Lukáš Pekárek
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pekarekl.bsky.social
Lukáš Pekárek
@pekarekl.bsky.social
540 followers 1.2K following 37 posts
Harnessing physics to understand life.
Pulling one RNA molecule at a time.
RNA, Biophysics, and Proteins sometimes.
Lame puns intended.
Currently sciencing at @tudresden.bsky.social
Posts Replies Media Videos
pekarekl.bsky.social
So happy and proud that my great supervisor and mentor Marcus Jahnel is one of those 13 scientists! Congratulations! 🥳
tudresden.bsky.social TU Dresden @tudresden.bsky.social · 13h
Starkes Zeichen für die Qualität der Spitzenforschung: 13 TUD-Mitglieder sind unter den weltweit meistzitierten Forschenden. 🧑‍🔬 Damit zählt die #TUDresden erneut zu den am stärksten vertretenen Einrichtungen in 🇩🇪 bei den #HighlyCited2025 von @clarivateag.bsky.social.
ℹ️ tu-dresden.de/tu-dresden/n...
Foto von den Großbuchstaben "TUD" auf der Wiese hinter dem Hörsaalzentrum der TU Dresden im Herbst.
November 12, 2025 at 7:57 PM
Reposted by Lukáš Pekárek
venpopov.bsky.social
The academic publishing system is so rotten, it must be completely dismantled. Not partially, and not improved. Dismantled and rebuilt from the ground up.

When I tell non-academic friends how it all works they stare at me in disbelief. Not only that it exists, but that we still allow it to.
hansonmark.bsky.social Mark A. Hanson @hansonmark.bsky.social · 1d
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 12, 2025 at 9:24 AM
Reposted by Lukáš Pekárek
gabrielaughey.bsky.social
Always shocking to see these kinds of data collected together. "[publishers made]US$12 billion in profits between 2019 and 2024" - That's $12 billion diverted away from actual research or materially supporting the community - these are disgusting numbers.
hansonmark.bsky.social Mark A. Hanson @hansonmark.bsky.social · 1d
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 1:20 PM
Reposted by Lukáš Pekárek
disabilitystor1.bsky.social
Call me controversial, but technology that leads vulnerable people into crisis and even holds their hand as they die by suicide should not be endorsed by schools and universities, we should not be giving discounted subscriptions to this monstrous tech to young people AT ALL
fionakatauskas.bsky.social Fiona Katauskas @fionakatauskas.bsky.social · 5d
The boyfriend of a friend of my son's has spent several weeks in a psych ward due to Chat GPT induced psychosis. He isn't suicidal but AI encouraged him down a toxic and paranoid wormhole until he became completely delusional. Evil stuff.
disabilitystor1.bsky.social Aparna Nair @disabilitystor1.bsky.social · 5d
1.This is not the only known example we know of ChatGPT cheering on a vulnerable young person to die by suicide, this time it is a recent Texas A&M grad
2. Every single university that has invited OpenAI into our midst should be asked to account for their choices.
www.cnn.com/2025/11/06/u...
November 7, 2025 at 12:51 PM
Reposted by Lukáš Pekárek
olivierduss.bsky.social
Excited to share my first PhD student’s @biorxivpreprint.bsky.social!

Tracking 5 dyes simultaneously Kavan Gor @embl.org tracks nascent #RNA folding during #ribosome assembly to correlate structural with functional information on single RNA molecules!

Check it out!

www.biorxiv.org/content/10.1...
November 1, 2025 at 5:56 AM
Reposted by Lukáš Pekárek
vanessaloi.bsky.social
I´m hiring!
Please share 🪴 🧪 🌈
I´m hiring a lab technician! | Vanessa Loiacono
I´m hiring a lab technician! The position is at the beginning (from September 1) part-time but with possibility of full-time with negotiating salary as it can be additionally funded by a 12 mil CZK PR...
www.linkedin.com
July 18, 2025 at 12:28 PM
Reposted by Lukáš Pekárek
zachhensel.bsky.social
🧵Remember the preprint claiming SARS-CoV-2 has a "synthetic fingerprint"?

It said a restriction map was "extremely unlikely to have arisen by random evolution.”

I took its claims seriously.

The "synthetic fingerprint" hypothesis collapses. My new preprint explains why.

arxiv.org/abs/2510.23833
22-Oct 2022 headline from The Economist A new paper claims SARS-CoV-2 bears signs of genetic engineering But it has yet to be peer reviewed. And others strongly disagree
October 29, 2025 at 7:32 AM
Reposted by Lukáš Pekárek
astrokatie.com
Chatbots — LLMs — do not know facts and are not designed to be able to accurately answer factual questions. They are designed to find and mimic patterns of words, probabilistically. When they’re “right” it’s because correct things are often written down, so those patterns are frequent. That’s all.
June 19, 2025 at 11:21 AM
Reposted by Lukáš Pekárek
redpenblackpen.bsky.social
What's in yer basement?
October 15, 2025 at 7:21 PM
Reposted by Lukáš Pekárek
schlierflab.bsky.social
3 more days to apply for a PhD position within our training program on biomolecular condensates 👇👇. 12 positions within our a focus from physics and theory to experimental biophysics to biology and medicine/disease.
schlierflab.bsky.social Michael @schlierflab.bsky.social · Oct 7
Are you interested in Biomolecular Condensates and looking for a PhD training? Check out the 12 (!) open PhD positions (also 1 on smFRET & condensates 🙃) in Dresden @rtg3120.bsky.social @tudresden.bsky.social starting April 2026. Apply latest by 24 Oct 2025 here: dresdencondensates.org/join-us/
Join Us – RTG 3120 Biomolecular Condensates
dresdencondensates.org
October 21, 2025 at 10:20 AM
Reposted by Lukáš Pekárek
kristalerista.bsky.social
Dear funding agencies,

I know we all want to discover the wonder drug that will cure the horrible diseases, but to do that, we need to invest in basic, unsexy, foundational research on how the systems work. Funding can’t all be drug development.

Sincerely,
Looking for basic research grants.
October 14, 2025 at 7:24 PM
Reposted by Lukáš Pekárek
richardsever.bsky.social
AI in biology: "I read about some new computational method...get excited because it’s exactly what I need...I try the method...Most of the time things don’t work...I have seen this play out so many times my default assumption is nothing is going to work" blog.genesmindsmachines.com/p/we-still-c...
We still can’t predict much of anything in biology
Biology is hard. Yes, even for AI.
blog.genesmindsmachines.com
October 9, 2025 at 6:13 PM
Reposted by Lukáš Pekárek
alexis-verger.cpesr.fr
AI-generated papers
AI-generated peer-review reports
AI-generated images
AI-grant writing
Algorithms to spot promising science

I'm very worried, we should all be very worried
October 3, 2025 at 12:46 PM
Reposted by Lukáš Pekárek
mehr.nz
here are some helpful steps for academics who are considering creating genAI images to use for lab branding:

1. don't
September 29, 2025 at 12:07 AM
Reposted by Lukáš Pekárek
vaclav-veverka.bsky.social
How do flexible regions of histone chaperones team up to handle histones? Together with Fred Winston’s lab
@harvardmed.bsky.social, we reveal new insights in our study just out in Mol Cell. Hats off to James Warner and Vanda Lux @iocbprague.bsky.social for their key contributions! dlvr.it/TNB145
September 21, 2025 at 7:31 PM
Reposted by Lukáš Pekárek
matthewkraushar.bsky.social
Rainer and I did our last experiment together in the Kraushar Lab @molgen.mpg.de on Sunday - like many such days since our postdocs. Rainer will soon lead a team in the Emmanuelle Charpentier Dept @MPUSP - stay tuned for more!
September 19, 2025 at 8:05 AM
Reposted by Lukáš Pekárek
larshubatsch.bsky.social
Amazing!!! 🧪 The 2025 Ig Nobel prize goes to scientists from the @mpipks.bsky.social for discovering a bullet proof version to make the classic pasta alla cacio e pepe! Including a deep understanding of the pasta sauce in terms of phase separation physics 😃
Congrats @gbart.bsky.social et al!
Links👇
September 19, 2025 at 5:52 AM
Reposted by Lukáš Pekárek
juliusbrennecke.bsky.social
Love RNA biology?

Join us to explore the piRNA pathway with structural and genetic approaches (see 👇👇).

PhD student/postdoc position co-supervised by Clemens Plaschka & myself.

DM or email us if you’d like to know more!

@vbcscitraining.bsky.social @imbavienna.bsky.social @impvienna.bsky.social
juliusbrennecke.bsky.social Julius Brennecke @juliusbrennecke.bsky.social · Sep 17
PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity.

But how does piRNA-guided target interaction translate into silencing?

PhD student Júlia Portell Montserrat has an intriguing answer

www.cell.com/molecular-ce...
September 18, 2025 at 2:34 PM
Reposted by Lukáš Pekárek
jesseveenvliet.bsky.social
This is indeed a unique opportunity for @ec.europa.eu. But to ensure that „excellence thrives where it is enabled, protected & shared“ the % of funded proposals needs to stay the same (or actually increase). Otherwise it’s just a waste of talent.
ec.europa.eu European Commission @ec.europa.eu · Sep 11
The 2025 call for #MSCA Postdoctoral Fellowships drew 17,058 applications worldwide.

A 64.6% increase from 2024, it's the most popular call in over four decades.

Excellence thrives where it is enabled, protected and shared — and Europe provides that environment.

→ europa.eu/!jcnGgP

#ChooseEurope
A scientist in a lab coat looks through a microscope in a laboratory, with other researchers blurred in the background. Overlaid text reads: “Record Applications – Choose Europe: EU research fellowships attract record 17,058 applications.” The European Commission logo appears in the bottom right corner.
September 14, 2025 at 3:16 PM
Reposted by Lukáš Pekárek
markrubin.bsky.social
"Hostility, exclusion and academic bullying should be formally recognised as research integrity issues because they directly impact who gets to succeed and whose voices are silenced."

By @maddipow.bsky.social
Research integrity needs a kindness agenda or we will lose ECRs
Responding to early-career researchers’ honest questions with accusations of misconduct is a travesty of open science, says Madeleine Pownall
www.timeshighereducation.com
September 9, 2025 at 6:28 AM
Reposted by Lukáš Pekárek
boghuma.bsky.social
Health misinformation and disinformation are the biggest and most under prioritized threats to public health in the 21st century. They are eroding decades of progress in the control and spread of diseases in real time. If we do not address this like the existential threat it is, we risk everything!
August 26, 2025 at 1:11 PM
Reposted by Lukáš Pekárek
jukebarosh.bsky.social
My Friday night hot take is that replication studies are largely a waste of time & $

If a result is worth following up on, it's better to address from a different angle & see if it holds water. Strong ideas withstand this

Conversely, there R infinite ways a replication can fail that teach you zip
August 16, 2025 at 1:47 AM
Reposted by Lukáš Pekárek
elisecutts.bsky.social
"...if we deploy LLM assistants in decision-making roles... they will implicitly favor LLM-based AI agents and LLM-assisted humans over ordinary humans"

Translation: Use the product, or the product will discriminate against you.

Great
AI–AI bias: Large language models favor communications generated by large language models | PNAS
Are large language models (LLMs) biased in favor of communications produced by LLMs, leading to possible antihuman discrimination? Using a classica...
www.pnas.org
August 13, 2025 at 8:26 PM
Reposted by Lukáš Pekárek
illdottore.bsky.social
You hear stories about what an academic household does to children but today at bedtime my precocious rising kindergartner said “father will you read me a story about university leaders who believe LLM-based chatbots have made language teaching irrelevant?” and fortunately I had just the thing
I *really* like slop! By Mo Willems
August 14, 2025 at 12:34 AM
Reposted by Lukáš Pekárek
tanentzapflab.bsky.social
The goal of a PhD is not to learn some facts or read a few papers or learn a bunch of techniques. The goal of a PhD is to learn independence, problem solving, how to finish things you start, resilience, & gain the ability to adapt & think creatively. Learning these things is hard.
August 13, 2025 at 5:28 PM