The dream: just one shot

We are engaged in an arms race with the flu virus, but we have a secret weapon hidden in our DNA.  We can make antibodies that neutralize a bunch of different flu variants.

Viruses are little packets of DNA cloaked in proteins.  We make antibodies that target the outer protein shell, flagging the virus as an invader to be destroyed.  In the arms race, viruses evade detection by making constant changes to that outer coating.  But not the whole coating, just a piece of it that is referred to as the “head.”  We might gain a foothold in this race because the flu keeps the same “stem” region across many of its flavors, including H1N1 and the much-talked about H5N1 (avian flu).  In response to the pandemic 2009 H1N1 infection, some people made broadly neutralizing antibodies directed against that stem region. We all have the gene to do it; the trick seems to be finding the right immunogen to show to the immune system.  The seasonal vaccines we get at the doctor’s office haven’t been able to elicit such a response, yet, though people who have been exposed to many flu vaccines are more likely to have broadly neutralizing antibodies.  So all those shots you got weren’t for nothing.

Research is bringing us closer to that dream of a universal flu vaccine.  It’s been making headlines in the big journals this month. A paper published in Nature this week shows what makes for a good universal antibody and how the immune system needs to display it.  A paper in Science Express earlier this month found that people can make broadly universal antibodies that target both influenzas A and B.  If all the pieces come together, it could be the end of annual flu vaccines for future generations.

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Watching the world go by

Stingless bees live in dense tropical forests with canopies that reach over 40 meters (130 feet) high.  Lush as tropical forests seem to us, competition for resources is tough if you’re a bee.  When they find new food, they keep going back.  And they’ll bring friends.  How do bees remember where they found that last tasty morsel in a vast three-dimensional world?

Honey bees use a “visual odometer”, which gauges how far they’ve traveled based on the flow of images across their visual fields.  New research by a team from UCSD shows that the distantly related stingless bee does, too.  By papering stripes on the inside of tubes, which contained feeders of unscented sugar water, the researchers were able toy with the stingless bees’ visual odometer.  As the bees fly through the tubes, they see alternating black and white stripes.  Seeing the stripes pass by, the bees learned exactly how far into the tube they had to fly to find sugar water.  Once they were all trained up, the researchers altered the tubes and looked to see how the bees navigated. By varying stripe width (and therefore the number of stripes bees pass by on their way to food), they confirmed that stingless bees don’t count stripes.  Rather, they rely on their visual odometer, which tracks how fast the world passes by to estimate how far they’ve flown.  That visual odometer breaks down when the stripes run the length of the tube and their world looks…exactly the same.  Making the tube narrower or wider messes the bees up in a whole new way: the bees perceive the stripes moving at a different rate, and they navigate accordingly- going either too far, or not far enough.  Lastly, the researchers found that stingless bees use their visual odometer to measure distances in all three dimensions, not just laterally from the nest.  A good thing for bees that live in the forest’s understory.

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My lemonade’s only half done.  Tell me more about these stingless bees!

Stingless bees don’t do the “waggle dance” like the honey bee.  They have their own form of communication: they jostle, vibrate, and make noises to share information with the colony.  Most of the information seems to be on the order of:  “I found food!  It’s super sweet!  And close!”  Not “go here for food.”  For the purposes of guiding hive-mates, they leave scent trails that can last about 10 minutes and they lead expeditions back to new food sources.  Stingless bees and honey bees are distantly related, though the stingless bee is much older, with the oldest known fossil dating back 80 million years.

References:

A stingless bee can use visual odometry to estimate both height and distance.  Eckles MA, Roubik DW, Nieh JC.  The Journal of Experimental Biology, Sept 15, 2012. doi:10.1242/jeb.070540

Signals and cues in the recruitment behavior of stingless bees.  Barth FG, Hrncir M, Jarau S. Journal of Comparative Physiology, 2008.  DOI 10.1007/s00359-008-0321-7

Image credit:  David Cappaert, available under CCL.  Source:  http://tolweb.org/Apinae

Let the musical (r)evolution begin

The noise was fit enough to reproduce, so its genes were passed on to its daughters.

Can we use the scientific method to understand how music evolves?  Evolution, with all the trappings of tenth grade biology: heritable traits, genetic recombination and mutation, and survival of the fittest?  To find out, scientists in London and Japan wrote DarwinTunes, a computer program that applied the tenets of evolution to 8-second loops of computer-generated noise.  Then they watched as popular choice turned noise into music.

The noises were assigned a “genetic code” that could be shuffled around and mutated, much like our DNA.  Thousands of people voted on how much they liked (or hated) the noises.  The best loops were allowed to “reproduce,” or pass on their traits to the next generation.  Then people voted again.  This cycle went on for more than 2500 generations.  Through this process of (quasi-)natural selection, the researchers found that music quickly came from noise, complete with western rhythm and chordality.   You can listen to the evolution for yourself, here.

But then it stopped evolving.

Computer simulations aren’t the only place that musical change has plateaued.  It’s happening in real life, too. Scientists in Spain analyzed almost half a million popular songs recorded from 1955-2010, looking for changes in pitch (harmony, chords, melody), timbre (instruments used), and loudness (not how loud you blast it in your headphones, rather intrinsic loudness).  They analyzed these three traits within songs and across time.

The results are in.  If you grumble every time you turn on the radio, prepare your soapbox.  Newer songs basically sound the same, with simpler chord progressions and less instrumental variety.  Not only is this uninspiring to listeners, it could prove problematic for song recognition programs.  As for what has changed:  everything keeps getting louder.

Maybe social media will save us.  Yes, popular songs have the same ring.  But we have an Internet full of digital music.  As people explore and share songs that fall outside of this homogenous norm, we will probably see musical evolution pick up again.  Which gets back to the role of the audience in shaping new music.  As the creators of DarwinTunes point out, the line between audience and artist is easily blurred in our digital day and age.  Digital music allows people to tweak and re-share the original piece.  Audience-induced mutations could introduce a selective advantage that evolution just might favor.  Or, put more simply, seek out music that’s different, and mix up the stuff that’s not.

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Photo credit:  Mark Runyon/ConcertTour.org

Original Papers:

Evolution of Music by Public Choice.  MacCallum et al.  PNAS July 24, 2012 vol. 109 no. 30 12081-12086

Measuring the Evolution of Contemporary Popular Western Music.  Serra et al.  Scientific Reports 2, Article #521.  July 26, 2012.  DOI:10.1038/srep00521

The (soil) cycle of life

Decomposition is a great housekeeper: it takes care of dead plants and animals by breaking them down into simple molecules.  A variety of fungi, insects, worms, and bacteria are involved in decomposition.  The end result is that nutrients are returned to the soil for use by the next generation of plants.

Decomposition is important for maintaining the ecosystem, because there is a finite amount of matter in the world.  Think of it like a bunch of Legos: you can build a whole town, but then all your bricks are used up.  To build something new, you have to take apart the cars and buildings that you’re done playing with.  Then you can build something else with the freed-up pieces.

If you live in a town or city, you might not think about decomposition very often.  But out in the woods, you can’t miss it.  You’re often tromping on a thin layer of dead leaves that are square in the middle of being decomposed.  It’s long been thought that the main factor affecting the return of nutrients to the soil was simply how many plants were around to be decomposed.

Turns out it might be more complex than we thought.  In a study published in Science on June 15th 2012, Dror Hawlena, a post-doc in the Schmitz lab at the Yale School of Forestry, and his colleagues show that the rate of plant decomposition is affected by the predators in an ecosystem.

And it’s not because predators are eating the plants.

Hawlena and his colleagues stressed grasshoppers by raising them with a natural predator: a spider, but one whose mouth was glued shut.  The grasshoppers were under the impression that they could be dead at any minute.  Grasshoppers lived their lives, with or without the spiders present, died, and decomposed by the hand of microbes in the soil.

When prey animals, like grasshoppers, feel their lives are in danger, they want a constant supply of ready energy in case they have to make a break for it.  So, they eat more carbohydrates and break proteins in their bodies down into sugar.  While these behavioral and metabolic changes give the grasshoppers energy, they also alter the chemical composition of their bodies.  Carbohydrates have lots of carbon and not a lot of nitrogen, and the proteins that they dismantled were loaded with nitrogen. The combined effect of these changes is that stressed grasshoppers have a higher carbon-to-nitrogen ratio than unstressed grasshoppers.  Dead grasshoppers become part of the microbial diet.  True to the old adage, “you are what you eat,” that carbon/nitrogen imbalance is passed on to the microbes.

When the researchers piled dead grass on top of the soil where the grasshoppers had been, they found a surprise: microbes that broke down stressed grasshoppers were 200% less efficient at breaking down the grass.  The reason this is so surprising is that there was only a 4% difference in the carbon-to-nitrogen ratio between stressed and unstressed grasshoppers.  That small difference in body chemistry exploded into a huge effect on the rate of plant decomposition.

So, microbes eating stressed grasshoppers get less nitrogen.  Nitrogen is what microbes use to grow and to make the enzymes that break down dead plants.  Less nitrogen in the microbial diet probably means fewer microbes and fewer digestive enzymes in the soil, hence slower decomposition.

This doesn’t mean that we should mount a campaign against grasshopper stress.  Nature has a way of finding the right balance when left to its own devices.  But humans have a way of mucking with nature, so we need to keep in mind that the endangerment or extinction of high-level predators could have a ripple effect on the entire ecosystem; one that reaches deeper than we originally thought.

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More reading:

Fear of predation slows plant-litter decomposition. Science. 2012 Jun 15;336(6087):1434-8.

Headbutting fish

In the wild, male animals use headbutting to defend their territory, among other things. We have always thought of land animals, like bison and rams, as the ones that headbutt.  Now we know that fish do it, too.  Specifically, the giant bumphead parrotfish.

The bumphead parrotfish was named for the giant bump on the front of its head.  Turns out they also actually bump heads under water. You can see them doing it here:

Bumphead parrotfish headbutting

It’s hard to tell from the pictures, but these are huge fish.  They can grow four to five feet long and weigh 100 pounds, making some of them as big as a 13-year old.  They are also a potentially endangered species (PDF).  Their lifestyle makes them easy targets for overfishing: they hang out in groups in shallow water, where spearfishers get them.  The fish have learned, though, and are now skittish of humans.  It’s hard to know what they do when no one’s watching:  there aren’t many of them around, and when do we find them, they quickly swim away.

There are a few marine areas where bumphead parrotfish are protected.  In these areas the fish still thrive, and they don’t know to be afraid of people.  It was in one of these areas that scientists first heard, and then saw, the fish headbutting.

People thought that the fish use their heads to bump into the reef and break off chunks to eat.  However, the bony plates on female heads are not as big as the ones on males, and the females have no trouble eating (you can see a picture of the male/female difference in the original paper).  Now we may know what those plates are really used for:  a mating ritual, and territorial defense.

Headbutting aside, the bumphead parrotfish are thought to be gentle giants.  Their diet mainly consists of coral reef. In fact, they are the biggest plant-eating fish on coral reefs. Being so big, they can eat a lot: up to five tons of reef each year, per fish.  No other fish eats that much reef, and without the bumphead parrotfish, the reef would just keep growing.

The scientists observed the fish in the video at Great Barrier Reef off the coast of Australia, where are still plenty of bumphead parrotfish.  The fish eat the reef as fast as it grows. Without them chomping away on it, the whole reef would change, and probably for the worse: the reef would get too big and become unstable.  Also, different species would move in.  This would disrupt the ecology of the entire reef system.

The scientists’ discovery was a surprise benefit of bumphead parrotfish protection.  Not only is the reef healthier, and the fish are surviving, but we’ve also learned something totally unexpected about fish. And that’s what science is all about!

Note:  This is my the first “Family Day at The Beach” post.  Try sharing it with kids.  I’d love to hear what you think.

Image credit:  http://underwater.com.au/image/id/9476/

Please pass the science

I was once a high school science teacher. From there, I found my way back to the lab, and then into graduate school, and now I suppose I’m officially a scientist.  However, seven moves later, I’m still carting around boxes of my old teaching materials.

As they follow me, so too the question: how do we do a better job of educating students in science and math?

The Program for International Student Assessment, or PISA, is a test given every year to 15-year olds around the world.  Students are tested for math, science, and reading competence.  The US is not kicking butt.  In 2009, we ranked 31st in math (below average) and 23rd in science (about average).

Being number one on tests like PISA may come at a cost, such as a more structured and rigorous childhood.  When I was young, I had the freedom to just be a kid.  My childhood involved healthy doses of goofing off, reading, playing, and being bored.  At least that’s how I remember it.

But I was also part of a family that prioritized learning.  As early as first grade, my parents installed a desk in my bedroom, so that I would have a special place to do homework.

I couldn’t wait for my first assignment.

Kids love learning things.  Parents of young children realize this, and take time to teach their kids about the world.  When those same kids go off to school, there is no torch that gets passed from parents to the teachers that relieves parents of the responsibility to educate their children.

So I’d like to throw my two cents into the “how to improve science education” debate: talk about science at home. Let your kids be makers, or scientists in their own right.  You don’t even need to buy a chemistry kit, if that sounds scary and explosive.  Early scientists started out observing the world with basic, if any, equipment.

In case you are about to protest that you are unqualified (perhaps you were die-hard humanities major): you don’t need to be a scientist to encourage science. There is a lot of cool science out there for both kids and adults to love.  Science can have a place in anyone’s home. To that end, I’m going to give a shot at writing a few columns aimed at parents and kids.

In keeping with the blog’s theme, I’ll call it “Family Day at The Beach.”  My hope is that a good post might fuel a family dinner conversation.  My babbling baby is too young a test subject for this idea, and it could be a total flop when he gets to be old enough.  My son will probably be running the dinner show as soon as he can string together a few sentences. I won’t be able to get a non sequitur in edgewise.

How else will I bring up headbutting fish?