Explore Utah Science - Explore Utah Science - Displaying items by tag: Life http://exploreutahscience.org Mon, 22 Jan 2018 01:29:06 -0700 en-gb Extracting the Human Story From Our DNA--Blog http://exploreutahscience.org/explore-utah-science-blog/item/147-blog-extracting-the-human-story-from-our-dna http://exploreutahscience.org/explore-utah-science-blog/item/147-blog-extracting-the-human-story-from-our-dna Extracting the Human Story From Our DNA--Blog

New advances in DNA testing allow us to delve deeper into our ancestry than ever before.

New advances in DNA testing allow us to delve deeper into our ancestry than ever before.

Most of us wonder about those that lived before us. Some people go beyond mere curiosity, recording family stories and tracking down ancestors' documents. Thanks to convenient access to a multitude of records, either in archives or online databases, genealogists today are developing extensive family trees.

After becoming interested in genealogy in 2007, I spent hours examining parish records, determined to follow a line of male ancestors as far in the past as possible. My research took me back nine generations, to anDescendants of Georg Linseder: My great-grandfather Franz, railroad engineer, poses with his sons in Sarajevo, Kingdom of Serbs, Croats and Slovenes, around 1926.Grandchildren of Georg Linseder attended this schoolhouse in Sitzendorf an der Schmida, Austria, in the late 17th century. The building was previously a hospital and dates to the 15th century. ancestor who had migrated to Buda (now Budapest, Hungary) in the 1730s. Genealogists and archivists overseas helped me extend that line by three more generations, terminating with Georg Linseder who lived in Grosshaselbach, Austria, in the 17th century.

Its unlikely, though, that I'll discover any ancestors beyond Georg: oral histories and paper documents can take us only so far. Most people of European descent can't trace ancestors prior to the 16th century, when recording of baptisms, marriages, and interments was first mandated by the Roman Catholic Church. For others, the delicate paper trail ends much sooner−either because documents related to their heritage don't go far into the past, or because the documents perished in wars or unfortunate accidents.

Yet distant ancestors are not lost to us−we're all living repositories of humanity's history. In every cell within our bodies, DNA provides a molecular record that goes back tens of thousands of years into the past. We may not know the names of distant ancestors, but our DNA is showing us something much greater−that all people on Earth belong to a single human family tree.

Nowadays, learning about ancestry is easy: one can select a DNA testing company, collect their DNA sample, and send it out for analysis. Small changes in DNA, called mutations, are key for determining the relatedness and ancestry of individuals. Two people with greater differences in their DNA will have a common ancestor further in the past than two people with similar DNA. Using this new technology it will be possible to find out whether my ancestors lived elsewhere, perhaps Asia or the Middle East, during the two hundred thousand year long interim between paper documentation and the origins of humanity in Africa.

The desire to learn more about one's deep ancestry is spreading across the globe like wildfire. According to Spencer Wells, a Rhodes visiting professor at Cornell University, "consumer genomics has gone mainstream," with 2013 likely to emerge as the year of inflection for anthropological DNA analysis. In the decade preceding 2013, nearly 1 million people submitted their DNA for analysis to various nonmedical institutions. But just within the current year, another million will likely follow.

Several things have contributed to this phenomenon: DNA has become a household word, and many people today are comfortable sharing their private information. There's also the power of word-of-mouth−satisfied participants tend to pique others' interest in ancestry, and the more people who offer their DNA for anthropological analysis, the better, as it becomes easier to find DNA matches among participants.

Scientists rely on two types of DNA to unravel our distant ancestry−the Y chromosome (Ycs) and mitochondrial DNA (mtDNA). Most of our genetic material is organized into 23 pairs of chromosomes, made of tightly folded DNA and proteins. Among these chromosomes is a single Ycs, found only in men. The Ycs is passed on directly from father to son, and informs about a person's paternal lineage.

All people, however, have mtDNA. Separate from chromosomes, mtDNA is located in a small cellular compartment called the mitochondrion. But because mtDNA is passed on only from a mother to her children, it reveals a person's maternal lineage. Even though women lack an Ycs they can still learn about their paternal lineages from the analysis of their father's or brother's Ycs.

Genetic information can be used for much more than just a personal analysis of each of our own family trees, uncovering ancient migrations and intermingling between our species, Homo sapiens, and other hominins that occurred tens of thousands of years ago. Since 2005, the Genographic Project, which is led by Wells and overseen by the National Geographic Society, the Genographic Consortium and an international advisory board, has used advanced DNA analysis to understand how humans came to populate the Earth. To date, about 72,000 people from 1,000 indigenous populations contributed their DNA to the Genographic Project for this purpose. Based on variations in their mtDNA and Ycs, these people have been assigned to different groups, called haplotypes.

Study of geographic localities of indigenous peoples and frequencies of different haplotypes across the globe can help unravel many migration mysteries. For example, scientists have long been baffled by fossil records, which suggested that ancestors of indigenous Australians were among the first humans to venture out of Africa. A risky oceanic migration seemed unlikely, but paleontologists were unable to find any fossil remains suggesting a land migration across southern Asia. But when Wells and collaborators studied Ycs of southern Indians, they discovered individuals with an "M130" haplotype, which matched that of indigenous Australiansi. Ancestors of indigenous Australians most likely trekked across the coast of southern Asia, which has long since been submerged. And though fossil evidence of these early migrants is now underwater, their DNA survives in India to this day.

The newest kit offered by the Genographic Project, Gene 2.0, can also uncover other branches of the hominin family tree. Tens of thousands of years ago, we were not the only hominins roaming the Earth. Humans likely encountered Neanderthals after moving into the Middle East and Central Asia no later than 47,000 years agoii. Denisovans and humans met and mated in Asia about 45,000 years agoiii. Neither Neanderthals nor Denisovans bestowed us with much of their DNA−the mtDNA and Ycs haplotypes discovered to date are distinctly human. But a small amount of genetic material from our hominin cousins still lives on today in chromosomal DNA (other than Ycs) of some people, contributing to the wealth of our heritage.

Though my genealogy adventure revealed ancestral hometowns, professions, and families, it did not go beyond 12 generations of ancestors. My next step, submitting DNA for analysis, should eventually uncover migratory paths of thousands of nameless ancestors−human and, possibly, Neanderthal. For anyone interested in genealogy, looking deep into their DNA−and that of relatives'−allows them to go far beyond where the paper trail has gone cold. Yet unless a male Linseder descendant sends in his DNA, my ancestor Georg's Ycs lineage will remain a mystery. Far superior to the paper trail, even DNA analysis has its limitations.

i. Spencer Wells (2006). Deep Ancestry: Inside the Genographic Project. National Geographic, Washington D.C.

ii. Sriram Sankararaman, Nick Patterson, Heng Li, Svante Pääbo and David Reich (2012). "The Date of Interbreeding between Neandertals and Modern Humans." PLoS Genetics 8(10): e1002947. doi:10.1371/journal.pgen.1002947

iii. Pontus Skoglund and Mattias Jakobsson (2011). "Archaic Human Ancestry in East Asia." PNAS 108(45): 18301-18306.

smiljka_kitanovic@yahoo.com (Smiljka Kitanovic) Explore Utah Science Blog Mon, 07 Jul 2014 19:39:39 -0600
Sounds of the West http://exploreutahscience.org/science-topics/life/item/137-sounds-of-the-west http://exploreutahscience.org/science-topics/life/item/137-sounds-of-the-west Angels Landing, Zion National Park

Thousands of animal and ambient sounds from eleven western states have been recorded and archived in a digital library in Utah. While fascinating in their own right, sounds can also be used to track environmental change.

Thousands of animal and ambient sounds from eleven western states have been recorded and archived in a digital library in Utah. While fascinating in their own right, sounds can also be used to track environmental change.

Some people like to hunt animals, not to kill them, but to record the sounds they make.

Conservationists, scientists, volunteers, and state and federal agency employees have contributed over 2600 animal sounds that are now housed at the biggest library of its kind in the west, called the Western Soundscape Archive. The project was founded by recording engineer Jeff Rice and digital librarian Kenning Arlitsch in order to document the sounds of animals living in the west and to make people aware so they will want to protect the environments where these animals live.

The digital sound archive is kept at the University of Utah's J. Willard Marriott Library. Anna Neatrour was a project manager for a grant from the Institute of Museum and Library Services, awarded to Rice and Arlitsch, to develop the archive.

"The Western Soundscape Archive is a site that collects animal sounds centered on eleven states in the American West," says Neatrour. "And it provides a really good overview of all the species that live in our states as well as ambient sounds for National Parks. Quite a variety of sounds that people can listen to from their computers."

While the project no longer has funds to collect and annotate new sounds, Neatrour says archiving animal sounds is important because when people think about environmental issues and declining landscapes, they usually think about the visual aspects.

"The sounds associated with these natural landscapes change as well. So preserving that now for the future is very useful," she adds.

But recording the sounds is not always easy. Many animals are active early in the morning and can be in hard to reach locations. Different microphones are needed for different jobs. By using a parabolic microphone it's possible to pick up weak sounds from a few meters away, while a small remote microphone can be dropped into burrows in the ground, or holes in trees. Some sound enthusiasts go even further.

"If you search the archive for 'ant interview,' you can hear a story of a scientist describe how he recorded the vibrations that ants make by holding them between his teeth," says Neatrour. "It shows how devoted people are for capturing these sounds.

[Interview with Dr. Hayward Spangler]

The recordings include over 500 bird species, 300 mammals, dozens of snakes, turtles, lizards, and frogs, as well as multiple insects. Many of the recordings are paired with predicted species distribution maps and pictures of the animals, which can be found by common or scientific name.

"We have some sounds from animals that you think would not make sounds, like earth worms for example," explains Neatrour. "And in that case the sound for that sound clip, it's more like the dirt falling as the earthworm moves through the ground."

[Earthworm sounds]

The individual animal sounds are important, but so are collections of sounds from particular landscapes. These collections, or soundscapes, include sounds of animals, geophysical features such as wind and streams, and human-produced sounds collected over the course of a day from different locations in the natural world.

[Ironwood Forest National Monument at dawn]

Soundscapes are frequently represented visually as spectrograms. The images of daily acoustic patterns can be used to better understand the area's biodiversity and health. Donated by the National Park Service, there are over 10,000 spectral images from 24 National Parks in the Western Soundscape Archive.

[Spectrograms from Zion National Park]

"You can actually look at these sound wave graphs and pinpoint things like airplane flights going overhead and disrupting the landscape versus variations in the ambient noise you might get in the different season," says Neatrour. "So that is something that can appeal more if people are doing research in that area."

Scientists are realizing that the auditory environment is as important as the visual landscape in understanding the health of an ecosystem. And the National Park Service is actively searching for ways to better protect the natural environment from the impact of human sounds, since studies suggest the acoustical environment is important for animals to find mates, protect their young, and to communicate about territories.

So the next time you are out in nature, remember to listen as well as look.

kim@exploreutahscience.org (Kim Schuske) Life Thu, 05 Dec 2013 14:31:01 -0700
Blog: A Bighorn Sheep and Ranger Meet http://exploreutahscience.org/explore-utah-science-blog/item/116-blog-a-bighorn-sheep-and-ranger-meet http://exploreutahscience.org/explore-utah-science-blog/item/116-blog-a-bighorn-sheep-and-ranger-meet Blog: A Bighorn Sheep and Ranger Meet

Ranger Kathryn Burke has a close encounter with a bighorn and writes about it in her blog.

Canyonlands Ranger Kathryn Burke writes about her close encounter with a bighorn sheep in her blog Ranger Kathryn's Arches.

exploreutahscience@gmail.com (Explore Utah Science) Explore Utah Science Blog Thu, 02 May 2013 06:06:14 -0600
The Secret Lives of Dinosaurs http://exploreutahscience.org/science-topics/life/item/112-the-secret-lives-of-dinosaurs http://exploreutahscience.org/science-topics/life/item/112-the-secret-lives-of-dinosaurs The Secret Lives of Dinosaurs

Author Brian Switek’s new book discusses new discoveries about how dinosaurs looked, lived, and had sex

Salt Lake City based author Brian Switek wrote the recently released book, My Beloved Brontosaurus, to explain why our perceptions of dinosaurs have changed dramatically over the past 20 years. Gone is the imagery of scaly, slothful animals, replaced by dynamic, and sometimes feathered creatures. Modern paleontology is gleaning from fossils more details about dinosaur lives than ever before. Switek spoke with Explore Utah Science contributor Julie Kiefer.

JULIE KIEFER: What were you hoping to accomplish by writing, My Beloved Brontosaurus?

BRIAN SWITEK: There is always a lag between scientific discoveries and how science permeates public perceptions. I wanted to explain the current knowledge about dinosaurs by highlighting the tension between what scientists know and what the public knows.

Jurassic Park, which first came out 20 years ago, gave this idea that dinosaurs are very scaly and relatively drab. Now that the fourth movie is coming out, this is during a time when we know that many dinosaurs, like the Velociraptor, that are closely related to birds, were covered with feathers and fuzz and were relatively striking in color. It’s kind of a disappointment to hear the film director say there’s going to be no feathers in the next movie because fans prefer the old scaly way. I’m trying to make the case that dinosaurs are cooler than they’ve ever been.

JULIE KIEFER: How do scientists know that some dinosaurs had feathers?

BRIAN SWITEK: In China, there are many dinosaurs preserved with feathers intact, and there are also dinosaur feathers preserved in amber. Also on arm bones of the Velociraptor there are little bumps called quill knobs. You see the same thing on the arm bones of the turkey vulture. Those are where the pen-like attachment for some of the long wing feathers go. Even though the Velociraptor couldn’t fly, based on the skeletal evidence, it had pretty advanced plumage.

If you look at the evolutionary tree, there is a particular group of dinosaurs called the coelurosaurs that birds belong to as well. Every lineage within this group had some sort of fluff or feathers or fuzz in it, suggesting this is a common trait for this group. Even though no one has found direct evidence of feathers on Tyrannosaurus rex, it’s a good bet that they probably did have some kind of feathery body covering because it’s a coelurosaur.

JULIE KIEFER: What else is new research telling us about how dinosaurs looked?

BRIAN SWITEK: As a kid I was told we would never know what color dinosaurs are, and now paleontologists are starting to figure that out. I mentioned that some dinosaurs are preserved with feathers. If you take something like a scanning electron micron microscope and zoom in on them, you’ll see little blobs. They’re in certain shapes and arranged in a certain density. A paleontologist figured out that these were melonosomes, pigment carrying bodies that are also in the feathers of birds.

Some colors like browns, reds, blacks and greys are made by a reaction from light bouncing off structures in the feathers. If you have these structures in fossils, and you can look at the feathers in modern birds where you know what the color is, and match up the patterns of melonosome shape and distribution, then you can reverse engineer what color that dinosaur feather would’ve been. The first one to be fully reconstructed was a pigeon-sized dinosaur, called Anchiornis. It kind of looked like a magpie. It was mostly black with some white on the feathers, and a slash of red feathers on top of its head.

The ability to know dinosaur color creates all sorts of opportunities. If you have a big enough sample size and reconstruct the colors of many animals, maybe we can figure out whether some animals died with their breeding plumage on, or if there are color differences between males and females. I’m totally fascinated to see where this goes.

JULIE KIEFER: Are there ways to learn about how dinosaurs lived their daily lives?

BRIAN SWITEK: Yes, but they’re not always the most direct. A dinosaur trackway is recorded behavior. It’s an actual few moments in an animal’s life where you can see what direction it was moving, how quickly it was moving, and interactions between dinosaurs.

There is also evidence from bone pathologies. Paleontologist Andy Farke took models of Triceratops skulls and said, ok if these animals are really locking horns, what positions would actually work? Based upon that he went back to fossil skulls and found lesions and other damage right where the models predicted. That’s pretty decent evidence that these animals were actually locking horns and fighting each other.

JULIE KIEFER: You conjure some interesting mental imagery when you write about dinosaur sex. You write, “I envisioned a pair of amorous Brachiosaurus … each one waiting for the other to make the first move. But try as I might, I couldn't quite figure out the mechanics of what should come next.” Why take on this topic?

BRIAN SWITEK: It may seem like a silly topic, but I wrote about it because it’s important in dinosaur lives. In the book, I present an anecdote that helped show that we put our own values into our study of sex and mating in nature. In the early 20th century, naturalists on an Antarctic expedition observed sexual behavior among Adélie penguins that was considered out of the norm. That section of the report was taken out of the final monograph that was published. It was a century before this document with important, original observations was rediscovered.

Beyond the taboos, for a long time for dinosaurs it seemed like an ancillary topic that almost anyone could speculate on because there was almost nothing substantial to be said. Now that is changing.

It has only been recently that we’ve been able to tell what sex dinosaurs are. We’ve found females that happened to be laying eggs when they died. They have a special kind of bone tissue inside their long bones that we can identify.

In terms of sexual behavior, we can’t observe dinosaurs trying to woo each other, but we can use other methods. We are using evolutionary logic and looking to birds and crocodiles. By seeing what they share in common, we can deduce what might have been present in a dinosaur’s physical anatomy. New fossil evidence has also helped. There are hips of female dinosaurs that still contain eggs in it. The number of eggs and their position tell us something about the reproductive anatomy.

JULIE KIEFER: Besides reading and writing about paleontology, how do you satisfy your dinosaur cravings?

BRIAN SWITEK: I volunteer at the Natural History Museum of Utah, and during the summer months I go out into the field with them as often as I can. It’s fantastic to be looking for scraps of teeth, or tracks, or something that someone has never seen before that will lead to a new understanding of dinosaurs and prehistoric life.

JULIE KIEFER: Where is your favorite place to go fossil hunting?

BRIAN SWITEK: My favorite place in terms of visual beauty is Dinosaur National Monument on the Utah/Colorado border. It contains more exposures of different teleological periods than any other national park. You can stand in some places and see oceans going in and going out, replaced by deserts, replaced by flood plains, and another ocean comes in and recedes. You can see millions and millions of years of history just laid out in front of you.


My Beloved Brontosaurus is available in hardcover on Amazon, and as an audiobook on iTunes and Audible. Hear an excerpt from the book through the audio player near the top of this page.

Brian Switek also authors the National Geographic blog, Lealaps.

Brian Switek





 Brian Switek

julie@exploreutahscience.org (Julie Kiefer) Life Thu, 18 Apr 2013 00:00:00 -0600
Advances in Medicine Have Gone to the Dogs http://exploreutahscience.org/science-topics/life/item/109-advances-in-medicine-have-gone-to-the-dogs http://exploreutahscience.org/science-topics/life/item/109-advances-in-medicine-have-gone-to-the-dogs Advances in Medicine Have Gone to the Dogs

Advances in veterinary care present new hope for ailing pets, and tough choices for pet owners.

Advances in veterinary care present new hope for ailing pets, and tough choices for pet owners.

Scout, an active black Labrador Retriever, had always loved her daily walks with owner Brandi Williams. But, when she was just six years old, things started to change. Her daily walks became shorter and shorter, and eventually she could no longer run. After a trip to the vet, Brandi learned Scout had arthritis, primarily in her right elbow, and was faced with the decision of how to care for her companion.

With advances in veterinary medicine, increasingly animals have the same options for treatment that are offered to humans with similar conditions. There are kidney transplants for animals with disease, and radiation and chemotherapy treatments for pets with cancer. For animals with arthritis, like Scout, joint replacement is now an option.

Specialty treatments, however, can come with a hefty price tag. According to the American Veterinary Medicine Association, U.S. households spent an average of $375 on veterinary care in 2011, but such statistics can be deceptive. Advanced medical procedures, such as knee replacement or chemotherapy, can run more than $4,000. For many of the six-out-of-ten pet owners who consider pets as family, hundreds or even thousands of dollars is a small price to pay for the ability to improve quality of life.

Like any devoted pet owner, Williams did everything in her power to help relieve Scout's pain. Because the front legs of a dog support 60% of their weight, Scout's arthritic leg was under intense stress. Her local veterinarian, Rob Bagley, prescribed non-streroid anti-inflammatory drugs, and recommended weight management and daily activity, the most common approach for arthritis in animals.

After about 2 years of intensive treatments, there was no noticeable improvement. Williams researched Scout's condition to learn whether there was something more she could do. "I felt like Scout just had years ahead of her, and if I could do something, then her quality of life would be better or at least maintain where it was."

Although amputation is sometimes recommended in severe cases of trauma, Williams wanted to save the leg and Scout's left foot was also starting to show signs of arthritis. She opted instead for a total elbow replacement. Bagley says that while this orthopedic procedure has been available since the 1980s it "is still not a mainstay." At first, the procedure was highly invasive and required a long recovery time. Many newer procedures and replacements have since been developed that are less invasive and have a shorter recovery time.

The TATE elbow, developed in 2007, is one such advancement. The prosthetic replicates the motion of the elbow joint with two C-shaped components that nest inside each other. Fitting into the elbow joint, the prosthetic cups the humorous bone, with the rounded side facing the radius and ulna. Unlike other prostheses, it is not cemented in place but rather was developed for the bone to grow into it, similar to some prosthetic joint options available for humans. Veterinarian Randy Acker of Sun Valley Animal Center in Idaho invented the TATE elbow, named after his yellow lab who, like Scout, had arthritis. Williams decided this was the best option for Scout, and paid $3500 for the procedure.

At first, it looked like Scout would be able to return to her active lifestyle. "Right off the bat she was able to walk, which Dr. Acker said was normal," says Williams.
However, as with many medical procedures, complications developed. For Scout, "the upper piece attached to the humorous didn't heal or attach – the bone didn't grow into it," says Williams. She says Scout's recovery has reached a plateau.

Williams is now working with Dr. Bagley to improve Scout's condition. She's now taking a different pain medication and due to improved management Scout has a better outlook. "We can make it around the block on some days. It's a pretty small walk. But it's a 10-minute walk instead of a 4 or 5-minute walk. And she's a happy dog."

Even though the prosthetic didn't fix Scout's problem, Williams stands by her decision. "You have to weigh the pros and cons yourself and the quality of life for your dog - it's a tough decision. I believed I was doing what was best for my dog."

With more veterinarians specializing in subtypes of care, and continued advancements in veterinary medicine, pet owners will be presented with increasing treatment options in the future. Dr. Bagley has practical advice for pet owners who may be faced with a decision like Williams. "It's important for a pet owner to become educated about different options and it is the vet's job to understand the risks and benefits of each option. We're on the same team and the best solution depends on the pet and the situation."

alexandraporpora@gmail.com (Alex Porpora) Life Sun, 07 Apr 2013 19:58:23 -0600
A Voyage of Discovery on an Ancient Sand Sea http://exploreutahscience.org/explore-utah-science-blog/item/79-a-voyage-of-discovery-on-an-ancient-sand-sea http://exploreutahscience.org/explore-utah-science-blog/item/79-a-voyage-of-discovery-on-an-ancient-sand-sea A Voyage of Discovery on an Ancient Sand Sea

A paleontologist's work can be incremental and grueling. But once in a while, they're lucky enough to be a part of an incredible discovery.

Utah is an undeniably hot and arid place, but in the Early Jurassic, 190,000,000 years ago, things were much worse. At that time a vast sea of desert sand covered some 850,000 square miles of intermountain west. In northeastern Utah, the sediments of that desert are known to geologists as the Nugget Sandstone.

Despite being an extreme and generally inhospitable environment, over time, plants and animals evolved and adapted to live there. To understand more about how this transition took place , a group of paleontologists and students from Dinosaur National Monument, the University of Nebraska, Brigham Young University, and the University of Utah, has been investigating the area for the past several years. Nugget field work is not for the faint of heart. Patience and perseverance is essential and you must be prepared for many hot and frustrating days when no fossils can be found. But hey, if working in the Nugget was easy someone would have already done the research!

Left to right, Drs. George Engelmann (University of Nebraska), Dan Chure (Dinosaur National Monument), and Brooks Britt (Brigham Young University) at the Saints and Sinners Quarry.

Much of what we know comes from trace fossils, the trails, trackways, and burrows made by animals going about their lives in and around the dune fields. We have found the trackways of various kinds of herbivorous and carnivorous dinosaurs. At one site, hundreds of Brasilichnium footprints record the ancient passage of small mammal-like reptiles as they walked up the steep fronts of large dunes. As in modern deserts, arthropods were common, and we have numerous trails of scorpions and spiders, as well as small burrows made by adult and larval arthropods of various types, and burrows of large scorpions. In most cases, trace fossils are the only evidence we have of those organisms.

A small Brasilichnium footprint in the Nugget Sandstone.

Then there are those moments when the miraculous happens. I will never forget the day we found the Saints and Sinners Quarry --- stepping onto a sandstone surface and spying more than fifty dinosaur bones naturally exposed. In that instant we knew we had made the find of a lifetime. We eventually uncovered a phenomenal deposit of thousands of bones preserved in a small desert lake. Most of these fossils belong to a new, small, predatory dinosaur, but bones of several other kinds of small reptiles have also been recovered. While optimism is essential for paleontologists, never, in our wildest dreams, did we imagine finding such a treasure trove of fossils! This one quarry has produced orders of magnitude more bones than all previous work in the rocks of this ancient desert.

A spectacularly complete foot of a small reptile from the Saints and Sinners Quarry.

Uncovering the abundance at Saints and Sinners Quarry was just the beginning. Our diverse group continues to explore, excavate, prepare, map, and analyze the remarkable fossils of this ancient desert, from SSQ and beyond. Work continues in both the field and in the lab, and the first manuscripts about our SSQ findings are in preparation. But more remains to be done and summer field work is approaching. Who knows what that may bring?

Part of a long scorpion trackway (Paleohelcura) from the Nugget Sandstone.
The upper jaw of a carnivorous dinosaur from the Saints and Sinners Quarry.
Footprint of a large predatory dinosaur in the Nugget Sandstone.
Visit Dan Chure's Blog: Land of the Dead
dan_chure@nps.gov (Dan Chure) Explore Utah Science Blog Mon, 14 Jan 2013 00:15:22 -0700
Natural History Museum Spotlights Plight Facing Utah Frogs http://exploreutahscience.org/science-art-and-community/item/62-natural-history-museum-spotlights-plight-facing-utah-frogs http://exploreutahscience.org/science-art-and-community/item/62-natural-history-museum-spotlights-plight-facing-utah-frogs Natural History Museum Spotlights Plight Facing Utah Frogs

Globally frogs and toads may be facing a mass extinction. At the Natural History Museum, scientists explained what they're doing to save local populations.

"Come on in, we're talking frogs here!" says state biologist Paula Trater. The most dressed up you'll ever see her, she is wearing dark green rubber waders, khaki hiking pants, and a colorful frog patterned shirt. Trater's most distinctive feature, however, is that she is passionate about frogs.

Trater shared her love of frogs at the 77th Scientist in the Spotlight at the Natural History Museum of Utah. This bimonthly series features scientists from around the state in an open house format, creating a "unique opportunity to get face-to-face with a scientist," says gallery programs coordinator Paul Michael Maxfield.

Trater taught visitors how to sneak up on, catch, weigh, measure, and track frogs over multiple years. Besides getting their hands dirty, the work challenged visitors to think about how amphibians in Utah fit into the global picture.

By current estimates, more than 30% of amphibian species worldwide are threatened with extinction. With semipermeable skin that makes them highly sensitive to pollution, radiation, and diseases, they are among the first species in an ecosystem to react to climate change. Their demise doesn't bode well for everything else.

In some ways, the state of amphibians in Utah is a microcosm of their global plight. At one time or another, local frogs and toads also faced extinction. How these species are doing today signals how well humans are managing the changes that are happening to the natural world.

In the early 1990s, the state hired Trater to monitor the quickly declining Columbia spotted frog populations. Counting frogs by the number of egg masses, she tallied just a few hundred annually back then. Although each egg mass can contain up to 1,000 embryos, only about 5% of them make it to adulthood.

The primary contributor to the species' downfall was habitat destruction due to land development and use. Two major water projects, construction of the Jordanelle Dam and straightening of the Provo River, within the past 60 years had eliminated many of the marshy areas where the frogs lay their eggs. In 1997, the spotted frog was listed as a Utah Sensitive Species.

To restore wildlife habitats, the Provo River Restoration Project, initiated in 1999, re-created wetland areas by re-establishing the natural curves of the river. "If there was an established colony nearby, they [new frogs] would move right in," Trater says. The spotted frog population recovered, and Trater now counts upwards of a 1,000 egg masses annually.

But just as spotted frogs were gaining ground, a new threat came online. The Chytrid fungus, which had already devastated amphibian populations worldwide, was detected in Utah spotted frogs in 2001. Trater recalls that when she heard the news, "it was like hearing your whole family was going to die."

To her surprise, the dramatic decline she had been bracing for never came about. Trater suspects that spotted frogs are resistant to the disease. "We know the disease is there, but the frogs aren't dying," she explains. "Our frogs are rugged."

Unlike Columbia spotted frogs, boreal toads haven't been so lucky. Once prevalent in the Wasatch, they are now so scarce that Utah Division of Wildlife Resources (DWR) biologists rely on hikers to relay sighting information. Mark Grover with the DWR believes that Chytrid is the culprit, but says the fungus is "not the global boogyman that's responsible for everything."

Environmental stresses, some triggered by pollution or varying water years, may be increasing the susceptibility of boreal toads to the disease. Once scientists determine the root cause, Grover hopes they can design a recovery plan to stabilize the population. With each amphibian species as an environmental indicator, one can't help but wonder what the toads are telling us.

This realization struck a chord with Scientist in the Spotlight participant, Eugenia Richins of Salt Lake City. She says she has fond memories of catching frogs as a kid, but doesn't see many these days. With a new appreciation for the issues facing amphibians today, Richins views these populations as a "barometer of the climate of our world with pollution and global warming." Now motivated, she vows to volunteer to help save them.

Scientist in the Spotlight, featuring geneticists to paleontologists, is scheduled for the first and third Fridays at 2:00pm at the Natural History Museum of Utah, 301 Wakara Way, Salt Lake City. At the next event on December 7th, a zooarcheologist will demonstrate what animal remains reveal about climate change.

Kaitlin.Basham@hci.utah.edu (Katie Basham) Science Art and Community Thu, 29 Nov 2012 06:14:23 -0700
Saving the Rain Forest By Using It to Find Drugs http://exploreutahscience.org/science-topics/life/item/56-saving-the-rain-forest-by-using-it-to-find-drugs http://exploreutahscience.org/science-topics/life/item/56-saving-the-rain-forest-by-using-it-to-find-drugs Saving the Rain Forest By Using It to Find Drugs

Scientists at the University of Utah apply knowledge from their basic science research to save rain forests in Panama.

Few people can say that their work has helped to save an island. But Phyllis Coley and Tom Kursar are not ordinary scientists.

The island is Coiba, a chunk of land off the coast of Panama. Since the early 1900s, Coiba had been the site of a Panamanian prison. The relative lack of activity on the island meant that 80 percent of its natural habitat was still intact. This included trees and animals that had disappeared from the mainland, such as the Crested Eagle and Scarlet Macaw, as well as several animal subspecies.

However, in 2004, the remaining prisoners were moved from the island, leaving the Panamanian government to decide what to do with Coiba. One option was to turn it into a tourist destination, complete with golf courses and hotels.

Bioprospecting in Panama

Enter Coley and Kursar, researchers from the University of Utah who study the interaction between plants and the herbivores that feed upon them. As a married couple, they spent their life together doing research in the world's tropical rain forests. However, many of their research sites had fallen prey to logging and commercial development.

"We find our survey of ecology of plant defenses absolutely a fascinating puzzle but rain forests are disappearing. What can we do about it?" Coley remembers thinking at the time. "If we could find something that was valuable in rain forests then there would be an incentive for those countries to save the rain forests."

Coley and Kursar came up with a solution, modeled after a program in Costa Rica: bioprospecting. Instead of searching for gold, bioprospectors 'mine' plants, bacteria, and fungi for novel, often toxic, biological compounds that combat illnesses such as cancer and infectious diseases.

Mature leaves are one of the most common biological samples collected by bioprospectors. However, through their studies the Utah scientists found that it is young leaves that are particularly tasty to herbivores because they are tender, nutritious, and full of nitrogen. "We're really interested in why the world is green, why the insects or herbivores haven't eaten up all the plants," says Coley.

To defend themselves against herbivores, new leaves produce poisons; in fact, 50 percent of their dry weight is made up of toxic compounds, much greater than mature leaves. For this reason the scientists thought it would be more efficient and productive to focus bioprospecting efforts on young leaves.

In 1995, Coley and Kursar started a program to look for potential drugs in the jungles of Panama. Since then, program scientists have isolated a total of 216 biologically active compounds, some from young leaves. One of the most promising is Coibamide A, which was found to inhibit growth of cancer cells. Isolated from cyanobacteria (blue-green algae) off the coast of Coiba, the compound was patented in 2011. Other compounds have the ability to destroy bacteria and kill parasites responsible for leishmaniasis, malaria and Chagas disease.

There is still a long way to go before any of the compounds can be turned into marketable drugs. Only one out of 50 drugs make it to clinical trials, with associated costs estimated at $880 million per drug.

More than Drug Discovery

Central to Coley and Kursar's plan was that as much of the work as possible be done in Panama by Panamanian scientists and students. "We said, right at the very beginning, that [sending samples back to the US] was ridiculous," says Kursar. "They [Panamanians] need to get immediate benefits." According to Coley and Kursar, these efforts have helped Panamanians to become researchers themselves and realize the value of their rainforests, the program's biggest success.

The program was eventually funded by the International Cooperative Biodiversity Groups (ICBG), a coalition of U.S. government agencies that use drug discovery programs as incentives for conservation, and has brought in $8.5 million in grant money for research efforts in Panama. Currently, the program is administered by the Smithsonian Tropical Research Institute and includes U.S. scientists, Panamanian scientists, and private companies.

What started seventeen years ago as a small program in Panama has now garnered the attention of the world. In 2005, Coiba and its surrounding islands were designated a World Heritage Site, an internationally recognized protected status. Earlier this year, the group received one million dollars from the Global Environmental Facility (GEF) to continue the drug discovery program in Panama and serve as an example for other countries.

"We wanted it [the Panama project] to be an example. [But] we want it to be much, much bigger than Panama," says Kursar. "We're not interested in being politicians. And that's why it was really good to get this GEF attention because...we're hoping it will grow and develop."

Referring to the success of the program, Coley says, "My mother always said, 'Well, what earthly good is that? Who cares about caterpillars eating baby leaves?' If we hadn't spent 25 years doing the basic science with no obvious application, it [the bioprospecting program] never would have occurred to us...This whole project was a labor of love."

Coley and Kursar have since turned over the reins of leadership for the project to Panamanians. Currently they are working in other S. American tropical rain forests, continuing their work researching the interaction between herbivores and plants.


kirstin.roundy@gmail.com (Kirstin Roundy) Life Mon, 19 Nov 2012 05:37:32 -0700
Explosion in Urban Beekeeping Raises Concerns for Honeybee Population http://exploreutahscience.org/science-topics/life/item/37-explosion-in-urban-beekeeping-raises-concerns-for-honeybee-population http://exploreutahscience.org/science-topics/life/item/37-explosion-in-urban-beekeeping-raises-concerns-for-honeybee-population Explosion in Urban Beekeeping Raises Concerns for Honeybee Population

Experts fear that negligent hobby beekeeping could spur a disease outbreak that devastates commercial hives.

Millions of buzzing residents have moved into Utah, as the number of new beekeepers registering with the state has increased eightfold since 2006.

That’s good news for local farmers and gardeners who depend on honeybees to pollinate their crops. The bad news is that the new arrivals could be bringing with them a rash of problems.

Several honeybee experts worry that in the hands of novice beekeepers, all those hives could become incubators for viruses and pests ready to hitch a ride to any of the thousands of commercial hives around the state.

Clint Burfitt suggests that this concern has been fueled by a fundamental shift in the scale of risk that face beekeepers today. “In the past, a [commercial] beekeeper could keep 1000 hives and might lose a few [to disease], but now a commercial beekeeper can have losses of 60 percent.” Burfitt is a state entomologist at the Utah Department of Agriculture and Food.

Colony Collapse Disorder, the nationwide phenomenon that first hit the news in 2006, contributes to these losses. By some estimates, the disorder is blamed for killing one quarter of the nation’s bees, resulting in a $12 billion loss to the agricultural economy.

Some beekeepers fear that should pest and viral infection spread to commercial apiaries, the results could be similarly devastating. “If one person isn’t knowledgeable or just doesn’t understand how to recognize or treat for [pests and pathogens], that jeopardizes everybody in that system,” says Burfitt.

The greatest opportunity for contamination comes when honeybees rob nectar from each others’ hives, inadvertently taking fungal spores, mites, and viruses with them. The varroa mite, the most common problem facing beekeepers, introduces viruses and bacteria directly into the bloodstream of bees. A rarer threat, the American foulbrood turns normally glistening, white honeybee larva into brownish goo that smells like dirty socks

“People get all fired up about [starting their new hives]. It goes pretty well at first, but summer gets busy and they let it languish. If it craps out, this time of year, robbers come looking for weak hives. Robber bees come in, pests jump ship and join the new hives,” says Chris Rodesch, Salt Lake County bee inspector. This activity can initiate a cycle that quickly infects an entire neighborhood of hives.

However, Rodesch maintains that commercial bees experience more risk of exposure when they are rented to farmers to pollinate crops, a common and lucrative practice. They are often trucked long distances and forage alongside bees from other parts of the country.

Should an outbreak of a particularly pernicious virus occur, the Department of Agriculture and Food is equipped to notify registered beekeepers and offer advice on symptoms and treatment. The Utah Bee Inspection Act mandates that all beekeepers register their hives with the department within 15 days of setting them up.

Nevertheless, there are shortcomings to the system. The inspection act does not require beekeepers to submit notification of hive losses. Such a requirement could make a big difference in identifying pests and pathogens before they reach the level of outbreak.

Further, many of the state’s beekeepers are either unaware of the registration requirement or unwilling to register their hives. Rodesch says that only half of the hives that he visits are registered with the state.

“Unless you see a lot of hives it’s hard to know if what’s happening in yours is normal or something that needs to be addressed,” says Rodesch. “That’s why the [beekeeping] clubs are really important.”

Cory Stanley, an entomology professor and honeybee specialist with Utah State University gives live demonstrations of various hive management techniques throughout the state, “I think that it is important to let the young beekeepers know the value of asking questions.”


photo credit: Caroljean Rodesch

Chris Rodesh checking on his bees


noelleswan@gmail.com (Noelle Swan) Life Wed, 24 Oct 2012 23:15:15 -0600
How Dogs Came to Be—Part 2 http://exploreutahscience.org/science-topics/life/item/9-how-dogs-came-to-be—part-2 http://exploreutahscience.org/science-topics/life/item/9-how-dogs-came-to-be—part-2 How Dogs Came to Be—Part 2

For thousands of years dogs have wandered the world with humans. Researchers have begun to unravel how that happened.

Dogs come in every conceivable shape and size. They can be six pounds or 200 pounds. They can be six inches tall or three feet tall. Researchers have begun to decipher the genetics behind this variation in dogs. And they've found that only a few genes can cause major differences.

In the 1800s, people were fascinated with dogs. Breeding dogs for extreme physical traits was a hobby for many. Breeds were created with short or long legs, pointy or floppy ears, smooth or coarse hair—in all possible combinations. In fact, 80% of the 300 plus dog breeds we have now, were created during this time. Robert Wayne, professor of ecology and evolution at UCLA, calls this period the third stage of dog evolution.

“We like to think of three stages, the first being this very early one where wolves interacted with hunter gatherers moving around the landscape. Then a second stage during the development of agriculture when human societies were more sedentary people began to live in small towns. Then we like to think of the third stage as the Victorian explosion of dog forms. What we see today is principally a product of that explosion over the last few hundred years.”

No other animal species in the world comes in such different sizes and shapes than dogs. How were breeders able to do this? Dog geneticists like Elaine Ostrander with the National Human Genome Research Institute are now solving this mystery. Ostrander says in twenty short years, dog researchers have now put together most of the tools needed to tell the story of the dog. She adds, genetic maps and sequencing the dog genome has allowed researchers to focus on many questions. “Whether it was behaviors, morphologic traits, why are dogs big, why are dogs small. Or diseases, why does this breed get cancer, why does this breed get epilepsy, why does this breed get diabetes.”

One of the first researchers to connect physical traits of dogs with genes was Gordon Lark, Professor Emeritus at the University of Utah. He started with the Portuguese water dog, which was bred to help Portuguese sailors on their fishing ships. One member of this breed, Bo, is now living with the Obama family in the White House. Lark started the project when his dog Georgie died.

“This dog, which I loved very much, when it died I realized the cure for this was to get another one fast. So I was looking for another Portuguese water dog and finally found a breeder who would let me have one. She said, ‘but I need to know what you do because sometimes people do things that are inappropriate for having this type of dog.’ So I said I was a soybean geneticist and what she seemed to hear was blah blah genetics blah blah.”

Lark says the breeder called him two or three times a week to talk only about genetics. “So when the time came for me to get the dog I said ‘well you know this has been a lot of fun talking and so on, but we haven’t talked money, I need to send you a check.’ And she said, ‘I’m giving you a very expensive dog free so that you will work on dog genetics.’ And that was actually the start of it.”

Lark and his colleagues contacted breeders and owners who gave DNA samples, X-rays, and all types of measurements of their dogs including body size, tail and ear length. “Well the first thing we found out blew us away. There is a trade off in shape, for instance in the legs being long and thin or being short and thick. And at the same time whether the pelvis was fairly robust or was like popeye the sailor man, a very narrow pelvis. And we were working with a colleague Dave Carrier here and he said ‘well that’s the difference between a greyhound and a pit bull. It’s the difference between energy efficient speed and power but slow.’”

Lark says the data helped explain how breeders could easily mix and match physical traits because they found only a few genes are controlling pelvis and leg shape at the same time. Lark, Ostrander and others have since discovered that a small number of genes have a big impact on many other traits. For example, one key gene is critical for whether a dog is big or small. By contrast, in humans it’s thought that height is controlled by at least 50 genes, says Ostrander. “We began to realize that there was a recurring theme in our work and that is for most of the traits that we study. It isn’t as though there are hundreds and hundreds of genes controlling that trait, but there really seem to be a small number of major effective factors.”

Surprisingly, just like what was found for physical traits, scientists are finding that a few genes are also responsible for diseases in dogs. Ostrander says because of inbreeding, purebred dogs are frequently prone to getting certain diseases. It turns out that many of these diseases are ones that humans also get. “Almost any disease I named off the top of my head that was common to humans occurred in dogs. Whether it be cataracts, epilepsy, or cancer, or diabetes.”

UCLA’s Robert Wayne says the simple genetics in dogs makes it easier to identify genes, including disease genes. By finding the genes first in dogs, it might narrow the search for disease genes in humans. “Because of the nature of how dogs were selected, very intensely by humans. It tends to be a simple genetic basis for many of the traits we observe. One or a few genes explain most of the variation we observe. So that makes the task of finding a gene much easier.”  

The gene for the sleeping disorder narcolepsy was found in dogs in 1999. This discovery led researchers to the cause of the disease in humans one year later. Recently a gene for Obsessive Compulsive Disorder was found in Doberman Pinchers. Researchers are now looking at that same gene in humans who suffer from OCD. And there many other promising studies, including for cancer that are currently under way.

Gordon Lark says the interesting thing about dog genetics research is that it’s a partnership with dog owners. “The dogs have never been kept in a laboratory, they are all owned by people. It’s just like human genetics. These owners really wanted to help.”

Once again dogs and people are working together, this time to advance our knowledge about how genes controlling physical traits and disease came to be.

This story originally aired 9/27/09

kim@exploreutahscience.org (Kim Schuske) Life Sun, 21 Oct 2012 00:00:00 -0600