Dolphins, Sharks, and Whales: Adventures in Biodiversity

“Space is the last great frontier.”  Space is indeed spectacular, but maybe not the last frontier of discovery, especially when completely new species pop up with some regularity on your own planet.  Due to an inability to grow gills, humans have yet to sprawl into the ocean, so many of these new species are water-dwelling, surprisingly big, and good at hiding.  A few of these new species we are newly distinguishing from their neighbors, and others we’ve just gotten to know.  But these sharks and squids and jellyfish have been here all along, and are now rolling their eyes at the uninformed humans.  Here are some quick introductions to our newly-identified global neighbors.

The half snake, half two-ducks-in-a-costume creature you see waddling around in the video above is a new species of walking shark, also known as carpet sharks.  Named Hemiscyllium halmahera, it was discovered off the coast of the eastern Indonesian island of Ternate, the 16th member of the Hemiscyllium walking shark genus.  This species is a mini version of its relations- on average 12 cm smaller than the 40 cm length of other species- and has distinctive snake-like dark bands running down its back.  The nocturnal members of the genus Hemiscyllium prefer shallow, warm tidal pools, which have one major drawback as a habitat.  As the pools are cut off from the ocean at high tide, any resident Hemiscyllium gradually use up the available oxygen, leaving them in a state of extreme oxygen depletion, known as hypoxia.  They have evolved to survive until the tide comes in by carefully regulating blood flow, even ‘turning off’ – reducing the metabolism – of some areas of its brain.  For an animal that looks like a cartoon creature come to life, that’s quite a talent.

Read the rest of this entry »


Human Minds Vs. Large Numbers, Round 2

Meet Bob. He’s in his late fifties, a quiet guy, wears rimless spectacles, and likes to read poetry. Do you think Bob is a classics professor or a truck driver?


If you answered classics professor, you’re with the vast majority of people asked this question. Quiet, spectacles, poetry reader, all of it pretty well fits the common image of a classics professor and not so much our image of a truck driver. But while there are approximately 7500, maybe at a stretch 10000 classics professors in the US, that number is blown out of the water by a couple orders of magnitude when compared with how many truck drivers there are. The American Trucking Association’s website says there are 3,500,000 truck drivers in the country, making it much, much more likely that Bob is a quiet, poetry-reading truck driver. He may not fit the NASCAR-loving truck driver stereotype, but it’s still more likely.

It’s much more likely, but that’s not the way we think. Humans look for patterns, make categories, and form stereotypes in order to make sense of the world. If our early ancestors heard a scream, they did not sit down to calculate the probability that their friend Og had trod on a surprise thorn bush versus the probability that Og had just been snack for a saber-toothed tiger. No, they used their learned pattern of scream = bad and got the hell out of there.

Read the rest of this entry »

Human Minds Vs. Large Numbers

Imagine 70 sextillion of these.  Got it? Ok, that's an estimate of how many stars are in the universe.

Imagine 70 sextillion of these. Got it? Ok, that’s an estimate of how many stars are in the universe.

A few months ago I was playing with my cousin’s kids at a beach- sandcastles and kicking sand and burying feet and the lot. One of the two was three and a half, the other one and a half. Their mother came down with a new set of sand toys and we all got excited. “Do you know which one of these sand toys looks like an animal that doesn’t exist any more?” I asked.

Ellie, the younger one, pointed to the sand toy in the shape of a penguin. “Are you being mischievous?” I asked. “A world without penguins would be a sad one!” I got a seriously blank look in return. Then it hit me- they had no idea what mischievous meant. Time to talk little-kid. “It’s the dinosaur,” I said, “all of the dinosaurs died out a long long time ago.”

“When I was a baby?” Abby asked, the three and a half year old. Uh-oh. No concept of time or numbers, either. “No,” I said, “a long, long, long, long, looooonnnng time ago. Before you were born.”

Read the rest of this entry »

A Gift From A Steamship, or, Why We Can Still Get Good Wine From Europe

The southern Rhone Valley in 1866 France was a wine maker’s heaven. A warm Mediterranean climate offered warm winters and plenty of sunshine, with just enough rain to keep the vines happy. Heaven, that is, until death struck. 13 acres of vines mysteriously died, without leaving a suicide note or cause-of-death notice or anything. In the middle of a good weather year, the leaves shriveled up, the grapes turned into bitter raisins, and the whole vine died quickly.

Death spread quickly, extending out in all directions from the original field. The mysterious disease killed off large swaths of vinyards who had withstood pests and bad weather for hundreds of years already, only to be laid low by the newcomer. By July 1868 winemakers were so worried that a special council was appointed to determine the cause of all this death.

image“There was no rot… but suddenly under the magnifying lens of the instrument appeared an insect, a plant louse of yellowish color, tight on the wood, sucking the sap,” wrote Jules-Émile Planchon, a professor of botany and pharmacy at the nearby university in Montpellier and one of the council members. “It is not one, it is not ten, but hundreds, thousands of lice… They are everywhere.” A suspect had been found.

Read the rest of this entry »

Ocean Exploration, Without The Claustrophobic Submarine

Google Earth is a magnificent production- you can virturally tour the whole world from a computer chair. Or so everyone thought, until one Sylvia Earle pointed out the major flaw in this idea. “My children, my grandchildren think it is great to see their backyard, fly through the Grand Canyon, visit other countries,” she said to John Hanke one day at a conference. Hanke happened to be the Director of Google Earth and Maps, and Earle had a bone to pick with him. “But, John, when are you going to finish it? You should call Google Earth ‘Google Dirt’. What about the ¾ of the planet that is blue?”

Sylvia Earle is an oceanographer and explorer, currently a National Geographic Explorer-In-Residence, formerly the chief scientist at the National Oceanic and Atmospheric Administration (NOAA) and recipient of 22 honorary degrees. She is a well-traveled aquanaut, diving in subs and scuba gear many times over, setting records for depth, including a solo sub dive to 1000 meters. Earle has spent her many decades studying the ocean and watching it change, and many countries and organizations have awarded her their highest honors. She has some serious credits. Earle had just met Hanke at a conference in Spain. “I had a chance publicly to say how much I love Google Earth,” she wrote later. And to point out that the then-current version of Google Earth was not complete. She wanted the vicarious exploring to extend to “the real Hawaiian islands, not just the mountain tops that poke through the ocean’s surface.”

Read the rest of this entry »

No PhD Needed

Sebastian Seung could have hired an army of undergraduates to do crucial legwork in his neuroscience lab at MIT.  Even with the help of powerful computers that would have taken years.  Instead, he and his lab turned it into a game, called it Eyewire, and 10,000 people played it on the first day.  Many are still at it.  These players hold all conceivable occupations, but in their free time they are neuroscientists: a prime example of scientists partnering with the public in citizen science projects.  Collecting or organizing vast amounts of data might take one or two scientists years, but with thousands of people helping, data sets are complete in months or weeks, and discovery accelerates.

Several neurons fully mapped by by Eyewire playersfrom Wikimedia Commons

Several neurons fully mapped by by Eyewire players
from Wikimedia Commons

The goal of Eyewire is to trace individual neurons in the the tangles of a mouse’s retina.  Many people map the same neuron, and results are averaged for better accuracy.  Accuracy against the average wins points, though sometimes a player has to be the trailblazer, the first one to map a new neuron, slowly expanding the map.  Collectively, the players turn tangles into data, mapping neuron types, connections, and extensions.  Seung is hoping to map the retina as a stepping stone to mapping the whole brain, developing a set of connections he thinks may be unique to each person.  This connectome, he says, may  make each of us who we are.  But to map this vast connectome, the pathways of billions neurons in each person’s head, Seung needed help from both a powerful artificial intelligence, the computer game, and thousands of citizen scientists around the world playing it.

Read the rest of this entry »

Nature and Nurture and Something Else (Plus Bees)

What makes you, you?  The nature vs. nurture debate has been going on for more than a century, and recent work with honeybees has managed to make it even more complex.  Researchers focused not on the nature part, the bees’ DNA, nor on the nurture part, how the bees grew up and lived, but on a fuzzy gray area in between.

All of the worker bees in a hive are sisters, descended from the same queen.  All of these bees grow up together sharing the same environment.  Worker bees divide into two groups: nurse bees, who take care of the eggs and larvae, and forager bees, who fly around collecting pollen and nectar.  Nurses’ and foragers’ missions are different, but the DNA of these sister bees is quite similar and their nurturing seems to have been the same.  How do they end up with different purposes?

Nurse bees working away

Enter epigenetics, a relatively new field that studies how the environment affects the expression of genes.  Genes were once thought to be instructions written in stone, unchangable directives for the cell.  The nurture effects were thought to go on after the instructions were read, a result of environmental factors, i.e. where a toxic chemical causes cancer or someone overcomes a natural stutter.  In reality, the genes themselves get buffeted by the winds of chance and circumstance from the outside world.  Epigenetics has found “tags” sitting on top of sections of DNA.  These tags control whether the cell will “read” a gene or if it will remain silent.  The DNA itself is not actually changed, but its accessibility is.  The whole set of DNA, called the genome, is overlaid with a pattern of these tags, called the epigenome.

This epigenome develops throughout life, starting with very few tags at birth.  Tags are added or removed due to environmental factors such as nutrition, stress, and disease, allowing cells access to some genes and not others.  Not only do these tags accumulate throughout one lifetime, some of them can be passed down to offspring.  Which means that parents, grandparents, and various distant relatives all gave some of their epigenome to an individual, contributing to how their genes are expressed.  They also contributed DNA, too, but unlike DNA, the epigenome is influenced by lifestyle choices.  Those grandparents’ actions and experiences, not just their genes, influence who you are.

Absolutly necessary dramatic cartoon.

After finding no difference between the genome and the epigenomes of the queen bee and workers right after birth, Dr. Andrew Feinberg and his colleagues at Johns Hopkins University examined the differences between the two castes of worker bees: nurses and foragers. These workers perform very different roles in the hive.  Usually, newly born bees start out as a nurses, and as older foragers die in the risky outdoors, some of them start foraging.  Researchers took care to compare the epigenomes of workers that were the same age, each nurse and forager getting the same amount of time to accumulate epigenetic tags.

In their experimental design, the researchers were sneaky. They took advantage of the ability of the workers’ ability to change jobs: switching back to nurse from forager if the need arises.  This doesn’t happen very often, but researchers created the need.  If we manipulate their hive a bit, and get some of the forager bees to change back to being nurses, they asked, what will their genome look like then?

While the forager bees were out foraging, the researchers moved the hives, so that the bees came back to another hive, empty of bees but not of honeycomb full of larvae that needed tending.  With a distinct need for nurse bees, half of the workers went back to their old jobs.  Researchers looked to see if foragers and nurses have different epigenomes, and what type of epigenome the foragers-turned-back-to-nurses had.

It turned out that not only did nurses and foragers have distinct epigenomes, but it seems the epigenome changed with the job.  When foraging worker bees were steered back to being nurses, their epigenome, and the genes it allowed to be expressed, reverted back to look like it did when it was a young nurse bee.  It was like flipping a switch attached to about 100 genes at the same time, turning them on or off if the worker was fulfilling a nurse role or a forager role.  These worker bees acted very differently, and the specific epigenome patterns seem to be the key to why.

Worker bee looking stylish.

This is, as the researchers note in very understated tones, “the first evidence in any organism of reversible epigenetic changes associated with behavior.”  Does our epigenome change our behavior or does our behavior change our epigenome?  No one knows, but this is evidence of the large role epigenetics plays in each individual.  And our epigenome is greatly affected by every facet of the environment we live in.  So how did you become you?  A murky causal soup of your environment, combined with your genes, combined with the gray area of environmentally-affected gene expression.  Epigenetics, and bees, have just made the nature-nurture debate much more interesting.