Xenobots, tiny living machines, can duplicate themselves.
Strange and complex behavior of frog cell blobs
A xenobot “parent,” shaped like a hungry Pac-Man (shown in red false color), created an “offspring” xenobot (green sphere) by gathering loose frog cells in its opening.
Tiny “living machines” made of frog cells can make copies of themselves. This newly discovered renewal mechanism may help create self-renewing biological machines.
According to Kirstin Petersen, an electrical and computer engineer at Cornell University who studies groups of robots, “this is an extremely exciting breakthrough.” She says self-replicating robots are a big step toward human-free systems.
Researchers described the behavior of xenobots earlier this year (SN: 3/31/21). Small clumps of skin stem cells from frog embryos knitted themselves into small spheres and started moving. Cilia, or cellular extensions, powered the xenobots around their lab dishes.
The findings are published in the Proceedings of the National Academy of Sciences on Dec. 7. The xenobots can gather loose frog cells into spheres, which then form xenobots.
The researchers call this type of movement-induced reproduction kinematic self-replication. The study's coauthor, Douglas Blackiston of Tufts University in Medford, Massachusetts, and Harvard University, says this is typical. For example, sexual reproduction requires parental sperm and egg cells. Sometimes cells split or budded off from a parent.
“This is unique,” Blackiston says. These xenobots “find loose parts in the environment and cobble them together.” This second generation of xenobots can move like their parents, Blackiston says.
The researchers discovered that spheroid xenobots could only produce one more generation before dying out. The original xenobots' shape was predicted by an artificial intelligence program, allowing for four generations of replication.
A C shape, like an openmouthed Pac-Man, was predicted to be a more efficient progenitor. When improved xenobots were let loose in a dish, they began scooping up loose cells into their gaping “mouths,” forming more sphere-shaped bots (see image below). As many as 50 cells clumped together in the opening of a parent to form a mobile offspring. A xenobot is made up of 4,000–6,000 frog cells.
Petersen likes the Xenobots' small size. “The fact that they were able to do this at such a small scale just makes it even better,” she says. Miniature xenobots could sculpt tissues for implantation or deliver therapeutics inside the body.
Beyond the xenobots' potential jobs, the research advances an important science, says study coauthor and Tufts developmental biologist Michael Levin. The science of anticipating and controlling the outcomes of complex systems, he says.
“No one could have predicted this,” Levin says. “They regularly surprise us.” Researchers can use xenobots to test the unexpected. “This is about advancing the science of being less surprised,” Levin says.
More on Science
DANIEL CLERY
3 years ago
Can space-based solar power solve Earth's energy problems?
Better technology and lower launch costs revive science-fiction tech.
Airbus engineers showed off sustainable energy's future in Munich last month. They captured sunlight with solar panels, turned it into microwaves, and beamed it into an airplane hangar, where it lighted a city model. The test delivered 2 kW across 36 meters, but it posed a serious question: Should we send enormous satellites to capture solar energy in space? In orbit, free of clouds and nighttime, they could create power 24/7 and send it to Earth.
Airbus engineer Jean-Dominique Coste calls it an engineering problem. “But it’s never been done at [large] scale.”
Proponents of space solar power say the demand for green energy, cheaper space access, and improved technology might change that. Once someone invests commercially, it will grow. Former NASA researcher John Mankins says it might be a trillion-dollar industry.
Myriad uncertainties remain, including whether beaming gigawatts of power to Earth can be done efficiently and without burning birds or people. Concept papers are being replaced with ground and space testing. The European Space Agency (ESA), which supported the Munich demo, will propose ground tests to member nations next month. The U.K. government offered £6 million to evaluate innovations this year. Chinese, Japanese, South Korean, and U.S. agencies are working. NASA policy analyst Nikolai Joseph, author of an upcoming assessment, thinks the conversation's tone has altered. What formerly appeared unattainable may now be a matter of "bringing it all together"
NASA studied space solar power during the mid-1970s fuel crunch. A projected space demonstration trip using 1970s technology would have cost $1 trillion. According to Mankins, the idea is taboo in the agency.
Space and solar power technology have evolved. Photovoltaic (PV) solar cell efficiency has increased 25% over the past decade, Jones claims. Telecoms use microwave transmitters and receivers. Robots designed to repair and refuel spacecraft might create solar panels.
Falling launch costs have boosted the idea. A solar power satellite large enough to replace a nuclear or coal plant would require hundreds of launches. ESA scientist Sanjay Vijendran: "It would require a massive construction complex in orbit."
SpaceX has made the idea more plausible. A SpaceX Falcon 9 rocket costs $2600 per kilogram, less than 5% of what the Space Shuttle did, and the company promised $10 per kilogram for its giant Starship, slated to launch this year. Jones: "It changes the equation." "Economics rules"
Mass production reduces space hardware costs. Satellites are one-offs made with pricey space-rated parts. Mars rover Perseverance cost $2 million per kilogram. SpaceX's Starlink satellites cost less than $1000 per kilogram. This strategy may work for massive space buildings consisting of many identical low-cost components, Mankins has long contended. Low-cost launches and "hypermodularity" make space solar power economical, he claims.
Better engineering can improve economics. Coste says Airbus's Munich trial was 5% efficient, comparing solar input to electricity production. When the Sun shines, ground-based solar arrays perform better. Studies show space solar might compete with existing energy sources on price if it reaches 20% efficiency.
Lighter parts reduce costs. "Sandwich panels" with PV cells on one side, electronics in the middle, and a microwave transmitter on the other could help. Thousands of them build a solar satellite without heavy wiring to move power. In 2020, a team from the U.S. Naval Research Laboratory (NRL) flew on the Air Force's X-37B space plane.
NRL project head Paul Jaffe said the satellite is still providing data. The panel converts solar power into microwaves at 8% efficiency, but not to Earth. The Air Force expects to test a beaming sandwich panel next year. MIT will launch its prototype panel with SpaceX in December.
As a satellite orbits, the PV side of sandwich panels sometimes faces away from the Sun since the microwave side must always face Earth. To maintain 24-hour power, a satellite needs mirrors to keep that side illuminated and focus light on the PV. In a 2012 NASA study by Mankins, a bowl-shaped device with thousands of thin-film mirrors focuses light onto the PV array.
International Electric Company's Ian Cash has a new strategy. His proposed satellite uses enormous, fixed mirrors to redirect light onto a PV and microwave array while the structure spins (see graphic, above). 1 billion minuscule perpendicular antennas act as a "phased array" to electronically guide the beam toward Earth, regardless of the satellite's orientation. This design, argues Cash, is "the most competitive economically"
If a space-based power plant ever flies, its power must be delivered securely and efficiently. Jaffe's team at NRL just beamed 1.6 kW over 1 km, and teams in Japan, China, and South Korea have comparable attempts. Transmitters and receivers lose half their input power. Vijendran says space solar beaming needs 75% efficiency, "preferably 90%."
Beaming gigawatts through the atmosphere demands testing. Most designs aim to produce a beam kilometers wide so every ship, plane, human, or bird that strays into it only receives a tiny—hopefully harmless—portion of the 2-gigawatt transmission. Receiving antennas are cheap to build but require a lot of land, adds Jones. You could grow crops under them or place them offshore.
Europe's public agencies currently prioritize space solar power. Jones: "There's a devotion you don't see in the U.S." ESA commissioned two solar cost/benefit studies last year. Vijendran claims it might match ground-based renewables' cost. Even at a higher price, equivalent to nuclear, its 24/7 availability would make it competitive.
ESA will urge member states in November to fund a technical assessment. If the news is good, the agency will plan for 2025. With €15 billion to €20 billion, ESA may launch a megawatt-scale demonstration facility by 2030 and a gigawatt-scale facility by 2040. "Moonshot"
Jamie Ducharme
3 years ago
How monkeypox spreads (and doesn't spread)
Monkeypox was rare until recently. In 2005, a research called a cluster of six monkeypox cases in the Republic of Congo "the longest reported chain to date."
That's changed. This year, over 25,000 monkeypox cases have been reported in 83 countries, indicating widespread human-to-human transmission.
What spreads monkeypox? Monkeypox transmission research is ongoing; findings may change. But science says...
Most cases were formerly animal-related.
According to the WHO, monkeypox was first diagnosed in an infant in the DRC in 1970. After that, instances were infrequent and often tied to animals. In 2003, 47 Americans contracted rabies from pet prairie dogs.
In 2017, Nigeria saw a significant outbreak. NPR reported that doctors diagnosed young guys without animal exposure who had genital sores. Nigerian researchers highlighted the idea of sexual transmission in a 2019 study, but the theory didn't catch on. “People tend to cling on to tradition, and the idea is that monkeypox is transmitted from animals to humans,” explains research co-author Dr. Dimie Ogoina.
Most monkeypox cases are sex-related.
Human-to-human transmission of monkeypox occurs, and sexual activity plays a role.
Joseph Osmundson, a clinical assistant professor of biology at NYU, says most transmission occurs in queer and gay sexual networks through sexual or personal contact.
Monkeypox spreads by skin-to-skin contact, especially with its blister-like rash, explains Ogoina. Researchers are exploring whether people can be asymptomatically contagious, but they are infectious until their rash heals and fresh skin forms, according to the CDC.
A July research in the New England Journal of Medicine reported that of more than 500 monkeypox cases in 16 countries as of June, 95% were linked to sexual activity and 98% were among males who have sex with men. WHO Director-General Tedros Adhanom Ghebreyesus encouraged males to temporarily restrict their number of male partners in July.
Is monkeypox a sexually transmitted infection (STI)?
Skin-to-skin contact can spread monkeypox, not simply sexual activities. Dr. Roy Gulick, infectious disease chief at Weill Cornell Medicine and NewYork-Presbyterian, said monkeypox is not a "typical" STI. Monkeypox isn't a STI, claims the CDC.
Most cases in the current outbreak are tied to male sexual behavior, but Osmundson thinks the virus might also spread on sports teams, in spas, or in college dorms.
Can you get monkeypox from surfaces?
Monkeypox can be spread by touching infected clothing or bedding. According to a study, a U.K. health care worker caught monkeypox in 2018 after handling ill patient's bedding.
Angela Rasmussen, a virologist at the University of Saskatchewan in Canada, believes "incidental" contact seldom distributes the virus. “You need enough virus exposure to get infected,” she says. It's conceivable after sharing a bed or towel with an infectious person, but less likely after touching a doorknob, she says.
Dr. Müge evik, a clinical lecturer in infectious diseases at the University of St. Andrews in Scotland, says there is a "spectrum" of risk connected with monkeypox. "Every exposure isn't equal," she explains. "People must know where to be cautious. Reducing [sexual] partners may be more useful than cleaning coffee shop seats.
Is monkeypox airborne?
Exposure to an infectious person's respiratory fluids can cause monkeypox, but the WHO says it needs close, continuous face-to-face contact. CDC researchers are still examining how often this happens.
Under precise laboratory conditions, scientists have shown that monkeypox can spread via aerosols, or tiny airborne particles. But there's no clear evidence that this is happening in the real world, Rasmussen adds. “This is expanding predominantly in communities of males who have sex with men, which suggests skin-to-skin contact,” she explains. If airborne transmission were frequent, she argues, we'd find more occurrences in other demographics.
In the shadow of COVID-19, people are worried about aerosolized monkeypox. Rasmussen believes the epidemiology is different. Different viruses.
Can kids get monkeypox?
More than 80 youngsters have contracted the virus thus far, mainly through household transmission. CDC says pregnant women can spread the illness to their fetus.
Among the 1970s, monkeypox predominantly affected children, but by the 2010s, it was more common in adults, according to a February study. The study's authors say routine smallpox immunization (which protects against monkeypox) halted when smallpox was eradicated. Only toddlers were born after smallpox vaccination halted decades ago. More people are vulnerable now.
Schools and daycares could become monkeypox hotspots, according to pediatric instances. Ogoina adds this hasn't happened in Nigeria's outbreaks, which is encouraging. He says, "I'm not sure if we should worry." We must be careful and seek evidence.
Michael Hunter, MD
2 years ago
5 Drugs That May Increase Your Risk of Dementia
While our genes can't be changed easily, you can avoid some dementia risk factors. Today we discuss dementia and five drugs that may increase risk.
Memory loss appears to come with age, but we're not talking about forgetfulness. Sometimes losing your car keys isn't an indication of dementia. Dementia impairs the capacity to think, remember, or make judgments. Dementia hinders daily tasks.
Alzheimers is the most common dementia. Dementia is not normal aging, unlike forgetfulness. Aging increases the risk of Alzheimer's and other dementias. A family history of the illness increases your risk, according to the Mayo Clinic (USA).
Given that our genes are difficult to change (I won't get into epigenetics), what are some avoidable dementia risk factors? Certain drugs may cause cognitive deterioration.
Today we look at four drugs that may cause cognitive decline.
Dementia and benzodiazepines
Benzodiazepine sedatives increase brain GABA levels. Example benzodiazepines:
Diazepam (Valium) (Valium)
Alprazolam (Xanax) (Xanax)
Clonazepam (Klonopin) (Klonopin)
Addiction and overdose are benzodiazepine risks. Yes! These medications don't raise dementia risk.
USC study: Benzodiazepines don't increase dementia risk in older adults.
Benzodiazepines can produce short- and long-term amnesia. This memory loss hinders memory formation. Extreme cases can permanently impair learning and memory. Anterograde amnesia is uncommon.
2. Statins and dementia
Statins reduce cholesterol. They prevent a cholesterol-making chemical. Examples:
Atorvastatin (Lipitor) (Lipitor)
Fluvastatin (Lescol XL) (Lescol XL)
Lovastatin (Altoprev) (Altoprev)
Pitavastatin (Livalo, Zypitamag) (Livalo, Zypitamag)
Pravastatin (Pravachol) (Pravachol)
Rosuvastatin (Crestor, Ezallor) (Crestor, Ezallor)
Simvastatin (Zocor) (Zocor)
This finding is contentious. Harvard's Brigham and Womens Hospital's Dr. Joann Manson says:
“I think that the relationship between statins and cognitive function remains controversial. There’s still not a clear conclusion whether they help to prevent dementia or Alzheimer’s disease, have neutral effects, or increase risk.”
This one's off the dementia list.
3. Dementia and anticholinergic drugs
Anticholinergic drugs treat many conditions, including urine incontinence. Drugs inhibit acetylcholine (a brain chemical that helps send messages between cells). Acetylcholine blockers cause drowsiness, disorientation, and memory loss.
First-generation antihistamines, tricyclic antidepressants, and overactive bladder antimuscarinics are common anticholinergics among the elderly.
Anticholinergic drugs may cause dementia. One study found that taking anticholinergics for three years or more increased the risk of dementia by 1.54 times compared to three months or less. After stopping the medicine, the danger may continue.
4. Drugs for Parkinson's disease and dementia
Cleveland Clinic (USA) on Parkinson's:
Parkinson's disease causes age-related brain degeneration. It causes delayed movements, tremors, and balance issues. Some are inherited, but most are unknown. There are various treatment options, but no cure.
Parkinson's medications can cause memory loss, confusion, delusions, and obsessive behaviors. The drug's effects on dopamine cause these issues.
A 2019 JAMA Internal Medicine study found powerful anticholinergic medications enhance dementia risk.
Those who took anticholinergics had a 1.5 times higher chance of dementia. Individuals taking antidepressants, antipsychotic drugs, anti-Parkinson’s drugs, overactive bladder drugs, and anti-epileptic drugs had the greatest risk of dementia.
Anticholinergic medicines can lessen Parkinson's-related tremors, but they slow cognitive ability. Anticholinergics can cause disorientation and hallucinations in those over 70.
5. Antiepileptic drugs and dementia
The risk of dementia from anti-seizure drugs varies with drugs. Levetiracetam (Keppra) improves Alzheimer's cognition.
One study linked different anti-seizure medications to dementia. Anti-epileptic medicines increased the risk of Alzheimer's disease by 1.15 times in the Finnish sample and 1.3 times in the German population. Depakote, Topamax are drugs.
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Evgenii Nelepko
3 years ago
My 3 biggest errors as a co-founder and CEO
Reflections on the closed company Hola! Dating app
I'll discuss my fuckups as an entrepreneur and CEO. All of them refer to the dating app Hola!, which I co-founded and starred in.
Spring 2021 was when we started. Two techies and two non-techies created a dating app. Pokemon Go and Tinder were combined.
Online dating is a business, and it takes two weeks from a like to a date. We questioned online dating app users if they met anyone offline last year.
75% replied yes, 50% sometimes, 25% usually.
Offline dating is popular, yet people have concerns.
Men are reluctant to make mistakes in front of others.
Women are curious about the background of everyone who approaches them.
We designed unique mechanics that let people date after a match. No endless chitchat. Women would be safe while men felt like cowboys.
I wish to emphasize three faults that lead to founders' estrangement.
This detachment ultimately led to us shutting down the company.
The wrong technology stack
Situation
Instead of generating a faster MVP and designing an app in a universal stack for iOS and Android, I argued we should pilot the app separately for iOS and Android. Technical founders' expertise made this possible.
Self-reflection
Mistaken strategy. We lost time and resources developing two apps at once. We chose iOS since it's more profitable. Apple took us out after the release, citing Guideline 4.3 Spam. After 4 months, we had nothing. We had a long way to go to get the app on Android and the Store.
I suggested creating a uniform platform for the company's growth. This makes parallel product development easier. The strategist's lack of experience and knowledge made it a piece of crap.
What would I have changed if I could?
We should have designed an Android universal stack. I expected Apple to have issues with a dating app.
Our approach should have been to launch something and subsequently improve it, but prejudice won.
The lesson
Discuss the IT stack with your CTO. It saves time and money. Choose the easiest MVP method.
2. A tardy search for investments
Situation
Though the universe and other founders encouraged me to locate investors first, I started pitching when we almost had an app.
When angels arrived, it was time to close. The app was banned, war broke out, I left the country, and the other co-founders stayed. We had no savings.
Self-reflection
I loved interviewing users. I'm proud of having done 1,000 interviews. I wanted to understand people's pain points and improve the product.
Interview results no longer affected the product. I was terrified to start pitching. I filled out accelerator applications and redid my presentation. You must go through that so you won't be terrified later.
What would I have changed if I could?
Get an external or internal mentor to help me with my first pitch as soon as possible. I'd be supported if criticized. He'd cheer with me if there was enthusiasm.
In 99% of cases, I'm comfortable jumping into the unknown, but there are exceptions. The mentor's encouragement would have prompted me to act sooner.
The lesson
Begin fundraising immediately. Months may pass. Show investors your pre-MVP project. Draw inferences from feedback.
3. Role ambiguity
Situation
My technical co-founders were also part-time lead developers, which produced communication issues. As co-founders, we communicated well and recognized the problems. Stakes, vesting, target markets, and approach were agreed upon.
We were behind schedule. Technical debt and strategic gap grew.
Bi-daily and weekly reviews didn't help. Each time, there were explanations. Inside, I was freaking out.
Self-reflection
I am a fairly easy person to talk to. I always try to stick to agreements; otherwise, my head gets stuffed with unnecessary information, interpretations, and emotions.
Sit down -> talk -> decide -> do -> evaluate the results. Repeat it.
If I don't get detailed comments, I start ruining everyone's mood. If there's a systematic violation of agreements without a good justification, I won't join the project or I'll end the collaboration.
What would I have done otherwise?
This is where it’s scariest to draw conclusions. Probably the most logical thing would have been not to start the project as we started it. But that was already a completely different project. So I would not have done anything differently and would have failed again.
But I drew conclusions for the future.
The lesson
First-time founders should find an adviser or team coach for a strategic session. It helps split the roles and responsibilities.
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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Matt Ward
2 years ago
Is Web3 nonsense?
Crypto and blockchain have rebranded as web3. They probably thought it sounded better and didn't want the baggage of scam ICOs, STOs, and skirted securities laws.
It was like Facebook becoming Meta. Crypto's biggest players wanted to change public (and regulator) perception away from pump-and-dump schemes.
After the 2018 ICO gold rush, it's understandable. Every project that raised millions (or billions) never shipped a meaningful product.
Like many crazes, charlatans took the money and ran.
Despite its grifter past, web3 is THE hot topic today as more founders, venture firms, and larger institutions look to build the future decentralized internet.
Supposedly.
How often have you heard: This will change the world, fix the internet, and give people power?
Why are most of web3's biggest proponents (and beneficiaries) the same rich, powerful players who built and invested in the modern internet? It's like they want to remake and own the internet.
Something seems off about that.
Why are insiders getting preferential presale terms before the public, allowing early investors and proponents to flip dirt cheap tokens and advisors shares almost immediately after the public sale?
It's a good gig with guaranteed markups, no risk or progress.
If it sounds like insider trading, it is, at least practically. This is clear when people talk about blockchain/web3 launches and tokens.
Fast money, quick flips, and guaranteed markups/returns are common.
Incentives-wise, it's hard to blame them. Who can blame someone for following the rules to win? Is it their fault or regulators' for not leveling the playing field?
It's similar to oil companies polluting for profit, Instagram depressing you into buying a new dress, or pharma pushing an unnecessary pill.
All of that is fair game, at least until we change the playbook, because people (and corporations) change for pain or love. Who doesn't love money?
belief based on money gain
Sinclair:
“It is difficult to get a man to understand something when his salary depends upon his not understanding it.”
Bitcoin, blockchain, and web3 analogies?
Most blockchain and web3 proponents are true believers, not cynical capitalists. They believe blockchain's inherent transparency and permissionless trust allow humanity to evolve beyond our reptilian ways and build a better decentralized and democratic world.
They highlight issues with the modern internet and monopoly players like Google, Facebook, and Apple. Decentralization fixes everything
If we could give power back to the people and get governments/corporations/individuals out of the way, we'd fix everything.
Blockchain solves supply chain and child labor issues in China.
To meet Paris climate goals, reduce emissions. Create a carbon token.
Fixing online hatred and polarization Web3 Twitter and Facebook replacement.
Web3 must just be the answer for everything… your “perfect” silver bullet.
Nothing fits everyone. Blockchain has pros and cons like everything else.
Blockchain's viral, ponzi-like nature has an MLM (mid level marketing) feel. If you bought Taylor Swift's NFT, your investment is tied to her popularity.
Probably makes you promote Swift more. Play music loudly.
Here's another example:
Imagine if Jehovah’s Witnesses (or evangelical preachers…) got paid for every single person they converted to their cause.
It becomes a self-fulfilling prophecy as their faith and wealth grow.
Which breeds extremism? Ultra-Orthodox Jews are an example. maximalists
Bitcoin and blockchain are causes, religions. It's a money-making movement and ideal.
We're good at convincing ourselves of things we want to believe, hence filter bubbles.
I ignore anything that doesn't fit my worldview and seek out like-minded people, which algorithms amplify.
Then what?
Is web3 merely a new scam?
No, never!
Blockchain has many crucial uses.
Sending money home/abroad without bank fees;
Like fleeing a war-torn country and converting savings to Bitcoin;
Like preventing Twitter from silencing dissidents.
Permissionless, trustless databases could benefit society and humanity. There are, however, many limitations.
Lost password?
What if you're cheated?
What if Trump/Putin/your favorite dictator incites a coup d'état?
What-ifs abound. Decentralization's openness brings good and bad.
No gatekeepers or firefighters to rescue you.
ISIS's fundraising is also frictionless.
Community-owned apps with bad interfaces and service.
Trade-offs rule.
So what compromises does web3 make?
What are your trade-offs? Decentralization has many strengths and flaws. Like Bitcoin's wasteful proof-of-work or Ethereum's political/wealth-based proof-of-stake.
To ensure the survival and veracity of the network/blockchain and to safeguard its nodes, extreme measures have been designed/put in place to prevent hostile takeovers aimed at altering the blockchain, i.e., adding money to your own wallet (account), etc.
These protective measures require significant resources and pose challenges. Reduced speed and throughput, high gas fees (cost to submit/write a transaction to the blockchain), and delayed development times, not to mention forked blockchain chains oops, web3 projects.
Protecting dissidents or rogue regimes makes sense. You need safety, privacy, and calm.
First-world life?
What if you assumed EVERYONE you saw was out to rob/attack you? You'd never travel, trust anyone, accomplish much, or live fully. The economy would collapse.
It's like an ant colony where half the ants do nothing but wait to be attacked.
Waste of time and money.
11% of the US budget goes to the military. Imagine what we could do with the $766B+ we spend on what-ifs annually.
Is so much hypothetical security needed?
Blockchain and web3 are similar.
Does your app need permissionless decentralization? Does your scooter-sharing company really need a proof-of-stake system and 1000s of nodes to avoid Russian hackers? Why?
Worst-case scenario? It's not life or death, unless you overstate the what-ifs. Web3 proponents find improbable scenarios to justify decentralization and tokenization.
Do I need a token to prove ownership of my painting? Unless I'm a master thief, I probably bought it.
despite losing the receipt.
I do, however, love Web 3.
Enough Web3 bashing for now. Understand? Decentralization isn't perfect, but it has huge potential when applied to the right problems.
I see many of the right problems as disrupting big tech's ruthless monopolies. I wrote several years ago about how tokenized blockchains could be used to break big tech's stranglehold on platforms, marketplaces, and social media.
Tokenomics schemes can be used for good and are powerful. Here’s how.
Before the ICO boom, I made a series of predictions about blockchain/crypto's future. It's still true.
Here's where I was then and where I see web3 going:
My 11 Big & Bold Predictions for Blockchain
In the near future, people may wear crypto cash rings or bracelets.
While some governments repress cryptocurrency, others will start to embrace it.
Blockchain will fundamentally alter voting and governance, resulting in a more open election process.
Money freedom will lead to a more geographically open world where people will be more able to leave when there is unrest.
Blockchain will make record keeping significantly easier, eliminating the need for a significant portion of government workers whose sole responsibility is paperwork.
Overrated are smart contracts.
6. Tokens will replace company stocks.
7. Blockchain increases real estate's liquidity, value, and volatility.
8. Healthcare may be most affected.
9. Crypto could end privacy and lead to Minority Report.
10. New companies with network effects will displace incumbents.
11. Soon, people will wear rings or bracelets with crypto cash.
Some have already happened, while others are still possible.
Time will tell if they happen.
And finally:
What will web3 be?
Who will be in charge?
Closing remarks
Hope you enjoyed this web3 dive. There's much more to say, but that's for another day.
We're writing history as we go.
Tech regulation, mergers, Bitcoin surge How will history remember us?
What about web3 and blockchain?
Is this a revolution or a tulip craze?
Remember, actions speak louder than words (share them in the comments).
Your turn.