[Introduction from Mike. I’m on the OKFN’s open-access mailing list, where we’re currently embroiled in a rather tedious reiteration of the debate about the merits of the various open-access licences. On Monday, veteran of the OA wars Jan Velterop posted a message so perfect that I immediately asked him for permission to re-publish it as a guest post here on SV-POW!. He kindly agreed, so over to Jan for the rest of this post. The only changes I’ve made are to highlight what I consider the key passages.]

I’ve been following this discussion with increasing bemusement. Frankly, it’s getting ridiculous, at least in my humble opinion. A discussion such as this one about licensing and copyright only serves to demonstrate that copyright, once conceived as a way to stimulate and enable science and the arts, has degenerated into a way to frustrate, derange and debilitate knowledge exchange.

I’m not the first one to point out that absolutely anything, under any copyright licence or none, could be abused for evil purposes or, in more mild circumstances, lead to misunderstandings and accidental abuse. I agree with all those who said it.

The issue here is what science and scientific results stand for. Their purpose is emphatically not “to be copyrightable items”. Copyright, invented to combat commercial abuse, has become a means of commercial abuse. The purpose of science and scientific results is to enrich the world’s knowledge. Any commercial advantage – appropriate for industrially funded research – can be had by 1) keeping results secret (i.e. not publishing them), or 2) getting a patent. Science, particularly modern science, is nothing without a liberal exchange of ideas and information.

Ideally, scientific publications are not copyrightable at all, and community standards take care of proper acknowledgement. We don’t live in an ideal world, so we have to get as close as we can to that ideal, and that is by ameliorating the insidious pernicious effects of copyright with CC-Zero and CC-BY licences.

The existence of the NC rider or stipulation for CC licences is unfortunate and quite damaging. Mainly because of the vagueness and ambiguity of what ‘commercial use’ means. Ideas in published articles can be freely used for commercial purposes of any kind, as ideas are not copyrightable. Only “the way the ideas have been formulated” is covered by copyright, and thus by the NC clause in copyright licences. In my interpretation that means that most usage of published material that is not a straightforward selling of text or images can be freely done. But that’s my interpretation. And that’s exactly where it rubs, because all the NC clause does is introduce hypothetical difficulties and liabilities. As a result of which, NC practically means: “stay away from using this material, because you never know with all those predatory legal eagles around”. In other words, it’s virtually useless for modern, sophisticated scientific knowledge discovery, which doesn’t just consist of reading papers any longer, but increasingly relies on the ability to machine-process large amounts of relevant information, as human ocular reading of even a fraction of the information is not possible anymore. At least not in most fast-moving areas of the sciences. Read this article, or similar ones, if you want to be convinced: On the impossibility of being expert, BMJ 2010; 341  (Published 14 December 2010 – unfortunately behind a paywall).

The taxpayer angle (“must be open because the taxpayer paid for it”), leading to Kent Andersonian notions of knowledge protectionism (“results of research paid by US taxpayers should not be available to non-US citizens unless they pay for it”), is a most unfortunate, visceral and primitive reaction and a complete red herring. For many reasons, not least because the taxpayer, or vicariously the taxman, isn’t the party that pockets any money payed for paywalled information. Besides, how far do you go? Americans not being allowed to stay alive due to a cure that was developed with public money in Switzerland unless they pay through the nose for it to the Swiss tax authorities? The “as-long-as-I-am-well-the-rest-of-you-can-go-to-hell” personality disorder. The whole idea is so against the ethos of science that those even thinking in that direction must be taken to be utterly and entirely unsuitable to any role in the scientific community.

Access control and restriction via copyright was at best a necessary evil in the print era; the ‘necessary’, though, has disappeared in the web environment.

Have a nice day!

Jan Velterop

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AN ALIEN IS COMING!

February 19, 2012

Re-posted with permission.

Of course, these these days John is better known for this work on the evolution of musculature on the line to birds, tyrannosaur hindlimb mechanics, and elephant anatomy.  But it seems the world lost a promising novelist.

[Originally posted on Twitter, by John.]

See also: Acaren and the Evil Wizards.

[This is a guest post by frequent commenter Heinrich Mallison.  Heinrich is maybe best known to SV-POW! readers for his work on digital modelling of sauropodomorphs, though that may change now that his paper on sauropod rearing mechanics is out.  Read on …]

Maybe this post should have been titled “How sauropods breathed, ate, and farted”. Or maybe not. But breathing, eating and fermenting the food will play an important role.

Last week held a special pleasure for me. I spent it in New York, digitizing sauropods bones in the American Museum of Natural History’s Big Bone Room. Treasure trove that this room is, the museum still held something even better: the opening of a new special exhibit titled The World’s Largest Dinosaurs. While all such exhibits are of general interest to me, this one is special. Mark Norell, famous palaeontologist and curator at the AMNH, had a co-curator for this exhibit, Martin Sander of Bonn University, who is the head and speaker of the German Research Foundation Research Unit FOR 533 “Sauropod Biology”. As a member of FOR 533, and having received funding for both my PhD work and my first post-doc project, I am obviously somewhat biased, so please take this into account when you read this report.

The exhibition does not show a large amount of sauropods material. Not that it wouldn’t make for a nice exhibit, as the AMNH’s Hall of Saurischian Dinosaurs doesn’t really have that many sauropods (one Apatosaurus mount, to be exact, with a mashed up Barosaurus vertebral column half-hidden away and a wonderful but obviously depressed “prosauropod”, my old friend Plateosaurus, thrown in to make up a bit for the many, many stinkin’ theropod specimens). But instead of showcasing some of the usually hidden-away bones of the AMNH collection (and believe me, there is some wonderful stuff there), it rather focuses on those parts of the animal that are usually missing: the soft tissues. “How did sauropods get so big?”, or, reversing the question: “Why did and does no other group of terrestrial vertebrates reach such gigantic body sizes?” These were the questions our research group has been busily investigating for the last six years, and the answers to these question are what the exhibit now tries to communicate to the public. And it does so quite successfully!

The centerpiece of the AMNH exhibit: the belly of Mama Mamenchisaurus.

The centrepiece is a full-sized, fleshed out model of a sauropod (Mamenchisaurus hochuanensis), but on one side the skin and superficial musculature has been cut away. The visitor can see the neck vertebrae, the trachea, the carotid artery, and the ribcage. And the ribcage is also a projection area, on which a video is played that shows the internal organs and how they work.

With a voice-over that explains the actions in simple terms, the principle of the avian-style unidirectional lung and the air sacs is explained (albeit with a small error, as lung physiologist and FOR 533 member Steve Perry was quick to point out – the AMNH has promised to fix things), as well as the basic principles of sauropod reproduction (high number of offspring). Many things are not said or shown here, which is a good thing as it allows for the normal short attention span of the average museum visitor for one piece of exhibit. Instead, interesting stuff like how much fodder a sauropod needed per day (or even per hour), a comparison of a sauropod’s and an elephant’s heart, and of a giraffe’s and a sauropod’s neck vertebra (wow, how light the sauropod one is!) are explored at small science stations spread around the room. I won’t go into a detailed description here, you can find that elsewhere on the web. The AMNH did a blogger’s preview a while ago, and invited the press for a press conference and walk-through of the exhibit with the chance to interview the scientists present on Wednesday, so much info has already been plastered all over the web. Instead, I’ll just show you some pics and talk a bit about the concept of the exhibition, and how various issues were handled that can make or break a show.

One thing is how to catch the attention of visitors and direct it to the content of the exhibit. You don’t want people just going “aw, sh*t! That is one HUGE bone/animal!” and wandering off into the next room. If you want to educate them (and that, may I remind you, is the central purpose of a museum exhibit), you need to get them interested in stuff. Get them to read texts, look at stuff (not just let their eyes wander across it for a few seconds), try to get their brains going. The sauropod exhibit manages this by, first of all, being behind a closed door you can’t see through. Usually, the AMNH halls are accessible either through an open doorway, or in a few cases through glass doors. Secondly, the exhibit, especially the rather confined area you enter first, is dark. Very dark. Again a marked contrast to the AMNH’s usually well-lit halls. Just a few plants greet the visitor, and it takes a second to adjust to the dark – enough time to look around a bit and notice the neck and head of Argentinosaurus (fleshed out model) above.

My esteemed colleague Vivian Allen from Royal Veterinary College London going "Aw, sh*t! That is one HUGE sauropod!"

Next, the visitor is channeled along, with only a very few specimens to catch his attention. Well done, because these few pieces (sauropod leg, Komodo dragon skeleton, human skeleton, etc.) focus on getting the main message across (sauropods = way larger than everything else), aided by the largest animals (or their silhouettes) or various groups painted on the wall. Only once the message has been driven home, as I could detect from the comments I overheard, are the visitors released into the main area that contains the sauropod model and the various detail exhibits around it.

The next thing is giving people time to check things out. If you herd them too much, they will get driven along by the masses. That’s why the larger, opener area around the sauropod model and the smaller bits around it works so well: people can sit down to see the projected videos on the sauropod belly, or they can drift around from one specimen or science station to the next.

The stations are not just glass cabinets with some bones in them. Instead, at many of them you can DO things. One allows you to measure either an adult or baby sauropod femur or your own, and then calculate how heavy a sauropod of that size was. At another you can pump a sauropod’s and an elephant’s lung. One I liked very much simply had an unpainted sauropod model, and two sets each (adult and children height) of oculars. One showed a colorful “show-off” version, the other a “camouflage” one. “Which one is true? We don’t know!” is how I’d paraphrase the text that goes with it. One that innocently hides in the corner is among the most impressive: a 5 ½ ft cube (1.7 m, for the civilized) made from Plexiglas filled with sauropod food. A serving sufficient for one day! On it, also, the various plant groups available in the Mesozoic were rated for various factors, getting an easily understood rating in stars. That’s another big thing: make things easily understandable, visualize them!

Yummy! 100% Recommended Daily Value for your average sauropod.

With all these things well done, there remains only one more thing: make things fun for kids! And the AMNH did just that by adding a kids’ dinosaur dig. OK, it is one of those cheesy things where you use brushes and stuff to brush sand off fossils (cast), but it was done well enough that kids lined up like there was no tomorrow.

Overall, the exhibit gets two big thumbs up from me. If you make it to NY while it is on, or to any of its future stations, go see it! However, as FOR 533 member Steve Perry was quick to point out: if you’re in it only for the size, you’ll be disappointed! Aside from a few isolated bones, not much of the largest dinosaurs (Argentinosaurus and Amphicoelias) is to be seen in bone. It is the biological details that matter!  But don’t get me started about the tail musculature, especially the caudofemoralis, of the big model.

And then, there is the other thing about it that is closely tied to shameless self-promotion: the AMNH did not produce a catalogue or anything similar. Instead, the latest book from the “Life of the Past” series (Editor: James Farlow) of Indiana University Press was presented at the press conference. The lucky reporters all even got a free copy! The title is Biology of the Sauropod Dinosaurs: Understanding the Life of Giants, edited by N. Klein, K. Remes, C. T. Gee and P. M. Sander. And by now, I am sure, you have figured out who the authors are … It is intended to be a summary of the research findings of the first (and part of the second) funding period of FOR 533, and yours truly has two chapters in it. The first doesn’t really give much new information; most is already contained in my two papers here and here. The second, however, presents novel research that didn’t make it into the AMNH exhibit. But hey, why spoil the surprise – go and buy our book!) Overall, it is quite a technical book, so laypeople beware, but we did try to make the research as accessible as possible while retaining a high standard. For the even more technically minded there is the summary of our research group’s work (which cost the DFG ~€6.000.000) to be found in Sander et al. 2010. However, reading that paper is not half as much fun as the book, or the exhibit.

References

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.