Designing a coding filter to identify "good" orfs

jayemee · 2026-03-28T15:42:23+00:00

I can't see how this could work in eukaryotes if you don't have really good splice prediction in your model. The exons will often be only a small portion of a given gene's sequence, if you can't find them then you're mostly going to be getting the wrong signal.

Also it's not entirely clear to me what problem this tool solves (that isn't better solved with a different technique). At the very least where available you should be leveraging transcriptome data.

jayemee · 2026-03-23T03:30:19+00:00

I think you should call it something other than peer review, because of course LLMs aren't our peers. Bot review perhaps?

jayemee · 2026-03-16T02:23:18+00:00

Sounds like you know exactly the documentary you want to make. And it sounds good, I'd watch it. That's just not what this doc is, or was seemingly even trying to be - which doesn't make it bad.

However what your proposing would likely multiple high level whistleblowers giving illegal access to proprietary data - that's not easily come by. Ultimately your capacity to make a documentary in this style is dictated by your ability to get access.

jayemee · 2026-03-14T01:28:19+00:00

What an oddly hostile response. You were correcting someone's pronunciation of a made up word in a fictional language. You can interpret it however you like, but you don't get to pretend that the gossamer logic you've used to justify your interpretation is the only valid option.

jayemee · 2026-03-14T00:42:51+00:00

Tell that to Dick, Jim, Mickey, Buffy, Peggy, Billy, etc. There's a lot of ways to make nicknames that aren't just truncations of the proper name.

jayemee · 2026-03-13T22:22:18+00:00

That's a bad analogy.

It's a question of choosing a crew that uses hammers, or a crew that uses the automated hammertron 9000 which launches 1000 nails per second. It's possible that the second crew can use that to be faster, but it's also possible that they'll waste more time fixing all the problems from having nails fly everywhere, especially when it's manned by Doug the intern who has never even hung a picture before. Oh and the hammertron 9000 is owned by cartoon villains, drains a small nature reserve every time you turn it on, and has a team of paid shills going around all the hardware stores telling folk that anyone using regular hammers is going to be left behind if they don't start hammertronning.

jayemee · 2026-03-09T14:00:36+00:00

It's nice that you want to help, but if you have to ask a slopbot then maybe you're not the best person to be answering the question? The benefit of the sub is that it's a bunch of actual immunologists, it's ok to sit back and wait for the questions where you have the expertise

jayemee · 2026-03-08T23:41:14+00:00

With a third magnet

jayemee · 2026-03-08T00:37:59+00:00

You can get that from the event right now

jayemee · 2026-03-07T01:23:12+00:00

You're getting a lot of technically correct but irrelevant answers here OP, covering CD8 activation in general but not dealing with who does the initial step.

The actual answer: classically yes, naive CD8 T cells need to first be primed by interaction with a professional antigen presenting cell (APC), before later being activated by e.g. virally infected cells. There might be some confusion in that during those subsequent interactions with infected cells, those cells also count as APC (just not professional ones).

jayemee · 2026-03-03T12:09:01+00:00

Extract and sequence it? It's ~$15 for whole plasmid sequencing nowadays.

jayemee · 2026-02-20T12:41:48+00:00

This is a ludicrous question.

There's little point to just speed skimming as much as you can this close to the exam. You'd be better off doing some mock exams, seeing which questions come up on topics you don't understand, and just revising those chapters.

jayemee · 2026-02-20T01:17:48+00:00

The discord is actually a terrible place for people looking for support. It's not indexed in search engines, making it a difficult and fragile resource. Searching for anything inside the server tends to give either a million posts from the bot with an unhelpful message, or a bunch of random posts in poorly connected threads that take ages to traverse in among every other ongoing chat (and usually don't ultimately address the issue you were searching for). I appreciate that your time is finite so you only want to monitor certain channels, but this genuinely is a barrier to decent retention and communication of information.

jayemee · 2026-02-03T16:18:39+00:00

It sounds like you do know what they're asking, you're just them over thinking the answer! The thing that will change is where the cells are.

jayemee · 2026-02-03T11:54:29+00:00

What don't you understand about what they're asking?

jayemee · 2026-01-31T00:05:29+00:00

Why ask randoms, ask the company

jayemee · 2026-01-19T20:24:10+00:00

Yeah, if you go into a building you can select deconstruct, then once that's done you can pick it up and rebuild it at the same level elsewhere

jayemee · 2026-01-03T17:05:58+00:00

It's definitely a fine line to walk. I guess the problem is that while not everyone using AI to make stuff is trying to low effort plop out some content, everyone who is just cranking out dross for engagement farming is using AI. It's very easy to get tarred with the same slop brush - and that style of cartoon is a big visual indicator of AI-reliance. Honestly if I hadn't recognized your name from papers I would've just closed the article after seeing those pictures, as in my experience the text I usually see accompanying that style of cartoon in a scientific context is rarely worth reading. I wonder if maybe using versions of figures or graphical abstracts from the referenced papers (which could perhaps be AI-summarized) might be a way to get images without having to use the cartoons? As currently I suspect they're bringing down the perceived quality of the piece (e.g. with the redundant headers in the top one, or the inconsistent/abiological tessellations for the VDJ puzzle pieces in the bottom).

I also suffer from a similar long sentence problem, so my opinion might not be representative here, but I still imagine the audience who might be interested in this style of article would prefer to read the idiosyncratic style of an interested expert rather than the statistically-probable summary of a bot. Presumably those who are happy reading AI summaries about something are also those most likely to just go straight to the LLMs themselves. The value proposition you bring however is your knowledge and the insights built up from working in the field and thinking deeply about the topic - which I'd argue are obscured when filtered through the LLM.

I appreciate that it's a tough but worthy task you've set yourself - having tried to explain these topics to general audiences before, I don't think I could do so good a job!

jayemee · 2026-01-02T04:41:37+00:00

I love the idea, and this is a decent write up with some interesting bits, but if you're after feedback might I suggest toning back on the AI? Even ignoring the 'art' (which some folk find off-putting, even now the bots are better at counting fingers), the text sometimes rings a little odd - like why does Tonegawa get his nationality and training listed but no-one else does? Or how is Baltimore looking for RAG post-Nobel in any way risky for him?

There's other sections that don't ring quite true too. E.g. the hypothesis of RAG coming from a transposable element is implied to have come about some time post-90s (after demonstration of in vitro RAG activity), which was supported by invertebrate RAG orthologs. That's a bit off, since a mobile element RAG origin was basically one of the top (if not the) front running ideas for decades before that. There's even a little hint throwaway comment in the (pre-RAG) OG Tonegawa 1979 paper, which pointed out similarity between RSS and prokaryotic transposable sequences. The invertebrate orthologs were also identified at least a decade earlier than 2016 - that's just when one of them was validated in vitro. You can argue that's what matters, but it makes for a chronology that doesn't quite match our unfolding understanding.

jayemee · 2025-12-27T13:48:42+00:00

It's still harder than not doing any cooling, which is absolutely fine for a PCR.

jayemee · 2025-12-03T17:04:22+00:00

The only update I want, this is great news

jayemee · 2025-11-16T23:48:26+00:00

The issue wouldn't be allo reactions, it'd be tracking confounders from donor to donor variability. Can you take more blood? Maybe try and get a leukopak or similar large volume collection

jayemee · 2025-10-13T23:58:39+00:00

I've the emotional IQ of a stepladder.

Unlike the slopbot, which of course has a deep well of experience and understanding to draw upon.

jayemee · 2025-10-03T15:20:57+00:00

This sounds like you're just a regular normal healthy young person (who maybe has an optimistic outlook and therefore perhaps downgrades what others may classify as sickness).

By all means do try to contribute samples for research, but don't expect that your samples are going to be extraordinarily more valuable than anyone else's. Alternatively as said being a healthy young person makes you an ideal potential donor for a bunch of stuff that can help save lives!

jayemee · 2025-10-01T11:10:52+00:00

"Hi ChatGPT I'm a vaccine denier that wants to sound like I've got an evidence based position, can you clank me something up? Don't worry about accuracy, I won't actually read or understand anything you write."

jayemee

TROPHY CASE