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 5, 2012

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

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

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

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 3, 2012

The Skeptic Society has an educational resource page, and you should check it out. If you can, you should support it.

On with the show!

Light microscopy at its ultimate, the shadow of a single atom. That is light microscopy, which we typically say is only able to resolve images no larger than a small bacteria or particularly large virus, so I think WOW is appropriate. This was accomplished by holding a single atom in place in vacuum via some pretty cool electrical physics, shining light on the atom, and then using an extremely high resolution sensor to record the shadow cast. This could lead to some pretty amazing images being made of very delicate structures.

There is currently an outbreak of Legionaire’s in Edinburgh, Scotland. Legionaire’s is a fascinating disease, and it is amazing that there aren’t more outbreaks considering how widespread the causative organism is. Legionaires’ disease is a serious bacterial pneumonia caused by the legionella bacteria, and makes for a great disease to examine for class discussions. Legionella appear to live at least part-time in freshwater protozoa such as acanthameoba when they aren’t infecting humans, making them doubly interesting.

Topics can range from the history of the disease, from when it was discovered during an outbreak at an American Legion conference in  Philadelphia, to how human activity has produced niches for the legionella to thrive (fountains, cooling towers at power plants and factories, air conditioning catch pools), and how weather and climate can affect disease spread (cases increase after storms). This pathogen is especially important as many nations have an aging population, and the elderly are particularly at risk for Legionaires’ disease.

Linkity linkity link

Moth eyes inspire nano level structures that enhance xray imaging.
The Gaurdian has a video explaining what the Higgs boson is in laymans terms, which are just right for me.
More on the wonderful tiny phorid flies that were featured yesterday.
I find the concepts within evolutionary medicine to be fascinating, if not always useful… Science Based Medicine has a good examination of the topic. Make sure you read the comments, especially Drs. Gorski and Crislip.

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?