Sign in

James McInerney

@jomcinerney.bsky.social
4.3K followers 6.9K following 369 posts

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

PostsRepliesMedia
James McInerney @jomcinerney.bsky.social · 08/10/2026
A biorxiv preprint that describes it functionality is here: www.biorxiv.org/content/10.6...
biorxiv.org
CRAIC: interactive interrogation of multiple sequence alignment uncertainty
Multiple sequence alignments (MSAs) are often treated as a solved problem. However, ambiguously or incorrectly aligned regions are the source of much error in phylogenetics and comparative genomics. C...
051
James McInerney @jomcinerney.bsky.social · 08/10/2026
The github repo is here: github.com/mol-evol/craic
github.com
GitHub - mol-evol/craic: CRAIC: Interactive Interrogation of Multiple Sequence Alignment Uncertainty
CRAIC: Interactive Interrogation of Multiple Sequence Alignment Uncertainty - mol-evol/craic
100
James McInerney @jomcinerney.bsky.social · 08/10/2026
The documentation is here: mol-evol.github.io/craic/
mol-evol.github.io
CRAIC
CRAIC — Conserved-Region Alignment by Iterative Convergence
100
James McInerney @jomcinerney.bsky.social · 08/10/2026
I have put this program online. I use it mostly for teaching about alignments, though it is a genuine aligner wrapper, as well as having a ProbCons-like aligner itself. www.youtube.com/watch?v=Zljs...
youtube.com
CRAIC Features
YouTube video by James Talks Genetics
1107
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.
051
Reposted by James McInerney
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.
02510
Reposted by James McInerney
Jonathan Howard @joho.bsky.social · 15/08/2026
I am unshocked
3359
Reposted by James McInerney
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.
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
Prof Francois Balloux
@BallouxFrancois
·
Jul 31
This tweet reads like a spoof intent on painting academics in a bad light ...
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
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
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
361118290
Reposted by James McInerney
Ramya balasubramanian @rabal97.bsky.social · 05/08/2026
A thoroughly engaging read!
011
Reposted by James McInerney
Cahir O'Kane @cahirokane.bsky.social · 05/08/2026
Genetics lessons from the Irish famine
031
Reposted by James McInerney
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.
0227
Reposted by James McInerney
Joshua B. Plotkin @jplotkin.bsky.social · 27/07/2026
… Time to prune
041
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
134
Reposted by James McInerney
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.”
092
Reposted by James McInerney
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"
0296
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.
59014
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"
0296
James McInerney @jomcinerney.bsky.social · 22/07/2026
Interesting study: www.sciencedirect.com/science/arti...
051
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.
010
Reposted by James McInerney
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?
1223
James McInerney @jomcinerney.bsky.social · 17/07/2026
That’s so kind of you, Laura.
010
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?
1223
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.
0227
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
0113
James McInerney @jomcinerney.bsky.social · 05/06/2026
Thanks Annie. Your comment made my Friday :)
020
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
1356
Reposted by James McInerney
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.
12610
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.
12610
James McInerney @jomcinerney.bsky.social · 28/05/2026
Indeed.
010
James McInerney @jomcinerney.bsky.social · 28/05/2026
He was laughing in this photo.
010
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.
2130
Reposted by James McInerney
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
033
James McInerney @jomcinerney.bsky.social · 17/05/2026
I don’t know if that answer is much help. I don’t think I do things much differently to other people I have talked to. I don’t have any special insights. It mostly helps pull together my diffuse thoughts.
110
James McInerney @jomcinerney.bsky.social · 17/05/2026
I think most computational scientists are using these tools now or will be soon, and I’d encourage transparency about it. If I was to talk about “treading lightly” it would be to use TDD and be skeptical about any code or output. Don’t try something if you don’t know what the output should look like
110
James McInerney @jomcinerney.bsky.social · 17/05/2026
Sure. I use LLMs as coding assistants for data analysis scripts, simulations, and building web tools (the blog, the FAQ page, etc.). The scientific reasoning and evolutionary biology framework is mine.
210
James McInerney @jomcinerney.bsky.social · 17/05/2026
I’ve invoked things like the massive census population of some bacteria - the gene is in some part of the network, being neutral or beneficial, and the combination of mobility and pop size means that this “solution” can be found quickly from external sources.
110
James McInerney @jomcinerney.bsky.social · 16/05/2026
Please do. I always imagine that whatever bacteria do, viruses do it on fast forward.
220
Reposted by James McInerney
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
311537
James McInerney @jomcinerney.bsky.social · 13/05/2026
I feel these points refine the model, but don't contradict it. but I'd be happy to know your thoughts. 10/10
100
James McInerney @jomcinerney.bsky.social · 13/05/2026
Short version: yes, h_eff = r × p_ext is the right decomposition; my h values were intended as h_eff, not as bare r; for genes with very small p_ext the predicted equilibrium f is correspondingly small, which is consistent with the very rare tail of the pangenome distribution. 9/n
100
James McInerney @jomcinerney.bsky.social · 13/05/2026
I haven't done that explicitly and it is definitely an interesting extension, particularly for asking which genes are pool-supported vs. self-supported, and for relating "open" vs. "closed" pangenomes to gene-pool diversity rather than to r alone. 8/n
100
James McInerney @jomcinerney.bsky.social · 13/05/2026
You are prompting me to write a cleaner version than what I actually wrote. The honest framing is a coupled system: focal species f tracked against a broader gene pool with its own dynamics, with h_eff = r × p_ext doing the bookkeeping. 7/n
100
James McInerney @jomcinerney.bsky.social · 13/05/2026
Genes that are uniformly rare across the broader pool do give small h_eff, and the model predicts correspondingly low equilibrium f. The U-shape architecture is robust to this — the rare peak just sits closer to the floor. 6/n
100
James McInerney @jomcinerney.bsky.social · 13/05/2026
On your specific worry that p_ext should pull h_eff way down: it depends on the gene. AMR cassettes on broad-host-range conjugative elements have substantial p_ext across Enterobacteriaceae and beyond, so h_eff stays moderate. 5/n
100
James McInerney @jomcinerney.bsky.social · 13/05/2026
calibrated to empirically observed transfer rates that already include the realistic availability of donor DNA, not bare recombination rates with p_ext = 1. 4/n
100
James McInerney @jomcinerney.bsky.social · 13/05/2026
So the values I quoted (~10⁻² for conjugative plasmids down to ~10⁻⁶–10⁻⁸ for chromosomal homologous recombination) are net per-cell per-generation rates of gene *re-entry* into lineages that have lost the gene 3/n
100
James McInerney @jomcinerney.bsky.social · 13/05/2026
The h = r × p_ext decomposition really is the mechanistic underpinning. What I have been doing is treating h as an effective net rate that already absorbs p_ext, rather than a bare per-encounter recombination rate. 2/n
100
James McInerney @jomcinerney.bsky.social · 13/05/2026
Thanks Ben...and you're right. The model as stated needs h to represent external input — pure intra-species recombination just redistributes f without sustaining it against selection, so the equation f = h / |s_net| only works if h is largely external. 1/n
100