David A. Markowitz

It's increasingly tempting to believe frontier models truly understand concepts and their relationships like humans do. Then I get a figure like this from today's leading model and the illusion is ruined. <sigh>

Very excited to dive into this paper

My children are descended from Holocaust survivors. 80 years later, they have always needed armed guards at their school and places of worship because antisemitic violence remains so common. I work in national security to make them safer. But hate takes generations to undo.

Connectomics is Method of the Year 2025!!
@natmethods.nature.com
just released the news nature.com/articles/s41... In my perspective piece, I afford some predictions into the future and compare how we are doing vs. genomics www.nature.com/articles/s41...

1 year later and wow, exciting to see big things in the works!!!

Our new paper showcasing molecular connectomics with pan-expansion microscopy is out in @natbiotech.nature.com! www.nature.com/articles/s41...
This wonderful collaboration with @bewersdorflab.bsky.social was led by Ons M'Saad (now founder/CEO of Panluminate) and @allisonphysics.bsky.social. (1/5)

We still need a massive improvement in compute efficiency of binder design tools to make this a financially compelling alternative to CROs for the average user.

Furthermore, the above cost of binder design in the cloud doesn't include the cost of experimental validation of your candidates, which would be needed to achieve the same results as a CRO. Might be another few K in labor and materials, plus time needed to make the thing.

Lots of excitement around open source computational binder design (BoltzGen FTW!), but as far as I can tell it's still ~2x more expensive per target than a traditional campaign with a CRO.

(60k runs/target) x (2 mins/run) x ($5/hr for an A100) = $10k/target

vs ~$5k with a CRO

Incorporating open connectomics data into teaching neuroscience Learn to analyze open neuroscience data and introduce dry lab modules into your existing classes at the Incorporating Open Connectomics data into...

I will be co-teaching a summer course at Allen Institute on connectomics education please apply. Travel support, new connectomics data sets and learning directly from the scientists who built these datasets. Details here: alleninstitute.org/events/incor...

Jaxley: differentiable simulation enables large-scale training of detailed biophysical models of neural dynamics - Nature Methods Jaxley is a versatile platform for biophysical modeling in neuroscience. It allows efficiently simulating large-scale biophysical models on CPUs, GPUs and TPUs. Model parameters can be optimized with ...

I am super happy to share that our project on training biophysical models with Jaxley is now published in Nature Methods: www.nature.com/articles/s41...

It's increasingly tempting to believe frontier models truly understand concepts and their relationships like humans do. Then I get a figure like this from today's leading model and the illusion is ruined. <sigh>

Maybe it's specific to AI tools? As a comp, this non-AI announcement + blog post from last year did much larger numbers on Bluesky, well before the paper was released. People were happy to like and share: bsky.app/profile/andr...

Is there an academic/industry divide in attitudes about using AI to support discovery? I noticed this post has 3.6k likes on X but only 6 likes on Bluesky. It deserves more attention here!

For a decade, my white whale as a neuroscientist has been working to convince public+private funders to "go big" on post-mortem human tissue analysis, so we can define circuit disruptions in disease and just maybe link them with molecular drivers. This remains as tough a sell today as 10 years ago.

Haven't seen Carlos in forever, but reading this gleeful post in his voice made my morning. Super cool work

Today, we're announcing Kosmos, our newest AI Scientist, available today. Kosmos makes fully autonomous scientific discoveries at scale by analyzing datasets and literature, and is the most powerful agent for science so far. Beta users estimate that Kosmos does 6 months of work in a single day.

‘A true genocide’: RSF kills ‘at least 1,500 people’ in Sudan’s el-Fasher Saudi Arabia, Egypt, Turkiye, Jordan and Qatar express alarm as more evidence emerges of mass killings by paramilitary forces in Sudan&#039;s in el-Fasher.

As this widely reported genocide plays out in real time and Arab nations express growing horror, it's sad to see the continued apathy toward it in the West. Silence on both left and right wing social media. No demonstrations, no boycotts... www.aljazeera.com/news/2025/10...

YouTube video by Science A global mission to restore vision | PRIMA by Science

Very excited that the clinical trial results for our PRIMA retinal prosthesis are published today in the New England Journal of Medicine! This is the first time that patients who are blind due to photoreceptor loss have been able to intuitively see again.

www.youtube.com/watch?v=J_qT...

Whole-brain, bottom-up neuroscience: The time for it is now Applying new tools to entire brains, starting with C. elegans, offers the opportunity to uncover how molecules work together to generate neural physiology and how neurons work together to generate…

Applying new tools to entire brains, starting with C. elegans, offers the opportunity to uncover how molecules work together to generate neural physiology, and how neurons generate behavior, write @kordinglab.bsky.social and @eboyden3.bsky.social.

#neuroskyence

bit.ly/48EzEO8

Combinatorial protein barcodes enable self-correcting neuron tracing with nanoscale molecular context https://www.biorxiv.org/content/10.1101/2025.09.26.678648v1

bsky.app/profile/nyti...

‘We watch the graveyards from space’: satellites track Sudanese city under siege Paramilitary forces have cut off El Fasher, the military government’s final stronghold in the western Darfur region

Update From Doctors Without Borders: "This is one of the worst situations I have seen” ... "It really is quite unique in terms of the volume of affected people, the level of suffering and also the underfunding of the international response” www.ft.com/content/d331...

Wow, VERY interested to see this paper!

Settle a debate for me: If you could hook up a fruit fly brain to a completely new set of end effectors, could it learn to use them for goal-directed behavior? To what extent is an insect brain evolutionarily specialized for controlling its body? #FlyBCI

Mapping the Brain for Alignment | IFP How to map the mammalian brain’s connectome to solve fundamental problems in neuroscience, psychology, and AI robustness

How to make frontier AI models safer and accelerate drug discovery with the connectome. We are featured in this
@ifp.bsky.social article by @adammarblestone.bsky.social & @andrewcpayne.bsky.social

ifp.org/mapping-the-...

Starvation spreading in Sudan as aid convoys blocked by siege, UN says Situation is worsening in El Fasher, which is enduring a daily bombardment of artillery shelling and drone attacks by RSF fighters

The latest on this humanitarian catastrophe, one of several happening in the world right now, yet strangely neglected in the public discourse: www.theglobeandmail.com/world/articl...

There is a famine currently affecting 640k children in Sudan, driven by military action funded by a key US ally in the Middle East. It's been widely reported in the media since 2023. Yet no condemnation by public figures, no demonstrations in the US. Why does no one care?