iiinova — where your digital self keeps evolving

Bat info here! mean about twice as high as birds, but also a 'weirdly' tight distribution across the 140 assemblies.

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Orthoptera: "Hold my beer" www.biorxiv.org/content/10.1...

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Thanks for pointing me at it - I wasn't aware of the resource, and the extra safeguards! Do let me know, I'd love to index them in a fair way if folks are onboard.

At the moment no: in an attempt to keep the backend as small as possible, I'm currently just tallying NCBI records as they release (and retaining full metadata only for a few months). But if there's a database that can be periodically scraped, I might be able to set it up?

god damn this is cool! So the origin is probably lost to the Jurassic.....

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Joe Hanly @hanliconius.bsky.social · 15h

I wonder how they achieved that......

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amazing, thanks. I'll investigate if i can set up a github action to do a onetime trawl.

Joe Hanly @hanliconius.bsky.social · 15h

It could be interesting to track the genomes of eukaryote disease vectors - do you know if anyone maintains a curated list that is easily checkable?

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A few more and we’ll be able to see New Zealand on the map!! 😅

@felixvaux.bsky.social here we go! you might need to force a browser refresh with ctrl-shift-r. Happy to play around adding more features, and let me know if it does end up being helpful!

Oh that sounds interesting! Let me see what I can cook up XD

Joe Hanly @hanliconius.bsky.social · 08/10/2026

this plot also hides the poor orthoptera, who can get as big 30Gb.

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I'm surprised by how well behaved bird genomes are!

Joe Hanly @hanliconius.bsky.social · 08/10/2026

genome sizes in animal and fungal orders. (note different scales). hanliconius.github.io/genome-obser...

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Joe Hanly @hanliconius.bsky.social · 06/10/2026

according to Genome Observatory, we have 6 chromosomal genomes from extinct species. That includes one of the only genomes from a named and famous individual, Lonesome George the Giant Tortoise hanliconius.github.io/genome-obser...

A table showing the 6 chromosomal genomes of extinct species.

a picture of the Abingdon Island Giant Tortoise, "Lonesome George".

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GitHub - Hanliconius/eukaryote-genome-watch: applet for viewing live stats about genome sequence publication

Honestly there was a heavy vibe-coding AI assist from ChatGPT, and the code is all open on github; I'm more than happy for anyone to follow up on this, and i'll answer any questions I can github.com/Hanliconius/...

github.com

applet for viewing live stats about genome sequence publication - Hanliconius/eukaryote-genome-watch

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Sure! honestly for the viz, I took inspiration from "national grid live", a dashboard that shows power generation by source in the UK. Other than that, I knew the info I wanted would all be on NCBI, and that I needed to find ways to tally records without downloading all the metadata for every sample

You can now explore who is doing the sequencing. (the punchline: almost all of it is being done by @sangerinstitute.bsky.social !)

I suppose NCBI could add a "type" field to the metadata for each chromosome... but then someone has to go and back-fill 18k genomes :/

I've continued to make little quality of life and data vis updates to Genome Observatory. I've really enjoyed how with frankly very minimal work, I've been able to generate a usable tool hanliconius.github.io/eukaryote-ge...

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some verts for the so-inclined: hanliconius.github.io/eukaryote-ge...

I also updated the Taxon Viewer to allow for comparisons, and to have a map function. I'm insect biased so looked at this first:

Joe Hanly @hanliconius.bsky.social · 01/10/2026

Today's Genome Observatory Tidbits: 1. the shift in dominance from Illumina to PacBio for genome assembly. 2. the increasing ubiquitousness of HiC.

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Joe Hanly @hanliconius.bsky.social · 01/10/2026

While this Wired piece does have some nuance, it shows exactly why I'm so angry about this 'review': academic journals should not be doing free advertising for sketchy startups with strong associations to eugenics. @cellpress.bsky.social, you should retract it. www.wired.com/story/biotec...

wired.com

A Biotech Founder Makes the Moral Case for Gene-Editing Human Embryos

The practice of editing the genes of embryos remains highly controversial and risky, but Origin Genomics founder Cathy Tie argues its a “moral imperative” to address hereditary diseases.

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sorry for like, being pesky about this but @adamrutherford.bsky.social what exactly is one supposed to do about stuff like this?!?

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ah yes, the old "was it an ethical, moral and scientific scandal or was it just some pesky paperwork" dilemma.

From the Guardian "Tie is a bold performer, determined to build her reputation as a respectable voice for her field. Whether she can [...] remains to be seen. Perhaps it won’t matter, if she succeeds." Apparently she CAN, with your help @cellpress.bsky.social

And suddenly, it does feel inevitable to me that this is going to happen. It has already happened. Whether Tie will be the person to get regulations changed to allow it to happen legally is another matter. But there are enough people prepared to put money, time and effort into this technology – and enough demand for it – that it feels like a question of when, not if.

Tie steps down from the stage. “The tide is turning!” she tells me, with a broad, triumphant grin.

On these hallowed New York stages, in this company, Tie is a bold performer, determined to build her reputation as a respectable voice for her field. Whether she can shake the spectre of her previous collaborations – with the Manhattan Project, with the Los Angeles Project, with He Jiankui – remains to be seen. Perhaps it won’t matter, if she succeeds.

Arnaud Martin @evolvwing.bsky.social · 30/09/2026

Reposted by Joe Hanly

Cell Press giving a rather biased, pro-eugenics platform to self-proclaimed "Biotech Barbie", former a Thiel Fellow who briefly married He Jiankui, and fails to properly frame the debate on germline editing. Partly bonkers, partly important, check out this thread 🤯

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Indeed, it's fantastic to see!

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I'm sorry, but there's no way to describe this but as a pro-eugenics Op-Ed disguised as a scientific review, and is a complete failure of editorial and ethical standards at @cellpress.bsky.social . This article should be retracted. 5/5

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The author also has strong ties to noted eugenicist and convicted criminal He Jiankui 4/

Cathy Tie's ex-husband is controversial Chinese biophysicist He Jiankui, who gained global notoriety as "China's Frankenstein" for creating the world's first CRISPR gene-edited babies.
Key Details of Their Relationship
• Marriage: The Canadian entrepreneur Cathy Tie married He Jiankui in April 2025 in Beijing after a whirlwind romance.
• Separation: Just three months later, in July 2025, Tie announced on social media that they were separating and pursuing separate paths, later clarifying that they had not been legally married.
• Context: The split followed travel complications when Tie was blocked and denied entry to China during a layover in Manila, leaving her operations rooted in North America while He remained in China.

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As if it weren't clear enough, this whole thing smacks of eugenics, and the author's history of funding highlights this, having received funding from people like Peter Thiel. 3/

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Firstly, the author is the founder of a company selling this technology and lobbying for legal changes to make it possible 2/

C.T. is the Founder, Chief Executive Officer, and an equity holder in Origin Genomics, a company developing technologies related to human genome editing. C.T. also serves on the board of directors of the Cold Spring Harbor Laboratory Association.

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@cellpress.bsky.social has just released an.... interesting new 'short review' on pre-implantation gene editing, in which author Cathy Tie argues for the ethical imperative of pushing for this technology. www.sciencedirect.com/science/arti... There are, to put it mildly, a few issues here. 1/

Medicine has a responsibility to develop interventions that safely reduce human suffering. Therapeutic germline gene editing should be judged by the scientific evidence supporting it, not by the history of the field. If rigorous clinical evaluation demonstrates that it is safe and effective, continued prohibition would itself require ethical justification.

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Just a quick note on this, I couldn't find a way to reliably parse UV systems because V turns up frequently in cases where chromosome names are Roman Numerals. There's a risk that the X could poison the info for XY too, but I don't really know how to fix that.

Today's Genome Observatory tidbit: different countries have very different trends in what type of genomes they are focusing resources on. The UK output is overwhelmingly "first time species", whereas the US is mainly reference improvements. hanliconius.github.io/eukaryote-ge...

A chart of genomes submitted by UK institutions since 2005, showing a current 30 day rate of 20.5 a day, with 5472 total, 4811 of which are first time genomes.

A chart of genomes submitted by US institutions since 2005, showing a current 30 day rate of 1.2 a day, with 3139 total, 1160 of which are first time genomes.

There's a win-win solution: include diagrams of squid guard.

This let me add an extra panel of observed vs expected sex chromosomes.

The median eukaryote has 16 chromosomes. It’s perhaps surprisingly unimodal. All this and even more here: hanliconius.github.io/eukaryote-ge...

Histograms for genome size and chromosome number in all eukaryote genomes.

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AHA!! I was hoping someone would prove me wrong! Thanks!

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Joe Hanly @hanliconius.bsky.social · 28/09/2026

I’m definitely on team “totally spoilt by being a lepidopterist”

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Have you put any thought into having some form of Ancestral Recombination Group-based naming system? There's potential for ARG-naming to be future-proof, but then doesn't solve historical databasing etc.....