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How to Make Your Own 3D

In the last post, I covered good places to find 3D fossils. This post I want to cover how to make your own 3D images using photogrammetry. Photogrammetry is the process of turning a bunch of 2D photos into an interactive 3D image. Since I am not an expert on doing this, I am simply going to link you to a series of tutorials put together by Dr. Heinrich Mallison. Dr. Mallison describes himself as “a dinosaur biomech guy working at the Museum für Naturkunde Berlin.” If you would like to read more of his work, I suggest you check out his blog, Dinosaurpaleo, in which he blogs about his research. He also has links to a lot of his research papers and will happily send you pdfs of any other papers of his you want. Dr. Mallison is an expert on making 3D reconstructions using photogrammetry and has already done the legwork to give you all the information you need to get started.

Image

 

Getting the Right Photo

Photogrammetry tutorial 1 begins with the logical starting point: the equipment. He recommends getting a good DSLR camera with a Life View touchscreen, circular polarizing filter, good tripod, turntable, and a ring flash for optimal pictures. Also, don’t forget the scale bar and stickers. The stickers will be helpful if you have to take our photos in two sets (for instance, if you have to move the object between sets). This will require making two models and stitching them together, which will be aided by small stickers that will serve as easily findable common points so you can properly align the models.

Photogrammetry tutorial 2 discusses general suggestions on how to take good pictures that you can use for the 3D model. Here he gives advice, such as maximizing the F-number to increase depth of field, balancing your exposure, the use of HDR (high dynamic range) images, and proper cropping of the images.

 

Mallison's 3D CAD model illustrating good camera shots.

Mallison’s 3D CAD model illustrating good camera shots.

Photogrammetry tutorial 3 covers the use of turntables. He covers the type of specimens that work best, how to place the camera for the needed pictures and how to photograph with an eye for aligning the 3D models you create.

Photogrammetry tutorial 4 discusses techniques for photographing large, bulky specimens.

Photogrammetry tutorial 5 provides a ideo of the turntable method described in part 3.

Making the 3D Model

Part of a Diplodocus limb Dr. Mallison modeled.

Part of a Diplodocus limb Dr. Mallison modeled.

Finally in tutorial 6, Dr. Mallison finally gets around to actually building the model from the photos. If this indicates to you that getting good photos is essential to making good models, you would be correct. To add more to this, the writers of the blog Sauropod Vertebra Picture of the Week, or SV-POW, have a series of useful posts on how to take good photographs, manipulating them for good effect, making stereoscopic images, and much more great advice.

In this tutorial, Dr. Mallison discusses some of the programs that are available. He prefers Photoscan Pro from Agisoft. The downside to this program is that it costs $549, which is probably out of the price range for many people. The upside is that it is a versatile program designed for non-specialists. He discourages use of Autodesk 123D even though it is free because all of your work becomes the property of Autodesk 123D. He also states that others prefer Image Modeler, which is the professional version of Autodesk. It can do more than Photoscan Pro, but it will cost you much more. He also mentions VisualSFM and Meshlab, open source programs which together can be used to make 3D models and provides a link to a tutorial by a fellow paleontologist, Peter Falkingham, who tells you how to use those programs.

From there, Dr. Mallison goes into scaling and aligning the models. If you want to see some of the finished work, try here and here.

Other Options

Of course, this isn’t the only wayto make 3D objects. Photogrammetry is only way to make quality 3D images. Laser-scanning is another great way to do so. If you have a few thousand dollars, I might recommend the NextEngine 3D laser scanner. It is not as expensive as some of the other laser scanners and does quite a bit at a comparable or better quality. As a caveat, neither the photogrammetry nor the 3D laser scanning will create the most detailed images. If you want truly detailed, high resolution images, then you really need a computed tomography, or more commonly just called CT, scanners. The downsides to that is that CT scans do not preserve the color of the objects, so you lose surface details related to color, and they are hideously expensive. But at least they are not as expensive as synchotron scans. Synchotron scanners are similar to CT scanners, but are much more powerful and can create images with much greater detail, but with only five available scanners, probably not something your average paleontologist, much less a hobbyist, is going to ever see.

Once you have your 3D objects of course, there is always the next possibility: 3D printing! For that, contact your local high-tech Maker Spaces, such as the Arkansas Regional Innovation Hub. There are several places you can go to buy your own 3D printer, such as Quintessential Universal Building Device, or QU-BD, in Little Rock, AR.

Full Disclosure: I have no monetary interests or any other vested interests in any of the people or companies linked to in this essay.

3D: It’s Not Just for Movie Theaters

Jim Lane is talking about something that has been on the mind of a lot of education researchers lately. If you read much in the way of education literature at all, I am sure you will have run across many a discussion of how to improve learning by engaging the students with materials they find interesting and challenging them to solve relevant problems in a creative manner. Doing that means moving beyond the simple worksheets and memorization. It means using the newly available tools to bring the material to life and having the students work on, as one of Mr. Lane’s students called it, the edge of science.

Some of those new tools are in the realm of 3D scanning and modelling. This has allowed many museums and researchers to put some of their work online in a way that allows much more interaction than simple photos. You can, for instance, examine the head of a 2,200-year-old Chinese terracotta warrior housed at the Emperor Qin Shi Huang’s Mausoleum Site Museum or skeletons in an underwater cave from the comfort of your own home. This has great benefits for conservation and research, allowing digital preservation of fragile artifacts and researchers from all over the world to view the objects without having to spend the money to physically examine them. Much of the time, researchers will still want to see the real thing, but there are numerous studies that can be done with only the scanned images. There is even some research that can only be done on the scanned items, making the scans in a way, more important than the item itself. More to the point here, 3D scanning also opens up the object to viewing by people the world over, the vast majority of whom will never have the chance to visit the museum and see the real item.

So where can you see some of these items? There are several places on the net you can go. Here we will focus on those useful for evolutionary topics, such as fossils and anatomy (comparative anatomy with modern organisms is the heart of paleontological research). Many of the sites allow you to download the scans and print them out if you have access to a 3D printer, which are becoming increasingly common as the prices drop down to the point many individuals can buy their own and schools are starting to make them available to their students. Be warned, interactive 3D elements generally take a lot of graphics computation, so try to limit any other graphics you have up, i.e. close other browser windows, don’t try running a game in the background, the general rules of using a program with a lot of graphics. But as long as you have an up-to-date browser with Quicktime and Java, most computers these days should be able to handle it just fine (although a warning about Java, the security updates in the past year or so have made the more recent versions of java incompatible with earlier versions, so unless the developer for the site has updated their program, it may not work).

The following sites are in no particular order, so with that in mind, the first place on this list you might want to visit is Smithsonian X 3D, a website the Smithsonian recently put up showcasing objects from their collection they have scanned. At the moment, there is not a lot, but the site is new and they will be adding much more as they go along, so be sure to check back regularly. Right now, you can see 3D images of whale fossils, a mammoth, a blue crab, an orchid, a bee, and several other historical objects. Included in the collection is a scan of President Obama, the first ever 3D Presidential portrait. The basic 3D viewer is easy to use, although a few of the more advanced controls are not altogether intuitive. The website provides a brief description of each item, along with articles and videos on some of the items and the process of scanning them, including a page for educators on the use of the objects in the classroom. The Smithsonian also has more 3D collections on their human origins site. You might think that they would only have human fossils, but they have much more. You can certainly find hominid fossils, but along with them are numerous primates from Aye-Ayes to gorillas, and a large variety of other animals, from bears and cheetahs to komodo dragons and vultures. While you are there, you can a diverse array of information on human evolution, including teacher guides, lesson plans, multimedia, current research, everything you need to teach a human origins unit.

Another place you will want to check out is the Visual Interactive Anatomy pages by Dr. Lawrence Witmer at Ohio University. He and his students spend a lot of time scanning fossils and modern animals using a medical CT scanner at nearby O’Bleness Hospital or a micro-CT scanner on campus. They have put together several pages that illustrate the anatomy of several modern animals, including an opossum and the heads of a human, rhino, iguana, alligator hatchling, and ostrich. They have also collaborated with Dr. Casey Holliday on an adult alligator. The adult alligator page even has individual pages for every bone in the skull. On these pages, you will find interactive 3D pdfs and videos of the scans and reconstructions, which have a variety of structures labeled, identifying the bones, brain cavity, nasal passages, etc. In addition, you will find news and behind the scenes excerpts, and links to the published research on the specimens. On the 3D Visualizations page, you will find similar movies and 3D pdfs for a variety of dinosaurs (including Tyrannosaurus rex, Majungasaurus, and Euoplocephalus, along with several birds) and mammals from the platypus to deer to Archaeotherium, one of the group of animals often called “terror pigs”.

A website that is sure to grow is the NIH 3D Print Exchange. This site allows people to share their own 3D files for other people to download and use. The website focuses on biomedical applications, but currently you can find a variety of brains, bones, molecules, DIY lab equipment, and more. The more part I am sure will grow as people explore the site and add their own models. You can also find tutorials for making your own 3D models using 3D visualization software, and links to open source software such as Blender, FreeCAD, and Google Sketchup, as well as 3D printing services such as i.materialize and Makexyz and others.

Digimorph, or more properly Digital Morphology, a National Science Foundation Digital Library, is a site run by the CT facility at the University of Texas at Austin, one of the premier CT facilities in the country and the primary place American paleontologists go to get their fossils scanned. Digimorph provides access to these scans for the public and researchers the world over. On this site, you can find videos of scans and 3D reconstructions, some of which can be downloaded for 3D printing, for hundreds of animals, including a variety of avian and non-avian dinosaurs, along with extinct and modern species of mammals, reptiles, amphibians, fish, and even plants, coral,  crustaceans and other invertebrates. Along with the scans and 3D reconstructions, you can find descriptions of each specimen, a bibliography of research published on them, and links to useful sites for software, information on CT scanning, and other related sites. The downside to the site is they provide nothing specific for educators and the specimens that have downloadable 3D renderings are a small fraction of the total specimens available in video form, and none of them of the dinosaurs, which are only available as video animations. Nevertheless, for sheer quantity of 3D images for a diversity of animals, there is no place better.

The final site on the list is swiftly becoming the place to go for virtual fossils.GB3D Type Fossils Online project, or simply GB3D, is a website run by the British Geological Survey, Amgueddfa Cymru (National Museum of Wales), Oxford University Museum of Natural History, and the Sedgwick Museum of Earth Sciences. As the name suggests, the site is a repository for information of “type” fossils. If you don’t know what a “type” is, they have a handy guide explaining the different types. In this case, they aren’t talking about what kind of fossil it is, but things like holotypes, fossils designated in the original description of the fossil, which all others are compared to, which make them very important to scientists studying those kinds of fossils. If you want to see United Kingdom fossils, this is the place to go. They have hundreds of fossils in 3D and hundreds more in 2D. On this site, you will find a great diversity of plants and animals with high quality photographs, many of them also have stereophotos (get your 3D glasses with those red and blue lenses) and 3D models. In addition, you will find information about the fossil, such as what it is, when and where it was collected, how old it is, and contact information for the institution that holds the fossil itself. They also have a page describing the more commonly found fossils, all of which happen to be various invertebrates or fish. You will also find free programs used to view and work with 3D images you can download. They have available MeshLab, SPIERSview, and Adobe 3D Pdf Reader. Finally, you will also find links to a variety of educational resources for primary and secondary schools, universities, and the public.

Hang gliding in the Oauchita Mtns. Photo by www.mena-ark.com

Hang gliding in the Oauchita Mtns. Photo by http://www.mena-ark.com

If you want to inspire people to learn, you have to bring them right up to the edge of that knowledge cliff so they can peer over it at the wondrous space beyond, exposing them to the unknown in all its glorious mystery. Help them understand the foundations of the cliff, teach them how to build their own wings, and then push them off that cliff so they can soar into uncharted regions. When they return, they will have a better grasp of how the cliff is formed and what its boundaries are. They just might also find that cliff sticking out a little farther than when they flew off it. And when they do, you won’t have to push them, they will leap on their own. Of course, you will then have another problem: keeping up with your students. So keep your own wings in good repair. I do hope I have helped you build your wings a little stronger. If you know of any other sites that may be of use, please let us know in the comments section.

I will let Dr. Witmer finish this out and let him explain a bit about his projects and why approaches like this, particularly with dinosaurs, are useful educational tools.

 

Best Introduction to Evolution Textbook

The Tangled Bank: An Introduction to Evolution

ImageBy Carl Zimmer

Publication date (2nd ed.): 2013 according to publisher (my copy says 2014), 452 pg.

Roberts and Company Publishers. ISBN: 978-1-936221-44-8.

Author: Carl Zimmer is one of the best science writers in the business. You can keep up with him on his blog, which is part of the National Geographic “science salon” called Phenomena, a collection blogs by Carl Zimmer, Brian Switek, Ed Yong, Virginia Hughes, and Nadia Drake, all of whom are experienced science writers with a talent for accuracy and clarity. They cover everything from dinosaurs to DNA to dark matter and are the first place I go to in the morning for interesting science news. If it sounds like I am selling them, I am in order to convince you that a book by Carl Zimmer is both more accurate than the current textbook you are using and better written. Zimmer and the others are not just authorial guns for hire, they care about science communication and they do it well. My first introduction to Carl Zimmer was a book called “Parasite Rex“. You probably are thinking that a book about parasites would not be the most interesting of books, but you would be wrong. Read it and it will open up a whole new (albiet disturbing) world for you.

The name of the book is derived from the opening line of the last paragraph in The Origin of Species, by Charles Darwin, a fitting name for a book introducing evolutionary topics. While I have a few complaints, none are major and I highly recommend the book. My chief complaints are that I always want more, but there is only so much one can put into a book, especially an introductory text.

The book is filled with high quality pictures and graphs that break up the text, but whereas many books have flashy graphics that serve little purpose other than to distract from the text, all the figures in the book clearly relate to the topic at hand without excessively cluttering up the book. They also provide data that get the reader to go beyond the “because I told you” format so many books use and actually look at some of the data supporting the scientific concepts (and serve as a great way to integrate math, geography, and art standards into the science). Each chapter also have a list of resources for further reading and an extensive bibliography, so anyone can check the data presented in the primary and peer-reviewed literature for themselves.

One thing that might make some teachers and students a little annoyed is that important terms are not in bold font, nor does it have problem sets. However, it explains all the terms as they come up, it does not require flipping to the end of the book for every new term, although there is also a glossary for those that need it. The book is designed to be read, not just skimmed through while one picks out the bold words, like so often happens. However, there is also a study guide for the book written by Dr. Alison Perkins, which includes all the learning objectives, questions, activities, and pedagogical suggestions that teachers are looking for.

The book begins with a detailed discussion of whale evolution as an example to introduce several general concepts of evolution and various ways in which evolution may be studied. It covers fossils, placing them into phylogenetic and geologic context, DNA studies, embryology, and ecology from their earliest beginnings to today. Zimmer doesn’t go into the disputes that arose about whale origins, instead just focusing on what has become the consensual understanding, which I find a bit disappointing, but perfectly understandable for the context of this book and especially this introductory chapter. Nevertheless, I like presenting disputes because it shows the dynamic nature of science as an exploration, not just a book of facts. He presents the exploration through a discussion of the fossils being discovered and how they were interpreted, he just cleans up the historical path and makes it neater than it really was.

Chapter 2 brings a history of evolutionary thought, starting in the 1600s and the development of evolutionary concepts before Darwin. Zimmer correctly explains that Darwin was not the first to conclude that organisms evolved, but he did provide a plausible mechanism for how it happened. He then continues with a discussion of the changes and additions to evolutionary theory in the decades since Darwin. He tackles the important misconceptions of evolution, including the common misunderstanding of what a scientific theory really means, which form the basis of most people’s arguments against evolution.

Chapter 3 presents geological data, including how radioactive decay is used to date rocks and biomarkers to detect traces of life within rocks. He tells us how fossils tell us about the past, followed by a brief overview of the major transitions in life from the dawn of life to today.

One of the many phylogenetic trees in the book showing the evolution of, in this case, birds from dinosaurs.

One of the many phylogenetic trees in the book showing the evolution of, in this case, birds from dinosaurs.

Chapter 4 is probably one of the most important chapters that is left out of many introductory biology texts. Zimmer tells us what phylogeny is and how to read a phylogenetic tree to understand evolutionary relationships. It is particularly disturbing so many books skip this step because it is vital to understanding much of what comes after. Misunderstandings here reverberate throughout one’s ability to understand evolutionary theory, yet reading phylogenetic trees is not as intuitive as most teachers think.  He talks about homology and how that affects our understanding of evolution. After he introduces the concepts, he demonstrates the concepts through a series of phylogenetic trees, such as early mammals, dinosaurs, and hominids.

Chapter 5 talks about DNA and how variation is introduced. Zimmer does a great job of discussing the various types of mutations and showing the typical view of point mutations is but the smallest way of introducing variation. His discussion of the role of sexual selection in creating diversity is short, although his description of Mendel’s experiment with peas helps somewhat. He also gives short shrift to lateral (aka horizontal) gene transfer, in which genes are transferred not through descendants but sometimes through completely unrelated organisms by, for instance, viruses. Zimmer also completely ignores endosymbiosis, which helped create mitochondria and chloroplasts, and hybridization, which makes this chapter not as satisfying for me.

Chapter 6 covers the role of genetic drift and selection well, although he leaves out a discussion of gene flow from one population to another. I like that he talks about fitness in terms of more than one gene, showing that what may be good for one gene is not necessarily good for another in terms of fitness, so that evolution is limited by the interplay between genes that each have their own optimal conditions. This would have been a good place to address the misunderstanding of “survival of the fittest,” which is commonly viewed as a tautology (the fittest survive, but how do you determine who is fittest? The ones that survive) but he does not mention it. This is a very common misconception. First, the phrase was never used by Darwin and is incorrectly and second, it is being incorrectly interpreted. It is not the overall fitness of a particular organism that matters, but a measure of how many offspring successfully survive and reproduce. It doesn’t matter evolutionarily if you are the toughest guy on the block if you don’t breed and produce successful offspring.

Chapter 7 discusses molecular phylogenies, figuring out evolutionary relationships from their DNA or protein sequences. One complaint I have here is that he talks about how successful the molecular clock is, how you can tell time using the amount of mutations separating species. In all actuality, the molecular clock has some serious issues, as in, it doesn’t work very well. Fortunately, he does discuss some of the challenges of the molecular clock (genes don’t mutate at the same rate either between each other or within different parts of the same gene, or through time, it requires fossils to calibrate and then tries to claim better results than the fossil data, etc.). The problems with the molecular clock mean that its usefulness and accuracy are limited and requires statistical manipulation of the data to try to take into account the known issues. Unfortunately, the figures lead one to believe the molecular clock actually acts clock-like, reducing the impact of the text describing its problems and the examples in the text downplay the problems. A bonus to this chapter is that he brings back the topic of horizontal gene transfer and shows its importance in a box at the end of the chapter. I might have put this in the last chapter and discussed it more, but it could be that Zimmer thought it might confuse people by introducing too much complexity at once and wanted the readers to develop a bit more understanding before throwing another wrench in the works.

Chapter 8 gives a great discussion of adaptation, taking it from the gene to species evolution. I particularly like his discussions showing how gene duplications and rewiring without the need for further point mutations can make huge differences. This is a really important concept to understand, that variation is more than just the single point mutations most people think about. He ends the chapter with a discussion of the limits of evolution based on physical limits and baggage from previous evolutionary steps, although I would have liked to see a brief mention at least of the constraints imposed by having genes with different optimal conditions that all have to be balanced.

Remember when I said chapter 5 gave short shrift to variation through sexual reproduction? That is because chapter 9 is completely devoted to the topic. Here he goes into several aspects of sexual selection, including trade-offs that may limit evolution in any one particular direction. Trade-offs in this case refer to the fact that improving one thing takes away from another. The genes with different optimal conditions are an example of this. Improve and you hurt another until a balance is achieved.

Formation of the Chicxulub crater formed at the end of the Cretaceous.

Formation of the Chicxulub crater formed at the end of the Cretaceous.

Chapter 10 defines what a species is (which is nowhere near as easy as it sounds) and how species evolve into other species. Chapter 11 extends that to evolution on a grand scale, showing the development of global biodiversity through time. I would have preferred to see a discussion of the difficulties in determining fossil biodiversity, such as the relationship between the amount of outcrops of a particular time and the number of species known, but there is only so much one can put into a textbook. Inevitably, the chapter discusses the major extinctions of the world, although he only talks about two of them, the Permo-Triassic and the Cretaceous-Paleocene extinctions, probably because they are better known by far than the others. His discussion of the Permian extinction doesn’t mention that the reason the volcanoes at the time put out so much carbon dioxide was that they apparently burned through huge coal deposits, which pumped up the carbon dioxide way beyond what the volcanoes would have done alone, but he gets the gist of the cause of the extinction. He also discusses briefly the debate in why the extinction occurred at the end of the Cretaceous, which is good. The chapter ends with a discussion of the current mass extinction taking place and the causes for it.

Chapter 12 discusses coevolution, both mutualistic and antagonistic. Here Zimmer finally discusses endosymbiosis and the important role it played in evolutionary history. Chapter 13 is an interesting discussion about the evolution of behavior in both plants and animals.

Chapter 14 will of course be the most controversial chapter because it deals with human evolution. Zimmer does a good job with this chapter, although I would have preferred a clearer statement that hominids and apes both evolved from a common ancestor, but where our ancestors became adapted for savanna life, the apes evolved more towards forest life. He talks about the interbreeding that happened between neanderthals and Homo sapiens, as well as with the Denivans, according to the genetic research published recently, which will make a few people uncomfortable, but is the truth nevertheless. The chapter wraps up with a discussion of some evolutionary psychology, which is highly controversial, but the parts he discusses are well supported by experimental evidence.

The last chapter is arguably the most important one in the book. Here Zimmer discusses the role of evolution in medicine, with examples of disease progression, vaccines, antibiotics, and cancer. If, by the time people have worked their way through the book and are still asking themselves why it is important they understand evolution, this chapter is a sledgehammer wake-up call. One cannot finish the book without having a strong understanding of the importance of this concept of evolution and why biologists consider it the central tenet of all biology. As Dobzhansky said, “Nothing in biology makes sense except in the light of evolution.”

 

Website Review and the Misconception of a Theory

In a quick review, I would like to discuss the website by Lin and Don Donn, http://earlyhumans.mrdonn.org/evolution.html.

This website is part of a much larger website that is filled with a lot of information on all sorts of history. As Mr. Donn states, they do not claim to be experts in anything, so do not claim everything on the site is correct, although they do try. It is clear they have put a great deal of time and effort into making a substantial site with the honest intention of providing accurate and useful information to teachers. They have won awards for an impressive site. However, in the evolution of humans, they seriously fall down.

The early humans website has several links to good resources. Unfortunately, it has two things that destroy the science educational credibility of the site completely. The first is a link to a presentation teaching Biblical creationism, a subject that has no place in a public school as it is both scientifically invalid and pushes one specific religious view, which is illegal in the United States. Regardless of whether one believes in creationism or not, it is not legal to teach a specific religion in public schools and it is especially not valid to teach that religious view in a science class. The only way to make this legal would be to teach the creationism stories of every other religion equally, without comment as to which one the teacher believed, which would be impossible. Even then, it would have to be in a religious studies class, not a science class. If we are to preserve everyone’s First Amendment rights to freedom of religion, we simply cannot have government-run public schools teach one religious view and we certainly cannot teach that view as a scientifically valid theory. I am hitting this point especially hard because it is a serious point of controversy in the United States, but it should not be. Keeping creationism out of the schools is not an attempt to suppress anyone’s views. It is an attempt to preserve everyone’s right to make their own religious choices without government interference.

That leads me into the second problem, one which is stated boldly right up front. One of the big problems we have in science literacy is that many people do not understand the difference between the colloquial use of the term “theory” and the scientific meaning of the term. To quote the website: “A theory is a guess based on some facts.  Remember a theory is not proven.  One of the great controversies of our time has been the theory of evolution.” This is massively wrong in two areas.

The term they have defined is NOT a theory. What they defined was SPECULATION. Anyone can come up with an idea, but that does not make it a scientific theory. First, one must have a hypothesis, which is a testable idea, based on observation, that explains a relationship between two or more measurable things. There are two critical parts to this. The observations, so it must be an attempt to explain something we actually see in the real world. Second, that explanation must be testable. If there is no conceivable way to test it, the idea remains in the realm of speculation and can never be taken as a scientific theory, or even a valid hypothesis.

Image

Great hypothesis, but not the way to do science.

Once one has a series of hypotheses that have been tested by many people, none of whom have been able to disprove the hypotheses, one can formulate a scientific theory. That theory ties the hypotheses together, explaining numerous detailed observations into an explanatory framework that applies broadly. An example of this is the Theory of Gravity. Numerous observations were made showing gravity exists, there is no doubt about that. Many observations showed precisely how it worked and the relationship of different masses to each other, both on earth and in the universe as a whole. However, to make a theory, we needed more than these observations, we needed a way to accurately describe and predict these relationships. Isaac Newton discovered a mathematical equation that could be used to predict the motions of the planets. That equation was then tested many times and found to be valid everywhere, at least at the speeds attained by most things in the universe. Einstein went further with his Theory of Relativity, which extended our understanding of gravity into realms beyond the experience of everyday existence. Even here, these started out as hypotheses, requiring many people to test over and over gain. Not only has no one been able to prove them wrong, but no one has come up with an explanation that better fits the data. Therein lies the key, testing and testing and basing the acceptance of the theory on data, evidence that either supports or disproves the theory. Without that, it is not a theory.

parachute

As such, there is no Law of Gravity. We know it exists, it is fact that is undeniable. The Theory of Gravity provides a framework in which gravity works that has been put to the test. In a similar fashion, there is no Law of Evolution. We know it exists, it is a fact that is undeniable. Why? Because the idea that biological life forms change over time is something that cannot be argued against. All one has to do is acknowledge we are not clones of our parents, or look at the diversity of changes brought about by dog and cat breeders, sheep and cow breeders. We see biological change all around us. Evolution is therefore a fact, just like gravity. The Theory of Evolution put forth by Darwin is more properly called the Theory of Natural Selection, which explained this change through the aforementioned natural selection. It has been tested numerous times and shown to work. Is natural selection the only way in which species change? No, but it is a major mechanism. But the point here is that it has been tested and retested. Like all scientific theories, it is not simply a guess based on a few facts. It is permissible to argue about specific mechanisms, but trying to argue whether or not evolution occurs is like arguing whether or not the earth is flat or that we need air to survive.

Evolution and Gravity are Theories (Humor)

Dino Sites to Avoid

I have been working on lectures on early amniote evolution, along with the following reptilomorph and synapsid lectures for my vertebrate paleontology course. We will be getting into dinosaurs and the other Mesozoic animals very soon, hooray! However, in preparing these talks, it has brought to my attention just how prevalent two sites in particular are: Reptileevolution.com and Pteresaurheresies.wordpress.com.

 Image

When I did a search for “pterosaur”, Google actually responded by saying “Did you mean pterosaur heresies” and provided images that all but one are either from the site or sites complaining about the site.

This is quite unfortunate. Both sites present an abundance of beautiful artwork done by a stellar paleoartist. There is an abundance of information on the animals and their relationships. All in all, the websites look fantastic and are quite the draw for paleo-enthusiasts.

But it is all wrong.

None of the hypotheses presented on these pages is accepted by virtually any other paleontologist. The techniques used to gather the information is not considered valid and no one who has tried to reproduce the data using the methods have had any success.

I won’t get into details about why the websites are wrong. I am frankly not qualified enough to provide a step-by-step breakdown of the problems (not being an expert in either pterosaurs or basal tetrapods), nor do I really have the time. I will say that many years ago, I heard the author of these websites give a talk about his evidence for a vampiric pterosaur and even as a young undergraduate, it was clear to me that neither the technique nor the conclusions were valid. I found it very unfortunate because the idea of a vampiric pterosaur was incredibly cool and the technique, which involves detailed image study, is useful in many contexts. However, it is very easy to let personal biases enter into conclusion based on these methods, to allow oneself to extrapolate well beyond anything the data can actually support. Oftentimes, those biases are completely unknown to the observer simply due to the way our brains interpret sensory input and modifies them based on past experience. We really do not see everything we think we see, which is why the scientific method requires other scientists examining your conclusions and your methods and trying to poke holes in your ideas. So it is vital to recheck one’s conclusions with many detailed images from various angles and lighting methods and, most importantly, detailed examination of the fossil itself.

So instead, I will point you to articles written by people who are experts in the very animals that are discussed on those pages and what they have to say about them. The first is an article by Dr. Christopher Bennett, who is an expert on pterosaurs. In this article, he discusses the validity of the techniques and discusses specific claims of two pterosaurs in particular, Anurognathus and Pterodactylus. Anurognathus is a very odd-looking pterosaur and is quite aptly named “frog mouth.” Pterodactylus is probably the most famous pterosaur next to Pteranodon and is why so many people mistakenly refer to all pterosaurs as pterodactyls.  Dr. Bennett does an excellent job critiquing the science in a professional and readable way.

Dr. Bennett's article.

Dr. Bennett’s article.

The second article is a blog post by Darren Naish, a noted researcher and science author that has researched pterosaurs and many other animals who has a deep understanding of both the accepted science and the author of these websites and the work presented therein. Here is what he says: “ReptileEvolution.com does not represent a trustworthy source that people should consult or rely on.Students, amateur researchers and the lay public should be strongly advised to avoid or ignore it.” The emphasis is completely his. The post is quite long and discusses several aspects of the work, discussing the accepted science and the material on the websites that is not accurate, including the techniques used to arrive at the conclusions, both accepted techniques and those by the website author that are not.

The next site is an article by Pterosaur.net, a website devoted to research on pterosaurs by pterosaur researchers. It is a brief article that uses Naish’s article as a starting point and continues on with a discussion of why they think it important for people to know why these sites should be avoided. To quote: “The issue taken with ReptileEvolution.com is not that it exists, but that it’s internet presence has grown to the point that it is now a top-listed site for many palaeo-based searches. Tap virtually any Mesozoic reptile species into Google and either ReptileEvolution.com or the Pterosaur Heresies is likely to be in the first few hits. The situation is even worse for image searches, which are increasingly dominated by the many graphics that Peters’ uses on his sites.” This would not be a problem that the sites are so well known if they were correct, but their prevalence presents a highly flawed version of what scientists really think. People are taking these sites as truth, when in fact they are regarded by professionals as seriously wrong.

Finally, Brian Switek, a science writer who authors the blog Laelaps, which moved from Wired Science Blogs to National Geographic and the now-defunct blog Dinosaur Tracking for the Smithsonian,  wrote a piece on the site, in which he urged more paleontologists and paleontology blogs to call out misleading websites like these.  In that spirit, I hope I can help some avoid getting a mistaken impression of dinosaur science and help steer them to better, more reliable sources.

* If you are wondering why I say “the author” or “the artist” rather than using the person’s name, it is because I don’t want this to be about the person, but the information. I don’t personally know the author, nor have I ever had direct contact, so I have nothing to say about the person. The work, however, can be and should be open for criticism, just like any other researcher, including my own.

Mystery Monday and Walking With Dinosaurs Movie Review

Mystery Monday

Last Friday I posted clues to a mystery fossil. The clues were 1) I lived in AR during the Mississippian Period roughly 330 million years ago and am a very common fossil to find here. 2) Many people think I’m a coral, but I’m not. 3) I am named after a famous Greek mathematician and inventor. Who, or more precisely, what am I? Allie Valtakis got the right answer as the bryozoan, Archimedes.  Here is what the Arkansas Geological Survey says about it.

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The Bryozoa grow attached to the sea-floor as do corals, but they differ significantly from corals in terms of soft-part anatomy.  The bryozoans are exclusively colonial and fall into two broad groups, the lacy colonies and the twig-shaped colonies.  Individual “houses” (zooeciums) lack the radial partitions found in corals, but they are divided transversely by partitions called diaphragms (Fossils of Arkansas).  Bryozoans can also grow as incrustations on the shells of other organisms and are commonly associated with reef structures.

“Bryozoans are tiny colonial marine animals that are present in marine and fresh water today.  They are sessile benthonic animals (fixed to seabed) that are filter feeders and prefer shallow seas, living fairly close to shore (neritic).  One bryozoan called Archimedes (see picture below) is abundant in Mississippian age rocks in Arkansas and is so plentiful that one of the rock formations called the Pitkin Limestone was once referred to as the “Archimedes Limestone”.  Generally, only small pieces of bryozoans that resemble “fronds” are preserved in Mississippian and Pennsylvanian age rocks in the Ozark Plateaus Region.

References:

Freeman, Tom, 1966, Fossils of Arkansas:  Arkansas Geological Commission

Bulletin 22, 53 p., 12 pls., 15 figs., 1 map.

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Archimedes “fronds”

Way to go, Allie!

Can you guess this week’s fossil? I will do things a bit differently this time. Unlike previous fossils, in which I told people on the Facebook page as soon as someone provided the correct answer, I will not reveal the answer until Friday, so you have plenty of time to give it a try. In addition to the picture (note the scale) below, I will provide one clue every day until Friday. Good luck!

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Clue 1: It’s from the Cretaceous.

Clue 2: It’s modern day relatives are widely considered a delicacy.

Clue 3:  This is no wilting lily. This creature is big and bold. It shows how twisted it is on the outside for all the world to see. Dude, that’s heavy.

Come back tomorrow for the answer! You can also find it on the Facebook page.

 

Walking with Dinosaurs 3D movie review

I went to see Walking With Dinosaurs 3D this weekend. My kids were interested in seeing the movie and I liked the BBC “Walking with Dinosaurs” TV mini-series, so we were all eagerly anticipating the movie. I had read a few reviews of the movie, some by paleo people, who said the dinosaurs were great, but the voices were terrible, which gave me pause, but it’s a BBC movie on dinosaurs, how bad could it be, right?

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Sadly, not like this.

Sad to say, I have to agree with most of the reviewers. This movie may be much more enjoyable if you can’t hear it. To begin with, whatever expectations you may have, forget them. If you are going in expecting to see a big screen version of the BBC “Walking with Dinosaurs,” you will be disappointed by the cartoon voices and plot. If you are looking for light entertainment for little kids, you might be a bit surprised by the rather jarring breaks providing a subpar, documentary-style educational interlude which will kick everyone out of the story.

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More like this, but with better graphics.

The film reminded me nothing so much as a cross between the BBC documentary-style series and The Land Before Time movie series, failing at both. I think the reason for this is because it seemed to clearly start off with the idea of it being a kid-friendly movie along the lines of the TV series, but some executive decided after it was made that it was not going to draw enough kids. So the movie was recut and really bad dialogue added to it instead of the normal narration one would expect in a nature documentary, along with completely superfluous modern scenes bookending the film, wasting the talents of otherwise fine actors. The voices were obviously added as an afterthought because the dinosaurs do not act like they are speaking. I could even occasionally hear the original dinosaurian bleating and honking in the background even as they are supposedly talking. The dialogue, as Brian Switek noted in his review, destroyed any emotion that may have been evoked by the scenes that were supposed to be emotionally powerful. What should have been poignant, heart-tugging scenes were drained of any impact by juvenile pratterings that never ceased. I found myself wishing for the dinosaurs to just shut up once in a while. As a result, it is a movie that may be enjoyable for a little kid, but eminently forgettable. Bambi was a much more riveting emotional experience, not to mention more educational about the lives of deer.

The story line was inconsistent with the idea of a nature documentary and a poor choice for a dinosaur movie. Whether or not the worst aspects of it were in the original script, I don’t know, but the final plot, while suitable for a cartoon Land Before Time, was wholly inappropriate for a nature “fauxmentary.” For a film that was supposedly educational, it pushed moral viewpoints which are only valid in human cultural environments and completely invalid in the natural world. The idea that intelligence and courage will overcome the thoughtless, testosterone-fueled belligerence of the larger alpha males is a noble sentiment and may work in a human context, but not in the depicted dinosaur society. Control of a herd of large herbivores that have evolved extravagant displays will never pass to the runt of a litter because he saves the herd in a time crisis due to his quick thinking. The plot line for the movie is far more appropriate to an after-school special involving actual, human children, not dinosaurs. As such, it completely destroys any educational effectiveness of the movie. The only education that remains is that dinosaurs lived in a snowy Alaska and that some dinosaurs had feathers, particularly the smaller theropod carnivores. I really like this aspect of the movie, but its authenticity in these aspects was completely undermined by the silliness of the rest of the movie.

To make it even more confusing in terms of genre plotting, the movie shows that females in the herd are dominated by the alpha male, but glosses over what that means in terms of sexual dominance. In a kid-based movie, this understandably only goes as far as hanging out with each other. In the natural world (and post-adolescent human worlds), as every adult in the audience will understand, it means the female submits to the alpha male’s sexual advances. In terms of a human kid’s movie, it sends very poor messages about the role of females in society. In terms of an educational nature show, it is intentionally misleading to spare the typical parental sensibilities of what is appropriate for kids to see.

In short, if you go to see this movie (which I would really recommend waiting until a rental, as it is not worth spending the price for a 3D movie), go expecting to see a mindless 80 minutes of passable, but forgettable, entertainment for children with no real educational value other than to say look, aren’t dinosaurs neat? Enjoy the graphics, ignore the rest.

It’s Big, It’s Golden, and it’s Dinosaurs

The Big Golden Book of Dinosaurs

By Dr. Robert T. Bakker

Ilustrated by Luis V. Rey

Publication date: 2013. 61 pg.

Golden Books, Randomhouse. ISBN: 978-0-375-96679-8.

biggbofdinosb2Do these books look familiar? One is the classic book that most people old enough to be parents grew up on, first published in 1960 and continuing through 1981. The second is the new, Big Golden Book of Dinosaurs, a new, totally updated edition that came out in 2013. The book is written by Dr. Robert Bakker, known by many as the bushy-bearded, cowboy hat-wearing paleontologist of many documentaries and the author of such books as the Dinosaur Heresies and Raptor Red. Illustrations are by Luis Rey, a talented artist already mentioned here due to his work illustrating Dr. Holtz’s Dinosaurs book. Dr.Holtz’s book was written for a wide audience, geared towards children of middle school age and upwards. This book, like its predecessor,  is geared for elementary kids. So it is not as detailed, but it is even more lavishly illustrated and will definitely hold the interest of younger kids.

From the front cover to the last page, those who know and love the original book, will find it echoed here, but updated with the latest information. inside the front cover is a map of the world as it existed in the Triassic and early Jurassic, with dinosaurs dotting the landscape, showing where various dinosaurs have been found. The map is matched on the inside of the back cover with a Cretaceous map. Both maps have the names of each of the dinosaurs illustrated so you know what you are looking at. There is also an index and handy pronunciation guide for all the animal names.carboniferousb

While the book is of course heavily weighted towards dinosaurs, like the previous book, it does not focus entirely upon them. In the brief introduction, it makes a point to place the dinosaurs in context as part of an evolving ecosystem, not as isolated creatures. The book then dives into the Devonian seas,introducing us to the fish that began the walk towards becoming landlubbing tetrapods (animals with four legs). It continues with a few pages on the Carboniferous and Permian Periods, with giant insects, early amphibians and reptiles, and even animals like the iconic Dimetrodon, properly identifying its kin as ancestral to modern mammals, even explaining key features showing it’s related to us. Only then do we get to the Triassic, the beginning of the Age of Dinosaurs and even then, it starts the discussion with pterosaurs and the ancestors of crocodylians. After a mention of the earliest dinosaurs, it then mentions the proto-mammals.

AmphicoeliasFinally, we reach the Jurassic Period and it is here that dinosaurs take center stage, with gigantic, long-necked sauropods and other well-known dinosaurs. Even so, they don’t forget the small, mouse-like early mammals under foot. After a brief interlude to discuss the great sea reptiles that appeared during this time, as well as the pterosaurs, that were now much bigger and diverse than in the Triassic, they return to a discussion of dinosaurs, this time focusing on a bit of history explaining how our views have changed over the decades.

YutyrannusThe book moves then into the Cretaceous, showing how dinosaurs adapted to diverse environments, such as the sand dunes of central Asia to the snows of the poles. There is a chapter on different ways dinosaurs communicated with each other, including singing, after a fashion, much like birds and animals call to each other today, although he goes a bit overboard in this area and speculates beyond what most in the field would say is reasonable. Of course, no elementary book would be complete without a chapter devoted to Tyrannosaurus rex and its battle with an armored herbivore, in this case, the ankylosaurid Euoplocephalus and a battle with Triceratops.  While the book makes much of the use of horns and frill by the Triceratops in battling T. rex, they were almost assuredly evolved to battle other Triceratops as dominance displays, like bison or antelope today, although that of course, doesn’t rule out their use as defensive weaponry against predators.

There is the required chapter on dinosaur extinction and it does a good job of mentioning several possibilities. However, it gives a bit of short shrift to the most accepted asteroid hypothesis and a bit more space to Bakker’s favorite hypothesis of disease, which is almost assuredly not true as a hypothesis of widespread extinctions on such a large scale. To his credit, he ends with the likely possibility that no one hypothesis is sufficient for explaining everything.

The book ends with what animals actually benefited from the extinction, that being mammals. The book ends with noting that not all dinosaurs died out and acknowledging the influence that dinosaurs had on the evolution of early mammals, thereby connecting the story of the dinosaurs to us. Besides the great illustrations, that I think, is the key strength of this book, never letting the reader forget that dinosaurs were but a part (a big, incredibly impressive part) of a bigger ecosystem, with each piece influencing the others. No group was isolated from the others, all are interconnected.

Overall, while I had a few minor quibbles, as i mentioned above, I can definitely recommend this book for any elementary library. Some middle school kids will like it too, although those older than that will likely be reading it for nostalgia of the original book, who will find this version a worthy successor.

Other than the image of the 1960 book, all images are illustrations from the book.

Why do artists draw dinosaurs the way they do?

Scaly Spotted Feathered Frilled: How Do We Know what Dinosaurs Really Looked Like?

scalybookBy Catherine Thimmesh

Publication date: 2013. 58 pg.

Houghton Mifflin Harcourt. ISBN: 978-0-547-99134-4.

Author: Catherine Thimmesh is an author of several books aimed at children in elementary to middle school. Her books have primarily focused on people, particularly women, doing science and politics, while bringing a wealth of information along with the human stories. As a result, her books should appeal to many people, helping them draw personal connections to the material. Two of her books, Girls Think of Everything and The Sky’s the Limit, have been listed as Smithsonian Notable Books, the latter book also listed as an Outstanding Science and Social Studies Trade Book for Children in 2002. Her book, Team Moon, discussing all the people besides the astronauts that made the moon landings a success, won the Sibert Award in 2007.

Iguanodon by Waterhouse Hawkins, 1850s

Iguanodon by Waterhouse Hawkins, 1850s

Illustrator: The book is beautifully illustrated by several well-known paleoartists, including John Sibbick, Greg Paul, Mark Hallett, Sylvia and Stephen Czerkas, and Tyler Keillor, as well as Charles Knight, the artist who created the classic pictures shaping the view of dinosaurs for more than a generation. Moreover, there are pictures of skeletons, sketches showing reconstruction from bone to skin, as well as Greg Paul’s classic silhouetted skeletons. As an added bonus, she includes a page at the end with a paragraph about each artist and a fun fact about each one. For instance, Mark Hallett was the person who coined the term “paleoartist.”

I have mentioned this book previously from a review by Brian Switek (for a librarian’s perspective, try the SLJ review here), but I finally got my hands on a copy so I can provide my perspective on it and I have to say, I agree with the other reviews. this is an excellent book well worth including in any elementary or middle school library or classroom. If you know someone who likes dinosaurs and likes to draw, they will like this book. This book gives a great discussion of how artists bring fossils to life, using new discoveries that are changing our views of how dinosaurs looked and comments straight from the artists crafting those visions.

KnightbrontoThe book wastes no time, providing information on the inside covers. At the beginnig is a timeline showing the different Periods of the Mesozoic Era, with a short description of the overall climate, apleogeography, and notable fauna and flora of the time for each Period. Inside the back cover is a breakdown of the three major dinosaur groups, with a few general facts describing the dinosaursin each group and listing several representative dinosaurs for each group (along with page references for where they appear in the text). Other things that puts the book on my recommended list is a nice index, glossary, and references; things not often found in childrens’ books, which makes this book a cut above. This book does not take the sadly all too common tack of using the “it’s a childrens book” excuse to talk down to the audience and not worry about the facts 9except for one point mentioned by Switek which I will get to later).

Seismosaurus. Mark Hallett, 2006

Seismosaurus. Mark Hallett, 2006

The book starts with a discussion of questions the artists ask about the fossils themselves and what scientists can determine from them, such as what can the bones tell us about how they moved and what they ate. Further questions are asked about the plant fossils found in the rocks and what the rocks themselves say about the environment. Was it a desert? A beach? Shallow marine? Once they have what is known, then they can fill in what is not known. The next few pages provide a short history of dinosaur science and the art that sprung from it, such as the early Waterhouse Hawkins Crystal Palace sculptures in London during the 1850s and the Charles Knight paintings adorning the American Museum of Natural History. The book continues with information gleaned from trackways and new technologies helping to spur more discoveries. A discussion of the skeletons leads into reconstructing soft tissues such as muscle and eyes over the bones.

One area in which views have changed significantly is in the skin, which is discussed next. The book describes how new fossils are helping to inform new views, such as feathered raptors, although the book does not mention that we even have evidence of feathers on tyrannosaurs now. This is one area in which the book could have gone farther, it did not discuss much of the diversity of feathers, quills, and assorted spines we have recently found on a variety of dinosaurs. The use of modern animals and analogs and mechanical constraints, such as skin around joints, is also discussed. The problems and possibilities of how one decides on a color is discussed, ending on a mention of new fossils that are beginning to give us amazing insight into actual colors of some dinosaurs.

yutyrannus-feathered-dinosaur_50973_600x450

Yutyrannus, by Brian Choo via nature. 2012. Not in book.

The information here is not presented as definite conclusions, but as a puzzle, in which the scientists and artists take the various clues and try to piece them together. Sometimes, mistakes are made, such as the thumb spike of Iguanodon was originally thought to be a nose horn. The descriptions demonstrate how vibrant and dynamic the work is. As new fossils and new information comes to light, views change accordingly. The workers must constantly adapt as their knowledge base grows, with each new find getting us closer to a more accurate understanding.

The one quibble I would make with the book is one which Switek also mentioned. The book begins by stating that no one has ever seen a real, live dinosaur, which is not true. We see them every day. They are in fact the most diverse group of vertebrate animals outside of fish. The book mentions that dinosaurs and birds are thought to be related. In fact, it is often said that birds are dinosaurs because birds evolved from earlier dinosaurs. So just like children are still in the same family as their parents, birds are in the same family as all the other dinosaurs. This relationship is a key point in reconstructing fossil dinosaurs. Of course, a lot of people find it bothersome to constantly have to refer to non-avian dinosaurs to refer to only those that lived during the Mesozoic, so it is justifiable to say dinosaurs and birds, so long as it is made clear at the beginning that dinosaurs in that context are only referring to the Mesozoic ones. this book doesn’t do that, which is the only big gripe about the book. Still, a relatively minor complaint compared to the rest of the book, which is done wonderfully.

Life is one big family

tolTeaching how all life is interrelated is a whole lot easier if you can show something akin to a family tree for living organisms. The Paleobiology Database has all the fossils organized by taxonomic  relationships to help you find things in the database, but it is not very useful for visualizations. The Encyclopedia of Life has lot of information and multimedia available for over a million individual species and shows how they are classified and is quite useful if one is looking for information on a particular species. But again, it is not very visual.

The Tree of Life website is an excellent website providing a great deal of information on phylogenetic relationships (for good discussion of phylogenetics, try here and here), providing abundant references on the primary literature discussing how scientists think various organisms are related. They work in collaboration with the Encyclopedia of Life, with the EOL focusing on species pages and TOL focusing on relationships. On TOL, one can start at the base of the tree and click on various branches following different groups into smaller and smaller groups, with each page providing what groups are descended from the starting group. For instance, the base of the tree starts with links to eubacteria, eukaryotes, and archaea, with viruses with a question mark. Each one is hyperlinked to a page discussing relationships within that group. It also provides a discussion of possible alternative branchings as well. Thus, the relationships are not presented as “we know this to be true,” but as an active, ongoing process of discovery and research. It is often highly technical, but would be extremely useful for high school students working on an evolutionary or biodiversity topic.

tol1

The Tree of Life and the Encyclopedia of Life are great sources for information on species and their phylogenetic relationships, but if you want better visualizations of the sum total of biodiversity, there are other websites that are definitely worth your time.

The first I would like to mention is the Tree of Life interactive by the Wellcome Trust and BBC. Watch the great video with David Attenborough first, then dive into the tree itself. The tree simplifies life to about 100 representative species. It is seriously weighted toward mammals, so provides a very skewed version of biodiversity, but the presentation should appeal to those who are most interested in the overall development from bacteria to humans. If once clicks on any individual species, it highlights the path to the base of the tree and provides a text description and in some cases pictures, a video, and locations. Click on another species and the path to the last common ancestor of the two selected species is highlighted. All the files are open source and available for free download, including the images and videos.

tolinteractive

timetree_poster_finalAnother interesting site is the Time Tree. This site has a poster that shows 1610 families of organisms available for free download. The poster does a better job of showing the true diversity, but is still heavily weighted towards eukaryotes. However, the real purpose of the site is to provide divergence dates between two species. Simply type in two species names using either scientific (say, Homo sapiens and Gallus gallus) or common name (say, human and chicken) and it will provide how long ago their last common ancestor lived. It should be noted here that the dates listed are estimates based on molecular data. They should not be considered as conclusive dates or anywhere near as precise as listed. Indeed, the value given is a mean value of several estimates, with the median value also given, as well as what they call an “expert result” (which they sadly do not explain). In addition, they provide the scientific references the results came from and the dates provided for each, which can be quite broad. In the example above, those values range from 196.5 to 328.4 million years ago, but of the nine studies listed, all but two fall within 317.9 and 328.4 million years ago. There is also a mobile version of the site, as well as an iPhone/iPad app, as well as a book.

Another site of interest is Evogeneao.com.  They have an interesting Great Tree of Life, as they call it, which like most others is heavily weighted toward eukaryotes. They have good explanations of evolution, along with a set of resources for teachers, including an interesting suggestion for how to introduce evolution to students. The interesting part of this site is their discussion of evolutionary genealogy, in which they extend the idea of a family tree farther back than it typically seen. They provide methods to calculate how far removed you are from other species. You can pick from a list of animals and it will tell you how closely you are related. For instance, choosing dolphin returns an estimate of 27 millionth cousin, 9 million times removed. That nicely encapsulates not only the idea of relatedness, but the immense scales of time we are talking about.

evo-large

itolThe Interactive Tree of Life, or iTOL, is another interesting site that may be of interest to high school teachers. This site utilizes genomic data as the basis of its trees and, unlike the others, provides a better visual indicating how truly diverse prokaryotes are in relation to us.  It also allows you to print out phylogenetic trees in different formats, depending on your preferences and what sort of information you want to display. You can even upload your own data if you wish, but most teachers will likely choose to stick with the displays already provided, as there are simpler programs to deal with trees that any but the most precocious senior high school student (or college student for that matter) may wish to create.

There are a few other interactive trees out there that may be more appropriate to younger viewers. One is at the London Natural History Museum website. This one is very simplistic, having only sixteen branches, with four of them being primates, but it gets the point across. This interactive is limited to providing the link between any two branches and the name of the group containing both. For instance, clicking on the banana and the butterfly gives the name Eukaryota.  Another site provides an interactive for the poster Charles Darwin’s Tree of Life. This interactive allows one to zoom in on any part of the tree and if one clicks on an animal, a short description of the animal is provided. Sadly, the two best interactives I have yet seen are not available on the internet. I had the opportunity to explore DeepTree at the Harvard Natural History Museum and it is truly spectacular, as is their FloTree. If you get a chance to see them, you should. Hopefully, one day they will be available in a broader format than now.

All of this assumes of course, that people actually know how to read these trees, which is a false assumption in that most people really do not. So it would be useful to spend some time getting familiar with proper interpretation of them before using them in class. There are several resources explaining this (such as here and a really excellent video here), so I will not put a tutorial on here unless there are requests to do so.

All images posted here are from the websites being discussed and are copyrighted to them.

You were here: Maps for seeing geography through time

It may seem that the earth is pretty stable. You can always count on the mountains being there when you look for them. But the Earth is a dynamic place. Volcanoes, floods, landslides, and earthquakes all change the landscape in ways we can see quickly.  What we don’t typically see is that if we expand these processes over long periods of time, those same processes alter the landscape far beyond our experiences. The surface of the Earth is covered in a crust broken up into numerous plates, which are constantly shifting and moving. The plates only move between 2.5 – 15 cm/year (the previous link contains information on how this is measured and provides activities for teachers for use in the classroom), but add this up over millions of years and the Earth looks quite different. Add into this mountain-building and erosion wearing down the mountains and you get radically different geographies for the planet.

094So what did the Earth look like in the past? There are two excellent sources providing maps of the planet through time. The first is the PALEOMAP Project, by Dr. Christopher Scotese. On this website, you will find maps ranging from 650 million years ago to the modern day and even into the future. There are 3D animated globes and interactive maps. He includes a methods section for how the maps wer put together and a list of references and publications. There is also a climate history section providing brief descriptions of the climate at various points in time. For teachers, there are several educational resources available, some of which are free, but others are available for a fee. There is even an app for the iPhone/iPad. It is not available yet for either android or Windows, but that has been admirably taken care of by the Howard Hughes Medical Institute with their Earthviewer app and they have done a wonderful job. the app is fully interactive, allowing easy scrolling through time and full rotation of the globe. You can also track atmospheric oxygen and carbon dioxide, day length, important fossils, biological and geological events, and major meteor impacts. The app even provides a bibliography of their source material. In addition to the maps from Dr. Scotese, the app extends the timeline back to 4.5 billion years (although this extension is obviously not nearly as detailed as the Scotese maps due to the greatly extended time and the greatly decreased amount of available data). All in all, a great app, also reviewed by the NSTA.

NAM_key-paltect_image

The second site that will be of interest is the Library of Paleogeography run by Dr. Ron Blakely. These maps cover approximately the same time frame as those provided by Dr. Scotese and are not animated. However, Dr. Blakely provides maps in different projections and provides regional coverage beyond that of global maps. So if you are specifically interested in paleogeographic maps of North America and Europe, this is an excellent resource.

A third site also provides paleogeographic maps which are very useful. In this case, the maps are secondary to the main purpose of mapping fossil locations. The Paleobiology Database contains records of fossil locations that have been published in  the primary literature. One can perform a search by organism or group, country, rock unit or type, time interval, paleoenvironment, or publication. The results from the search are mapped onto global maps based on the PALEMAP Project.

Dromeosaur fossils in 70 million year old rocks.

Dromeosaur fossils in 70 million year old rocks.

All of these sources are available to the public and are used by professional researchers. Therefore, one can safely assume they represent accurate assessments of current, generally accepted thoughts on our Earth through time. You may notice that maps from Scotese and Blakely may not completely agree on all aspects. This is because it is very hard to piece together all the evidence and trace the movements of the continents backwards through time. Often, the data is incomplete and they have to make judgment calls based on the available evidence. Not everyone makes the same choices. This is true even for maps of current geography and is even more so for paleogeography.  As we get more data and better techniques, those disagreements become fewer and fewer, but there is still much work to be done, so these maps can and will most likely be refined in the future to reflect new research.