Science Tidbits for July 5, 2012

One more reason why smoking can lead to ectopic pregnancies. Not only does nicotine paralyze the cilia in the Fallopian tubes, slowing the rate the egg moves from the ovary to the uterus, but cotinine, a breakdown product of nicotine, alters gene expression of BAD, which may make Fallopian tube cells resemble uterus cells.

How does nicotine get to the Fallopian tubes? When a person inhales smoke, nicotine enters the bloodstream and goes everywhere, not just the brain. The cillia in the Fallopian tubes aren’t the only ones affected. Airway cilia, which help to clear mucus (and anything stuck in it) from the lungs are also slowed down. This is one reason for the characteristic smoker’s cough.

Not much else grabbed my attention, so enjoy this excerpt (direct link to the PDF) of The Rocks Don’t Lie by David R. Montgomery from the NCSE website on the scientific evidence that demonstrates that creationist claims about the formation of the Grand Canyon are false.

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Science tidbits for July 2, 2012

Lots of tidbits, lots of links, enough to make a few tidbytes, even (8 tidbits = 1 tidbyte).

Feathers may have been an early adaptation, perhaps even basal, of Saurischian dinosaurs (which includes therapod dinosaurs), appearing so early in the evolutionary tree that many therapod dinosaurs (if not most) may have had feathers. Saurischian dinosaurs are one of the two major orders of dinosaurs, the other being Ornithischia, both named for the structure of their pelvic bones. Saurischian dinos have a lizard like hipbone, while Ornithischia has a bird like hipbone. Interestingly, it is the Saurischian group that is thought to have given rise to birds.

What kind of feathers, though? There are eight feather types that are documented within modern and extinct birds, all the way back to feathered dinosaurs.

Xu, X. and Guo, Y. (2009). The origin and early evolution of feathers: insights from recent paleontological and neontological data. Vertebrata PalAsiatica 47 (4): 311-329. – Hosted at wikipedia

Quoting wikipedia’s article on Feathers > Evolutionary stages

Feather evolution was broken down into the following stages by Xu and Guo in 2009:

  1. Single filament
  2. Multiple filaments joined at their base
  3. Multiple filaments joined at their base to a central filament
  4. Multiple filaments along the length of a central filament
  5. Multiple filaments arising from the edge of a membranous structure
  6. Pennaceous feather with vane of barbs and barbules and central rachis
  7. Pennaceous feather with an asymmetrical rachis
  8. Undifferentiated vane with central rachis

However, Foth (2011) showed that some of these purported stages (stages 2 and 5 in particular) are likely simply artifacts of preservation caused by the way fossil feathers are crushed and the feather remains or imprints are preserved. Foth re-interpreted stage 2 feathers as crushed or misidentified feathers of at least stage 3, and stage 5 feathers as crushed stage 6 feathers.

Modern birds have feather types 4, 6, 7 and 8 (chicks have filament feathers similar to type 1). The dinosaur that is the subject of the research paper that sciencenews is presenting a press release on a 150 million year old fossil of Sciurumimus albersdoerferi, which has type 1 feathers. A dino covered with type 1 feathers would have looked kind of fuzzy, like a kiwi. Not the fruit, the bird. This supports other evidence for feathered dinosaurs in the therapod group existing as far back as 160 million years ago. Therapods are the dinosaurs come to mind when you think of Tyranosaurs or Velociraptors.

What I am most interested in is that feathers are made of a protein called keratin. Keratin is the waterproof filamentous protein that makes up the outer layer of your skin, hair and nails. Keratin is also present, in one form or another, in all vertebrates. Hooves, horns (like those of a rhino) and baleen are all also made of keratin. Amphibians produce keratin, but only on their feet and perhaps belly, as protection against abrasion, while lizards, snakes and all other reptiles produce keratin all over their skin, and it is one of the major evolutionary adaptations that let reptiles live away from water. Carl Zimmer, one of my personal science journalism heroes, has an article at NatGeo on the evolution of feathers, as well as the evolution of our understanding of the evolution of feathers. I highly recommend reading it and passing it along to interested students of all levels.

Depending on how and where they are expressed, they can make up very different structures, which is one of the primary concepts within evolution. Inventing the wheel is quite easy when the parts you need are already present and only need a modification here and an alteration there. With minor mutations here and expression changes there, scales become modified into feathers, which become altered into more complex feathers with further mutations, each becoming useful for different purposes. And all of this from one group of proteins with incredible versatility.

CERN is getting ready to tell couldn’t take the excitement and told us something about the Higgs boson. Great fun for physicists. I have no clue what it means. Dammit, I’m a doctor (biologist), not a doctor (particle physicist)! Luckily, there are people that can explain it.

BoingBoing has a great article up as a piece on cell division and embryogenesis in sea urchins. The videos there would make for great media pieces in the multimodal classroom.

You can learn a lot from fossils, even fossil poop. Yeah, sometimes, feces fossilize (and are called coprolites), and we can learn about the diet of the animal that produced it. In this case, the New Zealand Moa’s coprolites have been examined, and these exceptionally large flightless birds ate plants, and don’t seem to have been too picky. This can relate to the classroom quite easily in any lab where students examine owl pellets. This is a very similar experiment in some ways, examining the contents, but without the carbon dating and DNA analysis.

What drove the moa to extinction around 1500 CE? Humans arrived on the island before this point, and apparently moa were delicious. If only they had survived, I could have a 12 piece New Zealand Fried Moa bucket.

Eugenie Scott of the NCSE talking at the Global Atheist Convention 2012, via Token Skeptic. This talk has some great pearls of knowledge for regarding creationist attempts to do science, and how they don’t mesh with the evidence. (evidence they conveniently ignore)

I love parasites. They are seriously cool. For every animal that feeds itself, there is an animal that lives off of it as a parasite. Some of those parasites have parasites of their own.

The smallest of ants were thought to be safe from phorid flies, a parasite that lays eggs in the heads of ants. The larva emerges, eats the goodies in the ant’s head, and when it is ready to emerge as an adult fly, the head falls off and the fly comes out.

Well, size doesn’t matter to a newly described species of fly that is smaller (0.4 mm long) than any previously described member of the family. So far, the researchers have no idea what the host of this tiny parasite is, but you can be sure they are looking.

In any discussion of how organisms gain their food, parasitism comes up, and visceral examples like this fly can be very interesting to students.

Edited to add this video


Miscelania linkelist

Coffee. Need I say more? OK, history and pharmacology of coffee.
Via Jerry Coyne, wild macro photography of some very cool caterpillars, some of which should be hands off. BTW, the description on the page goes with the insect on the next page.
I would never work with chimpanzees. Even before you get to the ethical issues, they scare the E. coli out of me.
Ants that farm and raise aphids for honeydew and for food have altered the evolution of their livestock.
Mass extinctions can have subtle effects on evolution.
Want to have some fun in an ecology class? Give your students a paper on modeling bigfoot reports!
Interested in a challenging discussion on how to change behavior in a third world setting? Give the class this.
Via BoingBoing, reasons to hate standardized tests. My number one pick from this WaPo piece, ” because they measure only “low level” thinking processes.” Bloom’s Taxonomy? Anybody? Hello?

Science Tidbits for June 25, 2012

First things first, the Houston Museum of Natural History (@HMNS) is running a fundraiser, calling on donors to “adopt” a prehistoric pet. Depending on the donation, you can adopt a different animal and can receive a variety of thank you gifts including drawings or replicas of your pet, certificates, or tickets to the museum, but most importantly, the knowledge that you are helping a home of public learning and science advocacy. If I get the job I’m hoping for, I might just adopt a triceratops. I hope it stays small. I hear they can get rather big…

Now on with the Science!

For the last week, I have been posting “science tidbits” as my own take on teaching tidbits. The idea behind a “tidbit” is that you can drop it right into a lesson plan in order to enrich the lesson, make it more relevant to students, or to tie it into current events. I try to mix in ideas about how to use them in the classroom and if you have an idea, please share it in the comments.

When you think of sharks, you usually think of fast predators, moving just under the waves, carefully stalking its prey… The Greenland shark fits all of those ideas except for “fast.” Scientists knew that the greenland shark ate seals from examination of stomach contents, but figured that they scavenged dead seals. Seals are really fast, so a shark that swims at a speed slower than a mile per hour is an unlikely predator. There is a new hypothesis, though…

“Arctic seals sleep in water to avoid predation by polar bears (Ursus maritimus), which may leave them vulnerable to this cryptic slow-swimming predator,” wrote the authors of a recent study on Greenland sharks’ speed, published in the Journal of Experimental Marine Biology and Ecology.

Where does this fit into a lesson? Any discussion of a food web in the Arctic would include polar bears as an apex predator, and adding the greenland shark into the mix stresses the diversity of the environment and the importance of what happens beneath the ice. You could also describe the shark, where it is found, how fast (or slow) it is, and ask students to come up with ideas about what an animal like this would eat.

Beyond that, the greenland shark isn’t the best known or best studied of sharks, which can make it an interesting creature for an “internet” scavenger hunt, where students hunt for information about the slowest shark, or smallest deer or a venomous mammal, or a good topic for a short group presentation on lesser known organisms.

Making the tidbits again, a chance to talk about zoonotic diseases. Koala bears are one of the cutest animals on the planet. Who doesn’t love them?

Wild koala numbers started dropping last decade, and researchers asked the obvious question, why? (Brainstorm opportunity) It turns out that there are three different organisms attacking koalas, one of which is a retrovirus that is attacking their immune system. The other two are different strains of the Chlamydia, Chlamydia pecorum and Chlamydia pneumoniae, and at least the C. pneumoniae strain can infect humans.

Unfortunately, C. pneumoniae can be transmitted to humans. Koala’s incredible cuteness works on the disease’s behalf. People enjoy picking them up, but like many tree-dwelling animals, koalas don’t much care where they urinate. If an infected koala urinates on a person, they can possibly transmit the strain of chlamydia to the human.

It is frighteningly easy to pick up diseases from animals, wild or domestic, so being aware of these risks is a good idea. Another opportunity for discussion comes in with what people can do to help the koalas. There is a vaccine that appears to work for the retrovirus, but the only treatment for chlamydia sp. is antibiotics. This can quickly lead to a secondary discussion of antibiotic resistance, as there is nothing to prevent reinfection or to prevent resistance from arising. Since humans can be infected with C. pneumoniae, it would be a very bad thing to encourage the bacteria to develop resistance in the wild as it would limit which antibiotics could be used to treat infected humans. This closely mirrors discussions of the use of antibiotics in livestock.

The opportunities for dropping this topic into lessons about infectious diseases, antibiotic resistance, ecology… are endless. Its a good topic for high school on, with advanced undergraduate and any graduate student delving deeper, perhaps presenting short talks on the topic.

The concept of a “living fossil” is a messy one. It suggests that an organism is completely changeless over millions of years, which can be very misleading. Many so called living fossils closely resemble their ancient relatives, while others have undergone morphological changes. The coelacanth isn’t just a single species of lobe finned fish, but is a large group of both modern and extinct species with many morphological differences and falls into several species. Beyond that, they are no longer thought to be the group most likely to have given rise to land dwelling tetrapods.

This isn’t just a good discussion topic, but can be a good topic for small group discussions in high school and undergraduate courses. Give students a list of misconceptions about evolution (a very long list can be found here) and have them examine and present the science behind them. This has great risks and great rewards. Students teaching each other can be one of the most effective ways to learn, and breaking down bad ideas is an important step in the process of learning evidence based science. Remember what Chuck said,

False facts are highly injurious to the progress of science, for they often endure long; but false views, if supported by some evidence, do little harm, for every one takes a salutary pleasure in proving their falseness.

-Charles Darwin

Giving students the tools to replace false facts with true ones is vital in teaching topics that are controversial in culture, but not among scientists. The talk origins database is one of the best ones you can offer for evolution, with Skeptical Science a great one for climate change (from real skeptics, not ones using the title for PR purposes). However, if you get a student that wants to present personal beliefs instead of what the evidence says, or if you pick a topic that is too broad or too narrow, it can end up as a mess.

The other risk/landmine is that you absolutely should avoid discussing religion in a public school classroom, and if you are teaching at a religiously affiliated private college (or even a public institution), you need to be careful to make sure that your administration backs you up. Creationist organisations can put a tremendous amount of pressure on a college and the list of educators that have lost their positions due to the controversy that they can bring to bear is very long and grows longer every year. Be careful to stay within the boundaries of science. No matter what you think of NOMA personally, it is a good guideline for the classroom. If you limit discussion topics to things like living fossils, missing links, the existence of transitional fossils, or why gaps in the fossil record are not only expected but are not a problem for evolution, you should be fine. If you need advice, talk to the NCSE (link above).

If you are using the previous tidbit, or are sending students to use the internet for sources, this is a good read for you and for more advanced students. Lots of material on the internet is accurate, but lots of it is simply junk. If students are doing a presentation, go over their sources with them, and look to make sure that they are reliable.

And one for the teachers, when you are teaching a difficult concept, one that students typically respond to by saying that they will never use it… you need to respond immediately with real world uses, or defuse it before it starts. That can be easy for me. Not understanding evolution kills people via a bad understanding of antibiotic resistance, genetic and evolutionary causes of medical problems, etc. Students can grasp the importance of medicine, poisons, venoms, cancer. But not everything is so easy. Tidbits help a lot. That is the purpose of sharing them and always looking for new ones.

Teach on.

Science Tidbits June 19, 2012

Fast one today, as I spent a fair bit of time today at the Lexington Humane Society making friends with the cats and dogs. It’s June, which means that there are lots of adorable little kittens out there in need of homes, but don’t overlook the wonderful adult animals out there. We have three cats from LHS, two of which were adopted as adults. It is easier to place kittens into loving homes than adult cats who lack the tiny furball cuteness of the larval cat. With an adult cat, though, you have the knowledge of what the cat’s personality is and you know that you have brought home a special friend that may have spent several months in a small cage. If you can’t give a cat a good home right now, consider making a donation of food or money (call first and find out what they need).

On with the show.

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Top story, and for good reason, a Chicago woman has been cured of Sickle Cell Anemia! This isn’t a first ever, but is wonderful to see! Her bone marrow was killed via radiation and bone marrow carrying the gene for normal hemoglobin was transplanted. This is a pretty major intervention, as you can imagine, but it is great to see that some people are getting relief from this painful disease.

Most courses on genetics use Sickle Cell as an example of a disease where people carrying one copy of the gene are protected against malaria, but people with two copies have a lethal disease unless the disease is treated. Even then, most patients have a much shorter lifespan and have to deal with a painful disorder and side effects from the treatment. This gives us hope that better treatments could be within reach… but will require a much improved donor database.

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Its National Pollinator Week, and Bug Girl has information on the importance of our pollinators. For a person who has kept honeybees, this is a week I can dance for. Insect collecting and photographing can be great projects for students from elementary school all the way up to undergraduate, with identification exercises, learning about habitat and ecological niches as needed. If some students are particularly interested, 4-H programs offer a chance for students to direct their own learning and to practice their public speaking skills.

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Class discussion topic for all ages and a chance to discuss the history of the exploration of space: Is it time to return to the moon?

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Following up on yesterday’s tidbit about mating strategies, the Giant Cuttlefish shows its colors.

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A fast Toxic Tuesday, a returning feature of this blog, a quick list of several incredibly deadly proteins, running the gamut from ricin, produced by a bean, to botulinum, produced by a bacteria.

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Finally, news on the textbook controversy in South Korea. Creationist groups had pressured publishers to remove evolution from textbooks without input from scientists. Scientists will now get their say, and hopefully this misadventure will end with science back in science texts.

Teach on.

Dear Gov. RE: Creation Amusement Park

Dear Governor Beshear.

It was with great sadness that I learned of the severe injury done to the Commonwealth of Kentucky’s reputation. It is a sad day when Kansans can look down on Kentucky, that at least Kansas is not trying to attract an amusement park catering to the unscientific concept of young earth creationism.

Worse still, Kentucky is offering tax incentives to attract further development by Answers in Genesis, a group that can only further decrease our reputation as a state that values higher learning. All this in a state that is home to such treasures of paleontology as Big Bone Lick and the rich history of hundreds of millions of years of evolutionary history are visible to anybody who bothers to look at every road that cuts through a hill.

It wouldn’t be a slap in the face to all of my fellow alumni of the University of Kentucky, devaluing the doctoral diploma that I proudly display in my office and  denigrating the verifiable and evidence based science taught in our land grant universities and private colleges if Kentucky wasn’t looking to help fund an ethically bankrupt amusement park. The presence of the Creation “Museum” is embarrassment enough, but to know that my tax dollars may help to fund its expansion, when researchers at UK and University of Louisville face tight budgets while performing ground breaking scientific research, it is simply too much.

Today, you helped to tarnish my hard won degree with the scorn of the academic community. In an instant, my years of scholarship became worth a tiny little bit less. I will have to defend my state as I once did as a child. “Yes, we wear shoes,” becomes, “No, we aren’t all stuck in a scientific stone age.”

What hue and outcry would there be if Ken Ham’s execrable organization was teaching children that God’s way was to learn that left and right are actually right and left? And if you don’t follow the Ham’s specific and narrow interpretation of biblical direction, society will collapse entirely. This is the scientific equivalent of creationism. Students come prepared to ignore anything taught in biology classes, and no level of evidence will convince them that learning about how life evolves is of value, but will guarantee their damnation.

Imagine then, students unable to read their English texts from left to right, as their interpretation of those directions means that no book can make sense to them. Students walking through a line in the cafeteria, gathering their food in their hands and finally depositing it on a tray. Students inoculated against evidence don’t even know that their educational skills are stunted until they are faced with an honest presentation of evolution at the college or university level.

Perhaps saddest of all of this is that the tens millions of dollars already spent on this monument to prideful ignorance goes not to feed the hungry or clothe the poor (or even to clothe the hungry) but to enrich the purveyors of a plainly dishonest interpretation of all types of scientific evidence, biological, chemical, physical and astronomical.

And to what end? The hope that if people remain ignorant of the reality surrounding them, the facts of evolution, explained by the modern synthesis of the theory of evolution by natural selection, that their faith can remain intact.

Ignorance is bliss to Ken Ham and Answers in Genesis, ignorance and fear of a wrathful and genocidal god. I wonder, shall the amusement park include a wave pool filled with the simulated bobbing bodies of the dead, as the Museum cheerfully displays the Genesis account of the Great Flood via computer animation and artistic dioramas of the wholesale slaughter of the world? Having been to this “Museum”, I can say that no depth is too low to subject young minds to in order to scare them away from inquiry and learning.

What shall I expect next from the government of our fair Commonwealth? Should UK and the University of Louisville begin to offer degrees in astrology? Will the UK medical school offer coursework in homeopathy? Perhaps you could establish a Department of Divination to direct the government’s future goals and to offer you a morning horoscope? Or should I expect some other discipline of magical thinking to be given the stamp of approval of the state?

Why did you choose to encourage what can only harm our state’s reputation? Was it a promise of 30 pieces of silver (a temporary increase in construction jobs) to betray our good name?

Please do not count on my vote in the next primary election. I will remember your intentional step backwards on that day and cast my vote for any challenger. And should I look to spend money on a day at an amusement park, I will do so without guilt in neighboring Ohio, at King’s Island.

Sincerely and Remorsefully,

Robert Bevins, PhD

A Creation Petting Zoo?

I decided to take some time and write a follow-up piece to my adventure at the petting zoo at the Creation “Museum” and fulfill Mr. Hammer’s offer of guest posting.

A little about myself… I finished my PhD in Toxicology in 2005 at the University of Kentucky and am now teaching part time at my undergraduate alma mater. I used to blog as a graduate student, mostly on politics and religion, and gradually slacked off. After the SSA visit to the Creation “Museum”, I decided it was time to come back, and put together a blog on what is happening in the biological sciences today, and how you could present that information in a manner that would engage students and promote learning. Daniel offered to let me write up a guest post on the visit, and so, here I am.

You can probably guess how I responded to the faux science of this place. The good news is that it seems like an incredibly boring place to take a kid. The bad news is that lots of kids get hurried through there, and find themselves lied to about how science works. Of course, that makes my job harder, because the theory of evolution is a central concept in biology, and without it, there are lots of unconnected lines of evidence, begging for something to unite them. Answers in Genesis hopes to provide a replacement concept in a very narrow interpretation of Genesis, and hell take you if you dare to disagree. The problem is, even if they were able to disprove evolution by natural selection, it wouldn’t make a six day version of biblical creationism, by default, correct. The worst part is that they can’t even come up with any new claims. They are stuck with arguments that are decades, sometimes more than a century old, and all long debunked. Even intelligent design isn’t a new concept.

Science is a system by which we attempt to remove our bias and prejudice, and seek naturalistic and materialistic explanations for what we find in the world around us. The supernatural doesn’t enter into our examinations, unless somebody makes the claim that the supernatural can be measured or otherwise proved to exist. So far, nobody who makes those claims has been able to offer any concrete evidence for their claims and while it is impossible to disprove them, the “Museum” is being academically dishonest and is ethically bankrupt by plainly admitting that they start with a conclusion and ignore any evidence that doesn’t support their conclusion. They abandon any pretense of science from their starting point and they don’t even know it.

Keeping up with the amusement church theme found on the rest of the grounds, Profit Prophet Ham has a lovely little petting zoo, perhaps one of the two interactive exhibits available to catch the attention of children.

Continue reading

The Creation “Museum”

Why would I go to a creation museum?
creozerg robsterFCD 109
I don’t believe in a special creation, to put it bluntly. I have no question that evolution by natural selection is fact as well as solidly grounded theory.  I find the whole concept of a 27 million dollar facility pushing a narrow interpretation of a creation myth to be offensive, when one could have sent those millions to, say, upgrade the facilities of a teaching hospital in Africa, or fund clinics in the slums of central America, or promote polio vaccination programs worldwide… the list of real charitable projects would go on and on and on. And if you would prefer those dollars be used for US charities, try Habitat for Humanity or the Susan G. Komen breast cancer charity, or the Secular Students Alliance (more on this group in a post to come).

Why? Because my students come from varied backgrounds and with this “museum” only a 90 minute drive from home, some will have visited this place. While I am familiar with most of the claims of creationists of many stripes, thanks to TalkOrigins and The Counter Creationist Handbook (which I am holding above, and if you are a science educator, you should own this book and keep it in your office or classroom), it is always best to see these claims firsthand so that you can see their claims firsthand, how they are presented, etc so that you can be better prepared to respond.

Also, because there was a large group going, I didn’t have to pay $22 to get in, just ten. I’ll be offsetting that with donations and dues payments to a variety of pro science education groups or skeptical organizations, such as the NCSE, CSI and SSA, among others. Consider it Idiocy Offset Credits, sort of like offset credits of the carbon type.

Finally, PZ Myers, lord of the squid, was going, and I wanted to get a chance to see if fire really did shoot from his eyes and if bats darkened the skies with their leathery wings above him, blotting out the sun. Sadly, his reputation in this manner has been greatly exaggerated.

creozerg robsterFCD  096

My tie has the periodic table on it. I was ready to teach the controversy between four elements and all those hundred or so elements that scientists keep adding to every now and then. PZ’s tie, on the other hand is one of two crocoducks, the other belonging to Richard Dawkins.

What did I find? Continue reading