Read the first chapter of The Bare Bones

BareBmecDue to requests for a sampler of my forthcoming book from Indiana University Press, The Bare Bones, I am now making available a PDF of the first chapter. I think this will give you a feel for the tone of the book.

Thanks to everyone for all of the interest and enthusiasm for the book. It was truly a labor of love, and I hope many of you will find it enjoyable to read and useful to those who may use it as an educational resource.

The Bare Bones, Chapter 1

I am also giving another sneak preview at one of the figures, this one from Chapter 2:

Carnivorous mammals, such as a cat, tend to have a jaw joint in line with their sharp, shearing teeth, much as the handles of a pair of scissors align with the blades.  This puts the best cutting surface towards the back of the jaws.  In contrast, herbivorous mammals such as horses have a jaw joint located above the tooth row, allowing their teeth to simultaneously contact one another like a nutcracker.

Carnivorous mammals, such as a cat, tend to have a jaw joint in line with their sharp, shearing teeth, much as the handles of a pair of scissors align with the blades. This puts the best cutting surface towards the back of the jaws. In contrast, herbivorous mammals such as horses have a jaw joint located above the tooth row, allowing their teeth to simultaneously contact one another like a nutcracker.

Also remember, you can preorder The Bare Bones through Indiana University Press or Amazon.

If you are into e-books, it can also be purchased as an e-book. See the Indiana University Press website for links to the appropriate retailers.

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The NAMS Research Symposium at Stockton University – Friday, April 17

Just a brief announcement that the NAMS Research Symposium, which features research by NAMS students with faculty, is this Friday, April 17 in the C/D Atrium on the Main Campus of Stockton University. Students will be at their posters between 3-5PM.

You can see the research our students are doing by downloading the NAMS Research Symposium Abstract Booklet 2015.

You can tweet about the event with the hashtag #OspreySci

You can also join us on Facebook.

The BFF Lab Students and Faculty in the Spotlight!

Black Beard the Bearded dragon,

Black Beard the Bearded dragon. Photo (c) Susan Allen/ The Richard Stockton College of New Jersey

I am excited to report that the Best Feet Forward (BFF) Lab has had its first local news story! Susan Allen at the Office of News & Media Relations at Stockton College has written a wonderful article that was distributed to the associated press today.  We thank Susan for this wonderful story, which we reproduce here in this post (see below).  All photos are copyright Susan Allen / The Richard Stockton College of New Jersey.

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Stockton College Researchers Analyze Locomotion of Modern Day Reptiles, Mammals to Understand How Dinosaurs Moved

By Susan Allen, Office of News & Media Relations, Richard Stockton College of New Jersey

Galloway Township, NJ- Caleb Bayewu, a junior Biochemistry major, cradled a bearded dragon in his hands as Cory Barnes, a senior Biology major, attached tiny reflective beads to the bumpy skin on the patient reptile’s forearm.

Caleb Bayewu, a junior Biochemistry major (left), cradled a bearded dragon in his hands as Cory Barnes (right), a senior Biology major, attached tiny reflective beads to the bumpy skin on the patient reptile’s forearm.

Caleb Bayewu, a junior Biochemistry major (left), cradled a bearded dragon in his hands as Cory Barnes (right), a senior Biology major, attached tiny reflective beads to the bumpy skin on the patient reptile’s forearm. Photo (c) Susan Allen / The Richard Stockton College of New Jersey

Black Beard, as the lizard is nicknamed, is one of three juvenile bearded dragons at The Richard Stockton College of New Jersey taking part in an animal locomotion research project aimed at better understanding how dinosaurs once moved across our planet.

After body measurements were recorded, Black Beard was placed on a treadmill surrounded by a system of three infrared cameras and plastic containers that serve as safety nets in case a reptile runner strays off course.

As soon as Bayewu shook a clear jar of jumping crickets, Black Beard sprang into action. Alex Lauffer, a junior Biology major, flipped the conveyor belt switch, the treadmill kicked on and the cameras began transmitting data to Dr. Matthew Bonnan, associate professor of Biology, and Dr. Jason Shulman, assistant professor of Physics.

Caleb Bayewu, a junior Biochemistry major from Maywood in Bergen County, shakes a jar of jumping crickets to motivate a beaded dragon to run on the treadmill. From the left, Alex Hilbmann, a sophomore Biology major from West Deptford in Gloucester County, Alex Hilbmann, a sophomore Biology major from West Deptford in Gloucester County, and Corey Barnes, a senior Biology major from Seaville in Cape May County, stand by.

Caleb Bayewu, a junior Biochemistry major from Maywood in Bergen County, shakes a jar of jumping crickets to motivate a beaded dragon to run on the treadmill. From the left, Alex Hilbmann, a sophomore Biology major from West Deptford in Gloucester County, Alex Hilbmann, a sophomore Biology major from West Deptford in Gloucester County, and Corey Barnes, a senior Biology major from Seaville in Cape May County, stand by.  Photo (c) Susan Allen / The Richard Stockton College of New Jersey

Sophomore Biology majors Kieran Tracey and Alex Hilbmann stood close by, making sure Black Beard stayed on the treadmill.

Kieran Tracey, a sophomore Biology major from Sea Isle City in Cape May County, guides a beaded dragon to the treadmill as Caleb Bayewu, a junior Biochemistry major from Maywood in Bergen County, holds a jar of crickets. Photo (c) Susan Allen/ The Richard Stockton College of New Jersey

Kieran Tracey, a sophomore Biology major from Sea Isle City in Cape May County, guides a beaded dragon to the treadmill as Caleb Bayewu, a junior Biochemistry major from Maywood in Bergen County, holds a jar of crickets. Photo (c) Susan Allen/ The Richard Stockton College of New Jersey

While Black Beard ran in place, the cameras captured the motion of each reflective bead sending real experimental data at the overwhelming rate of 120 frames-per-second to a computer program that can read and display the data as moving dots.

From behind their monitor, Bonnan, of Hammonton, and Shulman, of Egg Harbor Township, watched each step on their screen.

Dr. Matthew Bonnan, associate professor of Biology, and Dr. Jason Shulman, assistant professor of Physics, are working together with students to model dinosaur movement by studying modern day reptiles and mammals. “Given that the earliest mammals and dinosaurs had a forelimb posture not unlike lizards, they are acting as a model to test hypotheses about the transition from sprawling to upright forelimb postures,” said Bonnan. Shulman has been instrumental in analyzing the data, which is captured at 120 frames-per-second by a system of infrared cameras. “He is a big part of why we're able to do this. Without him, interpreting the data would be difficult at best,” said Bonnan. (c) Photo: Susan Allen/ The Richard Stockton College of New Jersey

Dr. Matthew Bonnan, associate professor of Biology, and Dr. Jason Shulman, assistant professor of Physics, are working together with students to model dinosaur movement by studying modern day reptiles and mammals. “Given that the earliest mammals and dinosaurs had a forelimb posture not unlike lizards, they are acting as a model to test hypotheses about the transition from sprawling to upright forelimb postures,” said Bonnan. Shulman has been instrumental in analyzing the data, which is captured at 120 frames-per-second by a system of infrared cameras. “He is a big part of why we’re able to do this. Without him, interpreting the data would be difficult at best,” said Bonnan. Photo (c) Susan Allen/ The Richard Stockton College of New Jersey

Stepping Back in Time

“Without a time machine, we can’t put dinosaurs on a treadmill,” said Bonnan, who has been fascinated with dinosaurs since he was 5 years old. Instead, bearded dragons, ferrets, rats and a Savannah monitor are “standing in for their ancestors” at the Best Foot Forward (BFF) Laboratory on the main Galloway, NJ campus.

Bridget Kuhlman, a senior Biology major, of Little Egg Harbor in Ocean County, left, and Kelsey Gamble, a senior Anthropology and Biology major, of Williamstown in Gloucester County, were in the Best Foot Forward Laboratory to gather data on ferret movement patterns. Kuhlman, said, “It’s a dream come true being able to work with ferrets. It’s getting me ready for vet school,” she said. She works as an EMT and personally owns five ferrets. Photo (c) Susan Allen/ The Richard Stockton College of New Jersey

Bridget Kuhlman (left), a senior Biology major, of Little Egg Harbor in Ocean County, left, and Kelsey Gamble (right), a senior Anthropology and Biology major, of Williamstown in Gloucester County, were in the Best Foot Forward Laboratory to gather data on ferret movement patterns. Kuhlman, said, “It’s a dream come true being able to work with ferrets. It’s getting me ready for vet school,” she said. She works as an EMT and personally owns five ferrets. Photo (c) Susan Allen/ The Richard Stockton College of New Jersey

“Given that the earliest mammals and dinosaurs had a forelimb posture not unlike lizards, they are acting as a model to test hypotheses about the transition from sprawling to upright forelimb postures,” said Bonnan.

The fossil record offers scientists a motionless slice of history. Bonnan and his team have turned to optical tracking technology to tell more of the story.

“Our ultimate goal is to realistically model and place constraints on how fossil vertebrates, such as dinosaurs and early mammals, moved their forelimbs,” Bonnan explained.

The team is quantitatively illustrating the motion of modern day reptiles and mammals and using bone shape as a common denominator to make comparisons between their laboratory stand-ins and dinosaurs.

Bonnan’s lifelong desire has been to “reconstruct long-dead animals and breathe life into old bones.”

Step-by-step, his vision is coming to life with the support of colleagues, student researchers and staff within the School of Natural Sciences and Mathematics.

Blending Physics and Biology

To model motion, math and physics come into play. Bonnan’s friend and colleague, Dr. Jason Shulman, joined the team lending his numerical analysis expertise. “Jason Shulman is a big part of why we’re able to do this. Without him, interpreting the data would be difficult at best,” said Bonnan.

Early in the Physics curriculum, students learn to calculate angles and speed, which means that undergraduates are prepared to take part in real research outside of textbook exercises Shulman said.

Sometimes Physics majors wonder why they need to study Biology and vice versa. The animal locomotion research is an example of how the sciences work together. “It’s important for students to understand concepts outside of their field—that’s an important lesson I hope we convey.

The interdisciplinary collaboration is perfect for Physics students,” said Shulman.

Campus-wide Support

The bearded dragons were donated to Bonnan by student Kiersten Stukowski, of Gloucester in Camden County. Scientists rarely have the opportunity to work on a long-term project with the same specimens as they mature explained Bonnan.

Justine Ciraolo, director of Academic Laboratories and Field Facilities, connected Bonnan with her sister, who is loaning her ferrets to the team.

One of our ferrets, "Mocha."

One of our ferrets, “Mocha.” Photo (c) Susan Allen/ The Richard Stockton College of New Jersey

When the reptiles and mammals aren’t in the lab, they are cared for by John Rokita, principal animal health lab technician, who has been instrumental in acquiring specimens for Bonnan.

“None of this would have been possible without the support of the School of Natural Sciences and Mathematics and Stockton’s Institutional Animal Care and Usage Committee. It is rare for undergraduates to get this experience. On every level this is teamwork and everyone has been incredibly helpful,” said Bonnan.

The Student Researchers

Alex Hilbmann, a sophomore Biology major, of West Deptford in Gloucester County, says he’s learned all about lizards while building a foundation to better understand the kinematics (or science of motion) during his independent study. “It wasn’t always easy to get them to run,” he admitted. Hilbmann plans to go on to medical school after Stockton.

Caleb Bayewu, a junior Biochemistry major who’s from Maywood in Bergen County, started out working with rats on the treadmill, but “they didn’t always want to move.” Since he joined the team, he’s witnessed the differences in movement among different species.

Corey Barnes, a senior Biology major, of Seaville in Cape May County, took Comparative Anatomy with Dr. Bonnan, which he says opened up his interest along the evolutionary tree. The research has really illustrated “how different their walking habits are.” Barnes is a veterinary technician at Beach Buddies Animal Hospital in Marmora and hopes to attend veterinary school.

Alex Lauffer, a junior Biology major, of Point Pleasant in Ocean County, has always had an interest in dinosaurs and reptiles. The research project was “right up my alley,” he said. The aspiring veterinary assistant has three snakes, one tarantula, one dog and a pond of koi fish. However, it was in the BFF Lab that he held his first bearded dragon. They are surprisingly calm, he said.

Kieran Tracey, a sophomore Biology major, of Sea Isle City in Cape May County, said, “I’m having a lot of fun working with lizards and watching them run,” and added that the experience is giving him important exposure to research in preparation for medical school. He looks forward to “analyzing how [the data] relates to dinosaurs.”

Bridget Kuhlman, a senior Biology major, of Little Egg Harbor in Ocean County, said, “It’s a dream come true being able to work with ferrets. It’s getting me ready for vet school,” she said. She works as an EMT and personally owns five ferrets.

Bridget Kuhlman (left) and Kelsey Gamble (right) attach tracking beads to the ferret nick-named, "Mocha" as Drs. Bonnan and Shulman look on.

Bridget Kuhlman (left) and Kelsey Gamble (right) attach tracking beads to the ferret nick-named, “Mocha” as Drs. Bonnan and Shulman look on. Photo (c) Susan Allen/ The Richard Stockton College of New Jersey

Kelsey Gamble, a senior Anthropology and Biology major, of Williamstown in Gloucester County, said, “Working with live animals is an interesting experience. It’s a lot different than my anthropology work,” she said. “We are looking at the forelimbs and how they move.” The search for patterns and constructing relationships between form and function blend her Biology and Anthropology interests.

Kelsey Gamble, a senior Anthropology and Biology major, of Williamstown in Gloucester County, said, “Working with live animals is an interesting experience. It’s a lot different than my anthropology work,” she said. “We are looking at the forelimbs and how they move.” The search for patterns and constructing relationships between form and function blend her Biology and Anthropology interests. Pictured, she holds a ferret that is taking part in the animal locomotion research project at Stockton College. Photo (c)

Kelsey Gamble, a senior Anthropology and Biology major, of Williamstown in Gloucester County, said, “Working with live animals is an interesting experience. It’s a lot different than my anthropology work,” she said. “We are looking at the forelimbs and how they move.” The search for patterns and constructing relationships between form and function blend her Biology and Anthropology interests. Pictured, she holds a ferret that is taking part in the animal locomotion research project at Stockton College. Photo (c) Susan Allen/ The Richard Stockton College of New Jersey

Contact:         Susan Allen
                        Office of News & Media Relations
                        Galloway Township, NJ 08205
                        Susan.Allen@stockton.edu
                        (609) 652-4790

Ferret on a treadmill — you read that correctly

When you’re interested in documenting forelimb locomotion to help you infer what was going on extinct reptiles and mammals, it pays not to be picky.  So when the opportunity came to analyze the gaits of two ferrets materialized, how could the BFF lab say no?  Ferrets have a unique body morphology and certainly have a much more upright forelimb than the rats and reptiles we typically work with, so they help form a nice point of contrast and comparison.

What happens when you place a GoPro camera at the end of the treadmill?  Success, that’s what.  BFF student Bridget Kuhlman did just that the other week in our lab during our data capture sessions, and she got this brilliant bit of POV video.  You don’t see Bridget directly in the video, although you do see her finger which has a tasty smear of FerretVite which we use to coax the ferrets to walk in the line of the infrared cameras.  In the background, modulating the treadmill, is BFF student Kelsey Gamble.

You will notice that this Ferret, nick-named “Latte,” walks and then rides the treadmill backwards, then walks again.  Science is messy — no animal is going to walk in perfect rhythm with the treadmill from start to stop.  What we do is capture all the data, and then find the motion capture portions where “Latte” and our other animals are keeping pace with the treadmill.  Incidentally, we measure various body dimensions on the animals each session (in case they grow or put on/lose weight) and we note the treadmill speed so we can calculate how fast they are moving.

“Latte,” and his room-mate “Mocha,” have been temporarily loaned to us thanks to the generosity of Jen Ciraolo.

News from the BFF Locomotion Lab

Just a brief post to point out we’ve updated our main lab page and that we have many new student members.  We’ve also seen our first lab alumni graduate or move on to other projects.

Just a reminder that you can follow us on Twitter: @BFFLocomotion and Facebook.

 

Why I love bearded dragons -or- Putting lizards through their paces in the BFF Lab

This has been an exciting week for my students and I in the BFF locomotion lab.  We have finally worked out multiple bugs in our system and have a bunch of very peppy and cooperative bearded dragon (Pogona vitticeps) lizards.  Corey Barnes, one of the BFF undergraduate seniors and PreVet Biology major, captured one of our trials on a young beardie we affectionately named Greenbeard.  As you can see in the video below, we entice the lizards to walk and run by tempting them with their favorite treats – crickets!  Although the lizards cannot get the treats immediately (we need the incentive), they each get a tasty cricket after each trial to reward them for a job well done.

Yes — these are juveniles … adult bearded dragons will be filmed as well.

The data we are collecting will form the basis of a comparative study of the relative movements of lizard forearms relative to the body across several species.  Given that the earliest mammals and dinosaurs had a forelimb posture not unlike lizards (in some respects, lizards have “held on to” the ancestral forelimb posture and anatomy of early reptiles and mammals), they are acting as a model to test hypotheses about the transition from sprawling to upright forelimb postures.

The treadmill was custom made for us by JogADog, and we’re capturing data from reflective markers using the OptiTrack V120 Trio system for motion capture.

The "Bonnan Beardies" crew with our treadmill (center) and motion capture system (left).  From left to right, Alex Lauffer, Kieran Tracey, Alex Hilbmann, and Corey Barnes.

The “Bonnan Beardies” crew with our treadmill (center) and motion capture system (left). From left to right, Alex Lauffer, Kieran Tracey, Alex Hilbmann, and Corey Barnes.

Why science definitions matter: a response to the NCSE’s Misconception Mondays

Dear fellow scientists and science educators: may I suggest the time has come to work together to standardize the major terminology of our field?  I don’t mean the terminology of specific disciplines, I am getting at the fundamentals here: what is science, and how do we effectively and efficiently communicate what a hypothesis, law, and theory are?

I am writing this post because I read with some dismay the recent National Center for Science Education’s blog Misconception Mondays: Hypotheses, Theories, and Laws, Oh My! by Stephanie Keep.  I encourage my readers to read her blog post and form your own opinions.  I want to be clear from the beginning that this is nothing personal about Stephanie Keep — her post simply caught my attention and serves as a spring board for discussing what I read and hear all too often from many of my colleagues.

The take home message from Keep’s post is this: it doesn’t matter what labels we give concepts in science, so long as science is being taught.  In essence, don’t get bogged down in semantics and lose the forest for the trees — it is more important that students understand the science.  At face value, this seems reasonable: don’t be pedantic be practical.

On deeper reflection, however, this attitude (an attitude shared by many in the sciences) is troublesome, because definitions and the meanings we attach to words do matter, especially for students and the public who vote on science issues.  Keep says:

People—especially scientists—like firm definitions. Science is full of technical terms that we learn to master (or learn to quickly look up on the Internet), and thanks to a mixture of precedent and state standards, many teachers keep making kids learn definitions for theory, law, and hypothesis in the introductory weeks of a new class. I’m not suggesting that kids shouldn’t learn what a hypothesis is—of course they should! Forming and testing hypotheses are fundamental parts of any scientific endeavor. But I am suggesting that we be willing to admit that there is often no good reason why something is called a law vs. a theory, or a hypothesis vs. a theory—and that’s okay.

But therein lies the fundamental problem with this approach — not just Keep’s approach, but, I would argue, the approach so many of us have been taught to take.  How can you teach a student how to test a hypothesis if you simultaneously tell them that we can’t tell if it’s a hypothesis or a theory?  These definitions do matter.

Something else is troublesome in Keep’s statement that, “many teachers keep making kids learn definitions for theory, law, and hypothesis in the introductory weeks of a new class.”  In any discipline, you learn what it is and how it works in the beginning so that you have a common language through which to teach and make sense of the core material.

If we are charged with doing science and with educating the public about science, shouldn’t we able to say: here is what science is, here are it’s limits, and here’s how the toolkit works?  Especially at the beginning of a class?  As scientists and science educators, we seem on the whole to be so circumspect about this because, I suspect, we appreciate that science is not about certainty but about probability.  Therefore, we are loathe to say we have a concrete definition because we fear that what we convey is an absolutism rather than messy reality.  Believe me — I understand and appreciate wanting to avoid teaching our students that science = unassailable truth.  But if this is a fear of looking too authoritarian, in my opinion, it has led to much confusion both among ourselves and the public at a time when science is under attack.

Dear scientists and science educators: it is okay to have firm definitions that define and describe what we do, and we need to give ourselves permission to be okay with that.  It is no longer okay for us to say to students, in essence, we can’t really describe or define what it is we do precisely, but you’ll know it when you see it.

It would be arrogant and presumptuous on my part to suggest I have the definitive answer or definitions for what we do, nor do any of us work and teach in a vacuum — much of what I teach my students is cobbled together from what I have found works for me as an instructor (borrowed and morphed from many gifted individuals), particularly the approach of a former graduate mentor, Dr. Ron Toth at Northern Illinois University.

But I would like to start a conversation about fundamentals.  Surely, science as a discipline is not an amorphous thing.  I suspect most of us would define it as a tool for understanding the natural world.  Many of us test hypotheses – these are predictive statements that can be tested and falsified which guide our research.  We often test our hypotheses under an explanatory umbrella we call a theory.  As an example, a paleontologist might test the relationships of various dinosaurs (a hypothesis called a phylogeny) using data collected from fossils, working under the explanation that they are closely or distantly related through common ancestry (a theory called biological evolution).

Laws, I will admit, often stick in many of our craws.  I have come to see scientific laws as testable descriptions of repeatable phenomena or processes.  If we define scientific laws in this way, we are now more clear about what should qualify.  For example, in her essay, Keep says,

Have you ever noticed that most of the “laws” in science tend to be in the physical sciences and astronomy? There aren’t a lot of “laws” in biology—in fact, I can’t think of any aside from Mendel’s Laws. Why is that? Is it because biology is a “soft science” while physics and astronomy are “hard sciences”? Not at all. It’s because people in those fields really liked the term “law.” No, really. That’s pretty much it.

I would argue that we do have laws in all the branches of science, we just don’t always call them that.  If a scientific law is a repeatable phenomenon or process, Genetic Dogma (DNA is transcribed and translated by RNA into proteins) is a law — it happens continuously in all living things, always the same — a repeatable phenomenon or process.  Natural Selection is a Law — all individuals vary, more individuals in a population are born than can survive, and those with variable traits that allow them reproduce viable offspring are “selected.”  Look at any population in the living world, and this process is on-going and repeatable.  How about calling the Cell Theory, the Cell Law?  After all, that living things are made of cells is pretty much a repeatably observable phenomenon.

This works for me and for teaching my students, but I am not suggesting I have the market cornered on this definition.  Rather, my point here is that when we have a clear definition, we can more easily comprehend what we are communicating to one another and to our students.  If I am testing a hypothesis, you and others know I am probably working under an explanation, a theory.  If I am testing a law, you and others know that if I find variation or the phenomenon does not repeat, I may be in a position to reject or modify that law.

We need to have this conversation because definitions do matter in science.  What you call something does matter, especially when you need it to convey a particular set of qualities.  True, there will always be exceptions to the definitions and the natural world is messy, but don’t let perfection be the enemy of progressScience is and should be definable — we don’t just know it when we see it.

I welcome any constructive feedback and ideas from all of my colleagues as to how we can and should move forward.  I want to thank Stephanie Keep for sparking this conversation.

For those who don’t know and who might be interested, I have outlined and explained my own approaching to teaching science and evolution.