Meet the group trying to build a Noah’s Ark for threatened species DNA – Morning Brew

As many as 1 million species of plants and animals are facing extinction due to the actions of humans. Thousands of these could be lost in the coming decades.

Some organizations are already working on the technology to make a sort of de-extinction a reality, including the team at Colossal a biotech startup that recently raised $15 million to bring back the woolly mammoth.

And, for its part, the Vertebrate Genomes Project (VGP) is working on a digital Noahs Ark to preserve many of their DNA sequences. VGP aims to collect the genetic information of every vertebrate species on Earthmore than 70,000 individual genomesin the hopes that humans could eventually bring back some of the animals we may push into extinction.

VGP is chaired by Erich Jarvis, a professor and head of the Laboratory of Neurogenetics of Language at The Rockefeller University in New York, as well as an investigator for the Howard Hughes Medical Institute, one of the largest private biomedical institutions in the US.

Since the Human Genome Project began in 1990, the cost of sequencing DNA has dropped drastically and the accuracy has improved, Jarvis told Emerging Tech Brew. While that project required nearly $3 billion, sequencing the genome of a single species is estimated to cost significantly less now. When next-generation sequencing tech became available, the price dropped to about $100,000 per genome, Jarvis explained. Today the process costs between $1,000 and $10,000, he said.

We spoke to Jarvis to get more detail on how far DNA sequencing technology has come, and why the data his team is collecting is so important.

This conversation has been edited for length and clarity.

What is the purpose of sequencing the genome of every vertebrate?

All the information of what makes a speciesall the code, all the instructionsis in the DNA. So if we can save that genetic code nowwithout the possibility of saving an animal or the speciesmaybe 100 years from now (or less, according to Ben [Lamm] and George Church), we can take that genome and resurrect the species. For that reason, our database where were putting these high-quality genome assemblies, we call it Genome Ark. This is an ark thats storing the genetic code of life.

The way we do experiments in the lab is we change something, and then by changing a reaction, we find out how it worked. Thats how we figured out the mechanisms of biology, chemistry, and so forth. We tinker around with things and see the outcome.

Well, nature has done that naturally with millions of species. If we sequence all these genomes of all of life and then create a database of all their different traitsnot just for blue eyes, brown eyes, or height, but for all these species that fly, those that cant, those that live in cold environments, those that live deep in the oceanit will make it easier for us to find the genetic code of the proteins and so forth that generate those traits.

If all these species go extinct that we dont have that genetic code, were losing all of that natural history thats been around for millions of years.

What are the other implications of this data collection process?

Many people, including many scientists, dont realize that even the human genome that cost $3 billion, and many others after it, is like Swiss cheese [and ]has holes in it of missing data, repetitive sequences.

Sort of like pieces of a puzzle, if you have two pieces that look similar, its hard to figure out where in the puzzle [that] goes. And this is the problem when you have repeat sequences in your DNA, and those repeat sequences actually turned out to be biologically important in many cases. This is causing many scientists to have errors in their scientific analysis, and many experiments to be actually done in a misinformed way because of having inaccurate or error-prone genomes.

Another error we were findingeach cell in our body has chromosomes from mom and dad. You get half your DNA from mom. You get the other half from dad.

What were finding out is that in a lot of genome assemblies, the sequences from mom and dad were so different that some of the computer algorithms were considering them as two separate genes, as opposed to moms version and dads versions.

Were finding thousands of [these false duplications] in the older sequencing. So people were mistakenly adding 5,000 or 6,000 genes to the genome as extra copies of various different genes, which werent true.

The implications of adding more genes that are false is that people start studying these genes that are really just divergent from each other and not two separate copies. And they make false conclusions about the evolution of the genes, false conclusions about the differences in the biology from one copy and another. Its just terrible.

How much progress has VGP made?

Back in 2017, we started producing this high-quality genome data. For vertebrates, we decided to do what we call all orders of vertebrates. Species are classified into orders, family, genera, so we take one species, like a parakeet that you buy in the pet shop, representing all 300 parrots, representing the order of parrots. A human and a chimpanzee representing primates...

Were halfway through the 260 [species that represent all vertebrate orders].

How have you seen this technology change over time?

[The VGP has] worked with all the major sequencing technology companies, tested out all their different protocols. We scientists and academia pulled together the technology of various companies and made a hybrid. The hybrid technology is whats giving us the highest-quality genome data to date. We spent about five years developing the best technology, and its continuing to develop. Were not perfect yet.

We had two breakthroughs. One breakthrough is that the enzymes that were reading the genetic code and then making reactions that the computer detects sometimes would make it wrong. They wouldnt get the G right or wouldnt get the C right. So itll call a G a C or vice versa. And so its making these mistakes we dont like. So the enzymes have gotten better in not making mistakes.

Then the technology plus the enzymes have gotten better at the length of the DNA thats actually read into the computer. So there isnt any technology out there that can just take a chromosome and read through the entire 10 million base pairs without errors or just as one large chunk. You have to chop the DNA up into pieces, sequence each piece and then stitch it back together in the computer.

Its like taking something, throwing it on the ground, breaking it into pieces, and then trying to put all the pieces back together. The bigger the piece, the easier it is to figure out how to put it together. We call it long-read technology, and thats a big improvement.

How long do you expect it will take to actually de-extinct a species?

Id be surprised if [Colossal generates] a woolly mammoth in five years. But I do think the day will come where we can, based upon the DNA sequence alone, resurrect a species.

There is a saying that applies to the time you automatically think it will take to complete a project: You tend to overestimate what you can do in two years and underestimate what you can do in 10 years.

Lets say in 20 to 50 years from now, something like this might be done. Ten years ago, I never thought that Id be leading an international project to sequence the genomes of all species on the planet, of all life. Or even think that I could do it in my lifetime. Im an ambitious person, but I have some practicality as well.

What would you say to people who might question if bringing species back is a good idea?

One answer I have to that is its just for our own survival. If enough species goes extinct, well go extinct, too. Well do self-extinction, even without nuclear bombs.

Were starting the sixth mass extinction, and its humansnot a meteorite or something else. We are responsible for the extinction and the coming extinction of many species, so I think we should be responsibleif they goto bringing them back.

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Meet the group trying to build a Noah's Ark for threatened species DNA - Morning Brew