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The best-laid plans of mice and men often go astray

—Robert Burns
To a Mouse, on Turning Her Up in Her Nest with the Plough, 1785

Last week I was in New York City, working on the incredible fossils stored at the American Museum of Natural History, as part of a long-planned museum-hopping tour to see important specimens in New York, Philadelphia, Yale, Harvard, Amherst, and then down to the University of Florida Museum before returning home. I’m on sabbatical, and this research reviewing the evolution of North American peccaries or javelinas (pig-like creatures mainly found in Latin America, but only distantly related to true pigs of the Old World) is the focus of my sabbatical this fall. The trip itself was scheduled over six months ago, since it was the only time I could get away before the kids go back to school and my wife resumes teaching on Labor Day weekend. I flew in on Sunday night, Aug. 21, and was filled with flashbacks of my wonderful six years there as a Ph.D. student at Columbia University and the American Museum (1976-1982). Back then, as a young grad student,  I was footloose and fancy free (although poor) and enjoyed the opera (day of performance standing-room ticket was all I could afford), jazz in the Village, half-price Broadway show tickets at TKTS, all the while working like a maniac on those incredible fossils to publish enough research before I finished my doctorate, in order to have a small chance at a job. (Fewer than 20% of Ph.D.’s in vertebrate paleontology get a decent job in a related field).

For the first four days, the weather was great (low 80s and not too humid, very unusual for New York in August), and I was getting a lot of research done. I was also reveling in the sounds and sights and smells of Manhattan, and even the steam-bath humidity of the subway tunnels and the frequent arguments that break out in the subways didn’t bother me. I’d seen a lot of them in 6 years of living there, especially in the pre-Guiliani days when the city was a lot dirtier and more dangerous, and bums harassed you much more aggressively. It was great to see the amazing exhibits at the American Museum again, stroll around the Park and seeing the sights of Downtown again, or go people-watching along Broadway or Columbus on the Upper West Side. I visited my old building on West 87th just off Riverside (I once had a tiny rent-controlled fourth-floor walkup in a brownstone that cost me only $160/month in 1978, now worth many thousands a month), hung out at Lincoln Center (no time for a concert, and they’re not performing in August anyway), and walked past my favorite haunts on Broadway. It was fun to rediscover the foods, too: a Nathan’s Famous hot dog or a REAL New York bagel and schmear in a genuine Jewish deli, savor the delicious smells at Zabars, or have a slice or two at Ray’s Pizzeria. I walked past the Dakota building where John Lennon was murdered (I was just a few blocks away that night in 1980). I tried to find the Blarney Castle, an Irish bar on 72nd St. where I once took a final exam over pitchers of beer in a seminar taught by Niles Eldredge, but it had changed names and ownership.

High above the Earth from aboard the International Space Station, astronaut Ron Garan snapped this image of Hurricane Irene as it passed over the Caribbean on Aug. 22, 2011. Even though it was only a Category 1 storm, it covered an area the size of Europe (Photo credit: NASA)

But by Wednesday I was getting worried about the reports of Hurricane Irene and what it would do to New York, and by Thursday night the reports of the hurricane forced me to cancel my swing through New England and Florida, and rebook my JetBlue flight back on Saturday night. It was clear that the storm would make it impossible to get to those New England museums on Monday or Tuesday, let alone expect the collections managers to show up and help me out. My long-planned museum tour would have to be postponed, and I’d have to spend more scarce grant money trying to do it all over again before my sabbatical ended. (continue reading…)

TO ALL TEACHERS AND PROFESSORS who are teaching courses in skepticism, critical thinking, science and pseudoscience, science and the paranormal, science studies, history or philosophy of science, the psychology of paranormal beliefs, religious studies, and the like…

Please send us your course syllabuses, reading lists, video/YouTube links, classroom demonstration ideas, student projects and experiments, research project ideas, and the like to my graduate student Anondah Saide. I want to add them to my own course syllabus on Skepticism 101, and create an online Skeptical Studies Program at Skeptic.com for teachers and professors everywhere to go to in a creative commons/open source system so that we can build a new academic field going forward with skepticism into academia. (continue reading…)

It probably comes as no surprise to any reader here that Ann Coulter is not a scientist, nor does she give any evidence of scientific literacy. Why, then, is she writing about science?

In a recent article entitled The Flash Mob Method of Scientific Inquiry, she repeats claims she made in a prior book that evolution is pseudoscience – the demented belief system of atheist liberals. I am not interested in Coulter‘s politics – she is just another polemicist rallying the troops. In fact, evolution has nothing to do with being liberal or conservative, except that some conservatives want to make it about this.

Evolution is a solid scientific theory backed by a mountain of evidence. It not a political or religious issue. It is only the political or religious ideology of some that attempts to make it so. And that’s what Coulter is doing.

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OK, I’ll admit this is a fairly lightweight blog post. I’ve been on vacation with my family for the past week, and spent the previous three weeks cramming in five Skeptoid episodes. Lightweight, yes, but still very cool. (continue reading…)

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Last week I returned from an amazing Skeptic Society cruise along Alaska’s Inside Passage. During the cruise, we held a conference with 200 other Skeptics on “Glaciers and the Science of Climate Change,” with presentations by scientific experts on glaciers and climate. On day 3, we witnessed the glaciers melting away before our very eyes. At Glacier Bay National Park, we saw tons of ice calving away from Margerie and Johns Hopkins glaciers, causing huge booms to echo across the fjord. As our resident expert Dr. Bruce Molnia of the USGS pointed out during his presentation, over 95% of the glaciers of Alaska are stagnant or shrinking, and we saw several examples of these. Molnia has been studying Alaska’s glaciers for decades, and he showed stunning images of how much they have retreated in just the past century (such as the images of the retreat of Muir Glacier below, shot in 1941  and in 2004). If you recall the images of the vanished glacier’s in An Inconvenient Truth, some of those were from Molnia’s research. We billed the trip as “See ‘em before they vanish” but in the case of most of the glaciers, it’s already too late. If my 6- and 8-year-old sons repeat this trip decades later as grown men, there will be almost no glaciers to see at all.

Naturally, the conference focused on the scientific evidence about glacier retreat and global climate change. Our moderator Michael Shermer challenged us to show us the evidence that climate change is real and anthropogenic, and our speakers did so in spades. Much of this evidence was outlined in Chapter 10 of my new book Catatastrophes!, so I will not repeat all of it here. But some of the key points that came up again and again in the conference were:

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Image by Daniel Loxton with Jim W. W. Smith. © 2011. All Rights Reserved.

Finally! After a year (and more) of work and months of anticipation, I’m able to reveal my newest children’s book: Ankylosaur Attack, from Kids Can Press.

Illustrated by the Junior Skeptic art team of yours truly with Jim W. W. Smith, Ankylosaur Attack is a full-color hardcover storybook about a day in the life of a dinosaur. It’s intended for my youngest audience yet: ages four and up. (It’s approved by my own five-year old, whose discerning taste in dinosaurs is unparalleled.)

Ankylosaur Attack is in stock now at Amazon.com and available for pre-order at Amazon.ca. (The official release date is September 1, 2011. Skeptic.com and most other major North American booksellers will have it in stock in the coming days.)

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You have probably heard of the crocoduck – the impossible chimera that exists only in the pseudoscientific imagination of Kirk Cameron and Ray Comfort. There is also the duckcroc, which is a real creature – an extinct crocodilian with a duck-like snout.

Well now, meet crocochicken. This creature does not yet exist, but only because the scientists who are tinkering with its genetic program are not allowed to let it hatch. Arkhat Abzhanov is an evolutionary biologist at Harvard University. He is engaged in a research program, the goal of which is to reverse some of the evolutionary changes that resulted in birds evolving form theropod dinosaurs. In essence, he want to reverse the evolutionary clock and produce a chicken with more reptilian features.

The particular feature he is working on is the duck’s bill. He is coaxing it down a different developmental path so that it ends up looking more like a crocodiles snout – hence the name “crocochicken.”

There is another researcher also doing similar research. Hans Laarson of McGill University and colleagues are also trying to reverse chicken DNA to develop along more primitive path – he is working at the other end, trying to get chickens to grow a dinosaur-like tail. His creation has been dubbed “dinochicken,” which is a much better term as chickens actually evolved from dinosaurs and not crocodilians.

The two teams, working independently as far as I can tell, are not tweaking the DNA directly. Rather they are altering proteins that control how the DNA is expressed, and specifically how DNA controls the development process. The research is teaching us a lot about this process. You can imagine the development of an embryo into a mature creature as all the different body parts following a winding and twisting developmental pathway. Proteins, themselves coded by genes, and other biochemical signal turn on and off genes in different cell populations and are thereby steering development down these various paths.

This means that the introduction of a key regulatory protein at a key time in development could take the embryo down a different path, and result in a different morphology. At some point, for example, the chicken’s tail is given a signal to stop growing. If you block or change that signal, then the tail will continue to grow and end up more like the dinosaur tail of its ancestors.

There are a couple points worth emphasizing here. The first is that the researchers are not changing the actual DNA of the chicken embryos. They are simply introducing altered protein signals that influence the expression of DNA and therefore the developmental process.

The second, and more profound, point I wish to emphasize is that the chicken’s DNA is capable of creating dinosaur-like structures, with simple prodding here and there. The chicken DNA, and indeed the developmental process that leads to a chicken, is not a clean and direct process. It does not appear as if the chicken were created out of nothing as a chicken. Rather, the developmental process is messy and meandering, and reflects the long and chaotic evolutionary history of the chicken. These researchers are taking advantage of that fact, and exploiting the dino-DNA inside every chicken to alter those developmental meanderings into a more dinosaur direction (at least for some parts of the chicken).

I know this by itself is not “proof” of evolution – but it is one more line of evidence that supports evolutionary theory. This kind of thing should be true if evolution is a fact. It is similar to prior evidence that chickens can grow teeth. Researchers can famously coax chicken embryos into growing teeth by methods similar to the dinochicken and crocochicken experiments. They just introduce the right signals at the right time in development.

The implication of this (pointed out by Stephen Gould) is unavoidable – chickens have the genes for teeth, they are just dormant and turned off. We can turn those genes back on and voila – a chicken with teeth (smilochicken?). We are getting pretty darn close to independent proof of evolution. I won’t say “undeniable” because (you guessed it) those loons at the Discotute do in fact deny this line of evidence.

Casey Luskin “explains” that the chicken teeth experiments must be mistaken because neutral mutations (without selective pressure against them in a vestigial gene) would render the genes for teeth useless within 6 million years. Yet, he argues, birds and dinosaurs diverged 60+ million years ago. Luskin does not have a coherent explanation for the experiments, he just wants to cast doubt on the evolutionary implications. He glosses over the assumptions of his point, however. He assumes that the genes that contribute to teeth in birds have no other purpose, and are therefore under no selective pressure. He also assumes that any loss of function dates to around the split of birds and reptiles, but relevant changes in gene expression could have occurred more recently. Further, the chicken’s teeth that result from these experiments are not perfectly formed – they are highly degraded, as one would expect.

We are now also moving far beyond just chicken teeth. The more recent experiments seek to reverse many developmental features of chickens to their more reptilian form. It is true that, because of mutations, the evolutionary clock cannot be perfectly turned back using these methods. We will not get a velociraptor from a chicken by tweaking development. But we will get a dinochicken. We would have to actually reverse a lot of the mutations that have accumulated over the last 80 million years to get an actual dinosaur from these experiments. And for that we would probably need some reference dino DNA, which is highly unlikely to have survived.

I do not rule out that future researchers will hit upon some workaround. We may have a Jurassic park yet. Not from these experiments, as cool and informative as they are.

What’s in a name? That which we call a rose by any other name would smell as sweet.

—William Shakespeare, Romeo and Juliet

ITEM: A few years ago there was a big fuss in the media about the fact that astronomers had demoted Pluto from one of the classic nine planets to a “minor planet,” just another body in the solar system. Some people were shocked and upset, since they had always learned that Pluto was the ninth planet and didn’t want to unlearn it, no matter what astronomers said. Astronomers pointed out that numerous other small icy objects had been found in the Kuiper belt outside Neptune, including some that were larger than Pluto—but no one was ready to promote 2060 Chiron to the 10th planet. Instead, the logical solution was to demote Pluto to the class of “dwarf planets” along with these other objects, since it really didn’t have much in common with the other eight planets. The state legislatures of Illinois (where Pluto discoverer Clyde Tombaugh was born), New Mexico, and California passed resolutions against the change (despite the fact they had no legal authority in the matter). Caltech astronomer Mike Brown, who spearheaded the change, wrote in his book How I Killed Pluto and Why it Had it Coming that “I’ve been accosted on the street, cornered on airplanes, harangued by e-mail, with everyone wanting to know: why did poor Pluto have to get the boot? What did Pluto ever do to you?” In 2007, the American Dialect Society recognized the neologism “to pluto” (meaning “to demote or degrade”) as the 2006 Word of the Year.

ITEM: In 2010, paleontologists Jack Horner and John Scannella suggested that Triceratops was just the juvenile form of the longer-frilled dinosaur Torosaurus. Once again, there was public outrage and protests. People complained that their beloved three-horned dinosaur was being snatched away from them. Unfortunately, the public and the media got the story completely backward. IF other scientists eventually agree with Horner and Scannella, and formally decide to ratify the idea that Triceratops and Torosaurus were the same animal, then the invalid name would be Torosaurus, not Triceratops. As Brian Switek pointed out in his blog “Relax—Triceratops really did exist”, Triceratops was named by Yale paleontologist O.C. Marsh in 1889; the same scientist named Torosaurus in 1891. According to the rules of the International Code of Zoological Nomenclature (ICZN), Triceratops has priority over Torosaurus, so no one will weep or gnash their teeth if Torosaurus becomes the invalid synonym and is officially demoted. (continue reading…)

This article first appeared as an alternative medicine opinion editorial for the American Medical Associations’s Virtual Mentor Journal, Volume 13, Number 6: 389–393, June 2011.

For many years now there has been considerable debate between so-called complementary and alternative medicine (CAM) and mainstream science-based medicine. In reality there is no debate because there is only science-based medicine and everything else that has yet to be tested. Most of CAM falls into this latter category. This does not automatically mean that all CAM claims are false; only that most of them have yet to be tested through the rigorous methods of science, which begins with the null hypothesis that holds that the hypothesis under investigation is not true (null) until proven otherwise. A null hypothesis states that X does not cause Y. If you think X does cause Y then the burden of proof is on you to provide convincing experimental data to reject the null hypothesis.

The statistical standards of proof needed to reject the null hypothesis are substantial. Ideally, in a controlled experiment, we would like to be at least 95–99 percent confident that the results were not due to chance before we offer our provisional assent that the effect may be real. Everyone is familiar with the process already through news stories about the FDA approving a new drug after extensive clinical trials. The trials to which they refer involve sophisticated methods to test the claim that Drug X (say a statin drug) improves outcomes in Disease Y (say cholesterol-related atherosclerosis). The null hypothesis states that statins do not lower cholesterol and thus have no effect on atherosclerosis. Rejecting the null hypothesis means that there was a statistically significant difference between the experimental group receiving the statins and the control group that did not.

In most cases CAM hypotheses do not pass these simple criteria. They have either failed to reject the null hypothesis, or they haven’t even been rigorously tested to know whether or not they could reject the null hypothesis. (continue reading…)

The Human Genome Project (HGP)- the project to map the entire human genome – was one of the big public science endeavors that captured the imagination. It started in 1990 and took 13 years to complete, completing the map in 2003 (but certainly not ending the project). Unusually for most such big projects, it was completed ahead of schedule and below budget. The project benefited tremendously from improved techniques and advancing computer power. Sequencing the first genome took about 300 million dollars. Today we can do it for about 10,000 dollars, and the price continues to fall geometrically (about half every 9 months).

By all accounts the HGP was a huge success. But 8 years after the completion of the first human genome map there is the vague sense in the public that the promise has not been fulfilled. The public was promised that the HGP would allow us to identify genes associated with diseases, and then craft cures based upon that knowledge. So where are all the genetic cures we were promised?

What is really going on is that even a big-picture successful science project like the HGP can be overhyped by the press. By mapping the human genome scientists were given a powerful tool with which to investigate disease. It still takes, however, a tremendous amount of research to translate that tool into specific knowledge about an individual disease, and then further translate that specific knowledge into a proven treatment. The pipeline for translating the basic knowledge of the HGP into an actual treatment is about 15-20 years optimistically (and that is after a specific disease is pursued genetically.

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