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.

Forelimb kinematics research off and running in the BFF Lab

Just a brief note: our forelimb kinematics research on lizards and mammals is off and running (pun intended) in the BFF Locomotion Lab.  This semester, several teams of undergrads from biology and physics are working with myself and Dr. Jason Shulman (Physics) on a variety of projects to explore the typical range of motion and posture in lizard and mammal forelimbs.

Corey Barnes (left) and Alex Lauffer are working with a bearded dragon lizards to determine the typical range of motion in their forelimbs.

Corey Barnes (left) and Alex Lauffer are working with bearded dragon lizards to determine the typical range of motion in their forelimbs.

A close up of one of our bearded dragons, decked out with optical tracking markers.

A close up of one of our bearded dragons, decked out with optical tracking markers.

Undergrad Bridget Kuhlman coaxing one of our ferrest, "Mocha," with ferret treats to walk on the treadmill.

Undergrad Bridget Kuhlman coaxing one of our ferrets, “Mocha,” with ferret treats to walk on the treadmill.

The BFF Lab is thriving thanks to the help of NAMS lab staff.  We particularly want to thank Justine Ciraolo, Chrissy Schairer, Bill Harron, Mike Farrell, and Mike Santoro for their invaluable help in acquiring lab space and with technical assistance, and Deanne Gipple for help with student safety and animal welfare training.  None of this would occur without the assistance and animal care provided by John Rokita and the animal lab staff and volunteers.  We also thank NAMS Dean Dennis Weiss and the Biology and Physics programs for their continued support and assistance with our research endeavors.  Finally, we give a special “shout out” to the Stockton Federation of Teachers for their strong encouragement of faculty research “without walls.”  Thanks everyone!

Sauropod forelimbs -or- why I was wrong -or- why I do research

An in-press, open access paper by Joel Hutson extensively cites my Bonnan (2003) paper while developing a hypothesis that quadrupedal dinosaurs did not evolve fully pronated forearms.  Hutson suggests, correctly, that the hypothesis linking hand morphology and pronation in Bonnan (2003) is falsified.  I agree.  I also agree with Hutson that dinosaur forearms are best understood in the context of other non-mammal tetrapods, and I agree that mammalian-style (and chameleon-style) pronation of the hand was not possible in known quadrupedal dinosaurs.  But I take issue with the tone of Hutson’s paper, and for what I think he misses about the process of science.  To put this in context, first a little history:

As odd as it may seem, the forelimb posture of quadruepdal dinosaurs is anything but settled.  This is due to several reasons, chief among them being that a large amount of articular cartilage encapsulated the ends of the long bones (see here and here, for example).  Since this tissue is rarely preserved, determining how the elbows and shoulders of dinosaurs went together, let alone their possible ranges of movement, is difficult to determine at best.  This makes determining how the bones were oriented in life difficult to resolve.  Regardless of how much cartilage was or was not there, a dinosaur forearm and that of a large, quadrupedal mammal are different.  Without going into a long, drawn-out discussion on the subject, suffice it to say that, like other archosaurs, the radius and ulna of most quadrupedal dinosaurs lie parallel to one another.  If the forearm was held as a relatively vertical support structure, it is difficult to envision how the hand would be pronated so that it moved in synchrony with the foot.  Large mammals accomplish this by significant crossing of the radius over the ulna: this turns the hand palm-side down (pronation) and essentially allows it to work effectively in tandem with the foot to push the animal forwards.  In other words, an elephant hand and foot push in the same direction.

In graduate school (mid-to-late 1990s), I noted what I believed were inconsistencies: 1) sauropod trackways show that the manus is often pronated (although not quite as much as mammals and certainly the palm did not face directly backwards); 2) the forearm bones articulated like they do in other archosaurs, like alligators, that cannot assume an upright, columnar forelimb posture with a pronated hand; 3) quadrupedal dinosaur forelimbs were often restored with the radius crossing the ulna to some degree, which cannot occur when you articulate the bones together.  In essence, there appeared to be a mismatch between trackways and bone morphology.

It had been well-known that the hands of most sauropods were a vertically-oriented, tubular metacarpus (palm) with stubby fingers and sometimes a large thumb claw, whereas the hind feet were more what you might expect in a big animal: a large foot spread across a fat pad.  Why the difference?  I began to notice that when the radius was articulated with the ulna, it was cradled on either side by ulnar processes at the elbow.  One of these processes was not present in “prosauropods,” theropods (including birds), and crocs.  It occurred to me that, perhaps, the radius had shifted internally in the forearm relative to the ulna, and this “new” process (the craniolateral process) evolved to buttress the humerus where the radius once resided ancestrally.  If the radius had shifted medially, this would further “drag” the hand into pronation.  There was also a lot of cool Evo-Devo stuff going on at the time, and I was absolutely enraptured with the concept of the digital arch that forms the hand in embryos.  Since this arch forms from the ulna side and spreads to the radius side, I hypothesized that a shift in radius position internally could bend the hand into a U-shaped structure.

I published on this in the Journal of Vertebrate Paleontology in 2003, and it is one of my most cited papers.  It was, to the best of my knowledge at that time, the simplest “solution” to two “problems” — pronation of sauropod hands and their U-shape.

Needless to say, a lot has happened since 2003.  Many, many more sauropods and “prosauropods” have been discovered, and other well-known species have been re-described.  In my 2003 paper, I predicted that when the earliest sauropods were found, if they had an ulna with a craniolateral process that hugged the radius, they should also have a U-shaped hand.  You know what?  I was wrong.  My first excursion out to South Africa cinched it for me — I got to examine the forelimb of Melanorosaurus, either an almost-sauropod or a basal sauropod.  That one animal blew up my hypothesis — it had a craniolateral process on the ulna, but a flattened hand.  End of story. Done.

Well, sort of.  Adam Yates and I published on the forelimb of Melanorosaurus in 2007, and we drew attention to this issue.  We suggested that the radius might still have shifted proximally at the elbow, but that it did not directly and radically effect the hand.  We suggested that the U-shaped hand seen in most “classic” sauropods evolved after this shift and may have enhanced pronation by assuming a U-shape.  But we definitely stated that the Bonnan (2003) hypothesis linking the possible shift in the radius and the U-shaped hand was falsified.  As we stated in the abstract for that paper:

The forelimb morphology of Melanorosaurus suggests that pronation of the manus occurred early in basal sauropods through a change in antebrachial morphology, but that changes to the morphology of the manus followed later in eusauropods, perhaps related to further manus pronation and improved stress absorption in the metacarpus. Thus, we conclude that changes to antebrachial morphology and manus morphology were not temporally linked in sauropods and constitute separate phylogenetic events.

So, to return to Hutson’s paper, I was surprised that he is apparently unaware of the Bonnan and Yates (2007) paper on Melanorosaurus where we clearly say, yes, there probably was no direct link between pronation and U-shaped hands.  Again — the hypothesis put forward in Bonnan (2003), based on what was available and known at the time, is falsified, so far as the U-shaped hand and radius-shift are concerned.

I was also surprised that Hutson claims, for example, that I formulated my original hypothesis within a restricted phylogenetic context.  At the time, I had dissected and studied bird and reptile forelimbs, and also examined and articulated where possible the forelimbs of “prosauropods” and theropods, and had examined a variety of mammalian forelimbs — keep in mind, this is all before it was feasible to easily digitize and manipulate sauropod dinosaur skeletons.  I reference all of these taxa in additional to numerous sauropods in my study.  To suggest my hypothesis was developed within a restricted phylogenetic context is specious.  Hutson also suggests that I was unaware of the plesiomorphic condition for pronation in tetrapod forelimbs.  I will leave that to my readers and to the scientific community to judge.

Throughout the paper, Hutson uses phrases like “Bonnan reasoned …,” “Bonnan relied upon a suggestion …,” and so forth that imply I did not examine material first-hand.  I did, and spent many many months and years agonizing over what I had examined, articulated, and dissected.

I could go on, but my point is this.  Science proceeds by making hypotheses, testing them, putting that through the process of peer-review, and the allowing the scientific world community to continue to test and modify those hypotheses.  As a scientist, you are going to be wrong, and wrong a lot.  Over time, new data are going to emerge, new approaches will crop up, and new eyes will look at old bones.  You do the best you can with what you have, but you can’t let perfection be the enemy of progress.  No paper and no study is perfect — hypotheses will be overturned.  If we waited to publish when everything was perfect, nothing would be.

When your hypotheses have been falsified, it is okay to admit that.  In 2007, that is precisely what Adam Yates and I did — we said, yep, Bonnan (2003) got some things wrong because we now have better data, and the data don’t agree with that hypothesis anymore.  And you know what?  That is going to keep happening — scientists evolve past their older papers, and science is self-correcting.  If I were still trumpeting from the hills that my Bonnan (2003) article was totally correct and unassailable, the scientific community would be right to castigate me in light of all the new data.

So I think Hutson misses the point.  There are statements in his paper such as, “Unfortunately, pronation research has suffered from a lack of awareness that semi-pronated forearm anatomy is plesiomorphic to Archosauria, and indeed all tetrapods.”  I know many colleagues who spend an inordinate amount of time carefully collecting and examining data from fossils and living animals.  The issue is not one of ignorance or lack of awareness, but one of difficulty — it is damn hard to elucidate evolutionary patterns of forelimb posture because of so many contingencies.  I have grown to appreciate these even more as I’ve ventured into collecting kinematic data on live animals.  It ain’t easy, and it never will be perfect.

I wish nothing but the best for Hutson and his future studies on what is admittedly an intriguing evolutionary history among the archosaurs. I do hope that he remembers, when his hypotheses are ultimately changed or falsified, that this is the process of science — and that that’s okay.

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.

Dr. Bonnan to give free dinosaur presentations at Southern New Jersey libraries

A short post to let all interested New Jersey parents and their children know that I will be giving a series of free dinosaur presentations at libraries throughout Atlantic County this July, 2014!  My presentations consist of fossils, bones, and dinosaur artwork featuring dinosaurs selected by audience members!

Check out the attached PDF link and poster below, and see when I’m coming to a library near you!

Atlantic County Library Presentations PDF Schedule 2014

Bonnan_Dinosaurs_July 2014

The NAMS Research Symposium Winners

Just a short post to make you aware that the winners of the 2014 NAMS Research Symposium are now posted on-line.

A big series of “thank you”s is necessary.  On behalf of Tara Luke and myself, we thank each and every one of our faculty and students for such an amazing turn-out at the NAMS Research Symposium this spring!  Thanks go out to all of the NAMS staff for their help with our student research. I also want to thank the judges for their time and input:  Adam Aguiar, David Burleigh, Justine Ciraolo, Nate Hartman, Marie Jelinski, and Chrissy Schairer.  We also want to again extend our thanks to David Dimmerman and his staff for coordinating the poster printing.  Finally, we thank Dean Weiss, Provost Kesselman, and President Saatkamp for their continuing support of our student research.