The Mount Diablo buckwheat, thought to be extinct, was rediscovered in 2005. Photo: Scott Hein / Save Mount Diablo.

This week, QUEST’s Science on the SPOT video will feature the Franciscan manzanita, a plant thought to be extinct until it was rediscovered in San Francisco’s Presidio in 2009. The Franciscan manzanita (Arctostaphylos franciscana) is not the only California plant deemed extinct and then rediscovered. My friend Mike Park, a grad student in Integrative Biology at Berkeley, rediscovered the Mount Diablo buckwheat (Eriogonum truncatum) while hiking in Mount Diablo State Park in 2005.

Mike was able to identify the plant thanks to its pale pink flowers, which were in full bloom; the species hadn’t been seen since 1936.Eight additional California plant species, listed as extinct in 1994, have since been re-found, including the fantastically-named Ventura marsh milk-vetch (Astragalus pycnostachyus var. lanosissimus), the northern adder's-tongue (Ophioglossum pusillum), and the water howellia (Howellia aquatilis).

It can be hard to determine whether a species is truly extinct. The difference between exceedingly rare and really extinct can rest on the lives of just a few individuals. The California Native Plant Society (CNPS) keeps track of plants that are likely extinct in the Online Inventory of Rare, Threatened and Endangered Plants of California. The list of plants thought to be extinct tells the story of land use change in California over the past 150 years. For each of the 29 plants, the possible reasons for extinction are listed: urbanization, conversion of river banks to agricultural areas, wetland modification, mining. Plants with distributions that were confined to the Channel Islands seem particularly vulnerable to extinction. For some plants, like the lost thistle (Cirsium praeteriens), it isn’t clear whether they were California species that went extinct soon after they were first described, or recently introduced European plants that failed to establish in the New World. Many plants on the list, like the hairless popcorn flower (Plagiobothrys glaber), may still be out there in small numbers, but we just don’t know.

To find out whether the plants on the extinct list are really alive and blooming (and whether the plants on the rare list should be shifted to the extinct list), CNPS has started the Rare Plant Treasure Hunt. They match amateur plant hunters with experienced botanists, and provide detailed maps of priority areas and info on plant identification. This is a great project for school clubs, scout groups, and anyone interested in doing some botanizing. And they’re particularly interested in recruiting people with GIS skills (geocaching enthusiasts, that’s you!).

Just because a plant hasn’t been seen in decades doesn’t mean it’s gone forever. It might be growing at your feet; you just need to know what to look for.

37.879329 -122.2463347

Rough-skinned newt. Photo: ap.

The newts are on the move again. Each fall, after the rains start, the newts of Berkeley’s Tilden Park start migrating from the woods to waters of Wildcat Creek, where they mate and lay their eggs. South Park Drive, popular with cyclists and Sunday drivers, crosses their migratory path. Each year from November 1 to April 1 the road is closed to cars, to prevent the newts from getting squished. (How did the newt cross the road? Not by being run over, that’s for sure.)

The newts in question are the California newt, Taricha torosa, brown with a yellow/orange belly, and the rough-skinned newt, Taricha granulosa, which also has an orange belly and, as its name suggests, has rough, brown skin. The newts’ orange bellies are warning signs to predators—both species produce tetrodotoxin, a powerful neurotoxin. However, the rough-skinned newt’s toxin is ten times more powerful than the California newt’s toxin.

Newts lay egg masses, like these, in ponds and slow-flowing streams. Photo: Jennifer Skene.While these two species are not technically threatened, their habitat has been impacted in recent years: their forests and fields have become our neighborhoods, roads have chopped their remaining habitat into fragments, and the streams and ponds where they lay their eggs have been degraded. The least we can do at this point is refrain from running them over!

Newts are amphibians, animals that spend the early part of their life in the water, and their adult life on land. Amphibians are going extinct at an alarming rate; their decline has been referred to as the world’s Sixth Mass Extinction. Habitat destruction is playing a role, but the main problem is an infectious fungus, called chitrid. San Francisco State professor Vance Vredenburg studies yellow-legged frogs in the high altitude lakes of the Sierra Nevada Mountains. He has seen hundreds of frog populations die out because of chitrid. Learn more about Vance’s work and amphibian declines in QUEST’s TV story, Disappearing Frogs, and in a recent New York Times article and accompanying audio slide show.

Chitrid hasn’t affected the newts in Tilden, but the closure of South Park Drive reminds us that amphibians worldwide face some serious threats.

37.883758 -122.228064

Maybe a clone of this guy will wander the Earth one day.A new study shows that scientists can clone a mouse that has been dead and frozen for 16 years. If they can apply what they've learned to a mammoth that has been dead and frozen for over 10,000 years, then maybe my kids can ride a mammoth one day. Or at least my grandkids can.

You Need More than DNA to Clone

Cloning isn't as simple as was shown in Jurassic Park. You can't take DNA and make a clone from it. Instead, you need an intact nucleus. And ideally, an intact nucleus in an intact cell.

The nucleus is where DNA is kept in our cells. The DNA is stored and packaged there in a way that only Mother Nature can do (for now). We can’t take our 6 feet of DNA and cram it into the tiny space of the nucleus.

Cloning 101.As I said, right now cloning uses intact cells. Here's how it works:

1) Take a cell from the animal to be cloned
2) Remove the nucleus from an egg (this is called an enucleated egg)
3) Fuse the two cells and let it divide a few times in a Petri dish
4) Implant the growing embryo into a surrogate mother
5) If everything goes well, a clone is born

This procedure requires living intact cells to be used. The problem with a frozen animal cell is that it is dead and ice crystals have torn it apart. It is not possible to fuse a beat up dead cell with an enucleated egg.

Cloning Using Frozen Cells

What the researchers in this new study did was change the protocol a bit. Instead of fusing two cells, they harvested nuclei from the frozen cells and injected them directly into the enucleated egg.

When they tried to clone the mouse that had been frozen for 16 years this way, it didn't work. But they managed to get 4 clones by adding an extra step. What they did was to make embryonic stem (ES) cells from the frozen mouse and use those cells to make a clone.

Basically they cloned the mouse but then instead of putting the embryo into a surrogate mother, they harvested its ES cells. Then they used the nuclei from these cells to create a clone in the usual way.

So we can now clone a long frozen mouse. The next step will be to try to clone an extinct animal like a mammoth.

Cloning a Mammoth is Trickier than a Mouse

Mammoth cloning will be no walk in the park. First off, we don’t have any mammoth eggs or cells to use. We'll have to use elephant ones. Hopefully, elephant eggs and/or cells will be compatible with a mammoth's nucleus. ( But there is some concern they they might not be compatible.)

Second, elephants are a lot harder to work with than mice. The experiments in this study used thousands of eggs to get a few clones. I don’t know enough about elephant biology but it seems like you'd need a lot of elephants to get that many eggs.

But this is definitely the first step in resurrecting long dead animals. For now we'll have to focus on the frozen ones. Maybe in the future researchers can figure out how to clone animals stored in formaldehyde. Or from pelts. Then we can start reviving species we humans have managed to kill off over the years.

37.332 -121.903