Science Tidbits for June 29, 2012

How cool are worms? Really cool. Worms are freaking neat. Annelids (the phylum including earthworms, leeches and polychaetes) are just flat out odd sometimes, and odd makes for teachable concepts.

Zombie worms are polycheates that live in the deep ocean, and have a very odd way of eating.

They don’t, not exactly.

They don’t have mouths. They don’t have stomachs, intestines or anuses either, and yet, they eat the bones of dead whales, and are called bone eating worms or osedax, which means bone eating in Latin.

They use a branching anchor with rootlike structures, covered in microvilli, to secrete acid, which breaks down the calcium structure, liberating fats, which are absorbed and then digested by bacteria living in the tissues of the worm. And zombie worms aren’t even the most grossly named of these critters. Behold the bone eating snot flower worm!

So they don’t eat, but do break down bone and absorb food from their surroundings.

It sounds a bit like a fungus, actually. And this can be a great chance for you to talk about how what a normal defining characteristic of a kingdom (ingesting food for Animalia, photosynthesis for Plantae) are sometimes abandoned, but the organism never hops to another kingdom. A ghost orchid that doesn’t photosynthesize is still a plant, existing as a parasite on fungi underground, only poking up to flower on rare occasion. Students often want to think of non-photosynthesizing plants as fungi, and might want to do the same with bone eating worms, but they still have all the other features of their kingdoms. The osedax still doesn’t have cell walls or mycorrhizae like a fungus. It still has closer genetic ties to other polychaetes and annelids than to anything else. The ghost orchid still has cellulose cell walls instead of chitin. It may not have chloroplasts, but it still is a plant. Great chance to have a lesson on phylogenetic trees.

Another topic you can bring up is the use it or lose it concept. Osedax don’t use a digestive tract and don’t need one. The genes for a digestive tract are turned off and over the millions of years since they evolved, the genes probably have become mutated into a non-functional state. It was once assumed that once you go down this tract, you can’t go back, but scientists have found that geckos have gained and lost their adhesive toe pads several times, and some lineages of scorpions have gone from surface to cave dwelling and back, and lost their eyesight and regained it. The longer you don’t use something and it remains unexpressed, the harder it is to reactivate, but it isn’t impossible.

I would really love to see a study of the early development of these worms, especially to see if their larval forms have digestive tracts.

One other cool detail… Osedax have both male and female sexes, but the males live in a larva like state inside the female.

Worms = cool

A new gene in the influenza virus has been discovered. Let me pick up my teeth. Influenza just went from a genome of 10-11 genes to 11-12.

The gene is hidden in the code of another gene, and it appears to limit the severity of the immune response. If the mouse model is correct, when this gene works, the flu symptoms are less severe. If it is mutated, the flu is more severe and is more likely to kill otherwise healthy people.

The gene wasn’t discovered until now because it is found after the main gene on segment three starts. It basically is a second open reading frame (this is the link to the original paper in the journal Science), and is activated by a ribosomal frame shift. (Does this sound like it may be for an undergraduate genetics course? Oh yeah. But don’t be afraid of handing it to a gifted high school student.)

Basically, the gene is transcribed as normal, making the viral mRNA. The mRNA is then translated, and when the ribosome reaches the start of the internal gene, it slips, missing a nucleotide and the rest of the protein is produced according to the internal gene. This is similar to eukaryotic alternative splicing, and is a very cool way to get two genes coded into the space of one.

This produces a protein that represses the genes of the cell, and probably inhibits the cell from putting up the little red flags that tell the immune system that it has been infected. Less immune response, less chance for a cytokine storm, the nightmare scenario for flu.

Misc science goodness:
Neutron star racing across space 
Graphene may make for an efficient way to make salt water into fresh
Nice way to explain the different parts of the electromagnetic spectrum (xrays to visible light to radio waves) and their significance to astronomy
Why does coal become rare in the fossil record around 300 million years ago? Fungus that could break down lignin evolved about that time.
A rare freshwater mussel is facing extinction.
Animals from the Ediacaran period preserved by volcanic ash.

Teach on.

Science Tidbits for June 28, 2012

Looking for something to blow some time while doing something for science? Help map the moon! (via Token Skeptic)

On with the show.

In the June 20 list of science teaching tidbits, I talked about what senses you could ascribe to plants, and somewhat dismissed the concept that plants could “see.” Well, I didn’t put enough thought into it, and failed to consider the range of what “sight” means. Sight in flatworms can be something as simple as detecting the presence of light and moving towards it.

Daniel Chamovitz, of Tel Aviv University, in a Scientific American 60 second science blog post, points out that plants “see colors, they see directions, they see intensities.”

And beyond that, they respond to direction, through a process called phototropism, where the plant grows towards light.

The great thing about science is that you can be excited by being wrong.

Also from Scientific American is one of the most ignored members of our phylum, chordata, the sea squirt. We rarely do more than mention tunicates and lancelets in passing and move on to the better known and more popular vertebrates, which is really a shame. These oddities of chordata are very useful in spicing up a lecture on diversity. What is more different from a mammal than an organism that only swims as a larva, then settles down, becomes sessile, grows a shell and lives as a filter feeder for the rest of its life, resembling a mussel more than anything else?


The particular sea squirt of interest is a food item, nay, a delicacy in Chile and Peru, and has some incredibly odd reproductive habits, from a human point of view.

Finally, an incredibly old impact crater was recently found in Greenland, as in around 3 billion years old. It isn’t the biggest, but its the oldest. There are impact craters all over the world, some in our own back yards, many of which are not much to look at from the ground, but can stick out on a satellite image. For example, put 38.305000,-86.500000 in as your coordinates on google maps. As you zoom out, you will begin to see a broken ring. This is thought to be the site of a meteor strike in the ancient past of Indiana (I don’t have my roadside geology guide handy, or I’d give more details), and the surrounding land bears the shocked quartz, deformed bedrock and sedentary fill, and even the gravity density of a meteor site. Completely invisible from the ground.

The Kentland, Indiana crater is better known, but all kinds of things are just under our metaphorical noses. You don’t have to go to Arizona to stand where the sky fell. This makes the rare meteor crater site on the other side of the country or world a bit more close to home, and therefore, interesting.

If you want to go a little further in a physics class, here is a nice little experiment that you can do with fairly little setup or expense.

Teach on.

The life of the incoming freshman

Its their first time away from home for more than a week. They have run through all their clothes, and it is time to brave… the coin operated laundromat. How do you keep from stepping on toes? Is there a code of conduct? Why yes there is. Some of it is obvious, don’t be rude stuff. Other parts require that you think ahead, have enough quarters and sort your load before you get there.

Should you wait to for your freshmen to come to you to ask you, their adviser or professor, for help?

Well, you could do that, or you could take the initiative and send useful information to them by way of email, or set up a website with useful links like local bus schedules, or even more importantly, an explanation of what terms like “best if used by” on food mean.Even if students have a meal plan, they may have a mini-fridge with some milk, lunch-meat, cheese, etc, or they may have stopped by the student center/union, grabbed some food and squirreled it away for later. Helping students stretch their food budget while keeping them from making themselves sick? Not only is that good for you, but building the self esteem of new students and improving their first year experience is priceless.

Students with less outside stress perform better, learn more, are happier, and all of these contribute to a major goal of any institution of higher education… retention.

Teach on.

Toxic Tuesday – Arsenic and old peppermints

Imagine popping a nice sweet into your mouth. It should be a pretty safe treat, right?

Not in Bradford, England, back in October of 1858.

Due to a mistake made by an assistant at a chemist’s shop, arsenic trioxide was sold instead of a filler called “daft.” The resulting batch of candies contained twice the lethal dose of arsenic in each candy.

Within days 25 people died, while at least 90 adults and 50 children became extremely ill. Counted among the stricken was Humbug Willie himself, who became sick from handling his own candies.

The aftermath of this accidental mass poisoning led to a requirement that arsenic include a coloring agent so that it would not be mistaken for other chemicals, as well as tighter regulation of arsenicals (chemicals containing arsenic). In the US, problematic patent medicines and disease outbreaks from food led to the passage of the Pure Food and Drug Act, which created the Food and Drug Administration.

This case reminds me of one of the truisms of toxicology, that laws regulating poisons are written in blood. (Laws regulating poisson are written in fish-hooks)

Science Tidbits for June 26, 2012

Two quick news items for today and one video.

First up, more information on the effect that the 2009 H1N1 pandemic virus had. The H1N1 “swine” flu inflicted a particularly severe toll based on an interesting application of a couple concepts from the world of epidemiology and public health.

There are multiple ways to describe the death rates of a disease, one of which is simply the number of people that die from the disease. This simple measurement of mortality doesn’t tell us everything. Influenza typically kills a mix of the very young and very old. The 2009 H1N1 pandemic flu killed far more young people than the seasonal flu normally does, which changes the effect on society.

The concept to stress here is that of patient or person years. Functionally, every person that lives one year lives a person year. If you have fifty people that live one year, you can express this as fifty person years. If they are patients, you would say that there were fifty patient years.

A good way to bring this to the classroom is to compare one young person and one older person. Let’s say that the young person can expect to live sixty more years, while the older person can expect to live twenty more years. If both people die from the same disease, at the same time, the young person lost more years than the older person. Sure, if either one of them had survived the disease, either could have been hit by a bus the very next day, but statistically, the death of the younger person was a greater loss of potential years of life. If we have a very large population, with perhaps tens of thousands of young people and old people falling into our patient group. For every young person that dies, three older people have to die to add up to the same number of patient years.

It sounds like a very cold and callous way to look at the lives and deaths of real people, but this system is used to determine what level of risk is acceptable for a medication. How many patient years are saved from the treatment and how many are lost from side effects? How severe was an outbreak? How useful was a new safety technology installed in automobiles? Many concepts in public health take an impersonal look at an issue because of the sheer number of people involved.

This can lead to a great discussion of the differences between patient and population centered medicine, if that is in the scope of the class you are teaching.

The second tidbit is a quick explanation of a piece that was in the news a couple of weeks ago. A woman eating parboiled squid bit into what appeared to be a tasty piece of meat, but was in reality a reproductive organ of the male meal. This can either be passed along to students asking if it was real, or be used in a zoology course when discussing the reproductive strategies of a variety of invertebrates.

Finally, a video that I have used in teaching about the process of mitosis.

I have shown the video as is to a course, muted it and described the steps in the video, pausing to point out specific features, and have included it as a link on a course website (both Moodle and Blackboard). However you approach the multimodal classroom, videos like this can be very useful in helping students understand how something like mitosis works, and can be used at multiple levels of difficulty, from simply learning the phases of mitosis in order to beginning to understand the function of spindle fibers.

Teach on.

Caturday’s common ancestor #1

PZ Myers decided some time ago to wage war against Caturday by posting things that are not cats. This past Saturday, he brought out the big guns, baby red pandas. Ouch.

Well, I’m feeling a bit accommodationist, so I thought I’d start something new. After all, red pandas (Ailurus fulgens) and housecats (Felis catus / Felis domesticus) aren’t that far apart, right?

So I plugged the in to Time Tree and here are the results.

Just 55.7 million years. See, not that different after all. Can’t we all just get along? Think of the kittens.

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.

Eugenie Scott – Why Creationism isn’t Science

I’m a big fan of Eugenie Scott and the National Center for Science Education‘s (NCSE) work to keep science education free from creationism. – Via RichardDawkins.net

The NCSE is branching out to fight climate denialism as well, which is a good move. They are well placed for such a move since climate denailists tend to use many of the same rhetorical tactics as creationists. The Skeptical Teacher has a video from Mark McCaffrey, the NCSE’s climate expert. BTW, they are currently looking for a second climate expert to round out their team.

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.

Fun science stuff, tidbits tomorrow

I had a very long day doing hard labor, so have some fun with these and I’ll put science news tidbits up in the morning (good thing that on Earth, its always morning somewhere).

Close your eyes and listen to the annoyed cat in this first video.

Is it saying anything? Can you make out specific words? Now play it back and watch the video. It all makes perfect sense with subtitles! If you want to really test this, play it a third time, eyes closed. Did you “understand” the cat now that you are primed to decode certain words?

This is an example of paredolia, specifically, audio paredolia. Your brain is very good at finding patterns, even where they aren’t really there, and if you prime it to pick up a pattern, it can be extremely hard not to notice it later on. We see faces in blobs, shapes in clouds or craters, and we think that certain cats are secretly pirates.

I have also had half of a class close their eyes and just listen, and the other half watch and listen and then poll the students to see if they could understand the cat. Its a great way to show how suggestible the mind is.

Want to show what calories look like? Just ask Dr. Bunhead.

Now aren’t you glad that your body releases that energy in little packets of ATP instead of all at once?

They laryngeal nerve is an excellent example of something you would expect from evolution, but not intelligent design. It runs from the brain, around the aorta and back up to the larynx. It works well for fish, but when you remodel the body a bit, a vital nerve that can’t be cut running around a vital artery that can’t be cut, with both developing early in the embryo means you are stuck with a minor tangle. Take that and apply it to a giraffe…

(giraffe autopsy, not for the squeemish)