Science: Playing with evolution

This post is long (sorry 🥺), but a lot of fun! 😊

Back in the mists of time, when dinosaurs roamed the Earth and cowboys with six-shooters on dinosaur-horses duked it out with feisty T. rex trying to eat the cattle and the always tasty and juicy women folk, a slug of biochemists and biologists made a man-made cell that could self-replicate. That was 2010.

In 2010, a 1079-kb genome based on the genome of Mycoplasma mycoides (JCV-syn1.0) was chemically synthesized and supported cell growth when transplanted into cytoplasm. Hutchison III et al. used a design, build, and test cycle to reduce this genome to 531 kb (473 genes -- 1 kb means 1,000 DNA base pairs). The resulting JCV-syn3.0 retains genes involved in key processes such as transcription and translation, but also contains 149 genes of unknown function. That was the start of man-made life and experimentation with it.

Quanta magazine writes about more recent research:

Even Synthetic Life Forms With a Tiny Genome Can Evolve

By watching “minimal” cells regain the fitness they lost, researchers are testing whether a genome can be too simple to evolve

Seven years ago, researchers showed that they could strip cells down to their barest fundamentals, creating a life form with the smallest genome that still allowed it to grow and divide in the lab. But in shedding half its genetic load, that “minimal” cell also lost some of the hardiness and adaptability that natural life evolved over billions of years. That left biologists wondering whether the reduction might have been a one-way trip: In pruning the cells down to their bare essentials, had they left the cells incapable of evolving because they could not survive a change in even one more gene?

Now we have proof that even one of the weakest, simplest self-replicating organisms on the planet can adapt. During just 300 days of evolution in the lab, the generational equivalent of 40,000 human years, measly minimal cells regained all the fitness they had sacrificed, a team at Indiana University recently reported in the journal Nature. The researchers found that the cells responded to selection pressures about as well as the tiny bacteria from which they were derived. A second research group at the University of California, San Diego came to a similar conclusion independently in work that has been accepted for publication.

“It turns out life, even such simple wimpy life as a minimal cell, is much more robust than we thought,” said Kate Adamala, a biochemist and assistant professor at the University of Minnesota who was not involved in either study. “You can throw rocks at it, and it’s still going to survive.” Even in a genome where every single gene serves a purpose, and a change would seemingly be detrimental, evolution molds organisms adaptively.

Electron micrograph of JCVI-syn3.0 cells, a strain developed in 2016 by reducing a synthetic version of the tiny genome of the goat-dwelling parasitic bacterium Mycoplasma mycoides to its bare essentials

“Increasingly, we are seeing evidence that this [minimal cell] is an organism that is not something bizarro and unlike the rest of life on Earth,” said John Glass, an author on the Nature study and the leader of the synthetic biology group at the J. Craig Venter Institute (JCVI) in California that first engineered the minimal cell.

The minimal cell “is a type of life — it’s an artificial type of life, but it’s still life,” Lennon said, because it fulfills the most basic definition of life as something able to reproduce and grow. It should therefore respond to evolutionary pressures just as gorillas, frogs, fungi and all other organisms do. But the overarching hypothesis was that the streamlined genome might “cripple the ability of this organism to adaptively evolve,” Lennon said.

No one had a clue what would really happen, however, because researchers have generally taken great care to keep minimal cells from evolving. When samples of the cells are distributed by JCVI to any of the roughly 70 labs that now work with them, they’re delivered pristine and frozen at minus 80 degrees Celsius. When you take them out, it’s like their first day on Earth, Lennon said: “These are brand new cells that had never seen a day of evolution.” 

[In one experiment to test whether minimal cells could evolve] they calculated that the original minimal cell had lost 53% of its relative fitness along with its nonessential genes. The minimization had “made the cell sick,” Lennon said. Yet by the end of the experiments, the minimal cells had evolved all that fitness back. They could go toe-to-toe against the ancestral bacteria.

“That blew my mind,” said Anthony Vecchiarelli, a microbiologist at the University of Michigan who was not involved in the study. “You would think that if you have only essential genes, now you’ve really limited the amount of evolution that … can go in the positive direction.”

Yet the power of natural selection was clear: It rapidly optimized fitness in even the simplest autonomous organism, which had little to no flexibility for mutation. When Lennon and Moger-Reischer adjusted for the relative fitness of the organisms, they found that the minimal cells evolved 39% faster than the synthetic M. mycoides bacteria from which they were derived.

I know, I know, the obvious question. What if  we ‘Let It Loose’ in the real world? Well, the data discussed here suggests that if they get lose and manage to survive wherever they get released into, they could wind up evolving into a new free-living form of life. We all know how that worked out when non-native pythons got released into the Everglades in Florida. It was and still is a freaking disaster. And whaddabout the possibility that  COVID-19 was man-made and accidentally leaked out of a lab? And, etc.?

But one thing is darned clear, the force of evolution is powerful and highly flexible. 

Illustration of the parasitic bacterium Mycoplasma mycoides, 

source of the genome for the man-made minimal cell, a new form of life

By Germaine: Science dude

Ain't science great!

(when it isn't scary)