Deepak Shilkar

Big experiments are only big if they can fail Some reflections on Arena Bioworks' unexpected wind down as a fellow institutional experimentalist

"We need more institutional experiments for science" makes sense to me @seemaychou.bsky.social. We might not like some of 'em and some'll fail, but given academic science often looks like a feudal system needing an industrial revolution trying things can't hurt.. seemay.substack.com/p/big-experi...

Already did! I hope this project becomes financially sustainable in the long term. Best wishes!

Alibaba has good stuff but takes forever to deliver.

Tried @qedscience.bsky.social by running our published paper through it. It identified 2 issues unknown to us. Amazing work, Dr. @odedrechavi.bsky.social and team. 👌👌👌

James Watson, Co-Discoverer of the Structure of DNA, Is Dead at 97

James Watson has died www.nytimes.com/2025/11/07/s...

Next paper title: "Over 99.99% Humans were born"

Does it play well with citations?

Agreed. Can't say equal talent. But I've met people over the years who took up odd jobs because they needed to support family, even though their talents and interests were elsewhere. That's life, right!? But wherever they are, they've made their mark in their own unique way.🙂

Well well. At the end of the day, snek ❤️ Snek

Gen AI didn't create this problem, but it has supercharged it. It has lowered the cost and time to produce a plausible-looking (but empty) paper from months to minutes. Would it be possible to uniquely identify the submitting parties and deplatform or ban them for certain number of years?

And another thing: I am far more concerned with data provenance and information/identity verification than peer review right now… 1/2 journals.plos.org/plosbiology/...

Changes to UniProt proteomes UniProt, the data resource for protein sequence and function information, is making major changes to its proteomes resource and to the UniProt Knowledgebase. UniProt has developed a new workflow that ...

UniProt is changing its reference proteomes resource.

Reference proteomes will remain in UniProtKB, while others will move to UniParc.

Read more about these changes:
www.ebi.ac.uk/about/news/u...

🧬 🖥️

Uniprot is a collaboration between EMBL-EBI, @sib.swiss & the Protein Information Resource.

Loved Season 4 the most. Liked Voyager only because there are character arcs. But I feel that Enterprise is kinda most underrated. The one from 2001.

Understatement!

Nature suggests you use their "Manuscript Adviser" bot to get advice before submitting

I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:

but...you shouldn't use a calculator when you are learning elementary math...the whole point is to develop the language of math...

letting elementary math students use a calculator to 'learn math' would be like letting elementary reading students use a voice reader to 'learn to read'

Excited to share our new work on transgenerational adaptation www.science.org/doi/epdf/10.... out today spearheaded by outstanding former undergraduate @kathleenkim.bsky.social. C. elegans adapt to repeated generational stresses and no longer display altered fertility, fat content, + longevity 1/9

Interesting work. Didn't think evo-devo framework could be applied like this. Will keep this paper on my weekend reading list.

Fleetwood Mac / Rumours

This is so good to see - a young baby has had a life changing treatable disease diagnosed early due to broad based (healthy baby) genome sequencing. He has a rare eye cancer gene, and has immediately been put into the effective treatment pathway.

A few alumni have collected in Rochester this weekend to say thank you and happy retirement to my PhD advisor Tom Eickbush, along with three other amazing evolutionary biologists: Allen Orr, John Jaenike, and Jack Werren.

My heart is filled with gratitude for having trained with them.

Constraints on chromosome evolution revealed by the 229 chromosome pairs of the Atlas blue butterfly The genome of the Atlas blue butterfly contains ten times more chromosomes than most butterflies, and more than any other known diploid animal. Wright et al. show that this extraordinary karyotype is ...

How many chromosomes can an animal have?

In our paper out now in @currentbiology.bsky.social we show that the Atlas blue butterfly has 229 chromosome pairs- the highest in diploid Metazoa! These arose by rapid autosome fragmentation while sex chromosomes stayed intact.
www.cell.com/current-biol...

Assistant Professor-Neurobiology All Job Postings will close at 12:01a.m. CST (1:01a.m. EST) on the specified Closing Date (if designated). If you close the browser or exit your application prior to submitting, the application progre...

Our department @lsu.bsky.social LSU Biological Sciences is hiring an Assistant Professor in Neurobiology.

Our department is amazing - come join us...

lsu.wd1.myworkdayjobs.com/LSU/job/0202...

We reward papers, not integrity, so we learn to play the publish-or-perish game instead of chasing philosophy. I was rejected from a few prestigious PhD programs because I did not have a research paper. So I ended up joining a research assistantship to generate and add some garbage on my profile.

cc: old time chemtwitter friends

@alexgoldberg.ca

Lol. Math has left the room.

Manipulation of the nucleotide pool in human, bacterial and plant immunity - Nature Reviews Immunology Modification of the nucleotide pool is emerging as key to innate immunity in animals, plants and bacteria. This Review explains how immune pathways conserved from bacteria to humans manipulate the nuc...

We wrote a review on the free nucleotide pool as a central playground in human, bacterial, and plant immunity – now out in Nature Reviews in Immunology

www.nature.com/articles/s41...

Was fun to write this piece with Dina Hochhauser!

Here is a thread to explain the premises

1/

A The major components of the CSF system include CSF, choroid plexus, and circumventricular organs. These systems change their properties across time of day, including those listed below each component. B Multiple inputs affect the CSF system across time of day.

How does the brain 🧠 change around the clock 🕰️? Can this inform treatments?

Learn more in a new review from the lab 'Harnessing the #circadian nature of the choroid plexus and cerebrospinal fluid' ➡️ npj Biological Timing & Sleep | #Nature @natureportfolio.nature.com
www.nature.com/articles/s44...

Malaria parasite population genomics during an elimination program in Eastern Myanmar https://www.biorxiv.org/content/10.1101/2025.05.21.655408v1

I will be recruiting new postdocs with start dates end 2025 - early 2026. If you'd like to work at the Pasteur Institute in the heart of Paris surrounded by amazing scientists, reach out to discuss possible projects on SynBio / Bacterial Immunity!