Stop-and-go mammals and “warm-blooded” dinosaurs

Ever since Thomas Huxley opined that dinosaurs and birds might be related, a debate has waxed and waned over whether dinosaurs were simply inflated, “cold-blooded” reptiles or active, “warm-blooded” creatures.  Tied into these metabolic “states” have been judgement calls as well: we mammals tend to have warmer feelings for endotherms than for ectotherms (pun very much intended).

Our best data for inferring dinosaur physiology comes to from studies of the microscopic structure of long bones in thin cross-sections, a science called histology.  Bone is a dynamic, living tissue that provides a record of the relative speed at which its tissues were laid down during growth and development.  Bone growth and development rely on a good blood supply, and in a typical long bone cross-section, one can see the conduits that once carried life-sustaining blood vessels.  These circular rings of bone are called Haversian canals.

The rate or speed at which bone tissues are laid down effects how they look in cross-section, an observation first made by the famous Italian researcher Amprino and known as Amprino’s Law.  When bone grows slowly, fewer blood vessels are necessary to sustain the growth, and consequently there are few Haversian canals.  In contrast, when bones grows quickly, many blood vessels are needed to supply fuel for the growth, and therefore Haversian canals abound.  Additionally, slow-growing bone has time to lay itself down in nice, concentric layers like the rings of a tree.  This type of bone is called lamellar because of its distinctive layering.  In contrast, fibrolamellar bone occurs when bone is being laid down quickly — somewhat like a mason throwing together a wall of bricks as fast as possible and in no particular order.  In other words, fibrolamellar bone can look a mess compared with lamellar bone.

Ectothermic vertebrates like an alligator tend to have lamellar bone with few Haversian canals, whereas endotherms such as a bird will show fibrolamellar bone pocked with many Haversian canals.  But there’s a wrinkle: in addition to these features, we will also see dark, concentric rings called Lines of Arrested Growth (LAGs) representing times when long bone growth temporarily ceased.  Traditionally, it was thought that slow growth and seasonal cessations of that growth produce LAGs, such as the seasonal warming and cooling of “reptiles” from Spring and Summer to Fall and Winter.  However, there have been sporadic reports of LAGs in otherwise fast-growing mammals and birds, and it has been suggested that changes in diet might play a role here.

And this is where a lot of controversy has come in: dinosaur long bones often show LAGs in section, yet are often fibrolamellar with many Haversian canals.  What gives?  If there is any consensus currently, it is apparent that all dinosaurs had some fibrolamellar bone, and most researchers recognize that this indicates a qualitatively rapid growth rate elevated at least somewhat above “reptiles.”  But what about those pesky LAGs?

Enter a new study by Kohler and colleagues published in Nature which shows that lines of arrested growth occur in numerous wild ruminants over a large range of climates.  That’s right — these are endothermic mammals, your cows and antelopes and other hoofed herbivores that have large, multichambered stomachs for processing grasses.  By examining the histological cross-sections of 115 femora from ruminants across Africa and Europe, Kohler and colleagues have shown many examples of LAGs in otherwise “good” endotherms.

What is going on here?  Seasons.  Kohler and colleagues matched the LAGs in their ruminant sample to average rainfall across the various biomes from which the ruminants lived.  What they discovered was that LAGs and slowed growth occurred during times when precipitation was low.  As you might expect, low rates of precipitation will effect plant biomass: fewer plants = fewer calories = less energy available for growth during the lean season.

LAGs in dinosaurs have often been pointed to as either definitive evidence of ectothermy or at least have raised flags concerning how well bone histology conserves information about growth and development.  This study by Kohler and colleagues pretty much ends that argument: LAGs are not associated with the underlying metabolic rate of the animal.  Instead, they reflect changes in bone growth due to the seasonal availability of food and water.

The authors actually say it best at the end of their paper:

The consistently seasonal formation of rest lines in homeothermic endotherms debunks the key argument from bone histology in support of dinosaur ectothermy. Our study instead suggests that the extensive vascularization of the fibrolamellar bone in most dinosaurs and other extinct vertebrates is tightly correlated with seasonal maxima of endogenous heat production, an association that should be explored in future studies. — Kohler et al. (2012), doi:10.1038/nature11264, p. 4

Is this “proof” that dinosaurs were endothermic?  Not exactly, but what is exciting about this new study is that it does indicate that what we are seeing in dinosaur long bone thin-sections is a realistic approximation of their growth rates and an indirect measure of their environments.

XROMM Days 3-5: Data, data, data

Again, if you’re just tuning in to this thread on XROMM, please refer to my previous posts on what XROMM is, why I am excited about using it, and what I have done so far, including 3-D animating a chewing pig.

The past few days have seen us busy and social.  We’ve now learned to do scientific rotoscoping, or the art of properly aligning three-dimensional, anatomically-accurate models of vertebrates with two X-ray movies shot from different angles.  I have previously described the basic steps involved in making these XROMM movies and coordinating and calibrating the X-ray movies, so I refer you to my previous post on this.

Unlike the method of XROMM I described previously that uses bone markers to synch the moving images and the bones, in scientific rotoscoping you manually align bones frame by frame with x-ray movies.  It can be tedious at times, but essentially it is, to quote Steve Gatesy, quoting Ken Dial, fitting a digital key (the bones) into a visual lock (the X-ray movies).  In other words, you are posing the skeleton in three-dimensional coordinates based on the constraints imposed by X-ray movies.  Put simply, if your digital skeleton deviates from the reality of the X-ray movies, you are doing something wrong.

What is perhaps most important to emphasize in all of this is that because you are fitting bones into a virtual reality space of what happened when the animal was filmed, you can now recover data about skeletal and joint movements.  That’s right: you can actually retrieve reliable, repeatably scientific data on gait and movement from these 3-D animations.  For example, you assign joint markers and then measure how much the mouth of a pig opens, or how much rotation is happening in a bird knee, or even how parts of a fish skull move in relation to the skeleton and muscles.

So, you are not just making a nice skeleton movie — you are recovering what would normally be unrecoverable data.  The sort of data that allows you to more objectively describe what happens in living vertebrates, and hopefully, data that can be used as a baseline constraint for limiting what fossil vertebrates may or may not have been capable of.

All in all, this has been a great experience.  I wish to thank Beth Brainerd, Steve Gatesy, David Baier, Ariel Camp, Sabine Moritz, and Erika Giblin for all their help, information, and assistance this week.  It has been a pleasure.

XROMM Day 2: This little piggy bites … in 3-D

Again, if you missed previous posts on XROMM, please read those first for better context of the discussion that follows: see what XROMM is all about, why I’m excited to be learning it, and what I’ve already done.

On our second day in the course, we took the next step to synch two different, simultaneous X-ray movies of a mini-pig eating with a three-dimensional model of its skull in the MAYA program.  These X-ray films were taken on the C-arm x-ray machines I mentioned in my previous post by Dr. Beth Brainerd and colleagues, and we were essentially learning by replicating their process.

Dr. B. and the Mini-Pig

Me and mini-pig’s skull. The original movie was filmed back in 2006, so the mini-pig that stars in the X-rays has since passed on to piggy heaven. Here I am holding the actual skull of the animal that you will see in the animation.

In XROMM, you essentially have a work-flow like this:

  1. Film an animal behavior from two directions using calibrated X-ray cameras.  The animal usually has tiny, spherical beads implanted surgically into a few of the bones of interest prior to the filming.  As an important note here, all such films and surgeries are done under strict animal welfare protocols and the animals are not harmed: the X-ray dosages are as low or lower than that of humans exposed to x-rays for diagnosis, and the beads are tiny and biologically inert.
  2. After filming the animal’s behavior, the skeleton’s three-dimensional geometry is often CT-scanned from the animal.
  3. The CT-scan bone data are converted into geometrically-accurate 3-D representations of the bones of interest.
  4. In MAYA and MATLAB, the films from the two x-ray cameras are virtually “projected,” and the beads implanted into the animal subject show up as little dots.  These dots show up as little spheres in the CT-scanned bones you import into the MAYA program.
  5. Things then get more technical, but suffice it to say that the beads you see in the X-ray films and the spheres in the CT bones are synched.  The movements of the beads (spheres) are digitized in three-dimensions calibrated from the two camera views, and then the virtual bones are “cemented” to these spheres.  Then, as the spheres move, the bones follow, and what you get is a three-dimensional reconstruction of the 2-D x-ray films!

Here is a screen shot of the animation made in XROMM today.

Mini-Pig X-ray and Reconstruction

What you get from XROMM: to the left is one of the two X-ray films, and to the right is the 3-D skull reconstruction of the mini-pig.

Here is an animation of what you get — I still can’t believe we can do this!

Dr. B. Contemplates the Mini-Pig

Dr. B. Contemplates the mini-pig skull.

And we’re not even done yet.  Stay tuned …

XROMM Day 1: Pig heads and C-arms

If you’re just tuning in, you may want to read my previous posts on what XROMM is and why I am thrilled to be learning this technique.

Today was a good, busy, productive day at the XROMM course.  Never let it be said that “simply” synching X-ray “movies” (cineradiography) is easy!  The students in the course are learning how to animate the three-dimensional jaw movements of a mini-pig, based on the research of Dr. Beth Brainerd and colleaguesThe XROMM site provides movies and animations of what we are attempting to duplicate.

You don’t simply take an X-ray movie and then transpose that into a 3-D animation, of course.  If you’re going to match up the three-dimensional models of the mini-pig skull to the chewing motions recorded on as cineradiographs, you have to get the animation program (MAYA) to synch with the frames of these movies.  And that involves a number of techniques including correcting for distortion (the tube that transmits the X-ray images to the camera has convex ends, which give the original footage a fish-eye lens distortion) and “registering” the simultaneous side and top or bottom views of the moving animal to virtual cameras and screens in MAYA.

In science, the tedious parts come from making absolutely sure you are doing everything to account for error and noise in your data.  This usually pays off with dividends in the end, but getting there is the hard work. Its not enough in this case to do all the technical things necessary simply to capture a moving animal’s skeleton in two planes.  Then you have to spend hours and days matching that raw data to your virtual skeleton — and all for a sequence of maybe 2-20 seconds in length.

Today we also were able to visit the two XROMM facilities at Brown.

Dr. Bonnan at XROMM facility

Dr. Bonnan in one of the two labs of the XROMM facility a Brown University. Note the two large, mobile X-ray machines to Dr. Bonnan’s left.

Physics came back to haunt me today, as part of doing the science of XROMM correctly and safely is putting knowledge of photons and radiomagnetic waves to good use. Physics was always a tough subject for me, but it is amazing what you can learn and apply when you really want to do something and when doing it incorrectly will result in long-term injuries from X-ray irradiation!

One of the rooms had mobile C-arm X-ray machines that demonstrate very well the basic concept of what you do when you capture the motions of an animal.

Small C-arms at XROMM

Two small C-arm X-ray machines in one of the XROMM labs, positioned perpendicular to one another. One is facing left, and the other is pointed away from you in this photo.

All of the XROMM faculty and staff have been wonderful and saintly in their patience with us as we learn a technique that is often as frustrating to learn as it is to explain many times over and over again.  A big thank you for their patience and help today … and I think my eyes are starting to uncross now.

To give you an idea of the time investment necessary to convert 2-D cineradiographs into 3-D moving models, consider this: we spent most of our time today simply registering points and synching virtual camera views … there has been no animation yet!

I see great potential for research and student involvement with XROMM, and I’m looking forward to having a chewing mini-pig skull in the next few days.

Stay tuned …

Seeing through vertebrates to see through time

While waiting in the airport for my last flight (long story) to Providence, RI, and on to Brown University for the XROMM course, I obtained a good WiFi signal and so I’m writing a brief post.

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Tomorrow will mark the beginning of learning new cineradiography techniques and skeletal modeling that I have jealously been wanting to do for a long time.  It is hard to convey in words how anxious and interested I am to begin learning and then using the XROMM techniques.  Perhaps this is a bit of an exaggeration, so forgive the hyperbole, but I feel somewhat like a physicist who first get access to an atom smasher or an astronomer learning for the first time how to peer into the cosmos through some technologically marvelous telescope.

For someone like myself who is interested in how the skeleton actually behaves as a machine, and how to apply this new XROMM technology to deciphering past vertebrates like dinosaurs, this is coming close to time travel.  Okay, perhaps a bit of an exaggeration again, but I believe that seeing through live vertebrates to understand quantitatively how their skeletons “tick” is seeing through time.  Conserved movement and novel functions in living relatives of dinosaurs help us realistically constrain and predict what those long-dead animals were doing when they moved, hunted, or vacuumed-up vegetation.

I’ll be updating this blog throughout the week, and of course you can follow me on twitter for up-to-the-minute thoughts and comments.

How to see the skeleton in action … in 3-D

I am interested in dinosaur locomotion.  In particular, I am interested in how the various parts of a dinosaur skeleton moved in relation to one another, especially when capped in cartilage, actuated by muscles and tendons, and ensheathed in flesh.  Of course, until time travel becomes reality or until Jack Horner brings to life his “chickenosaurus,” knowing just how dinosaurs moved is fraught with difficulties and unknown variables.

Take, for example, the recent, independent confirmations by Casey Holliday and colleagues, and that of my own group’s research, on archosaur long bone articular cartilage thickness and shape.  It turns out, frustratingly, that a good amount of joint shape and thickness are lost to time in dinosaurs.  Part of my current research focus is to develop empirical methods for reconstructing the missing cartilage shape at the ends of dinosaur long bones, but that is a long work in progress.

However, you would think that at the very least, we should be able to quite readily determine the range of movements and interactions of the living skeleton in crocodylians and birds.  Strange as it may seem, understanding how the skeleton of a vertebrate moves in real life is not easy.  An actual, physical skeleton of any given animal can only be articulated in one pose at a time, and in any case the limitations or freedom of movement resulting from soft tissues are very difficult to establish — just ask Larry Witmer and his group of dedicated students.  One could, of course, pose a dead animal in various ways and then CT-scan or take a radiograph (an X-ray photograph) of each pose, but dead animals don’t always assume natural poses.

Another technique used for a number of analyses of skeletal movement has been fluoroscopy combined with the capture of X-ray movies of live animals, called cineradiography.  Several papers have been published on various aspects of vertebrate animal movement, breathing, and other activities using cineradiography.  Whereas these previous studies have been invaluable in revealing heretofore unknown or unanticipated movements of the vertebrate skeleton (e.g., the furcula of birds acts as a flexible spring), they are limited in that they are 2-D.  All bones of the animal are compressed into a flat plane, and you have to be able to recognize and follow the movements of the bones you are interested in while they merge and pass over all the other bones in the movie.

Therefore, I am thrilled to report that I have been accepted into a 1 week course at Brown University where myself and other faculty, postdocs, and graduate students will learn a new, 3-D cineradiographic technology that enables accurate three-dimesnional animations of vertebrate skeletons!  Called XROMM (X-ray Reconstruction of Moving Morphology), this new technology uses combined, multiple fluoroscopic and standard video sequences of a moving animal in combination with three-dimensional representations of its bones to produce a scientifically accurate moving skeletal model of particular behaviors and motions.  The three-dimensional bones are obtained using standard CT-scan or laser-scanning technology.  Check out the following examples under the Movies link on the XROMM site:

  • Mini-pig feeding
  • Ray-finned fish mouth mechanics
  • Iguana breathing and rib movements
  • Bird hindlimb movements
  • Duck feeding

The advantages of XROMM over traditional fluoroscopic movies or the attachment of external markers to skin is easy to appreciate.  For the first time, you can watch the movement of bones in three dimensions from any angle and in any perspective.  Moreover, you can easily export the ranges of movements generated by the animation for further quantification and analysis of how the bones actual move in space, in time, and in relation to one another.

I will be blogging and tweeting (@MattBonnan) about my experiences in this course, which will take place Monday, June 11 through Friday, June 15, 2012.  This sort of experience will not only open new doors for the research of all those involved in the course, but it will inform projects I will conduct in the future with my students.

I wish thank the members of the XROMM course for such an amazing opportunity:

  • Beth Brainerd
  • Steve Gatesy
  • Dave Baier
  • Ariel Camp
  • Sabine Moritz

It is wonderful to be a paleontologist in the 21st century!

Let’s face it: birds are dinosaurs -Part 3-

In the last two posts, I outlined many of the reasons why birds and dinosaurs have been “estranged” and are now being reunited as members of the same clade: Dinosauria.  If you haven’t read these first two posts, check them out:

So, at this point if you’re still not convinced that birds are indeed the living dinosaurs among us, here is one more thing to consider.  Let me take you by the hand …

Embryologists who have studied the development of bird embryos for decades have always come away from studies of their hands with the following conclusion: five initial digits form in cartilage (technically called anlagen), but after awhile, only the three middle digits remain.  Technically, we number digits from the thumb out to the little finger.  So, your thumb would be digit I and your little finger would be digit V.  In birds, the three remaining digits that fuse into the hand are II, III, and IV.  Okay, great, so what?

So this: the earliest predatory dinosaurs had five digits, but the main three digits were I, II, and III, not II, III, and IV.  In fact, during predatory dinosaur evolution, digits IV and V decrease in size until all that is left are I, II, and III.  This contradiction between the digit identities of bird hands and predatory dinosaur hands has been held up as the ultimate “proof” that all the amazing similarities between birds and dinosaurs are just that: amazing convergence.

Enter the past two decades of embryonic science, studies of evo-devo (evolutionary development), and a proliferation of studies combining old-school developmental anatomy with new-school gene studies.  It turns out that the digit identities in the hand are not set like permanent blueprints, but develop from the expression of various developmental genes to concentrations of various proteins.  Without going into great detail, we now know that the identity that digits assume (that is, whether they become I or V or something else) depends on how much of a concentration of particular proteins these regions of the hand were exposed to during development.  Simply put, higher concentrations of certain proteins trigger genes that, when transcribed and translated (i.e., expressed), ultimately create proteins that form digit I, II, III, IV, or V.

Intriguingly, this means that the relative position of a digit in the embryo’s hand and what that digit actually becomes are different.  In other words, a digit in position II could become a digit I if the concentration of various proteins and the expression of certain genes are changed.  This has been called the Frame-shift Hypothesis.  In this case, the “frame” is the region of gene expression that gives digits their identities, whereas the how this gradient moves in the developing hand is the “shift.”  What this all means is that just because you develop a digit in your hand where digit II should be doesn’t at all guarantee that it will become digit II.  It might become digit I, for example, depending on the frameshift.

What this all means is that, hypothetically, at some point during predatory dinosaur evolution, the anlagens that were in positions II, III, and IV frame-shfited to I, II, and III.  This frameshift would, of course, “solve” the digital confusion between birds and dinosaurs, but of course this hypothesis has been questioned and there was no fossil evidence of it occurring in dinosaurs … until recently.

A new Jurassic ceratosaur (a primitive type of predatory dinosaur) from China called Limusaurus preserved a complete hand that looks like an embryonic bird hand!  See for yourself: Figure 2 in their paper.  Now, compare that figure of the ceratosaur hand back to the ostrich hand.  I find this absolutely fascinating and was floored to see a dinosaur hand that looked like something undergoing the hypothesized frameshift.  Here, captured in stone for millions of years, is what you would predict to see in a transitional form going from the primitive predatory dinosaur digit arrangement to the birdy one.  Note in the Limusaurus hand figure that where the first digit is is a splint, like in a bird embryo, and next to that, the digit in the typical place of digit II, is something that looks an awful lot like digit I.

So, to conclude my thread, let me say that it is not at all parsimonious at this point in time to separate birds from dinosaurs.  That is equivalent to separating you from mammals.  It is no longer enough to argue that all the similarities between dinosaurs and birds are due strictly to an amazing amount of convergent evolution.  We have unique skeletal features only birds and dinosaurs share, we have dinosaurs that could not possibly fly possessing feathers, and we even have fossil support to explain why bird and dinosaur hands match up after all.

And finally back to the recent paper that inspired this thread in the first place: Birds have paedomorphic dinosaur skulls.  Paedomorphosis is the retention of juvenilized features into adulthood.  In other words, the proportions of the larva, infant, or juvenile remain relatively unaltered as adults.  This occurs a lot more often in nature than you may realize.  Essentially, the scientists Bhullar and colleagues used a shape analysis technique I have used myself: geometric morphometrics.  This technique analyzes changes in bony landmarks across numerous specimens and provides a mathematical test to see whether the changes predicted are actually significant.  What Bhullar and colleagues discovered was that bird skulls grow as if they were juvenilized dinosaur skulls!  Yet another nail in the coffin (scientifically) for the vague claim that birds cannot be dinosaurs.

Let’s face it: birds are dinosaurs.  I emphasize that I say this in the scientific sense of “certainty.”  Although we can’t be 100% certain in science, these data show overwhelmingly that birds are part of the dinosaur family tree.  When you realize that there are over 10,000 species of living birds but only 4600 or so species of living mammals, you realize it is still the Age of Dinosaurs after all.

Let’s face it: birds are dinosaurs – Part 2 –

To continue from the last post, where were the feathered dinosaurs?  And how did paleontologists begin to reconcile that birds and dinosaurs should start to come together again in their family tree?

Throughout the 1970s and 1980s, the hypothesis of a dinosaur-bird relationship was revived in part because of re-study of the Archaeopteryx specimens, the discovery of the “raptor” known as Deinonychus, and a new approach to understanding evolutionary relationships called cladistics.

Archaeopteryx and Deinonychus are known and discussed in great detail in many sources.  Suffice it to say John Ostrom, among others, began to notice striking skeletal similarities between Archaeopteryx,Deinonychus, and dinosaurs generally.  It was eventually recognized that there are a number of special, shared traits that only seem to occur together in birds and dinosaurs, and especially among predatory dinosaurs and birds.  I could provide a substantial list, but here are a few, selected key features:

  • A fully erect stance where the shaft of the femur (thigh bone) is perpendicular to the femoral head. (Incidentally, the femoral head points inwards towards the pelvis, and this allows the femur to be held vertically.)
  • The ankle is a modified mesotarsal ankle joint.  What this means is that the proximal and distal ankle bones form a cylinder-like roller joint between themselves.  You can see the upper part of this roller joint at the end of a chicken or turkey drumstick, and you also see it in dinosaurs.
  • Predatory dinosaurs and birds have specialized, hollow bones.
  • Predatory dinosaurs and birds have a three-fingered hand, and Archaeopteryx has a clawed, three-fingered hand with deep ligament pits, just like other predatory dinosaurs.
  • A large majority of predatory dinosaurs are classified as tetanurans, and it has been discovered that the tetanuran predators and birds have a furcula.  Despite earlier suggestions to the contrary, many dinosaurs have clavicles and furcula.
  • Coelurosaurs are predatory dinosaurs with specialized wrist bones that allow the hand to swivel sideways.  In other words, the hand doesn’t flex and extend, it rotates sideways towards the ulna.  Guess what other group of vertebrates has this specialized wrist? Birds!
  • Within coelurosaurs are the maniraptorans, the predatory dinosaurs that include Deinonychus and the now universally-knownVelociraptor.  These dinosaurs have highly flexible necks, elongate forelimbs, and the ulna is bowed outwards — the only other vertebrates with these features? Birds.

These observations, while powerful on their own, really started to hit home when placed within a scientifically-testable framework called cladistics.  In a nutshell, cladistics relies on special, shared traits rather than overall similarities to determine common ancestry.  In extremely simplified form, cladistics attempts to do what your family tree does: group everyone together who is related by common ancestry.  Yes, we all have an uncle or group of relatives we wish were not part of our family, but our shared genetic traits still show our close relationships.

Cladistic analyses of dinosaurs among the vertebrates revealed what Huxley had hypothesized all those years ago: birds were not just relatives of dinosaurs, they were a branch of the predatory dinosaur family tree!  Birds were dinosaurs just like humans are mammals.

But where were the feathered dinosaurs?  Until the 1990s, all paleontologists could do is point to the special, shared traits of Archaeopteryx, predatory dinosaurs, and birds and infer that maybe some dinosaurs had feathers.  This ambiguity was seized on by opponents of the birds-as-dinosaurs hypothesis to again suggest all the features (and more) that we have listed here were simply due to an amazing amount of convergent evolution.

Enter the Cretaceous Chinese predatory dinosaur discoveries of the 1990s in the Liaoning Province.  Unprecedented soft-tissue preservation in these fossils showed what was predicted by cladistics, Archaeopteryx, the suite of features shared between dinosaurs and birds only, and even back to Huxley’s observations: unmistakable dinosaurs with unmistakable feathers*.  And not flight feathers, either.  Barb-like and downy-like feathers that ran along the lengths of dinosaurs that could not have flown.  These animals would have used the feathers for insulation and perhaps display, but many could not have flown.  To tick off a few on the list of feathered dinosaurs discovered since the 1990s:

And in the past few years, non-predatory dinosaurs and large predatory dinosaurs with feathers have appeared.  Among them:

This many dinosaurs with feathers, some nowhere near the bird-line let alone among the predatory dinosaurs at all, leads to what we call in science robust evidence.

*Now, the reason for the asterisk — to be absolutely clear and fair, “feather” can be a rather broad term.  Some of these dinosaur feathers are long, hollow barbs, and some don’t branch like modern feathers.  However, Richard Prum and Jan Dyck have demonstrated through detailed studies of feather development in modern birds how feathers begin and diversify.  They have “staged” feathers, meaning that he has hypothesized what the earliest types of feathers should be and so on.  Interestingly enough, the variety of filamentous structures found in the many so-called feathered dinosaur fossils fit these predictions very, very well.

But perhaps you’re still not satisfied that birds are indeed dinosaurs?  Okay, stay tuned …

Let’s face it: birds are dinosaurs – Part 1 –

Several recent papers on dinosaurs and birds have, for many of us paleontologists, more or less completely cinched the hypothesis (as much as can happen in science) that birds are living dinosaurs.  Two such papers are:

But it is still very common for their to be doubt about birds as dinosaurs, not only from the general public, but from some of our colleagues, including ornithologists.  Perhaps because of when I was born and the dinosaur books I was exposed to as a child and teenager, the discoveries over the past three decades have been magical but also very conclusive for me.  I still wonder why anyone serious about evolution can still question the link between dinosaurs and birds, and I wanted to explore that in a series of posts.

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I am a child of the late 70s and early 80s, which means that in addition to nostalgia about the Atari 2600, all that “cool” ’80s music and “classic rock,” and the Rubik’s Cube, my first and favorite books on dinosaurs were The Hot-Blooded Dinosaurs, Archosauria: A New Look at the Old Dinosaur, The Riddle of the Dinosaur, and, of course, The Dinosaur Heresies.  These books and many other popular works of that time brashly proclaimed that previous generations of paleontologists had got it all wrong: dinosaurs were hot-blooded, active, and intelligent animals, and their descendants were none other than our feathered friends, the birds.  Archaeopteryx, the “first bird,” was in fact the genetic lifeboat upon which dinosaurs would ride out their mistaken extinction at the end of the Cretaceous Period some 65 million years ago.

So it was a surprise to learn as an undergraduate that the hypothesis that birds are dinosaurs is not as new as I was led to think.  “Darwin’s Bulldog,” the evolutionary biologist Thomas Henry Huxley, had noticed the striking similarities between the skeleton of Archaeopteryx and other small dinosaurs known at the time, including the bird-like Compsognathus, a little predator the size of a chicken.

But what happened?  Why was the hypothesis of a dinosaur-bird relationship essentially discarded for most of the 20th century?  The history of the people and politics behind the removal of birds from dinosaurs and their eventual reunification have been covered and detailed numerous times in books, blogs, and articles too numerous to mention.  Instead, I wanted to focus on why birds were scientifically estranged from dinosaurs for so long.

First, let me briefly introduce a concept called parsimony.  Parsimony is the default setting under which modern evolutionary biologists and paleontologists reconstruct the evolutionary tree of life.  Boiled down to its basics, parsimony means that, all things being equal, the simplest explanation is preferred.  In the context of vertebrate relationships, it means that we assume the presence of shared, specialized traits is due to common ancestry.

To demonstrate how parsimony works, let’s start with a (hopefully) non-controversial statement: you are a mammal.  You share unique traits with dogs, naked mole rats, and the duck-billed platypus such as hair (yes, naked mole rats have some hair), the production of milk (in females), and a single lower jaw bone rather than multiple jaw elements.  Now, we could say that you, your dog, the naked mole rats, and the duck-billed platypus each evolved these traits independently — in other words, humans, dogs, and all other mammals each re-invented hair, milk, and the single lower jaw bone.  However, this would not be a very simple explanation (it would not be parsimonious).  But we wouldn’t simply reject this hypothesis because it wasn’t parsimonious — we would also reject it because it was not supported by data from the fossil record and mammal embryology.

The issue with dinosaurs and birds has revolved around the interpretation of various traits and argumentation over something called convergent evolution. Granted, not all similar-looking traits are related to common ancestry.  For example, a shark and a dolphin both have a stream-lined body form with fins.

Convergent evolution

Convergent evolution in body form. In this illustration, the shark and dolphin have a streamlined body form with fins. Despite this superficial similarity, dolphins share more trait states in common with other mammals such as cats than they do with sharks. The streamlined form is due, not to common ancestry, but to convergence on a form that allows the dolphin and shark to move quickly through the same medium, water. (c) 2012 M.F. Bonnan.

At face value, we might conclude that these traits were evidence that sharks and dolphins shared a recent common ancestor.  However, on closer inspection, we would begin to notice some large discrepancies.  The skeletal structure of the shark is cartilaginous whereas that of the dolphin is bone.  A shark’s skin is rough and covered in tooth-like scales, yet that of a dolphin is smooth and overlies a layer of blubber.  Sharks breathe using gills, but dolphins have lungs and must surface occasionally to take in fresh air.  Dolphins nurse their young on milk from mammary glands while shark pups must fend for themselves.

Eventually, it would occur to us that, more likely, the similar shapes of the shark and dolphin were not due to common ancestry but instead to a common environment: water.  Water is denser than air, and there are only so many “solutions” to swimming fast in it.  The shark and dolphin have converged onto a similar functional solution, the streamlining of their bodies and the possession of fins, to move fast in a dense medium.

So it has been argued for the striking similarities between birds and dinosaurs.  For example, both birds and predatory dinosaurs are bipeds, so perhaps their bone structure and posture evolved independently because of a shared functional “need.”  Both dinosaurs and birds are part of the broader Reptilia, and so perhaps the skeletal similarities in predatory dinosaurs and birds were independently evolved from a much early, reptilian skeletal framework.

Then there is the issue of what is missing.  Birds have a furcula, a bone made by fusing the two collar bones together into a strut that resists the large forces generated by their flapping wings. Archaeopteryx has a furcula, but it was long supposed that dinosaurs did not have this structure.  Embryonically, bird hands develop in such a way that it is the three middle digits that that remain (index, middle, and ring finger), whereas predatory dinosaurs have a thumb, index finger, and middle finger.  And, the key feature held out for a long time as evidence that birds were not at all dinosaur relatives was their feathers.  Where were the dinosaurs with feathers?

Stay tuned …