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Kevin Blake PhD

@kevinsblake.bsky.social
36 followers 37 following 60 posts

Scientist + Writer.

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Kevin Blake PhD @kevinsblake.bsky.social · 06/08/2026
Can we treat infectious disease *without* killing microbes? 🦠💊🧪 Scientists are investigating how to end the War on Bacteria with more "diplomatic" approaches. They are: 1. Disarming virulence 2. Building tolerance 3. Promoting colonization resistance Read more about it here 👉
kevinsblake.substack.com
Pathogens to Pacifists
Curing infections without killing bacteria.
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Reposted by Kevin Blake PhD
Saloni @scientificdiscovery.dev · 28/05/2026
We take it for granted today that DNA is the genetic code of life, but until the 1940s most scientists thought genes were made of protein! In a new piece, @kevinsblake.bsky.social tells the story of how scientists discovered that DNA is the code of life.
worksinprogress.co
How bacteria solved the mystery of inheritance - Works in Progress Magazine
In the 1940s, scientists made a discovery now fundamental to biology: genes are encoded in DNA. The story involves bacteria, dead mice, and a kitchen cream separator.
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Kevin Blake PhD @kevinsblake.bsky.social · 28/05/2026
The foundational discovery of modern genetics -- that genes are made of DNA -- came from an organism many doubted even had genes: bacteria 🧬🧫 Read more in my piece @worksinprogress.bsky.social worksinprogress.co/issue/how-ba...
worksinprogress.co
How bacteria solved the mystery of inheritance - Works in Progress Magazine
In the 1940s, scientists made a discovery now fundamental to biology: genes are encoded in DNA. The story involves bacteria, dead mice, and a kitchen cream separator.
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Kevin Blake PhD @kevinsblake.bsky.social · 05/05/2026
If you liked this, you can read more about it here 👉 open.substack.com/pub/kevinsbl...
open.substack.com
Mark Twain’s (Unpublished) Microbiology Book
Twain's story about a scientist who's turned into a "cholera germ" and sees the microbial world from a germ's-eye-view
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Kevin Blake PhD @kevinsblake.bsky.social · 05/05/2026
Did you know: Mark Twain wrote a book about a microbiologist who is accidentally transformed into a "cholera germ"? 🦠🧪 Though written over 100 years before the term “microbiome” was coined, its descriptions of the human body from the microbe’s-eye view could be home in any modern text.
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Reposted by Kevin Blake PhD
Pablo Ivan Nikel @pabnik.bsky.social · 27/01/2026
Should an iconic #bacterial #chassis be renamed without community consensus? Our @mbio.bsky.social #article vindicates the established identity of #Pseudomonas putida KT2440 & argues for continuity, community practice & common sense in naming · @vdlorenzo.bsky.social journals.asm.org/doi/10.1128/...
journals.asm.org
The disputed identity of Pseudomonas putida KT2440: when taxonomists rename your favorite microbe | mBio
Names matter; they are not mere labels. They operate as anchors of memory, social coordinates, and references of collective identity. When a name becomes established through long-term use and broad ad...
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Kevin Blake PhD @kevinsblake.bsky.social · 26/01/2026
You can read more about it here 👉 open.substack.com/pub/kevinsbl...
open.substack.com
After the "Cambrian Explosion in AI"
Finding clues to what's next in 500-million-year-old fossils.
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Kevin Blake PhD @kevinsblake.bsky.social · 26/01/2026
What might this mean for AI? Maybe nothing. (Don't blame me, I didn't make the metaphor.) But if the metaphor holds true, we're just before the decimation. Most AI companies, models, applications, etc. will go extinct. The survivors will not be the "best," but a lottery.
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Kevin Blake PhD @kevinsblake.bsky.social · 26/01/2026
S.J. Gould called this the "decimation." This captures the period's two key features: 1. Magnitude: About 90% of Cambrian forms went extinct. 2. Randomness: Survival wasn't based on fitness or skill, but a lottery.
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Kevin Blake PhD @kevinsblake.bsky.social · 26/01/2026
However, this wasn't the full picture. Later work revealed most animal forms evolved in the Cambrian went extinct! Life has not become more diverse over time, it BEGAN at its maximal scope. But most did not survive. The few which did diversified into forms we know today.
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Kevin Blake PhD @kevinsblake.bsky.social · 26/01/2026
Initially, scientists thought these were the ancestors of modern forms. The tree of life was like a "cone of increasing diversity." From a few basic branches came a continuously increasing number of subgroups. AI, it's argued, is growing and diversifying in the same way.
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Kevin Blake PhD @kevinsblake.bsky.social · 26/01/2026
The Cambrian explosion was a period ~500 million years ago when modern multicellular animals made their first appearance in the fossil record -- and with a bang. Virtually overnight (geologically speaking) a huge diversity of fossils evolved.
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Kevin Blake PhD @kevinsblake.bsky.social · 26/01/2026
Tech CEOs claim there's been a "Cambrian Explosion in AI." This is usually just marketing-speak for "rapid, transformative growth." But assuming the metaphor is accurate, maybe we can find clues for what's next--is there a bubble?--in what followed the ACTUAL Cambrian explosion?
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Reposted by Kevin Blake PhD
STCmicrobeblog @stcmicrobeblog.bsky.social · 26/01/2026
These Are the Times by Roberto — Microbiologists continue to advance the frontiers of knowledge.
smallthingsconsidered.blog
These Are the Times
by Roberto — Microbiologists continue to advance the frontiers of knowledge.
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Reposted by Kevin Blake PhD
CMI Communications @cmicomms.bsky.social · 01/12/2025
We are very excited to have launched this new collaboration with @gardp.bsky.social! 🚀 This first jointly published commentary on #AMR by @kevinsblake.bsky.social & Gautam Dantas can also be read on our journal page: www.cmi-comms.org/article/S295... #IDSky #clinmicro
cmi-comms.org
Ecological strategies to end the war on resistance
Military metaphors are pervasive in the language of antibiotics and resistance [1]. Bacterial pathogens are foreign invaders with whom we are at war. To fight them, we deploy antibiotic chemical weapo...
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Reposted by Kevin Blake PhD
Global Antibiotic R&D Partnership (GARDP) @gardp.bsky.social · 30/11/2025
📝 A new Antimicrobial Viewpoint by Kevin Blake and Gautam Dantas examines public framing of AMR and proposes alternatives to the war metaphor. The piece is jointly published on REVIVE and CMI Communications. 🔗https://tinyurl.pulse.ly/jjtqv3dn37 Got a topic idea? Write to revive@gardp.org
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Kevin Blake PhD @kevinsblake.bsky.social · 25/11/2025
It might! A key part to one theory is Fleming left a plate at room temp instead of incubating it. But why do that? Incubation affects the color of the staph colonies, which would be important for his agar art, so could be he didn’t incubate the plate because he was playing around with that.
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Kevin Blake PhD @kevinsblake.bsky.social · 24/11/2025
Every biologist knows the story of Fleming's chance discovery of penicillin. But is it true? Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.
press.asimov.com
The Penicillin Myth
Competing theories seek to explain inconsistencies surrounding Alexander Fleming’s famed discovery.
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Kevin Blake PhD @kevinsblake.bsky.social · 05/11/2025
I wrote about the history of the field of "experimental evolution" with @worksinprogress.bsky.social Read it here 👉 www.worksinprogress.news/p/evolution-...
worksinprogress.news
The evolution of bacteria
Generations of microbes evolve in hours, not millennia. By speeding up Darwin’s clock, scientists have watched evolution happen in real time, and it’s changed how we understand natural selection.
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Kevin Blake PhD @kevinsblake.bsky.social · 05/11/2025
Darwin thought evolution required thousands of years, and was therefore out of reach from human experimentation. But in one of the few forms of life he didn’t study -- microorganisms -- evolution can happen in mere months or weeks 🦠🧫
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Kevin Blake PhD @kevinsblake.bsky.social · 27/10/2025
Read about it in my commentary with Gautam Dantas on @gardp.bsky.social and @cmicomms.bsky.social 👉 www.sciencedirect.com/science/arti...
sciencedirect.com
Ecological strategies to end the war on resistance
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Kevin Blake PhD @kevinsblake.bsky.social · 27/10/2025
The "war on antibiotic resistance" won't end with brute force alone 💊🧫 Instead, eco-evo strategies take a more diplomatic approach. These seek to foster co-existence with microbes, rather than kill them. We metaphorize these as: disarmament, non-proliferation, and soft power.
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Kevin Blake PhD @kevinsblake.bsky.social · 29/09/2025
Read it here 👉 medium.com/the-quantast...
medium.com
The “Good” Side of Antibiotic Resistance
New tools to protect the gut microbiome come from an unlikely source: antibiotic-destroying enzymes from bacterial pathogens
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Kevin Blake PhD @kevinsblake.bsky.social · 29/09/2025
Antibiotic resistance is portrayed as the enemy of modern medicine. But nothing in biology is inherently evil. Could it be useful, even “good”? 💊🔬 I wrote about using resistance enzymes to protect the gut microbiome from antibiotics and prevent secondary infections. 🧫🦠
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Kevin Blake PhD @kevinsblake.bsky.social · 29/05/2025
Are chromosomes merely a laundry list of genes? I wrote for @stcmicrobeblog.bsky.social about new research which finds that natural selection has organized nearly 2/3s of bacterial genes into specific positions on the chromosome 🧪 🧫 🧬
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Kevin Blake PhD @kevinsblake.bsky.social · 22/05/2025
Where does antibiotic resistance come from? 💊🧫 I wrote for @asimovpress.bsky.social about proactive approaches for fighting resistance that shift focus from studying it in clinical pathogens to studying it at the source: soil-dwelling bacteria.
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Kevin Blake PhD @kevinsblake.bsky.social · 07/05/2025
Read my full article here 👉 medium.com/the-quantast...
medium.com
The Age of the Earth and La Tour Eiffel
If the Eiffel Tower were to represent the history of life on Earth, how far down would the history of Homo sapiens begin?
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Kevin Blake PhD @kevinsblake.bsky.social · 07/05/2025
🌸 First flowering plants: 1/4 down the spire 🦖 Origins of the dinosaurs: 1/2 down the spire 🐚 Cambrian explosion: Third-floor platform 🦠 First eukaryotes: Between the second and third floors 🧫 Origins of bacteria: Somewhere below the first floor
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Kevin Blake PhD @kevinsblake.bsky.social · 07/05/2025
Analogies like this can bring the 4.54 billion-year scope geological deep time, down to a more human level. Human origins might be just the "skin of paint" at the top but where does other life lie on the 1024 ft tower?
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Kevin Blake PhD @kevinsblake.bsky.social · 07/05/2025
Mark Twain wrote, “If the Eiffel tower were now representing the world’s age, the skin of paint on the pinnacle-knob at its summit would represent man’s share of that age.” 🧪🌐
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Kevin Blake PhD @kevinsblake.bsky.social · 30/04/2025
Multichannel pipette, in LEGO 🧪🔬
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Kevin Blake PhD @kevinsblake.bsky.social · 13/04/2025
Read it here: medium.com/the-quantast...
medium.com
Return of the Soil Bacteria
Discovery of a new class of broad-spectrum antibiotic, a lasso-shaped molecule call lariocidin, in slow-growing soil bacteria.
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Kevin Blake PhD @kevinsblake.bsky.social · 13/04/2025
I wrote about the discovery of lariocidin, a new class of antibiotic from slow-growing soil bacteria.
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Kevin Blake PhD @kevinsblake.bsky.social · 03/04/2025
You can check it out here: github.com/kevinsblake/...
github.com
GitHub - kevinsblake/NatParksPalettes: Color palette package inspired by National Parks
Color palette package inspired by National Parks. Contribute to kevinsblake/NatParksPalettes development by creating an account on GitHub.
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Kevin Blake PhD @kevinsblake.bsky.social · 03/04/2025
{NatParksPalettes} now has >10k downloads! 🧪🎨⛰️🏜️ Very cool to see this little side project (really, done to procrastinate thesis experiments) be used by so many people.
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Kevin Blake PhD @kevinsblake.bsky.social · 27/03/2025
LEGO’s DNA Helix Isn’t “Right” 🧪 #MicroSky kevinsblake.substack.com/p/legos-dna-...
kevinsblake.substack.com
LEGO's DNA Helix Isn't "Right"
The Evolution of STEM is a wonderful new set marred by an unfortunate scientific inaccuracy.
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Kevin Blake PhD @kevinsblake.bsky.social · 13/03/2025
Call me old fashioned, but I’d think the mission of the Environmental Protection Agency should be something like, “protecting the environment.”
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Kevin Blake PhD @kevinsblake.bsky.social · 23/02/2025
Also, if you think this work is cool, note that it was funded by the NIH NIAID. If federal funding for scientific research is cut, there will be a lot less of this kind of work!
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Kevin Blake PhD @kevinsblake.bsky.social · 23/02/2025
You can read the full paper here: www.nature.com/articles/s41...
nature.com
The tetracycline resistome is shaped by selection for specific resistance mechanisms by each antibiotic generation - Nature Communications
Bacteria can use different mechanisms to become resistant to the same antibiotic class. Here, the authors study bacterial strains that express genes conferring tetracycline resistance via different me...
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Kevin Blake PhD @kevinsblake.bsky.social · 23/02/2025
This showed that each tet generation preferentially selects for specific mechanisms of resistance, and in a pattern that matches the history of drug development and mech discovery in pathogens.
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Kevin Blake PhD @kevinsblake.bsky.social · 23/02/2025
Using mixes with only one mechanism per pot, we ruled out inter-mech interactions as driving this. We also ruled out MIC alone as driving this (e.g., several DES1s had MICs higher than any RPP in gen 2 drugs).
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Kevin Blake PhD @kevinsblake.bsky.social · 23/02/2025
But most interestingly, when that same starting mix was instead grown with gen 2 drug (DOX), the RPPs expanded to 90% the culture. And with a gen 3 drug (TIG), DES1s expanded to 95%.
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Kevin Blake PhD @kevinsblake.bsky.social · 23/02/2025
So we pooled strains at equal amounts to make a mixture with all strains starting at the same % relative abundance. We then grew that with a gen 1 drug (TET), and after 20 h counted the % relative abundance of ea strain. We observed EFF strains expanded from 25% to 80%!
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Kevin Blake PhD @kevinsblake.bsky.social · 23/02/2025
So we created CompAReSeq. Unlike the other methods, this differentiates strains by a 7-bp DNA barcode in the plasmid. To quantify the % relative abundance of each strain in a culture, just extract plasmid DNA, sequence the barcoded region, and count.
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Kevin Blake PhD @kevinsblake.bsky.social · 23/02/2025
The problem was counting these strains in mixed cultures. We need them to be identical except for the AR gene BUT still distinguishable. The usual methods—adding unique fluorescent or antibiotic markers—get unwieldy at high numbers and introduce their own fitness effects.
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Kevin Blake PhD @kevinsblake.bsky.social · 23/02/2025
But this was monoculture. Wanted to test it directly. We aimed to mix our strains, and grow them in the context of different gen drugs. If we're right, then each gen should lead to the expansion of specific mechanisms in a pattern matching the history of resistance discovery.
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Kevin Blake PhD @kevinsblake.bsky.social · 23/02/2025
Extrapolating this out to the population-level, we’d predict that in gen 1 EFF strains would increase in abundance because they have the fastest growth and high MIC. But with gen 3, DES1s now are the only resistant strains and so—despite their slow growth—would expand.
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Kevin Blake PhD @kevinsblake.bsky.social · 23/02/2025
To evaluate this, we created 24 tet-resistant strains expressing genes from each mechanism (6 ea). We know AR is a tradeoff between benefits (high MIC) and costs (slower growth). Quantifying these in monoculture, we found that the DES1s and RPPs have slower growth than EFFs.
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Kevin Blake PhD @kevinsblake.bsky.social · 23/02/2025
We asked: Why did it happen in this order? Why weren’t DES1s discovered earlier? Or EFFs later? Was it just chance? Or, could each gen have selected for specific mechanisms? Were DES1s discovered so late because, despite resistance to all drugs, they're worse in other ways?
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Kevin Blake PhD @kevinsblake.bsky.social · 23/02/2025
Did you notice a pattern in those timelines? The deployment of each new tet gen has been quickly followed by the discovery of a new mechanism of resistance: efflux after gen 1, ribosomal protection after gen 2, and destructases after gen 3.
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