Topical Tuesday: De-extinction and paleogenomics

Today started out with an 8 mile run, 6 of those miles were at tempo-effort. Near the end of it I saw an older lady walking a cat on a harness around Greenlake. The world is a weird and wonderful place if you wake up early.
This post isn’t about cat-walking. Today I have been thinking about genetic engineering. Discussing genetic engineering is one of the best ways to make people confused, frightened, angry, and sometimes itchy. I’m going to try to avoid blanket statements and dogma.
Genetic engineering in general warrants far more than a single blog post- indeed, the term itself has many different meanings. “Genetically Modified Organism” conjures up images of frankenfoodstuffs and creepy chimeras.

If you were a child of the 90s you know what this is…I didn’t have TV, but Nicktoons still made their way into my consciousness

However, if you, or anyone you know requires insulin, that life-saving peptide hormone was manufactured by a gigantic batch of genetically modified yeast.
My job would be impossible without genetic engineering; in fact, I spend a significant amount of time  manipulating the genomes of the Bacillus strains I work with so that I can ask questions about how DNA replication works.
Hey little GMOs, wanna do an experiment?
The topic is complex, which is why I plan to write follow up posts on genetic engineering and farming, emerging technologies, and what EXACTLY it is I do all day. 
I play with bacteria
Today I want to talk about a new, exciting, and, in my humble opinion, utterly useless and misguided application of genetic engineering: the de-extinction movement.
I learned about de-extinction from this article in the New York Times Magazine. Carl Zimmer wrote another great piece for National Geographic. Several groups (including the Paleogenomics facility at my alma mater, UCSC) are attempting to clone extinct species, and reintroduce them into the wild. I think that this is completely moronic, and that is not just because I was raised on Jurassic Park.

Never forget

These groups are focusing their efforts on resurrecting the Passenger Pigeon and the Wooly Mammoth. They have full genome sequences from both of these extinct species, which they are in the process of assembling and comparing to the genomes of the closest living relatives. The next step is to use next-gen genome editing to engineer an ancient genome from a modern genome by reversing any genetic changes that have built up in the DNA sequence over evolutionary time. Once they have made this synthetic genome, they’re just a hop, skip, and somatic-cell nuclear transfer away from making a chimeric ancient/modern transgenic species. The first filial generation (everybody remember their genetics?) from mating two chimeras will have a 100% ancient genome. Next up: the McMammoth Burger.
In all seriousness, these endeavors are very impressive from a technical and scientific standpoint. It takes a Herculean amount of effort to isolate and sequence ancient DNA; not only does the DNA degrade over time, separating out that degraded ancient DNA from all of the bacterial DNA that is ubiquitous in the environment is no easy feat. Additionally I think that there is a terrific amount of knowledge to be gained from the complete genome sequences of these organisms. Mammoths were supremely adapted to cold-weather living, elephants are not; what genes are responsible? The Passenger Pigeon went from being one of the most abundant birds in America to totally extinct, largely because it could not cope with human incursion into its habitat. Modern pigeons cope with humans just fine; is there a genetic basis to a species’ resilience? Can we use that information to search for traits that may help species currently on the brink? Finally, I think the massively multiplex genome editing technology that this group has developed is amazing! I want to do a whole post on cool biotechnology–stay tuned.
While I think that genetic research on extinct species is valuable and important, I maintain that attempting to recreate ancient species is a collosal waste of human time and capital. These groups claim that returning the Passenger Pigeon and Wooly Mammoth to North America will right ancient ecological wrongs wrought by humankind. Now, I agree that human beings have an unacceptable and unsustainable impact on our planet. It is a travesty that our species has directly caused so many extinctions. 
Never forget
However, and this is a big and conditional however, not EVERY extinction is necessarily a tragedy. Smallpox virus is, for all intents and purposes, extinct on this planet because of direct human action. We are trying our hardest to eradicate Polio right now, and I don’t see any “save the viruses” bumper stickers on the Priuses of Saeattle.
Sarah McLaughlin music just doesn’t feel appropriate for this image
I realize that I am citing extreme examples; I also realize that viruses aren’t necessarily the best entities to make ecological arguments about, given that it’s tricky to define a viral species, and that they aren’t technically alive.  Not to mention the fact that viruses are many things, but they are NOT cute.
Passenger Pigeon: cute.
Smallpox: cute? 
Regardless, it is a simple fact that sometimes lineages go extinct because they are no longer suited to their particular niche–when that happens, they are outcompeted by other organisms. This is called Natural Selection, or “how Cro Magnon Got His Groove Back.” The Mammoth likely went extinct because natural climate variations made conditions on the steppes unsuitable. The Passenger Pigeon was not well suited to sharing a niche with humans. In one case the selection likely had nothing to do with humans, in the other we probably have some responsibility. So is one of these extinctions more tragic than the other? Should we de-fund team mammoth and give their grant money to team bird? Those questions are so irrelevant, Charles Darwin just reached from beyond the grave to slap me upside the head.

The questions we should ask are: 

1)What in the world indicates that a Wooly Mammoth or Passener Pigeon, species that went extinct due to changing conditions, will ever be able to survive in modern  conditions? Are we going to brig these animals back to watch them go extinct all over again? You wouldn’t try and introduce a penguin into the Sahara, I imagine a Mammoth wouldn’t fare so well at modern-day Mammoth Mountain…

“My tusks don’t fit on the chairlift…”
2) What exactly, aside from shear novelty value, will the world gain by the reintroduction of these species?
3) How will introducing these species into the wild impact the current ecological niches? De-extinction would involve perturbing entire ecosystems with novel (ok- the animals themselves are ancient, but they would be new to current conditions) species, how is this any different or morally superior to introducing an invasive pest?

Blackberries: cute, and also invasive
In my opinion, the de-extinction movement is throwing good science, valuable human capital, and scarce research grant money after a pointless and trivial endeavor. As I mentioned before, I think that the genome sequencing and genome editing research is highly worthwhile, interesting, and could potentially yield some important results. These groups could (and should) stop there. Cloning ancient species represents a huge investment of time and effort that could be better directed elsewhere. I won’t even get into the fact that birds and large mammals are NOTORIOUSLY difficult to clone…if you insist on engineering an ancient species, why not start with an easier target as proof of principle. Something with a small genome that grows quickly, like an insect or a fish. The ethical issues surrounding the number of birds and elephants that will likely have to be sacrificed for this vanity project are deeply worrisome.

So, in summary, Sam is pro-ancient genomics, and decidedly anti-de-extinction. I’d love to hear anyone else’s thoughts on ecology, genetic engineering, Mammoths, or if you have any questions. I don’t pretend for one second to be an expert on any of these topics, I’m just a pragmatist at heart, and I like trying to understand an issue from all viewpoints. If I don’t know the answer, I like going and looking things up. If something I have said upsets you, sorry! Let me know, and I want to hear where you are coming from. I’d love to get a discussion going, but if you do comment remember: everyone is entitled to their own opinions (even if they are wrong), if you can’t criticize somebody’s point of view without criticizing the person you aren’t thinking hard enough, and, finally, if you can’t say anything nice sometimes it’s better to not say anything at all.

I had fun writing this. I think the next topic I will cover is genome editing.

3 thoughts on “Topical Tuesday: De-extinction and paleogenomics

Add yours

  1. OK- so I was googling around a little more on this topic, and I realized that some groups already HAVE succeeded in engineering some formerly extinct animals. This Australian group was able to clone the gastric brooding frog, a species that gives birth through its mouth! ( I couldn't find any follow up on whether they have successfully re-introduced the frog.This just reinforces my point that amphibians are easier to clone than birds and large mammals.

    I still think the whole de-extinction movement is silly


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