Cirque du Soleil - Totem - Red-Eyed and Reticulate Poison Dart Frogs

I was super-excited to see Totem because A) a friend who saw it in San Francisco raved about it, and B) it's about evolution! How cool is that? Cirque du Soleil says of their latest touring show, "TOTEM traces the fascinating journey of the human species from its original amphibian state to its ultimate desire to fly."

Wait. Amphibians?

Sure, humans (and dogs and horses and birds) evolved from amphibians. But our amphibian ancestors in turn evolved from fish, so you might just as well talk about our "original fish state." And the fish evolved from some kind of worm, which in turn evolved from something like an amoeba . . .

You know what? Let's just start with the origin of life on Earth, about 4 billion years ago. Pedantic scientist that I am, if I were to design a circus show about human evolution, I'd open with primordial soup. Perhaps a human ladder would construct itself from nucleic acids and proteins. Then there would be an aerial photosynthesis act (2.4 billion years ago) in which "light rays" swing down from above and pass their energy to "cells." The show's first climax would be an acrobatic act that grew ever more intricate as more and more performers joined in–the evolution of multicellularity (600 million years ago).

The creators of Totem decided to skip all this and start in media res, with amphibians–who evolved a scant 300 million years ago. However, I'm not exactly complaining, because the amphibian gymnastics are thrilling and their costumes spectacular. I went to the show with a friend who breeds frogs, and she instantly recognized the artists as red-eyed tree frogs and reticulated poison dart frogs. Score one for anatomical accuracy–but for the sake of evolutionary accuracy, I must point out that these are modern frog species, just as "evolved" as modern humans. They were not around 300 million years ago.

By starting with amphibians, though, and returning to the water theme throughout the show, Totem pays appropriate homage to our aquatic origins. Just a few seconds of beautifully orchestrated sound and background video place the audience beside a rushing river in one scene, a quiet pond in the next. And the ocean, ancient mother of all life, is not forgotten.

The show is hardly an evolutionary textbook, but who could ask it to be? Totem is a tribute to the transcendence of human imagination and hard work–Cirque du Soleil at its best. It'll be in San Jose until April 15. Go see the magic that science can inspire.

Crabfish - Sandra Yagi

Have you heard of the Poisonous Fiddlerfrog, whose tadpoles grow up into crabs? Or the Hummingshrew, who eats flies as well as nectar?

These animals aren't real, so you'd only know about them if you've seen Voyage Through a Hidden World. This collaboration between artist Sandra Yagi and writer Julie Benbow is currently on display at The Bone Room Presents in Berkeley. Yagi's hybrid creatures are paired with Benbow's journal entries, written from the perspective of fictional 18th century explorer Lady Lavinia.

Rhinobeetle - Sandra Yagi

Many members of the beautiful bestiary are puns incarnate. Real rhino beetles are large and oddly shaped, but Yagi's Rhinobeetle has the head of a literal rhinoceros. Leafy seadragons in our world are marine fish; the ones on Yagi's canvas crawl on reptilian limbs.

Yagi has always been fascinated by science. "I'd go to Body Worlds and take my sketchbook," she says. "I collect anatomy books." The artist is also lucky to have a personal fact-checker: "My partner works in medicine, so she'll tell me if I get anything wrong."

But aren't all hybrids "getting it wrong" in a spectacular way? In "Zonkeys are Pretty Much My Favorite Animal" (July 31, 2007 Outside), Jon Cohen points out that hybrids "strain credulity–even when they're staring you in the face." They flout the organized structure we've set up to understand nature. And yet real hybrids are more common, and possibly more important to evolution, than most of us realize. Have you ever heard of blynxes? Pizzlies? Humanzees?

But real-world hybrids are always produced by crosses between similar species. Remember the classification scheme you probably had to memorize in high school biology, with humans as an example:

Hummingshrew - Sandra Yagi

Kingdom (Animalia)
Phylum (Chordata)
Class (Mammalia)
Order (Primate)
Family (Hominidae)
Genus (Homo)
Species (sapiens)

A bobcat (Lynx rufus) and a lynx (Lynx lynx) belong to the same genus, and they can make a baby blynx. Polar bears (Ursus maritimus) and grizzlies (Ursus arctos) are also congeners, and can join forces to create a pizzly.

Hummingbirds and shrews, by contrast, belong to entirely separate classes, and frogs and crabs to separate phyla. Anatomical and chemical differences between these pairs are too extreme to allow hybridization.

So fiddlerfrogs and hummingshrews remain confined to our imaginations. Disappointment, or relief? Your choice!

Yeast like these are teaching us how simple evolution really is. Image courtesy of Masur, Wikimedia Commons

Unless, of course, the changes are easier than we imagine. For example, what if it is pretty easy to go from a single celled beast to a multi-cellular one? Or what if you can get increased complexity through easy to come by DNA changes? Then maybe it becomes easier to wrap your head around evolving complexity.

A couple of new studies in baker’s yeast are showing us just how easy it can be to build up complexity. Going from a single celled yeast into a multi-cellular one is pretty easy under the right conditions. And fairly common DNA changes can lead to increased complexity.

Taken together these two studies show us that increased complexity is easier to get than many people think. Certainly simpler than creating a 747 from a tornado in a junkyard!

I won’t have the space to deal with both studies in this blog. So I’ll talk about multicellularity in this one and then tackle the other, more complicated mutation example in my next entry.

How to Make a Multi-Cellular Yeast

In the first study, Ratcliff and coworkers used a very clever technique to end up with multi-cellular yeast. Basically they shook yeast in a big flask and only let those that were at the bottom reproduce.

After just two months, you had these beautiful beasts:

These aren’t just yeast cells stuck to each other either. That wouldn’t really be multi-cellular life.

No, as you can see in the video, these new creatures give birth to smaller multi-cellular instead of reverting back to single celled yeast. Being multicellular is now the default state of these yeast. This is true even when you stop the flask experiment and let them grow “naturally.”

Not only do they give rise to little versions of themselves, but they also have specialized cells within the snowflake cluster. For example, certain cells are willing to die so that the little juvenile snowflakes can separate from mom. No self-serving single cell would suicide like that unless it were part of a larger organism.

So the transition from one to many cells may be simpler than we thought. Which makes sense if current theories about life’s evolution are true. Scientists think multicellularity evolved dozens of times over the last few billion years.

Line up the blocks and help cure a disease!

Yesterday I discovered an online game called Phylo. No, it isn’t about Greek pastry dough. It has more to do with phylogenetics.

Phylogenetics is the study of how living things are related to each other. It takes advantage of the fact that DNA changes slowly over time. So the more distantly related two things are, the less DNA they will share.

You can also learn which bits of DNA are important for life (or good health) by seeing which ones stay pretty constant between various animals. Since these don’t change, they are probably being used for something. And if they get changed in people who have a disease, then they may be involved in that disease.

This is what Phylo is based on. In the game, you are trying to line up the DNA sequences of various animals to figure out which DNA is important and which isn’t. This is a lot harder than it sounds.

While DNA changes slowly, we’re dealing with some pretty long spans of time since two animals shared a common ancestor (i.e. had the same DNA). This means that the DNA can start to look pretty different.

Phylo gives you sets of DNA sequences that haven’t been lined up yet and has you try to line them up manually. Apparently people are still better at this than computers!

Lining these sequences up helps scientists discover which DNA bases are important. It can also give us some basic knowledge about the evolutionary relationship of various animals.

Since DNA sequence might be a little intimidating, Phylo uses colored blocks instead. Each different colored block represents one of the four DNA bases.

In the game, you have a certain amount of time to align the sequences as best you can. You want the fewest mismatches with the fewest gaps.

The game is pretty hard but it is engaging. And you’re doing your bit for science which is always a good thing.

What would make it even better is more explanation about what I am doing and why it is important. This could make the game fun and educational. (I’d also like to see the DNA sequences I aligned but that’s probably just me.)

So give it a whirl and do your bit to help humanity. And have a little fun in the process.

Nice list of top 5 citizen scientist games (Phylo is number 1).

As a hunting bat closes in on a flying insect, its echolocation calls get closer and closer together, and shorter and shorter in duration. The calls, more than 160 per second, give the bat rapid-fire information on the location of its ever-moving prey.

To the human ear, the calls register as one continuous sound. Researchers call it the “terminal buzz,” and until recently, scientists did not fully understand how bats produced it.

Bats use muscles in the larynx to produce sound, just like humans, but scientists had never found a mammal muscle that could turn on and off that quickly.

"You can tap your finger on a table, and you can try to tap your finger as fast as you possibly can," said Andy Mead, a biology graduate student at the University of Pennsylvania. Eventually, your muscles seize up and you can’t tap any faster, Mead said. “You can probably tap five, six, seven times a second if you really try.”

As part of a research team led by Coen Elemans from the University of Southern Denmark , Mead found muscles in a bat larynx that could turn on and off in less than one one-hundredth of a second, firing up to 180 times a second.

"It was instantaneously really shocking and exciting to see yes, this is a very, very fast muscle," Mead said.

The discovery marked the first evidence of a “superfast” muscle in a mammal. Superfast muscles are responsible for the rattle of a rattlesnake and the mating call of the bottom-dwelling toadfish and some songbirds, but the discovery of the muscles in mammals leads researchers to believe they may be more common than they thought. They are also key to the evolutionary success of bats, which are the only flying mammals to use echolocation to hunt.

See the original story from our partners at WHYY.

Additional Links

• Scientific community unites to save bats: Bats are dying at rapid rates of the mysterious white nose syndrome. Learn about efforts in Pennsylvania to study the disease.

By reversing evolution, scientists may be able to transform chickens into dinosaurs one step at a time.

You may remember that in Jurassic Park, scientists sequenced some dinosaur DNA from a mosquito trapped in amber. They made a copy of this DNA, filled in the gaps with frog DNA and then created a dinosaur.

Although cool, we're not likely to get dinosaurs this way in the near future for a bunch of different reasons. The biggest for now (besides not having any dinosaur DNA) is that we can’t clone anything bigger than a bacterium with just a piece of DNA. To clone a multi-celled creature like a dinosaur, we need frozen or even better, live cells.

While this might be possible for some extinct animals including mammoths, 65 million years is just too long to find any frozen or viable cells. But there may be another way to one day create Jurassic Park. By messing with a chicken’s genes.

Current theories are that birds evolved from dinosaurs. This means that all the information for making a dinosaur was contained in bird DNA at one time. The trick is to figure out what this dinosaur DNA looked like and to change bird DNA accordingly and/or to unlock any hidden dinosaur DNA that may still be in bird DNA.

After 65 million years you might think all traces of dino-DNA would be lost in birds. Surprisingly, you’d be wrong. It looks like there is still some T-rex lurking in a chicken’s DNA.

In the last decade, scientists have been able to make chickens look a bit more dinosaur-like by changing how the chickens use the genes they already have. For example, they have been able to make a chicken’s tail look a bit more like a dinosaur’s.

A big difference between birds and dinosaurs is that dinosaurs have much longer tails. But this doesn’t hold up in a chicken embryo.

At a very early stage of development, chicken embryos have what looks like a very reptilian tail with 16 vertebrae. Later in development, though, most of the vertebrae disappear until only five are left.

What this means is that if scientists can figure out how to keep the vertebrae from disappearing, they might end up with a long tailed chicken. And they’ve actually managed to sort of do this already.

By changing when certain genes are turned on or off, they have managed to create a chicken with a tail that has eight vertebrae. Not quite a dinosaur but a step in that direction.

They have also been able to create a chicken with teeth. And even a snout! All of this without fundamentally changing a chicken’s genes but instead changing how they are used.

Now they probably won’t be able to make the chicken-dinosaur transition simply by changing how chicken genes are used. There are bound to have been some significant changes in certain key genes that will have to be replicated to really make a dinosaur. And for that we’ll need to figure out what dinosaur DNA looked like.

But still, we can make a lot of progress towards making a dinosaur by simply using the toolkit of current bird genes. In the end, we’ll probably be able to recreate something very much like a dinosaur. The question will then become whether we should.

QUEST story on how scientists can figure out ancient DNA from modern DNA.

Scientists are redesigning bacteria like these to “speak” a new language.

All living things pretty much use the same language to read their genes. That is about to change.

Scientists in Boston are close to teaching a strain of bacteria a new dialect of the genetic code. In combination with some work done by a different group in 2010, we are now getting to the point where we can actually think about (re)designing life. Which is a big step from what we have been able to do up until now.

The genetic engineering we have done in the past has been pretty crude. We have mostly added pre-existing genes to cells to give the cells new properties or to have the cells make something for us.

So we add a human gene to bacteria so they will make insulin for us. Or we add a gene from bacteria to a plant to make the plant resistant to an herbicide like Round Up. Or we even add two genes to cause rice to make vitamin A like in golden rice.

Now we aren’t always this unsophisticated. We have managed to do some pretty elegant things with genes in mice. There we have tinkered with mouse genes to slightly change how they work or to control how they are expressed.

But these new experiments are different. This is changing the language of life so we can make a living thing do things nothing living has yet been able to do. Maybe this is even the start of intelligent design…

A big reason this is all possible is because nature has given us a very simple template to work with. Not only does the genetic code have just four letters and 64, three letter words, but many of its words also have the same meaning. It is this last point that has allowed researchers to futz with the code.

The researchers plan to teach bacteria a new language by co-opting one of the words in the genetic code and giving it a new meaning. There are two things scientists need to do to make this happen.

The first is to replace all instances of one word in the bacteria’s genes with an equivalent word. Now the bacteria’s genes all still code for all the same things but a word has been freed up so it can be given a new meaning.

The second step is to redefine the replaced word. This will probably be done by mutating the cell’s reading machinery using some pretty well established genetic techniques.

Church’s group has nearly finished the first step. They managed to create four strains of bacteria each with ¼ of all 314 instances of TAG changed to TAA. They are now in the process of combining these four strains in such a way to generate a single strain with no functional TAG’s. After this first step is done (which should be soon), this group of researchers will be ready to teach these bacteria a new language.

An easy first thing they can do is to change the definition of the TAG so it means the same thing as one of the other words. So the TAG will no longer mean STOP but instead will mean Met or Lys or some other amino acid. (The genetic words or codons really just tell a cell which amino acid to put where in a protein.)

Done correctly, this would probably make the bacteria immune to viral infection.* Which would be a boon for the biotech industry as it loses millions of dollars every year because of infected bacterial strains.

This is pretty pedestrian stuff though. The cool thing will be when they redefine TAG as a word that isn’t already in the genetic code. Then we’ll be able to easily create different proteins with properties useful as medicines, industrial enzymes or who knows what else. At least that is the hope.

And this is just one word. There are another 30-40 codons that may be able to be freed up and given new meanings as well.

We are stepping into a whole new area of research. We are retraining life to do what we want. Let’s hope we know what we’re doing…

*This is because viruses use a cell’s machinery to read its own genes. If the machinery changes, the virus will misread its own genes and die.

Sex may have evolved to cut down on genetic variation.

No, I don’t mean in the red light district of Amsterdam or at Mustang Ranch. What I am talking about is the high biological cost of sex. In fact, it is so expensive it can be hard to imagine how it ever evolved in the first place.

The main reason sex is so costly is it takes two parents to have a kid. Asexual creatures can do it on their own.

This doesn’t sound like much of an advantage, but it is. Some computer simulations show that a single asexual individual can overtake a population of one million sexual creatures in about 50 generations. That is about 1000 years for people and only 8 years for mice.

So sex needs to have some pretty big advantages to have ever evolved in the first place. Otherwise the first sexual creature would have been quickly swamped out by all of its asexual brethren as soon as it appeared.

In the past, scientists have pointed to variation as one of sex’s big advantage. This probably isn’t the whole story though. Or even most of it.

Sex does create additional variety through the mixing of genes but it probably isn’t enough to explain the rise of sex. You’d have to live in some pretty chaotic times for this variation to offer enough an advantage to an individual to overcome its cost. Eight or a thousand years just isn’t that long in an evolutionary time scale.

A new review out is bringing up an old idea that Muller came up with back in 1932. The main advantage of sex is to provide a safe time to recombine our DNA.

Recombination is simply the swapping of DNA between two identical (or nearly identical) pieces of DNA. For us that means swapping between the chromosomes we got from mom and dad. So DNA is swapped between our two chromosome 1’s our two chromosome 2’s and so on.

This is where part of that variation we were talking about earlier comes from. But more importantly, recombination actually helps repair DNA damage. You can see the effects of no recombination by looking at our sad little Y chromosome which is slowly disappearing because it has no one to recombine with except itself.

But recombination is a double edged sword. Cells need it to repair their DNA but it can cause lots of DNA damage if it isn’t controlled. For example, even with all of our controls in place, 1 in 1000 humans still ends up with one chromosome stuck to another.

You can see what happens with uncontrolled recombination by looking at cancer cells. These cells end up with extra chromosomes, chromosomes stuck together, and lots of other chromosomal problems because they recombine willy-nilly. They do well for themselves but are definitely bad for the individual.

So it makes sense to contain recombination to some easily controlled time. Sex may have arisen and took over the world because it provides a safer way to keep harmful DNA damage in check. The variation that everyone goes on about may simply have been a beneficial side effect.

After just nine generations, the sexual beasts on the left are already being swamped out by the asexual ones on the right.

See the following for more information:

Muller’s Ratchet
Extra chromosomes and new species

Dr. Rebecca Johnson is a systematic biologist and studies the evolution of color in sea slugs at the California Academy of Sciences.

In the slow paced world of marine sea slugs, a sedentary defense can be the difference between eating and being eaten. With shelled armor, stealthy camouflage or chemical warfare, defense strategies are not only fascinating, but are a potential source of novel cancer and cardiac therapies. Of the 3,000 species of nudibranchs, or "naked-gilled" slugs, many display beautiful, vivid color patterns. These colors warn predators that the slugs are toxic.

Post-doctoral researcher at the California Academy of Sciences, Dr. Rebecca Johnson studies the evolution of color patterning in these brazen beauties. Her specialty lies within a family of 300 species called the chromodorid nudibranchs, which mainly live in shallow tropic waters worldwide.

Chromodorid nudibranch (Risbecia tyroni) Photo credit: Stephen Childs

Most nudibranchs take something from their prey to use as their own chemical defense. For example, the chromodorid nudibranchs selectively feed on sponges and steal toxic chemicals from the sponge originally intended to keep animals from living and growing on the sponge. The slugs redistribute those chemicals throughout their tissues to use for defense.

Species that eat sea anemones and other cnidarians can capture the stinging cells from their prey and store them in their tissues. The aeolid nudibranchs store these stinging cells in cerata, which are long finger-like projections that line the body.

A group of slugs that are closely related to nudibranchs, called sacoglossans, steal chloroplasts from algae prey. Instead of stealing for defense, these slugs steal for energy. They redistribute the chloroplasts throughout their tissues and can actually keep the chloroplasts photosynthesizing. These animals are essentially crawling plants.

Dr. Johnson has been named one of the 16 Rubenstein Fellows by the Encyclopedia of Life (EOL). “I am honored and excited to be a Rubenstein Fellow,” says Johnson. “With this award, I will use the Encyclopedia of Life as a platform with which to consolidate and organize historical data, new research findings, and information on chromodorid nudibranchs that is only found in the scientific literature, libraries, natural history museums, and scattered across the web.  As a fellow, I look forward to sharing the beauty of these animals with a larger audience and to making scientific information about them more widely available.”

In addition to working as postdoctoral researcher at the Academy, Johnson also works with the Gulf of the Farallones National Marine Sanctuary to train tide pool naturalists at Duxbury Reef—a marine protected area in Marin County—and contributes to the Academy’s exhibits and education programs, including a recent display on the Farallon Islands.

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A walrus takes flight to deal with global warming. Image: Monterey Bay Aquarium.

The Monterey Bay Aquarium has a fun new video about climate change, called Change for the Ocean, to go with their exhibit Hot Pink Flamingos. Narrated by John Cleese and produced by Free Range Studios, the animated video is cute, funny, and pretty effective at conveying the fact that people can change their ways much faster than sea life can adapt to climate change.

Though their point is that human behavior can change quickly while animal evolution happens more slowly, the video shows some pretty fast animal evolution. Flamingos grow longer legs in a matter of seconds, and walruses instantly and miraculously modify their flippers into wings. If you weren’t listening to John Cleese as he says “Sadly, animals evolve far too slowly,” you might just get the wrong idea about how evolution works.

Evolution is generally a slow process. But, as humans can ride bikes to work instead of driving in cars, animals can make behavioral changes in response to climate change, too. Some animals spend more time in the shade, or move to cooler habitats. Others do more than just relocate themselves. In response to the heat, the Arabian oryx, a species of antelope, becomes less active during the day, when it’s hot, and more active at night, when it’s cooler. Other animals, through changes in their behavior, can actually change their physiological response to high temperatures The intertidal sea star Pisaster ochraceus takes up cold water into a cavity in the middle of the body—and this mass of cold water keeps its body cool during low tide. Scientists at the Bodega Marine Lab found that sea stars take up extra water when conditions are hot, and can thus maintain their body temperature. These kinds of changes are not evolution in action—rather, these animals are modifying their behavior to deal with the heat.

Like the animals, we humans can change our behavior to deal with a warming world. But we have a second option, which the animals don’t have: we can change our behavior—in big ways—to prevent the world from getting quite so warm in the first place.

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