Micha Sam Brickman Raredon
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msbr89.bsky.social
Micha Sam Brickman Raredon
@msbr89.bsky.social
1.1K followers 1.6K following 170 posts
Scientist/Engineer. Assistant Professor of Anesthesiology @ Yale. Tissue Biology, Lung Regeneration, Data Visualization. Here to learn. https://RaredonLab.com
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msbr89.bsky.social
Micha Sam Brickman Raredon @msbr89.bsky.social · Oct 1
United States Disappeared Tracker

public.tableau.com/views/United...
Reposted by Micha Sam Brickman Raredon
biorxiv-devbio.bsky.social
Mapping embryonic mouse lung development using enhanced spatial transcriptomics https://www.biorxiv.org/content/10.1101/2025.11.22.688293v1
November 25, 2025 at 6:31 PM
Reposted by Micha Sam Brickman Raredon
hormiga.bsky.social
You know those labs that keep harming students, again and again? Some reflections on why it's so hard to stop this from happening and where our responsibilities lie.

scienceforeveryone.science/bad-mentors-... 🧪
Bad mentors hurt people
What to do about bad mentors?
scienceforeveryone.science
November 25, 2025 at 6:38 PM
Reposted by Micha Sam Brickman Raredon
haoyin.bsky.social
Lab-in-the-loop therapeutic antibody design with deep learning

Targets
EGFR
IL6
HER2
OSM

11 lead Ab➡️ 4 rounds with > 3X ⏫binding affinity➡️ > 1800 Ab designs

Hope this system can yield antibodies with better immunohistochemical performance as well

bioRxiv 2025
www.biorxiv.org/content/10.1...
November 18, 2025 at 12:26 PM
Reposted by Micha Sam Brickman Raredon
arula-ratnakar.bsky.social
These people are detrimental to science. Imagine how much more we would have figured out about the universe if young women people like Summers and David Sabatini targeted were left to focus on their research in peace instead of having to fend off old creepy men in positions of power.
November 16, 2025 at 5:41 PM
Reposted by Micha Sam Brickman Raredon
tommytang.bsky.social
Making a heatmap is an essential skill for a bioinformatician. But you probably do not understand heatmap. 7 reading resources to understand heatmap! 🧵
November 16, 2025 at 2:45 PM
Reposted by Micha Sam Brickman Raredon
melina-iras07572.bsky.social
#Galaxy cluster Abell 2813 with #JWST NIRCam (filters: F277W, F356W, F444W) with lots of bright gravitational lenses. 🔭

program: VENUS www.stsci.edu/jwst-program...
Bright large white galaxies. More distant greenish and orange galaxies, sometimes with strong gravitational lenses.
November 15, 2025 at 6:31 AM
Reposted by Micha Sam Brickman Raredon
natcellbio.nature.com
☕The authors identify a chemical cocktail to generate #totipotent - like cells, which they then use to build an #embryo model. This model captures a developmental spectrum from early #embryogenesis to post-implantation events.
bit.ly/4oHxUZp
A continuous totipotent-like cell-based embryo model recapitulates mouse embryogenesis from zygotic genome activation to gastrulation - Nature Cell Biology
The authors identify a chemical cocktail to generate totipotent-like cells, which they then use to build an embryo model. This model captures a developmental spectrum from early embryogenesis to post-...
bit.ly
November 15, 2025 at 8:17 PM
Reposted by Micha Sam Brickman Raredon
howtoreadthisch.art
Part of this week’s newsletter was inspired by the post below. Was there a way to show the distance between normal Americans and the super wealthy?
1/8
www.howtoreadthisch.art/putting-the-...
November 15, 2025 at 4:55 PM
Reposted by Micha Sam Brickman Raredon
haoyin.bsky.social
My continued biomedical education

Shaping neutrophil morphology & function
The importance of a segmented nucleus

Polylobular nuclei likely help Neutrophil with
👉Motile flexibility
👉Differentiation
👉NETosis
👉Rapid switching b/w A/B compartments

#NatRevImmunol 2025
www.nature.com/articles/s41...
November 15, 2025 at 12:17 PM
Reposted by Micha Sam Brickman Raredon
jcellsci.bsky.social
Rudolfo Karl, Elvira Mass, Dagmar Wachten @wachtenlab.bsky.social and colleagues discover that renal tissue-resident macrophages promote cystogenesis in early polycystic kidney disease.
#JCSciliaSI
journals.biologists.com/jcs/article/...
Figure showing that tissue-resident macrophages promote cytogenesis in an in vitro 3D model system.
November 14, 2025 at 2:14 PM
Reposted by Micha Sam Brickman Raredon
mm-jj-nn.bsky.social
"Solving a Million-Step LLM Task with Zero Errors", from the inimitable Elliot Meyerson (et al.)
Solving a Million-Step LLM Task with Zero Errors
LLMs have achieved remarkable breakthroughs in reasoning, insights, and tool use, but chaining these abilities into extended processes at the scale of those routinely executed by humans, organizations...
arxiv.org
November 13, 2025 at 9:39 PM
Reposted by Micha Sam Brickman Raredon
nature.com
Nature research paper: iPEX enables micrometre-resolution deep spatial proteomics via tissue expansion

go.nature.com/4qRtP6F
iPEX enables micrometre-resolution deep spatial proteomics via tissue expansion - Nature
Isotropic tissue magnification is integrated with matrix-assisted laser desorption/ionization mass spectrometry imaging to enable untargeted spatial proteomics at micrometre resolution and with high protein identification rates in multiple tissue types.
go.nature.com
November 13, 2025 at 11:17 AM
msbr89.bsky.social
www.sciencedirect.com/science/arti...
Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions
Chromatin structure is a key determinant of gene expression in eukaryotes, but it has not been possible to define the structure of cis-regulatory elem…
www.sciencedirect.com
November 13, 2025 at 12:14 PM
Reposted by Micha Sam Brickman Raredon
medsci.ox.ac.uk
NEWS: Oxford scientists capture genome’s structure in unprecedented detail

@rdm.ox.ac.uk scientists have achieved the most detailed view yet of how DNA folds and functions inside living cells, using a new technique called MCC ultra .
Oxford scientists capture genome’s structure in unprecedented detail
Radcliff Department of Medicine scientists have achieved the most detailed view yet of how DNA folds and functions inside living cells, revealing the physical structures that control when and how genes are switched on.
www.medsci.ox.ac.uk
November 13, 2025 at 11:00 AM
Reposted by Micha Sam Brickman Raredon
danbrockington.bsky.social
Profits from scientific publishing are eye-watering, costing us billions. In ‘The Drain of Scientific Publishing’ (arxiv.org/abs/2511.04820), (building on ‘The Strain of Scientific Publishing’ doi.org/10.1162/qss_a_00327) we show how it is harmful – and unnecessary.
The Drain of Scientific Publishing
The domination of scientific publishing in the Global North by major commercial publishers is harmful to science. We need the most powerful members of the research community, funders, governments and ...
arxiv.org
November 12, 2025 at 11:41 AM
Reposted by Micha Sam Brickman Raredon
greenwell.bsky.social
What a thrill to be part of @talkingpointsmemo.com's series about the past 25 years of digital media! I wrote about why private equity goons destroyed Deadspin and why it matters.
There Are No Weird Blogs Anymore Cause It’s More Fruitful to Drive Them Out of Business
I learned many surprising lessons from my 20 months as editor-in-chief of...
talkingpointsmemo.com
November 11, 2025 at 3:24 PM
Reposted by Micha Sam Brickman Raredon
hansonmark.bsky.social
Back on track:

Funders hold all the cards. There's this flawed view that authors are consumers and journals are producers. Wrong.

Funders and institutes are consumers. They contract authors to produce research, and they pay for journals to QC the work.

Funders are the consumers.

8/n
November 11, 2025 at 11:52 AM
Reposted by Micha Sam Brickman Raredon
hansonmark.bsky.social
Fundamentally, what we need is leadership. But we break with the chorus of most #OpenScience initiatives here and emphasize very strongly that this leadership must come from funders and institutions.

We researchers can support the battle, but we cannot lead the charge. Funders hold the cards.

6/n
The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
November 11, 2025 at 11:52 AM
Reposted by Micha Sam Brickman Raredon
hansonmark.bsky.social
More fundamentally, every active scientist has been brought up in a system where The Drain was already normalized.

This system hasn't always existed. For-profit publishers are a recent invention. Their value proposition has always been awful, and now they are actively eroding trust in science.

5/n
2. Stopping the drain Back in the 1950s, when for-profit journal publishing was just getting going, British scientific leaders predicted that ‘the moment commercial gain began to dominate this field, the welfare of the scientific community would suffer’ (1). They were right – and it is past time that we acted. The first step we must take is to recognize the seriousness of the problems that scientific publishing’s engagement with for-profit publishing have become.
November 11, 2025 at 11:52 AM
Reposted by Micha Sam Brickman Raredon
hansonmark.bsky.social
For-profit journals are supposed to improve research quality, yet they're perversely incentivized to churn out whatever they can monetize. This was happening before AI (see Strain: bit.ly/43gJPUM), and AI will make it worse.

It's insane that we volunteer our time to help them do so.

4/n
November 11, 2025 at 11:52 AM
Reposted by Micha Sam Brickman Raredon
hansonmark.bsky.social
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision. A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
November 11, 2025 at 11:52 AM
Reposted by Micha Sam Brickman Raredon
slavov-n.bsky.social
The protein concentration in the cytoplasm is so high that the average protein has a water hydration shell with a thickness of only ≈ 10 water molecules separating it from the adjacent protein hydration shell.

1/2
November 10, 2025 at 12:57 PM
Reposted by Micha Sam Brickman Raredon
chrismurphyct.bsky.social
Bullies gain power when their misconduct succeeds in causing righteous people to yield in the face of wrongdoing. That’s why voting for Trump's continuing resolution - without any protection against his health care cuts or his growing illegality - is a mistake.

I voted NO.
November 10, 2025 at 2:19 AM
Reposted by Micha Sam Brickman Raredon
rbreich.bsky.social
Meanwhile, CEOs make 280 times the typical worker today.

The system is rigged.
November 8, 2025 at 8:30 PM
Reposted by Micha Sam Brickman Raredon
statsepi.bsky.social
The advances we've made in statistics, experimental study design, and causal inference over the past century are remarkably useful for understanding our world. But there is never been a push to make people use them like we are seeing with generative AI. Perhaps take a moment to consider why.
November 7, 2025 at 9:07 AM