An old dinosaur learning new tricks

Okay, so I’m the “old dinosaur” here, although I was informed recently that I could still pass as a graduate student.

I am happy to report that I am back on the campus of Brown University this week with one of my undergraduates, Radha Varadharajan, to begin what I hope to be the first in a long series of studies on the evolution of amniote (reptile, bird, mammal) forelimb posture.  We (my “rat pack” students and I) are using the XROMM technology I have detailed here on this blog to understand how the three-dimensional movements of the forelimb bones of rats actually occur.  The long-term goal of this initial study is to document how these movements facilitate hand placement and posture, and how these details of locomotion are related to bone shape.  My ultimate goal is to use the somewhat primitive forelimb posture of rats as a template to understand how some early fossil mammals may have moved.

Today, Radha and I, under the tutelage of Dr. Elizabeth Brainerd, began the process of setting up the so-called C-arm fluoroscopes that will allow us to take calibrated X-ray movies of a number of rats as they walk, run, and perhaps do other activities that we happen to capture.  This was especially exciting and informative for me, because these are the “new tricks” this “old dinosaur” wants to learn.  Tomorrow, we begin in earnest filming the skeletal movements of the rats.

You will notice in the pictures posted here that Radha and I are suited up in lead aprons and thyroid collars because, as you might anticipate, we do not want to expose ourselves to X-ray radiation during the data capture.  In fact, she and I have participated in numerous safety trainings and tests to ensure we stay safe.

Here I am behind the two C-arm fluoroscopes. In front of the scopes, you can spy the wooden plank walk-way for the rats, and an acrylic box that the rats will walk or run through in the vicinity of the X-ray fields.

Here is Radha learning x-ray capture at the Brown C-arms lab.

We also spent time today with Dr. David Baier learning how to set up what is called a rig in the MAYA software program that will later animate the skeletons of the rats we film.  Essentially, a rig in this case means creating a joint system that can be calibrated with the X-ray films and “attached” to the 3-D bone geometry from CT-scans of the rats used in the study.  I further shook some of the rust out of my head reviewing and practicing how to import calibrated data from X-ray digital movies and syncing them with 3-D bone geometry — skills I first acquired almost one year ago during Brown’s 2012 XROMM course.

All of this setup and learning is key for me and my students, not only because we want to do the science right, but also for other reasons I shall divulge in future posts.

Everyone at Brown has once again been incredibly helpful, and I am especially indebted to Dr. Brainerd for her encouragement and help over the past year with XROMM.

Please stay tuned … this week promises to get more interesting …

Academic “evolution”

Recently, one of my former undergraduate honors students, Collin VanBuren, did something remarkable: he not only was accepted into Cambridge University, but was also the recipient of the Gates Cambridge Scholarship!  What is the Gates Cambridge Scholarship?  It is a prestigious award for outstanding applicants from countries outside the U.K. to pursue full-time postgraduate work in any subject available at the university. For Collin VanBuren, this is well-deserved indeed.

Collin, like many of my students, came to me as an eager undergrad with an interest in zoology, and in particular he was interested in marine mammals.  So, I put him to task studying the morphology of the cetacean radius bone (a bone in the forearm) because of my broader interests in forelimb posture among mammals and dinosaurs.  Collin, like many of my students, far exceeded my expectations: he not only collected a lot of data on cetaceans and other mammals, but he desperately wanted to pursue reptile and dinosaur radius morphology.  I warned him it would not be easy and that he was under a short time constraint.  Collin assured me it could be done, and over 400 bones later, he was correct!  He presented his undergraduate work at the Society of Vertebrate Paleontology (as an oral talk, no less — and it was his first ever SVP presentation!) and he and I are now revising what I expect will be a well-received paper … and very much due to his diligence!

During all of this research, Collin headed the Zoology Club at WIU, he participated on several digs in the Late Jurassic Morrison Formation of Utah with me, other eager students, and the Burpee Museum, and was one of many active members of our Functional Morphology and Evolutionary Anatomy (FMEA) Lab, co-directed by Dr. Jess White.  Collin then was accepted into Dr. David Evans’s M.S. program at the University of Toronto, where he has continued to excel, before this latest award.

Seeing my former WIU students succeed always makes me smile and remember the many fun dissections, interesting discussions, and sense of a cohort we often had.  I am singling out Collin now, of course, but I could and will write updates about my other students, including among many others: Ashley Morhardt, now a successful Ph.D. student in Dr. Larry Witmer’s lab; Hillary Parks, who successfully defended her M.S. at WIU and went on to be a key member of the Burpee Museum; Kristy Tuttle who did an M.S. at WIU on rodents and will now be working with Dr. Virginia Naples at Northern Illinois University on her Ph.D.; Simon Masters, one of my first M.S. students at WIU, who is currently one of the best dinosaur paleontology field hands out there; Katie Reiss who did an excellent undergraduate project on shark tail morphology and has gone on to earn her M.S. in shark toxicology; and many more I could and need to mention in the near future.

It is often remarked in academic circles that we have our own academic family as well as our biological one.  In other words, we are “descendants” of our advisors, who are descendants of theirs, and so on, and we can trace back our scientific roots, if you like.  For me, my academic “ancestor” is J. Michael Parrish, and I believe that his encouragement and support of me during my formative years as a scientist have now been passed to another generation. As a scientist or other academic, your students are your “children,” and I hope that, like a “parent,” these students succeed and stand on their own two feet.  I cannot take but a shred of credit for them, because they were all self-motivated, but I am glad to know them and especially glad to hear when they do well.

Again, many congratulations to Collin, and, as I begin to advise a new and eager crop of students here at Stockton, I hope they get to meet and be inspired by my former WIU students.  Would that be cross-pollination or interbreeding?

The “Rat Pack” Succeeds

A lot has happened in the Bonnan Lab at Stockton these past few months.

First, the “Rat Pack” as I fondly call them (Evan Drake, Kadeisha Pinkney, and Radha Varadharajan), presented their research proposals for 3-D rat locomotion and kinematics to the Northeastern Regional Vertebrate Evolution Symposium (NERVES) on March 22nd, 2013, at the New York Institute of Technology (NYIT) College of Osteopathic Medicine.  Their talks were very well received and we had excellent suggestions from colleagues and scholars.  I was especially proud of these undergraduates because they were able to give technical talks to a scientific audience having only worked with me for a few months on their projects. Bravo!

A special thank you to the Symposium’s organizers, Drs. Brian Beatty and Matthew Mihlbachler!

You can read their NERVES talk titles below.

Next, they put their collective heads together and, with my input, created a very nice poster for the 2013 NAMS Research Symposium at Stockton.

You can read their NAMS research abstract below as well.

The “Rat Pack” presented their preliminary research on rat locomotion to the 2013 NAMS Research Symposium. Left to right: Kadeisha Pinkney, Radha Varadharajan, and Evan Drake.

Kadeisha (left) and Radha (right) explain the joys of rat locomotion to interested students.

The “Rat Pack” attracted quite a crowd.

Last, but not least, Radha Varadharajan received the first Robert L. Fines scholarship awarded at Stockton, April 26, 2013, for her work on this research and her future career goals in veterinary medicine.  Dr. Fines is a former Stockton alumnus (1975) and is one of the premiere M.D. researchers successfully fighting pancreatic cancer.  He is the Herbert Irving Associate Professor of Medicine in the Division of Medical Oncology at the Columbia University College of Physicians & Surgeons in New York, New York.  I am honored and proud that Radha has received this award from such a prestigious alumnus.

The scholarship will allow Radha to travel with me to Brown University the week of May 20-24, where we will work with Dr. Elizabeth Brainerd and colleagues X-ray filming the rats walking, running, and landing at their XROMM C-arms facility.  Stay tuned and we’ll keep you posted on our time and research activities while at Brown.

Finally, I must acknowledge the help of our campus veterinarians, Drs. Ralph Werner and Mary Wilkes, for their efforts in helping me with the rats, as well as our animal caretaker, John Rokita, for his constant help and suggestions on rodent protocols and biology.

I feel truly grateful to have made such a jump to a new college and to already be surrounded by supportive faculty, eager students, and the chance to pursue 3-D kinematics research.

NERVES Talk Titles

Varadharajan, Radha and Bonnan, Matthew F. 2013. Exploring 3-D long bone kinematics in the White Rat (Rattus norvegicus) as a model for inferring forelimb posture in early mammals: Contribution of the scapula.>

Pinkney, Kadeisha and Bonnan, Matthew F. 2013. Exploring 3-D long bone kinematics in the White Rat (Rattus norvegicus) as a model for inferring forelimb posture in early mammals: Contribution of the humerus.

Drake, Evan and Bonnan, Matthew F. 2013. Exploring 3-D long bone kinematics in the White Rat (Rattus norvegicus) as a model for inferring forelimb posture in early mammals: Contribution of the radius and ulna.

NAMS RESEARCH SYMPOSIUM ABSTRACT

Forelimb movements in Rattus norvegicus (white rat) and their relationship to pronation: implications for early mammal forelimb posture

Varadharajan, Radha; Pinkney, Kadeisha; Drake, Evan; and Bonnan, Matthew F.

 

Rattus norvegicus (the white rat) is a therian mammal with a forelimb morphology similar to that of early non-cursorial mammals. Currently, early mammal limb posture is controversial, with reconstructions ranging from sprawling to parasagittal. With this current ambiguity, the study of forelimb shape and movements in R. norvegicus may provide a model to infer the locomotor patterns of earlier mammals.  Previous research, most notably by Jenkins (1971, 1974), indicates that the forelimb posture of rats does not follow simple, pendulum-like mechanics but rather a more complex, less-upright range of movement. For the first time, we will study the 3-D morphology and kinematics of the forelimb in R. norvegicus by utilizing three-dimensional moving X-ray animations generated through the XROMM (X-ray Reconstruction of Moving Morphology) technique.  Specifically, we will focus on the three-dimensional movements of the scapula, humerus, and antebrachium (radius and ulna), and their combined contribution to pronation (placing the hand palm-side down).  To this end, we will test three interdependent hypotheses on the contribution of each of these limb segments to pronation. For the scapula, we examined the serratus anterior, supraspinatous, infraspinatous, spinotrapezius, acromiotrapezius, and rhomboids major and minor. Data gathered on the rat scapula through literature and dissection lead to the hypothesis that this element contributes in a significant way to pronation. Specific features of the humerus distinguish the parasagittal from the sprawling stance in early fossil mammals: degree of torsion, condylar structures of the elbow joint, width of the intertubercular groove, and the relative sizes of the lesser and greater tubercles.  These features are associated with major locomotor muscles such as the pectoralis major and minor, deltoids, and pronator teres. We hypothesize that the humerus will contribute in a significant way to the pronation of the hand in the white rat. In humans, the radius can rotate about the ulna to pronate the hand because these elements are bowed, creating the space necessary to allow such movements. The pronator teres and pronator quadratus pull on the radius and rotate it about the ulna, whereas the supinator and biceps brachii act as antagonists to return the bones to a parallel position. Unlike humans, the radius and ulna of Rattus norvegicus fit tightly together like two spoons stacked together, with little, if any, space available in which the radius can rotate about the ulna.  Moreover, the pronator quadratus has not yet been described or identified in our rat dissections. Instead, the radius and ulna appear “fused” by the interosseous membrane and rendered incapable of supination. Rats have little need to supinate the forelimb because the forelimbs are primarily used in locomotion. It is therefore hypothesized that all pronation and supination occur in the humerus and scapula in rats because the radius and ulna are in such close proximity to each other that we infer they participate little, if any, to pronation.  After we capture the three-dimensional movements of these bones with XROMM, we will test our hypotheses and perhaps gain insight into the posture of early mammals.

The NAMS Research Symposium — a Stockton Success!

On behalf of Tara Luke and myself, a huge thank you to everyone at Stockton for helping to make this year’s NAMS Symposium such a success!

Please thank all of your students for doing such an excellent job.

Also, thank you to Dean Weiss, to Tana Tracey who helped set up the food services and location before she retired, thanks to David Dimmerman and all in A&S who helped with printing the volumes of posters, and of course the judges: Jason Shulman, Eva Baranowski, Mark Sullivan, Russ Mason, Dick Colby, and Adam Aguiar.  And, last but not least, thanks to Provost Harvey Kesselman for attending the event and offering such great words of encouragement to our students.

Pictures of the winners and the event can been seen by clicking here.

Abstracts and Poster Numbers for Stockton NAMS Research Symposium now on-line

This brief post is to notify students, faculty, and all of those interested that the NAMS Research Symposium Abstracts and Poster Numbers have now been published on this blog.  Again, the NAMS Research Symposium will be held on April 19, 2013, from 3-5 PM in the atrium between the C&D wings.

For students and faculty involved in presenting research: follow the link to the on-line NAMS Research Symposium abstracts and locate the number of your poster.  Posters are listed in alphabetical order by the first author.  There will be numbers posted in the Atrium between the C&D wings on Friday, April 19, by 11:00 AM.  From 11:00 AM to 2:50 PM, students should hang their posters under their designated poster number.  Drs. Tara Luke and Matthew Bonnan will be available during these times to assist students with setting up their posters.

Given that we have 46 presentations, please make sure that you place your poster under the correct number that you have been assigned.

Thanks to all the students and faculty for submitting so many interesting research abstracts, and we invite the Stockton community and anyone else who can attend to come and see this work.

Stockton Science Students will be presenting their original research April 19, 2013

Just a quick post to let students and anyone in the Stockton community know that on April 19, 2013, we are hosting the Natural Sciences and Mathematics (NAMS) Research Symposium.  Any students in NAMS who are actively working on faculty-sponsored research are encouraged to participate.

For more information, and to submit an abstract, please see the NAMS Symposium page on this blog.

You can also follow us on Twitter at #OspreySci

The Facebook Event page for our NAMS Research Symposium: http://www.facebook.com/events/330868603701753/

Oh, Rats!

Dr. Bonnan and three undergraduates at the Richard Stockton College have begun to investigate the forelimb anatomy of the white lab rat (Rattus norvegicus).

White lab rat. Source: http://upload.wikimedia.org/wikipedia/commons/1/1d/Albino_Rat.jpg

This mammal is well-known and has been the center of many studies, but we would now like to take what is known about forelimb locomotion into 3-D by using XROMM technology in cooperation with Brown University.  Currently, three undergraduates are working on different aspects of rat forelimb anatomy, and each will scan and describe the three-dimensional morphology of bones in the rat forelimb.  This summer (2013), XROMM data collected by Dr. Bonnan at Brown will be analyzed in conjunction with the undergraduate students and their long bone scans to reconstruct forelimb movements related to pronation in white rats.  Why are we doing this and what does this have to do with dinosaur locomotion?

Student Radha Varadharajan dissecting rat forelimbs – she will focus on describing movements of the scapula.

Student Kadeisha Pinkney – she is dissecting rat forelimbs and will be describing the contribution of the humerus to pronation.

Student Evan Drake – he is dissecting rat forelimbs and will focus on the contribution of the radius and ulna to pronation.

We will begin blogging and tweeting about our lab’s work in the near future … stay tuned!

Dead dinosaurs and reasons for hope

“Time will turn us into statues, eventually.”

– Saint David Grohl, a fighter of foo

As we enter this time of the holidays in the United States, many of us become reflective on the year and take stock of our lives.  For my family and I, this year has been absolutely wonderful, dreadful, fantastic, unnerving, scary, and hopeful.  Why?  There has been a lot of change in our lives: see my lonely post from September for more details and my farewell to my previous institution.  This would also explain my dearth of blog posts, although a weird and interesting topic snuck in this November.

I am also finishing my dinosaur course here at Stockton, and that means I give my final lecture on “What I hope you have learned from dinosaurs.”  It struck me today that this would make an excellent little blog post as well.

One of my grandfathers was fond of asking me, “Why study dinosaurs?  What’s the point?” When you are asked that question enough times, you eventually develop a repertoire of answers.  I don’t know if these ever satisfied him, but I do hope they satisfy those willing to listen:

There are the Big Picture Reasons:

• First off, dinosaurs are just so damn cool.  Those who need convincing haven’t been paying much attention to the plethora of amazing discoveries that have continued at an ever-accelerating pace since the late 1800s.
• Dinosaurs put our place in the world into perspective – this is not a world meant for us, but one we have had the happy fortune to inherit from previous generations of life.
• Dinosaurs were the most successful group of terrestrial vertebrates the world has seen … and they are still among us as beautiful, feathered treasures.  Oh, birds are not dinosaurs?  Like the Honey Badger, the data don’t care … and the support for birds as dinosaurs is as overwhelming as the data for humans as mammals.

And then there are the Practical Reasons:

• Dinosaurs are the perfect ambassadors for science – they bring scientific concepts and the nature of science to children and the public like nothing else I know.
• While the doctors and veterinarians of the world are busy saving those people and pets you love, the vertebrate paleontologists are in the trenches at the universities and colleges, teaching the next group of practitioners their anatomy.  That’s right – most vertebrate paleontologists are excellent anatomists.  A certain Larry Witmer comes to mind …
• Want to understand why vertebrate anatomy is the way it is?  Ask a vertebrate paleontologist – we have to know all that embryology and evolution stuff to inform our research and to blow your mind. =)  The bottom line has always been the anatomy is the result of embryology and evolution … who better to teach that we dinosaur-o-philes?  And so that I’m being fair – all vertebrate paleontologists are this excellent, not just the dinosaur ones!

Yes, you say, but we’ve heard these platitudes before.  You spoke of hope … where is that?  If dinosaurs have taught me nothing else, it is an appreciation for human life.  As successful as dinosaurs were, their Encephalization Quotient (their EQ, or brain size) was never too generous.  We mammals, on the other hand, have had the evolutionary fortune of inheriting a rather different brain with a typically much higher EQ.  To be fair, the birdy dinosaurs around us have enlarged brains compared to their predecessors.

Why is EQ size a reason for hope?  Well, EQ by itself is not, but it is what we Homo sapiens do with it that is.  I am no anthropologist, but speaking in general terms, here are two things one can say about humans that cannot, so far as I know, be applied to other vertebrate animals:

1. We can both anticipate the future and act on it.
2. We can use imagination to bring positive things into concrete existence.

For all of their significance and success, the non-avian dinosaurs could not have anticipated their demise, nor could they have done anything to act on it.  Apart from ancient aliens imbuing dinosaurs with a sense of imagination (I can imagine a particular channel of history losing all its credibility), these mighty animals could not have brought forth everything from medicine to concepts of social justice.  As a species, we are certainly still working on a lot and have a long, long way to go, but have you ever stopped to think of how unbelievably special and unique it is that we can act on knowledge and create our future?

So this holiday season, and throughout the year, I hope you may reflect on the fact that whereas for non-avian dinosaurs history’s lessons were inaccessible, they are very much an open book for us.  If we can anticipate what the future will bring, we can act on it.  If we decide to put our imagination to good use, we can create positive change in the world.

The non-avian dinosaurs could not learn from their past, but perhaps we can learn from them … and from our own ancestors.

“So have a toast and down the cup, and drink to bones that turn to dust.” — Oingo Boingo (Danny Elfman’s rock band)

Danny Elfman, creator of the Simpson’s Theme Song, can’t be wrong …

References

Fastovsky, D. and Weishampel, D. 2009. Dinosaurs: A Concise Natural History. Cambridge University Press. 379 pp.

Penis worms, anuses, and evolution

Now that I have your attention, what is a penis worm?  Technically, they are invertebrate animals called priapulids which, if you know your Latin, has the word “penis” in there.  What exactly are they?  They are sausage-shaped, segmented worm-like animals with an extensible, toothy proboscis they use to capture prey.  Here is what a priapulid looks like:

A priapulus “worm” — the proboscis is pointing up in this picture.

What do these weird-looking and rather unknown animals have to do with evolution?  A whole lot, as it turns out.

The group of creatures we call Animals is incredibly diverse, and most of us have only a passing familiarity with a small fraction of these denizens.  It turns out that once you get past sponges, jellyfish and their kin, and a weird band of animals called comb jellies, there is a great clade of animals called the Bilateria.  Sounds formal, but basically the name means that this group of animals is bilaterally symmetrical – that is, these animals have symmetry about their midline and have right and left sides.  Look in the mirror – congratulations, you, too, are a member of Bilateria!

The diversity of Bilaterian animals.

You may not appreciate it, but one of the key developments of bilaterian animals is forming a distinct mouth and anus.  This involves the formation of a gut tube, and like all tubes it has to start somewhere.  That somewhere is a puckered indentation called a blastopore that forms early during their embryonic development.  Yes, even we humans develop a blastopore as the beginning of our gut tract.

Among the bilaterian animals, there has traditionally been a split proposed that divides these organisms into two groups based on a fundamental difference in the way their digestive tracts develop.  In one group called Protostomes, the blastopore becomes the mouth, and the gut tract develops until it “punctures” the other end of the animal, forming the anus.  The word Protostome means “mouth first.”  Protostomes include a huge variety of animals such as insects, crustaceans, earthworms, mollusks, and most other “creepy-crawlies” you are familiar with.

In the other group, called Deuterostomes (meaning “mouth second”), the blastopore becomes the anus and the digestive tract stretches from hind to fore, eventually “punching” through the head region to form the mouth.  As I like to tell my students, Deuterstomes develop from the bottom up – you may now groan.  Something that may make you groan all the more is the fact that we vertebrates are members of the Deuterostomes.

The development of the mouth and anus in Protostomes and Deuterostomes.

What does all this have to do with Priapulids?  Everything.  You see, the big evolutionary question is which came first, Protostome development or Deuterostome development?  Which is the original condition in the common ancestor?  Knowing this would inform our understanding of how other changes in development downstream from this evolutionary event were effected, and what we should predict to see in various animal lineages.

So, in a recent study by Martin-Duran and colleagues (2012) in which they followed the development of this engimatic worm, they found … drum roll … that priapulids develop as Deuterostomes, with the blastopore forming the anus.  Why is this shocking?  Because: priapulids share all the major DNA and anatomical characteristics with those of Protostomes!  In fact, they are nested among the members of the Ecdysozoa, the exoskeleton-bearing animals that include insects, nematodes, and crustaceans.  All of those animals have protostomic development … why would priapulids be any different in this regard?

Martin-Duran and colleagues (2012) suggest that we have it wrong when it comes to these evolutionary divisions of animals.  It turns out that we may be too hung up on what the blastopore forms.  Instead, Martin-Duran et al. (2012) suggest that it is the separation of the mouth from the anus that is the major adaptation to focus on in Bilaterian animals.  Given that a number of Protostome animals are similar to priapulids in having all the protostome characteristics except that their blastopore forms the anus, it seems that the Deuterostome condition was the most primitive.  In other words, the Protostome condition is derived, and probably developed independently several times.

Figure 4 from Martin-Duran et al. (2012) showing their evolutionary hypothesis for Bilaterian animal development.

What does all this mean?  It means that we now need to re-explore animal relationships and the fossil record to re-test whether the way we understand the evolution of the major animal groups is in need of re-tooling.  Who would have thought that a penis worm and the origin of its anus would have such an evolutionary significance?

References

• Freeman, S. 2011. Biological Science, 4th Edition. Pearson.
• Martin-Duran, J.M., Janssen, R., Wennberg, S., Budd, G.E., and Henjol, A. 2012. Deuterostomic development in the Protostome Priapulus caudatus. Current Biology, http://dx.doi.org/10.1016/j.cub.2012.09.037

Settling into our new home, settling into Stockton College

This is a brief blog post to let everyone know:

1. My family and I are finally settling into our new home base of Stockton College.
2. That we survived a complex and at times horrendous move.
3. That our livestock, including me, made the trip from Illinois to New Jersey reasonably unscathed.
4. That Dr. White and I are enjoying teaching our first new crop of students at Stockton.
5. That the blur and rush of uprooting and planting ourselves in “foreign” soil is subsiding.
6. That my brain now has the luxury of thinking about dinosaurs and other past life again.

Cheers and thanks to all my blog followers for hanging in there.  Extra special thanks to friends and family who made a difficult move and career change less painful.

Be well and soon(ish), new posts about dinosaurs and all other things paleontological shall commence.