Blue Collar Scientist

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.

Over the last fifteen or so years, physics instructors have done a good deal of research on how students think about physics, and what sort of misconceptions they are prone to. They have used the results of this research to improve the quality of physics teaching - they’ve come up with workshop activities, demonstrations, and other teaching tools, all of which do a much better job of informing students about physics than previous, more traditional methods.

As (primarily) an astronomy outreach instructor, some of this has trickled down to my awareness, and changed how I talk about and teach concepts in astrophysics.

Today, by far the biggest apparent crisis in science education is in biology. The foundational knowledge of biology is evolution. The theory is so well confirmed, so powerful in its predictive abilities, and so wide-ranging and integrating that evolution dominates parts of many other disciplines as well - including biochemistry, ecology, genetics, paleontology, geology (especially stratigraphy), and so forth. Despite this, evolution is casually dismissed as untrue by religious extremists who want it to be untrue for complicated reasons relating to their desired religious hegemony - because, in short, they believe knowledge leads to poor morals. Their propaganda confuses the issue for otherwise sound-thinking individuals.

From my own experience I feel comfortable asserting that biology students, at least at the high-school level, often do not appreciate the nature of biological processes at the cellular level. The tendency is to believe that cellular processes are directed. This belief has in common with evolution denialism an insufficient appreciation of the character and power of random occurrences, and a lack of awareness of where randomness ends and direction begins. However, I have not previously been aware of any research supporting this notion.

Now, much like physicists, biologists have begun to do research on student misconceptions about their subject area. A paper in last month’s PLoS-Biology, Recognizing Student Misconceptions through Ed’s Tools and the Biology Concept Inventory, details some interesting methods and results of such research.

The research began with the construction of a concept inventory, which was done by asking students several open-ended questions about biological processes. Responses to the questions, as well as interviews with the students, were analyzed in order to determine where student misconceptions were rooted.

Results from the BCI indicate a striking lack of understanding on two questions related to randomness, even after three major’s courses in Molecular, Cell, and Developmental Biology at the University of Colorado at Boulder—we suspect that similar results would be found widely.

(Emphasis mine.) Misconceptions on randomness do not surprise me; high school students are the raw material of college freshmen. But I was surprised that the misconceptions persisted after three college courses in the subject.

A common observation … was that students were unwilling to see random processes as capable of directed effect in themselves—they routinely seek alternative rational explanations, the dominant one being the presumption of drivers that are actually responsible for the observed effects.

It will be noted that this amounts to the cognitive strategy adopted by intelligent design creationists - deny, without having a reason, that randomness can produce an effect, and then go make something up to fill the void.

This research therefore serves as a very large arrow pointing at where biology, presumably including outreach, is having educational failures. It also points out that these failures are in the same concept domain that intelligent design creationists are having propagandistic success.

In discussing the cognitive effect of these misconceptions, the authors note:

From an evolutionary perspective, it leads to “just-so” stories that project meaning onto every variation, whether meaningful or not, and obscures the basic mechanisms that make evolutionary theory so valuable.

This strokes a pet peeve of my own, which is that those doing biology outreach frequently overemphasize selection, sometimes misleading students into believing that selection is the cause of variation.

The paper authors make some concrete recommendations, including one that I believe would have high value:

From the perspective of course and curriculum content, we need to provide students with opportunities to work with random systems, and explicitly state (and confront) their assumptions.

At the level of late gradeschool and middle school students, I can imagine a demonstration involving a clear acetate box, with, say, 20 ping-pong balls inside. Four of the ping-pong balls have velcro on them. Shaking the box will result in a pretty stochastic motion of balls, and yet the four balls should stick to one another in fairly short order. This sort of demonstration might address something like the authors’ description of a student misconception that ATP synthase seeks out and grabs ADP - appropriately simplified for the grade level. (Such a demonstration has the virtue of allowing bright colors, loud noises, and vigorous physical activity into the classroom, which tends to appeal to this age group.)

The paper is focused on college-level students and instructors, but it nevertheless suggests several strategies for outreach and educators in lower grades. It is recommended reading for anyone doing outreach that touches on biology.

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This blog post is about:

Klymkowsky, M.W., Garvin-Doxas, K. (2008). Recognizing Student Misconceptions through Ed’s Tools and the Biology Concept Inventory. PLoS Biology, 6(1), e3. DOI: 10.1371/journal.pbio.0060003

It’s science fair season in Alaska, and apparently in Minnesota too. PZ Myers writes about the Twin Cities Creation Science Fair today. He describes one project:

As a perfect example of ID inanity, one student demonstrated irreducible complexity by taking a motor apart and showing that it didn’t work any more. Thank you, Michael Behe, for trying to make your feeble “insight” a part of the science curriculum.

Huh. I judge about five or six science fairs every year up here in Alaska, and this was a project a kid did at one of those fairs last year.

Are the IDiots actually organized to the point of suggesting specific projects to their minions?

Serious question. Please answer if you can. I don’t read much of their blathering anymore.

I owe a small debt of gratitude to Martha Knox for pointing something out that I had not realized: that “irreducible complexity” would be found in organisms was a prediction of evolutionary biology made by a Nobel prizewinning geneticist in 1918 - and not the “discovery” of intelligent design creationists in 1996.

If you already know what irreducible complexity is, feel free to skip ahead to the triple-asterisks. Otherwise, settle in and I’ll explain.

“Irreducible complexity” is the pseudoscientific claim that some biological systems are too complex to have evolved from more primitive, less complete predecessors. It was originated as an argument against evolution, or at least popularized for this purpose, by Michael Behe in 1996. He defined an irreducibly complex system as one “composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning”¹. In other words, the creationist claim is that any biological part which cannot be broken down into smaller parts and still remain useful (a) cannot have evolved, and (b) therefore must have been created by an intelligent designer - presumably god, or space aliens².

Behe gives several examples of biological “parts” that he claims are too complex to have evolved but his work in this field is deeply ignorant, and every example he has put forth has been blown apart by a massive amount of research by real scientists. This was demonstrated, perhaps most dramatically, at the Dover trial, which at one point turned into a massive review of the research in the fields Behe has made his claims. His work did not stand up to scrutiny well - in fact, Behe couldn’t even convince a conservative judge appointed by George W. Bush that he wasn’t full of baloney. Wikipedia has a decent summary of Behe’s humiliations at that trial, so there’s no real reason to go over his failures here.

***

Anyway, it turns out that all this is in some ways a moot issue. Behe and his minions consider the appearance of “irreducible complexity” in organisms to be really good evidence against evolution. But it isn’t.

It is actually evidence supporting evolution, as was explained in a research paper ninety years ago.

In 1918, Hermann Muller published a paper about his pioneering work with fruit flies. It was called by the appealing title “Genetic Variability, Twin Hybrids, and Constant Hybrids, in a Case of Balanced Lethal Factors.” Muller’s paper is available online [pdf], and it contains a description of irreducible complexity, along with an explanation of how it comes about through the simplest of evolutionary means. It amounts to a prediction that “irreducible complexity” will actually be found in organisms, and it begins on page 42 of the pdf file (which is the same as page 463 of the original journal):

Most present-day animals are the result of a long process of evolution, in which at least thousands of mutations must have taken place. Each new mutant in turn must have derived its survival value from the effect which it produced upon the “reaction system” that had been brought into being by the many previously formed factors in cooperation; thus a complicated machine was gradually built up whose effective working was dependent upon the interlocking action of very numerous different elementary parts or factors, and many of the characters and factors which, when new, were originally merely an asset finally became necessary because other necessary characters and factors had subsequently become changed so as to be dependent on the former.

Now, what exactly is he saying here? It is a lot simpler than it sounds. Genes mutate, and when they do, they can change in such a way that they become absolutely dependent upon their interaction with some other gene to fulfill their function. If those genes interact to make a particular piece of anatomy, and you take one of those interacting genes away, you will have a non-functioning, pointless biological structure as a result of this dependence.

That looks to me to be what Behe defines as irreducible complexity, all laid out in a very accessible way in a well known paper, by a very famous Nobel prizewinning researcher, who did this fundamental work in evolution seventy-eight years before Behe published his book.

It is simply bizarre to consider that, convinced he had found irreducible complexity in real organisms, Behe somehow thought that finding it soundly refuted the prediction of evolutionary theory that it would be found!

1. Darwin’s Black Box, page 9 [↩]
2. Space aliens are seriously entertained as creators of life by some intelligent design creationists. Other intelligent design creationists will not admit to believing that the intelligent designer is a god, but also won’t admit they believe in space aliens. So I’m just going to stick with the two candidates that I know of - god and space aliens. <shrug> [↩]

Evolution education in this country (the United States) is in some serious trouble. As is well known, we have a large population of people whom the schools have failed, who believe that the theory of evolution makes claims that it does not. In place of the reality of evolution, they have chosen to believe the creation myth of a bronze-age middle eastern religion, which was largely plagiarized from four earlier Mesopotamian myths. The worldview of this “alternative” asserts that knowledge is essentially undiscoverable and unchangeable, that observations of the universe must conform to limits that are pre-defined by these myths, and that people who do not agree with the repressive system of “morality” that accompanies these mythic beliefs are unfit to exist in society.

Accordingly, it is very nice to find a free periodical resource designed to aid those doing education and outreach on the topic of evolution. Springer has a journal called Evolution: Education and Outreach, designed to help instructors of K-16 with their activities. And they have decided that during 2008, anyone may receive the journal free online. This is stale news; somehow I missed it when it was launched last November.

Free access is good, very good indeed! And Springer should be commended for this.

On the other hand, they’ve made it painfully difficult to get a copy of the journal online. As far as I can tell, it is actually impossible to get a copy of the journal online.

What you can do instead is get a separate copy of each article in the journal, requiring at least 21 separate downloads for a single issue of the journal.

To do this, go to the very counterintuitive page that apparently lists issues of the journal. As I write, there is only one issue of the journal available. But don’t be confused by the link to “Online First,” because that’s not it. What we’re looking for is Number 1 / January, 2008 - click on that instead.

Once you have done that, you’ll be on a page that lists the articles in this issue of the journal. At the top of each section are the article titles. Other than the title, there’s no way to determine what the article is about. If you click the title, you don’t get the article - you get an abstract (sometimes), and you get some information about who, if anyone, has cited back to that article. Clicking the title is about as expensive in terms of effort and download time as just downloading the article and skimming the first couple paragraphs to learn if it is topically relevant with what you are doing. So there’s no real point to clicking on the title.

To get the article, you need to look a few lines below the title, to the “Text:” field, and click on either PDF or HTML, depending on which format you want to read the article in. I’ve now read a few articles in each format. Strangely, PDFs download a lot faster than HTML (sometimes HTML articles simply won’t load at all). And if you click on the HTML link, you may wonder why nothing happens, depending on what browser you are using and how it is configured - the HTML link insists on opening a new tab or window without telling you, and this can be puzzling if the new page opens hidden behind another one.

Anyway, if you do all this properly, you can read the whole journal only after an absolute minimum of 24 clicks (and 21 save-as dialogs if you are saving PDFs locally to read offline). Everywhere else on the web, one click would do to read a PDF version of a journal. And don’t fool around with the “save this item” or “download this list” icons, because they don’t do what normal web users think.

This system sucks, and it will obviously discourage people from reading. I know Springer is a journal publisher, and I know publishing journals in this way makes sense when your readers are highly focused on specific topics. But they’re publishing an EPO aid in this case, not a research journal, and most of its audience is not going to be savvy to Springer’s proprietary online journal publishing system. Nor will they find its bells and whistles useful.

The contributors to and publishers of this journal need to take a look at what we’re up against: a horde of ignorant evangelists who enjoy single-click downloading of articles at their primary “research” sites such as Answers in Genesis.

The resource content is actually pretty good. I recommend going and reading it if you are doing science EPO that ever touches on evolution, as I am.

Springer: Single-click download, please. Until then, you get a D-.

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.

After writing up the account of my trip to the Oregon Museum of Science and Industry on Saturday night in the Portland airport, I went to one of those strange airport bookstores and bought Your Inner Fish, by Neil Shubin, so that I’d have something to read on the plane. And I read it - I started it as we were taking off, and I finished it a few moments before we landed.

Shubin is one of the discoverers of Tiktaalik, and the book opens with an outstanding account of the discovery and its significance:

In the midst of the press hubbub [following the announcement of Tiktaalik], my son’s preschool teacher asked me to bring in the fossil and describe it. I dutifully brought a cast of Tiktaalik into Nathaniel’s class, bracing myself for the chaos that would ensue. The twenty four- and five-year-olds were surprisingly well behaved as I described how we had worked in the Arctic to find the fossil and showed them the animal’s sharp teeth. The I asked what they thought it was. Hands shot up. The first child said it was a crocodile or an alligator. When queried why, he said that like a crocodile or lizard it has a flat head with eyes on top. Big teeth, too. Other children started to voice their dissent. Choosing the raised hand of one of these kids, I heard: No, no, it isn’t a crocodile, it is a fish, because it has scales and fins. Yet another child shouted, “Maybe it is both.” Tiktaalik’s message is so straightforward even preschoolers can see it.

Indeed. I’m left wondering how useful it would be to mention Isaiah 11:16 to the evolution deniers.

The rest of the book is an incredibly accessible and entertaining account of the evolutionary history of the human body. It is much deeper than merely the transition from fish to quadruped - the book goes into fascinating details about human development and how it differs from that of other animals, and how it is similar. It is the best science book I’ve read in some years - perhaps since Carl Zimmer’s At Water’s Edge.

For better or worse, the book has probably changed me for life - among other things, I dumped on “those damn amphibians” when someone mentioned hiccups earlier today. This bit of trivia from the book is almost certainly going to get worked up into one of my evolution resources….