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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Dowd explores the idea of sin as going backwards on the evolutionary track and that when we are sinning we let the primitive, instinctual, aggressive, fear-driven part of our brain take charge.

Call it the Devil, or evil, or sin, or whatever, something is not quite right in the world. Read a newspaper or turn on the news. Study history. Study your own history. Live life and you’ll find that out. Mystics from all traditions will say that the problem is the way we perceive the world.

Augustine, a Fourth Century Bishop and a Catholic Saint, is credited with conceiving the notion of “original sin”. He found something not quite right in the human mind and human will. But because we have reason, with the help of God, we can chose to do good rather than evil. Julian of Norwich, a Fourteenth Century Christian mystic who lived in Norwich, England, wrote a document describing a series of visions that she had, called Showings or Revelations of Divine Love. Actually, she wrote it about 20 years after she had the visions. She lived in a small room attached to a church. People would come to her to share their problems and pain. She lived through the plague in her town. She would have seen dead bodies in the streets outside her room. But she wrote that sin is “behovely”, or necessary, and that “All shall be well.”

Thomas Merton, a Trappist monk who lived in a Kentucky monastery and died in 1968, thought that life was about recovering our true nature that has been lost. I like this idea of Merton because life, it seems to me, is something like a journey home. As we grow, we can become more comfortable with who we are and less concerned about what others think of us. Paul Tillich, a Protestant theologian and contemporary of Merton thought of sin as separation. We are born separated from our real selves, other people, and God. Modern theologians might add that we also think of ourselves as separated from the Earth and that this sense of separation has led to environmental degradation, species extinction, and perhaps eventually it will lead to our own extinction. Some have called the Devil the Father of Lies. In this case the lie is that we are separated from our best selves, one another, and the Earth.

But what do scientists think about sin? I’ve recently read a book that provided an interesting connection between the biological idea of evolution and sin. The book, by Michael Dowd, an Evangelical Christian, is called Thank God for Evolution. In the book, Dowd explores the idea of sin as going backwards on the evolutionary track and that when we are sinning we let the primitive, instinctual, aggressive, fear-driven part of our brain take charge. We stop thinking and words become weapons; our heart rate goes up and the body releases lots of stress hormones into our bloodstream. Like when we are mad at the person who just cut us off in traffic. We’re not our best selves in these moments, or living as full human beings. And we tend to be selfish and inconsiderate when we’re trying to tailgate the person who cut us off; and we don’t notice the child in the back seat of the other car. Later we might say, “I wasn’t myself”.

(FYI: The Center for Theology and the Natural Sciences at the Graduate Theological Union in Berkeley is sponsoring a two-day event, Exploring the Frontiers of Science and Religion, April 23-24, 2010.)

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"For every five hours of cable news, less than a minute is devoted to science" – Chris Mooney, Author of Unscientific America

Chris has been a lightning rod for controversy ever since he released the bestseller, The Republican War on Science, in 2006. Chris cites some famous stats that scientific illiteracy is increasing: 46 percent of Americans reject evolution and think the Earth is less than 10,000 years old. In his new book, he points the finger at a profit driven media, science phobic politicians, and the arrogance of scientists themselves. (Chris' recent showdown with famous science blogger PZ Myers is widely documented). His main point: this gap hinders productivity and has us falling behind in global innovation.

Then there was the recent Pew survey showing a widening gap between scientists and the public on key issues of global warming, evolution, and use of animals in research. The survey also looked at scientific illiteracy using a 12 question quiz (Take the quiz yourself!) with some surprising results:

• 54% incorrectly identified electrons as bigger than atoms
• 46% thought antibiotics kills viruses as well as bacteria
• 24% failed to correctly a basic question on plate tectonics

But it isn't all doom and gloom, Chris outlines his strategy for closing that gap including sexing up science and training a new generation of science ambassadors in society at large.

Chris Mooney: Unscientific America

When: Monday, August 3^rd 630 PM – 830 PM

Where: Kellogg Auditorium, Silicon Valley Bank, 3005 Tasman Dr., Santa Clara, CA

Time: 6:30 p.m. check-in, 7 p.m. program, 8 p.m. book signing

Cost: $15 members and non-members advance. $20 members and non-members at the door, Tickets

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Scientists used evolutionary theory to figure out where
to find the bones of this fishibian.

What is so great about this book for a scientist is that it gives the big picture on evolution. This sort of thing can be hard to get sometimes because we scientists are so specialized. As I like to tell people, I worked on a single amino acid of a single human protein for my postdoctoral project. For three years.

Coyne's book synthesizes genetics, anatomy, biogeography, physiology, paleontology, geology, and lots of other "ologies" to show how strong the case is for evolution. This is great for me because, of course, I tend to focus on genetics and molecular biology and spend less time on the other fields. Which means I miss important, subtle nuances to some big findings.

For example, I had heard about the fossil of Tiktaalik roseae that was found in 2004 that linked fish to amphibians. This was a huge deal because the animal that the bones came from had characteristics of both fish and amphibians. And it appeared in the fossil record at the right time to be a transitional animal between the two.

What I hadn't fully appreciated was that the scientists decided to look where they did based on how old they thought the fossil should be. In other words, they were able to use the theory of evolution to predict where to find the fossil they were looking for.

They knew from previous fossil finds that something like Tiktaalik roseae would have appeared between 360 and 390 million years ago. The scientists also knew from previous research that the beast would have been in freshwater. So they got out a geological map and looked for places that met these criteria. They settled on Ellesmere Island in Canada and after five years, they found this marvelous fossil.

This is important for a lot of reasons. One is that it obviously tells us a lot about how vertebrates emerged onto dry land. Another is that it provides further validation of geological dating methods. They had to rely on these methods to know where to look for the fossil and the methods worked.

This find is also important because it is based on a prediction made by evolutionary theory. Around 390 million years ago, the only vertebrates were fish. By 360 million years ago, there were four-footed vertebrates on land. So the scientists looked in a place that was 375 million years old.

Scientists used evolution to make a testable prediction that turned out to be true. And evolution came through with flying colors like any good scientific theory should.

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