Erik Poppleton

New to RNA design? Please try pyFuRNAce! Looking forward to your feedback 🧬

Tenure Track Professorship (W1 with Tenure Track to W3) in “Molecular Biology" (f/m/d) - Heidelberg job with Universität Heidelberg | 12850668 The Center for Molecular Biology of Heidelberg University (ZMBH) and the Faculty of Biosciences invite applications for a   Tenure Track Professors...

We are recruiting a tenure track professor in the broader area of molecular biology @zmbh.uni-heidelberg.de at Heidelberg University! www.nature.com/naturecareer... Please share and apply!

Will you incorporate LLMs and AI prompting into the course in the future? No. Why won’t you incorporate LLMs and AI prompting into the course? These tools are useful for coding (see this for my personal take on this). However, they’re only useful if you know what you’re doing first. If you skip the learning-the-process-of-writing-code step and just copy/paste output from ChatGPT, you will not learn. You cannot learn. You cannot improve. You will not understand the code.

In that post, it warns that you cannot use it as a beginner: …to use Databot effectively and safely, you still need the skills of a data scientist: background and domain knowledge, data analysis expertise, and coding ability. There is no LLM-based shortcut to those skills. You cannot LLM your way into domain knowledge, data analysis expertise, or coding ability. The only way to gain domain knowledge, data analysis expertise, and coding ability is to struggle. To get errors. To google those errors. To look over the documentation. To copy/paste your own code and adapt it for different purposes. To explore messy datasets. To struggle to clean those datasets. To spend an hour looking for a missing comma. This isn’t a form of programming hazing, like “I had to walk to school uphill both ways in the snow and now you must too.” It’s the actual process of learning and growing and developing and improving. You’ve gotta struggle.

This Tumblr post puts it well (it’s about art specifically, but it applies to coding and data analysis too): Contrary to popular belief the biggest beginner’s roadblock to art isn’t even technical skill it’s frustration tolerance, especially in the age of social media. It hurts and the frustration is endless but you must build the frustration tolerance equivalent to a roach’s capacity to survive a nuclear explosion. That’s how you build on the technical skill. Throw that “won’t even start because I’m afraid it won’t be perfect” shit out the window. Just do it. Just start. Good luck. (The original post has disappeared, but here’s a reblog.) It’s hard, but struggling is the only way to learn anything.

You might not enjoy code as much as Williams does (or I do), but there’s still value in maintaining codings skills as you improve and learn more. You don’t want your skills to atrophy. As I discuss here, when I do use LLMs for coding-related tasks, I purposely throw as much friction into the process as possible: To avoid falling into over-reliance on LLM-assisted code help, I add as much friction into my workflow as possible. I only use GitHub Copilot and Claude in the browser, not through the chat sidebar in Positron or Visual Studio Code. I treat the code it generates like random answers from StackOverflow or blog posts and generally rewrite it completely. I disable the inline LLM-based auto complete in text editors. For routine tasks like generating {roxygen2} documentation scaffolding for functions, I use the {chores} package, which requires a bunch of pointing and clicking to use. Even though I use Positron, I purposely do not use either Positron Assistant or Databot. I have them disabled. So in the end, for pedagogical reasons, I don’t foresee me incorporating LLMs into this class. I’m pedagogically opposed to it. I’m facing all sorts of external pressure to do it, but I’m resisting. You’ve got to learn first.

Some closing thoughts for my students this semester on LLMs and learning #rstats datavizf25.classes.andrewheiss.com/news/2025-12...

PyFuRNAce: an integrated design engine for RNA origami - Nature Communications RNA nanotechnology creates structural and functional RNA architectures for biomedicine, synthetic biology and beyond. Here, the authors introduce pyFuRNAce, an intuitive browser-based RNA design tool....

PyFuRNAce is an intuitive browser-based RNA design tool. 
@monari-luca.bsky.social @kgoepfrich.bsky.social @uniheidelberg.bsky.social realized the largest cotranscriptionally folded RNA nanostructures to date. #BiotechNatureComms

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

"are you enjoying duo mobile" does a hamburger enjoy being made of quarks. does a fish enjoy linear time. does the mountain enjoy the first taste of a cup of hot chocolate when you get back to the ski lodge. your question means nothing to me. i couldn't enjoy duo mobile even if i tried

Nobody tell them about melodeath 🤫🤫🤫

Enumerating possible pseudoknots that a sequence can form with nearest-neighbor models is an NP-hard problem. Even evaluating these structures is challenging, let alone designing them. So it’s great to see data-based models starting to crack the RNA structural design problem! 🧬🧪

Mors Principum Est is a group I’ve loved for a long time, and somebody recommended Der Weg winner Freiheit to me yesterday!

How do you make your graphic? Is there a template you use, or is it manual?

An early and authoritative drop on the AOTY lists! I’ve only listened to two of these, so time to see if they have rude words for my tentative list.

Duolingo year in review showing 36537 XP is also 98%

98% is apparently a very wide percentile in the distribution…

PyFuRNAce: an integrated design engine for RNA origami - Nature Communications RNA nanotechnology creates structural and functional RNA architectures for biomedicine, synthetic biology and beyond. Here, the authors introduce pyFuRNAce, an intuitive browser-based RNA design tool....

The latest from RNA-designer extraordinaire
@monari-luca.bsky.social is out in @natcomms.nature.com. We introduce PyFuRNAce.de, a design tool for RNA origami. It simplifies design with a rich motif library and automatic 2d/3d modeling and routing optimization 🧬

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

Huh! So he is! He’s not in chapters 4 or 6, but there’s a lot I haven’t read yet.

Wait, what?? Did he do art for it, or did he write a section? 🧬

$2.37?

An obviously AI-generated figure with AI slop and fake text all over it, recently published in Scientific Reports.

Since AI slop is again all over Scientific Reports, a thread on the economics of grey-zone publishing.

Why does slop keep getting published? What does it mean for science? How can we stop this?

Background readings:
Understand the strain: tinyurl.com/2b6wxx5r
Stop the drain: tinyurl.com/3jfscscy

And then you sink into the drifts and find yourself listening to Hex, or Printing in the Infernal Method from Earth…

Owwwwww

Self-assembled cell-scale containers made from DNA origami membranes - Nature Materials Through the programmable self-assembly of lipid-inspired radially symmetric DNA, porous molecular membranes and cell-sized compartments are formed with applications in bottom-up biology and soft robot...

The long-awaited Dipids paper is finally out www.nature.com/articles/s41...! Check out the largest containers ever self-assembled from DNA origami🧬, and the amazing person and story behind it www.linkedin.com/feed/update/... Congrats to Christoph🎉 and thanks for letting me be part of this journey🥹!

Ahhh, I love the smell of academic fraud in the morning.

No nonononononono! If you reach g you’ve probably made a terrible mistake imho

The Salt Lake Tribune will drop its paywall next year, CEO tells donors at NewsMakers gala After years of requiring people to pay for online news content, The Tribune announced an upcoming change during its 2025 annual NewsMakers Gala.

Remember last year when we said we would drop The Tribune's paywall if we raised enough money to support the transition to free? About that… 😁

I think I’m gonna have to retract this meme I made… 🧬

Hmmm thanks! This makes things not look so bad for robotaxis, if they’re at 44% with a smaller fleet than ridehail (as the original article points out, a small fleet can lead to increased pickup distances). But they’re not showing that they can be significantly better, at the moment.

How does that compare to the deadheading rates for Uber/Lyft/traditional taxis?

For the first time in the history of the universe, it wasn’t, in fact, DNS.

I really wish there was some sort of easy, (probably paid) way to host your own feed within Bluesky. As far as I can tell, setting up your own firehose consumer and feed builder is minimum $20/month, but for that much you can make 1 feed or 5, so there’s an economy of scale to be had.

I gotta say, you have three genres of posts, all of them are aspirational.

Pretty sure this would ban every lab I’ve ever been a part of from getting any US government funding…

Basic light pollution diagram showing four different streetlight set ups ranging from more light pollution on the left to less light pollution on the right. The most pollution option, labelled "very bad" is a street lamp with a round uncovered bulb on top, making a sphere of light in the air. The next option, labelled "bad" has a tiny cap on top, that limits the upward pollution a bit. The "better" option is mostly uncovered on top, limiting pollution above the streetlight. The final option, labelled "best" has a full shroud overtop, limiting the light to only below the streetlight, where it is needed for pedestrians and vehicles.

Lots of folks captioning aurora photos like "for a few minutes we didn't think about politics"

guess I'm built different, every time I'm out trying to see night sky stuff I frequently think about how much light pollution is entirely preventable with just a tiny bit of regulation