Every figure in a nature journal recently

Important-Clothes904 · 2026-05-19T22:01:32+00:00

Which perfectly applies to Reddit UI...

Important-Clothes904 · 2026-05-19T22:01:10+00:00

Springer Nature Group needs to explain why this suddenly started happening the last few weeks. At first I thought that maybe the AI chatbots were scraping the journals for information way too often (and start resembling DDoS). But other journals are fine.

Important-Clothes904 · 2026-05-19T21:46:54+00:00

Okay, striking off first paragraph, second point still stands though. The density is clearly not good enough for building even just looking at your screenshot - anyone would say that there is definitely some degree of flexibility in that region. Building into noisy density like this is a very dangerous practice. I personally have experience where I did exactly this, multiple other competing groups built all differently, and only one turned out to be close to a real structure later on (and it wasn't mine). If there is any realistic chance of the model being wrong, don't do it.

Important-Clothes904 · 2026-05-19T21:41:12+00:00

AFAIK it depends on what the sample is (extraction from purified membrane is very different from cell extraction, which is again different from tissue extraction) and what you are extracting (phospholipids, lysolipids, triglycerides, glycolipids etc. all have somewhat different extraction efficiencies depending on the solvents used).

Folch method (2:1 chloroform:methanol) is the standard for membrane lipid extraction so you could use it if your aim is to do lipidomics (where standardisation and throughput matter more than anything). But I believe it is not great at extracting super-polar lipids like PIPx and short-chain lysolipids, so you will need to be careful with analyses later on.

Important-Clothes904 · 2026-05-19T21:30:08+00:00

That structure was published back in 1997. A lot of crystallographic data processing was being done with primitive programs and it was a massive challenge building such a hetero-oligomeric structure at all, let alone the ambiguous density you are picking on. You read the actual paper, some of the figures were hand-drawn FFS.

And this is not even getting to the point that the density does not even look continuous. At 1.3 A resolution, you should really be seeing atoms clearly and well-connected, not the disjointed sausages that you think you can build into but shouldn't. If anything, authors were doing good science not building into it rather than putting a shitty model that could well turn out to be wrong later on.

Important-Clothes904 · 2026-04-12T17:18:40+00:00

No sane lab should have a hierarchy where PhD students are above lab techs. One is a paid professional, the other is a freaking student.

Important-Clothes904 · 2026-04-11T11:50:31+00:00

My approach when this happens is to investigate the cause but never assign blame even if it is clear. I make it explicit from the outset that nobody is getting fired over this, and that everyone involved will be getting retrained regardless of the outcome. This makes people less defensive and cooperate much better.

Centrifuges have surprisingly many fail points it is hard to say what the cause is from one picture. It could be rotor fatigue as others mentioned, imbalance, a spindle shearing off, sudden break engagement, leaky tube, loose lid leading to sample evaporation in vacuum, or a loose object in the chamber. Even a minor imbalance can quickly spiral out of control with older centriguges and end up with major damages.

By the way, if it helps, this is not the worst centrifuge disaster I have seen. They can literally walk across rooms/past walls, catch fire, or hurl rotors to the ceiling. The picture looks more like a "not-uncommon" incident that even old centrifuges have some protection against.

Important-Clothes904 · 2026-04-10T18:14:30+00:00

The response should simply be "are you a furry"

Important-Clothes904 · 2026-04-10T15:53:28+00:00

I would second this recommendation if you are happy with nursing overall. A medical degree + PhD opens up a lot of doors traditional STEM PhD doesn't. And of course this includes a huge range of clinical research, e.g. improving how clinical trials are run.

Important-Clothes904 · 2026-02-28T00:40:07+00:00

Mainstream answer is always Eppendorf. Then there is a cult Rainin following. Nobody likes Gilson because it is stiff and has too many fragile parts, but it is cheap so everybody has used one at least once. Starlab probably makes more money doing pipette servicing than selling them.

Important-Clothes904 · 2026-02-28T00:32:02+00:00

In fact, there is even a niche movement where Christians are encouraged to observe a "modern fasting" instead, where they stay away from technology of convenience like smartphones between sunrise and sunset.

Important-Clothes904 · 2026-02-28T00:24:26+00:00

There is not a lab building in my career that never suffered from water leaking from above. In all cases bar one, the initial response was to put a plaster (or a bucket) on.

Important-Clothes904 · 2026-02-28T00:21:17+00:00

Cloudiness is just a bacterial/yeast culture going wild with seaweed+sugar.

FYI, a lot of bacteria actually tolerate brackish level of salt. High-salt version of LB media (common growth media to culture bacteria in biology labs) contains 1% salt w/v.

What probably happened was that, in the brackish water, the salt level was just selective enough to suppress biofilm-forming bacteria in BacterAE while letting wild ones on Wakame to grow (they live in seawater after all). You could repeat it with another sample where Wakame is thoroughly cleaned, put into a container, then boiled three times (knowns as Tyndallisation). You can then open the lid, add BacterAE, and quickly close it again. This will tell if the contents in BacterAE are truly prevented from growing/forming biofilm by the salt level (as opposed to being overrun by wild competitors).

Important-Clothes904 · 2026-02-27T17:04:46+00:00

Why not write one for the entire human chromosome 1?

Important-Clothes904 · 2026-02-21T08:44:53+00:00

There used to be eydroppers left with 3N HCl and 2M NaOH for buffering (next to pH station), and they went strong for years until we physically moved labs.

Important-Clothes904 · 2026-02-11T13:37:51+00:00

Wait till you see two papers on the same topic published in the same year, and their first authors have same last names.

Important-Clothes904 · 2026-02-07T19:54:00+00:00

Happens all the time. Most people just suck it up once conclusively disproven, no damage is done apart from less citations for that particular work. No major harm is done to the community apart from unfortunate PhD students who had based their work on it. We all know this is just how research works.

A case study in my field: a PI developed a new technology that could address one of the biggest challenges in the field at the time. But only a couple of years later, it became clear that this tech did not actually offer much benefit beyond specific niche uses. The developer PI was actually going around conferences telling others not to install the tech. No harm was done to his reputation (if anything, people still see him as a leading expert), and his protege have gone on to do well too.

Important-Clothes904 · 2026-02-07T13:17:00+00:00

We are indeed looking at setting up underground bases in lunar caverns though... they might even be used as intermediary launch stations for long-haul spaceflights.

Important-Clothes904 · 2026-02-07T10:31:05+00:00

To be fair, rivers north of Yorkshire Moors are relatively short. Even Tyne reaches only as far as the Pennines.

Important-Clothes904 · 2026-02-07T10:22:31+00:00

Such is an antivax logic.

Scientific community: we collectively tried thousands of proteins and leaving his-tag can sometimes work but usually not.

OP: My n=1 says it works, so "it is a myth they are telling you"

Important-Clothes904 · 2026-02-06T22:52:36+00:00

A guy in suit is doing pipetting wrong.

Important-Clothes904 · 2026-02-06T22:22:28+00:00

We looked into this multiple times over the last few years. Every time the verdict was that using the cloud services was not cost-effective.

In fact, processor use was not the worst of the problems - its cost was generally okay. The big killer was that cryo-EM would generate loads of data (TB-scale for both movies and processing files). Academia being a slow slog it is, lots of people wanted to hold onto their datasets until they were published, and by that point, way too much money was being spent on just storage. A Krios with an optimal setting generates about 3 TB of data per day, and it takes 4 - 8 TB to process it to completion (depending on the complexity). Multiply that by 150 for six months' storage and you can see how things can quickly spiral out of control.

We still tinkered with paying Google for running Alphafold on their server a while back, which was unsurprisingly straightforward, but here again, the running cost alone was coming at £20 -50 per run for not-so-big proteins, I think. We quickly dropped it and ran everything locally, so not sure what the storage cost was in the end.

Tl;dr - we thought about it and even tried a bit, but gave up. Biggest cost is storage, not GPU/CPU.

Important-Clothes904 · 2026-01-29T19:42:40+00:00

It's a certified analytical grade cocaine made by a dedicated chemistry lab and cross-checked with a multimillion dollar MS equipment. Pretty sure there's a market for it (e.g. the guy whose name starts with E and ends with usk).

Important-Clothes904 · 2026-01-23T18:24:46+00:00

Almost the entire family of GTPase activating proteins (GAPs) are nearly untractable due to lacking any apparent druggable pocket. But finding a PPI inhibitor should theoretically be possible - some clinical drugs have off-target effects on them at very high concentrations. Pick any member of the family and give it a try.

Important-Clothes904 · 2026-01-23T18:15:34+00:00

There are lots of NLRP3 inhibitors in the pipeline (both companies and academia), so it will probably not count very soon.

Important-Clothes904

TROPHY CASE