Dr. Stone is a manga and anime story that aims to portray science in a more entertaining way than the average school classroom. With protagonist Senku Ishigami being an expert in physics, chemistry, medicine and other realms of the subject, author/artist team Riichiro Inagaki and Boichi do their best to portray his endeavors as accurately as possible. They get so close, in fact, that Dr. Stone has to come with warnings stating that recreating Senku's experiments can be dangerous and illegal.
For the sake of the narrative, however, scientific accuracy sometimes comes second to telling a good story. One of Dr. Stone's biggest instances of this occurs in Season 1, after Senku learns the history of Ishigami Village. Though he became chief by winning the Grand Bout, it turns out that the position was his birthright, as everyone in the village is descended from Senku's father and five other people. Narratively, this is an emotional moment for Senku and expands on his father, Byakuya. Scientifically, however, this could never have happened.
Why Dr. Stone's Ishigami Village Couldn't Have Survived Thousands of Years
In terms of a narrative, making Byakuya a larger figure than just Senku's role model makes him a stronger character. This connection also brings a more emotional side out of Dr. Stone's goal-oriented protagonist. In seeing Byakuya's part of the story unfold, the audience learns where Senku got some of his best qualities, namely his love of science and endless determination. In terms of a story beat, the idea isn't farfetched at all.
This idea of very few creatures repopulating the world is ingrained into fiction. It can even be found in religious texts from modern Christianity to ancient Norse mythos. Yet scientifically, this is impossible -- Ishigami Village would not have lasted nearly as long as it has with so few people creating a gene pool.
Byakuya’s group was made up of six people, three men and three women. This was most likely a conscious decision by Inagaki, as the six become three pairs who each have children as time goes on. It's the most diversity one could ask for when the characters all come from a small space station orbiting the planet. While larger than the stereotypical Adam and Eve setup, it's still far from enough for a colony to survive for thousands of years.
The True Science Behind Dr. Stone's Plot Twist
The science of minimum viable populations (MVP) is a threshold that estimates the smallest number of individuals in a species needed to prevent its extinction. While the results are estimates, these numbers are used to help conserve and manage populations that are on the decline. Minimum populations vary by the species, as each has its own timetable for reproduction and life span. This number is the minimum that a species would need to survive for several generations.
A widely accepted rule in this line of science, though debated to this day, is the 50/500 rule. Simply put, in order to prevent severe defects caused by inbreeding, a species needs a minimum of 50 individuals. For the species to thrive and continue to evolve, the population needs to be over 500. This number does not mean total individuals, but those capable of reproducing at any given time.
As a person or animal ages, its ability to reproduce changes. Using Dr. Stone as an example, characters like Suika and Kaseki wouldn't count because they are either too young or old. Meanwhile, the likes of Senku and Kohaku would count. The population would also need to maintain an even distribution of males and females. So realistically, the population would have to be even higher than these standards.
As a series that prides itself on its scientific accuracy, diverging from it in such a drastic way can be jarring. Dr. Stone can be spot-on when it comes to making alcohol in the Stone Age, but can also simplify or twist facts for the sake of the story. In this case -- and surely others as the series progresses -- the rules of science are broken entirely.
That said, every piece of fiction is a mixture of fantasy and reality. If stories completely adhered to realism, there would be no surprises. The genre of fiction may not exist at all if media followed this path. At the end of the day, Dr. Stone's goal is to make science fun for its target audience, and it does that in spades.