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That's awesome. It must have been a giant mushroom, because that's the coolest possible outcome. It's like I'm in Vvardenfell all over again...
Giant living spires? Better watch out for mutalisks then ...
I first heard about this in Paul Stamet's book Mycelium Running.

Its too bad they include this period of Earth's history more prominently in high school.

It's a mushroom, It's a fungus, And they're growing all around us and among us
Why is it assumed that these mushrooms would grow straight and tall? Trees grow tall to maximize their exposure to their primary energy source, which is of course light. But why would a mushroom need to grow really tall. Don't they obtain all their energy from the land?
Exposure to air. The higher, the windier, the farther the spores get.
Plausible, but not apparently a problem from most fungi currently alive. I would guess that the trade-off in terms of marshaling resources vs. increase in spore distribution would not be favorable enough. I expect that's why the lichen argument appeared - we can easily see why being tall is a plus for photosynthesis.
Part of the reason a mushroom would be so tall is that when the cap opens, the stem is connected to the middle. So a mushroom top that is say, 10 feet across, would be at the very least 5 feet tall. As the top gets heavier the stem would have to be larger in diameter to hold up the increased weight.

It's also not uncommon to find fungi that are several feet long growing on trees and such. Not sure if the article specifically said mushroom or if it was just a fungi they found a fossil of.

It's assumed they grew that way because that's what the fossils look like.

If a fungus had a photosynthetic symbiont, it would have a good reason to compete for height. In fact, an algal symbiont is a leading theory, based on chemical traces that point to algae in the fossils.

Interestingly, lichens do this today: they are composite organisms of fungus and photosyth (algae or cyanobacteria). They don't currently get very high, but perhaps that's just because plants are so much better at height that all tall forms have gone extinct.

If there's no photosynthesis going on, it's harder to explain. Perhaps it's handy in a very low-growing world to lift most of your energy-storage mass or hard-won water above the ground, away from predators?

They also must eat something... I still expect them to do some kind of photosynthesis, just like lichens, and that would explain their height.
What an interesting idea, I can't help but visualize Zangermarsh[1] :-) Interesting question about what it might gain evolutionarily by being tall, perhaps more moisture exposure but as others have pointed out fungal mats get that by just being wide and covering a lot of area. Of course if you were competing with a fungal mat being tall might be one strategy.

[1] Its a World of Warcraft zone

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The fruiting body of a fungus is typically a reproductive mechanism. Bigger mushroom = more spores (ie. size does matter).
And by taller than others the spores would be more likely to be carried over everything else by the wind and travel further distances. A short mushroom's spores might end up only traveling a few feet before hitting, say, another mushroom.
Haha that zone totally came to my mind too. It's actually quite cool how many different types of zones Blizzard has made in that game... I wonder if they'll ever run out of ecosystems.
Smurfs were real, and normal size! It's the mushrooms that were big enough to carve houses inside.
Interesting. Could fungi photosynthesize? I thought not. Unless the earth was covered as a marshland, it would be unlikely mushrooms covered earth. It is likely they are popular around coastal area.
No known fungus does--though there are "radiotrophic" fungus, that use gamma radiation as an energy source.

However, fungus are found with photosynthetic symbionts. Lichen, for example, are a combination of fungus and algae (or similar). It's possible the Prototaxites were giant lichen, which would allow them to live in non-fungus-friendly locales, rather like a tree.

Makes one wonder if the pipes in Super Mario Bros. led to not where- but when?
I wonder what those fungus lived on? This was in the era before fungus could metabolize cellulose. Maybe, unlike modern fungus, they just grew bit by bit? The fact that dead wood couldn't easily be digested is part of the reason the Earth's O2 level was so high back in the day, and why you could get coal or oil deposits even without anoxic conditions.

EDIT: All interesting information above from friends who know way more about the subject than me, who I told about the article. Any mistakes are probably mine.

Was there really a lot of cellulose to consume that early? Remember, no trees so no dead wood to consume.
Am I just a huge anime nerd, or did anyone else immediately think of the early Miyazaki film "Nausicaa and the Valley of the Winds"?
Nope, I thought the same!

Spoiler Good thing we weren't around to poison the Earth back then or these would be sprouting toxins like no one's business.

I was thinking more Super Mario. They were not far off at all
Not much of an anime nerd,but I love Miyazaki's work, so yeah, that makes sense now that you say it
Cool! I've often imagined alien worlds that had nothing resembling plants or animals, and they invariably ended up with giant fungi. Turns out many of the craziest life forms we can imagine have already existed on Earth.
So... Jules Verne was right about YET ANOTHER thing? RE: Ancient giant mushrooms dotting the shore of the prehistoric coast in Journey to the Center of the Earth.
That's exactly what I thought when I read the title! I'm right now in the process of reading Journey to the Center of the Earth and this struck me. Jules Verne really was quite the visionary...
Considering that the fungus theory was raised by Dawson in 1859 (and widely debated), and JttCotE was written in 1864, it's likely Verne was influenced by modern scientific debate.
Of course, he was also wrong about a lot of things. I recall in 20,000 Leagues they travel under the Antarctic ice all the way over the pole... because there was no land there in 1870, I guess.
We don't know that there isn't a way to go under the Antarctic ice mass .. there may well be large enough rivers under the ice, navigable with fancy machines.
Back then, gravity was a lot less, so soft bodies can grow huge. Now they can't.
Seems there's no acceptance round here for the possibility of the Expanding Earth Theory...
Tech people tends to be close minded.
This discussion has a pretty amazing number of references to fantasy or science fiction worlds. I count eight so far.

* WoW - Zangermarsh

* Elder Scrolls - Vvardenfell

* StarCraft - Mutalisks

* Smurfs

* Mario Brothers

* Jules Verne - Journey to the Center of the Earth

* Miyazaki - Nausicaa and the Valley of the Winds

* Paul Stamet - Mycelium Running

Don't forget: * Minecraft - Mushroom Biome
And Tintin - The Shooting Star.
The first thing that came to mind: Minecraft.
Dude in article pic looks like he's an expert on mushrooms
As these broke down and broke down other things around them, they probably created soil (as funguses still help to do) which enabled more advanced plant life to thrive. Love it
Actually reading the article, came across:

"So science is messy, and despite more than a century of digging, we still don’t really know, for sure, what these huge spires that dominated the ancient Earth really were."

So despite the link-bait title, we still don't know and they may not be giant mushrooms.

Sure, we're not certain, but giant mushrooms are our best guess.
har har morrowind har har...
The article clearly states that no consensus has been reached over the fossils origin. It might be a Fungus. Misleading title that everyone seems to be ignoring.