Welcome to The Nonlinear Library, where we use Text-to-Speech software to convert the best writing from the Rationalist and EA communities into audio. This is: Why Are Bacteria So Simple?, published by aysja on February 6, 2023 on LessWrong.

As far as we can tell, bacteria were the first lifeforms on Earth. Which means they’ve had a full four billion years to make something of themselves. And yet, despite their long evolutionary history, they mostly still look like this:

Bacteria belong to one major class of cells—prokaryotes. The other major class of cells, eukaryotes, arrived about one billion years after bacteria. But despite their late start, they are vastly more complex.

Prokaryotes mostly only contain DNA, and DNA translation machinery. Eukaryotes, on the other hand, contain a huge variety of internal organelles that run all kinds of specialized processes—lysosomes digest, vesicles transport, cytoskeletons offer structural support, etc.

Not only that, but all multicellular life is eukaryotic. Every complex organism evolution has produced—eukaryotic. Trees, humans, worms, giant squid, dogs, insects—eukaryotic. Somehow, eukaryotes managed to blossom into all of these complex forms, while bacteria steadfastly remained single-celled, simple, and small. Why?

The short answer is that prokaryotes have vastly less DNA than eukaryotes—four to five orders of magnitude less, on average—and hence can’t do nearly as much stuff. The long answer is the rest of this post, which investigates two related questions: first, why are eukaryotic genomes so long? And second, how exactly does more DNA allow for more complexity?

Why Are Eukaryotic Genomes So Long?

Scalable Energy Production

Using DNA—replicating, transcribing, and translating it into proteins—isn’t free. Cells need energy (such as ATP) to power these reactions and, all else equal, longer genomes will require more of it.

Both prokaryotes and eukaryotes pay similar energetic costs to maintain genes. The difference is that eukaryotes have way more energy and hence can afford to have longer genomes. But why this disparity?

Prokaryotes generate ATP along their cell membrane. Which means that as they increase in size, their surface area—and hence their energy production—will scale sublinearly with their volume. So a prokaryote that doubles in size, for example, will only end up producing half as much ATP per unit volume. Because prokaryotes become less metabolically efficient as they get bigger, most are quite small—six orders of magnitude smaller than eukaryotes, on average.

There are some exceptions. For instance, individual bacteria in the species Thiomargarita can reach up to one centimeter in size, visible to the naked eye! But its cell structure suggests the exception proves the rule—80% of its volume is a vacuole, essentially empty space. So in effect, evolution expanded its surface area without concomitantly expanding its functional volume—a neat trick!

But how do eukaryotes avoid this surface area constraint? Well, eukaryotes generate energy using mitochondria, which are inside the cells. As a result, their number of mitochondria—and hence their energy production—scales with their volume. This allows them to afford both larger cell sizes than prokaryotes, and also longer genomes.

Tolerance for Junk

But bioenergetic constraints aren't the whole story. Even leaving aside the direct energy costs, prokaryotes face way more selection pressure toward having short genomes.

Empirically, bacteria are very quick to rid themselves of genes once they're no longer useful. For example, if you insert DNA into a bacteria that affords antibiotic resistance, it will keep those genes as long as antibiotics are around. But once you remove the antibiotics, it will jettison that DNA within a few hours.

Eukaryotic DNA, on the other hand, is much more weakly selected against. While bacteria are sensitive to additions of DNA fewer than ten base pairs in length, eukaryotes will keep additions of ove...