicators like capital expenditure, or how much businesses (and governments) invest in infrastructure, factories, etc. It reflects whether businesses are projecting future demand growth. Like other gauges, this one is at the 40th percentile.
What one does with it is a tactical choice. While the reversal has been significant, future earnings discounting remains high historically. In either case, bubbles tend to overcorrect (sell off more than the fundamentals suggest) rather than simply deflate. But I wanted to share these updated readings with you in light of recent market activity.
Isaac Benson
3 years ago
What's the difference between Proof-of-Time and Proof-of-History?
Blockchain validates transactions with consensus algorithms. Bitcoin and Ethereum use Proof-of-Work, while Polkadot and Cardano use Proof-of-Stake.
Other consensus protocols are used to verify transactions besides these two. This post focuses on Proof-of-Time (PoT), used by Analog, and Proof-of-History (PoH), used by Solana as a hybrid consensus protocol.
PoT and PoH may seem similar to users, but they are actually very different protocols.
Proof-of-Time (PoT)
Analog developed Proof-of-Time (PoT) based on Delegated Proof-of-Stake (DPoS). Users select "delegates" to validate the next block in DPoS. PoT uses a ranking system, and validators stake an equal amount of tokens. Validators also "self-select" themselves via a verifiable random function."
The ranking system gives network validators a performance score, with trustworthy validators with a long history getting higher scores. System also considers validator's fixed stake. PoT's ledger is called "Timechain."
Voting on delegates borrows from DPoS, but there are changes. PoT's first voting stage has validators (or "time electors" putting forward a block to be included in the ledger).
Validators are chosen randomly based on their ranking score and fixed stake. One validator is chosen at a time using a Verifiable Delay Function (VDF).
Validators use a verifiable delay function to determine if they'll propose a Timechain block. If chosen, they validate the transaction and generate a VDF proof before submitting both to other Timechain nodes.
This leads to the second process, where the transaction is passed through 1,000 validators selected using the same method. Each validator checks the transaction to ensure it's valid.
If the transaction passes, validators accept the block, and if over 2/3 accept it, it's added to the Timechain.
Proof-of-History (PoH)
Proof-of-History is a consensus algorithm that proves when a transaction occurred. PoH uses a VDF to verify transactions, like Proof-of-Time. Similar to Proof-of-Work, VDFs use a lot of computing power to calculate but little to verify transactions, similar to (PoW).
This shows users and validators how long a transaction took to verify.
PoH uses VDFs to verify event intervals. This process uses cryptography to prevent determining output from input.
The outputs of one transaction are used as inputs for the next. Timestamps record the inputs' order. This checks if data was created before an event.
PoT vs. PoH
PoT and PoH differ in that:
PoT uses VDFs to select validators (or time electors), while PoH measures time between events.
PoH uses a VDF to validate transactions, while PoT uses a ranking system.
PoT's VDF-elected validators verify transactions proposed by a previous validator. PoH uses a VDF to validate transactions and data.
Conclusion
Both Proof-of-Time (PoT) and Proof-of-History (PoH) validate blockchain transactions differently. PoT uses a ranking system to randomly select validators to verify transactions.
PoH uses a Verifiable Delay Function to validate transactions, verify how much time has passed between two events, and allow validators to quickly verify a transaction without malicious actors knowing the input.
Kyle Planck
3 years ago
The chronicles of monkeypox.
or, how I spread monkeypox and got it myself.
This story contains nsfw (not safe for wife) stuff and shouldn't be read if you're under 18 or think I'm a newborn angel. After the opening, it's broken into three sections: a chronological explanation of my disease course, my ideas, and what I plan to do next.
Your journey awaits.
As early as mid-may, I was waltzing around the lab talking about monkeypox, a rare tropical disease with an inaccurate name. Monkeys are not its primary animal reservoir. It caused an outbreak among men who have sex with men across Europe, with unprecedented levels of person-to-person transmission. European health authorities speculated that the virus spread at raves and parties and was easily transferred through intimate, mainly sexual, contact. I had already read the nejm article about the first confirmed monkeypox patient in the u.s. and shared the photos on social media so people knew what to look for. The cdc information page only included 4 photographs of monkeypox lesions that looked like they were captured on a motorola razr.
I warned my ex-boyfriend about monkeypox. Monkeypox? responded.
Mom, I'm afraid about monkeypox. What's monkeypox?
My therapist is scared about monkeypox. What's monkeypox?
Was I alone? A few science gays on Twitter didn't make me feel overreacting.
This information got my gay head turning. The incubation period for the sickness is weeks. Many of my social media contacts are traveling to Europe this summer. What is pride? Travel, parties, and sex. Many people may become infected before attending these activities. Monkeypox will affect the lgbtq+ community.
Being right always stinks. My young scientist brain was right, though. Someone who saw this coming is one of the early victims. I'll talk about my feelings publicly, and trust me, I have many concerning what's occurring.
Part 1 is the specifics.
Wednesday nights are never smart but always entertaining. I didn't wake up until noon on june 23 and saw gay twitter blazing. Without warning, the nyc department of health announced a pop-up monkeypox immunization station in chelsea. Some days would be 11am-7pm. Walk-ins were welcome, however appointments were preferred. I tried to arrange an appointment after rubbing my eyes, but they were all taken. I got out of bed, washed my face, brushed my teeth, and put on short shorts because I wanted to get a walk-in dose and show off my legs. I got a 20-oz. cold brew on the way to the train and texted a chelsea-based acquaintance for help.
Clinic closed at 2pm. No more doses. Hundreds queued up. The government initially gave them only 1,000 dosages. For a city with 500,000 LGBT people, c'mon. What more could I do? I was upset by how things were handled. The evidence speaks for itself.
I decided to seek an appointment when additional doses were available and continued my weekend. I was celebrating nyc pride with pals. Fun! sex! *
On tuesday after that, I felt a little burn. This wasn't surprising because I'd been sexually active throughout the weekend, so I got a sti panel the next day. I expected to get results in a few days, take antibiotics, and move on.
Emerging germs had other intentions. Wednesday night, I felt sore, and thursday morning, I had a blazing temperature and had sweat through my bedding. I had fever, chills, and body-wide aches and pains for three days. I reached 102 degrees. I believed I had covid over pride weekend, but I tested negative for three days straight.
STDs don't induce fevers or other systemic symptoms. If lymphogranuloma venereum advances, it can cause flu-like symptoms and swollen lymph nodes. I was suspicious and desperate for answers, so I researched monkeypox on the cdc website (for healthcare professionals). Much of what I saw on screen about monkeypox prodrome matched my symptoms. Multiple-day fever, headache, muscle aches, chills, tiredness, enlarged lymph nodes. Pox were lacking.
I told my doctor my concerns pre-medically. I'm occasionally annoying.
On saturday night, my fever broke and I felt better. Still burning, I was optimistic till sunday, when I woke up with five red splotches on my arms and fingertips.
As spots formed, burning became pain. I observed as spots developed on my body throughout the day. I had more than a dozen by the end of the day, and the early spots were pustular. I had monkeypox, as feared.
Fourth of July weekend limited my options. I'm well-connected in my school's infectious disease academic community, so I texted a coworker for advice. He agreed it was likely monkeypox and scheduled me for testing on tuesday.
nyc health could only perform 10 monkeypox tests every day. Before doctors could take swabs and send them in, each test had to be approved by the department. Some commercial labs can now perform monkeypox testing, but the backlog is huge. I still don't have a positive orthopoxvirus test five days after my test. *My 12-day-old case may not be included in the official monkeypox tally. This outbreak is far wider than we first thought, therefore I'm attempting to spread the information and help contain it.
*Update, 7/11: I have orthopoxvirus.
I spent all day in the bathtub because of the agony. Warm lavender epsom salts helped me feel better. I can't stand lavender anymore. I brought my laptop into the bathroom and viewed everything everywhere at once (2022). If my ex and I hadn't recently broken up, I wouldn't have monkeypox. All of these things made me cry, and I sat in the bathtub on the 4th of July sobbing. I thought, Is this it? I felt like Bridesmaids' Kristen Wiig (2011). I'm a flop. From here, things can only improve.
Later that night, I wore a mask and went to my roof to see the fireworks. Even though I don't like fireworks, there was something wonderful about them this year: the colors, how they illuminated the black surfaces around me, and their transient beauty. Joyful moments rarely linger long in our life. We must enjoy them now.
Several roofs away, my neighbors gathered. Happy 4th! I heard a woman yell. Why is this godforsaken country so happy? Instead of being rude, I replied. I didn't tell them I had monkeypox. I thought that would kill the mood.
By the time I went to the hospital the next day to get my lesions swabbed, wearing long sleeves, pants, and a mask, they looked like this:
I had 30 lesions on my arms, hands, stomach, back, legs, buttcheeks, face, scalp, and right eyebrow. I had some in my mouth, gums, and throat. Current medical thought is that lesions on mucous membranes cause discomfort in sensitive places. Internal lesions are a new feature of this outbreak of monkeypox. Despite being unattractive, the other sores weren't unpleasant or bothersome.
I had a bacterial sti with the pox. Who knows if that would've created symptoms (often it doesn't), but different infections can happen at once. My care team remembered that having a sti doesn't exclude out monkeypox. doxycycline rocks!
The coworker who introduced me to testing also offered me his home. We share a restroom, and monkeypox can be spread through surfaces. (Being a dna virus gives it environmental hardiness that rna viruses like sars-cov-2 lack.) I disinfected our bathroom after every usage, but I was apprehensive. My friend's place has a guest room and second bathroom, so no cross-contamination. It was the ideal monkeypox isolation environment, so I accepted his offer and am writing this piece there. I don't know what I would have done without his hospitality and attention.
The next day, I started tecovirimat, or tpoxx, for 14 days. Smallpox has been eradicated worldwide since the 1980s but remains a bioterrorism concern. Tecovirimat has a unique, orthopoxvirus-specific method of action, which reduces side effects to headache and nausea. It hasn't been used in many people, therefore the cdc is encouraging patients who take it for monkeypox to track their disease and symptoms.
Tpoxx's oral absorption requires a fatty meal. The hospital ordered me to take the medication after a 600-calorie, 25-gram-fat meal every 12 hours. The coordinator joked, "Don't diet for the next two weeks." I wanted to get peanut butter delivered, but jif is recalling their supply due to salmonella. Please give pathogens a break. I got almond butter.
Tpoxx study enrollment was documented. After signing consent documents, my lesions were photographed and measured during a complete physical exam. I got bloodwork to assess my health. My medication delivery was precise; every step must be accounted for. I got a two-week supply and started taking it that night. I rewarded myself with McDonald's. I'd been hungry for a week. I was also prescribed ketorolac (aka toradol), a stronger ibuprofen, for my discomfort.
I thought tpoxx was a wonder medicine by day two of treatment. Early lesions looked like this.
however, They vanished. The three largest lesions on my back flattened and practically disappeared into my skin. Some pustular lesions were diminishing. Tpoxx+toradol has helped me sleep, focus, and feel human again. I'm down to twice-daily baths and feeling hungrier than ever in this illness. On day five of tpoxx, some of the lesions look like this:
I have a ways to go. We must believe I'll be contagious until the last of my patches scabs over, falls off, and sprouts new skin. There's no way to tell. After a week and a half of tremendous pain and psychological stress, any news is good news. I'm grateful for my slow but steady development.
Part 2 of the rant.
Being close to yet not in the medical world is interesting. It lets me know a lot about it without being persuaded by my involvement. Doctors identify and treat patients using a tool called differential diagnosis.
A doctor interviews a patient to learn about them and their symptoms. More is better. Doctors may ask, "Have you traveled recently?" sex life? Have pets? preferred streaming service? (No, really. (Hbomax is right.) After the inquisition, the doctor will complete a body exam ranging from looking in your eyes, ears, and throat to a thorough physical.
After collecting data, the doctor makes a mental (or physical) inventory of all the conceivable illnesses that could cause or explain the patient's symptoms. Differential diagnosis list. After establishing the differential, the clinician can eliminate options. The doctor will usually conduct nucleic acid tests on swab samples or bloodwork to learn more. This helps eliminate conditions from the differential or boosts a condition's likelihood. In an ideal circumstance, the doctor can eliminate all but one reason of your symptoms, leaving your formal diagnosis. Once diagnosed, treatment can begin. yay! Love medicine.
My symptoms two weeks ago did not suggest monkeypox. Fever, pains, weariness, and swollen lymph nodes are caused by several things. My scandalous symptoms weren't linked to common ones. My instance shows the importance of diversity and representation in healthcare. My doctor isn't gay, but he provides culturally sensitive care. I'd heard about monkeypox as a gay man in New York. I was hyper-aware of it and had heard of friends of friends who had contracted it the week before, even though the official case count in the US was 40. My physicians weren't concerned, but I was. How would it appear on his mental differential if it wasn't on his radar? Mental differential rhymes! I'll trademark it to prevent theft. differential!
I was in a rare position to recognize my condition and advocate for myself. I study infections. I'd spent months researching monkeypox. I work at a university where I rub shoulders with some of the country's greatest doctors. I'm a gay dude who follows nyc queer social networks online. All of these variables positioned me to think, "Maybe this is monkeypox," and to explain why.
This outbreak is another example of privilege at work. The brokenness of our healthcare system is once again exposed by the inequities produced by the vaccination rollout and the existence of people like myself who can pull strings owing to their line of work. I can't cure this situation on my own, but I can be a strong voice demanding the government do a better job addressing the outbreak and giving resources and advice to everyone I can.
lgbtqia+ community members' support has always impressed me in new york. The queer community has watched out for me and supported me in ways I never dreamed were possible.
Queer individuals are there for each other when societal structures fail. People went to the internet on the first day of the vaccine rollout to share appointment information and the vaccine clinic's message. Twitter timelines were more effective than marketing campaigns. Contrary to widespread anti-vaccine sentiment, the LGBT community was eager to protect themselves. Smallpox vaccination? sure. gimme. whether I'm safe. I credit the community's sex positivity. Many people are used to talking about STDs, so there's a reduced barrier to saying, "I think I have something, you should be on the watch too," and taking steps to protect our health.
Once I got monkeypox, I posted on Twitter and Instagram. Besides fueling my main character syndrome, I felt like I wasn't alone. My dc-based friend had monkeypox within hours. He told me about his experience and gave me ideas for managing the discomfort. I can't imagine life without him.
My buddy and colleague organized my medical care and let me remain in his home. His and his husband's friendliness and attention made a world of difference in my recovery. All of my friends and family who helped me, whether by venmo, doordash, or moral support, made me feel cared about. I don't deserve the amazing people in my life.
Finally, I think of everyone who commented on my social media posts regarding my trip. Friends from all sectors of my life and all sexualities have written me well wishes and complimented me for my vulnerability, but I feel the most gravitas from fellow lgbtq+ persons. They're learning to spot. They're learning where to go ill. They're learning self-advocacy. I'm another link in our network of caretaking. I've been cared for, therefore I want to do the same. Community and knowledge are powerful.
You're probably wondering where the diatribe is. You may believe he's gushing about his loved ones, and you'd be right. I say that just because the queer community can take care of itself doesn't mean we should.
Even when caused by the same pathogen, comparing health crises is risky. Aids is unlike covid-19 or monkeypox, yet all were caused by poorly understood viruses. The lgbtq+ community has a history of self-medicating. Queer people (and their supporters) have led the charge to protect themselves throughout history when the government refused. Surreal to experience this in real time.
First, vaccination access is a government failure. The strategic national stockpile contains tens of thousands of doses of jynneos, the newest fda-approved smallpox vaccine, and millions of doses of acam2000, an older vaccine for immunocompetent populations. Despite being a monkeypox hotspot and international crossroads, new york has only received 7,000 doses of the jynneos vaccine. Vaccine appointments are booked within minutes. It's showing Hunger Games, which bothers me.
Second, I think the government failed to recognize the severity of the european monkeypox outbreak. We saw abroad reports in may, but the first vaccines weren't available until june. Why was I a 26-year-old pharmacology grad student, able to see a monkeypox problem in europe but not the u.s. public health agency? Or was there too much bureaucracy and politicking, delaying action?
Lack of testing infrastructure for a known virus with vaccinations and therapies is appalling. More testing would have helped understand the problem's breadth. Many homosexual guys, including myself, didn't behave like monkeypox was a significant threat because there were only a dozen instances across the country. Our underestimating of the issue, spurred by a story of few infections, was huge.
Public health officials' response to infectious diseases frustrates me. A wait-and-see approach to infectious diseases is unsatisfactory. Before a sick person is recognized, they've exposed and maybe contaminated numerous others. Vaccinating susceptible populations before a disease becomes entrenched prevents disease. CDC might operate this way. When it was easier, they didn't control or prevent monkeypox. We'll learn when. Sometimes I fear never. Emerging viral infections are a menace in the era of climate change and globalization, and I fear our government will repeat the same mistakes. I don't work at the cdc, thus I have no idea what they do. As a scientist, a homosexual guy, and a citizen of this country, I feel confident declaring that the cdc has not done enough about monkeypox. Will they do enough about monkeypox? The strategic national stockpile can respond to a bioterrorism disaster in 12 hours. I'm skeptical following this outbreak.
It's simple to criticize the cdc, but they're not to blame. Underfunding public health services, especially the cdc, is another way our government fails to safeguard its citizens. I may gripe about the vaccination rollout all I want, but local health departments are doing their best with limited resources. They may not have enough workers to keep up with demand and run a contact-tracing program. Since my orthopoxvirus test is still negative, the doh hasn't asked about my close contacts. By then, my illness will be two weeks old, too long to do anything productive. Not their fault. They're functioning in a broken system that's underfunded for the work it does.
*Update, 7/11: I have orthopoxvirus.
Monkeypox is slow, so i've had time to contemplate. Now that I'm better, I'm angry. furious and sad I want to help. I wish to spare others my pain. This was preventable and solvable, I hope. HOW?
Third, the duty.
Family, especially selected family, helps each other. So many people have helped me throughout this difficult time. How can I give back? I have ideas.
1. Education. I've already started doing this by writing incredibly detailed posts on Instagram about my physical sickness and my thoughts on the entire scandal. via tweets. by producing this essay. I'll keep doing it even if people start to resent me! It's crucial! On my Instagram profile (@kyleplanckton), you may discover a story highlight with links to all of my bizarre yet educational posts.
2. Resources. I've forwarded the contact information for my institution's infectious diseases clinic to several folks who will hopefully be able to get tpoxx under the expanded use policy. Through my social networks, I've learned of similar institutions. I've also shared crowdsourced resources about symptom relief and vaccine appointment availability on social media. DM me or see my Instagram highlight for more.
3. Community action. During my illness, my friends' willingness to aid me has meant the most. It was nice to know I had folks on my side. One of my pals (thanks, kenny) snagged me a mcgriddle this morning when seamless canceled my order. This scenario has me thinking about methods to help people with monkeypox isolation. A two-week isolation period is financially damaging for many hourly workers. Certain governments required paid sick leave for covid-19 to allow employees to recover and prevent spread. No comparable program exists for monkeypox, and none seems to be planned shortly.
I want to aid monkeypox patients in severe financial conditions. I'm willing to pick up and bring groceries or fund meals/expenses for sick neighbors. I've seen several GoFundMe accounts, but I wish there was a centralized mechanism to link those in need with those who can help. Please contact me if you have expertise with mutual aid organizations. I hope we can start this shortly.
4. lobbying. Personal narratives are powerful. My narrative is only one, but I think it's compelling. Over the next day or so, i'll write to local, state, and federal officials about monkeypox. I wanted a vaccine but couldn't acquire one, and I feel tpoxx helped my disease. As a pharmacologist-in-training, I believe collecting data on a novel medicine is important, and there are ethical problems when making a drug with limited patient data broadly available. Many folks I know can't receive tpoxx due of red tape and a lack of contacts. People shouldn't have to go to an ivy league hospital to obtain the greatest care. Based on my experience and other people's tales, I believe tpoxx can drastically lessen monkeypox patients' pain and potentially curb transmission chains if administered early enough. This outbreak is manageable. It's not too late if we use all the instruments we have (diagnostic, vaccine, treatment).
*UPDATE 7/15: I submitted the following letter to Chuck Schumer and Kirsten Gillibrand. I've addressed identical letters to local, state, and federal officials, including the CDC and HHS.
I hope to join RESPND-MI, an LGBTQ+ community-led assessment of monkeypox symptoms and networks in NYC. Visit their website to learn more and give to this community-based charity.
How I got monkeypox is a mystery. I received it through a pride physical interaction, but i'm not sure which one. This outbreak will expand unless leaders act quickly. Until then, I'll keep educating and connecting people to care in my neighborhood.
Despite my misgivings, I see some optimism. Health department social media efforts are underway. During the outbreak, the CDC provided nonjudgmental suggestions for safer social and sexual activity. There's additional information regarding the disease course online, including how to request tpoxx for sufferers. These materials can help people advocate for themselves if they're sick. Importantly, homosexual guys are listening when they discuss about monkeypox online and irl. Learners They're serious.
The government has a terrible track record with lgtbq+ health issues, and they're not off to a good start this time. I hope this time will be better. If I can aid even one individual, I'll do so.
Thanks for reading, supporting me, and spreading awareness about the 2022 monkeypox outbreak. My dms are accessible if you want info, resources, queries, or to chat.
y'all well
kyle