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.

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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.

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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.”

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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.

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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.”

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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.

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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.

A Sweet Tooth Goes to Potions Class

Very few people get in a snit over cookies.  But even though most people like them, everybody has a different idea about what makes a perfect cookie.  Should it be chewy, thick, crunchy, or crisp?  It turns out there is some fascinating food chemistry behind cookie texture.  A lot depends on how much a cookie spreads, and when it sets.  When you know how different fats, proteins, and sugars act in cookie dough, you can mix and match for your perfect cookie texture.

Imagine you’re making cookies.  You put nice balls of dough on a cookie sheet, pop them in the oven, and a few minutes later these round, flat things come out.  What happened to the balls of dough?  They have spread as various ingredients liquify and interact. One of the biggest factors in the chewy or crispy fate of a cookie is the rate at which the cookies spread, as well as when they start spreading.  The bottom line is, the more spreading that happens, the thinner and crispier the cookie, and vice versa.

So the cookies are in the oven, spreading out into cookie shapes.  Now, when the cookie sets has a lot to do with the final texture of the cookie.  Setting is baking terminology for when the proteins from the eggs and flour gluten physically rearrange before rejoining in a new overall structure.  Once the proteins have settled in a new framework, the cookie has set.  The cookie dough is no longer cookie dough, but an underbaked cookie.  The faster a cookie sets, the less it spreads, making a thicker, denser cookie, and vice versa.

How to control rates of spreading and setting?  Keep an eye on the type and amount of fat, protein, and sugar you use.  Simple, right?  Except there are a myriad of options and possible combinations.

the perfect cookie?

To promote spreading, use a solid fat in your cookies, such as butter or margarine.  Solid fats tend to melt at lower temperatures, causing cookies to start spreading earlier and spend more total time spreading out into a thin, crispy cookie.  It takes a higher temperature to get the molecules in liquid fats, such as vegetable oil or melted butter, up and dancing.  Cookies containing liquid fats start to spread at higher temperatures, after more time in the oven.  Starting the spreading process late means they do less of it, and end up thicker and denser.

The type of sweetener you use also affects the final cookie texture.  Sugar is hydroscopic, meaning it readily absorbs water, both liquid and from surrounding air.  When more water is absorbed, less of it evaporates during baking, leaving a moister, chewier cookie.  Some sweeteners are more hydroscopic than others, however.  White granulated sugar turns out to be not very good at absorbing water.  Honey, maple syrup, molasses, or brown sugar are examples of more hydroscopic sources of sugar.  Brown sugar, much more hydroscopic, will keep absorbing water even after baking, keeping cookies moist and ready to go in your mouth.  Because cooking with white sugar leaves a fair amount of water moisture still in the cookie dough, this also helps it spread more than dough made with brown sugar.

Chewy cookie lovers- avoid this stuff!

Fats, sugars, and… proteins!  The two main protein sources in cookies are flour and eggs.  Flour provides the protein gluten, which binds ingredients together and provides chewiness. Different types of flour have different gluten content, with cake flour on the low end of the scale and bread flour at the high end.  Eggs, or more specifically the egg yolk, also provide binding proteins.  The higher the protein content (from gluten and eggs or egg yolks) in cookie dough, the less it will spread, as the proteins reassemble and latch onto each other into a new solid framework.  No matter how much protein you have, high amounts of fat and sugar will get in the way of the proteins finding each other, and the cookie setting.  Reducing amounts of fat and sugar in the recipe helps cookies set more quickly- the proteins can find each other faster!

The last key ingredient in cookies is… air.  How much air is incorporated into the dough affects the final density and the crispiness of the cookie.  Liquid fats can’t trap as much air into the dough as solid fats can, especially when the recipe calls for softened butter to be creamed with the sugar, incorporating even more air.  When cooked, this air steams up and creates air pockets in the cookies as they set.  Without the air, the cookies end up much more dense.  Butter and margarine also contain a fair amount of water, which, once it evaporates off as steam, leaves air pockets and a crispy cookie.  Egg whites, which  are approximately ninety percent water, and only ten percent protein, also add air pockets as their water evaporates, along with some extra protein.  Beating them before adding adds even more air, resulting in cookies of the crispy and not-so-dense  variety.

Salivating for a rich, moist, chewy, thick, dense cookie?  Pull out the brown sugar and melt the butter or use vegetable oil.  Find the bread flour, maybe add an extra egg or egg yolk.  Don’t use very much of the sugar or fat.  Or would you rather a crispy, crunchy, thin, not-so-dense cookie?  Go for the solid fats and whip them up with lots of air and sugar.  Get some cake flour, and add an egg white beyond what the recipe calls for.

Of course, rarely do all of the stars line up and you have several cups of both brown sugar and bread flour in your pantry, in addition to remembering to melt the butter.  But now you know why cookie recipes say to cream the butter and the sugar, why they often call for some white sugar and some brown sugar, and why the number of eggs varies with every recipe.  You’ve always wondered, right?  Now you can be your own potions master, and whenever you’re hankering for the perfect cookie, you know how to make it.  And you’ll know why it works.

Ready, Set, Tell Me A (Science) Story

The friendly takeover is complete!  We’re all excited to start gold digging for stories in the world of science, and share what we sift out with you. And we would like to introduce ourselves, those doing the taking-over, before we plunge in as new bloggers.  We’re an eclectic bunch, but we’re all interested in translating science into compelling stories.

Alex Kasprak comes to us from Brown University, where he recently earned a M.S. in geological sciences. There, he studied marine, environmental, and ecologic change during one of the largest biotic catastrophes known to the fossil record – the end-Triassic mass extinction. His favorite geologic age is the Hettangian, his favorite animal is the mouse lemur, and his favorite element is sulfur.

Jean Mendoza graduated from Brown University with a degree in English and biology, passions which she combined into science writing at Johns Hopkins. Her interests span from the intersection of science and superstition to medicine and astrophysics. She draws inspiration from Hemingway, Fitzgerald, Joan Didion, Jenny Boully, and Annie Dillard.

Gabe Popkin has come most recently from Madison, WI, and before that from the Washington, DC area, where he worked full-time for the American Physical Society for several years.  Gabe has a physics degree from Wesleyan University, and over five years of professional science writing, editing, and communication experience. He loves writing about physics, ecology, and everything in between–with a particular interest in the interactions between humans, our environment, and the rest of life on earth.

Kelsey Calhoun spent last year as a neuroscientist playing with rats, and is here to play with words because rats really can’t keep a discussion going when it comes to the physics of harpsichords, or the chemistry of chemotherapy.  She’s interested in almost every field of science, but particularly neuroscience, genetics, ecology, and anything interdisciplinary.  When not writing, she enjoys making music, biking, and watching live tropical fish cams.

If you have a comment, idea, suggestion, or question after reading what we write, please comment (we love discussing these cool stories).  We’re on twitter too, @the_sieve.  If you like what you read, share it!  We hope you enjoy our stories, wonderings, and explorations.


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