Where the heck did all those structures inside complex cells come from?

Great article. These parts of the cell are still mysterious.

Lynn Margulis’s work also suggests that structures like cilia and flagella, that seem like integral parts of the cell, are actually “captured” symbionts that used to be independent organisms.

Lift at that level is pretty weirds. The simple macro view thought in school (a tree with progression from roots to tips) is misleading and barely informative.

Back in the 1990s I spent a long time playing with Tierra (https://en.wikipedia.org/wiki/Tierra_(computer_simulation) ) and actually wrote my own distributed version[1] so it could run over multiple machines (computers were really slow back in 1991), and a simplified instruction set. Now I know that Tierra has a number of serious shortcomings compared to real evolution. Nevertheless it does really surprising things if you let it run long enough and then examine the cells that evolve in the system. Some cells become parasites, some become really large. I also saw really surprising optimizations happen spontaneously that I wouldn't have thought about.

Anyway given that the real thing has been running for 3 or 4 billion years, I'm not surprised that it has generated incredible complexity.

[1] http://oirase.annexia.org/dlife/

I find it fascinating how many bizarre, wide gaps we have in evolution where we are left wondering how something could have possibly come into existence at all in the first place.

And clearly, the questions are completely valid. From the most basic "how did life start" to questions like in this article (where did mitochondrion come from?) ... it is very difficult to make sense of. The timescales involved are long, any evidence of the in-between steps is long gone, and simply the odds of these random things occuring would seem to be astronomical.

Taking even just the first premise in this article, that mitochondrion came about due to a cell ingesting another cell, I can see that occuring. Given enough cells, and enough time, I can see it happening repeatedly. I mean, putting a cell in a cell doesn't get you mitochondrion, but you can start with the idea. But how do all these separate isolated occurances, which have no impact on each other in the vast ocean or wherever it is assumed this was taking place, move to the next step?

One single one of those events, then somehow needs not only confer an advantage, but also have the ability then to recreate that "cell within a cell", and then over time that not only needs the survival advantage, it has to undergo further continuous refinement to where, what was a simple merger of two similar things, has become specific internal machinery doing things that confer advantages to the whole.

Just trying to imagine this occuring due to things literally bumping into each other in the ocean already makes my brain start thinking "there's no way". But it is billions of years, there's theoretically a lot of these "primative" cells everywhere, and I just accept that part as seemingly impossible, yet obviously wasn't. And this is all still to try to figure out how only the most basic stuff came about. When you start bringing in complex structures that have to orchestrate with other ones in order to function, it only becomes more difficult and confusing.

At the end of the day, it's obviously evolution. There's literally nothing else it can be. Even if you think it came in on an asteroid, it had to start somewhere. The only other option that I can think of is that none of it is real and the simulation we're living in is glossing over some important details! But I'll stick with evolution.

But it's still very mysterious, to the point it seems to border on the impossible.

One thing I didn’t see mentioned in this article, that I thought was one of the major motivators for realizing that mitochondria originally came from outside the body, is that mitochondria have their own DNA independent of the cell’s nuclear DNA. But I wasn’t aware that any other animal organelles do (chloroplasts in plants do, and those are also assumed to have originally been an independent bacteria).

The article doesn’t mention that nuclei, mitochondria, and chloroplasts all have double membranes. If I had to guess, I would bet that those are the organelles that were formed by endosymbiosis.

I take this fact as suggesting that there may be more to the frequency illusion than just illusion.

How it feels is similar to like what you get when you run GTA on a system with finite VRAM. - The game uses the same assets over and over again, so you see the same cars and pedestrians too frequently to be random.

Can't really wrap my head around it though. It just seems unreasonable to demand that our reality has infinite capacity for complexity.