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Jack Shepherd

Jack Shepherd

3 years ago

A Dog's Guide to Every Type of Zoom Call Participant

More on Society & Culture

Enrique Dans

Enrique Dans

2 years ago

What happens when those without morals enter the economic world?

IMAGE: Gerd Altmann — Pixabay

I apologize if this sounds basic, but throughout my career, I've always been clear that a company's activities are shaped by its founder(s)' morality.

I consider Palantir, owned by PayPal founder Peter Thiel, evil. He got $5 billion tax-free by hacking a statute to help middle-class savings. That may appear clever, but I think it demonstrates a shocking lack of solidarity with society. As a result of this and other things he has said and done, I early on dismissed Peter Thiel as someone who could contribute anything positive to society, and events soon proved me right: we are talking about someone who clearly considers himself above everyone else and who does not hesitate to set up a company, Palantir, to exploit the data of the little people and sell it to the highest bidder, whoever that is and whatever the consequences.

The German courts have confirmed my warnings concerning Palantir. The problem is that politicians love its surveillance tools because they think knowing more about their constituents gives them power. These are ideal for dictatorships who want to snoop on their populace. Hence, Silicon Valley's triumphalist dialectic has seduced many governments at many levels and collected massive volumes of data to hold forever.

Dangerous company. There are many more. My analysis of the moral principles that disclose company management changed my opinion of Facebook, now Meta, and anyone with a modicum of interest might deduce when that happened, a discovery that leaves you dumbfounded. TikTok was easy because its lack of morality was revealed early when I saw the videos it encouraged minors to post and the repercussions of sharing them through its content recommendation algorithm. When you see something like this, nothing can convince you that the firm can change its morals and become good. Nothing. You know the company is awful and will fail. Speak it, announce it, and change it. It's like a fingerprint—unchangeable.

Some of you who read me frequently make its Facebook today jokes when I write about these firms, and that's fine: they're my moral standards, those of an elderly professor with thirty-five years of experience studying corporations and discussing their cases in class, but you don't have to share them. Since I'm writing this and don't have to submit to any editorial review, that's what it is: when you continuously read a person, you have to assume that they have moral standards and that sometimes you'll agree with them and sometimes you won't. Morality accepts hierarchies, nuances, and even obsessions. I know not everyone shares my opinions, but at least I can voice them. One day, one of those firms may sue me (as record companies did some years ago).

Palantir is incredibly harmful. Limit its operations. Like Meta and TikTok, its business strategy is shaped by its founders' immorality. Such a procedure can never be beneficial.

umair haque

umair haque

2 years ago

The reasons why our civilization is deteriorating

The Industrial Revolution's Curse: Why One Age's Power Prevents the Next Ones

Image Credit: Nature

A surprising fact. Recently, Big Oil's 1970s climate change projections were disturbingly accurate. Of course, we now know that it worked tirelessly to deny climate change, polluting our societies to this day. That's a small example of the Industrial Revolution's curse.

Let me rephrase this nuanced and possibly weird thought. The chart above? Disruptive science is declining. The kind that produces major discoveries, new paradigms, and shattering prejudices.

Not alone. Our civilisation reached a turning point suddenly. Progress stopped and reversed for the first time in centuries.

The Industrial Revolution's Big Bang started it all. At least some humans had riches for the first time, if not all, and with that wealth came many things. Longer, healthier lives since now health may be publicly and privately invested in. For the first time in history, wealthy civilizations could invest their gains in pure research, a good that would have sounded frivolous to cultures struggling to squeeze out the next crop, which required every shoulder to the till.

So. Don't confuse me with the Industrial Revolution's curse. Industry progressed. Contrary. I'm claiming that the Big Bang of Progress is slowing, plateauing, and ultimately reversing. All social indicators show that. From progress itself to disruptive, breakthrough research, everything is slowing down.

It's troubling. Because progress slows and plateaus, pre-modern social problems like fascism, extremism, and fundamentalism return. People crave nostalgic utopias when they lose faith in modernity. That strongman may shield me from this hazardous life. If I accept my place in a blood-and-soil hierarchy, I have a stable, secure position and someone to punch and detest. It's no coincidence that as our civilization hits a plateau of progress, there is a tsunami pulling the world backwards, with people viscerally, openly longing for everything from theocracy to fascism to fundamentalism, an authoritarian strongman to soothe their fears and tell them what to do, whether in Britain, heartland America, India, China, and beyond.

However, one aspect remains unknown. Technology. Let me clarify.

How do most people picture tech? Say that without thinking. Most people think of social media or AI. Well, small correlation engines called artificial neurons are a far cry from biological intelligence, which functions in far more obscure and intricate ways, down to the subatomic level. But let's try it.

Today, tech means AI. But. Do you foresee it?

Consider why civilisation is plateauing and regressing. Because we can no longer provide the most basic necessities at the same rate. On our track, clean air, water, food, energy, medicine, and healthcare will become inaccessible to huge numbers within a decade or three. Not enough. There isn't, therefore prices for food, medicine, and energy keep rising, with occasional relief.

Why our civilizations are encountering what economists like me term a budget constraint—a hard wall of what we can supply—should be evident. Global warming and extinction. Megafires, megadroughts, megafloods, and failed crops. On a civilizational scale, good luck supplying the fundamentals that way. Industrial food production cannot feed a planet warming past two degrees. Crop failures, droughts, floods. Another example: glaciers melt, rivers dry up, and the planet's fresh water supply contracts like a heart attack.

Now. Let's talk tech again. Mostly AI, maybe phone apps. The unsettling reality is that current technology cannot save humanity. Not much.

AI can do things that have become cliches to titillate the masses. It may talk to you and act like a person. It can generate art, which means reproduce it, but nonetheless, AI art! Despite doubts, it promises to self-drive cars. Unimportant.

We need different technology now. AI won't grow crops in ash-covered fields, cleanse water, halt glaciers from melting, or stop the clear-cutting of the planet's few remaining forests. It's not useless, but on a civilizational scale, it's much less beneficial than its proponents claim. By the time it matures, AI can help deliver therapy, keep old people company, and even drive cars more efficiently. None of it can save our culture.

Expand that scenario. AI's most likely use? Replacing call-center workers. Support. It may help doctors diagnose, surgeons orient, or engineers create more fuel-efficient motors. This is civilizationally marginal.

Non-disruptive. Do you see the connection with the paper that indicated disruptive science is declining? AI exemplifies that. It's called disruptive, yet it's a textbook incremental technology. Oh, cool, I can communicate with a bot instead of a poor human in an underdeveloped country and have the same or more trouble being understood. This bot is making more people unemployed. I can now view a million AI artworks.

AI illustrates our civilization's trap. Its innovative technologies will change our lives. But as you can see, its incremental, delivering small benefits at most, and certainly not enough to balance, let alone solve, the broader problem of steadily dropping living standards as our society meets a wall of being able to feed itself with fundamentals.

Contrast AI with disruptive innovations we need. What do we need to avoid a post-Roman Dark Age and preserve our civilization in the coming decades? We must be able to post-industrially produce all our basic needs. We need post-industrial solutions for clean water, electricity, cement, glass, steel, manufacture for garments and shoes, starting with the fossil fuel-intensive plastic, cotton, and nylon they're made of, and even food.

Consider. We have no post-industrial food system. What happens when crop failures—already dangerously accelerating—reach a critical point? Our civilization is vulnerable. Think of ancient civilizations that couldn't survive the drying up of their water sources, the failure of their primary fields, which they assumed the gods would preserve forever, or an earthquake or sickness that killed most of their animals. Bang. Lost. They failed. They splintered, fragmented, and abandoned vast capitols and cities, and suddenly, in history's sight, poof, they were gone.

We're getting close. Decline equals civilizational peril.

We believe dumb notions about AI becoming disruptive when it's incremental. Most of us don't realize our civilization's risk because we believe these falsehoods. Everyone should know that we cannot create any thing at civilizational scale without fossil fuels. Most of us don't know it, thus we don't realize that the breakthrough technologies and systems we need don't manipulate information anymore. Instead, biotechnologies, largely but not genes, generate food without fossil fuels.

We need another Industrial Revolution. AI, apps, bots, and whatnot won't matter unless you think you can eat and drink them while the world dies and fascists, lunatics, and zealots take democracy's strongholds. That's dramatic, but only because it's already happening. Maybe AI can entertain you in that bunker while society collapses with smart jokes or a million Mondrian-like artworks. If civilization is to survive, it cannot create the new Industrial Revolution.

The revolution has begun, but only in small ways. Post-industrial fundamental systems leaders are developing worldwide. The Netherlands is leading post-industrial agriculture. That's amazing because it's a tiny country performing well. Correct? Discover how large-scale agriculture can function, not just you and me, aged hippies, cultivating lettuce in our backyards.

Iceland is leading bioplastics, which, if done well, will be a major advance. Of sure, microplastics are drowning the oceans. What should we do since we can't live without it? We need algae-based bioplastics for green plastic.

That's still young. Any of the above may not function on a civilizational scale. Bioplastics use algae, which can cause problems if overused. None of the aforementioned indicate the next Industrial Revolution is here. Contrary. Slowly.

We have three decades until everything fails. Before life ends. Curtain down. No more fields, rivers, or weather. Freshwater and life stocks have plummeted. Again, we've peaked and declined in our ability to live at today's relatively rich standards. Game over—no more. On a dying planet, producing the fundamentals for a civilisation that left it too late to construct post-industrial systems becomes next to impossible, with output dropping faster and quicker each year, quarter, and day.

Too slow. That's because it's not really happening. Most people think AI when I say tech. I get a politicized response if I say Green New Deal or Clean Industrial Revolution. Half the individuals I talk to have been politicized into believing that climate change isn't real and that any breakthrough technical progress isn't required, desirable, possible, or genuine. They'll suffer.

The Industrial Revolution curse. Every revolution creates new authorities, which ossify and refuse to relinquish their privileges. For fifty years, Big Oil has denied climate change, even though their scientists predicted it. We also have a software industry and its venture capital power centers that are happy for the average person to think tech means chatbots, not being able to produce basics for a civilization without destroying the planet, and billionaires who buy comms platforms for the same eye-watering amount of money it would take to save life on Earth.

The entire world's vested interests are against the next industrial revolution, which is understandable since they were established from fossil money. From finance to energy to corporate profits to entertainment, power in our world is the result of the last industrial revolution, which means it has no motivation or purpose to give up fossil money, as we are witnessing more brutally out in the open.

Thus, the Industrial Revolution's curse—fossil power—rules our globe. Big Agriculture, Big Pharma, Wall St., Silicon Valley, and many others—including politics, which they buy and sell—are basically fossil power, and they have no interest in generating or letting the next industrial revolution happen. That's why tiny enterprises like those creating bioplastics in Iceland or nations savvy enough to shun fossil power, like the Netherlands, which has a precarious relationship with nature, do it. However, fossil power dominates politics, economics, food, clothes, energy, and medicine, and it has no motivation to change.

Allow disruptive innovations again. As they occur, its position becomes increasingly vulnerable. If you were fossil power, would you allow another industrial revolution to destroy its privilege and wealth?

You might, since power and money haven't corrupted you. However, fossil power prevents us from building, creating, and growing what we need to survive as a society. I mean the entire economic, financial, and political power structure from the last industrial revolution, not simply Big Oil. My friends, fossil power's chokehold over our society is likely to continue suffocating the advances that could have spared our civilization from a decline that's now here and spiraling closer to oblivion.

The woman

The woman

3 years ago

The renowned and highest-paid Google software engineer

His story will inspire you.

Made by me with Midjourney

“Google search went down for a few hours in 2002; Jeff Dean handled all the queries by hand and checked quality doubled.”- Jeff Dean Facts.

One of many Jeff Dean jokes, but you get the idea.

Google's top six engineers met in a war room in mid-2000. Google's crawling system, which indexed the Web, stopped working. Users could still enter queries, but results were five months old.

Google just signed a deal with Yahoo to power a ten-times-larger search engine. Tension rose. It was crucial. If they failed, the Yahoo agreement would likely fall through, risking bankruptcy for the firm. Their efforts could be lost.

A rangy, tall, energetic thirty-one-year-old man named Jeff dean was among those six brilliant engineers in the makeshift room. He had just left D. E. C. a couple of months ago and started his career in a relatively new firm Google, which was about to change the world. He rolled his chair over his colleague Sanjay and sat right next to him, cajoling his code like a movie director. The history started from there.

When you think of people who shaped the World Wide Web, you probably picture founders and CEOs like Larry Page and Sergey Brin, Marc Andreesen, Tim Berners-Lee, Bill Gates, and Mark Zuckerberg. They’re undoubtedly the brightest people on earth.

Under these giants, legions of anonymous coders work at keyboards to create the systems and products we use. These computer workers are irreplaceable.

Let's get to know him better.

It's possible you've never heard of Jeff Dean. He's American. Dean created many behind-the-scenes Google products. Jeff, co-founder and head of Google's deep learning research engineering team, is a popular technology, innovation, and AI keynote speaker.

While earning an MS and Ph.D. in computer science at the University of Washington, he was a teaching assistant, instructor, and research assistant. Dean joined the Compaq Computer Corporation Western Research Laboratory research team after graduating.

Jeff co-created ProfileMe and the Continuous Profiling Infrastructure for Digital at Compaq. He co-designed and implemented Swift, one of the fastest Java implementations. He was a senior technical staff member at mySimon Inc., retrieving and caching electronic commerce content.

Dean, a top young computer scientist, joined Google in mid-1999. He was always trying to maximize a computer's potential as a child.

An expert

His high school program for processing massive epidemiological data was 26 times faster than professionals'. Epi Info, in 13 languages, is used by the CDC. He worked on compilers as a computer science Ph.D. These apps make source code computer-readable.

Dean never wanted to work on compilers forever. He left Academia for Google, which had less than 20 employees. Dean helped found Google News and AdSense, which transformed the internet economy. He then addressed Google's biggest issue, scaling.

Growing Google faced a huge computing challenge. They developed PageRank in the late 1990s to return the most relevant search results. Google's popularity slowed machine deployment.

Dean solved problems, his specialty. He and fellow great programmer Sanjay Ghemawat created the Google File System, which distributed large data over thousands of cheap machines.

These two also created MapReduce, which let programmers handle massive data quantities on parallel machines. They could also add calculations to the search algorithm. A 2004 research article explained MapReduce, which became an industry sensation.

Several revolutionary inventions

Dean's other initiatives were also game-changers. BigTable, a petabyte-capable distributed data storage system, was based on Google File. The first global database, Spanner, stores data on millions of servers in dozens of data centers worldwide.

It underpins Gmail and AdWords. Google Translate co-founder Jeff Dean is surprising. He contributes heavily to Google News. Dean is Senior Fellow of Google Research and Health and leads Google AI.

Recognitions

The National Academy of Engineering elected Dean in 2009. He received the 2009 Association for Computing Machinery fellowship and the 2016 American Academy of Arts and Science fellowship. He received the 2007 ACM-SIGOPS Mark Weiser Award and the 2012 ACM-Infosys Foundation Award. Lists could continue.

A sneaky question may arrive in your mind: How much does this big brain earn? Well, most believe he is one of the highest-paid employees at Google. According to a survey, he is paid $3 million a year.

He makes espresso and chats with a small group of Googlers most mornings. Dean steams milk, another grinds, and another brews espresso. They discuss families and technology while making coffee. He thinks this little collaboration and idea-sharing keeps Google going.

“Some of us have been working together for more than 15 years,” Dean said. “We estimate that we’ve collectively made more than 20,000 cappuccinos together.”

We all know great developers and software engineers. It may inspire many.

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Daniel Clery

3 years ago

Twisted device investigates fusion alternatives

German stellarator revamped to run longer, hotter, compete with tokamaks

Wendelstein 7-X’s complex geometry was a nightmare to build but, when fired up, worked from the start.

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 twisting inner surface is now water cooled, enabling longer runs

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.”

Leonardo Castorina

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:

  1. 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.
  2. Instructions for using Obsidian, managing notes, reading lists, and useful plugins. This section demonstrates how I use Obsidian, my preferred knowledge management tool.
  3. 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:

  1. It had to be private, and nobody had to be able to read the entries.
  2. 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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Sam Hickmann

Sam Hickmann

3 years ago

A quick guide to formatting your text on INTΞGRITY

[06/20/2022 update] We have now implemented a powerful text editor, but you can still use markdown.

Markdown:

Headers

SYNTAX:

# This is a heading 1
## This is a heading 2
### This is a heading 3 
#### This is a heading 4

RESULT:

This is a heading 1

This is a heading 2

This is a heading 3

This is a heading 4

Emphasis

SYNTAX:

**This text will be bold**
~~Strikethrough~~
*You **can** combine them*

RESULT:

This text will be italic
This text will be bold
You can combine them

Images

SYNTAX:

![Engelbart](https://history-computer.com/ModernComputer/Basis/images/Engelbart.jpg)

RESULT:

Videos

SYNTAX:

https://www.youtube.com/watch?v=7KXGZAEWzn0

RESULT:

Links

SYNTAX:

[Int3grity website](https://www.int3grity.com)

RESULT:

Int3grity website

Tweets

SYNTAX:

https://twitter.com/samhickmann/status/1503800505864130561

RESULT:

Blockquotes

SYNTAX:

> Human beings face ever more complex and urgent problems, and their effectiveness in dealing with these problems is a matter that is critical to the stability and continued progress of society. \- Doug Engelbart, 1961

RESULT:

Human beings face ever more complex and urgent problems, and their effectiveness in dealing with these problems is a matter that is critical to the stability and continued progress of society. - Doug Engelbart, 1961

Inline code

SYNTAX:

Text inside `backticks` on a line will be formatted like code.

RESULT:

Text inside backticks on a line will be formatted like code.

Code blocks

SYNTAX:

'''js
function fancyAlert(arg) {
if(arg) {
$.facebox({div:'#foo'})
}
}
'''

RESULT:

function fancyAlert(arg) {
  if(arg) {
    $.facebox({div:'#foo'})
  }
}

Maths

We support LaTex to typeset math. We recommend reading the full documentation on the official website

SYNTAX:

$$[x^n+y^n=z^n]$$

RESULT:

[x^n+y^n=z^n]

Tables

SYNTAX:

| header a | header b |
| ---- | ---- |
| row 1 col 1 | row 1 col 2 |

RESULT:

header aheader bheader c
row 1 col 1row 1 col 2row 1 col 3