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Comment Re:How are they Known? (Score 3, Informative) 28

More or less. The paper looked at bacteria which are present in the Genome Taxonomy DataBase, which uses a range of marker genes/proteins in a genome to identify the species the genome is from and to build a tree of life based on that data. This includes a lot of shotgun sequencing data which produces DNA data from across the genome, compared to a PCR-based technique which normally focuses on a specific part of a genome. The environmental samples (soil, water etc.) this is done on will contain many different microbes, and a very large proportion of microbes in that data will never have been cultured or specifically studied. They just happened to be in the area when someone took a quick survey of the local microbial community. Even if a microbe has had a paper published on it, we probably know next to nothing about it. It is common for people to isolate a microbe, deposit it in a culture collection so other people can buy samples of it, and then publish a paper with a very high-level, general description of it. We'd still know next to nothing about the organism, or how it interacts with the world. Many organisms in culture collections have publicly accessible genome sequences, which can be helpful, but even that isn't a guarantee of anything. DNA is genetic potential, but there's a whole load of factors which control whether or not that DNA is actually expressed. This is why culturing hasn't been made obsolete by sequencing, and why you really need culture-based papers studying specific microbes to understand them rather than just a genome sequence.

Comment What could go wrong (Score 3, Insightful) 163

Might artificial intelligence (AI) steal its crown?

Oh sure, take the bit of software which causes errors because of obscure gotchas, and give it AI so it can blindly blunder into those gotchas without any human input at all. I can't possibly understand why AI PCs aren't flying off the shelves.

Comment Re:Venus is pretty cool (Score 1) 24

The idea, even remote, that there could be life in the atmosphere is worth exploring

So one of those theories was that phosphine gas in the atmosphere was a byproduct of life (we know terrestrial microbes appear to make it, although not how). The team who published that said that it was unlikely that the phosphine was volcanic in origin, as Venus wasn't volcanic enough for that: they claimed Venus would need to have at least 200 times as much volcanic activity as Earth for that to make sense. The paper published in the title claims Venus may be around as volcanically active as Earth, but that's based on old data from two regions of the planet. It'll be interesting to see how a closer look at the volcanic activity with more modern equipment factors into that equation.

Comment Re:Some direction is better than none (Score 4, Interesting) 57

I love Firefox. Most configurable browser (through about:config).

Unless you use Firefox for Android, where they disabled about:config because "not many people use it" and "it can become unstable" . Yes, Firefox Nightly for Android still has it, but I don't think disabling it in the main release bodes well.

Comment Re:This worries me (Score 3, Funny) 258

"conduct an open, inclusive, and scientifically rigorous" Do they really need to mention "inclusive"? "Open" and "scientifically rigorous" should also cover "inclusive", right? Right?

I don't know, a couple of years ago a bunch of very significant changes to microbial taxonomy came into effect off the back of a vote of 22-odd people, to the surprise of many microbiologists who had no idea this was even being discussed. Hopefully "inclusive" means "we are actually going to include opinions from across the community, starting by announcing this clearly ahead of time", as just because something is open doesn't necessarily mean people know it is going on and can ask to be included in it.

As Douglas Adams said:
"But the plans were on display”
“On display? I eventually had to go down to the cellar to find them.”
“That’s the display department.”
“With a flashlight.”
“Ah, well, the lights had probably gone.”
“So had the stairs.”
“But look, you found the notice, didn’t you?”
“Yes,” said Arthur, “yes I did. It was on display in the bottom of a locked filing cabinet stuck in a disused lavatory with a sign on the door saying ‘Beware of the Leopard'".

Comment Re:Fragments? (Score 3, Insightful) 47

Are these just fragments of RNA from bacteria, human cells, viruses, that were destroyed and are now just floating around in specific bacteria in the gut?

At a quick glance, they claim that these are fragments "with no evident homology to the NCBI BLAST (nt or nr) databases", and those databases are pretty comprehensive repositories of what we know. They've claimed that the genomes contain patterns indicative of genes/proteins, but that these and their predicted proteins mostly have no significant sequence or structural homology to anything we know. Some predicted proteins have tertiary structures which hint that they might have ribozyme activity, which suggests a replicative process similar to some viroids. So no, it looks like they've confidently ruled out that this is RNA from the host or microbiota, but it looks like they're still missing definitive proof that obelisks are some sort of new reproducing genetic element.

Comment Re: Goes to show how uneducated people are (Score 1) 52

I think it's a bit more obvious though. I have a Valve Index, which is a great piece of kit which I don't use often enough, and after a bout of Beat Saber those foam gaskets get sweaty, and then smelly. Given that the face gaskets are a lot closer to your nose than the handheld controllers are, you notice how stale they are pretty easily. It doesn't take many microbes to help that process along. As someone else pointed out, this is why the Index has magnetic gaskets which take seconds to swap out. If Meta isn't doing that then they're doing it wrong. It's just a shame that the Index gaskets aren't cheap.

Comment Re:What about the water? (Score 3, Interesting) 32

There are blind transparent shrimps who just love swimming about in the acid. I missed the bit about what the shrimps live on. Fermented biologists, I expect, but I admit that is baseless speculation on my part.

Most of these cave systems have a water source which brings dissolved minerals and gasses into the cave. Chemosynthetic microbes consume those to grow, and a whole food-web is built on top of them. So, something grazes on the bacteria, something eats the grazers, etc. The sulphuric acid production is usually due to microbes oxidising hydrogen sulphide gas for energy, seeing as it's a bit difficult to photosynthesise in a dark cave.

Perhaps a worthy topic of study would be if there are cloudy communities of living things on our own planet, who live out their lives in ephemeral droplets.

This isn't really my field, but I know there is some work on it already (no prizes for guessing where Bacillus stratosphericus was isolated from). This article (shouldn't be paywalled)? suggests there is evidence that microbes actively metabolise and reproduce in the atmosphere, but we still seem to be missing a lot of information.

It would be a good deal cheaper to investigate that, than to send a robot probe to Venus.

That doesn't mean that Venus isn't worth knowing about. By that same logic, most people wouldn't ever leave home to explore other parts of the world.

Comment Re:Brexit means Brexit? (Score 3) 81

But the EU science program is for EU nations

And associated nations, e.g. Israel. If I remember right, the deal is that EU nations pay into the pot depending on the size of their economy, but they can take out as much money as their research teams can win in the competitive application process. The UK used to get more money for science out of this scheme than it put in. However, associated nations have to pay for thier end of any research programmes, the benefit being that they can be part of large funded collaborations focusing on different aspects of the same topic.

The UK was down for associate status as part of the withdrawal agreement, but given that Boris has made it clear he wants to unilaterally change the NI border protocol, the EU is now saying "well if you won't abide by the withdrawal agreement then we won't abide by parts of it either".

In other words, it's not even "you can't be part of an EU scheme if you've left the EU". It's "You can't leave the EU, negotiate an agreement, and then unilaterally pick and choose which bits of that agreement you actually want to abide by after signing it".

Comment Re:The *filaments* are peanut-size, not the cells (Score 5, Interesting) 53

Eh, the filaments don't seem to be made of discrete cells though, so it's sort of arguable. The authors claim that the genome is lacking in key genes for binary fission, so it looks like the cells extend themselves as if they were going to go through fission, fail to separate, and then just keep extending. There seems to be a vacuole which runs the whole length of the filament, and there don't appear to be any septa throughout the filament, so it does seem to be a single, long cell, even if it looks like it pinches at points. Oddly it looks like cells at the end of the filament pinch off into individual cells to go off and form their own colonies, but at a glance the authors don't seem to have tried to explain how that happens if the main filament doesn't have the genes for doing that. Some of the genes involed in the fission process which this organism is missing were named "Fts" for "Filamenting temperature-sensitive mutant", as E. coli mutants in these genes would fail to separate and would form long filaments at high temperatures. It sounds like this organism does it as a matter of routine. I've seen cells which do this under the microscope, but never to this scale (say, 10-15 um long instead of 2).

Comment Re:Investigated != Guilty (Score 5, Insightful) 85

At least it used to be that way in the past. Just because some software flags some irregularity doesn't mean you are guilty

I work in an institute which also uses Canvas. Don't get me wrong, it has a lot of great features and I don't know how we could have taught over the last year without it, but we've also found a few bits of jank in the way it operates, which have sometimes required us to remark work, rejig how we handle submitted work, or not use the built-in system for something because under the hood it conflicts with how we actually want the system to work. I'd definitely not want to come down hard on someone just because Canvas flagged something, without some serious manual checking to make sure this wasn't also a quirk of Canvas. We ended up giving the students the benefit of the doubt when it comes to exams, and haven't used any serious proctoring/anti-cheating systems. Yes, we've had a bit of grade inflation and a few students probably got away with things they otherwise couldn't have, but given the privacy issues, the hassle getting both students and staff up to speed on how to use the software, and the potential for this sort of thing happening we thought it just wasn't worth it. The really serious stuff which separates good and bad students is project work, which is much more individual and harder to cheat.

Comment Re:Consequences (Score 5, Insightful) 48

There's absolutely no point in trying to sterilise materials for the ISS, or other human-crewed stations, because as soon as a human boards the station they bring all of their microbiomes with them. Niche applications (e.g. analytical equipment) will have thier own cleanliness policies but with humans, microbial hitchhikers are just a fact of life. Aside from giving most things a wipe down after they're finished and pre-screening the crew for obvious issues (which I'm sure already happens) there's not much more to be done really. There have been experiments in the past to check the effects of zero gravity etc. on microbial growth and pathogenic potential (e.g. through the Biorack program) so this isn't a new concern, but so far nothing dramatically worrying seems to have been seen. I think parts of the ISS get swabbed regularly for sequencing too just to keep an eye on what is around.

Comment The table has been totally reformatted (Score 3) 28

For anyone else who was confused as hell by the table in that link they've updated it to have notes which aren't stupid. I don't know why they thought it was a good idea to use a big green tick to mean both "Yes, it is encryped end-to-end" and "No, it doesn't drain your battery".

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