More on Science

Katrina Paulson
3 years ago
Dehumanization Against Anthropomorphization
We've fought for humanity's sake. We need equilibrium.
We live in a world of opposites (black/white, up/down, love/hate), thus life is a game of achieving equilibrium. We have a universe of paradoxes within ourselves, not just in physics.
Individually, you balance your intellect and heart, but as a species, we're full of polarities. They might be gentle and compassionate, then ruthless and unsympathetic.
We desire for connection so much that we personify non-human beings and objects while turning to violence and hatred toward others. These contrasts baffle me. Will we find balance?
Anthropomorphization
Assigning human-like features or bonding with objects is common throughout childhood. Cartoons often give non-humans human traits. Adults still anthropomorphize this trait. Researchers agree we start doing it as infants and continue throughout life.
Humans of all ages are good at humanizing stuff. We build emotional attachments to weather events, inanimate objects, animals, plants, and locales. Gods, goddesses, and fictitious figures are anthropomorphized.
Cast Away, starring Tom Hanks, features anthropization. Hanks is left on an island, where he builds an emotional bond with a volleyball he calls Wilson.
We became emotionally invested in Wilson, including myself.
Why do we do it, though?
Our instincts and traits helped us survive and thrive. Our brain is alert to other people's thoughts, feelings, and intentions to assist us to determine who is safe or hazardous. We can think about others and our own mental states, or about thinking. This is the Theory of Mind.
Neurologically, specialists believe the Theory of Mind has to do with our mirror neurons, which exhibit the same activity while executing or witnessing an action.
Mirror neurons may contribute to anthropization, but they're not the only ones. In 2021, Harvard Medical School researchers at MGH and MIT colleagues published a study on the brain's notion of mind.
“Our study provides evidence to support theory of mind by individual neurons. Until now, it wasn’t clear whether or how neurons were able to perform these social cognitive computations.”
Neurons have particular functions, researchers found. Others encode information that differentiates one person's beliefs from another's. Some neurons reflect tale pieces, whereas others aren't directly involved in social reasoning but may multitask contributing factors.
Combining neuronal data gives a precise portrait of another's beliefs and comprehension. The theory of mind describes how we judge and understand each other in our species, and it likely led to anthropomorphism. Neuroscience indicates identical brain regions react to human or non-human behavior, like mirror neurons.
Some academics believe we're wired for connection, which explains why we anthropomorphize. When we're alone, we may anthropomorphize non-humans.
Humanizing non-human entities may make them deserving of moral care, according to another theory. Animamorphizing something makes it responsible for its actions and deserves punishments or rewards. This mental shift is typically apparent in our connections with pets and leads to deanthropomorphization.
Dehumanization
Dehumanizing involves denying someone or anything ethical regard, the opposite of anthropomorphizing.
Dehumanization occurs throughout history. We do it to everything in nature, including ourselves. We experiment on and torture animals. We enslave, hate, and harm other groups of people.
Race, immigrant status, dress choices, sexual orientation, social class, religion, gender, politics, need I go on? Our degrading behavior is promoting fascism and division everywhere.
Dehumanizing someone or anything reduces their agency and value. Many assume they're immune to this feature, but tests disagree.
It's inevitable. Humans are wired to have knee-jerk reactions to differences. We are programmed to dehumanize others, and it's easier than we'd like to admit.
Why do we do it, though?
Dehumanizing others is simpler than humanizing things for several reasons. First, we consider everything unusual as harmful, which has helped our species survive for hundreds of millions of years. Our propensity to be distrustful of others, like our fear of the unknown, promotes an us-vs.-them mentality.
Since WWII, various studies have been done to explain how or why the holocaust happened. How did so many individuals become radicalized to commit such awful actions and feel morally justified? Researchers quickly showed how easily the mind can turn gloomy.
Stanley Milgram's 1960s electroshock experiment highlighted how quickly people bow to authority to injure others. Philip Zimbardo's 1971 Stanford Prison Experiment revealed how power may be abused.
The us-versus-them attitude is natural and even young toddlers act on it. Without a relationship, empathy is more difficult.
It's terrifying how quickly dehumanizing behavior becomes commonplace. The current pandemic is an example. Most countries no longer count deaths. Long Covid is a major issue, with predictions of a handicapped tsunami in the future years. Mostly, we shrug.
In 2020, we panicked. Remember everyone's caution? Now Long Covid is ruining more lives, threatening to disable an insane amount of our population for months or their entire lives.
There's little research. Experts can't even classify or cure it. The people should be outraged, but most have ceased caring. They're over covid.
We're encouraged to find a method to live with a terrible pandemic that will cause years of damage. People aren't worried about infection anymore. They shrug and say, "We'll all get it eventually," then hope they're not one of the 30% who develops Long Covid.
We can correct course before further damage. Because we can recognize our urges and biases, we're not captives to them. We can think critically about our thoughts and behaviors, then attempt to improve. We can recognize our deficiencies and work to attain balance.
Changing perspectives
We're currently attempting to find equilibrium between opposites. It's superficial to defend extremes by stating we're only human or wired this way because both imply we have no control.
Being human involves having self-awareness, and by being careful of our thoughts and acts, we can find balance and recognize opposites' purpose.
Extreme anthropomorphizing and dehumanizing isolate and imperil us. We anthropomorphize because we desire connection and dehumanize because we're terrified, frequently of the connection we crave. Will we find balance?
Katrina Paulson ponders humanity, unanswered questions, and discoveries. Please check out her newsletters, Curious Adventure and Curious Life.

Nojus Tumenas
3 years ago
NASA: Strange Betelgeuse Explosion Just Took Place
Orion's red supergiant Betelgeuse erupted. This is astronomers' most magnificent occurrence.
Betelgeuse, a supergiant star in Orion, garnered attention in 2019 for its peculiar appearance. It continued to dim in 2020.
The star was previously thought to explode as a supernova. Studying the event has revealed what happened to Betelgeuse since it happened.
Astronomers saw that the star released a large amount of material, causing it to lose a section of its surface.
They have never seen anything like this and are unsure what caused the star to release so much material.
According to Harvard-Smithsonian Center for Astrophysics astrophysicist Andrea Dupre, astronomers' data reveals an unexplained mystery.
They say it's a new technique to examine star evolution. The James Webb telescope revealed the star's surface features.
Corona flares are stellar mass ejections. These eruptions change the Sun's outer atmosphere.
This could affect power grids and satellite communications if it hits Earth.
Betelgeuse's flare ejected four times more material than the Sun's corona flare.
Astronomers have monitored star rhythms for 50 years. They've seen its dimming and brightening cycle start, stop, and repeat.
Monitoring Betelgeuse's pulse revealed the eruption's power.
Dupre believes the star's convection cells are still amplifying the blast's effects, comparing it to an imbalanced washing machine tub.
The star's outer layer has returned to normal, Hubble data shows. The photosphere slowly rebuilds its springy surface.
Dupre noted the star's unusual behavior. For instance, it’s causing its interior to bounce.
This suggests that the mass ejections that caused the star's surface to lose mass were two separate processes.
Researchers hope to better understand star mass ejection with the James Webb Space Telescope.
Daniel Clery
3 years ago
Twisted device investigates fusion alternatives
German stellarator revamped to run longer, hotter, compete with tokamaks
Tokamaks have dominated the search for fusion energy for decades. Just as ITER, the world's largest and most expensive tokamak, nears completion in southern France, a smaller, twistier testbed will start up in Germany.
If the 16-meter-wide stellarator can match or outperform similar-size tokamaks, fusion experts may rethink their future. Stellarators can keep their superhot gases stable enough to fuse nuclei and produce energy. They can theoretically run forever, but tokamaks must pause to reset their magnet coils.
The €1 billion German machine, Wendelstein 7-X (W7-X), is already getting "tokamak-like performance" in short runs, claims plasma physicist David Gates, preventing particles and heat from escaping the superhot gas. If W7-X can go long, "it will be ahead," he says. "Stellarators excel" Eindhoven University of Technology theorist Josefine Proll says, "Stellarators are back in the game." A few of startup companies, including one that Gates is leaving Princeton Plasma Physics Laboratory, are developing their own stellarators.
W7-X has been running at the Max Planck Institute for Plasma Physics (IPP) in Greifswald, Germany, since 2015, albeit only at low power and for brief runs. W7-X's developers took it down and replaced all inner walls and fittings with water-cooled equivalents, allowing for longer, hotter runs. The team reported at a W7-X board meeting last week that the revised plasma vessel has no leaks. It's expected to restart later this month to show if it can get plasma to fusion-igniting conditions.
Wendelstein 7-X's water-cooled inner surface allows for longer runs.
HOSAN/IPP
Both stellarators and tokamaks create magnetic gas cages hot enough to melt metal. Microwaves or particle beams heat. Extreme temperatures create a plasma, a seething mix of separated nuclei and electrons, and cause the nuclei to fuse, releasing energy. A fusion power plant would use deuterium and tritium, which react quickly. Non-energy-generating research machines like W7-X avoid tritium and use hydrogen or deuterium instead.
Tokamaks and stellarators use electromagnetic coils to create plasma-confining magnetic fields. A greater field near the hole causes plasma to drift to the reactor's wall.
Tokamaks control drift by circulating plasma around a ring. Streaming creates a magnetic field that twists and stabilizes ionized plasma. Stellarators employ magnetic coils to twist, not plasma. Once plasma physicists got powerful enough supercomputers, they could optimize stellarator magnets to improve plasma confinement.
W7-X is the first large, optimized stellarator with 50 6- ton superconducting coils. Its construction began in the mid-1990s and cost roughly twice the €550 million originally budgeted.
The wait hasn't disappointed researchers. W7-X director Thomas Klinger: "The machine operated immediately." "It's a friendly machine." It did everything we asked." Tokamaks are prone to "instabilities" (plasma bulging or wobbling) or strong "disruptions," sometimes associated to halted plasma flow. IPP theorist Sophia Henneberg believes stellarators don't employ plasma current, which "removes an entire branch" of instabilities.
In early stellarators, the magnetic field geometry drove slower particles to follow banana-shaped orbits until they collided with other particles and leaked energy. Gates believes W7-X's ability to suppress this effect implies its optimization works.
W7-X loses heat through different forms of turbulence, which push particles toward the wall. Theorists have only lately mastered simulating turbulence. W7-X's forthcoming campaign will test simulations and turbulence-fighting techniques.
A stellarator can run constantly, unlike a tokamak, which pulses. W7-X has run 100 seconds—long by tokamak standards—at low power. The device's uncooled microwave and particle heating systems only produced 11.5 megawatts. The update doubles heating power. High temperature, high plasma density, and extensive runs will test stellarators' fusion power potential. Klinger wants to heat ions to 50 million degrees Celsius for 100 seconds. That would make W7-X "a world-class machine," he argues. The team will push for 30 minutes. "We'll move step-by-step," he says.
W7-X's success has inspired VCs to finance entrepreneurs creating commercial stellarators. Startups must simplify magnet production.
Princeton Stellarators, created by Gates and colleagues this year, has $3 million to build a prototype reactor without W7-X's twisted magnet coils. Instead, it will use a mosaic of 1000 HTS square coils on the plasma vessel's outside. By adjusting each coil's magnetic field, operators can change the applied field's form. Gates: "It moves coil complexity to the control system." The company intends to construct a reactor that can fuse cheap, abundant deuterium to produce neutrons for radioisotopes. If successful, the company will build a reactor.
Renaissance Fusion, situated in Grenoble, France, raised €16 million and wants to coat plasma vessel segments in HTS. Using a laser, engineers will burn off superconductor tracks to carve magnet coils. They want to build a meter-long test segment in 2 years and a full prototype by 2027.
Type One Energy in Madison, Wisconsin, won DOE money to bend HTS cables for stellarator magnets. The business carved twisting grooves in metal with computer-controlled etching equipment to coil cables. David Anderson of the University of Wisconsin, Madison, claims advanced manufacturing technology enables the stellarator.
Anderson said W7-X's next phase will boost stellarator work. “Half-hour discharges are steady-state,” he says. “This is a big deal.”
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Karthik Rajan
3 years ago
11 Cooking Hacks I Wish I Knew Earlier
Quick, easy and tasty (and dollops of parenting around food).

My wife and mom are both great mothers. They're super-efficient planners. They soak and ferment food. My 104-year-old grandfather loved fermented foods.
When I'm hungry and need something fast, I waffle to the pantry. Like most people, I like to improvise. I wish I knew these 11 hacks sooner.
1. The world's best pasta sauce only has 3 ingredients.
You watch recipe videos with prepped ingredients. In reality, prepping and washing take time. The food's taste isn't guaranteed. The raw truth at a sublime level is not talked about often.
Sometimes a radical recipe comes along that's so easy and tasty, you're dumbfounded. The Classic Italian Cook Book has a pasta recipe.
One 28-ounce can of whole, peeled tomatoes, one medium peeled onion, and 5 tablespoons of butter. And salt to taste.
Combine everything in a single pot and simmer for 45 minutes, uncovered. Stir occasionally. Toss the onion halves after 45 minutes and pour the sauce over pasta. Finish!
This simple recipe fights our deepest fears.
Salt to taste! Customized to perfection, no frills.
2. Reheating rice with ice. Magical.
Most of the world eats rice. I was raised in south India. My grandfather farmed rice in the Cauvery river delta.
The problem with rice With growing kids, you can't cook just enough. Leftovers are a norm. Microwaves help most people. Ice cubes are the frosting.
Before reheating rice in the microwave, add an ice cube. The ice will steam the rice, making it fluffy and delicious again.
3. Pineapple leaf
if it comes off easy, it is ripe enough to cut. No rethinking.
My daughter loves pineapples like her dad. One daddy task is cutting them. Sharing immediate results is therapeutic.
Timing the cut has been the most annoying part over the years. The pineapple leaf tip reveals the fruitiness inside. Always loved it.
4. Magic knife words (rolling and curling)
Cutting hand: Roll the blade's back, not its tip, to cut.
Other hand: If you can’t see your finger tips, you can’t cut them. So curl your fingers.
I dislike that schools don't teach financial literacy or cutting skills.
My wife and I used scissors differently for 25 years. We both used the thumb. My index finger, her middle. We googled the difference when I noticed it and laughed. She's right.
This video teaches knifing skills:
5. Best advice about heat
If it's done in the pan, it's overdone on the plate.
This simple advice stands out when we worry about ingredients and proportions.
6. The truth about pasta water
Pasta water should be sea-salty.
Properly seasoning food separates good from great. Salt depends is a good line.
Want delicious pasta? Well, then kind of a lot, to be perfectly honest.
7. Clean as you go
Clean blender as you go by blending water and dish soap.
I find clean as you go easier than clean afterwords. This easy tip is gold.
8. Clean as you go (bis)
Microwave a bowl of water, vinegar, and a toothpick for 5 minutes.
2 cups water, 2 tablespoons vinegar, and a toothpick to prevent overflow.
5-minute microwave. Let the steam work for another 2 minutes. Sponge-off dirt and food. Simple.
9 and 10. Tools,tools, tools
Immersion blender and pressure cooker save time and money.
Narrative: I experienced fatherly pride. My middle-schooler loves science. We discussed boiling. I spoke. Water doesn't need 100°C to boil. She looked confused. 100 degrees assume something. The world around the water is a normal room. Changing water pressure affects its boiling point. This saves energy. Pressure cooker magic.
I captivated her. She's into science and sustainable living.
Whistling is a subliminal form of self-expression when done right. Pressure cookers remind me of simple pleasures.
Your handiness depends on your home tools. Immersion blenders are great for pre- and post-cooking. It eliminates chopping and washing. Second to the dishwasher, in my opinion.
11. One pepper is plenty
A story I share with my daughters.
Once, everyone thought about spice (not spicy). More valuable than silk. One of the three mighty oceans was named after a source country. Columbus sailed the wrong way and found America. The explorer called the natives after reaching his spice destination.
It was pre-internet days. His Google wasn't working.
My younger daughter listens in awe. Strong roots. Image cast. She can contextualize one of the ocean names.
I struggle with spices in daily life. Combinations are mind-boggling. I have more spices than Columbus. Flavor explosion has repercussions. You must closely follow the recipe without guarantees. Best aha. Double down on one spice and move on. If you like it, it's great.
I naturally gravitate towards cumin soups, fennel dishes, mint rice, oregano pasta, basil thai curry and cardamom pudding.
Variety enhances life. Each of my dishes is unique.
To each their own comfort food and nostalgic memories.
Happy living!

Jari Roomer
3 years ago
Successful people have this one skill.
Without self-control, you'll waste time chasing dopamine fixes.
I found a powerful quote in Tony Robbins' Awaken The Giant Within:
“Most of the challenges that we have in our personal lives come from a short-term focus” — Tony Robbins
Most people are short-term oriented, but highly successful people are long-term oriented.
Successful people act in line with their long-term goals and values, while the rest are distracted by short-term pleasures and dopamine fixes.
Instant gratification wrecks lives
Instant pleasure is fleeting. Quickly fading effects leave you craving more stimulation.
Before you know it, you're in a cycle of quick fixes. This explains binging on food, social media, and Netflix.
These things cause a dopamine spike, which is entertaining. This dopamine spike crashes quickly, leaving you craving more stimulation.
It's fine to watch TV or play video games occasionally. Problems arise when brain impulses aren't controlled. You waste hours chasing dopamine fixes.
Instant gratification becomes problematic when it interferes with long-term goals, happiness, and life fulfillment.
Most rewarding things require delay
Life's greatest rewards require patience and delayed gratification. They must be earned through patience, consistency, and effort.
Ex:
A fit, healthy body
A deep connection with your spouse
A thriving career/business
A healthy financial situation
These are some of life's most rewarding things, but they take work and patience. They all require the ability to delay gratification.
To have a healthy bank account, you must save (and invest) a large portion of your monthly income. This means no new tech or clothes.
If you want a fit, healthy body, you must eat better and exercise three times a week. So no fast food and Netflix.
It's a battle between what you want now and what you want most.
Successful people choose what they want most over what they want now. It's a major difference.
Instant vs. delayed gratification
Most people subconsciously prefer instant rewards over future rewards, even if the future rewards are more significant.
We humans aren't logical. Emotions and instincts drive us. So we act against our goals and values.
Fortunately, instant gratification bias can be overridden. This is a modern superpower. Effective methods include:
#1: Train your brain to handle overstimulation
Training your brain to function without constant stimulation is a powerful change. Boredom can lead to long-term rewards.
Unlike impulsive shopping, saving money is boring. Having lots of cash is amazing.
Compared to video games, deep work is boring. A successful online business is rewarding.
Reading books is boring compared to scrolling through funny videos on social media. Knowledge is invaluable.
You can't do these things if your brain is overstimulated. Your impulses will control you. To reduce overstimulation addiction, try:
Daily meditation (10 minutes is enough)
Daily study/work for 90 minutes (no distractions allowed)
First hour of the day without phone, social media, and Netflix
Nature walks, journaling, reading, sports, etc.
#2: Make Important Activities Less Intimidating
Instant gratification helps us cope with stress. Starting a book or business can be intimidating. Video games and social media offer a quick escape in such situations.
Make intimidating tasks less so. Break them down into small tasks. Start a new business/side-hustle by:
Get domain name
Design website
Write out a business plan
Research competition/peers
Approach first potential client
Instead of one big mountain, divide it into smaller sub-tasks. This makes a task easier and less intimidating.
#3: Plan ahead for important activities
Distractions will invade unplanned time. Your time is dictated by your impulses, which are usually Netflix, social media, fast food, and video games. It wants quick rewards and dopamine fixes.
Plan your days and be proactive with your time. Studies show that scheduling activities makes you 3x more likely to do them.
To achieve big goals, you must plan. Don't gamble.
Want to get fit? Schedule next week's workouts. Want a side-job? Schedule your work time.

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 :)
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