James McInerney
@jomcinerney.bsky.social
Writing a book about horizontal gene transfer and non treelike evolution. Bioinformatics, Evolutionary Biology. Pangenomes. https://profmcinerney.substack.com/ 🇮🇪 https://mol-evol.github.io/
The latest in my “what has four billion years of evolution taught us” series. Always free. Always about evolution. Take a look. open.substack.com/pub/profmcin...
Drift and Luck
In 1968, a Japanese geneticist named Motoo Kimura published a paper that changed how every evolutionary biologist thought about evolution.
open.substack.com
Continuing my writing on evolutionary biology and life. Another 6-ish minute read. Always free. "Never Bet It All" open.substack.com/pub/profmcin...
Never Bet It All
What potatoes, a gambler and your own genome knows about surviving a future you can't predict
open.substack.com
“You modify your surroundings, your social network, your informational diet, your daily routines, and then your modified environment modifies you, every day, whether you think about it or not.”
James McInerney@jomcinerney.bsky.social · 2w agoTake a few minutes to read. This is the next in my series about what we learn from evolutionary biology. Free to read, as always. open.substack.com/pub/profmcin...
Take a few minutes to read. This is the next in my series about what we learn from evolutionary biology. Free to read, as always. open.substack.com/pub/profmcin...
I’ve seen trees you people wouldn’t believe. Deep branches collapsing off the shoulder of a saturated site, unresolved. I watched long-branch attraction glitter in the dark near the root of the Archaea. All those topologies will be lost in time… like tips in a polytomy.
Take a few minutes to read. This is the next in my series about what we learn from evolutionary biology. Free to read, as always. open.substack.com/pub/profmcin...
Paul Nurse responds to the changes in scientific leadership in the uk today: royalsociety.org/news/2026/07...
Changes to government science department | Royal Society
The new Prime Minister has merged the Department for Science, Innovation and Technology into a new Department for Business, Innovation, Science and Trade.
royalsociety.org
Another Friday slow read. Modularity and what it could mean. As always it is free, so please subscribe. open.substack.com/pub/profmcin...
Modularity
Why is everything not an integrated, undifferentiated system?
open.substack.com
Another Friday slow read. Modularity and what it could mean. As always it is free, so please subscribe. open.substack.com/pub/profmcin...
Modularity
Why is everything not an integrated, undifferentiated system?
open.substack.com
The latest in my “what has four billion years of evolution taught us” series. Always free. Always about evolution. Take a look. open.substack.com/pub/profmcin...
Drift and Luck
In 1968, a Japanese geneticist named Motoo Kimura published a paper that changed how every evolutionary biologist thought about evolution.
open.substack.com
I'm mostly doing "Slow Reads" over on substack (it's always free), so you might get through a cup of coffee reading this one. Make sure you read to the end. profmcinerney.substack.com/p/good-enough
Good enough
What we have learned from absurd evolution
profmcinerney.substack.com
New Post: Genomes are models of the world. Click here -> open.substack.com/pub/profmcin...
Genomes are models of the world
What machine learning revealed about predictability in a bacterial pangenome
open.substack.com
in case you missed it: profmcinerney.substack.com/p/the-pangen... "The Pangenome Is Not A Parts List"
The Pangenome Is Not a Parts List
The pangenome is the total genetic repertoire of a group of organisms. It is a property of populations, maintained by evolutionary processes.
profmcinerney.substack.com
in case you missed it: profmcinerney.substack.com/p/the-pangen... "The Pangenome Is Not A Parts List"
The Pangenome Is Not a Parts List
The pangenome is the total genetic repertoire of a group of organisms. It is a property of populations, maintained by evolutionary processes.
profmcinerney.substack.com
I took this photo of E. O. Wilson on this day in 2013, when he gave a short talk in Harvard (I was a visitor there for a year). It was a fun evening, though he was clearly in ill health, he was lovely and charismatic.
The WHO has declared an Ebola outbreak in the Democratic Republic of the Congo and Uganda a “public health emergency of international concern”. For more information on Ebola, our cross-portfolio collection of articles on the virus is freely available to all: https://microb.io/4uUT6ht
Love this quote: "We used to make fun of Edgar Anderson by saying that he was finding hybrids under every bush. Then we realized that even the bushes were hybrids." academic.oup.com/jeb/article/...
Hybridization and speciation*
Abstract. Hybridization has many and varied impacts on the process of speciation. Hybridization may slow or reverse differentiation by allowing gene flow a
academic.oup.com
Sir David Attenborough is older than horizontal gene transfer. Well, he was born before the first experiments that demonstrated HGT. #clickbait #NotTheSameThing
"If the accessory genome was truly dispensable, then the interesting part of pangenomics would, of course, be the core."
James McInerney@jomcinerney.bsky.social · 3mo agoA short piece about what "the pangenome" is and is not. open.substack.com/pub/profmcin...
A short piece about what "the pangenome" is and is not. open.substack.com/pub/profmcin...
The Pangenome Is Not a Parts List
The pangenome is the total genetic repertoire of a group of organisms. It is a property of populations, maintained by evolutionary processes.
open.substack.com
Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...
New Preprint: Species-specific transformer models of bacterial gene order and content for genomic surveillance tasks www.biorxiv.org/content/10.6...
biorxiv.org
This robot installs 80 panels/hour. One every 45 sec. 1,920/day ≈ 0.0008 GW/day per line. Sounds small. It’s not. Scale this across thousands of lines and #solar becomes manufacturing, not construction. 👉 10,000 lines = 8 GW/day. That’s HOW China is winning the energy game.
New Preprint: Species-specific transformer models of bacterial gene order and content for genomic surveillance tasks www.biorxiv.org/content/10.6...
biorxiv.org