Particles of Thought

HAKEEM:

So, let's do two things now. Let's define some things for our audience. So, the two things that I want to define or describe from you. One is what does it really mean to de-extinct and the second thing I want you to get into is how do you do it. What's happening in the lab?

BETH:

How long is this podcast?

HAKEEM:

As long as you want it because I'm interested. How often do I get this opportunity? I got Dr. Beth Shapiro, I'm asking ... I want to know.

BETH:

So, our goal with de-extinction is to be able to create versions of these extinct species that are able to thrive in habitats of today that resurrect using DNA, using ancient DNA, extinct traits. And by creating these extinct species, by bringing extinct species back to life, our goal is to restore missing ecological interactions so that we can make ecosystems more robust and more resilient. So, Romulus, Remus and Khaleesi, we intended to bring back traits including the size and the musculature and we really liked the light-colored coat. We didn't know that dire wolves were light-colored until we sequenced the ancient DNA and were able to see in the sequence of their DNA that the animals whose genomes we'd sequenced both had light-colored coats. And this is actually a really important way of really showcasing how we are concentrating on de-extinction but also on animal welfare.

So, we knew that we wanted to make these light-colored animals. The gene variants that were in our ancient dire wolf fossils were in a gene that, in modern gray wolves, if individuals have variants in those genes, they can sometimes be blind or deaf. It's not the same variant that we saw in the dire wolf fossils but it's in the same gene and we thought that's a little bit risky. But since our goal is to bring back phenotypes, we know that we can make a gray wolf background into a white animal because there are white gray wolves today. So, we will use those variants to bring back, to de-extinct this dire wolf light-colored coat and, in this way, we are ensuring that we are bringing back, we are de-extincting dire wolf traits in the safest, most ethical way possible. So, how do we do it? Okay.

HAKEEM:

Wait, wait, let me ask a question about that. So, I've heard this with respect to the human genome but you can map specific physical characteristics to specific genes and you can say, "Okay, this particular gene," for example, light skin occurring in humans and anatolia or something like that, we know what gene created that. So, is it the case that you take a existing genome of, say, a gray wolf ... Oh, you know what? I'm getting to the question I'm about to ask you and then you say, "Okay, let me add the particular genes that give me the dire wolf characteristics to that existing one." Or, do you say, "Hey, I have this incomplete dire wolf DNA profile and let me fill in the gaps with living gray wolf." Which ...

BETH:

You know what? That is the Jurassic Park versus the way we're actually doing it conversation which you had said. So, I think that's why people are confused because Jurassic Park, which can I just remind everyone who's watching right now that Jurassic Park was not a documentary, that this was a science fiction. I think sometimes people get a little confused and they think this is what we're doing. And I'm also going to admit that I am an ancient DNA scientist who has attempted to extract DNA from insects preserved in amber and the hardest ... Of course, I did. And the hardest part about that was actually smashing the amber because it's so sticky. I had to freeze it really hard and then take a sledgehammer and whack the crap out of it so it would shatter and then try to find the pieces with the ... Anyway, there is no authentic insect ancient DNA or authentic dinosaur ancient DNA in amber.

HAKEEM:

Got it.

BETH:

Amber's actually a really bad material for the long-term preservation of DNA because it forms in really hot places and that's terrible for DNA preservation. It's also super porous so microbes can get into those pores and they'll just chew up the DNA that's in there and that is also terrible for DNA preservation. The oldest DNA that has been recovered so far is from mammoth bones that were preserved in Siberia, in permafrost, frozen dirt. So, the bones were defleshed probably by predators and then buried and then frozen solid and they are probably around one to two million years old which is really old. Most of the DNA we have dates to within the last 50,000 years or so. There's actually DNA that's been isolated from dirt, directly from sediment from Greenland-

HAKEEM:

Yeah, I saw that, yeah.

BETH:

... from a place called Copenhagen which is potentially slightly older, Pliocene in age, just before the ice ages started. It's really hard to know exactly how old things are around that time point but that could be the oldest DNA. Still, dinosaurs have been extinct for more than 66 million years and so we do not have DNA that is that old. So, in Jurassic Park, they got dinosaur DNA, which isn't possible, out of amber, which doesn't have DNA, and they pieced it together and then they saw that there were holes in this, not surprising, giant holes as in none of it was real but we're going here because this is the thing, it's a movie. All right. So, these things were there and then they thought there are holes in DNA, I'm going to use frog DNA to fill in those gaps which was a weird choice even then because we already knew that birds are dinosaurs but, whatever, frogs shoved in the middle and that meant that somehow they turned into girls. Is that what happened? I can't really remember the beginning.

HAKEEM:

Something like that, yeah, yes.

BETH:

Anyway, yeah. So, set it up, this is how it had to happen. So, now, when people imagine what we're doing, they're thinking, oh, you're going out, you're getting these DNA sequences directly from these bones and you're somehow holding onto them maybe with a really tiny pipetter and then you have another one with another tiny pipetter and you're super gluing those things together and you still can't do it. And it's not going to work, the DNA is broken in a way and it's also really hard. We actually have a much easier way to be successful doing de-extinction. Think about the mammoth project, for example. We know that mammoths and Asian elephants, that's their closest living relative. Hey, fun fact, mammoths and Asian elephants are more closely related to each other than Asian elephants and African elephants are related to each other.

HAKEEM:

Whoa.

BETH:

All right. So, we have mammoths and Asian elephants that are only about five million years diverged from each other, that means that they share a lot of their DNA. In fact, they share more than 99% of the DNA sequence between them, they're identical to each other, somewhere around 99.5%, depending on how you count. Which means, if you want to change an Asian elephant into a mammoth, that is a lot easier of a task than piecing together a mammoth by taking little, tiny fragments of DNA with little tiny tweezers and shoving them together which is also impossible. So, now you have this great, great shortcut that you can use where you can start with Asian elephant cells growing in a dish in a lab and you can use the tools of genome editing. The most famous one that most people have heard about now is CRISPR because it allows us some really nice precision to be able to make these changes.

And then, if you can think about it like this, gradually go in and cut out the version of the elephant DNA and paste in its place the mammoth version. So, we're cutting and pasting our way to a mammoth starting with this template that is already 99.5% mammoth. So, that is way easier than piecing it together.

HAKEEM:

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So, here's a question now. So, is this DNA manipulation happening outside the context of a cellular nucleus? It's free floating in some medium?

BETH:
No, it is happening in the nucleus of living cells that are growing in media, in a dish in a lab, yes.

HAKEEM:

Okay, I see.

BETH:

But we've missed a really important part that you actually highlighted earlier which is how do we know what to change. Being 99.5% the same is great but that 0.5% difference is still a lot of genetic differences between a mammoth and an Asian elephant. And we can't make hundreds of millions or tens of millions or even millions of changes right now, the technology isn't there yet. It will get there eventually but we're not there yet.

HAKEEM:

So, you're limiting the number of changes you can make.

BETH:

We're limited. And at Colossal, we're really trying to push the limit of that. How many edits can we make simultaneously, can we cut and paste large pieces of DNA maybe even to the scale of whole chromosome arms at some point so we can make lots of changes at the same time. Because, every time we go into that nucleus of the cell with the machinery that we need to make the edits, we stress that cell out and the cell has to be able to recover after that before it can do something else. So, we have to focus on keeping cells healthy, on maximizing the number of changes we can make at the same time so that the number of times we stress out the cell can be really limited. So, these are all the technologies that we're pushing forward here. And, I like to point this out, as we make these changes, as we figure out how to do multiplex genome editing which is just making lots of changes at the same time or replacing whole genes, these are technologies that can be immediately applied to human health, to animal health.

Once we figure out how we can edit birds and pass those DNA changes down between generations of birds, we could do things like modified genomes in Hawaiian honey creepers so that they can be resistant, resilient to avian malaria so that these species may not become extinct. These technologies are critical tools in what should be an advanced toolkit for biodiversity preservation and those tools are being developed right now on the path to a mammoth and a dodo and a moa and a thylacine. And to me it's such an exciting environment to be part of but we still haven't gotten to a very hard thing that you pointed out at the beginning which was how do I know what to change and that is where these ancient genomes come in handy.

So, we can go out into Siberia and we can collect hundreds, thousands of mammoth bones and extract DNA from them and piece together, using these tiny fragments and computers, sequences of mammoth genomes and we can compare all of these to each other and compare them to elephant genomes and ask where are all the mammoth genomes the same as each other but different from elephants. Because if they're the same as each other, then that means that they're probably important to making them a mammoth. You and I, for example, share a lot of our genomes, 99.9 blah, blah, blah, blah, blah percent because we're both anatomically modern humans. We're pretty much identical genetically, right?

HAKEEM:

Yeah, yeah.

BETH:

But you could compare our genomes to Neanderthals and to Denisovins, the other archaic homonin that's our cousin that has a genome sequence that's been ... And you could ask where are we the same as each other and different from them and that will start to narrow it down what it is that makes all of us, what it is that makes anatomically modern humans distinct as a lineage.

One thing we can also do there that's very useful for us is we can look at where you are different from me and where we are different from anybody else that we encounter and we can say those aren't important changes to being a human because they're not shared by all humans so we can throw those out. That is important because that means we can throw out a whole bunch of places in the genome where the mammoths are all different from each other because those aren't things we have to change, we know that they're not important to making a mammoth a mammoth.