Blue Collar Scientist

Here’s a pretty clever scientific technique. Let’s say you’ve got a source of amber - lots of amber - and you want to check it for fossils. The problem, though - the amber is impure, or it has nonbiological inclusions, or it is badly scratched up - whatever the reason, you can’t see through it and can’t tell what is inside. It looks like this:

Researchers have come up with a pretty cool technique to get around this problem. They are x-raying it instead.

This may sound pretty obvious, but it isn’t. The surface texture of amber scatters x-rays like mad, and this makes it very difficult to get an image of what is inside. The researchers came up with a clever way around this. The density of amber ranges from 1.05 to 1.15 grams per cubic centimeter. That’s really close to water, at 0.998 grams per cubic centimeter. Since scattering occurs preferentially when electromagnetic radiation encounters a density variation, the researchers simply put their amber samples into water. The water flows into the scratches and fills them up, making the surface of the amber look a lot smoother to the x-rays than it otherwise would.

The researchers used a very specific imaging technique, with the winsome name propagation phase contrast microradiography. Someday, I hope to understand exactly how that works in x-rays, but I know about phase contrast micrography in optical wavelengths, and that’s a tangent I think is worth exploring. To do this in visible-light microscopes, you start with partially coherent light, and you shine it through a ring, and then focus it on your specimen with a condenser lens. Once it has gone through the specimen, it goes through the objective, and then passes through a ‘negative’ ring - instead of a piece of material that has a donut-shape cut out of it to let light through, this piece of material is a donut-shape that blocks light (but allows light through the donut hole as well as though the outside of the donut). Once the light passes through this apparatus, you focus it into an image, and you get a really weird effect. Diffraction converts small changes in the phase of the light into large differences in amplitude - or brightness. The result is that stuff you have a real hard time seeing any other way leaps out at you. It is such an impressive technique that its inventor, Frits Zernike, won the Nobel Prize for coming up with it. Nikon has an excellent discussion of the optical technique.

Presumably, the x-ray apparatus works on similar principles. In any case, they’ve come up with this:

The top image is a standard x-ray, while the bottom image utilizes the phase contrast technique. Amazing.

The scientists imaged 640 pieces of amber from the Charentes region in southwestern France. They discovered 356 fossil animals, going from wasps and flies, to ants or even spiders and acarians.

Acarians, by the way, are mites and ticks, and one of them that was found in the amber was only 0.8 millimeters in size. Quite impressive. And I really recommend you click over to the press release, which has lots of pictures well worth seeing. The researchers report they’ve been able to determine the families of 53% of the inclusions, in some cases from 3-dimensional images. I don’t know how that compares to optical techniques on transparent amber, but it is certainly good enough to be useful. The method could potentially shed a lot of light on the evolution of small arthropods.

There are two really cool things about this. The first is that most amber is opaque - 80% of it at Charentes, where the researchers took their samples. The second is that there’s probably lots of opaque amber sitting around in museums that has been kept because it is interesting for some reason or other. This amber can now be studied.

Want the original paper?

M. Lak, D. Néraudeau, A. Nel, P. Cloetens, V. Perrichot and P. Tafforeau, Phase contrast X-ray synchrotron imaging: opening access to fossil inclusions in opaque amber, Microscopy and Microanalysis, Forthcoming article, doi: 10.1017/S1431927608080264

Zach Miller at When Pigs Fly Returns has an outstanding post called An Edmontosaurus named Dakota. Dakota is a fossil dinosaur mummy that is getting news coverage yesterday and today for no immediately apparent reason.

Leveraging the power of TIVO, I watched a National Geographic Channel show on this dinosaur a couple weeks ago. It was promoted with high-hype breathlessness as a major discovery that had completely overturned our knowledge about dinosaurs - or at least hadrosaurs - and I got sucked in. Unfortunately, the actual show disappointed me.

From memory, there were only two things the program asserted had been learned from Dakota:

• Dakota had differently-sized scales in patterns that are similar to the way differently-sized scales in lizards indicate differently colored areas of skin.
• Dakota’s tail vertebrae were not fused nor in contact with one another, but were separated from each other by about 10% of their length (so my memory of the graphic would suggest, at least).

The documentarians showed a reconstruction of a hadrosaur with the tail vertebrae in contact with one another, and this mount was seized upon by Daktoa’s principle investigator, Phillip Manning, to make a dramatic - dare I say histrionic? - statement on-camera along the lines of, “we thought we had this all figured out, but we were WRONG!”

Well, first off, of course we were wrong. Ignorance has a way of doing that. Until you find an articulated fossilized hadrosaur skeleton, you’re likely going to make a few mistakes putting such things back together. Second, if you spend any amount of time at all working in science, you are going to find out that you are wrong all the time, and that this is neither very dramatic nor very significant. But finally, and more fundamentally, I’m virtually certain I’ve seen hadrosaur mounts that have the tail vertebrae separated by an inch or two. It made me suspect that a straw man was being cooked up by the documentarians. Are we to understand that one incorrectly-done mount signifies a serious and drastic error throughout the whole of dinosaur paleontology? Or is my recollection false, and it really was is thought that hadrosaur tail vertebrae were in contact in life?

Or maybe the mount that was shown was one that Manning had put together himself and he was shocked at having made such an error? I’m really not sure. Anyway, Manning came off as smarmy - and in another part of the documentary, as unprepared and a little less than competent.

Manning and his team took the mummy to Boeing, where they have a giant CAT scanner. The idea was to fit the mummy on the scanner, scan it, and see what was inside. The program gave the impression that the process was largely a debacle. The largest piece of the mummy (which is apparently in at least two pieces) could barely be lifted by the lifting equipment. Once that problem was solved the piece couldn’t be fit on the scanner. I think this was solved by knocking off some excess matrix. (Did anyone think about using a tape measure before hauling the fossil all the way out there? The documentary didn’t say.) When they finally got the specimen on the scanner, with inches of clearance at most, they couldn’t see anything inside. There was too much matrix, I guess, or maybe the fossil itself was too extincting of the X-rays. In any case, they got some images that were perfect specimens of noisy astronomical CCD images with no signal - dark frames, in the parlance.

Couldn’t an assay of extinction at the energies of the CAT scanner have been done prior to hauling the mummy halfway across the country? I would have thought yes, that doing this would have been easier than moving the fossil, but what do I know.

And why didn’t they just try for a CAT scan after the matrix had been removed? My vague understanding was that they wanted to use the CAT scan results to guide the removal of matrix, but that impression might be a result of a desperate mental need to find sense and meaning in the inexplicable spectacle that I was seeing. I’m not suggesting that Manning’s team was incompetent in fact; but the documentary made it look that way, by playing up setbacks as dramatic moments without also discussing the kinds of preparation that the team undertook and the reason the risks were being taken.

So much for the big piece of the mummy. A smaller piece was scanned as well, and lo, there were the aforementioned tail vertebrae. And that was about that. The mummy was sent to another location and preparators worked on taking off the matrix. I walked away from that documentary thinking that they had a potentially nice specimen, but that watching an hour of TV about it had been a pretty pointless thing to do.

Now Zach weighs in on his blog:

This fossil has been known since 1999, its genus was just released today, and its species is still unconfirmed.

Whoah. Nine years just to identify the genus. I hadn’t been aware of that. The documentary kind of glossed over the fact that they didn’t really know what dinosaur they had on their hands.

…it’s curious that not a single peer-reviewed publication exists about Dakota, yet two books have been penned (one of them a kid’s book, one an awful popular science book). The National Geographic channel has aired two specials about Dakota, too. Dakota needs to be studied and published.

I hadn’t been aware that nothing scientific had been published. Again, the documentary kinda glossed that over. This is insane, to be fast approaching the decade anniversary of the fossil’s discovery, and still have nothing in the scientific literature about it at all. It is true that a thorough study of a good dinosaur mummy will probably take twenty years or more, but you need to start somewhere. Twenty years are half up and the PI has no results.

Zach rightly points out that Manning, or his funding sources, appear to be trying to do science by press release with this mummy. Someone, like his scientific peers perhaps, needs to give Manning a kick in the pants to actually publish something. If an astronomer had sat around on similarly significant discovery for ten years without publishing anything, their institution or funding sources would probably have kicked them off the job and found a new PI for the project by now.

Quick - have a look at these YouTube videos before some creationist cooks up a fraudulent DMCA copyright infringement claim to have these taken down.

Both videos explore phylogeny from the transitional fossil record in an interesting and compelling way, and set to some wonderful music.

Hat tip to Panda’s Thumb.

Microraptor fossil. The image is from Wikimedia Commons, where it is licensed under the Creative Commons Attribution ShareAlike 2.5 license. Unfortunately, no author name is provided.

I’ve just finished watching the latest Nova, which aired last night (all praise be to TIVO). The episode was about Microraptor.

The early part of the documentary set up some controversy by contrasting the ideas of Larry Martin with those of various AMNH paleontologists and staff, and their collaborators at other institutions. Martin proposes that the development of flight from ground-dwelling dinosaurs¹ doesn’t make much sense, without really giving any compelling reasons. He also says that this model is necessary for the evolution of birds from dinosaurs, and again, I don’t fully understand why he thinks that. As I’m fond of saying here, just because you say something doesn’t make it true. I’m unable to think of a reason that arboreal dinosaurs developing flight means that birds can’t have evolved from dinosaurs.

He did make a reproduction of Microraptor which featured splayed femurs. The documentary covered pretty convincingly why the reproduction was not plausible - even I could see that Martin’s pelvis was flatter than a pancake. The documentary covered the similarity of the splayed rear-limb model to lizard anatomy, but I don’t think I really understood why Martin believed - even if everything else he said was true, which I wasn’t convinced of - that Microraptor could not have secondarily splayed rear limbs.

Anyone?

The AMNH team certainly seemed to be doing the better science from what Nova presented. Not only was their model constructed with some pretty rigorous methods, they recruited a multidisciplinary team of experts in various fields and hiked out to a wind tunnel to test it. It made Martin’s approach look a bit parochial. The latter half of the documentary seemed to abandon any further coverage of Martin’s work.

The wind tunnel scene was pretty interesting. I’ve been part of similar groups of scientists trying out and testing new ideas, and what Nova showed is pretty much how scientists act - on the whole very competitive, but very collegial and with few exceptions willing to admit it when the data proves them wrong. As usual, Nova was well worth watching.

1. the “ground-up” model, as he puts it, which for some reason has me picturing dinosaurs flying into airplane propellers end ending up as ingredients in my hamburger [↩]

Researchers at the University of Oslo Natural History Museum have announced the discovery of an enormous marine reptile - a 50-foot (15 meter) pliosaur.

The pliosaur was found in the arctic island chain of Svalbard (the BBC reports it was found on Spitzbergen) by a “team of Norwegian paleontologists and volunteers from the University of Oslo Natural History Museum” and their principal investigator, Jørn Hurum. But at least one Alaskan, Patrick Druckenmiller, was involved with the find. A plesiosaur specialist at the University of Alaska Museum, he’s quoted in the press release as saying:

“Although we didn’t get the entire skeleton, we found many of the most important parts, including portions of the skull, teeth, much of the neck and back, the shoulder girdle, and a nearly complete forelimb (paddle)” said Druckenmiller, “Amazingly, the paddle alone is nearly 10 feet long.”

In a bit of a departure from established taxonomy practices and the usual reticince to announce such things before a paper has passed peer review, the PI says:

“From the bones we have finished stabilizing so far this absolutely looks like a new species” Jørn Hurum tells enthusiastically.

The fossil is 150 million years old, putting it in the late Jurassic.

One of the things interesting to me about this find is how many significant fossils are coming out of the arctic or nearctic in the last decade or so. Finds like Tiktaalik roseae, the Axel Heiberg champsosaurs, the Victoria Island acritarchs, the Colville River finds, the Bathurst Island vascular plants, Greenland’s Ichthyostega, and so on. This could be for any or all of a number of reasons:

• The arctic is well-mapped geologically, mainly by the oil companies, allowing paleontologists to conduct well-planned digs at carefully selected locations.
• More easily accessible areas are already pretty well prospected.
• Arctic areas don’t have a lot of trees on the ground to interfere with access to fossils.
• Until relatively recently, access was prohibitively expensive, especially if you wanted to transport fossils out.
• In this case, the Svalbard Tourism Board made the prospect of a working vacation irresistable.

Anyway, now we can chalk up another interesting arctic find. According to the BBC, they’ve done a literature search, and this is apparently the biggest pliosaur ever.

I recently did a little public outreach about astronomy, and because there were no clear skies to be had, we did a little lecture and question-answer session instead. In the last year or so, I’ve been making it a habit to start off the talk with a brief presentation on an unrelated science subject that is in the news. This time, I talked about Mesozoic crayfish and trace fossils from Australia. I hope to have the presentation file downloadable from here shortly; stay tuned.

Regular readers might remember that I covered this subject before - and now I have more of the story.

Dr. Anthony Martin, paleontologist at Emory University, is an acknowledged expert on trace fossils - that is, fossils that don’t preserve the body of an organism, but do preserve some indication of its anatomy and its behavior, such as footprints, burrows, and droppings. He’s also an expert about dinosaurs. He’s written important books about both subjects, as well as being heavily published in journals, mostly as the principal investigator.

He visited the Dinosaur Dreaming fossil site in Australia back in February, 2006. As he was walking around looking at the site on his first day, he discovered two large theropod dinosaur tracks. On the second day, he found a complex of crayfish burrows.

Crayfish burrows, 116 million years old, from Dinosaur Dreaming, Victoria, Australia. The scale card in this image is 10 centimeters long, or about four inches. Photo courtesy of Anthony Martin. Click to enlarge.

Paleontologists had been walking past the burrows for fourteen years, but either nobody noticed them, or nobody appreciated what they were. Martin saw them mainly because he was experienced and educated about what to look for - as they say, luck favors the prepared. At about 116 million years old, the burrows were an important find. Crayfish currently live on every continent except Antarctica and Africa. But many of the continents that crayfish are found on today are separated by large expanses of salt water, where crayfish can’t survive. Therefore, scientists thought that crayfish evolved and dispersed at a time when the continents they are found on were crammed together.

At the end of the Jurassic and beginning of the Cretaceous, Australia, Madagascar, South America, and India were all connected, but they had begun to move apart. If southern hemisphere crayfish had originated in Australia in the early Cretaceous, they would have had only a short time to expand to other continents. If this hypothesis were true, it suggests some specific predictions that could be made: Africa was already separated, so they wouldn’t be found there - and they aren’t. They might not have had enough time to make it to India, so they may not be found there either. It turns out that crayfish aren’t found in India, and neither are their fossils. So far, so good. And crayfish are found on Madagascar, South America, New Zealand, and Australia - all of which were connected, so this is consistent with the continental features of the time.

Another prediction can be made from this scenario: If southern hemisphere crayfish originated in Australia and expanded out from there, it would make sense if Australia to had more crayfish species today than its southern hemisphere neighbors. If it didn’t, that wouldn’t falsify the hypothesis, but if it did, it would lend it some support. And it turns out Australia does have more crayfish species - about 85% of all southern hemisphere crayfish species are found there.

There was a problem, though: although some crayfish fossils from around 150 million years ago are known from the northern hemisphere, none older than about 40 million years had been known from any of the southern continents. If southern hemisphere crayfish originated in Australia, the prediction of evolutionary theory and the theory of plate tectonics would be that crayfish body and trace fossils should be found from the early Cretaceous in Australia - fossils from sometime before 90 million years ago.

So with this discovery of 116 million year old crayfish burrows, these predictions are fulfilled. The burrows are of the right size and configuration for crayfish, and no other organism is known to produce just this morphology in their traces. In addition, the geology of the area supports a freshwater habitat favorable for crayfish. Everything was pointing to a significant find.

Having recognized the crayfish burrows, Martin asked the site director, Lesley Kool, the obvious question: “Do you have any crayfish body fossils from here?” It turns out they did not, but a crayfish body fossil had been dug up in Dinosaur Cove, another fossil site in Victoria, almost twenty years before. It had been sitting in the Museum of Victoria unstudied all that time.

Crayfish fossil, 106 million years old, from Dinosaur Cove, Victoria, Australia. Photo courtesy of Erich Fitzgerald.

One of the remarkable things about this fossil is how close it came to being destroyed by a rock saw. You can clearly see the slot sawed into the rock coming up from the bottom of the picture, slicing through the pincer, and heading toward the crayfish abdomen. There’s another saw cut that took out a chunk of rock that made up this crayfish’s upper back. It just goes to show that not all fossils - and not all important fossils, at that - are as clean and polished as the dinosaurs we see in museums. In addition to this fossil, fossilized claws from two other crayfish were found in the museum’s collections.

So, as a result of happening across the burrows, which led to asking about body fossils, Dr. Martin was able to describe the only crayfish fossils from the age of the dinosaurs in the southern hemisphere. Having written the paper, he saw it rejected twice, but got it published on the proverbially charmed third try.

In such haphazard ways is human knowledge advanced. In a lot of cases, paleontologists have already found interesting and important fossils - they just haven’t had an expert on that field around to recognize them or appreciate their significance. Gaps in our knowledge are caused not only by not having discovered important fossils (yet!), but also by not having studied the ones that have been discovered. This is how science works - it isn’t always in clean labs with white coats and microscopes, and it isn’t usually with perfect specimens. Sometimes it is considerably harder - and luckier - than that.

Intelligent Design Creationists have said for some time that bats pose a problem for evolutionary theory.

Things are even tougher for the evolutionist with the knowledge that the ‘oldest known’ complete fossils of bats … show indications of a fully-developed echolocation system.

Evolutionary theory predicts that in such cases, transitional forms did exist, and are possibly waiting to be discovered in the fossil record. And today, Carl Zimmer reports on his blog about a newly discovered bat fossil.

The ear bones in its head don’t have the distinctive shape found in living bats that echolocate, suggesting that it had to rely on sight and sound to catch prey–insects, judging from its teeth. Flight evolved first in bats … and echolocation only came later.

Oh. That must really suck to be an intelligent design creationist who thinks that bats popped out of nowhere with echolocation fully developed, then.

It turns out this bat fossil is the most primitive bat ever found, and it has several other transitional attributes:

1. Evolutionary theory predicts that early bats would have body proportions similar to that of the walking mammals from which bats evolved. This fossil has shorter arms, and longer legs, than modern bats. Prediction fulfilled!
2. Almost all modern bats have only a single claw. Evolutionary theory predicts that early bats should have a full compliment of claws, and that bats who lived in between these times should show a gradual loss of claws. Many bat fossils are single-clawed with vestigial claws on other fingers, thus fulfilling the prediction as far as was able. But this bat completes things - it has claws on all five fingers, just like evolution predicts.
3. Evolutionary theory predicts that as a lineage evolves flight, early fliers will be less strong, less powerful flyers than later ones. Some evolutionary biologists have also hypothesized that powered flight most likely evolved from early gliding. Most modern bats fly with a full-time power stroke, flapping their wings continually during flight. But this fossil’s wings suggest that it alternated between flapping and gliding. Prediction fulfilled!

This is just a summary - go read Carl’s story. It’s outstanding, and it has pictures.

The BBC, LiveScience, and others are reporting on the discovery of a new pterosaur found in north-east China. The find also confirms a prediction of evolution. From the BBC story:

“It is very likely that this pterosaur represents a lineage of arboreal creatures that lived and foraged for insects in the gymnosperm forest canopy of north-east China during the Early Cretaceous,” the researchers write in PNAS.

They conclude this from curved bones in the feet, which are similar to those found in perching birds. This pterosaur is also smaller than most others, of a size that makes sense for perching on branches. Cladistics suggest that this pterosaur was close to the ancestors of the giant pterosaurs, including Quetzalcoatlus, which had a 30-foot wingspan. Thus the new fossil is transitional, being in some ways less derived than later specimens but more derived than the pterosaur’s hypothesized concestor.

“It is interesting to see some clear arboreal adaptations in this species,” said [Smithsonian paleontologist Matthew] Carrano, who was not on the research team.

“It confirms a suspicion we had, that pterosaurs were more diverse in their habitats than we knew from the [fossil] record.”

Let’s be a bit more direct here, in the interests of effective science outreach and clear communication. The notion that pterosaurs were more diverse (in their habitats, or in their phenotype - both apply) than the fossil record previously demonstrated is a prediction of evolutionary theory, not merely a suspicion of paleontologists. There are actually two predictions here, both of which are confirmed by this fossil.

1. Evolution predicts that some species will be absent from the (known) fossil record, and that some of them, if they were known, would illuminate the evolutionary development of their lineage. Here we have an example of a fossil which was unknown until recently, and which does just this. Score one for evolution.
2. Evolution makes the more specific prediction that, when you have lots of fossils of lots of species with specialized adaptations - such as pterosaur fossils - that less derived species will exist earlier in the lineage. Not only that, but it says that most of the characteristics that are common to most or all of the more specialized species will be present in the less derived one. Again, from what’s been published, this fossil confirms this prediction.

Seems I’m on a paleontology kick lately. Undoubtedly this is a result of spending so much time in museums over the last month, looking at fossils. Fair warning - there’s at least one more of these in the pipeline. I’ve had some interesting information and photos from the PI of the crayfish fossils I reported on earlier that I’m working up.