Scientists Waited Two and a Half Years to See Whether Bacteria Can Eat Rock | Hacker News Reader

Scientists Waited Two and a Half Years to See Whether Bacteria Can Eat Rock

blogs.scientificamerican.com

93 pointsheadalgorithm22 comments

Original paper: Napieralski, S., Buss H., Brantley S., Lee S., Xu, H. and Roden, E (2020). "Microbial chemolithotrophy mediates oxidative weathering of granitic bedrock." PNAS 116 (52) 26394-26401; DOI: 10.1073/pnas.1909970117.

PDF: https://www.pnas.org/content/pnas/116/52/26394.full.pdf?casa... (works, even though it seems like it shouldn't...)

This is exciting experimental evidence for the concept of lithotrophy [0]; while we knew about the mechanisms of action for a while, and have previously found rock-eating microbes within otherwise-unliving rocks, this experiment shows us that these microbes are part of the circle of life.

[0] https://en.wikipedia.org/wiki/Lithotroph

Bacteria are also used in mining to refine the ore: https://en.wikipedia.org/wiki/Bioleaching

Only 2.5 yrs? This reminds of https://en.wikipedia.org/wiki/Pitch_drop_experiment

Stop treating the Earth like dirt!

More muck-racking journalism from Scientific American:

Would You Like a Side of Dirt with That?

https://www.scientificamerican.com/article/would-you-like-si...

Pay Dirt: Martian Soil Fit for Earthly Life

https://www.scientificamerican.com/article/martian-soil-fit-...

Eating Dirt: The Benefits of Being (Relatively) Filthy

https://blogs.scientificamerican.com/food-matters/eating-dir...

Dirt Doesn’t Smell like Dirt

https://blogs.scientificamerican.com/artful-amoeba/dirt-does...

Why Researchers Need Better Space Dirt

https://www.scientificamerican.com/article/why-researchers-n...

Secrets of Life in the Soil

https://www.scientificamerican.com/article/secrets-of-life-i...

How Dirt Cleans Water

https://www.scientificamerican.com/article/how-dirt-cleans-w...

Dirt Poor: Have Fruits and Vegetables Become Less Nutritious?

https://www.scientificamerican.com/article/soil-depletion-an...

How Dirt Can Clean the Air

https://www.scientificamerican.com/article/how-dirt-can-clea...

Jesus, this is a bad article. It's filled with several very bad attempts at humor and buries the lede but my main problem is that it's just wrong.

"there is an enduring mystery to dirt: where does it come from?", "Mystery of dirt’s origins is a thorny experimental problem"

Why would they try to pretend nobody knows where soil comes from!? Did they not even bother to Google the word "soil"? "Soil formation" is the third heading on Wikipedia. There's an entire field dedicated to soil formation: pedogenesis! Soil science isn't some new start-up field where everything's unknown - soil scientists can give you a pretty damned good estimate of not only where soil comes from but how many nutrients it will have over time, what microbes are in it, what will happen to the soil over time, etc etc.

Unfortunately this kind of thing seems to be par for the course for SciAm. A writer picks out some random new research and writes about it as if it's groundbreaking. Unfortunately, 99.5% of research isn't the discovery of DNA, it's "we tested if bacteria A has more xyz than bacteria B and the difference was not statistically significant."

I'm reminded of https://xkcd.com/683/

Logically, all xkcd references in comments resolve to https://xkcd.com/386/ including this one.

Nice. Did you just come up with that?

Are you saying that we should expect that websites who try to portray themselves as "experts" or "sources" shouldn't be called out?

I've always read that xkcd as someone arguing with someone on social media, not with a magazine who markets themselves as an organization who has "expert insights on the most important and awe-inspiring advances in science and technology", or "Scientific American is the essential guide to the modern world".

Normally we'd change the title to something neutral, but in this case the article is so sodden with it that it has soaked the thread as well. That happens sometimes. I'm not sure if it's getting more common; I rather think it isn't, actually; fingers crossed.

TLDR- yes it can.

"The minerals incubated with microbes appeared ragged or pitted — as if they had been dipped in acid, not bacteria — after their 864-day incubation. The sterile control minerals, by contrast, retained sharp, smooth edges."

misleading title, they did not wait, wait means something completely different

they ground the rock up, placed it in a tube, put it in a drawer, then took it out two years later and performed some measurements

the minerals turned out to be less jagged than sterile minerals kept for the same amount of time. The scientists concluded that the bacteria ate the rock by stripping electrons.

Now a possible alternative explanation (not explored by the journalist) is that the bacteria lived off the remaining organic materials in the rock and the byproduct of their life were substances that dulled the crystals.

"then took it out two years later" sure sounds like waiting to me.

It's just a language ambiguity. Nobody's wrong here. I first read it as, "they waited two years before they began investigating the topic."

Here are the relevant senses of the word from OED:

- "To remain in a place, defer one's departure until something happens."

- "colloquial. to wait about: to linger expectantly, ‘hang about’ where something is likely to happen. Also (chiefly U.S.) to wait around."

- "To defer action until some event has taken place; also with infinitive, to delay to do something."

I think there's ambiguity in what's being awaited:

- I think your parent comment assumes the scientists are awaiting a result

- I think you assume the scientists are waiting for some mount of time to pass

FWIW, when reading a headline, I'd definitely assume the first. "Scientists did other stuff for 2 years while a sample sat around" wouldn't be newsworthy enough to put in a headline. I think the headline was simply worded in a way that emphasises excitement over clarity.

A clearer headline would be "Scientists conducted a two and a half year experiment to [...]".

The alternative explanation is that they mined the rock for food? That's just as interesting.

I think that's actually the result!

I read @glofish's proposal as suggesting that bacterial excretions(?) indiscriminately dissolve the rock.

The paper (linked above) does try to address this in a few ways. Iron, the putative energy source, is specifically concentrated on the surface of the inoculated samples--but other metals aren't. The bacteria are also mostly found on the mineral edges. They discuss this near Figure 5/6 and in the supplement.

in a thread about misleading wording... usually "mining rock" means extracting rock, while "mining a mountain" means extracting minerals from the mountain. Your "mined the rock" means the latter sense of the word mine.

and as to the original "misleading title" claim, the way they meant the word wait was "scientists were willing to conduct a 2 year experiement because the data was worth the wait"

no what I meant is that during the process of grinding up the rock they mixed in the organic matter from the surface of the rock into the dust itself, the bacteria lived off that substance.

> Now a possible alternative explanation (not explored by the journalist) is that the bacteria lived off the remaining organic materials in the rock and the byproduct of their life were substances that dulled the crystals.

Is that your hypothesis or from an actual paper about the study?

I think this makes a lot of sense, because if there wasn’t left over organic material the bacteria could “eat” and was simply about bacteria stripping electrons from inanimate matter...I’m left wondering why the bacteria wouldn’t indiscriminately strip electrons including from say the test tube itself?

Reply on news.ycombinator.com