Vaccine resistance against pertussis (whooping cough)

This falls under the bad news category.

One thing to note, it has taken a long time for a vaccine resistant strain to show up. Vaccines don’t act as selection pressures in the same manner that antibiotics and antivirals do. Antibiotics act as immediate threats to survival, selecting for the mutants in a population that can survive in the presence of an antibiotic. Vaccines functionally increase the number of infectious particles needed to overcome immunity.

Think of it this way, once you start a course of antibiotics, you already have billions upon billions of pertussis bacteria playing pinochle in your snout, pleural cavity (where your lungs are) and elsewhere, and you have probably exposed everybody that lives with you and a majority of people that work or go to school with you. If they have not been vaccinated, or have not received a booster in the last decade or so, they will be infected.

If a person has been vaccinated and has strong immunity from the vaccine, only the bacteria that are already mutated in a manner to evade the vaccine have much of a chance of successfully starting an infection. Some bacteria are better than others at infecting a host, and a smaller number of bacteria are needed to kick off an infection. This is called an infectious dose. The infectious dose of pertussis is probably pretty low, since it is so easily transmitted (susceptible coworkers are 70-90% likely to catch whooping cough, and since kids have terrible hygiene, its even higher for them. Since we don’t know what that dose is, let’s just call it X. If the mutation to evade a vaccine is only present in one out of a million bacteria (a very generous guess), the infectious dose for a vaccinated individual is one million times X. This makes it a lot harder for a vaccine evading strain of a bacteria like pertussis to get started than an antibiotic resistant strain. Luckily, when antibiotic resistant strains show up, they don’t tend to spread very well, probably because the level of vaccination is decently high.

Caturday’s common ancestor #2

PZ Myers is continuing to wage war against Caturday. OK, nudibranches are quite gorgeous, but not exactly cuddly. Those scavenged cnidocytes can make for a bad day for nudibranch snugglers. Think of slugs, but all dressed up and with a whole ocean for having fun (link to the video).

Continuing as a cat / non-cat accommodationist, how far apart are nudibranches (the specific one shown munching away at a Portuguese man o’ war in the video is a blue dragonGlaucus atlanticus)   and housecats (Felis catus / Felis domesticus)? This is a painful one. They are very far apart, as one would expect for members of different phylums.

Timetree didn’t recognize the species, but it knew the family Glaucidae, and here is the time to most recent common ancestor

782.7 Million Years Ago (or worse, as much as 910mya). Precambrian, late proterozoic… Um. Hey it isn’t as far back as cats and catnip, right?

I’m concerned that this cat / not cat is driving us away from what should be our real focus, which is that we shouldn’t trust those weird prokaryotes. No nucleus, no way. Cats have cells with nuclei, which is fine by me.

Science Tidbits for July 17, 2012

Right. I’ll get to the science stuff in a minute. There’s a meteorite that hit the ground near here. I want to check it out. It won’t take long.

If you are teaching an astronomy class, I have a challenge for you. Introduce your students to minority astronomers. Neil deGrasse Tyson isn’t the only black astronomer! When I teach introductory biology I make sure to teach about women that are scientists and at the end of the semester, I often give a bonus point on the final if students can name a single female scientist that isn’t Marie Curie. Some can, some can’t.

Via Boing Boing, a heartwarming discussion of how your bellybutton is a special place for bacteria. OK, so it isn’t heartwarming, but what class from high school biology on up doesn’t involve sampling skin bacteria and growing them on petri dishes. It becomes slightly more intensive when you get into actually identifying all the bacteria present, but this is probably something that upper level courses might consider, if they have the required technology and resources.

Speaking of bacteria, and why not, since we are just walking, talking bacteria hosts and vectors, is this neat little bit on how certain bacteria have distinct smells. A well stocked lab with good safety controls could easily show off some of these lovely little bugs and remind students to use all their senses when making observations.

This piece actually reminds me of something I came across years ago about the naming of several short chain fatty acids (which happened to tie into my dissertation, another story for another day) and guess what, thank the interwebs, it still exists! If you are teaching a primary, secondary or introductory chemistry course, this would be a neat little thing to toss into a lab. It would only take a few minutes, perhaps while something else is going on, but having some samplers of things like butyric acid and a bit of rancid butter to compare it with would be a neat sensory lab. I’m not sure how you get a goat to compare caproic (hexanoic) acid with, but maybe some goat hair would do?

Worrying response to fatal shark attacks off the coast of Australia. While five fatal attacks in ten months sounds like it should be a definite concern, is it a trend marking a change in behavior? I’m not so sure.

If you look at the number of fatal attacks for all of Australia for the last decade, there is no clear trend that can be discerned. It is highly disturbing that there are now calls for a hunt for the shark responsible for the most recent attack. Attempting to hunt down the one large great white shark in an ocean that attacked a person is simply not a feasible idea. Great white sharks can roam dozens of miles in a day and can migrate thousands of miles seasonally. Without clear identification of the shark, checking stomach contents of a killed shark would be the only way to determine if you had caught and killed the right shark.

Revenge hunts won’t convince other sharks not to attack. People watching for sharks in the vicinity of beaches is a good preventative, but is not any more functional with a long coastline.

Tara C. Smith describes using zombies to teach about diseases, pandemics and other public health issues. How cool is that? What an excellent opportunity for discussion and fostering an active learning environment!

More joy from the Philipines, sea turtles saved from poacher’s nets. This probably should be viewed in the context of a larger dispute over territorial waters claimed by both China (where the poachers were from) and the Philipines, as noted in the link.

Lemurs are facing some serious threats and may be at risk of extinction.

Apparently moon dust is bad for you. Well, I could have told you that! Sharp pieces of regolith could get in your eyes and scratch your cornea or irritate your airways, not unlike inhaling ground glass. Here is the paper for specifics.

E. coli strain 0157 is a very nasty bug, and since there is no good reason to assume that the Germantown, Ohio outbreak came from meat (a recent outbreak was linked to feral hogs foraging in fields being used to produce vegetables), it will be interesting to see if a source is found. I’ll be keeping my eyes on the MMWR. In fact, students in any microbiology, disease ecology or public health course dealing with epidemiology should be asked to read and present reports from the MMWR as part of their course in order to see how the things they are studying are reflected in the real world.

There is a belief that lies can be detected via body language hint of looking up to the left. Apparently (surprise), it isn’t true, or at least is unreliable. Just like so many other lie detection tools.

The placebo effect is a very important concept to understand when examining any claim that a drug, intervention, device, whatever, has a positive effect. Well designed clinical trials can help researchers separate false effects from real ones (which is why alternative medicine seems powerful in small trials with poor statistical power, but when examined in large randomized double blind trials, the effect is no different from placebo. Hope plus effective treatment is very powerful. Hope plus nothing may make a person feel good in the short term, but in the long run can lead to dangerous delays in treatment.

People are less familiar with the nocebo effect, wherein something has a negative effect, even if there is nothing there.

In one study, 44 percent of lactose-intolerant people reported gastrointestinal problems after taking a fake lactose tablet. (Impressively, a quarter of people without lactose intolerance also reported digestive troubles after taking the tablet.) And in a somewhat cruel prostate drug study, one group of subjects was told that sexual dysfunction was a possible side effect, while the other group wasn’t. The better-informed group reported sexual side effects at a rate of 44 percent, compared to only 15 percent in the blissfully ignorant group.

People can actually make themselves more likely to experience side effects by simply knowing about them. Medical and nursing students would be well served by reading and discussing how this affects their interactions with patients and communicating risks of treatments. There is a fine line between communicating and providing informed consent and negatively influencing a patient’s treatment.

Undergraduate students in psychology or communication courses would also benefit from class discussions about interactions and how they affect both patient expectations and patient compliance (the linchpin of slowing the development and spread of antibiotic resistance).

It can be difficult to express the sheer diversity of ferns, but this SA blog post does that in spades. Don’t just show your students a fern from the florist. Show them the wild variety of these ancient plants and toss in some examples of ferns from the fossil record. If you can afford it, add some to your personal or department fossil collection.

Mixing live virus vaccines that can mix genes is causing problems in chicken farms. Could this happen in humans? Except for the oral polio vaccine, no, because our live virus vaccines that are given simultaneously can’t mix genes. The oral polio vaccine can recombine, but this is uncommon, and the oral vaccine is only used where polio is still a common disease. Is this virus a risk to people? No, people can’t catch this particular virus. If this sounds like the flu strains swapping genes, it should.

I love cats and cats go so well with science. Cats aren’t just something that students are familiar with, but they have some great features that make them good teaching tools. For example, calico and tortoiseshell cats are almost always female because the mix of alleles that cause a tricolor cat can only occur in a cat with two X chromosomes. A male cat that is calico is going to be the feline equivalent of Klinefelter’s syndrome. If it is as common in cats as it is in people, an assumption for which I have absolutely no evidence, then only 1 in 500 to 1 in 1000 male cats would be feline Klinefelter’s, even before the color pattern is determined.

So why are calico cats important? Find me an introductory biology text that doesn’t have a picture of a tricolor cat in the section about X chromosome interaction. They give us a visible examples of the mosaics formed during development as one X chromosome or another is inactivated, and only the color gene on the active chromosome is expressed. The presence of two active X chromosomes in a cell is probably toxic on some level to the animal. This likely has to do with the effect that the dosage of genes on a single chromosome being just right, while two is too much. More on cats in the classroom and the effects of aneuploidy on cells in the future, just not simultaneously.

Gorgeous video of a variety of insects getting a tasty, nutrient rich snack of pollen. Don’t worry, the flower will probably benefit by having a little bit (just enough) pollen finding its way to a stigma and then on to an ovary. (via @BugGirl on the twitter machines)

And here is another video of a critically endangered Lord Howe Island stick insect emerging from its egg. Wow. How nice it must be to not have a hard exoskeleton immediately upon hatching! More info here.

Lord Howe Island Stick Insect hatching from Zoos Victoria on Vimeo.


Keep an eye out for baby spiders doing their best impersonation of beloved literary characters!


Auroras are pretty neat. Maybe I’ll get a chance to see one some time. I just hope it doesn’t come with a solar flare powerful enough to be visible in Central Kentucky. Phil Plait not only has coverage of the most recent flare, but like he suggests, check out his related links for far more information than I could possibly impart. Just don’t forget to enjoy this video of the aurora from the BBC.

Enjoy this 360 panorama view of the inside of the Large Hadron Collider.

Updates:

There are now suspects in the vandalism of a fossil bed in Alberta. I hope they get put away for geologic time.

Edinburgh’s Legionaires’ outbreak is continuing, with the total reported cases topping 100.

Ever wonder how creationists respond to major news items regarding evolution, say, regarding fossil dinosaurs with type 1 feathers? Check it out at Playing Chess with Pigeons.

And if you are on Twitter, Follow me!

Further, if you are on twitter, follow Joanne Manaster @sciencegoddess for some great science information and teaching goodies like this!

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 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 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.

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.

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 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.