Where do dinosaurs come from?

Posted on May 15, 2013 by Jonathan Mitchell — No Comments ↓

I recently got back from Argentina, and in a few months I’ll be headed out to Wyoming and Utah. And I’m not alone.

Every year, paleontologists all across the world load into vans and trucks and head out into the middle of nowhere. Most of us are huntin’ for dinosaurs.

Unfortunately, there’s a lot of ground to cover. Fortunately, paleontologists know (roughly) where to look. Fossils tend to be found in rocks of very specific types, and different dinosaurs are known from different periods of Earth’s history. So if you want to discover a new dinosaur of a certain type (say, a new, giant meat-eating carcharodontosaur), you go to 100 million year old rocks from low-lying rivers and lakes. Once you’re there, you start lookin’!

Three paleontologists about to hike around Patagonia.

As you shuffle around the wastes, you keep your head down and walk around the bottom (base) of the rock formation you predict has the fossils in it. The idea is that if you start finding tiny scraps of bone at the base, since fossils can only roll downhill, there must be a dinosaur in the rocks above you!

The dark rocks with gray tops and black, spongy undersides are bone sitting as-found in Utah.

So you climb up the hill, looking for bone the whole way. Once you stop finding bone on the surface, it means you’ve probably passed where the fossil is weathering out from. At this point, you want to make sure there IS bone in the ground, and not just an exploded bone on the surface. This means you start gently scraping off the dirt, and digging down with hand-tools to see if you can find any bone sticking out of the rock wall.

A bone sticking out of the rock wall in Utah.

Finding a dinosaur in the hill is only the begining. You mark the spot on your map and take notes on exactly what color the rock is, and how high up it is, and then you start bringing your gear. Pickaxes, shovels, jackhammers and big, BIG bags of plaster…

In Argentina, we brought 350lbs of plaster up on horseback and shoulders. We quickly ran out.

…so you can start digging!

You want to take all of the rock from above and around the skeleton out, while leaving just a little bit of rock directly over the bone for the moment. The idea is to make a flat area using jackhammers/big tools, but to also leave a few inches of rock over the bone to protect it from your heavy equipment. Once you haev the big platform carved out, you start digging down with hand tools.

The man in the foreground is where the cliff’s face used to be. Big dinosaur needs a big hole.

When you dig down and hit the bone directly, you DO NOT take it out! Bone is fragile, and if you remove it then-and-there it will crumble and break. You want to take it back to the museum, where fossil preparators, the heroes of paleontology, can gently take off the rock with steady hands, fine tools and powerful microscopes.

To protect the bones until you get them back to the lab, you make a “jacket”. Dig a deep trench all of the way around the bone, and cover the bone with a layer of paper and then several layers of plaster. This way, the rock around the bone helps keep it in one piece for its journey to the museum.

Let the plaster over the top dry for 1-3 days (longer is better), then flip the jacket and cover the bottom! Flipping the jacket can be stressful, because if you don’t do it both quickly and carefully, the contents can spill out and the fossil can be destroyed.

Once the bottom is dry, you have to carry the entire plaster jacket down off the hill.

Jackets are really heavy. For this one Patagonian dinosaur we removed about 20 jackets with anywhere from half to a half dozen bones in each (skull bones are pretty small). The bigger jackets couldn’t be carried down the hill safely, so we lashed them to a raft made of tires and bent sign and slide them down the sides slooooowly.

Then the REAL work begins. Fossil preparators labor for dozens to hundreds of hours carefully picking away the rock from around the bone with dental tools, tiny, air-powered jackhammers, tweezers and all manner of other fine implement. Once the bone has been carefully cleaned off, and any breaks or fragments glued back in place, the fossil is ready for study and/or display!

Mounted skeleton of Giganotosaurus, a close relative of the dinosaur we are digging in the above pictures, in Villa El Chocon.

(pictures by Akiko Shinya, Nate Smith, and Frank Endres)

Graduate Education in How Economics Shapes Science

Posted on March 21, 2013 by Ben Krinsky — No Comments ↓

In How Economics Shapes Science (1), a thorough and highly engaging book, economist Paula Stephan does an admirable job using the intellectual tools of economics to analyze the professional practice of science. The book covers a wide range of topics, including the economic incentives for a career as a researcher, the labor market for scientists, how research is funded, and the effects of research investments on innovation and economic growth.

As a graduate student myself, I was particularly intrigued by the aspects of the book that relate to graduate education. Various factors incentivize the pursuit of a PhD, and Stephan rightly points out that many (if not most) of us seek an advanced degree in science because of intellectual curiosity; we have a desire to know more about some aspect of nature and we get a certain thrill out of the problem-solving aspects of doing research. She also rightly points out that the decision to attend graduate school is sensitive to more typical economic indicators. For example, during the economic crisis of 2008, as the labor market was in precipitous decline, doctoral degree-granting institutions saw a spike in applicants. One can infer that college graduates saw fewer opportunities for immediate employment and many sought the “shelter” of continuing education, especially science PhD programs, which often have fully subsidized tuition plus a stipend.

One of the problems with our graduate education system, as Stephan describes at great length, is a lack of transparency regarding the various economic costs of pursuing a PhD. Continue reading →

Thoughts on science writing straight from the source – Q&A with Deborah Cramer

Posted on February 15, 2013 by Courtney Stepien — No Comments ↓

We here at Bio for the Win got in touch with science writer Deborah Cramer to talk about her experiences at the interface of science and communication.

Author Deborah Cramer, image from her website

Deborah Cramer is author of Great Waters: An Atlantic Passage (W.W. Norton), Smithsonian Ocean: Our Water Our World (Smithsonian Books/HarperCollins), the companion to the Ocean Hall at the U.S. National Museum of Natural History. She lives at the edge of a salt marsh and is currently writing a new book following the migration of shorebirds from one end of the world to the other, provisionally called On the Edge: a tiny bird, an ancient crab, and an epic journey. (Yale University Press.) www.deborahcramer.com www.seaaroundyou.com

BFTW: You didn’t have much formal training in writing or science prior to starting your career as a science writer. What were you up to prior to picking up the pen, and how you do think your background has informed your writing?

DC: My education and training cross several disciplines, and came into focus when I began writing. Great novels contain deep truths. A graduate degree in American literature showed me the many ways people move in the world and how their passions inform their lives. A graduate degree in urban studies and planning showed me how policies are and aren’t made, how they are and aren’t implemented, and how conflicts are and aren’t resolved in areas, like the coast, where the stakes are high.

Living on the marsh, and participating in the resolution of upland land-use conflicts, I watched how day after day, season after season, year after year, the rhythms of life ebb and flow. I also watched how human activities degrade marshes which are important sinks for carbon and which nourish important fisheries. I saw firsthand how land use decisions failed to adequately take into account the ecology of wetlands.

Continue reading →

The Caturation point: carrying capacity in human environments

Posted on January 31, 2013 by Tim Sosa — No Comments ↓

Cats are superior to dogs. We don’t need to revive old debates. But once you’ve seen the light and adopted a cat, what should you do with it? Should you confine it indoors, where it will sit twitching its tail in the window and chirping at the birds and squirrels in the tree outside? Or should you let it outside for exercise and excitement?

I made up my mind when I was 16, and one of the family cats went missing one night. We never knew what became of him–hit by a car, killed by a coyote, a swig of antifreeze–but he was only about three years old. In fact, outdoor cats typically live about one third as long as indoor cats. So if you want to have a long relationship with your pet, probability is on your side if you keep it indoors, because of the dangers that the environment poses to your cat. But what about the dangers your cat poses to the environment?

Most of you will have seen coverage in, for example, The New York Times of a meta-analysis (a study that dumps data from many other studies into a bucket and reanalyzes them all together) about cat predation on wildlife. The original reference is over at Nature. This study caught my eye for a couple of reasons: first, I like cats, and I also like wildlife. Second, he won’t remember me, but I was an undergraduate at the University of Minnesota when one of the authors, Scott Loss, was a PhD student. The authors estimate that about 2.4 billion birds and about 12.3 billion small mammals are cat victims, every year, just in the United States. Domestic cats kill only 11% of the mammals, but 11% of 12.3 billion is still about 1.35 billion. Feral and stray cats have a much larger impact (the other 89%).

So keeping your cat indoors is probably good for the mice, rabbits, squirrels, moles, sparrows, finches, and other small animals that live in your neighborhood. Now what about feral cats, who do the vast majority of the killing? This is trickier. Organizations like the ASPCA are proponents of Trap-Neuter-Return (TNR) programs, in which animal control and welfare organizations trap the cats, sterilize them, and release them back into the colonies where they live. The idea is that no new kittens will be born, resulting in a gradual diminution of the feral cat population. This is promoted as humane, a win-win for wildlife and cats.

However, the ASPCA also suggests that volunteers feed feral cats. This appeals to my compassionate side; supplemental human feeding no doubt makes a harsh winter easier to endure for a stray cat. But does it make ecological sense?

By Scott Granneman from St. Louis, MO, USA (Flickr) [CC-BY-SA-2.0], via Wikimedia Commons

Let’s talk about carrying capacity. Carrying capacity refers to the number of a given organism that a given environment can support. It’s a euphemism from ecology. Carrying capacity actually means, “the number of individuals that, if exceeded, will result in the suffering of individuals already present.” When a population grows so large that its environment can’t support it, individuals in that population begin to starve, or to fight over space, or otherwise have a bad time.

Supplemental feeding increases carrying capacity. When we feed the cats in a feral cat colony, there is suddenly food in the environment that wasn’t there before. There is more for cats to eat; therefore we get more cats, possibly having a bad time. This is true regardless of a TNR program, unless the TNR program is 100% effective. Nobody pretends that we can catch 100% of feral and stray cats and neuter them, even if we could pretend that no new strays would pop up after escaping from (or being ejected from) people’s homes. One study Schmidt et al. 2007 found that feral cats could successfully raise 3.6 kittens per litter, and cats can sometimes have multiple litters per year. This means that a single fertile pair of cats can produce a population of more than 1,000 cats in just three years (it won’t, because many will die–recall the short life expectancy).

These factors lead to an inescapable conclusion: TNR programs will only temporarily reduce feral cat populations for as long as people feed them. Why? Because new cats will be born, and new cats will escape. TNR programs in the absence of feeding will reduce it permanently, because the carrying capacity will decrease too. Neither approach, of course, will reduce the population to zero. As long we feed feral cats, we make it possible for cats to kill even more wildlife. This is particularly true because well-fed cats are more effective hunters, and any cat owner can tell you that cats do not kill only when they’re hungry.

I’m only speaking of the inevitable result of feeding cats, not the ethics. What we do with our new insight into cats’ effect on wildlife depends on which of two things is more important in our judgment: keeping feral cats alive, or keeping wildlife alive.

Ancestry.com for the evolutionary family tree

Posted on January 30, 2013 by Courtney Stepien — No Comments ↓

Ever seen other animals and wondered just how many years have passed since you shared a common ancestor with that chimp, or that bird? Well, wonder no more!

A sweet tool exists out there to help you – called Time Tree: The Timescale of Life. If you go far back enough in the history of humans, eventually we all lead to a single related population. All humans share a common ancestor (our great-great-great-great plus seven thousand more greats grandma) and we can trace our cousins’ and our family lineage to some common relative (like how 1/2 a percent of the world can trace their ancestry back to Genghis Khan). We can trace all of today’s living species to common ancestors that existed millions of years ago in a similar fashion. Time Tree is a tool that summarizes scientific literature to tell you the point in geologic time that a single lineage split into two – say, when the human and chimpanzee lineages split from a shared ancestor.

So you put in the names of two taxa:

From TimeTree

And check out the results:

Continue reading →

Communicating About the Environment – Tips from a Conservation Advocate

Posted on January 24, 2013 by Samantha Lockhart — 2 Comments ↓

Today we have a bit of an education for the scientist audience. We scientists are not known as exemplar communicators when it comes to sharing research results with the press, non-scientists or government. Conservation organizer and environmental advocate Samantha Lockhart shares her insight on translating science-speak into advocate-speak step by step, so you too can communicate your science meaningfully! ~Courtney

For years, scientists have had trouble communicating about their work to the general public. It’s part of why so many people continue to call evolution “just a theory” because no one can understand the difference between what “theory” means in the world of science and how that’s different than my theory that your boyfriend is cheating on you because of the way he just looked at that waitress.

This communication gap is particularly troubling when it comes to the environment. It wasn’t until James Hansen, the NASA scientist and foremost authority on the science of the climate crisis, decided that researching facts and publishing that research was not going to create the kind of massive political change that was necessary. There were too many stakeholders, too many people who saw something to lose should his findings be accurate. Unfortunately, the climate data were accurate and, if anything, too modest in describing the speed and intensity of global temperature rising and arctic ice melt. That’s why he decided to speak up, to push himself outside of his comfort zone and communicate publicly about his research to the press, to non-scientists and to Congress. You can listen to James Hansen’s compelling story for yourself in his TED-talk below.

The challenge when a climatologist decides they need to tell their story is the question of how to make a bunch of research and analysis not only understandable to the average person, but actually engaging, exciting and sexy. To make it something that gets non-scientists like me to hear the story and get fired up. To make it something that changes the course that humans are on; to make it something that fundamentally shifts the politics in the country in a way that responds to the problems that our nation’s research program has identified.

Telling Your Story

Continue reading →

The Angler Fish – a Rainbow of Ugly

Posted on January 18, 2013 by Courtney Stepien — No Comments ↓

This is an awesome video about angler fish – equal parts science and hilarity and well worth the two minutes.

Angler fish that live in the deep sea are another source of bioluminescent light in the deep ocean, like the light-show producing jelly fish that giant squid eat (the squid find the jellies so efficiently that scientists now use electronic light shows to attract squid to camera equipment). In this case, the angler fish uses light to both attract food and to attract mates, though based on the video it doesn’t end so well for the guys….

True Facts About The Angler Fish

Giant Squid lured by promise of snack, caught on video.

Posted on January 16, 2013 by Courtney Stepien — 1 Comment ↓

Scientists have developed a way to actually attract giant squid close enough to their cameras and equipment underwater to get video footage – by baiting the squid with a tasty electronic light show that mimics a favorite food. The use of this new tech with a nod to the natural light environment – the only light at these depths are bioluminescent light and what little sunlight remains from hundreds of meters above – allowed this expedition to succeed where many others had failed. The below clip is part of a ton of footage to be aired on January 27th on the Discovery Channel’s “Monster Squid: The Giant is Real.”

Giant Squid footage. Source: The Guardian.

The light show that attracts the squid (click on the image below for popup video) is pretty interesting – researchers created a light pattern that mimics a prey animal. From the Ocean Research and Conservation Association:

Dr. Widder was invited to join the expedition because of her successes with the Eye-in-the-Sea, a deep-sea camera observatory that she developed as a means of exploring the deep ocean unobtrusively. The Eye-in-the-Sea uses low light imaging in combination with far-red illumination that is invisible to most deep-sea animals. The primary motivation for its development was the desire to observe animals that would normally be disturbed or frightened away by the white lights and noisy thrusters used on standard observation platforms.

She also developed a novel optical lure that imitates certain bioluminescent displays, thought to be attractive to large predators. Known as the electronic jellyfish or e-jelly the lure imitates the bioluminescent burglar alarm display of the common deep-sea jellyfish Atolla wyvillei.

Click the image to play the e-jelly video, narrated by Dr. Widder. From ORCO.

Bioluminescent mimicry is a promising new way to attract deep-sea creatures. Check out the full story and some cool details about the equipment over at the ORCO site, and put the Discovery channel January 27th show on your calendar.

Notes From The Field: Germination and Beyond

Posted on December 10, 2012 by Hoi-Fei Mok — No Comments ↓

Germination is tricky process! I never thought it would be so difficult to get some seeds to grow, but the last month has proven me wrong.

Corn seeds, treated for herbicide use

About a month ago, we sowed the corn into the plots. This was done by our contractor who also machine sowed the fertilizer. Some of the bays weren’t exactly 5m wide, so the machine sometimes didn’t fit in the last row of the seed. More specifically, the wheels would end up on the mound and the mechanical tube that released the seeds didn’t dig into the ground, causing seeds to lie at the soil surface. Seeds need to be dug a certain depth into the ground to establish strong root systems, so it was problematic that some seeds were sitting at the surface.

Seed sowing with Agrisearch contractors!

It is common commercial practice to irrigate 2-3 days before sowing seeds so that the soil is sufficiently moist for the seeds, but dry enough for the machinery to drive over. Unfortunately for me, our first irrigation event was the first time we were trying out our new pipes. The flow rate from the pipes ended up being too high, so while we followed the 2/3 rule (flood irrigate the bay until the wetting front, or the very tip of the water, reaches 2/3 of the bay), the water mostly flowed straight off the bay without seeping into the ground. As a result, by the 3^rd day with really windy and sunny weather, the ground was already too dry for the seeds. We came back a week after sowing and found that nothing had emerged, even though corn is supposed to germinate after 4-6 days under normal conditions.

The first irrigation event. The flow rate was way too fast, causing much soil erosion and the water to simply run off

Agronomists generally advise against irrigating in the first two weeks of a corn seedling’s life cycle for several reasons. Irrigation can cause caking of the soil surface, making it difficult for seedlings to emerge. Even once emerged, moisture stress can be tolerated because the seedling is then encouraged to start developing a strong root system. However, this is all weather dependent and under hot windy conditions, irrigation is sometimes necessary. So we made the decision to irrigate in hopes that the seeds would germinate. This irrigation event plus a few days of hand sowing seeds (lucky for me, my site wasn’t THAT big, but it was still two painful days of crouching all day) probably saved the crops. A few days later, our first seedlings emerged!

Block 6D seedlings! Almost all the first seed lot germinated, so we spent a few days thinning them out

After the germination process, there were still a few problems to take care of. We noticed that our irrigation system wasn’t distributing water evenly across the bays. Flood irrigation works like the name suggests: water is released by a gate into a large flat, sloped paddock, it floods the paddock, and the gate is closed once the wetting front reaches 2/3 of the paddock. Flood irrigation and furrow irrigation are two of the most common irrigation systems used around the world, especially the developing world, and though it is not as efficient as sub-surface drip irrigation, it is more relevant to farmers who would most likely use wastewater for irrigation.

How flood irrigation normally works (image from FAO)

The problem with our irrigation system was that we didn’t have gates, we had single pipes emitting water at the head of the bay. The pipe causes a great deal more soil erosion where the water falls because of the high flow rate. Furthermore, since the pipes are at an angle resting on the mound, the distribution of water is not quite the same as a gate releasing water at ground level. In theory, the pipe can still flood the entire bay, but what we were seeing was parts of the top plot and sides that weren’t getting any water. This is why levelling of the bays is so important – if the bays aren’t sloped correctly, the water will not flow to all the parts. To be fair, the machinery that sowed the seeds and fertilizer also created little furrows that now seem to be the primary channels the water is using for getting down the bay.

We’ve been experimenting with putting pine logs and pavers at the top of the bay to try and redistribute the water more evenly. More importantly, we’re going to try and reangle the pipe so that it sits as parallel to the ground as can be. I think we might have to deal with uneven water distribution over the course of the study, but hopefully those changes will help with the distribution problem. The upside is that I will not be sampling or harvesting from the outer rows of the plot (due to fringe effects) and most of the dry spots are along the outer rows, so hopefully there won’t be a huge effect in the results. Fingers crossed that the rest of the crop makes it through!

Trying out new irrigation method. Hope it works!

Evolving Novelty: Beetle horns!

Posted on December 7, 2012 by Jonathan Mitchell — No Comments ↓

One of the major focuses of evolutionary biology is on the origin of complicated structures. Darwin himself wrote out an elaborate, step-by-step explanation of how, by starting with a single light-sensitive cell, the complex camera eye you and I have could evolve. Indeed, despite the factually-challenged claims of creationists, we have yet to encounter a structure in the biological world that could not have arisen by evolutionary processes (note: this doesn’t just mean natural selection! evolution’s complicated).

That said, coming up with hypothetical ideas for how novel structures arise is very different from actually testing specific notions. Unfortunately, testing these things can be hard. Evolution needs a long time to produce a really complicated structure, which means if we see a complicated structure in the natural world, the organism that has it is likely very far removed in time from the organism that first evolved said structure. Conversely, even the most complicated of adaptations have to start off simple, so the incredibly complicated structures of the future should appear, to us now, as relatively simple precursors. Without a time machine, it’s impossible to know what will end up being the next “winning” component.

What evolutionary biologists often do is use natural variation, and comparisons between different species. In order for the step-by-step assembly of a complicated structure to work, each and every incremental step must be (at least) non-detrimental and (potentially) advantageous. Which means that some species may have simpler versions of complex structures. For instance, squids and snails have very different lifestyles, and so they don’t need the same kind of eye. However, they both inherited an eye from their common ancestor. Snails, because they don’t need vision to live happy, snaily lives, haven’t modified their eye as much, while squid have. By comparing the eye structures across a range of related creatures we can learn more about how these structures evolve and develop.

Recently, the Committee on Evolutionary Biology hosted Armin Moczek, a professor from Indiana University. Dr. Moczek gave an excellent seminar on his work trying to understand the origin and evolution of complex horns in dung beetles. The horns of a dung beetle are used when the beetles engage in EPIC COMBAT!

It turns out, only some species of dung beetle have horns. Dr. Moczek noticed, however, that beetles with and without horns all have a weird bump on their body when they’re very young. Closer examination showed that this bump, which develops into the horns of adults in some species, helps all of the young dung beetles shed their “skin” (beetles, like all insects, have an exoskeleton, so to grow they have to literally crawl out of their old skin and grow a new, larger one).

Certain genes control the formation, and eventually loss, of this bump. Every now and again, in wild beetles of unhorned species, there arises a mutation in those certain genes that means the beetle keeps this bump as an adult. Careful studies pitting one beetle against another have shown that even a small bump is enough to give a beetle a distinct advantage in a fight. So a simple screw-up in a set of genes that let’s an adult beetle keep a left-over structure from its younger days results in the origin of a totally new organ: the beetle horn.

Not content with just documenting its origin, though, Dr. Armin carefully examined the genetics that control the beetle’s horn. It turns out that once the beetle’s got that liiiiiittle start of a random, small bump, they can use genes they already have to make it something more. Genes that make a limb grow from being a small bump when the limb’s first forming into a long, complicated structure can be used again to make a tiny, accidental bump into a massive, formidable weapon. And so the beetles’ have!

Living things, in general, don’t have that many genes. You don’t have a specific gene for each finger, or a specific gene for each hair on your head. Instead, we have a suite of genes that work together to create all the oddities of life. In a way, you can think of a gene like a word, and a structure like a sentence or story. Using the same, limited sets of words you can weave some awesome stories and using the same sets of genes you can weave some pretty awesome structures!