Science Tidbits for July 13, 2012

Its Friday the Thirteenth… I wonder what Neil would say.

Thanks, Dr. Tyson. On to the science. (Don’t forget to do some superstition bashing today!)

Wow. I’m behind by a whole week, and have a meetup to go to tonight, so this is going to be mostly links.

Paleontology

Via RDF,  a fossil of Australopithecus sediba has been found at the Malapa Site in the Cradle of Humankind in South Africa.

Geologists in Peru are working to preserve a 3.6 million year old “whale cemetery” containing at least 15, probably more fossil whales killed by a volcanic ashfall. Most of the preservation work will be to prevent erosion of the fossils due to exposure to harsh wind driven sand.

Fascinating examination of a fossil bird showing traces of various elements left over by the mineralization process. The copper present is likely to be from the eumelanin pigment, giving hints regarding the color pattern of this 120 million year old bird.

A fossil of an early bird egg has been found (these are pretty rare, apparently) and is shaped like a modern oval egg. This is similar to the egg shape of the therapod dinosaurs, from which it is thought that birds evolved.

I find myself wishing a case of diptheria on the people that destroyed a hadrosaur fossil at an Alberta dig site. Apparently, some idiots have made a habit of destroying the fossils while drinking. Don’t do that.

Anthropology

Bog bodies are strange, but this bunch of quasi-bog bodies is really weird. An articulated skeleton made from multiple bodies, buried for reasons only guessed at.

Via AmericaBlog, an interesting DNA study regarding the origins of Native Americans. This study suggests that three migrations from Siberia acted as the founding populations.

Medical science

The HPV vaccine may already be having an effect on herd immunity, with infection rates dropping in unvaccinated groups.

REM sleep behavior is one of my favorite sleep disorders, since I have yet to find any suggested link between it and the paranormal. Sleepwalking, night terrors, sleep paralysis… they all get blamed on ghosts, ghoulies, and aliens, but not this one. And it seems to have some link to neurodegenerative disorders in a majority of the cases.

Bicycling is fun, and I don’t get to do it nearly as much as I would like to… but knowing how to fit your bike properly is important. In fact, it can affect your sexual health.

What happens if you “get spaced” or “cold shirt it?” Your vacuum questions answered here. (I regularly get asked this one by students. It feels good to be right.

Genetics

Are we teaching genetics properly? Are we bogged down in the history of the science so much that we ignore the state of the art? It is beginning to look like it. If you are as interested in evidence based teaching as much as I am, you should read this and the paper that goes with it. Better course design = better courses.

Zoology

I’m sure you have seen this by now, but a shark stole this young woman’s fish! But did you immediately know what shark it was? Bull sharks swim upriver, in fresh water, for as much as hundreds of miles, so being in a coastal wetland is nothing out the ordinary.

Perfume often includes whale puke. Bleah. But some people are working on a substitute made from the product of a basalm fir gene.

Clam tongue? No. Clam foot. Call it whatever you want, I’m still not eating it.

Wonderful photos of the wee animicules of the ocean

Just the other day, I thought I heard cicadas. I did! I did! Brood I is out, and despite being in an area that has had almost all of its old trees removed and replaced with young trees, I was surprised to hear any at all. Cicadas live underground on tree roots for so long that removing the trees can put a real kink in their reproductive cycle. Go and see the great video at Bug Girl’s place.

Evolution

“What Darwin Didn’t Know” is a pretty good documentary on evolution and is now available online. Check it out.

The demise of evolution in the textbooks of South Korea was wildly incorrect. A short piece in one book that was scientifically incorrect was removed and is going to be updated. This was trumpeted in the world media as a complete removal of evolution… and nobody checked the sources. Always check your sources.

Botany

A new species of plant in the British Isles has been discovered. It resulted from the hybridization of two related invasive species, and is significant because speciation in the wild is not something we usually get to observe.

Antarctic moss finds an unlikely nutrient source. Ancient penguin poop.

Carnivorous plants do some neat things. This one “eats” nematodes. By eat, I mean kills and absorbs the nutrients from.

Environmental science

Excellent video on global warming / anthropogenic climate change. Not too long to use up a whole class period, but a good way to start discussion.

If we cut our CO2 levels now, will the oceans stop rising? Yeah, not so much. There is lag time between CO2 release and the effects that it has on climate.

Overexploitation of natural resources such as fisheries is a major problem for the environment. 30% of fish stocks are overexpoited, which will make it more and more difficult to make a living from fishing and can drive species to the brink of extinction, if not right over the edge.

Is the current batch of extreme weather events due to global warming / antropogenic climate change? We have to be careful making statements regarding this. Weather isn’t climate. Short term events are not long term trends. So, what we really need to do is take a look at what has been predicted based on climate models. Does this fit with those predictions? Yes. Is it likely due to global warming? Very likely. Should we be careful in our phrasing and how we talk about climate’s relationship with weather? Absolutely (although I think MarkCC is a bit hard on Phil). Sad thing is, nuanced discussion doesn’t go over with the media very well and is weak in the face of a lie told with certainty.

Good news, authorities in the Philipines (hello to my readers in the Philipines!) seized 1500 fish and 150 pieces of live coral bound for aquariums.

Physics

Why do non-Newtonian fluids act like they do? Physics. Its like three dimensional chain mail, becoming rigid under impact, The suspended particles are pressed together and form a structure that resists the pressure. Make some ooblek, play with it, teach.

Keep an eye out for Nobel prize winning physicists on street corners giving impromptu explanations of science.

Tech

Did you see Prometheus? Those cool LIDAR mapping probes that mapped the ruins, making a map that the lost scientists apparently didn’t use… That technology exists now.

Classroom

Can iPads be used as teaching tools? Apparently so. Hopefully, this technology can be put into a slightly less expensive tablet.

Getting undergrads used to reading scientific literature is a goal that every college and university STEM department should have. Here is one way to approach the challenge.

Everybody loves XKCD, right? Of course. And XKCD has given us a tool to describe how the eyes work.

 

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.

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.

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.