Snuppy is a real clone!

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Remember Snuppy, the cloned puppy? He’s been living under a cloud for a while now, since one of his creators was Woo-Suk Hwang, the Korean scientist who was found to have faked data and exploited his workers, and there was concern that perhaps the dog cloning experiment was also tainted.

Put those fears to rest. Two groups of researchers have independently analyzed Snuppy and its putative clone parent, and both agree that it is most likely a clone. The nuclear markers between the two were identical, while mitochondrial markers were different—exactly what you’d expect in this kind of clone, and not what you’d see from simple twins, for instance, or if someone had faked the samples.

Parker HG, Kruglyak L, Ostrander EA (2006) DNA analysis of a putative dog clone. Nature 440:E1-E2.

Seoul National University Investigation Committee, Lee JB, Park C (2006) Verification that Snuppy is a clone. Nature 440:E2-E3.

Hug a high school teacher today!

My morning was spent at the local high school today, talking to the biology classes about the evidence for evolution. This wasn’t in response to any specific worries—in fact, talking to the instructor, it’s clear that they’re doing a decent job of covering the basic concepts here already—but that my daughter is in the class, and she thought it would be fun to have her Dad join in the conversation. I will say that it was very obliging of the Chronicle of Higher Ed to publish this today:

In a packed IMAX theater in St. Louis last month, a middle-school teacher took the stage and lectured some of the leaders in the American scientific establishment. In a friendly but commanding style honed by three decades in the classroom, Linda K. Froschauer told scientists that it was time for them to get involved in elementary and secondary education.

“Go home. Identify science teachers in your own neighborhood. Offer to help them,” she said. “Go to the board of education and speak up.”

Excellent advice! It gives an overworked teacher a brief break, lets you see what’s going on in the classrooms, makes the students a little more familiar with college faculty, and maybe it makes a few of them think and gives them a tiny bit more background. It was generally a very positive experience, although it does make me appreciate the work our secondary ed teachers have to do.

I gave a very informal lecture in which I confronted the whole ‘controversy’ about humans evolving from apes. I brought along a few transparencies and a human skull, and gave them an overview of three lines of evidence: transitional fossils, similarities in genes and chromosome structure, and “plagiarized errors”. I kept it fairly simple, using little of the technical vocabulary and defining what little I had to use, but tried to introduce some important concepts, like the taxonomic hierarchy and diagnostic characters and repetitive DNA and pseudogenes. I was also impressed that the students asked good questions, so I think they were grasping what I was talking about.

Boy, but high school teachers have a very different burden than I do. Having to give the same talk 3 times in a row is challenging—I was getting bored with me! The students also range in ability and interest far more than I’m used to…there were many who were attentive and curious (more than I’d expected, which is a very good sign), and there were some who were bored and rather disruptive (but not as many as I’d feared.) I tried not to completely neglect the troublemakers and engaged them a few times with questions, but I had it fairly easy since the regular teacher was there to hover over them and keep them in line. There’s a bit of drill sergeant rigor required in high school teachers that I don’t need at the university as much, I think.

I’d do it again, gladly…as long as I’ve got a few weeks to recover between days at the high school. The grade schools are where we have the most need to get more science into play anyway, so it feels like a productive birthday for me when I can talk to a few 10th graders. And any high school teachers out there—you’re doing an important job, and those of us up in the ivory tower of the university really do care about what’s going on in our schools. Don’t be shy about asking your local college science departments if we’d be willing to contribute in your classroom, I think there is a fair number of us who’d be happy to share our perspective.

PZ Myers’ Own Original, Cosmic, and Eccentric Analogy for How the Genome Works -OR- High Geekology

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I’m teaching my developmental biology course this afternoon, and I have a slightly peculiar approach to the teaching the subject. One of the difficulties with introducing undergraduates to an immense and complicated topic like development is that there is a continual war between making sure they’re introduced to the all-important details, and stepping back and giving them the big picture of the process. I do this explicitly by dividing my week; Mondays are lecture days where I stand up and talk about Molecule X interacting with Molecule Y in Tissue Z, and we go over textbook stuff. I’m probably going too fast, but I want students to come out of the class having at least heard of Sonic Hedgehog and β-catenin and fasciclins and induction and cis regulatory elements and so forth.

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Swamps are lovely

Darksyde’s latest Science Friday is an interview with Michael Grunwald on the subject of the Florida Everglades. It’s a mostly bad news with threads of forlorn hope scattered throughout, like most environmental news.

The bad news is that the ecosystem is in a state of near-collapse. Lake Okeechobee is going to hell; it’s the color of espresso. The Caloosahatchee and St. Lucie estuaries are just gross. And CERP is already way over budget, behind schedule, and off track; Congress is losing interest in funding it. The good news is that there are signs that Floridians are beginning to recognize that their way of life is not sustainable. Posh towns like Fort Myers, Sanibel, Stuart and Jupiter are in revolt over the decline of the estuaries; retirees are having trouble breathing at the beach. Governor Bush shocked enviros by taking their side in a battle over sprawl in Miami-Dade County. A plan to build a massive biotech campus at the edge of the Everglades–maybe the biggest project in Florida since Disney–was blocked by an environmental lawsuit; now it looks like it’s going to move to a more sensible location. And remember: several million acres of the Everglades ecosystem is already in public ownership. So there’s hope.

Spider Kama Sutra

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I’ve been savoring this lovely used book I picked up a little while ago, The Book of Spiders and Scorpions by Rod Preston-Mafham, and am appreciating more than the fact that it is full of beautiful photography of spiders and lots of general information on arachnid behavior and physiology; it’s also true that spiders are awfully sexy beasts. They are playful and romantic and kinky and enthusiastic and ferocious and savage and exotic, and really know how to have a good time. I thought I’d share a few of the pretty pictures and details of the arachnid sex life with the readers of Pharyngula—so if you’re mature enough to handle it, exuberant enough to enjoy reading about interesting animals doing fun things, and aren’t too squicked out at the idea of closeups of spider genitalia, read on.

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Elsewhere next week

If you live near Austin, on 9 March there will be A Debate on the History of Life on Earth with Sahotra Sarkar and Paul Nelson. I scowl disapprovingly on the debate format: it means half the time is going to be wasted with some creationist babbling on stage. The topic, “Can the history of life on Earth be explained by purely natural processes?”, doesn’t sound particularly promising, and simply invites the creationist to say “no”, although he won’t have any evidence to support that conclusion. Go to hear Sarkar, though, which should be interesting.

New Yorkers can attend the Bridges symposium at NYU on 4 March. This is what I like: more young scientists presenting their work, with none of the creationist wibbly-wobbly nonsense in sight. Douglas J. Futuyma is the keynote speaker.

The expected Powerline slapdown

Powerline. Round about these parts, that name is pretty much a synonym for stupid, and I see they’re doing a good job of maintaining their reputation. You’d think they’d learn that whenever they step into the domain of science, their level of ignorance is even more palpably apparent than usual.

Their latest embarrassment was prompted by an egregiously idiotic article from Michael Fumento, which catalogs an error-filled collection of so-called biases in science. The assrocket’s conclusion?

The moral of the story is that the leading scientific journals have been taken over by liberals who value politics over truth. So any time you see a news report on a “scientific” journal article that ostensibly has political implications, you should greet it with skepticism.

Wow. So any science article that discusses, say, evolution, climate, energy, reproduction, conservation, petroleum geology, glaciers, pesticides, extinction, wetlands, materials science, transportation, agriculture, neurobiology, HIV/AIDS (shall I go on?), demographics, deforestation, habitat loss, human genetics (I could keep this up all day), influenza, psychiatry, ethanol production, sexually transmitted disease, medicine in general, stem cells, weather, sex (OK, enough), all issues that have political implications, and which are therefore automatically suspect and tainted by <hiss>liberals? Jeez, John and Michael, why not just say, “Science is EVIL” and be done with it?When all the scientists are disagreeing with you, though, maybe instead you should wonder if you, people with no scientific competence at all, might just be wrong.

I’m pleased to say that we here at scienceblogs.com seem to be presenting a united front on this one, unsurprisingly. Chris Mooney also points out the absurdity of rejecting in its entirety the so-called “liberal” academy, and Tim Lambert rips into the bogus interpretations of the Fumento article. I’ll have to gnaw on a few scraps that are left over.

Here, for example, is an instance of Fumento illogic.

Consider a report
by three environmentalist authors back in 1988 in Journal of the American
Medical Association (JAMA), analyzing male-female birth ratios between
1970 and 1990. The authors found male births declining, and predictably
blamed man-made chemicals. Yet public data going
back to 1940 showed gender ratios are always changing, for no obvious
reason. Years that disproved their thesis were simply sliced out.

Look at that bit where he cites public data, with a link to a report by the CDC. He claims that the interpretation of the report is that “gender ratios are always changing, for no obvious reason”—I can only assume that he figures absolutely no one who reads his column will actually, like, look at his links. The report says nothing of the kind. Right at the top of the report is a graph that shows year-by-year variation, with trend lines on it to show that there is an overall decline in the number of males born. The report specifically discusses the reasons for it, explaining that it only looks at a few relationships and listing others. Here’s the CDC’s conclusion, plainly stated in the final paragraph.

Changes in the sex ratio at birth in the United States have been
attributed to many different factors. The factors examined in this report
include age of mother, birth order, and race and Hispanic origin of
mother. Other factors not examined here but cited by others in determining the sex of a child and, thus, the sex ratio at birth are weight
of mother, stress, age of father, family size, geographic and climatic
conditions, environmental toxins, and a preference for male offspring.
As such, the effect of these factors should be considered in under
standing the annual variation and overall decline in the sex ratio at birth.

How does he get away with this? He cites a report and claims that its conclusions are the exact opposite of what it actually says!

Assrocket just gullibly swallows it all whole. There is a whole parade of similarly mangled science results in Fumento’s article, and another is the recent Hwang Woo Suk scandal.

Fumento’s second example is embryonic stem cell research, where the most important “science” underlying public enthusiasm for cloning turned out to be fraudulent:

Even Science’s awful stem-cell embarrassment wasn’t purely a matter of fraud. I have written repeatedly on how both Science and Nature have turned themselves into cheerleaders for any supposed advance in ES cell science, while opening their pages to laughable attacks on what many see as both medically and ethically superior — namely adult stem cells.

Neither Powerline nor Fumento understand this result. It was an important and expected step in stem cell research, but it was only one result, and certainly wasn’t the foundation of public or scientific enthusiasm for this line of research. Nor does it in anyway invalidate the promise or past results of stem cell researchers, and the claim that everyone is sitting around wondering “How could I have been fooled?” is ridiculous.

  • Hwang Woo Suk flat out lied. I don’t know how journalists, editors, and scientists are supposed to know that until it gets worked over by other researchers, as it was. Of course we can be suckered by someone who is malicious and dishonest, for a while at least; the point of science as a community enterprise is that there is frequent cross-checking and examination of result, which means the truth will eventually out.
  • The Korean teams have had a string of successes in stem cell technology that are valid and have been double-checked. This wasn’t some nobody coming out of nowhere, but a research team with a good track record.
  • This technique of transforming somatic nuclei has worked in other animals than humans. There is no reason to think it isn’t doable—and I expect the work will be done someday. The fraud picked a good target, one that is just within our reach, nothing too outrageous, and all he did was nudge himself over the finish line first, not invent something outrageous.
  • the ridiculous cheering over adult stem cells from a scientific ignoramus is absurd. Probably one of the most prominent researchers in adult stem cells is Dr Catherine Verfaillie, right here at the University of Minnesota, and she has flatly said that she thinks the embryonic stem cell research is an invaluable complement to her work. Get that? She’s a person with a strong vested interested in AS work, and SHE is saying we need more ES work. Do Hindrocket and Fumento think they know better than a genuine researcher in the field? (yeah, probably. Incompetents don’t know the limits of their competence.)

This happens every time Powerline mentions anything about science. I think we ought to encourage a new reflex: every time Powerline mentions the word “science”, come check out scienceblogs.com, and you’ll find several of us howling with laughter.

Lamprey skeletons

Bone is a sophisticated substance, much more than just a rock-like mineral in an interesting shape. It’s a living tissue, invested with cells dedicated to continually remodeling the mineral matrix. That matrix is also an intricate material, threaded with fibers of a protein, type II collagen, that give it a much greater toughness—it’s like fiberglass, a relatively brittle substance given resilience and strength with tough threads woven within it. Bone is also significantly linked to cartilage, both in development and evolution, with earlier forms having a cartilaginous skeleton that is replaced by bone. In us vertebrates, cartilage also contains threads of collagen running through it.

These three elements—collagen, cartilage, and bone—present an interesting evolutionary puzzle. Collagen is common to the matrices of both vertebrate cartilage and bone, yet the most primitive fishes, the jawless lampreys and hagfish, have been reported to lack that particular form of collagen, suggesting that the collagen fibers are a derived innovation in chordate history. New work, though, has shown that there’s a mistaken assumption in there: lampreys do have type II collagen! This discovery clarifies our understanding of the evolution of the chordate skeleton.

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Jurassic beaver

Say hello to Castorocauda lutrasimilis, a primitive mammalioform from the middle Jurassic—164 million years ago. Despite its great age, it has evidence of fur and guard hairs still preserved in the fossil, and was rather large for its time. It’s estimated to have weighed about 500g (about a pound) and was over 400mm (over a foot) long in life, and as you can see from the reconstruction, shows signs of being aquatic. In size and lifestyle, it probably resembled the modern platypus.

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