Complete with feathers

Despite the opening scene in the movie Jurassic Park where a team of paleontologists and their field hands sweep dirt (which looked like kitty litter) off a completely articulated “Velociraptor,” it is actually quite rare to get anything even remotely complete and articulated from the fossil record.  We paleontologists are often ecstatic if we get over 50% of a skeleton, and the higher that number creeps, the bigger our grins get.  As someone who has had the good fortune to find and name two dinosaurs, believe me — even a 40% complete skeleton is enough to throw a party about.  And that’s just if the skeleton is in pieces, let alone articulated in any semblance.

Hence the eternal question, “how do you really know what you have?  Aren’t you just speculating?”  The answer to that question involves cars and trip to the junkyard.  If you were an expert on automobiles, and you went to a junkyard and found bits and pieces of cars, you could still have some very good approximations of what was in the scrap heap.  You might, from pieces of engine block and chassis undergirding, be able to get down to the make or model, and even have a fair idea of how large the car was.  So it is with dinosaur skeletons.  Many of us know our anatomy well, and so even if the whole animal isn’t there, we can often say a lot, factually, about what was probably or almost certainly there.

Therefore, when we do find a complete or nearly complete dinosaur, it is truly rare and mind-blowing.  Such is the case with the newly discovered predatory dinosaur, Sciurumimus albersdoerferi, reported in the journal PNAS by Oliver Rauhut and colleagues.  The genus name, by the way, essentially translates to “squirrel mimic.”  This little, post-hatchling dinosaur was discovered in the same Late Jurassic sediments from Germany as its more famous feathered relative, Archaeopteryx.  This animal is complete, and I do mean complete.  To put this in the proper perspective, bear in mind that the delicate bones of the hands and feet and nearly every single tail (caudal) vertebra, elements that are normally lost to time, are preserved.  In fact, even the hyoid bone, the splint-like tongue-anchoring bone in all jawed vertebrates, is present, tucked just behind and beneath the chin.

This little predator is not on the line of dinosaurs that led to the birds (birds are dinosaurs?).  Instead it belongs to a family of predatory dinosaurs called megalosauroids that share more deeper, distant common ancestors with the coelurosaur line that led to birds.  And here’s where things get truly weird: this little predator had filamentous proto-feathers preserved at the base of its tail and along parts of its body.  Given the position of this predatory dinosaur in the family tree, it strongly suggests that all or nearly all predatory dinosaurs had some kind of feathers, proto-feathers, or filamentous structures adorning their bodies.  And here again, we have an animal with no hope of flying (the arms are much too small to have been effective wings) still sporting plumage or its equivalent.

With hindsight, we might now say that not only was Jurassic Park a bit off the mark with how it portrayed dinosaur discoveries, but it was also, perhaps, too conservative with its predatory dinosaurs, who might have sported filaments and feathers.  Perhaps this is something Steven Spielberg and friends could fix with the magic of CG when Jurassic Park is re-released on some future date in ultra hi-def surround holographic discs that do not yet exist.  Until then, you could always watch the parts with Velociraptor through a feather duster.

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.

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 …