I have just made a series of fairly major edits to the in-progress Checklist for new zoological genera and species, and wanted to explain what’s changed and why.

The important change is that the Checklist no longer attempts to encompass the creation of families, nor of all genus-group and species-group names — only genera and species.  I took this painful decision after a lot of consultation with various people, here and by email, despite wanting the utility of the Checklist to be a broad as possible.  In the end, it became apparent that the attempt to include these other ranks could only result in the Checklist becoming much much longer and more complex, or leaving loopholes, or more likely both.

  • The very terms “genus-group” and “species-group” are misleading to non-specialist taxonomists — they can easily be misunderstood as meaning “group of genera” and “group of species”.
  • While the Code indicates that the only species-group ranks are species and subspecies, superspecies are fairly often used as well, and we don’t want to get into discussing such matters.
  • Likewise, supergenera are sometimes used as well as genera, despite the lack of support in the Code.
  • Conversely, the Code’s definition of genus-group names (see the Glossary) include things called “collective groups”, whatever they may be.
  • Worse, the Code also talks about divisions, which are described in the Glossary, not particularly helpfully, as “(1) A rank that if treated as a division of a genus or subgenus is deemed to be of subgeneric rank for the purposes of nomenclature [Art. 10.4]. (2) A taxon at the rank of division.”  We just don’t want to get into that stuff.
  • Discussion of subgenera and related ranks on the ICZN mailing list has resulted in disagreement even between taxonomy specialists on that list, over matters such as whether a subgenus can be used as the type genus of a family.  When even experts disagree, it seems a fool’s errand for the Checklist to try to tersely summarise the rules.

In short, I became convinced that trying to have the Checklist cover ranks other than genera and species opened up all sorts of cans of worms, and that the target audience — zoologists who are not taxonomy specialists — will get more value from a checklist that is more limited in scope, simpler to understand, and shorter.

As usual, comments are closed on this brief update — not to stifle debate, but because I want to keep all discussion together in one place: so please head over to the draft Checklist, read through the current version, and post any comments you may have.

I am optimistic that we are converging now on a version that is as simple as possible but no simpler.  Once we freeze in a few days, we will hopefully move to the next phase … which I’ll tell you about at the time.

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Sorry to bump Matt’s awesome Rhea-neck post off the top of the SV-POW! home page, but I have news of the rapidly developing checklist for new zoological names.  As well as many, many minor and not-so-minor edits — and thanks to everyone who’s participated in this process — I have made a major structural change.

The list has been broken into two, first enumerating Requirements and then describing Best Practice. I have also reordered some of the points within lists. As a result, ALL NUMBERING HAS CHANGED; also some points have been split and others merged.

Please be sure to comment only on the most recent version.

I am worried that the Checklist is getting too big.  I just copied and pasted the substance of it — the introductory paragraph and the two lists — into a new OpenOffice in 12-point Times, and found that it runs to a page and a quarter.  Reduced to 10.5-point type it fits on a page, but that’s the way I want to go.  So suggestions for reducing the length without losing content will be particularly welcome.

(As before, comments are closed on this post, because I don’t want to split discussion between here and the checklist itself.)

When you last saw this rhea neck, I was squeezing a thin, unpleasant fluid out of its esophagus. Previous rhea dissection posts are here and here; you may also be interested in my ratite clearing house post.

We did that dissection back in 2006. Since then I finished my dissertation, got a tenure-track job, and moved twice. The rhea neck followed me, living in a succession of freezers until last spring.

Last spring I thawed it out, straightened it (it had been coiled up in a gallon ziploc), refroze it, and had it cut in half sagittally with a bandsaw. I did all of this for a project that is not yet ready to see the light of day, but there’s a ton of cool morphology here that I am at liberty to discuss, so let’s get on with it.

Throughout the post, click on the images for full resolution, unlabeled versions.

In the image above, you’ll notice that the saw cut was just slightly to the left of the midline, so that almost the entire spinal cord was left in the right half of the neck (the one toward the top of the image; the left half, below, is upside down, i.e. ventral is towards the top of the picture). The spinal cord is the prominent yell0w-white stripe running down the middle of the hemisectioned neck. It’s a useful landmark because it stands out so well. Dorsal to it are the neural arches, spines*, and zygapophyses of the vertebrae, and epaxial muscles; ventral to it are the vertebral centra and the hypaxial muscles.

* If you want to call them that–some of them are barely there!

Here’s the large supraspinous ligament (lig. elasticum interspinale), which is similar to the nuchal ligament of mammals but independently derived. Compare to the nuchal ligament of a horse (image borrowed from here):

Note how the actual profile of the neck is vastly different from what you’d suspect based on the skeleton alone. This is one of the reasons that necks lie. For more on the supraspinous ligament in rheas and its implications for sauropods, see Tsuihiji (2004) and Schwarz et al. (2007).

Birds also have very large interspinous ligaments (lig. elasticum interlaminare), each of which connects the neural spines of two adjacent vertebrae. In the above photo, the blunt probe is passing under (= lateral to) the unpaired, midline interspinous ligament. Rheas are unusual among birds in having such a large supraspinous ligament, and you can see that this interspinous ligament is almost as big. If you tear down the neck of a chicken or turkey, you will find huge interspinous ligaments, and the supraspinous ligament will be tiny if you can identify it at all.

Here’s something I don’t think we’ve ever shown before here on SV-POW!: a photograph of an actual pneumatic diverticulum. That’s the dark hole in the middle of the photo. You can see that we’re in the left half of the neck, lateral to the spinal cord, almost to the postzygapophysis, the articular surface of which is more lateral still (“below” or “deep to” the surface you see exposed in this cut). Usually at each intervertebral joint there is a connection between the lateral pneumatic diverticula that run up the side of the cervical column and pass through the cervical rib loops and the supramedullary diverticula that lie dorsal to the spinal cord inside the neural canal. That connecting diverticulum is the one exposed here.

NB: diverticulum is singular, diverticula is plural. There are no diverticulae or, heaven forbid, diverticuli, although these terms sometimes crop up in the technical literature, erroneously. (I hesitate to point this out, not because it’s not important, but because I’ll be lucky if I didn’t screw up a Latin term elsewhere in the post!)

Here are pneumatic diverticula in a transverse CT section of an ostrich neck (Wedel 2007b: fig. 6; compare to Wedel 2003: fig. 2, another slice from the same neck). In this view, bone is white, muscles and other soft tissues are gray, and air spaces are black. A, lateral diverticula running alongside the vertebral centra. B, air spaces inside the bone. C, supramedullary airways above the spinal cord. This section is close to the posterior end of a vertebra; the flat-bottomed wing-like processes sticking out to either side are the anterior portions of the postzygapophyses. If the slice was a few mm more posterior, we would see the prezygapophyses of the preceding vertebra in contact with them. Also, the vertical bars of bone connecting the centrum to the postzygs would pinch out, and we’d see the diverticula connecting the lateral (A) and supramedullary (C) airways–that’s the diverticulum revealed in the photo two images up.

Here’s another cool section showing a diverticulum and some muscles. Note the short interspinous muscles, which connect the neural spines of adjacent vertebrae. The probe indicates another open diverticulum, and the very tip of the probe is under one of the very thin layers of epithelium that line the diverticula. You can see that this diverticulum lies on the dorsal surface of the vertebra, posterior to the prezygapophysis and anterior to the neural spine. This supravertebral diverticulum is near and dear to my heart, because I have published an image of its traces before.

Lots going on in this photo (remember that you can click for an unlabeled version). This is a middle cervical vertebra of an emu, in anterodorsal view, with anterior towards the bottom of the picture. Bonus geek points if you recognized it as the basis for Text-fig. 9 in Wedel (2007a). I published this photo in that paper because it so nicely illustrates how variable the skeletal traces of pneumaticity can be, even from left to right in a single bone. On the right side of the photo (left side of the vertebra), the bone resorption adjacent to the supravertebral diverticulum produced a pneuamtic fossa, but one without distinct bony margins or a pneumatic foramen. On the other side, the fossa contains a pneumatic foramen which communicates with the internal air spaces, but the fossa is otherwise identical. Fossae like the one on the right are a real pain in the fossil record, because they might be pneumatic, but then again they might not be; such shallow, indistinct fossae can house other soft tissues, including cartilage and fat. This is what I was talking about when I wrote (Wedel 2009: p. 624):

If progressively more basal taxa are examined in the quest to find the origin of PSP [postcranial skeletal pneumaticity], the problem is not that evidence of PSP disappears entirely. It is that the shallow, unbounded fossae of basal dinosaurs are no longer diagnostic for pneumaticity.

For more on that problem, see Wedel (2007a) and the post, “X-Men Origins: Pneumaticity”.

The other labelled bits in the above photo are all muscle attachment points, and you may find Wedel and Sanders (2002), especially Fig. 2, a useful reference for the rest of the post. The dorsal tubercles, or epipophyses, are rugosities dorsal to the postzygapophyses that anchor most of the long, multi-segment epaxial muscles, which in birds are the M. longus colli dorsalis, which originates on the anterior faces of the neural spines, and M. ascendens cervicalis, which originates on the cervical rib loops. The crista transvers0-obliqua is a low, bony crest connecting each dorsal tubercle to the neural spine; it corresponds to the spino-postzygapophyseal lamina (SPOL) of sauropods (see Tutorial 4: Laminae!), and anchors the Mm. intercristales, a group of short muscles that span the cristae of adjacent vertebrae, like the Mm. interspinales only more lateral.

The carotid tubercles serve as points of origin for the M. longus colli ventralis, one of the largest and longest of the multi-segment hypaxial muscles; they have no obvious homolog or analog in sauropods. The lack of this feature might indicate that the hypaxial muscles were less of a big deal in sauropods, for whom lifting the neck was presumably a bigger problem than lowering it. Alternatively, the M. longus colli ventralis of sauropods might have attached to the medial sides of the parapophyses and the capitula of the cervical ribs, which tended to be larger and more ventrally-directed than in basal sauropodomorphs and theropods.

The unlabeled red arrows mark the lateral tubercles and crests of the cervical rib loop, to which we will return momentarily.

Here you can see a big bundle of long epaxial muscles, including both the M. longus colli dorsalis and M. ascendens cervicalis, inserting on the left dorsal tubercle of the vertebra on the right.  Note that the cut here is quite a bit lateral of the midline, and actually goes through the lateral wall of the neural canal in the vertebra on the right (that vert is the fifth back from the front of the section of neck featured in this post, which is incomplete). That is why you see the big, multi-segment muscles here, and not the shorter, single-segment muscles, which lie closer to the midline.

Here are some more muscle attachment points in a bird vertebra (a turkey this time, courtesy of Mike). The lateral crests and tubercles (tubecula ansae and cristae laterales, if you’re keeping track of the Latin) are the same bony features indicated by the red arrows in the photo of the emu vertebra up above. They anchor both the long M. ascendens cervicalis, which inserts on the dorsal tubercles of more anterior vertebrae, and the short Mm. intertransversarii, which span the cervical rib loops of adjacent vertebrae. Sauropods usually have at least small rugosities on their diapophyses and the tubercula of their cervical ribs (which articulate with the diapophyses) that probably anchored homologous muscles.

Here’s a dorsal tubercle above the postzyg on the neural arch of a juvenile Apatosaurus (cervical 6 of CM 555, shown in right lateral view). Notice that the spinopostzygapophyseal lamina (SPOL) and postzygodiapophyseal lamina (PODL) actually converge on the dorsal tubercle rather than on the postzyg. This is pretty common, and makes good mechanical sense.

Dorsal tubercles again, this time on the world’s most wonderful fossil, cervical 8 of the HM SII specimen of Giraffatitan brancai, in the collections of the Humbolt museum in Berlin. While you’re here, check out the pneumato-riffic sculpting on the lateral faces of the neural arch and spine, and the very rugose texture on the tip of the neural spine, SPOLs, and dorsal tubercles. In fact, compare the numerous pocket-like external fossae on this vertebra with the internal air cells exposed in the cross-sectioned rhea neck. I have argued here before that sauropod cervical vertebrae are pretty similar to those of birds; the main differences are that the cervical rib loops are proportionally much smaller in sauropods, and sauropod vertebrae mostly wore their pneumaticity on the outside.

Farther anteriorly in the neck–the three vertebrae pictured here are the third, fourth, and fifth (from right to left) in this partial neck–and somewhat closer to the midline. Now you can see some short epaxial muscles, probably Mm. intercristales and Mm. interspinales (the two groups grade into each other and are often not distinct), spanning adjacent vertebrae. As in several previous photos, the supravertebral diverticulum is visible, as well as the communicating diverticulum that connects the lateral diverticula to the supramedullary airways. I forgot to label them, but ventral to the centra you can see long, light-colored streaks running through the hypaxial muscles. These are the tendons of the M. longus colli ventralis, and in some of the previous photos you can see them running all the way to their origination points on the carotid tubercles. These extend posteriorly from the short cervical ribs of birds, and are homologous with the long cervical ribs of sauropods.

That’s all I have for this time. If you’d like to see all of this stuff for yourself, turkey necks are cheap and big enough to be easy to work with. Geese are good, too. You can see all the same bits in a chicken or a duck, it’s just harder because everything is smaller (if you’re a real glutton for punishment, try a Cornish game hen).

When I first started working on sauropods, their cervical vertebrae made no sense to me. They were just piles of seemingly random osteology. The first time I dissected a bird neck was an epiphany; ever since then, it is hard for me to look at sauropod vertebrae and not see them clad in the diverticula and muscles that shaped their morphology. Go have fun.

References

As we all know, the International Code of Zoological Nomenclature is a large and intimidating document.  As a result, zoologists naming new animals often do not read it in its entirety (I know I haven’t).  It’s probably because of this that many of the more avoidable nomenclatural mistakes occur.

Whatever might or might not eventually be possible in terms of simplifying the Code, everyone recognises that that would be a huge job, and something that would take years to do.  So let’s ignore that possibility for now.

In the short term, what would be much more useful would be if someone could work up a very short document — no more than a single page of A4 and hopefully much shorter — that states in simple bullet-points what MUST be done to ensure that a new name is valid.  Then there would be no excuse for zoologists venturing into nomenclature for the first time not to read such a document — let’s call it the ICZN Cheat Sheet.

Neural spine morphology along the vertebral series of Bonitasaurua salgadoi (MPCA-460) in anterior view. From Gallina 2011, doi:10.1590/S0001-37652011005000001

Because it’s easier to steer a moving ship, I wrote to the ICZN email list this morning proposing an initial set of bullet points.  I did not for a moment expect that they were complete, consistent or even necessarily correct; but I hoped that they could at least serve as a starting point for a very quick process of putting such a list together.

I am pleased to say that response on the list was fairly positive, and at the suggestion of one of the list members I have now posted the in-progress checklist as a page on this site, having revised it in accordance with several suggestions.

If you’re interested in contributing to this effort — helping us to derive a clear, concise and correct one-page guide to naming new zoological genera and species — please head over to the page and comment there.  (Comments on this post are closed, to avoid splitting discussion across two places.)

We’ve been running SV-POW! for three and half years now; in all that time we’ve never featured a guest post, because we think it’s better to keep a blog tight and focussed.  In general, that remains our policy.

But today, first the first and maybe only time, we present a guest post.  This article, What should everyone know about paleontology?, was first posted on the Dinosaur Mailing List, by Tom Holtz, in response to a question from Robert Takata.  We are now pleased to present it, in revised and expanded form.

Tom is best known for his work on those vulgar, overstudied theropods, the tyrannosaurs — their phylogenetic position (he was the first to demonstrate that they are coelurosaurs, a position now universally accepted), ecology (he gently but emphatically rebutted Jack Horner’s bafflingly popular Obligate Scavenger hypothesis), and much more.  But Tom is more than a tyrannosaur jockey: he’s one of the most natural teachers I’ve even known, and it’s largely due to his seeming inexhaustible stream of helpful explanations on the dinosaur mailing list that I ever made it past the Dino-Fanboy level into the world of actual science — in fact, I mentioned him in the acknowledgements of my dissertation for that very reason.  So it’s fitting that he, of all people, should be the first ever SV-POW! guest writer.

Take it away, Tom!

“What Should Everyone Know About Paleontology?”

Thomas R. Holtz, Jr.

The title question was recently asked by Roberto Takata on the Dinosaur Mailing List (http://dml.cmnh.org/2011Feb/msg00020.html).

I think that is a good question. What really are the most important elements of paleontology that the general public should understand? I took a shot at coming up with a list of key concepts (http://dml.cmnh.org/2011Feb/msg00027.html and http://dml.cmnh.org/2011Feb/msg00029.html), based on experiences with teaching paleontology and historical geology and with less-formally structured outreach to the public. I have offered this list (cross posted at the Superoceras and Archosaur Musings blogs) as a way for it to reach a wider audience. That this is Darwin Week makes it even more appropriate, as we should use this occasion to encourage a better understanding of the changes of Earth and Life through Time for the public at large.

Much as I might like to think otherwise, the specific details of the hindlimb function of Tyrannosaurus rex or the pneumatic features of brachiosaurid vertebrae really are not the most important elements of the field. Understanding and appreciating the nitty gritty details of the phylogeny and anatomy of any particular branch of the Tree of Life are not really necessary for everyone to know, any more than we would regard detailed knowledge of bacterial biochemistry or the partitioning of minerals in a magma chamber to be significant general knowledge. (Indeed, these latter two items are actually far more critical for human society than any specific aspect of paleontology, and so from a certain point of view really more important for people to know than the History of Life.)

That said, all human societies and many individuals have wondered about where we have come from and how the world came to be the way it is. This is, in my opinion, the greatest contribution of paleontology: it gives us the Story of Earth and Life, and especially our own story.

I have divided this list into two sections. The first is a list of general topics of paleontology, touching on the main elements of geology that someone would need to know for fossils to make any sense. The second is the more specific list of key points in the history of life.

(NOTE: as the idea of this list is that it should be aimed at the general public, I have tried to avoid technical terminology where possible.)

General

  • That rocks are produced by various factors (erosion -> sedimentation; metamorphism; volcanic activity; etc.)
  • That rocks did not form at a single moment in time, but instead have been and continue to be generated throughout the history of the planet.
  • That fossils are remains of organisms or traces of their behavior recorded in those rocks.
  • That rocks (and the organisms that made the fossils) can be thousands, millions, or even billions of years old.
  • That the species discovered as fossils, and the communities of organisms at each place and time, are different from the same in the modern world and from each other.
  • That despite these differences that there is continuity between life in the past and life in the present: this continuity is a record of the evolution of life.
  • That we can use fossils, in conjunction with anatomical, molecular, and developmental data of living forms, to reconstruct the evolutionary pattern of life through time.
  • That fossils are incomplete remains of once-living things, and that in order to reconstruct how the organisms that produced them actually lived, we can:
    • Document their anatomy (both gross external and with the use of CT scanning internal), and compare them to the anatomy of living creatures in order to estimate their function;
    • Examine their chemical composition, which can reveal aspects of their biochemistry;
    • Examine their microstructure to estimate patterns of growth;
    • Model their biomechanical functions using computers and other engineering techniques;
    • Investigate their footprints, burrows, and other traces to reveal the motion and other actions of the species while they were alive;
    • And collect information of the various species that lived together in order to reconstruct past communities.
  • However, with all that, fossils are necessarily incomplete, and there will always be information about past life which we might very much want to know, but which has been forever lost. Accepting this is very important when working with paleontology.
  • That environments of the past were different from the present.
  • That there have been episodes of time when major fractions of the living world were extinguished in a very short period of time: such data could not be known without the fossil record.
  • That entire branches of the tree of life have perished (sometimes in these mass extinction events, sometimes more gradually).
  • That certain modes of life (reef formers, fast-swimming marine predators, large-bodied terrestrial browsers, etc.) have been occupied by very different groups of organisms at different periods of Earth History.
  • That every living species, and every living individual, has a common ancestor with all other species and individuals at some point in the History of Life.

Specific

Honestly, despite the fact the specific issues about specific parts of the Tree of Life are the ones that paleontologists, the news media, the average citizen, etc., are more concerned with, they really are much less significant for the general public to know than the points above. Sadly, documentary companies and the like keep on forgetting that, and keep on forgetting that a lot of the public does not know the above points.

Really, in the big picture, the distinction between dinosaurs, pterosaurs, and crurotarsans are trivialities compared to a basic understanding that the fossil record is our document of Life’s history and Earth’s changes.

Summarizing the key points of the history of life over nearly 4 billion years of evolutionary history is a big task. After all, there is a tendency to focus on the spectacular and sensationalized rather than the ordinary and humdrum. As Stephen Jay Gould and others often remarked, from a purely objective external standpoint we have always lived in the Age of Bacteria, and the changing panoply of animals and plants during the last half-billion years have only been superficial changes.

But the question wasn’t “what should a dispassionate outsider regard as the modal aspect of the History of Life?”; it was “What should everyone know about paleontology?” Since we are terrestrial mammals of the latest Cenozoic, we have a natural interest in events on the land and during the most recent parts of Earth History. That is a fair bias: it does focus on who WE are and where WE come from.

That said, here is a list of key concepts in the history of life. Other researchers might pick other moments, and not include some that I have here. Still, I believe most such lists would have many of the same key points within them.

  • Life first developed in the seas, and for nearly all of its history was confined there.
  • For most of Life’s history, organisms were single-celled only. (And today, most of the diversity remains single-celled).
  • The evolution of photosynthesis was a critical event in the history of Earth and Life; living things were able to affect the planet and its chemistry on a global scale.
  • Multicellular life evolved independently several times.
  • Early animals were all marine forms.
  • The major groups of animals diverged from each other before they had the ability to make complex hard parts.
  • About 540 million years ago, the ability to make hard parts became possible across a wide swath of the animal tree of life, and a much better fossil record happened.
  • Plants colonized land in a series of stages and adaptations. This transformed the surface of the land, and allowed for animals of various groups to follow afterwards.
  • For the first 100 million years or so of skeletonized animals, our own group (the vertebrates) were relatively rare and primarily suspension feeders. The evolution of jaws allowed our group to greatly diversify, and from that point onward vertebrates of some form or other have remained apex predators in most marine environments.
  • Complex forests of plants (mostly related to small swampland plants of today’s world) covered wide regions of the lowlands of the Carboniferous.
  • Burial of this vegetation before it could decay led to the formation of much of the coal that powered the Industrial Revolution and continues to power the modern world.
  • While most of the coal swamp plants required a moist ground surface on which to propagate, one branch evolved a method of reproduction using a seed. This adaptation allowed them to colonize the interiors, and seed plants have long since become the dominant form of land plant.
  • In the coal swamps, one group of arthropods (the insects) evolved the ability to fly. From this point onward insects were to be among the most common and diverse land animals.
  • Early terrestrial vertebrates were often competent at moving around on land as adults, but typically had to go back to the water in order to reproduce. In the coal swamps one branch of these animals evolved a specialized egg that allowed them to reproduce on land, and thus avoid this “tadpole” stage.
  • These new terrestrial vertebrates—the amniotes—diversified into many forms. Some included the ancestors of modern mammals; others the ancestors of today’s reptiles (including birds).
  • A tremendous extinction event, the largest in the age of animals, devastated the world about 252 million years ago. Caused by the effects and side-effects of tremendous volcanoes, it radically altered the composition of both marine and terrestrial communities.
  • In the time after this Permo-Triassic extinction, reptiles (and especially a branch that includes the ancestors of crocodilians and dinosaurs) diversified and became ecologically dominant in most medium- to large-sized niches.
  • During the Triassic many of the distinctive lineages of the modern terrestrial world (including turtles, mammals, crocodile-like forms, lizard-like forms, etc.) appeared. Other groups that would be very important in the Mesozoic but would later disappear (such as pterosaurs and (in the seas) ichthyosaurs and plesiosaurs) evolved at this time.
  • Dinosaurs were initially a minor component of these Triassic communities. Only the tall, long-necked sauropodomorphs were ecologically diverse during this time among the various dinosaur branches. However, a mass extinction event at the end of the Triassic (essentially the Permo-Triassic extinction in miniature) allowed for the dinosaurs to diversify as their competitors had vanished.
  • During the Jurassic, dinosaurs diversified. Some grew to tremendous size; some evolved spectacular armor; some become the largest carnivorous land animals the world had seen by this point. Among smaller carnivorous dinosaurs, an insulating covering of feathers had evolved to cover the body (possibly from a more ancient form shared by all dinosaurs). Among the feathered dinosaurs were the ancestors of the birds.
  • Other terrestrial groups such as pterosaurs, crocodile-ancestors, mammals, and insects continued to diversify into new habits.
  • During the Jurassic and (especially) the Cretaceous, a major transformation of marine life occurred. Green-algae phytoplankton were displaced by red-algae phytoplankton (which continue to dominate modern marine ecosystems). A wide variety of new predators—advanced sharks and rays, teleost fish, predatory snails, crustaceans with powerful claws, specialized echinoids, etc.—appeared, and the sessile surface-dwelling suspension feeders that dominated the shallow marine communities since the Ordovician became far rarer. Instead, more mobile, swimming, or burrowing forms became more common.
  • During the Cretaceous one group of land-plants evolved flowers and fruit and thus tied their reproduction very closely with animals. Although not immediately ecologically dominant, this type of plants would eventually come to be the major land plant group.
  • The impact of a giant asteroid—coupled with other major on-going environmental changes—brought an end to the Mesozoic. Most large-bodied groups on land and sea, and many smaller bodied forms, disappeared. The only surviving dinosaurs were toothless birds.
  • The beginning of the Cenozoic saw the establishment of mammals as the dominant group of large-bodied terrestrial vertebrates. Early on mammals colonized both the sea and the air as well.
  • During its beginning the Cenozoic world was warm and wet, much like the Cretaceous. However, a number of changes of the position of the continents and the rise of mountain ranges caused the climates to cool and dry.
  • As the world cooled and dried, great grasslands developed (first in South America, and later nearly all other continents).
  • Various groups of animals adapted to the new grassland conditions. Herbivorous mammals became swift runners with deep-crowned teeth, often living in herds for protection. Mammalian predators became swifter as well, some becoming pack hunters.
  • Other new plant communities evolved, and new animal communities which inhabited them. The rise of modern meadows (dominated by daisy-related plants and grasses) saw the diversification of mouse-and-rat type rodents, many frogs and toads, advanced snakes, songbirds, etc.
  • A group of arboreal mammals with very big brains, complex social communities, and gripping hands—the primates—produced many forms. In Africa one branch of these evolved to live at mixed forest-grassland margins, and from this branch evolved some who became fully upright and moved out into the grasslands.
  • This group of primates retained and advanced the ability to use stone tools that its forest-dwelling ancestors already had. Many branches evolved, and some developed even larger brains and more complex tools. It is from among these that the ancestors of modern humans and other close relatives evolved, and eventually spread out from Africa to other regions of the planet.
  • About 2.6 million years ago a number of factors led to ice age conditions, where glaciers advanced and retreated. Various groups of animals evolved adaptations for these new cold climates.
  • The early humans managed to colonize much of the planet; shortly after their arrival into new worlds, nearly all the large-bodied native species disappeared.
  • At some point before the common ancestor of all modern humans spread across the planet, the ability to have very complex symbolic language evolved. This led to many, many technological and cultural diversifications which changed much faster than the biology of the humans themselves.
  • In western Asia and northern Africa (and eventually in other regions), modern humans developed techniques to grow food under controlled circumstances, leading to true agriculture. (Other cultures are known to have independently evolved proto-agricultural techniques).
  • This Neolithic revolution allowed for the development of more settled communities, specialization of individual skills within a community (including soldiers, metallurgists, potters, priests, rulers, and with the rise of writing, scribes).
  • From this point we begin to get a written record, and so the historians can take up the story…

This list is obviously not comprehensive, and there are many elements that I had to ignore to keep it relatively short. Still, I hope this overview helps put where we as a species fit into the larger perspective of Life’s long voyage, a voyage that could only have been traced by the study of fossils.

Millions long for immortality who don’t know what to do with themselves on a rainy Sunday afternoon.

–Susan Ertz, Anger in the Sky

If you’ve been following the past few tutorials, you now know how to get copies of academic papers (learn Google fu and ask politely) and how to become a paleontologist (write and publish papers). But what are you going to write and publish papers about?

My own experience, and my impression from talking with many others, is that when you move into a new field for the first time, it often  seems like all of the good projects are taken. Or you’ll have what feels like a great idea for a project and then find out that Romer already solved that problem back in the middle of the 20th century. My advice is going to seem trite, but it’s worked for me several times and it seems to be what most other people do as well. Are you ready?

Step 1: Work on something

Seems obvious, right? Of course you have to work on something. You can’t just be a generic scientist (the idea is attractive, but that occupation closed about four centuries ago), and you can’t accumulate papers on everything. You need a focus. But if you’re just starting out, how do you know what to work on while you decide what to work on? It’s a Catch-22.

There are basically two solutions: work on something that appeals to you, or let someone else pick something for you.

Don’t discount the second path. It’s a big benefit of having an advisor who can provide you with a starter project. I didn’t have any particular fascination for sauropods before Rich Cifelli put me to work on what would become Sauroposeidon; I fell in love with them along the way (Buddhists would call this my awakening). As far as I can tell, Mike took the first path, and started working on sauropods because they seemed cool, and fell more deeply in love with them along the way.

I don’t describe this as “falling in love” lightly. That’s what it feels like: a positive feedback loop wherein the more you engage with a subject, the more you enjoy engaging with it, and so on. A few rounds of that and you may find yourself in a committed relationship, also known as a “research program”, because that’s how you maximize your time with the object of your affection.

You may not fall in love with your first project. It might crash and burn. You might not even finish it. It’s really just there to be your runway, to get you up in the air and flying under your own power. One way or another, you’re going on to something else. If you get a paper or two out of it along the way, that’s gravy.

Some people may find all this talk about falling in love overwrought or goofy, and some people may not feel that way about what they work on. If that’s you, you have my full sympathy, and my advice is to keep trying new things until you find something that you really do fall in love with. It’s worth it. Also note that I am using the word “love” to mean something involving commitment, investment, and self-sacrifice, as opposed to infatuation; find something that gives you satisfaction, not merely pleasure.

The point of working on something, as opposed to taking a more general approach, is not just to cut the problem of becoming a scientist down to a manageable size. It’s also to give you some traction with real data and real arguments. If you tried to become a generic paleontologist, you’d have to fly at such a high level that you couldn’t afford to get engaged with the details of any one particular problem. If you go that route you will never “drill down” enough to make a useful contribution; you may become a very well-informed enthusiast, but you won’t be  a very productive researcher.

Step 2: Learn lots of stuff

“Data! Data! Data! I cannot make bricks without clay!”

— Sherlock Holmes, “The Adventure of the Copper Beeches”, by Sir Arthur Conan Doyle

Once you have a direction, even a vague and temporary one, you have to accumulate clay. The clay comes in the form of facts, hypotheses (tested and otherwise), ideas, suggestions, and so on, and you get it mostly from reading papers.

You need clay for two reasons. First, you simply have to have a foundation of knowledge before you’re going to be able to contribute anything. Furthermore–and this is the step that seems to trip up many who aspire to contribute–you really need to have a handle on where the field is right now, and how it got there.

It’s pretty common for internet cranks in general, and absolutely pandemic for dinosaur cranks in particular, to argue that Ivory Tower so-called experts are all blinkered by orthodoxy and that outsiders with no technical training are better suited to having the big ideas because they are unshackled by the weight of knowing all that has gone before. These people are almost always wrong, because they keep reinventing the wheel, and the wheels they reinvent are often square. Either they’re solutions to problems that have already been solved (behind the state of the art), or solutions to problems that don’t exist (they misunderstand the state of the art), or, more rarely, solutions no one could implement because the methods or evidence just aren’t good enough yet (too far ahead of the state of the art). A good idea for a project has to be testable, but so far untested. Which means that if you want to make a useful contribution, you have to catch up with the cutting edge, and then stay caught up.

If you trust yourself and believe in your dreams and follow your star, you’ll still get beaten by people who spent their time working hard and learning things and weren’t so lazy.

–Terry Pratchett, The Wee Free Men

It’s not a trivial amount of work, and it requires some humility. Rich Cifelli put me to work on what would become Sauroposeidon in the late spring of 1996, and we had a paper ready to submit in the late spring of 1999. Thanks to Brooks Britt and Kent Sanders, I started CT scanning and really thinking seriously about sauropod pneumaticity in 1998, and the major papers that came out of that were written in 2001 and published in 2003. So both of those major steps required about three years of work from inception to submission (and an additional year or two until publication). Not all of my papers have three years of work behind them, because as you progress you learn stuff that applies to more than one project and you get better at figuring out what you need to know to complete a project; the earlier ones involve more faffing about. But if you’ve never published, it wouldn’t be a bad idea to mentally prepare to spend a few years getting up to speed.

That’s another benefit of doing a formal degree program that Mike didn’t mention in Tutorial 10: it gives you some protected time in which to get up to speed. You can do it without doing a formal degree program. It will require more effort on your part, since you won’t have an advisor to guide you or fellow students to challenge you (although you may be able to find substitutes). But there’s no reason why it can’t be done.

Step 3: Think about things

When Newton was asked years later how he had discovered his laws of celestial dyamics, he replied, “By thinking of them without ceasing.”

— Timothy Ferris, Coming of Age in the Milky Way

This seems like the easy step, when you’re considering it at one remove, either because you haven’t plunged in or because you’ve already learned to swim. After all, what could be more fun than thinking about dinosaurs (to pick an example completely at random)? But when you first start pulling the clay together, it seems like all the good ideas have been taken, like everyone else in the world is working on something 100 times cooler than anything you could ever think of, and that you will surely be doomed to work only on the most trivial problems because you’ll never have any really good ideas.

(Aside: if you have loads of what seem like really good ideas, then either you have already grown through this stage, in which case get back to work, or you skipped Step 2, in which case I’ll be happy to talk with you–in about three years.)

Fear not, because as long as you keep at it, you are going to have good ideas. In fact, pretty soon you’ll be drowning in them, and it will happen a lot sooner than you think. And I’ll tell you exactly how that’s going to happen.

At first, you don’t know anything, and it seems like all the good ideas are taken, but that’s because you don’t know anything. But as you catch up with the cutting edge, you will start to notice holes in the fabric of science: things that no one has done before, ideas that haven’t been tested, established “facts” that seem a little wonky or that have been upset by new discoveries. Now you’re getting traction. Not all of these holes are going to be worth patching. As you learn more (Step 2 again, forever and ever, world without end), you may find that some things haven’t been tried because they’re just intractable, and that some established facts only seemed wonky because you didn’t fully understand them (beware–this happens a lot). So stay humble, and keep learning, and keep thinking.

By “thinking” here I don’t mean simply staring off into space (although that is sometimes a symptom of deep thought), or sitting down with a notebook and pencil and deciding to think, although that can be a useful exercise now and then. It’s more along the lines of living and breathing your work. You have to engage with your subject material on a deep level. It will become what you think about in the shower. It may even invade your dreams. This is what I meant up above when I described it as “falling in love”. When you fall in love with someone, it’s almost impossible to think about anything else. With any luck, you’ll find a problem that occupies your mind similarly, at least for part of the day. I wrote the GDI tutorial when I was doing a lot of mass estimation for a couple of upcoming projects, and I found that I was mentally rotating volumetric models of Plateosaurus in my head on the drive home  from work. Often I went to sleep with visions of translucent 3D sauropodomorphs dancing in my head.

At some point you are going to go through what I call the Big Flip, where the exponentially rising curve of your knowledge passes the exponentially falling curve of your perception of how much science has actually been done. As you attain some level of mastery of the field, you won’t see just a few holes in the fabric of science, you’ll see that science is mostly holes, and that what we know is tiny compared to what we don’t know, about just about everything. At that point, you’ll see potential projects everywhere you look. The problem then becomes not thinking of a project to work on, but deciding what to pursue from among the almost limitless array of things that you could work on, and that’s a problem for another tutorial.

Maybe. Neither Mike nor I have been active long enough to tell if we’re any good at sorting projects, and Darren is no help because his “solution” is simply to work on everything. About the only thing I know for sure is that sometimes you have to start a project to find out that it’s not worth finishing. Don’t feel bad about hopping off a project like that onto another, more promising one (to a point; you’re going to have to settle down and work sometime). Some projects actually get to the moon, and others burn up in the atmosphere, go into dead-end orbits, or blow up on the pad. Sometimes the only way to find out which is which is to strap yourself in and light the engines.

Surely, you think, I’m exaggerating about the “almost limitless” array of things to work on. But I’m not. Just as big-S Science is dwarfed by big-I Ignorance, pretty soon your own completed science will fall far behind your own potential science, and it will never catch up. Right now I have about a dozen published papers, and 35 folders on my hard drive for projects I have taken seriously enough to start working on. A handful of those will be published in the not-too-distant future, a few more are things I might work on after that, and the vast majority are things I’ll never get around to. Everyone I know who is active in science feels exactly like this (Darren Tanke has “about 55 writing projects on the go”, by his own count). In fact, one sign that you’ve had your Big Flip is when you look around at all of the stuff you have going on and realize that you are going to die with a lot of work left to do, whether that’s tomorrow or a century from now. When that realization hits, don’t despair. It means you’ve arrived. Dive into whatever looks the most promising at the moment, and vamp till fade.

Step 4. Be open

If we knew what it was we were doing, it would not be called research, would it?

–Albert Einstein

I can tell you from experience that parents with infants are hyper-alert, because they don’t want to drop their babies. For the first few hours and days, this alertness is almost exhausting. It’s like when you first learn to drive and you’re constantly twitching the steering wheel. Eventually you learn how to be hyper-alert and still do other things. The “don’t trip on that rug/avoid sharp corners/be prepared to fall on your back” program is still running, but you can have other windows open on your mental desktop. Evaluating the potential hazards in whatever space you’re in becomes reflexive.

When I say, “be open”, I’m talking about cultivating an alertness of that kind. Your research program will be running most of the time, even it it’s minimized or in the tray while you do other stuff, and it will constantly evaluate the facts and ideas you encounter and see if they fit. The other part of being open is feeding your brain a cosmopolitan diet. Inspiration comes from the most unpredictable sources. There’s no way to force inspiration to happen, but you can improve the odds by deliberately seeking out the unfamiliar.

There is a great bit in one of David Quammen’s essays in which Quammen is roaming the Montana State University library and he comes across Jack Horner sitting on the floor between two rows of shelves with journals spread out all around him. Quammen says, “Hey, Jack, what are you doing here?” Horner looks up and says, “Having ideas.” The best part is that the journals weren’t even paleo journals, they were ornithology journals. (Note to DMLers: including a positive anecdote about Jack Horner is an intelligence test. Try not to fail.)

The downside of deliberately seeking out new stuff instead of staying with the bounds of your research program (the Sofa of Science!) is that it will make you feel stupid. It doesn’t matter what line of work you’re in, whether it’s paleontology or programming or construction, there is something that you are an expert on now that you weren’t when you started, whether it is taphonomy or recursive subroutines or pouring concrete. But you weren’t an expert when you started, and when you started you probably spent a lot of time feeling stupid. But you learned quickly, partly because you were anxious to get past feeling stupid, and partly because trying dumb stuff is a good way to learn what works and what doesn’t. If you’re not feeling stupid, you’re too comfortable, and it might be time to do an audit and see if you’re actually contributing to science at all. Science requires a certain kind of stupidity (Schwarz 2008).

And once you’ve got a research program, it’s all potential grist for the mill. Throw facts and ideas in the air and see where they land (the whole idea is that you can’t predict that in advance). Some will land behind the cutting edge, some too far out in front, and some entirely off the map. But one or two might land on the cutting edge, or ideally just ahead, and then you can push the whole field forward, just a little bit.

Conferences are valuable because they give your mental program a huge slug of input. You don’t get sprinkled with new facts and ideas, you get carpet-bombed, and as the volume of fire increases, so do the chances for a successful hit. I got an idea for a sauropod neck paper from a talk on the foot morphology of perching birds at ICVM last summer. Another long-delayed project was inspired by a talk on the development of snail shells by a fellow grad student back at Berkeley. That’s one reason I like smaller conferences like SVPCA, with no concurrent sessions. If everyone is in one room, you’re bound to sit through talks you wouldn’t see otherwise, and those are where you’re most likely to get fresh ideas. At SVP I always opt for the dinosaur talks over the mammal talks, and that’s good for Step 2, but bad for Step 4, because I already know what most of the dinosaur talks are about. I’m adding a little clay, but possibly losing out on a lot of inspiration. If I was really taking my own advice, I’d go see the fish talks.

So, conferences are good, but really they’re just an intense version of something you can do all the time, which is choose to feed yourself new things.

Coda: Publish

“I was on an [email] list with Tom Clancy once.  Mr. Clancy’s
contribution to the list was, ‘Write the damn book’.”

–Greg Gunther.

I know Mike used that quote before, but it bears repeating.

This tutorial is not aimed at everyone. It’s aimed specifically at people who were inspired by Tutorial 10 but don’t know where to start. Well, now you know. Step 1 is a choice. Steps 2, 3, and 4 are habits to be cultivated, for the rest of your life. But you can pick a project, read all the papers you want, think about your topic constantly, and drench yourself in the rainstorm of new ideas, and none of it counts until you publish. It may be a great way to pass the time, it may be tremendously rewarding, and you may develop as a person, but it won’t be science until you communicate it in a form that other people can use (i.e., papers, not mailing list posts–you dino folks know who I’m secretly addressing).

Write the damn paper.

——————–

Disclosure: a couple of passages in this post are cribbed from the never-completed series, “Blundering toward productivity”, on my old blog. That series was a straight up pastiche of Paul Graham, but it includes a few more relevant ideas and might be of interest. Part 1, Part 2, Part 3, Part 4.

Finally: I can only link to things, I can’t put a gun to your head and force you to read them. But if I could, I’d make you read Schwarz (2008) first–it’s one page, and it’s important. After that, I’d make you read all the linked Paul Graham essays. If you have time to slog through my blatherations, you have time to read the better stuff that inspired me.

Update 2014-03-16: This post inspired a follow-up, and this much later post touches on some of the same issues.

Reference

Schwartz, M.A. 2008. The importance of stupidity in scientific research. Journal of Cell Science 121:1771.