Colossal Biosciences announced Wednesday a new AI platform to help accelerate its efforts to bring back extinct species, TechCrunch can exclusively report.
The platform, called GenoMorph, uses advanced 3D morphology, comparative genomics, and developmental biology to identify genes that could be edited in de-extinction projects with limited gene data. The is using it as part of its effort to bring back the dodo bird, for which there are limited genomes to work with.
For example, the company is working with only one Dodo genome compared to the 100 genomes it has been able to obtain as part of its woolly mammoth de-extinction project. DNA from the woolly mammoth is more plentiful because the colder climates the animal lived in preserve the DNA better than the tropics where the dodo lived, the company said.
“Normally, scientists can compare many genomes to understand which genetic differences are responsible for certain traits,” Colossal CEO and co-founder Ben Lamm told TechCrunch. “We don’t have that luxury with ancient DNA from extinct species whose DNA is severely limited, and we can only get a small number of complete genomes.”
To build GenoMorph, Lamm said the company collected a bunch of developmental data from “chickens, quail, ducks, and pigeons,” and combined it with the “genetic information and 3D skull measurements from more than 70 bird species.” He said it took more than a year of work to build this platform, which also builds on the company’s years of work in de-extinction.
“The AI learns which regions of DNA are active as different birds develop their beaks and facial structures, and uses that information to predict which genetic switches may have given the dodo its iconic appearance.” He said to think of the platform as a “treasure map for the dodo genome,” where, rather than searching through a bunch of potential genetic differences, GenoMorph can help the Colossal team find only the genetic differences that matter.
“So far we’ve identified approximately 2,300 promising DNA editing targets for the dodo cranial facial morphology that we can now test in the lab,” he continued. He said GenoMorph will help the company tackle one of its biggest bottlenecks in trying to de-extinct animals — finding out which changes actually make an extinct species unique. But Lamm said scientists also need to test whether those edits can create the physical traits they need.
“We’ve developed a new system that uses lipid nanoparticles to deliver gene-editing tools directly into developing bird embryos,” he said. This will help the team see how certain genetic changes impact the development of a bird “without having to wait through an entire breeding cycle that requires birds to reach sexual maturity.”
The company also announced Wednesday that its Nicobar pigeon colony now has 36 birds and that it has successfully created the essential cells that become eggs and sperm.
“Because the Nicobar pigeon is the dodo’s closest living relative, those cells are a critical part of our strategy for creating birds that carry dodo traits,” he said. Next, the company is hoping to prove what GenoMorph predicts in a lab. “What’s most exciting is that we’re reaching a point where the different technologies we’ve been developing are starting to converge together and help other projects we are working on in a completely different part of the tree of life,” Lamm continued.
When asked whether it was safe to edit genes this way, Lamm said the point of developing a technology like GenoMorph is to make genetic engineering “more precise, controlled, and testable.” He said the product doesn’t edit genes itself, but helps their team identify which genetic changes are worth investigating.
“Identifying a potential edit doesn’t mean we immediately introduce it into an animal or assume it’s safe,” he continued. “The more precisely we can identify and validate these changes, the more informed our decisions become throughout the process.”
