Reconstructing the genome of the earliest mammal

Ian Holmes is a brilliant bioinformatics hacker at UC Berkeley (and also an active happy mutant in our BB community). A few years ago, I wrote about Ian's efforts to apply Noam Chomsky's theories about language to the firehose of genetic data spewing from the multitude of DNA sequencing efforts going on these days. Ian just emailed me about his latest research in the mind-blowing area of "paleogenetics." He writes:

Thought you might be interested to know that we & our collaborators recently put together a DNA sequence for the earliest mammal genome, 75 million years old.

Sure, it's full of holes, but it's the first time anyone's done it on this scale!

This whole field, known as "paleogenetics", is really taking off. On the experimental side, you might have heard about the recent sequencing of the Neanderthal and the woolly mammoth.

The cool thing is that you can get a lot of information about ancestral genomes just by crunching probabilities -- even if you don't have any fossils, or mosquitos-trapped-in-amber, or time machines, or whatever.

The even cooler thing (to my bioinformatics-geek mind) is that the algorithms used for this are almost exactly the same ones that linguists use to reconstruct ancient languages, like "Indo-European" or "Gondwanese".

It's only a matter of time before we can actually synthesize these paleogenetic reconstructions. A very short time, according to the Carlson Curves (the Moore's Law of DNA synthesis). Which, of course, has its issues (I am currently trying to reconstruct viruses... no plans to actually synthesize them, I hasten to add...)

Still... I wonder what 75Myr-old mammal meat would taste like? What would be the medicinal properties of ancient herbs? How big were ancient octopi, or spiders? How many genes were in the first bacteria? How long was the first self-replicating RNA sequence?

What would you reconstruct, if you could? Dodo, trilobyte, velociraptor?

David Pescovitz is Boing Boing's co-editor/managing partner. He's also a research director at Institute for the Future. On Instagram, he's @pesco.

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rawbacon2

@9 Amen. Important research and all, but pretty soon we’ll have to synthesize cod.
Let’s concentrate on present day nature. Once stabilized, we can start to play around with t-rex, it’ll be hot enough by then.
buddy66

Good point, funny punch-line.
entheo

I think that we should go for the velociraptor. They would make great guard dog’s for houses abandoned during the economic crash, & I want to train one to use my hoverboard (once they get around to developing those).
David Pescovitz

Anonymous @2, You’re absolutely right. Sloppy mistake on my part. Of course I know the difference between sequencing and reconstructing a sequence. Thanks.
Joe

It would seem that this method of constructing a theoretical ancestral genome would be incomplete, because it could not include any genes that have completely disappeared. If genes were common in the past that became fatal liabilities under new conditions, those genes would be gone.

For example, all currently living Native Americans are, in a way, not representative of the pre-Columbian peoples: almost all Native Americans died from European diseases except for a small minority that had some resistance. Repeated waves of death killed 90%, and then a bit later killed 90% again. It wasn’t random, it was natural selection, and people who survived had something in common. We can’t look at modern-day indigenous peoples to find out why the European diseases were so deadly to their ancestors, because they are descended from the survivors.
Ian Holmes

Urederra @50: empirical = based on data. These are probabilistic reconstructions based on multiple observations of divergent modern-day descendant sequences. So yes, they are empirical estimates. You seem to have a bee in your bonnet, and I’m not sure why.
matt4077

@21: Somewhat correct, but not everything is lost in these cases. Remember that often a single mutation is enough to deactivate a gene. If some gene that makes you susceptible to a disease has mutation A in some people and mutation B in others, it would be inactive in both. Most of the sequence, though, is conserved, and when you assemble a consensus sequence, you get the intact version.
TroofSeeker

Mighten’t there be… remnants, of ancient indegenous, pre-columbian, disease-suseptible home boys? Somebody wanna raise a wild Indian?
Wait.
Maybe they are.
Grab that squint from the DNA lab, Danno!
Nylund

I vote for bringing back the aurochs. The giant ancestor to the modern cow. It went extinct less than 400 years ago.

http://en.wikipedia.org/wiki/Aurochs

2nd choice is the giant sloth. No real reason for either. I just like them.
ridl

entheo @ 19 you inspired me! It’s shitty and rushed (the building in the background apparently suffers from some rare degenerative disease), but here’s a glimpse of teh futures!
Halloween Jack

I wonder what 75Myr-old mammal meat would taste like?

Porkeef!
Modusoperandi

Takuan “the atmospheric oxygen content was higher back then.”
Yeah, and kids didn’t wear such baggy pants back then, neither!
Takuan

the music was better too!
arkizzle

STATLER: Boo!
WALDORF: Boooo!
S: That was the worst thing Iâ€™ve ever heard!
W: It was terrible!
S: Horrendous!
W: Well it wasnâ€™t that bad.
S: Oh, yeah?
W: Well, there were parts of it I liked!
S: Well, I liked alot of it.
W: Yeah, it was GOOD actually.
S: It was great!
W: It was wonderful!
S: Yeah, bravo!
W: More!
S: More!
W: More!
S: More!
Lauren O

All I’m saying is, Ian Holmes’ name is close enough to the guy who played Bilbo Baggins that I think we can do something about combining Jurassic Park and The Lord of the Rings.
- Antinous / Moderator
  
  Or a T Rex in a garden where leeks did grow.
urederra

The cool thing is that you can get a lot of information about ancestral genomes just by crunching probabilities — even if you don’t have any fossils, or mosquitos-trapped-in-amber, or time machines, or whatever.

So, I guess science is not empirical any more.

Oh, computers, they can do so much good for humanity, and yet a bunch of morons decided to use it to create garbage
TroofSeeker

Bring back the Giant Cave Bear.
And the Giant Carnivorous Penguin.
Sabertooth Lion, you best beware!
noen

“I think that we should go for the velociraptor. They would make great guard dog’s for houses abandoned during the economic crash”

Yeah but then they’d want a bailout too.

“What’s that? You’d like to renegotiate your mortgage? Ok, lemme see what I can do… do you have any collateral?”

“Oh…. Clever girl.”
Modusoperandi

Lauren O “All I’m saying is, Ian Holmes’ name is close enough to the guy who played Bilbo Baggins that I think we can do something about combining Jurassic Park and The Lord of the Rings.”
Lord of the Parks? Will Marlin Perkins narrate?
robulus

Oh, computers, they can do so much good for humanity, and yet a bunch of morons decided to use it to create garbage

Hey! That’s my giant spider you’re talking about!
TroofSeeker

Jurassic Shire.
Sean Connery has to narrate because,
wasn’t Marlin Perkins found dead, with a cactus apple in his throat?
Modusoperandi

He’s not dead! He’s just resting.
robulus

Ooh! Ooh! Ooh! Make the giant spiders! Make the giant spiders!
Takuan

you guys are all nuts
http://imagecache2.allposters.com/images/pic/MMPH/28674~Raquel-Welch-Posters.jpg
noen

No giant spiders please, those are all from Mars. I want the giant dragonflies with the two foot wingspan and the IQ of a dog. That would REALLY make the outdoors interesting!
robulus

So we should reconstruct Raquel Welch from “One Million Years BC”? Certainly removes a number of technical barriers.
Chrs

Shame about the “ten foot wingspan” thing, I don’t know of anything over Noen’s commented size for ancient dragonflies.

I know it’s a bad idea, but I still want to bring back the Terror Birds. Ten-foot-tall, hook-beaked death beasts? Count me in!
lisafergogo

#1- I believe you are talking about tiktaalik from “Your Inner Fish.”

I for one would LOVE one of those trilobites with the big horns coming off the top of its head, but I’ll settle for a giant spider if that’s what the group wants.
robulus

but I’ll settle for a giant spider if that’s what the group wants.

YES. That is exactly what the group wants. And I better not hear otherwise, OK? OK?
Modusoperandi

Start with the tastiest extinct animals.
TroofSeeker

Reading Attenborough got me thinking about that first creature to crawl out of the ocean- his name escapes me, but he was the bravest and the greatest pioneer in the history of time!

Afraid to swim out into deeper waters for fear of being eaten, he has changed his flippers to pull himself along soft mud at the shoreline and root around for bits of biomatter, but look! Just look at those bugs over there by the bushes! [His eyes have moved to the top of his head so he can see above the mud] Food galore, ripe for the taking!

I want to build a monument to this bravest of pioneers, this bold mudpuppy, but I’m afraid other Christians might crucify me.
TroofSeeker

The story of Stellar and Bering is quite a tale, and I’d love to see it made into a movie (including the up-to-28-foot Sea Cow). Are you listening, Ron Howard?
Anonymous

Fascinating story, but please change the title because it’s incorrect.

They did not sequence this extinct genome but reconstructed its sequence from the actual genome sequences of extant species (note that Ian writes, “put together”).

“Sequencing” would mean that they had actual DNA from this ancestral mammal, chopped it into bits, fed it into sequencers, and assembled the fragments. This is currently taking place with the Neanderthal genome, but 75 MYA is pretty far.

Thanks.
robulus

Mmmmm. Giant Spider.
arkizzle

Do it Troof!
CammoBlammo

Hmm. They tried recreating the ancestor of all mammals in a Scott Sigler novel once. It all ended very, very badly:

http://www.scottsigler.com/node/952
TroofSeeker

Stellar’s Sea Cow. 35 feet long, tender and delicious! Didn’t last 20 years after Bering’s first taste. I’m a-gonna raise them cows in my seaweed forest.
Takuan

perhaps ten feet shorter. Perhaps the Umi Bozu?
Anonymous

Those who ate Dodo reported it to be the finest tasting bird that could be found. Kinda explains why it went extinct. Sailors rounded them up by the dozens to take with them. Nothing like a fresh food supply on long voyages. Restoring the Dodo would also restore a nut tree that is down to its last member because it only reproduces if the nut first passes through a Dodos gut. They tried force feeding turkeys the nuts in hope that would be a good substitute; but as of last report nothing had happened.
arkizzle

Long Lost Bacon Tree?
oohShiny

Actually, the ability to ressurrect the Dodo might be something we should consider. By all reports they were friendly little buggers — new trade in un-extinct pets, anyone?
Ian Holmes

Noen @10: I’d love to buy an island off Costa Rica, but first I have to pay off the subprime mortgage on my volcano-top lair in the South Pacific.
ornith

@1 as a Christian who believes in evolution – go for it!

@3 if they’re anything like other birds, they’d crap all over your floor, making them not very good pets. But they might make really good meat sources.
arkizzle

Well, dodo is an acquired taste, apparently. So either no one will buy it, or it’ll become a super exclusive, uber-desired rarity.

My advice: Do it, or don’t.
Takuan

`In that case,’ said the Dodo solemnly, rising to its feet, `I move that the meeting adjourn, for the immediate adoption of more energetic remedies–’
Marcel

The one that gives me the creeps over all, and of course, holds my fascination as well, is the giant ancestor of the dragonfly, who, presumably had a wingspan of about 10 feet. They say it must have produced a sound level similar to an approaching helicopter.

Make one, but if they turn out to migrate over oceans and eat human heads, I will contact my lawyer.
Anonymous

Obviously, we should get some dinosaur dna, use our science powers to bring the dinos to life, and put them all together on an island amusement park. What could go wrong?
noen

Please let us know when Ian Holmes buys a small island off the coast of Costa Rica.
ridl

Can we just concentrate on keeping around the few species we have left?
Jesse M.

@7, we could only reconstruct the genomes of ancient creatures which are the last common ancestor of other creatures whose DNA we have, so unless the common ancestor of modern dragonflies (or some sub-group of modern dragonflies) was a giant dragonfly, we can’t reconstruct those giants.

We do have DNA of neanderthals and those Indonesian “hobbits” (Homo floresiensis), so we might be able to reconstruct the common ancestor of all of these, maybe something like a normal-sized Homo erectus or an even earlier form of hominid. And alligators/crocodiles are thought to be the reptiles most closely related to dinosaurs and their descendants the birds, so reconstructing the common ancestor of birds + alligators might result in some weird new dinosaur-like reptile, though probably not a very large one. The common ancestor of all modern cetaceans (whales and dolphins) might also be pretty interesting-looking, maybe a bit like the fossil Dorudon.
buddy66

H. floresiensis. Y markers erectus or sapiens?
Takuan

the atmospheric oxygen content was higher back then.
Brettspiel

Noen, don’t you mean Richard Attenborough (sp?) or are you thinking of another movie?

Wikipedia says the Dodo was probably tough but flavorful. Since the flavor depends quite a bit on what it eats itself, and the dodo was an active forager in the rainy season, subsisting on the plentiful ground berries on the island, I imagine the flavor would be good, though a little tough from all the activity.

Resurrected, fed on corn, and penned to limit movement, I imagine it would be tender and taste like chicken.
arkizzle

Brett Spiel, same movie, but featuring the man above.
Ian Holmes + Costa Rican island == Real Jurassic Park