Omar El Oakley
@ooakley.bsky.social
agent-based modelling (and some experiments) of cells doing adaptive self-organisation & pattern formation in the embryo - PhD student between the Crick/KCL - ask me about limb mesenchyme fibroblasts
Reposted by Omar El Oakley
An Asgard archaeon with internal membrane compartments
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
November 7, 2025 at 10:44 AM
An Asgard archaeon with internal membrane compartments
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Reposted by Omar El Oakley
Of course, some collections are fairly benign. Like Tom Brown, an Appalachian man who collects rare apples.
August 27, 2025 at 10:35 PM
Of course, some collections are fairly benign. Like Tom Brown, an Appalachian man who collects rare apples.
Reposted by Omar El Oakley
BIG NEWS: For the first time in six years, Britain's rarest breeding bird has successfully nested in the UK!
A pair of Montagu's Harriers have raised four healthy chicks, all of which have taken their first flights.
A pair of Montagu's Harriers have raised four healthy chicks, all of which have taken their first flights.
July 30, 2025 at 9:04 AM
BIG NEWS: For the first time in six years, Britain's rarest breeding bird has successfully nested in the UK!
A pair of Montagu's Harriers have raised four healthy chicks, all of which have taken their first flights.
A pair of Montagu's Harriers have raised four healthy chicks, all of which have taken their first flights.
Reposted by Omar El Oakley
Preprint:
"Why We Experience Society Differently: Intrinsic Dispositions as Drivers of Ideological Complexity in Adaptive Social Networks"
Work by Akshay Gangadhar
arxiv.org/abs/2504.078...
TL;DR:
If you seek a homogeneous, steady environment, your life gets eventful, ironically!!
"Why We Experience Society Differently: Intrinsic Dispositions as Drivers of Ideological Complexity in Adaptive Social Networks"
Work by Akshay Gangadhar
arxiv.org/abs/2504.078...
TL;DR:
If you seek a homogeneous, steady environment, your life gets eventful, ironically!!
Why We Experience Society Differently: Intrinsic Dispositions as Drivers of Ideological Complexity in Adaptive Social Networks
Understanding the emergence of inequality in complex systems requires attention to both structural dynamics and intrinsic heterogeneity. In the context of opinion dynamics, traditional models relied o...
arxiv.org
July 23, 2025 at 10:46 AM
Preprint:
"Why We Experience Society Differently: Intrinsic Dispositions as Drivers of Ideological Complexity in Adaptive Social Networks"
Work by Akshay Gangadhar
arxiv.org/abs/2504.078...
TL;DR:
If you seek a homogeneous, steady environment, your life gets eventful, ironically!!
"Why We Experience Society Differently: Intrinsic Dispositions as Drivers of Ideological Complexity in Adaptive Social Networks"
Work by Akshay Gangadhar
arxiv.org/abs/2504.078...
TL;DR:
If you seek a homogeneous, steady environment, your life gets eventful, ironically!!
Reposted by Omar El Oakley
The 3-decade-old competition that enabled the emergence and evaluate of AlphaFold has run out of NIH funding.
The program will be terminated in weeks.
This is terminating success.
www.science.org/content/arti...
The program will be terminated in weeks.
This is terminating success.
www.science.org/content/arti...
July 3, 2025 at 12:28 PM
The 3-decade-old competition that enabled the emergence and evaluate of AlphaFold has run out of NIH funding.
The program will be terminated in weeks.
This is terminating success.
www.science.org/content/arti...
The program will be terminated in weeks.
This is terminating success.
www.science.org/content/arti...
Reposted by Omar El Oakley
Does the brain learn by gradient descent?
It's a pleasure to share our paper at @cp-cell.bsky.social, showing how mice learning over long timescales display key hallmarks of gradient descent (GD).
The culmination of my PhD supervised by @laklab.bsky.social, @saxelab.bsky.social and Rafal Bogacz!
It's a pleasure to share our paper at @cp-cell.bsky.social, showing how mice learning over long timescales display key hallmarks of gradient descent (GD).
The culmination of my PhD supervised by @laklab.bsky.social, @saxelab.bsky.social and Rafal Bogacz!
Dopamine encodes deep network teaching signals for individual learning trajectories
Longitudinal tracking of long-term learning behavior and striatal dopamine reveals
that dopamine teaching signals shape individually diverse yet systematic learning
trajectories, captured mathematical...
www.cell.com
June 15, 2025 at 9:33 AM
Does the brain learn by gradient descent?
It's a pleasure to share our paper at @cp-cell.bsky.social, showing how mice learning over long timescales display key hallmarks of gradient descent (GD).
The culmination of my PhD supervised by @laklab.bsky.social, @saxelab.bsky.social and Rafal Bogacz!
It's a pleasure to share our paper at @cp-cell.bsky.social, showing how mice learning over long timescales display key hallmarks of gradient descent (GD).
The culmination of my PhD supervised by @laklab.bsky.social, @saxelab.bsky.social and Rafal Bogacz!
Reposted by Omar El Oakley
The Math is not the Territory looks to clear up debates surrounding a modelling approach in neuroscience, the free energy principle (FEP) by distinguishing between the contentless formal modelling framework and interpreted models developed therefrom. link.springer.com/article/10.1...
The math is not the territory: navigating the free energy principle - Biology & Philosophy
Much has been written about the free energy principle (FEP), and much misunderstood. The principle has traditionally been put forth as a theory of brain function or biological self-organisation. Criti...
link.springer.com
November 17, 2024 at 10:35 PM
The Math is not the Territory looks to clear up debates surrounding a modelling approach in neuroscience, the free energy principle (FEP) by distinguishing between the contentless formal modelling framework and interpreted models developed therefrom. link.springer.com/article/10.1...
Reposted by Omar El Oakley
Incredible:
0% of studies funded by the meat industry have found a link between red meat and cardiovascular ill-health.
73% of studies *not* funded by the meat industry have found a link.
www.thetimes.com/uk/science/a...
0% of studies funded by the meat industry have found a link between red meat and cardiovascular ill-health.
73% of studies *not* funded by the meat industry have found a link.
www.thetimes.com/uk/science/a...
Is red meat bad for your heart? Studies leave plenty to chew over
Scientists analyse industry-sponsored research on red meat and heart health
www.thetimes.com
June 4, 2025 at 9:29 AM
Incredible:
0% of studies funded by the meat industry have found a link between red meat and cardiovascular ill-health.
73% of studies *not* funded by the meat industry have found a link.
www.thetimes.com/uk/science/a...
0% of studies funded by the meat industry have found a link between red meat and cardiovascular ill-health.
73% of studies *not* funded by the meat industry have found a link.
www.thetimes.com/uk/science/a...
Reposted by Omar El Oakley
huge fan of the 70 year old german guy who uploaded this 360 degree interactive panorama of inside a corn flakes bag. it's in the corn flakes article on
May 23, 2025 at 6:59 AM
huge fan of the 70 year old german guy who uploaded this 360 degree interactive panorama of inside a corn flakes bag. it's in the corn flakes article on
Reposted by Omar El Oakley
Striking new study from @archaeon-alex.bsky.social's lab just out in @science.org on multicellular development induced by compression in Archaea: www.science.org/doi/10.1126/...
Tissue-like multicellular development triggered by mechanical compression in archaea
The advent of clonal multicellularity is a critical evolutionary milestone, seen often in eukaryotes, rarely in bacteria, and only once in archaea. We show that uniaxial compression induces clonal mul...
www.science.org
April 3, 2025 at 6:24 PM
Striking new study from @archaeon-alex.bsky.social's lab just out in @science.org on multicellular development induced by compression in Archaea: www.science.org/doi/10.1126/...
Reposted by Omar El Oakley
⭐️ Please Fwd. Are you in Paris on 16th May? See👇 poster of symposium on « Information processing in biological systems » @collegedefrance.bsky.social Fantastic line of speakers 🤩.
It is free, w/o registration, and it will be exciting.m!
Follows from my series of lectures at CdF last fall.
It is free, w/o registration, and it will be exciting.m!
Follows from my series of lectures at CdF last fall.
March 20, 2025 at 8:03 AM
⭐️ Please Fwd. Are you in Paris on 16th May? See👇 poster of symposium on « Information processing in biological systems » @collegedefrance.bsky.social Fantastic line of speakers 🤩.
It is free, w/o registration, and it will be exciting.m!
Follows from my series of lectures at CdF last fall.
It is free, w/o registration, and it will be exciting.m!
Follows from my series of lectures at CdF last fall.
Reposted by Omar El Oakley
Stoked to present our latest, superbly led by Chris et al & @torres-sanchez.bsky.social We tackled a fundamental problem – how tissues are patterned during development – found that geometry-constrained ECM fractures pattern the myocardium in the vertebrate heart 1/n www.biorxiv.org/content/10.1...
March 10, 2025 at 2:43 AM
Stoked to present our latest, superbly led by Chris et al & @torres-sanchez.bsky.social We tackled a fundamental problem – how tissues are patterned during development – found that geometry-constrained ECM fractures pattern the myocardium in the vertebrate heart 1/n www.biorxiv.org/content/10.1...
Reposted by Omar El Oakley
PREPRINT OUT ✨ "hack" your microscope to work as a 3D printer! print micrometer sized features at cm scale. a method for easy and cheap microfabrication, with a focus on biological applications. THREAD ↓
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
February 23, 2025 at 2:06 PM
PREPRINT OUT ✨ "hack" your microscope to work as a 3D printer! print micrometer sized features at cm scale. a method for easy and cheap microfabrication, with a focus on biological applications. THREAD ↓
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Omar El Oakley
Elon Musk's only profitable company, Tesla, has created a cumulative grand total net income of $34 billion in its more than 20 years of existence.
That's less than the total amount of US federal subsidies his empire has collectively received.
The economics of Elon Musk are as bad as the politics.
That's less than the total amount of US federal subsidies his empire has collectively received.
The economics of Elon Musk are as bad as the politics.
Elon Musk, who has said the beneficiaries of federal spending are a "parasite class," runs businesses that have pocketed $38 billion in taxpayer-funded subsidies, loans and contracts www.washingtonpost.com/technology/i...
February 26, 2025 at 3:44 PM
Elon Musk's only profitable company, Tesla, has created a cumulative grand total net income of $34 billion in its more than 20 years of existence.
That's less than the total amount of US federal subsidies his empire has collectively received.
The economics of Elon Musk are as bad as the politics.
That's less than the total amount of US federal subsidies his empire has collectively received.
The economics of Elon Musk are as bad as the politics.
Reposted by Omar El Oakley
Here's an attempt to bring together ALife researchers and enthusiasts here, who am I missing?
go.bsky.app/LgoJN2N
go.bsky.app/LgoJN2N
November 13, 2024 at 10:33 AM
Here's an attempt to bring together ALife researchers and enthusiasts here, who am I missing?
go.bsky.app/LgoJN2N
go.bsky.app/LgoJN2N
Reposted by Omar El Oakley
📚 Attention Readers & Researchers
More than 500,000 books have been removed from our lending library due to the publishers' lawsuit. Have you been affected? Share your story with us and help us fight to restore access. #LetReadersRead
👉 forms.gle/G2GXK6xwMZ3t...
More than 500,000 books have been removed from our lending library due to the publishers' lawsuit. Have you been affected? Share your story with us and help us fight to restore access. #LetReadersRead
👉 forms.gle/G2GXK6xwMZ3t...
Share Your Story: The Impact of Losing Access to 500,000 Books
The publishers' lawsuit against the Internet Archive (Hachette v. Internet Archive) has resulted in the removal of more than 500,000 books from our lending library, including over 1,300 banned and cha...
forms.gle
June 13, 2024 at 7:03 PM
📚 Attention Readers & Researchers
More than 500,000 books have been removed from our lending library due to the publishers' lawsuit. Have you been affected? Share your story with us and help us fight to restore access. #LetReadersRead
👉 forms.gle/G2GXK6xwMZ3t...
More than 500,000 books have been removed from our lending library due to the publishers' lawsuit. Have you been affected? Share your story with us and help us fight to restore access. #LetReadersRead
👉 forms.gle/G2GXK6xwMZ3t...
Reposted by Omar El Oakley
This year in Montréal, Diogo Melo and I are organising a symposium on the interplays between developmental bias and selection. We are enthusiastic in bringing together theoretical and empirical studies across systems. Please do consider submitting an abstract!!
evolutionmeetings.org/symposia.html
evolutionmeetings.org/symposia.html
April 21, 2024 at 3:47 PM
This year in Montréal, Diogo Melo and I are organising a symposium on the interplays between developmental bias and selection. We are enthusiastic in bringing together theoretical and empirical studies across systems. Please do consider submitting an abstract!!
evolutionmeetings.org/symposia.html
evolutionmeetings.org/symposia.html
Reposted by Omar El Oakley
"Left wing students are getting too censorious" turned into "arrest those left wing students for protesting" without even tapping the brakes
April 19, 2024 at 2:26 PM
"Left wing students are getting too censorious" turned into "arrest those left wing students for protesting" without even tapping the brakes
Reposted by Omar El Oakley
Please share: collaborative postdoc opportunity in microbial ecology and evolution at Indiana University Bloomington
NSF Biology Integration Institute (BII) on "Genomics and Eco-evolution of Multi-Scale Symbioses (GEMS)”
@GEMS_BII: tinyurl.com/4vyf6erd
indiana.peopleadmin.com/postings/23270
NSF Biology Integration Institute (BII) on "Genomics and Eco-evolution of Multi-Scale Symbioses (GEMS)”
@GEMS_BII: tinyurl.com/4vyf6erd
indiana.peopleadmin.com/postings/23270
March 6, 2024 at 3:02 PM
Please share: collaborative postdoc opportunity in microbial ecology and evolution at Indiana University Bloomington
NSF Biology Integration Institute (BII) on "Genomics and Eco-evolution of Multi-Scale Symbioses (GEMS)”
@GEMS_BII: tinyurl.com/4vyf6erd
indiana.peopleadmin.com/postings/23270
NSF Biology Integration Institute (BII) on "Genomics and Eco-evolution of Multi-Scale Symbioses (GEMS)”
@GEMS_BII: tinyurl.com/4vyf6erd
indiana.peopleadmin.com/postings/23270
Reposted by Omar El Oakley
I just published: What’s a toxic environment for a PhD student?
Being aware of potential red flags when selecting a host lab is crucial. Here are some issues I’ve witnessed over the years. #phdchat #AcademicChatter
link.medium.com/O5fd2PQ0GHb
Being aware of potential red flags when selecting a host lab is crucial. Here are some issues I’ve witnessed over the years. #phdchat #AcademicChatter
link.medium.com/O5fd2PQ0GHb
March 4, 2024 at 1:53 PM
I just published: What’s a toxic environment for a PhD student?
Being aware of potential red flags when selecting a host lab is crucial. Here are some issues I’ve witnessed over the years. #phdchat #AcademicChatter
link.medium.com/O5fd2PQ0GHb
Being aware of potential red flags when selecting a host lab is crucial. Here are some issues I’ve witnessed over the years. #phdchat #AcademicChatter
link.medium.com/O5fd2PQ0GHb
Reposted by Omar El Oakley
Here's one for Rob Insall who was looking for an image showing the three cytoskeleton components (actin⚪️ microtubules🔵 intermediate filaments🟠) - I hope it will help students see the beauty of cells! 🧪
January 15, 2024 at 10:58 PM
Here's one for Rob Insall who was looking for an image showing the three cytoskeleton components (actin⚪️ microtubules🔵 intermediate filaments🟠) - I hope it will help students see the beauty of cells! 🧪
Reposted by Omar El Oakley
New paper from @thaliawheatley.bsky.social, me, @stolkarjen.bsky.social & @lukejchang.bsky.social at Perspectives on Psychological Science!
"The Emerging Science of Interacting Minds"
Read about why we think that this is an auspicious moment for interaction science!
Link: doi.org/10.1177/1745...
"The Emerging Science of Interacting Minds"
Read about why we think that this is an auspicious moment for interaction science!
Link: doi.org/10.1177/1745...
December 18, 2023 at 6:31 PM
New paper from @thaliawheatley.bsky.social, me, @stolkarjen.bsky.social & @lukejchang.bsky.social at Perspectives on Psychological Science!
"The Emerging Science of Interacting Minds"
Read about why we think that this is an auspicious moment for interaction science!
Link: doi.org/10.1177/1745...
"The Emerging Science of Interacting Minds"
Read about why we think that this is an auspicious moment for interaction science!
Link: doi.org/10.1177/1745...
Reposted by Omar El Oakley
MSU-1 ROM hacks let you add CD quality audio to old SNES games. For @aftermath.site, I blogged about remasters, ROM hacking, how people relate to game music, and spoke to a few of the hackers from the Zeldix forums about the history of the project. aftermath.site/the-ultimate...
December 8, 2023 at 9:00 PM
MSU-1 ROM hacks let you add CD quality audio to old SNES games. For @aftermath.site, I blogged about remasters, ROM hacking, how people relate to game music, and spoke to a few of the hackers from the Zeldix forums about the history of the project. aftermath.site/the-ultimate...
Reposted by Omar El Oakley
Unsure how to do threads here yet but here's our latest preprint from GS Tyler Hill 🎉. He describes multiple feedforward and feedback mechanisms involving cGMP and Ca2+ that drive response adaptation on a timescale of mins in a single thermosensory neuron pair.
🧠🟦 🧪
www.biorxiv.org/content/10.1...
🧠🟦 🧪
www.biorxiv.org/content/10.1...
Feedforward and feedback mechanisms cooperatively regulate rapid experience-dependent response adapt...
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
December 6, 2023 at 11:35 PM
Unsure how to do threads here yet but here's our latest preprint from GS Tyler Hill 🎉. He describes multiple feedforward and feedback mechanisms involving cGMP and Ca2+ that drive response adaptation on a timescale of mins in a single thermosensory neuron pair.
🧠🟦 🧪
www.biorxiv.org/content/10.1...
🧠🟦 🧪
www.biorxiv.org/content/10.1...
Reposted by Omar El Oakley
to not leave this on 𝕏 only:
@ASMicrobiology
Dr. Esther Lederberg discovered lambda phage—the first known virus with a lytic-lysogenic life cycle. She reported on the findings in a 1953 paper, available at the Center for the History of Microbiology/ASM Archives: asm.social/1AV
#phagesky #MicroSky
@ASMicrobiology
Dr. Esther Lederberg discovered lambda phage—the first known virus with a lytic-lysogenic life cycle. She reported on the findings in a 1953 paper, available at the Center for the History of Microbiology/ASM Archives: asm.social/1AV
#phagesky #MicroSky
December 7, 2023 at 5:01 PM
to not leave this on 𝕏 only:
@ASMicrobiology
Dr. Esther Lederberg discovered lambda phage—the first known virus with a lytic-lysogenic life cycle. She reported on the findings in a 1953 paper, available at the Center for the History of Microbiology/ASM Archives: asm.social/1AV
#phagesky #MicroSky
@ASMicrobiology
Dr. Esther Lederberg discovered lambda phage—the first known virus with a lytic-lysogenic life cycle. She reported on the findings in a 1953 paper, available at the Center for the History of Microbiology/ASM Archives: asm.social/1AV
#phagesky #MicroSky