Let’s focus the power of Web3 on science & biotech’s problems

Issue 160 | January 21, 2022
22 min read
Capsid and Tail

Jessica’s TechBio Adventures is a new blog by Jessica Sacher on the intersection between tech and biology, a fast-growing area that could mean a refreshing new source of solutions to science and biotech’s problems!

Phage Directory started because Jan (a ‘tech person’) saw how his skills could help fix inefficiencies in Jessica’s field: phage biology. Now, more people like Jan are getting excited to focus on solving problems in science/biology/biotech (accelerated by COVID and the new Web3/blockchain era). Some are even looking at Phage Directory as an example of what success can look like!

To delve into this area and inspire more scientists and tech people to work together (maybe some of you!), Jessica has started a new ‘TechBio’ blog, Jessica’s TechBio Adventures! We’ve cross-posted her most recent post below.

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Submit your manuscript here for the March issue of PHAGE Journal!

Check out the top 2 downloaded articles from December’s Special Issue on Phage Informatics and AI:

  • From Trees to Clouds: PhageClouds for Fast Comparison of 640,000 Phage Genomic Sequences and Host-Centric Visualization Using Genomic Network Graphs — Guillermo Rangel-Pineros et al.

  • Phage Annotation Guide: Guidelines for Assembly and High-Quality Annotation — Dann Turner et al.

What’s New

Paper: Combination of pre-adapted bacteriophage therapy and antibiotics for treatment of fracture-related infection due to pandrug-resistant Klebsiella pneumoniae. — Anaïs Eskenazi et al

Phage TherapyResearch paper

Paper: Lambda phage ‘counts’ the number of coinfecting viruses and then uses this to assess the abundance of potential hosts and decide whether to become dormant. This single-cell tool illuminates how! — Tianyou Yao et al.

Phage biologyResearch paper

Paper: Bacteriostatic antibiotics promote CRISPR-Cas adaptive immunity by enabling increased spacer acquisition — Tatiana Dimitriu et al

CRISPRResearch paper

Preprint: Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion — Jeremy Garb et al.

Phage defense systemsPreprint

Olivier Zablocki shares an updated ecosystem of microbiome/virome apps and guides (iVirus 2), which are freely available to run on CyVerse & DOE KBase. Learn more with their new perspective piece.

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Latest Jobs

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Postdoc: Our lab focuses on mutation generation and their impact on evolution and adaption in bacteria and phages, using quantitative approaches such as visualisation of mutations in microfluidic setups. Here, we aim to investigate the origin of spontaneous mutations in phages, with a focus on the activity of the Mismatch Repair system.

Contact: [email protected]

PhD project
PhD candidate to join the Cyanobacterial research group to elucidate the role of bacteriophage encoded auxiliary metabolic genes (AMGs) on pigment biosynthesis and oxygenic photosynthesis during the infection process.
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Postdoc to study gut phages interacting with the intestinal barrier in Inflammatory Bowel Disease.
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Postdoc: novel strategies that improve the health of farmed fish, including phage biocontrol.
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Postdoc positions: use cryo-electron microscopy and tomography to determine three-dimensional structures of viruses and bacteriophages and characterize their infection of cells.
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Postdoc in phage engineering for therapeutic applications.
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Postdoc to study the impact of phage therapy on the transfer of conjugative plasmids within and between species of enteric bacteria using experimental approaches.
Biological Scientist II: bacteriology and virology research, including phage work.
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PhD project: Machine Learning Approaches to Support the Development of Phage Therapies

Community Board

Anyone can post a message to the phage community — and it could be anything from collaboration requests, post-doc searches, sequencing help — just ask!

CDC has some AMAZING new interactive visualizations for Antibiotic Resistance by species, geography, and indication. Great for educating people on how big the problem is. Check it out! — Contributed by Natalie Ma via Twitter

Antibiotic resistanceScience communicationTool

In an effort to help companies navigate the development of their bacteriophage product, IHMA’s VP Global Microbiology Services & CSO, Daniel Sahm has compiled a summary of key considerations to address prior to beginning clinical trials.

Clinical TrialPhage Therapy

Thanks to all who came out to the first iVoM Season 2 event of 2022!

Next: Feb 2 from 2-3 PM CET
Topic: Phage application in the One Health approach.
Speakers: Dr. Cath Rees, Prof. Mariana Piuri, Prof. Lone Brøndsted.

If you want to join this series, which will run through May, please register at https://ivom.phage.directory — as many of you know, ISVM is asking for a small contribution from senior scientists and industry for access to this series, which will support ISVM’s activities now and in the future.

Phage Directory is a proud partner of this event, and so are the local organizers for VoM 2022, the upcoming in-person/hybrid conference in Portugal July 18-22!

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Join Instill, a platform that facilitates collaboration and mentorship amongst the phage community.

Collaborator requests on Instill are seeking help with:

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IPATH invites the phage therapy community to the virtual screening and discussion event for the new documentary, Salt in My Soul. This film recounts the struggles and feelings of Mallory Smith, who lost her battle with cystic fibrosis and a rare superbug infection in November 2017. (Her story was the inspiration for Phage Directory!)

You’ll get a link Jan 25th to stream the film at your convenience, before the panel event on February 1st (4:00 PM - 5:00 PM PST) on Zoom.

The panel will feature Diane Shader Smith, the film’s director Will Battersby, Dr. Doug Conrad, and IPATH’s Drs. Robert Schooley, Saima Aslam, and David Pride, moderated by IPATH Co-Director, Dr. Steffanie Strathdee.

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Let’s focus the power of Web3 on science & biotech’s problems

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Phage microbiologist and co-founder of Phage Directory
Co-founderPostdoctoral Researcher
Iredell Lab, Phage Directory, The Westmead Institute for Medical Research, Sydney, Australia, Phage Australia

Phage characterization, Phage-host interactions, Phage Therapy, Molecular Biology

I’m a co-founder of Phage Directory and have a Ph.D in Microbiology and Biotechnology from the University of Alberta (I studied Campylobacter phage biology). For Phage Directory, I oversee community building, phage sourcing, communications, science, and our awesome team of volunteers.

As of Feb 2022, I’ve recently joined Jon Iredell’s group in Sydney, Australia as a postdoctoral research scientist for the Phage Australia project. I’m diving back into the lab to help get Phage Australia’s country-wide phage therapy system up and running here, working to streamline workflows for phage sourcing, biobanking and collection of phage/bacteria/patient matching and monitoring data, and integrating it all with Phage Directory’s phage exchange, phage alerts and phage atlas systems. I’m also delving into phage manufacturing and quality control.

This post originally appeared here in Jessica’s TechBio Adventures on January 16, 2022.

Scientist friends, it’s time we got up speed on Web3 so we can help bring this revolution to science, biology, and biotech.

TL;DR: Web3 is about WAY more than just Bitcoin and buying/selling jpegs online. It is probably the next revolution of our time (for most industries). And yet for once, science and biotech are not being left until last! Web3 brings both the power and the will to meaningfully shake up age-old problems in science and biotech, and it’s massively picking up lately. So you might as well dive into it with me now!

Thanks so much for being here for post #2 of Jessica’s TechBio Adventures! (Subscribe to get future posts here)

Launching this blog a couple weeks ago was a big leap for me, so it’s been really nice to see the words of encouragement that have come in!

Today I wanted to talk about Web3 and what it could mean for science and biotech. Web3 is a new era of the internet that is bringing together new tech + an influx of the best kind of people: talented, optimistic builders who like to share. And Web3Bio is made up of people like this who also care about working on science/biology/biotech problems. (Unicorns, basically 🦄).

The Web3Bio (also known as DeSci/DeBi; for now I’m using all these interchangeably) world is very new, but already off to a racing start. Already there are several Web3Bio organizations getting to work, like VitaDAO, LabDAO, Molecule, Opscientia, PsyDAO, and SCINET. (Jan and I are even thinking Phage Directory could fit into this group with a few tweaks). And by definition, Web3Bio is open for us all to pitch in and join the movement. (Yes, that means us too, fellow scientists, even if we’re new to the tech world).


P.S. There are TONS of other places to learn about Web3; this is just how I’m wrapping my head around it as a scientist who recently immigrated to the tech world.

If you want to dive more into the Web3 world, from people who know way more than me, I suggest starting with:

What is Web3, and why does it matter to science?

You may have heard of Web3 — the ‘third era of the internet’. Or maybe not! I hadn’t until very recently, but as I got into in my last post, Tech + Biology = Great possibilities, when you hang out with ‘tech people’ (you only need one!) you get to hear about these things.

Web3 is an umbrella encompassing many terms you may have seen floating around lately, like crypto, NFTs, blockchain, the metaverse, DAOs, DeFi, tokens, decentralization… (it’s an entire world of scary-seeming lingo, I know).

At first, I figured that stuff wasn’t for me. I’d let Jan (my cofounder/partner) and the other ‘computer people’ get into that, build us a metaverse, etc. I’d hang out in it once it’s built. In the meantime, I’d be over here working on science and biotech. But the more I’ve started to learn about Web3, the more I’ve become convinced that this new era/universe is a big deal! It represents a rapidly expanding abundance of new tools (new superpowers for computer people) and an influx of really smart, cool, innovative, committed, generous people. I think this stellar combination could help solve problems that have been facing science and biology for decades.

Science and biotech are inefficient, which means scientists waste a lot of time and people die

It’s no secret that scientific funding, publishing, and translation of scientific results into real-world impact is woefully inefficient compared to what it could be.

I think of three main problem areas:

  • Funding: who gets funds to do research? What gets funded? What doesn’t?

  • Knowledge dissemination: how is research shared / made available? How much is shared?

  • Intellectual property (IP) and research translation: who owns the fruits of research, and how is it leveraged to solve real problems in the world?

While there’s a lot that works about all three, there are big issues with each, and they run deep. Like many things (maybe everything?), it’s the way it is because of the incentive systems currently in place.

If you’re not well-versed in how scientific research works and the economic systems/incentives that drive it, or if you want to see it all concisely laid out, I highly recommend this article, Magna Carta Scientiae, by @atoms_org. I also recommend this post, How Life Sciences Actually Work: Findings of a Year-Long Investigation, by Alexey Guzey, founder of New Science.

Our age-old problems in science are fixable

I feel like many of us scientists have tended to think these issues with research funding, knowledge dissemination, and translation would probably never be solved (or not in our lifetime).

I for one have been mad/perplexed about the way things work in science for almost a decade, starting soon after I started in the lab in 2010. I’ve been told time and again that that’s our system, deal with it if you want to do science. It was disheartening to learn about how publishing and funding works, how much time playing those games takes out of a scientist’s day, how much it all dictates what happens in the lab. Not to mention how little scientists/science are actually valued, even though this work and the people who do it underpin such an important part of society’s foundation.

As I talked about in my last post, the more time I spend with people in the tech/startup space, the more I’m realizing that science’s problems come from manmade systems of incentives, not from fundamental truths of the universe. I’ve learned that, luckily for us, the status quo can be redesigned without needing to convince arbiters of the current system to change. (See Airbnb not getting permission from hotels to revolutionize traveling).

As I’m learning, what it often takes to shift systems (even big, entrenched ones like we see in science) is a combination of new incentives, some outside perspective, a conscious effort to adapt and mash-up ideas and methods that have worked in other industries, and a ‘how can we make this work’ attitude. This may be obvious to people already steeped in the tech/startups space, but it was not obvious to me as a biologist.

Web3: a new era, where innovation of all kinds will get easier

Thanks to explainers all over the internet, but especially Packy McCormick’s Not Boring blog, the simple way I now think of it is:

  • Web1 was the era of the internet that started back in the 90s (this brought us things like email and ‘http’, which lets us all see and use websites).

  • Web2 is the internet most of us are familiar with nowadays (think Facebook, Google, etc).

  • Web3 is this new era starting basically right now.

Web3 builds on the foundation of Web1 and Web2, in a sense taking the best of both worlds. It’s is a special combination of the openness/sharing practices of Web1, the modern tools and technologies brought about by Web2, and the existence and growing adoption of the blockchain.

In this next section I’ll try to explain how this combination leads to some really cool new ways of enabling and incentivizing people to get work done (together). While this can (and will) be useful for any industry, I think science and biotech needs this very badly, and society will benefit in a big way if we can make this happen.

How Web3 superpowers our ability to get things done (together)

TL;DR: Thanks to the blockchain, which is Web3’s foundation, in Web3 people can own things they help build on the internet. This means if you have a project, it’s easier to incentivize people to work with you, and if you have expertise, it’s easier to get compensated for sharing it. And most importantly, the ethos of Web3 (like the open source software movement) is to share what is built as building blocks for the next person, so everyone can riff off of what each other is doing, and make something even better, faster. (Like jazz meets compounding interest!) 🎺 📈

Web3 enables people to own what they help build on the internet

One big distinction between Webs 1, 2 and 3 relates to ownership. With Web1, most everything was open and shared; no one really owned it. In Web2, companies like Facebook have owned/profited from most of it. With Web3, theoretically anyone can own things on the internet and make money when they help build things on the internet. (More on this)

But how? This is in part because of blockchain technologies that Web3 is built on…

The blockchain helps us trust each other on the internet (or lets us work together even if we don’t)

The blockchain is an open public register (a ‘decentralized ledger’) that keeps track of things, such as transactions (buying/selling), contracts and more. All without the need of a trusted party to enforce it all. (This clearly goes way beyond Bitcoin! For example, learn about what the Ethereum blockchain can do/enable here).

🎨 One small example: If a piece of art were put on the blockchain, every time it’s sold to someone new, its creator could automatically get a cut of those future transactions in perpetuity (this arrangement would be built into the code and permanently linked to that piece of art).

For science, the first thing that comes to mind is what that could mean for a scientist who makes a discovery and registers it on the blockchain — could that scientist make a percentage of everything that comes of that discovery?

Web3 makes it easier for groups of people to coordinate, do work, make and allocate money together

Taking this concept of ownership a step further, what if you could own part of a company you helped build part-time on the internet? Web3 is enabling new types of organizations called DAOs to form, where many people can contribute to a project online, and earn part ownership in whatever comes of that project. Maybe it’s a company that sells products, maybe it’s a collective that invests together — it could be anything! With a wallet (essentially a bank account on the blockchain) that can be operated securely by multiple people, a group of members can vote on what happens to a co-owned pot of money, decide on strategy, and more.

Web3 tech makes it easier to incentivize work

Web3 tech makes it easier to compensate people for contributions using equity, not just cash, no matter where they live or how much time they can spare. This means anyone with an idea can incentivize the best people to help, even at the idea stage. People don’t have to leave their jobs to start contributing their expertise to a project they care about. This unlocks more of world’s expertise for even new/small projects, as long as the mission is attractive.

Of course, there’s lots about science that could benefit from this, since so many ideas never make it to the point of being fundable by current systems. (More on this in future posts).

A ‘build-share-repeat’ mentality means compounding progress

The underlying tech infrastructure is a big part of why Web3 is powerful, but this alone wouldn’t be enough. It’s not just the tools that matter, it is also the people and how they use them.

Web3 is being built by thousands of people and organizations at once. Fortunately for us all, it’s being built by people who share what they’re doing freely on the internet, so anyone can adopt their ideas/systems, and use them as building blocks to make other/better things. Packy McCormick calls this phenomenon ‘Idea Legos’.

In principle this is how science has operated for a long time, or at least this is the idealistic version of what it’s supposed to be (rumour has it that Jan is planning a post on how science is one of the original decentralized systems, can’t wait to read that!)

What if we focused the power of Web3 on science?

Once you think about it, it’s easy to see how Web3 will likely be revolutionary for countless industries. It’s generic like the internet — it’s a spotlight that can be pointed at anything. And it’s not theoretical, it’s happening. Projects are being started left and right, and everyone’s excited to get involved. The question now is, what to build?

What could we make happen if we aimed Web3 tech/people/ethos at science/biology/biotech’s problems?

There are at least three main areas I’m really excited about, and there are already vibrant Web3 organizations/communities working on each. For now, a brief overview:

1. What happens when Web3 meets lab work (doing experiments, sharing reagents, bioinformatics analyses)?

  • E.g. LabDAO is building an open, community-run network of biological laboratories (I’m excited to have jumped into helping out with LabDAO; more on this in future posts!)


2. What happens when Web3 meets biotech (biotech, intellectual property ownership and technology transfer, and drug development)?

  • E.g. Molecule is working on ‘IP-NFTs’ to put biotech IP on the blockchain and enable ‘fractionalized ownership’ (think the stock market, but for research discoveries)

3. What happens when Web3 meets science (research funding, academic publishing, peer review, citations, storing and sharing data, reproducibility)?

  • E.g. VitaDAO is funding longevity research and has already funded two research labs’ projects (and minted two IP-NFTs using Molecule’s system, which means VitaDAO owners will own what comes of this research, and will collectively govern what happens with it)


  • E.g. Opscientia (OpSci) is making open science research workflows findable, accessible, interoperable and repeatable (I’ve also started dabbling in what OpSci is doing, and am excited to find ways to help out!)

In future posts, I’ll go deeper into the groups tackling these areas. I’ll also share insights from the Web3Bio organizations/projects I jump into.

In the meantime, check out Jocelynn Pearl’s DeSci Wiki for a giant list of Web3 science and biology initiatives. (Maybe you’ll find one or two to join, or maybe you can add something to this growing resource!)

Let’s make Web3Bio happen!

In summary, science and biotech are rife with inefficiencies that most of us scientists thought we’d never solve. Luckily, in Web3, a ton of innovation is happening that is enabling people to start and organize new efforts, get compensated, and amplify their impact by contributing to a system that is designed to build on itself.

Web3’s combination of powerful new tech + people with a build-share-repeat mindset is going to be powerful. This could revolutionize any industry, but I for one want to make sure science and biotech doesn’t miss this wave.

Miraculously, a lot of these optimistic-builders-who-share are starting to see science and biotech’s problems as worth solving, and are choosing to focus their newfound Web3 superpowers in this direction. Having been on the receiving end of this phenomenon with Phage Directory (when a random encounter with a single one of these kinds of people (🦄) transformed my research impact from a low-impact virology article every other year to saving the lives and limbs of actual human beings), I am here to tell you this is a Very Good Thing!

Importantly, we scientists are needed to help the builders ground themselves in what our field really needs, and what the issues and intricacies are. We need to be actively joining these projects and helping them grow. We do not need to ‘leave science’ to do this. There are so many issues, and they are big, but there are so many of us too. And I know for a fact most of us thought we’d be having more impact by now. Well, now we have our chance!

In other words: fellow scientists, they need us in the new world; let’s join the fray and see what we can do together! 👩‍🔬

See you all next time, thanks so much for being here!

— Jessica

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