More on Web3 & Crypto

Marco Manoppo
3 years ago
Failures of DCG and Genesis
Don't sleep with your own sister.
70% of lottery winners go broke within five years. You've heard the last one. People who got rich quickly without setbacks and hard work often lose it all. My father said, "Easy money is easily lost," and a wealthy friend who owns a family office said, "The first generation makes it, the second generation spends it, and the third generation blows it."
This is evident. Corrupt politicians in developing countries live lavishly, buying their third wives' fifth Hermès bag and celebrating New Year's at The Brando Resort. A successful businessperson from humble beginnings is more conservative with money. More so if they're atom-based, not bit-based. They value money.
Crypto can "feel" easy. I have nothing against capital market investing. The global financial system is shady, but that's another topic. The problem started when those who took advantage of easy money started affecting other businesses. VCs did minimal due diligence on FTX because they needed deal flow and returns for their LPs. Lenders did minimum diligence and underwrote ludicrous loans to 3AC because they needed revenue.
Alameda (hence FTX) and 3AC made "easy money" Genesis and DCG aren't. Their businesses are more conventional, but they underestimated how "easy money" can hurt them.
Genesis has been the victim of easy money hubris and insolvency, losing $1 billion+ to 3AC and $200M to FTX. We discuss the implications for the broader crypto market.
Here are the quick takeaways:
Genesis is one of the largest and most notable crypto lenders and prime brokerage firms.
DCG and Genesis have done related party transactions, which can be done right but is a bad practice.
Genesis owes DCG $1.5 billion+.
If DCG unwinds Grayscale's GBTC, $9-10 billion in BTC will hit the market.
DCG will survive Genesis.
What happened?
Let's recap the FTX shenanigan from two weeks ago. Shenanigans! Delphi's tweet sums up the craziness. Genesis has $175M in FTX.
Cred's timeline: I hate bad crisis management. Yes, admitting their balance sheet hole right away might've sparked more panic, and there's no easy way to convey your trouble, but no one ever learns.
By November 23, rumors circulated online that the problem could affect Genesis' parent company, DCG. To address this, Barry Silbert, Founder, and CEO of DCG released a statement to shareholders.
A few things are confirmed thanks to this statement.
DCG owes $1.5 billion+ to Genesis.
$500M is due in 6 months, and the rest is due in 2032 (yes, that’s not a typo).
Unless Barry raises new cash, his last-ditch efforts to repay the money will likely push the crypto market lower.
Half a year of GBTC fees is approximately $100M.
They can pay $500M with GBTC.
With profits, sell another port.
Genesis has hired a restructuring adviser, indicating it is in trouble.
Rehypothecation
Every crypto problem in the past year seems to be rehypothecation between related parties, excessive leverage, hubris, and the removal of the money printer. The Bankless guys provided a chart showing 2021 crypto yield.
In June 2022, @DataFinnovation published a great investigation about 3AC and DCG. Here's a summary.
3AC borrowed BTC from Genesis and pledged it to create Grayscale's GBTC shares.
3AC uses GBTC to borrow more money from Genesis.
This lets 3AC leverage their capital.
3AC's strategy made sense because GBTC had a premium, creating "free money."
GBTC's discount and LUNA's implosion caused problems.
3AC lost its loan money in LUNA.
Margin called on 3ACs' GBTC collateral.
DCG bought GBTC to avoid a systemic collapse and a larger discount.
Genesis lost too much money because 3AC can't pay back its loan. DCG "saved" Genesis, but the FTX collapse hurt Genesis further, forcing DCG and Genesis to seek external funding.
bruh…
Learning Experience
Co-borrowing. Unnecessary rehypothecation. Extra space. Governance disaster. Greed, hubris. Crypto has repeatedly shown it can recreate traditional financial system disasters quickly. Working in crypto is one of the best ways to learn crazy financial tricks people will do for a quick buck much faster than if you dabble in traditional finance.
Moving Forward
I think the crypto industry needs to consider its future. This is especially true for professionals. I'm not trying to scare you. In 2018 and 2020, I had doubts. No doubts now. Detailing the crypto industry's potential outcomes helped me gain certainty and confidence in its future. This includes VCs' benefits and talking points during the bull market, as well as what would happen if government regulations became hostile, etc. Even if that happens, I'm certain. This is permanent. I may write a post about that soon.
Sincerely,
M.

Farhan Ali Khan
2 years ago
Introduction to Zero-Knowledge Proofs: The Art of Proving Without Revealing
Zero-Knowledge Proofs for Beginners
Published here originally.
Introduction
I Spy—did you play as a kid? One person chose a room object, and the other had to guess it by answering yes or no questions. I Spy was entertaining, but did you know it could teach you cryptography?
Zero Knowledge Proofs let you show your pal you know what they picked without exposing how. Math replaces electronics in this secret spy mission. Zero-knowledge proofs (ZKPs) are sophisticated cryptographic tools that allow one party to prove they have particular knowledge without revealing it. This proves identification and ownership, secures financial transactions, and more. This article explains zero-knowledge proofs and provides examples to help you comprehend this powerful technology.
What is a Proof of Zero Knowledge?
Zero-knowledge proofs prove a proposition is true without revealing any other information. This lets the prover show the verifier that they know a fact without revealing it. So, a zero-knowledge proof is like a magician's trick: the prover proves they know something without revealing how or what. Complex mathematical procedures create a proof the verifier can verify.
Want to find an easy way to test it out? Try out with tis awesome example! ZK Crush
Describe it as if I'm 5
Alex and Jack found a cave with a center entrance that only opens when someone knows the secret. Alex knows how to open the cave door and wants to show Jack without telling him.
Alex and Jack name both pathways (let’s call them paths A and B).
In the first phase, Alex is already inside the cave and is free to select either path, in this case A or B.
As Alex made his decision, Jack entered the cave and asked him to exit from the B path.
Jack can confirm that Alex really does know the key to open the door because he came out for the B path and used it.
To conclude, Alex and Jack repeat:
Alex walks into the cave.
Alex follows a random route.
Jack walks into the cave.
Alex is asked to follow a random route by Jack.
Alex follows Jack's advice and heads back that way.
What is a Zero Knowledge Proof?
At a high level, the aim is to construct a secure and confidential conversation between the prover and the verifier, where the prover convinces the verifier that they have the requisite information without disclosing it. The prover and verifier exchange messages and calculate in each round of the dialogue.
The prover uses their knowledge to prove they have the information the verifier wants during these rounds. The verifier can verify the prover's truthfulness without learning more by checking the proof's mathematical statement or computation.
Zero knowledge proofs use advanced mathematical procedures and cryptography methods to secure communication. These methods ensure the evidence is authentic while preventing the prover from creating a phony proof or the verifier from extracting unnecessary information.
ZK proofs require examples to grasp. Before the examples, there are some preconditions.
Criteria for Proofs of Zero Knowledge
Completeness: If the proposition being proved is true, then an honest prover will persuade an honest verifier that it is true.
Soundness: If the proposition being proved is untrue, no dishonest prover can persuade a sincere verifier that it is true.
Zero-knowledge: The verifier only realizes that the proposition being proved is true. In other words, the proof only establishes the veracity of the proposition being supported and nothing more.
The zero-knowledge condition is crucial. Zero-knowledge proofs show only the secret's veracity. The verifier shouldn't know the secret's value or other details.
Example after example after example
To illustrate, take a zero-knowledge proof with several examples:
Initial Password Verification Example
You want to confirm you know a password or secret phrase without revealing it.
Use a zero-knowledge proof:
You and the verifier settle on a mathematical conundrum or issue, such as figuring out a big number's components.
The puzzle or problem is then solved using the hidden knowledge that you have learned. You may, for instance, utilize your understanding of the password to determine the components of a particular number.
You provide your answer to the verifier, who can assess its accuracy without knowing anything about your private data.
You go through this process several times with various riddles or issues to persuade the verifier that you actually are aware of the secret knowledge.
You solved the mathematical puzzles or problems, proving to the verifier that you know the hidden information. The proof is zero-knowledge since the verifier only sees puzzle solutions, not the secret information.
In this scenario, the mathematical challenge or problem represents the secret, and solving it proves you know it. The evidence does not expose the secret, and the verifier just learns that you know it.
My simple example meets the zero-knowledge proof conditions:
Completeness: If you actually know the hidden information, you will be able to solve the mathematical puzzles or problems, hence the proof is conclusive.
Soundness: The proof is sound because the verifier can use a publicly known algorithm to confirm that your answer to the mathematical conundrum or difficulty is accurate.
Zero-knowledge: The proof is zero-knowledge because all the verifier learns is that you are aware of the confidential information. Beyond the fact that you are aware of it, the verifier does not learn anything about the secret information itself, such as the password or the factors of the number. As a result, the proof does not provide any new insights into the secret.
Explanation #2: Toss a coin.
One coin is biased to come up heads more often than tails, while the other is fair (i.e., comes up heads and tails with equal probability). You know which coin is which, but you want to show a friend you can tell them apart without telling them.
Use a zero-knowledge proof:
One of the two coins is chosen at random, and you secretly flip it more than once.
You show your pal the following series of coin flips without revealing which coin you actually flipped.
Next, as one of the two coins is flipped in front of you, your friend asks you to tell which one it is.
Then, without revealing which coin is which, you can use your understanding of the secret order of coin flips to determine which coin your friend flipped.
To persuade your friend that you can actually differentiate between the coins, you repeat this process multiple times using various secret coin-flipping sequences.
In this example, the series of coin flips represents the knowledge of biased and fair coins. You can prove you know which coin is which without revealing which is biased or fair by employing a different secret sequence of coin flips for each round.
The evidence is zero-knowledge since your friend does not learn anything about which coin is biased and which is fair other than that you can tell them differently. The proof does not indicate which coin you flipped or how many times you flipped it.
The coin-flipping example meets zero-knowledge proof requirements:
Completeness: If you actually know which coin is biased and which is fair, you should be able to distinguish between them based on the order of coin flips, and your friend should be persuaded that you can.
Soundness: Your friend may confirm that you are correctly recognizing the coins by flipping one of them in front of you and validating your answer, thus the proof is sound in that regard. Because of this, your acquaintance can be sure that you are not just speculating or picking a coin at random.
Zero-knowledge: The argument is that your friend has no idea which coin is biased and which is fair beyond your ability to distinguish between them. Your friend is not made aware of the coin you used to make your decision or the order in which you flipped the coins. Consequently, except from letting you know which coin is biased and which is fair, the proof does not give any additional information about the coins themselves.
Figure out the prime number in Example #3.
You want to prove to a friend that you know their product n=pq without revealing p and q. Zero-knowledge proof?
Use a variant of the RSA algorithm. Method:
You determine a new number s = r2 mod n by computing a random number r.
You email your friend s and a declaration that you are aware of the values of p and q necessary for n to equal pq.
A random number (either 0 or 1) is selected by your friend and sent to you.
You send your friend r as evidence that you are aware of the values of p and q if e=0. You calculate and communicate your friend's s/r if e=1.
Without knowing the values of p and q, your friend can confirm that you know p and q (in the case where e=0) or that s/r is a legitimate square root of s mod n (in the situation where e=1).
This is a zero-knowledge proof since your friend learns nothing about p and q other than their product is n and your ability to verify it without exposing any other information. You can prove that you know p and q by sending r or by computing s/r and sending that instead (if e=1), and your friend can verify that you know p and q or that s/r is a valid square root of s mod n without learning anything else about their values. This meets the conditions of completeness, soundness, and zero-knowledge.
Zero-knowledge proofs satisfy the following:
Completeness: The prover can demonstrate this to the verifier by computing q = n/p and sending both p and q to the verifier. The prover also knows a prime number p and a factorization of n as p*q.
Soundness: Since it is impossible to identify any pair of numbers that correctly factorize n without being aware of its prime factors, the prover is unable to demonstrate knowledge of any p and q that do not do so.
Zero knowledge: The prover only admits that they are aware of a prime number p and its associated factor q, which is already known to the verifier. This is the extent of their knowledge of the prime factors of n. As a result, the prover does not provide any new details regarding n's prime factors.
Types of Proofs of Zero Knowledge
Each zero-knowledge proof has pros and cons. Most zero-knowledge proofs are:
Interactive Zero Knowledge Proofs: The prover and the verifier work together to establish the proof in this sort of zero-knowledge proof. The verifier disputes the prover's assertions after receiving a sequence of messages from the prover. When the evidence has been established, the prover will employ these new problems to generate additional responses.
Non-Interactive Zero Knowledge Proofs: For this kind of zero-knowledge proof, the prover and verifier just need to exchange a single message. Without further interaction between the two parties, the proof is established.
A statistical zero-knowledge proof is one in which the conclusion is reached with a high degree of probability but not with certainty. This indicates that there is a remote possibility that the proof is false, but that this possibility is so remote as to be unimportant.
Succinct Non-Interactive Argument of Knowledge (SNARKs): SNARKs are an extremely effective and scalable form of zero-knowledge proof. They are utilized in many different applications, such as machine learning, blockchain technology, and more. Similar to other zero-knowledge proof techniques, SNARKs enable one party—the prover—to demonstrate to another—the verifier—that they are aware of a specific piece of information without disclosing any more information about that information.
The main characteristic of SNARKs is their succinctness, which refers to the fact that the size of the proof is substantially smaller than the amount of the original data being proved. Because to its high efficiency and scalability, SNARKs can be used in a wide range of applications, such as machine learning, blockchain technology, and more.
Uses for Zero Knowledge Proofs
ZKP applications include:
Verifying Identity ZKPs can be used to verify your identity without disclosing any personal information. This has uses in access control, digital signatures, and online authentication.
Proof of Ownership ZKPs can be used to demonstrate ownership of a certain asset without divulging any details about the asset itself. This has uses for protecting intellectual property, managing supply chains, and owning digital assets.
Financial Exchanges Without disclosing any details about the transaction itself, ZKPs can be used to validate financial transactions. Cryptocurrency, internet payments, and other digital financial transactions can all use this.
By enabling parties to make calculations on the data without disclosing the data itself, Data Privacy ZKPs can be used to preserve the privacy of sensitive data. Applications for this can be found in the financial, healthcare, and other sectors that handle sensitive data.
By enabling voters to confirm that their vote was counted without disclosing how they voted, elections ZKPs can be used to ensure the integrity of elections. This is applicable to electronic voting, including internet voting.
Cryptography Modern cryptography's ZKPs are a potent instrument that enable secure communication and authentication. This can be used for encrypted messaging and other purposes in the business sector as well as for military and intelligence operations.
Proofs of Zero Knowledge and Compliance
Kubernetes and regulatory compliance use ZKPs in many ways. Examples:
Security for Kubernetes ZKPs offer a mechanism to authenticate nodes without disclosing any sensitive information, enhancing the security of Kubernetes clusters. ZKPs, for instance, can be used to verify, without disclosing the specifics of the program, that the nodes in a Kubernetes cluster are running permitted software.
Compliance Inspection Without disclosing any sensitive information, ZKPs can be used to demonstrate compliance with rules like the GDPR, HIPAA, and PCI DSS. ZKPs, for instance, can be used to demonstrate that data has been encrypted and stored securely without divulging the specifics of the mechanism employed for either encryption or storage.
Access Management Without disclosing any private data, ZKPs can be used to offer safe access control to Kubernetes resources. ZKPs can be used, for instance, to demonstrate that a user has the necessary permissions to access a particular Kubernetes resource without disclosing the details of those permissions.
Safe Data Exchange Without disclosing any sensitive information, ZKPs can be used to securely transmit data between Kubernetes clusters or between several businesses. ZKPs, for instance, can be used to demonstrate the sharing of a specific piece of data between two parties without disclosing the details of the data itself.
Kubernetes deployments audited Without disclosing the specifics of the deployment or the data being processed, ZKPs can be used to demonstrate that Kubernetes deployments are working as planned. This can be helpful for auditing purposes and for ensuring that Kubernetes deployments are operating as planned.
ZKPs preserve data and maintain regulatory compliance by letting parties prove things without revealing sensitive information. ZKPs will be used more in Kubernetes as it grows.

Robert Kim
3 years ago
Crypto Legislation Might Progress Beyond Talk in 2022
Financial regulators have for years attempted to apply existing laws to the multitude of issues created by digital assets. In 2021, leading federal regulators and members of Congress have begun to call for legislation to address these issues. As a result, 2022 may be the year when federal legislation finally addresses digital asset issues that have been growing since the mining of the first Bitcoin block in 2009.
Digital Asset Regulation in the Absence of Legislation
So far, Congress has left the task of addressing issues created by digital assets to regulatory agencies. Although a Congressional Blockchain Caucus formed in 2016, House and Senate members introduced few bills addressing digital assets until 2018. As of October 2021, Congress has not amended federal laws on financial regulation, which were last significantly revised by the Dodd-Frank Act in 2010, to address digital asset issues.
In the absence of legislation, issues that do not fit well into existing statutes have created problems. An example is the legal status of digital assets, which can be considered to be either securities or commodities, and can even shift from one to the other over time. Years after the SEC’s 2017 report applying the definition of a security to digital tokens, the SEC and the CFTC have yet to clarify the distinction between securities and commodities for the thousands of digital assets in existence.
SEC Chair Gary Gensler has called for Congress to act, stating in August, “We need additional Congressional authorities to prevent transactions, products, and platforms from falling between regulatory cracks.” Gensler has reached out to Sen. Elizabeth Warren (D-Ma.), who has expressed her own concerns about the need for legislation.
Legislation on Digital Assets in 2021
While regulators and members of Congress talked about the need for legislation, and the debate over cryptocurrency tax reporting in the 2021 infrastructure bill generated headlines, House and Senate bills proposing specific solutions to various issues quietly started to emerge.
Digital Token Sales
Several House bills attempt to address securities law barriers to digital token sales—some of them by building on ideas proposed by regulators in past years.
Exclusion from the definition of a security. Congressional Blockchain Caucus members have been introducing bills to exclude digital tokens from the definition of a security since 2018, and they have revived those bills in 2021. They include the Token Taxonomy Act of 2021 (H.R. 1628), successor to identically named bills in 2018 and 2019, and the Securities Clarity Act (H.R. 4451), successor to a 2020 namesake.
Safe harbor. SEC Commissioner Hester Peirce proposed a regulatory safe harbor for token sales in 2020, and two 2021 bills have proposed statutory safe harbors. Rep. Patrick McHenry (R-N.C.), Republican leader of the House Financial Services Committee, introduced a Clarity for Digital Tokens Act of 2021 (H.R. 5496) that would amend the Securities Act to create a safe harbor providing a grace period of exemption from Securities Act registration requirements. The Digital Asset Market Structure and Investor Protection Act (H.R. 4741) from Rep. Don Beyer (D-Va.) would amend the Securities Exchange Act to define a new type of security—a “digital asset security”—and add issuers of digital asset securities to an existing provision for delayed registration of securities.
Stablecoins
Stablecoins—digital currencies linked to the value of the U.S. dollar or other fiat currencies—have not yet been the subject of regulatory action, although Treasury Secretary Janet Yellen and Federal Reserve Chair Jerome Powell have each underscored the need to create a regulatory framework for them. The Beyer bill proposes to create a regulatory regime for stablecoins by amending Title 31 of the U.S. Code. Treasury Department approval would be required for any “digital asset fiat-based stablecoin” to be issued or used, under an application process to be established by Treasury in consultation with the Federal Reserve, the SEC, and the CFTC.
Serious consideration for any of these proposals in the current session of Congress may be unlikely. A spate of autumn bills on crypto ransom payments (S. 2666, S. 2923, S. 2926, H.R. 5501) shows that Congress is more inclined to pay attention first to issues that are more spectacular and less arcane. Moreover, the arcaneness of digital asset regulatory issues is likely only to increase further, now that major industry players such as Coinbase and Andreessen Horowitz are starting to roll out their own regulatory proposals.
Digital Dollar vs. Digital Yuan
Impetus to pass legislation on another type of digital asset, a central bank digital currency (CBDC), may come from a different source: rivalry with China.
China established itself as a world leader in developing a CBDC with a pilot project launched in 2020, and in 2021, the People’s Bank of China announced that its CBDC will be used at the Beijing Winter Olympics in February 2022. Republican Senators responded by calling for the U.S. Olympic Committee to forbid use of China’s CBDC by U.S. athletes in Beijing and introducing a bill (S. 2543) to require a study of its national security implications.
The Beijing Olympics could motivate a legislative mandate to accelerate implementation of a U.S. digital dollar, which the Federal Reserve has been in the process of considering in 2021. Antecedents to such legislation already exist. A House bill sponsored by 46 Republicans (H.R. 4792) has a provision that would require the Treasury Department to assess China’s CBDC project and report on the status of Federal Reserve work on a CBDC, and the Beyer bill includes a provision amending the Federal Reserve Act to authorize issuing a digital dollar.
Both parties are likely to support creating a digital dollar. The Covid-19 pandemic made a digital dollar for delivery of relief payments a popular idea in 2020, and House Democrats introduced bills with provisions for creating one in 2020 and 2021. Bipartisan support for a bill on a digital dollar, based on concerns both foreign and domestic in nature, could result.
International rivalry and bipartisan support may make the digital dollar a gateway issue for digital asset legislation in 2022. Legislative work on a digital dollar may open the door for considering further digital asset issues—including the regulatory issues that have been emerging for years—in 2022 and beyond.
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Matthew Royse
3 years ago
5 Tips for Concise Writing
Here's how to be clear.
“I have only made this letter longer because I have not had the time to make it shorter.” — French mathematician, physicist, inventor, philosopher, and writer Blaise Pascal
Concise.
People want this. We tend to repeat ourselves and use unnecessary words.
Being vague frustrates readers. It focuses their limited attention span on figuring out what you're saying rather than your message.
Edit carefully.
“Examine every word you put on paper. You’ll find a surprising number that don’t serve any purpose.” — American writer, editor, literary critic, and teacher William Zinsser
How do you write succinctly?
Here are three ways to polish your writing.
1. Delete
Your readers will appreciate it if you delete unnecessary words. If a word or phrase is essential, keep it. Don't force it.
Many readers dislike bloated sentences. Ask yourself if cutting a word or phrase will change the meaning or dilute your message.
For example, you could say, “It’s absolutely essential that I attend this meeting today, so I know the final outcome.” It’s better to say, “It’s critical I attend the meeting today, so I know the results.”
Key takeaway
Delete actually, completely, just, full, kind of, really, and totally. Keep the necessary words, cut the rest.
2. Just Do It
Don't tell readers your plans. Your readers don't need to know your plans. Who are you?
Don't say, "I want to highlight our marketing's problems." Our marketing issues are A, B, and C. This cuts 5–7 words per sentence.
Keep your reader's attention on the essentials, not the fluff. What are you doing? You won't lose readers because you get to the point quickly and don't build up.
Key takeaway
Delete words that don't add to your message. Do something, don't tell readers you will.
3. Cut Overlap
You probably repeat yourself unintentionally. You may add redundant sentences when brainstorming. Read aloud to detect overlap.
Remove repetition from your writing. It's important to edit our writing and thinking to avoid repetition.
Key Takeaway
If you're repeating yourself, combine sentences to avoid overlap.
4. Simplify
Write as you would to family or friends. Communicate clearly. Don't use jargon. These words confuse readers.
Readers want specifics, not jargon. Write simply. Done.
Most adults read at 8th-grade level. Jargon and buzzwords make speech fluffy. This confuses readers who want simple language.
Key takeaway
Ensure all audiences can understand you. USA Today's 5th-grade reading level is intentional. They want everyone to understand.
5. Active voice
Subjects perform actions in active voice. When you write in passive voice, the subject receives the action.
For example, “the board of directors decided to vote on the topic” is an active voice, while “a decision to vote on the topic was made by the board of directors” is a passive voice.
Key takeaway
Active voice clarifies sentences. Active voice is simple and concise.
Bringing It All Together
Five tips help you write clearly. Delete, just do it, cut overlap, use simple language, and write in an active voice.
Clear writing is effective. It's okay to occasionally use unnecessary words or phrases. Realizing it is key. Check your writing.
Adding words costs.
Write more concisely. People will appreciate it and read your future articles, emails, and messages. Spending extra time will increase trust and influence.
“Not that the story need be long, but it will take a long while to make it short.” — Naturalist, essayist, poet, and philosopher Henry David Thoreau

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

M.G. Siegler
2 years ago
G3nerative
Generative AI hype: some thoughts
The sudden surge in "generative AI" startups and projects feels like the inverse of the recent "web3" boom. Both came from hyped-up pots. But while web3 hyped idealistic tech and an easy way to make money, generative AI hypes unsettling tech and questions whether it can be used to make money.
Web3 is technology looking for problems to solve, while generative AI is technology creating almost too many solutions. Web3 has been evangelists trying to solve old problems with new technology. As Generative AI evolves, users are resolving old problems in stunning new ways.
It's a jab at web3, but it's true. Web3's hype, including crypto, was unhealthy. Always expected a tech crash and shakeout. Tech that won't look like "web3" but will enhance "web2"
But that doesn't mean AI hype is healthy. There'll be plenty of bullshit here, too. As moths to a flame, hype attracts charlatans. Again, the difference is the different starting point. People want to use it. Try it.
With the beta launch of Dall-E 2 earlier this year, a new class of consumer product took off. Midjourney followed suit (despite having to jump through the Discord server hoops). Twelve more generative art projects. Lensa, Prisma Labs' generative AI self-portrait project, may have topped the hype (a startup which has actually been going after this general space for quite a while). This week, ChatGPT went off-topic.
This has a "fake-it-till-you-make-it" vibe. We give these projects too much credit because they create easy illusions. This also unlocks new forms of creativity. And faith in new possibilities.
As a user, it's thrilling. We're just getting started. These projects are not only fun to play with, but each week brings a new breakthrough. As an investor, it's all happening so fast, with so much hype (and ethical and societal questions), that no one knows how it will turn out. Web3's demand won't be the issue. Too much demand may cause servers to melt down, sending costs soaring. Companies will try to mix rapidly evolving tech to meet user demand and create businesses. Frustratingly difficult.
Anyway, I wanted an excuse to post some Lensa selfies.
These are really weird. I recognize them as me or a version of me, but I have no memory of them being taken. It's surreal, out-of-body. Uncanny Valley.
