Science or Fiction, July 2012

About once a month, I get together with several friends and colleagues for the Lexington Skeptics meetup for dinner and conversation. The topics tend to run from recent science discoveries, pseudoscience controversies, scams and flim flam. Discussion sometimes ranges into religion and politics, but is always polite.

Many people find their way to “scientific skepticism” by way of podcasts like The Skeptic’s Guide to the Universe (SGU) and one of my favorite parts of the SGU podcast (which you should be listening to) is the Science or Fiction segment.

Briefly, the host, Steve Novella asks the co-hosts and guests to pick one fake story from a set of three or four. The others are true, at least in a technical sense. If a true story is turned into a false one and the detail changed is a number, the number is changed to an unreasonably high or low number.

Tonight’s Science or Fiction was a fun one, and led to a discussion of why certain things were possible or not. Read over the following three items, try to pick out the fictional news piece and then click through (or just don’t scroll past the science cat).

  1. Milk thistle slowed the progression of Hepatitis C infection in a placebo controlled clinical trial.
  2. Bacteria are being used to grow spider silk with the tensile strength of black widow spider silk.
  3. Injuries from laser hair removal have led to calls for regulation in Britain.

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Toxic Tuesday 3 – Revenge of the Hybrid Grass

By now, the story of the GMO grass that gassed a herd of cows in Texas has gone round the world at least twice, perhaps more.

Truth is still trying to catch up, and Deborah Blum has a good dose of truth available at Wired.

First, and pointed out by Blum, Tifton-85 is not genetically modified. It is a hybrid grass. Two different grasses were bred to produce this tasty green grass that is easy to digest. And even if it was GM, drought stressed grasses tend to produce cyanide. Non hybrid, hybrid, GMO, all of them are capable of doing this, and by so doing, can become toxic to grazers. The fact that many people are afraid of GMOs led people to immediately assume that the cows were killed by careless mad scientists at the behest of multinational corporations. Meh.

Second, I am highly skeptical that the plants were producing much cyanide gas. The cattle that were grazing in the field were most likely poisoned by eating the grass, not from breathing in cyanide, which would have caused a much higher dose to the cattle. The farmer, not eating the grass, but breathing the same air, would not have been affected.

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 for June 21 and 22, 2012

Good Morning, Tokyo. I promised tidbits by morning, and it is still morning on the other side of the planet.

Whenever I teach about the cell cycle, I discuss cancer, and when I discuss cancer and the cell cycle, I talk about how some anticancer drugs work in relation to the cell cycle. While my own dissertation work focuses on using cell cycle dependent drugs and making them more effective by tricking the cell into dividing with a second drug, all before it has repaired damage caused by first, I’m always looking for recent work that hits on this topic. This press release talks about using just such a “one two punch” to attack cancer cells. The full paper can be found here, but access is subscription limited. I suppose I’ll be hitting up the University library.

I love talking about flu as an example of… well, lots of things. Mutation rates, genes, viruses, zoonotic pathogens, genetic recombination, etc. One of the things I talk about is how close we are to an H5N1 pandemic. Right now, the H5N1 strains that are being monitored don’t pass from human to human very efficiently, which is one thing that keeps it from running rampant through the population. All it takes is a few small mutations and the virus can pick up the ability to pass from human to human, and it is only a matter of time before just such a mutant strain evolves. Hopefully, by that point in time, we will have universal influenza vaccines ready, or at least have methods approved for rapid vaccine production via cell culture. The chicken egg method is just too slow.

Do you know that the color you call blue is seen in precisely the same way as another person? A wavelength of 460 nm is a specific shade of blue. Do you see the same exact shade as another person? Does your brain interpret in precisely the same way?

We have no good way of knowing if my color blue is the same as yours, since every person has different eyes and different brains. Your brain, when you look around you, is receiving information from the surrounding world from your eyes, transferred along the occular nerves, and is decoding it. As it does this, it produces a simulation from that information. You can’t see some things that are there. You can’t see pigments that reflect in the ultraviolet range, but they are present, and many insects can see them. Illusions and mirages are excellent examples of errors in your interpretation of the world and how it is in reality.

This is especially true if you have certain genes for colorblindness. The “normal” person has three different types of cone cells in their eyes. They have trichromatic vision. These cones detect different ranges of color, and for each type of colorblindness, you lose one of those ranges. Your simulation is reduced pretty significantly for each malfunctioning cone cell type.

It turns out that there aren’t only people that have one fewer cone cell type, but some people have one extra type of cone cell, and are called tetrochromatic.

This is one of those little details that you can toss in to a lecture about vision or sex linked genes (some types of colorblindness are sex linked, and tetrochromatic vision definitely appears to be). I find that these kind of teaching tidbits can be a useful way of keeping students that are at the top of the curve right there, involved. They may already know a decent portion of the material, but if you toss in a few bits of trivia that they haven’t seen before, they pay attention for the new things that they didn’t already know about.

More fun Pollinator Week stuff from Bug Girl. Ignore the Burt’s Bees commercial part of the video, and enjoy the information about how bees are the true masters of interpretive dance, and how they are involved in pollination. Oh, did I mention that it is one of Isabella Rossellini’s wonderful videos about nature? Because it is.

Are you teaching a class about reproduction? Are you teaching a minimally mature class? Then fill them in on the oddities of animal penises (via Discovery News). The duck one is actually kind of useful if you are talking about prezygotic barriers to reproduction as a means of speciation. Ducks have penises and vaginas that can be species specific, which can prevent one species from being able to mate with another.

Ever have a student ask why you get brain freeze when you eat or drink something cold? Here is a nice video explanation.
Oh, and if you haven’t heard that Europe is working on increasing the involvement of girls in STEM (Science Technology Engineering Math) education, then you have missed out on one of the worst PR bungles ever. Why is it bad (other than being painful to watch)?

Sexist imagery decreases the performance of female students on tests in STEM subjects. Nicole (NoisyAstronomer) points out the problems in the campaign and also gives some good examples of what women doing science look like. (If you are on Google+, follow her for great astronomy news and information) Kylie Sturgess at Token Skeptic also has some great examples of women in science and a good takedown of the ad as well (Kylie’s podcast is pretty great, too).

Their examples are what get people interested in science. Normal people doing interesting things. And the great thing about this is that when you show minority groups involved in science, it increases their involvement, and doesn’t discourage people in majority groups. Their functional privilege makes such differences invisible to them. Well, except for the ones that need their privilege reinforced, and require that all discussions be about them.

Have a nice weekend. I’ll be calling people to push poll on evolution.

Science Tidbits for June 20, 2012

How do plants communicate with each other? Most people have no idea that plants can communicate with other plants, and this can make for a fun active learning exercise during a botany lesson. Get students to brainstorm possible means of communications, either as a class or in small groups, and discuss how such signals would be detected. Changes in color? Plants don’t have any known means of detecting this. Smell? Well, plants don’t have noses, but many receptors exist inside cells and on the surface of cells. A volatile chemical can move through the air from one plant, be absorbed by another plant and cause changes in gene expression. You can make this as simple or complex as you like, including chemical names, genes expressed, or for primary school students, you can easily talk about one plant sending a message that it has been damaged by a grazer and another plant receiving the message and tasting bad to grazing animals.

That one has been known about for a while, but one that has just been discovered is communication by sound. Apparently, the roots of corn saplings (corn that has germinated and has begun to grow) both produce and detect a clicking noise…

And her intuition was right. She, along with fellow researchers Stefano Mancuso and Daniel Robert, used powerful acoustic instrumentation which allowed them to hear clicking sounds coming from the roots of corn saplings. They also found that when they suspended the young roots in water and played a continuous noise at 200 Hz – a similar frequency to the clicks – the plants grew towards the source of the sound.

Seriously? A sound influences root growth? Science is so cool! They have no idea how this works, but that is pretty cool in itself. This could make for a very interesting discussion as well, with students developing hypotheses as to how the plants are both making and detecting the sound. A great lesson to be had here is that there are always new things to discover, and not knowing the answer to a question means that there are still things to learn.

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Another fun discussion topic for any class can be about how strange beliefs spread through society. For instance, the claims that the world will end this year (2012), based on Mayan prophecy is a fun one. In fact, you can make this as simple or as complex as you like, asking students to look for articles that are both critical of or in support of these claims and discuss what makes for a good argument and what doesn’t. For a simple one, you can just talk about how the people that study Mayan history are completely annoyed by the 2012 hysteria. One easy visual is to show students a 2012 and a 2013 calender, pointing out that the world doesn’t end when you get to the end of one calender year.

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Of course, this tidbit and the previous one fit together neatly. How do you tell good information from bad? Apply your baloney detection toolkit, which is made easier with the careful use of the internet.

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Ever want to talk about exoplanets (planets orbiting other stars)? This is a good place to start… You can see all the planets that we have discovered so far (as of June 2012), with the knowledge that we are discovering more all the time. This can lead into a discussion of how we discover planets. Phil Plait gives a great video explanation, which makes for a good bit of media to add to the classroom.

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And how could I not mention that the REAL Skywalker ranch is getting some historic preservation attention. The set used in Episode IV of the Star Wars saga as the home of a Owen, Beru and a young Luke Skywalker is getting some well deserved maintenance and care. A trip to Tatooine… I mean Tunisia never sounded so good.

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.

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