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James McInerney

@jomcinerney.bsky.social
4.3K followers 6.9K following 365 posts

Writing a book about horizontal gene transfer and non treelike evolution. Bioinformatics, Evolutionary Biology. Pangenomes. profmcinerney.substack.com 🇮🇪 mol-evol.github.io

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James McInerney @jomcinerney.bsky.social · 09/09/2026
profmcinerney.substack.com/p/the-biolog...
profmcinerney.substack.com
The Biology of “We”
The self isn't a fortress. It's a permeable membrane, and that's what keeps you alive.
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Cahir O'Kane @cahirokane.bsky.social · 15/08/2026
I teach 5 lectures on genomics to 2nd-yr undergrads, including genome variation. I'd rather not waste time on eugenic garbage, but I feel I have to devote time to debunking it. I discussed Cofnas's stuff last year (not naming him) for the first time. Even more debunking needed in future years.
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Jonathan Howard @joho.bsky.social · 15/08/2026
I am unshocked
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Aparna Nair @disabilitystor1.bsky.social · 14/08/2026
On July 31, Simon Baron-Cohen urged people to tone down the rhetoric on twitter re Jason Arday, and pointed to his own research on autism and suicide. Alexander Kustov responded with "Shame" Elon Musk with "Evil," and a wide variety of people came out jeering. The kind of cruelty on display here.

Prof Ian Pace
@drianpace
If an academic is in such a condition that public scrutiny of his (equally public) work may cause suicidal urges, then as a matter of urgency he should take leave and receive care. Using this threat to try and silence critics is about as low as it gets.
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Simon Baron-Cohen
@sbaroncohen
·
Jul 31
In 2014 we published the first large-scale study of suicidality in autism, subsequently widely replicated, revealing that 1 in 4 autistic people have planned or attempted suicide. That’s why I’m very concerned about the impact of the media coverage on Professor Jason Arday who is
Prof Francois Balloux
@BallouxFrancois
·
Jul 31
This tweet reads like a spoof intent on painting academics in a bad light ...
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Simon Baron-Cohen
@sbaroncohen
·
Jul 31
In 2014 we published the first large-scale study of suicidality in autism, subsequently widely replicated, revealing that 1 in 4 autistic people have planned or attempted suicide. That’s why I’m very concerned about the impact of the media coverage on Professor Jason Arday who is
Richard Hanania
@RichardHanania
·
Jul 31
This is amazing. You can't call out plagiarism because SUICIDE. 

This is the cheapest argument imaginable. It's what the trans movement did to shut down debate.

I've lost respect for Simon Baron-Cohen. He should be henceforth considered an absurd figure.
Quote
Simon Baron-Cohen
@sbaroncohen
·
Jul 31
In 2014 we published the first large-scale study of suicidality in autism, subsequently widely replicated, revealing that 1 in 4 autistic people have planned or attempted suicide. That’s why I’m very concerned about the impact of the media coverage on Professor Jason Arday who is
John B. Holbein
@JohnHolbein1
·
Jul 31
I care deeply about people's mental health. 

However, this is not a satisfactory defense for at least two reasons. 

First, what about the mental health of the people who's work Arday stole? 

What about Paula Zwozdiak-Myers? Women face an elevated risk for certain mental health
Show more
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Simon Baron-Cohen
@sbaroncohen
·
Jul 31
In 2014 we published the first large-scale study of suicidality in autism, subsequently widely replicated, revealing that 1 in 4 autistic people have planned or attempted suicide. That’s why I’m very concerned about the impact of the media coverage on Professor Jason Arday who is
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Ramya balasubramanian @rabal97.bsky.social · 05/08/2026
A thoroughly engaging read!
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Cahir O'Kane @cahirokane.bsky.social · 05/08/2026
Genetics lessons from the Irish famine
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James McInerney @jomcinerney.bsky.social · 25/06/2026
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...
open.substack.com
Drift and Luck
In 1968, a Japanese geneticist named Motoo Kimura published a paper that changed how every evolutionary biologist thought about evolution.
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Joshua B. Plotkin @jplotkin.bsky.social · 27/07/2026
… Time to prune
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James McInerney @jomcinerney.bsky.social · 05/08/2026
Continuing my writing on evolutionary biology and life. Another 6-ish minute read. Always free. "Never Bet It All" open.substack.com/pub/profmcin...
open.substack.com
Never Bet It All
What potatoes, a gambler and your own genome knows about surviving a future you can't predict
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Becca Satterwhite @satterwhite.bsky.social · 02/08/2026
“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.”
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James McInerney @jomcinerney.bsky.social · 24/07/2026
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...
A beaver with the text "Niche construction: selection running in two directions", with the subtext: "We make the place where we will evolve". It is from profmcinerney.substack.com. The publication is called The Long Game"
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James McInerney @jomcinerney.bsky.social · 27/07/2026
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.
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James McInerney @jomcinerney.bsky.social · 24/07/2026
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...
A beaver with the text "Niche construction: selection running in two directions", with the subtext: "We make the place where we will evolve". It is from profmcinerney.substack.com. The publication is called The Long Game"
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James McInerney @jomcinerney.bsky.social · 22/07/2026
Interesting study: www.sciencedirect.com/science/arti...
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James McInerney @jomcinerney.bsky.social · 21/07/2026
Paul Nurse responds to the changes in scientific leadership in the uk today: royalsociety.org/news/2026/07...
royalsociety.org
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.
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James McInerney @jomcinerney.bsky.social · 17/07/2026
Another Friday slow read. Modularity and what it could mean. As always it is free, so please subscribe. open.substack.com/pub/profmcin...
open.substack.com
Modularity
Why is everything not an integrated, undifferentiated system?
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James McInerney @jomcinerney.bsky.social · 17/07/2026
Another Friday slow read. Modularity and what it could mean. As always it is free, so please subscribe. open.substack.com/pub/profmcin...
open.substack.com
Modularity
Why is everything not an integrated, undifferentiated system?
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James McInerney @jomcinerney.bsky.social · 25/06/2026
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...
open.substack.com
Drift and Luck
In 1968, a Japanese geneticist named Motoo Kimura published a paper that changed how every evolutionary biologist thought about evolution.
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James McInerney @jomcinerney.bsky.social · 09/06/2026
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
profmcinerney.substack.com
Good enough
What we have learned from absurd evolution
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James McInerney @jomcinerney.bsky.social · 05/06/2026
New Post: Genomes are models of the world. Click here -> open.substack.com/pub/profmcin...
open.substack.com
Genomes are models of the world
What machine learning revealed about predictability in a bacterial pangenome
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James McInerney @jomcinerney.bsky.social · 04/06/2026
in case you missed it: profmcinerney.substack.com/p/the-pangen... "The Pangenome Is Not A Parts List"
profmcinerney.substack.com
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.
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James McInerney @jomcinerney.bsky.social · 04/06/2026
in case you missed it: profmcinerney.substack.com/p/the-pangen... "The Pangenome Is Not A Parts List"
profmcinerney.substack.com
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.
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James McInerney @jomcinerney.bsky.social · 28/05/2026
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.
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Microbiology Society @microbiologysociety.org · 18/05/2026
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: microb.io/4uUT6ht
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 12/05/2026
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/...
academic.oup.com
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
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Jitka Polechová @polejit.bsky.social · 12/05/2026
Published at @pnas.org www.pnas.org/doi/epdf/10....
pnas.org
Evolution of species’ range and niche in changing environments
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James McInerney @jomcinerney.bsky.social · 08/05/2026
Sir David Attenborough is older than horizontal gene transfer. Well, he was born before the first experiments that demonstrated HGT. #clickbait #NotTheSameThing
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Jeroen Meijer @jeroenmeijer.bsky.social · 08/05/2026
"If the accessory genome was truly dispensable, then the interesting part of pangenomics would, of course, be the core."
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James McInerney @jomcinerney.bsky.social · 08/05/2026
A short piece about what "the pangenome" is and is not. open.substack.com/pub/profmcin...
open.substack.com
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.
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Sam Horsfield @samuelhorsfield.bsky.social · 05/05/2026
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...
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James McInerney @jomcinerney.bsky.social · 05/05/2026
New Preprint: Species-specific transformer models of bacterial gene order and content for genomic surveillance tasks www.biorxiv.org/content/10.6...
biorxiv.org
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Chris Meder @evcurvefuturist.com · 05/05/2026
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.
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James McInerney @jomcinerney.bsky.social · 05/05/2026
New Preprint: Species-specific transformer models of bacterial gene order and content for genomic surveillance tasks www.biorxiv.org/content/10.6...
biorxiv.org
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James McInerney @jomcinerney.bsky.social · 23/04/2026
I'm blogging over on substack - no subscription needed. open.substack.com/pub/profmcin...
open.substack.com
The Fourth Wave
Meditations for the anxious scientific mind
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James McInerney @jomcinerney.bsky.social · 22/04/2026
I’ll be there. Hup!!
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James McInerney @jomcinerney.bsky.social · 21/04/2026
open.substack.com/pub/profmcin...
open.substack.com
Why Evolution Plays the Lottery
On bet-hedging, the mathematics of survival, and the unexpected virtue of being a little bit disorganised
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 05/12/2025
Dissecting Phylogenetic Support: Unified Decay Indices, AU Tests, and Branch-Site Specific Visualizations. www.biorxiv.org/content/10.64898/20…
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James McInerney @jomcinerney.bsky.social · 31/03/2026
Interesting. www.rte.ie/brainstorm/2...
rte.ie
Why return to office policies are all pain and no gain
These policies have moved from being questionable to being a red flag and are now a strong indication of a badly run organisation
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DeepDNA — Go Deep Into Your Genes @deepdna.ai · 28/03/2026
What's even wilder is that models like scGPT and Geneformer are now doing this at the single-cell level — learning gene regulatory patterns from raw expression data with zero biological annotation. They're rediscovering cell types and disease states purely from the structure of the data.
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James McInerney @jomcinerney.bsky.social · 26/03/2026
A transformer model trained on raw DNA, with no biological instruction whatsoever, learned to distinguish between genetic codes. Nobody taught it what a codon is. That is just “wow”.
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James McInerney @jomcinerney.bsky.social · 19/03/2026
We have a new Masters programme in Liverpool. Please pass on to anybody you think might be interested: news.liverpool.ac.uk/2026/02/13/n...
news.liverpool.ac.uk
New MSc in Wildlife Health and Conservation launched in partnership with Chester Zoo - University of Liverpool News
New MSc in Wildlife Health and Conservation launched in partnership with Chester Zoo
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James McInerney @jomcinerney.bsky.social · 11/03/2026
This looks really great. I’ve been following this for a while.
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James McInerney @jomcinerney.bsky.social · 11/03/2026
On this last point: the implication is (and I wrote this in the paper) that evolution is not optimising biochemical (or other) activity as a primary focus, but the context-dependent function. And this is liable to change often.
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James McInerney @jomcinerney.bsky.social · 11/03/2026
I'm thankful to MBE for publishing this paper. I wan't sure anybody would. The handling editor (I now know was Jeff Townsend) was great, as were the 2 reviewers. It is not an outcome/product/discovery, it is my way of thinking about HGT & pangenomes 1/3 academic.oup.com/mbe/article/...
academic.oup.com
Genomic perplexity and the evolution of context-dependent function
Abstract. The fundamental principle that selection acts on a gene's function often assumes implicitly that this function is fixed and intrinsic. However, e
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James McInerney @jomcinerney.bsky.social · 05/03/2026
True story.
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Molecular Biology and Evolution @molbioevol.bsky.social · 04/03/2026
@jomcinerney.bsky.social proposes that genomes do not encode fixed functions but rather “probability distributions” over functional and phenotypic outcomes, and introduces “genomic perplexity” as a measure of gene-context incompatibility. 🔗 doi.org/10.1093/molbev/msag041 #evobio #molbio
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James McInerney @jomcinerney.bsky.social · 04/03/2026
@guigau.bsky.social Saw PanGBank earlier. Very nice 👍
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James McInerney @jomcinerney.bsky.social · 04/03/2026
This looks absolutely great. For those of us interested in pangenomes, I am sure this will be a super place to get data and the interface is very clean (plotly). Congrats to the authors (I don't know if they are on bsky): pangbank.genoscope.cns.fr
pangbank.genoscope.cns.fr
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