Fossil hunting with the Brain Scoop

We’re big fans of Emily Graslie’s natural history video series The Brain Scoop. The latest episode goes right to the source of the museum specimens that usually take center stage—a fossil hunting expedition.

Watch the whole thing, and you’ll learn some nifty paleontology jargon, like:

“It’s called the 18-inch layer.”

“Is it because it’s 18 inches?”

“Yeah.”

Random Natural History: Valley Oaks and their Galls.

Ok, time for a short bit of natural history. I live in the Sacramento Valley in northern California. The dominant tree species (outside of urban areas) seems to be the Valley Oak (Quercus lobata). Now, there aren’t a whole lot of trees in the valley, so it’s pretty lucky that Valley Oaks are fairly spectacular.

Valley oak (Quercus lobata) on Joseph D Grant County Park Canada de Pala Trail

They are also little ecosystems unto themselves. The first thing most people notice about them are oak apple galls, so called because they bear a disturbing resemblance to (rotting) apples.

"Oak apple" galls of California Gall Wasps (Andricus quercuscalifornicus, Cynipidae, Hymenoptera) on Valley Oak (Quercus lobata, Fagaceae)

Trees can often be so laden with them that they actually look like cultivated apple trees. The galls are woody, though, not squishy like actual apples. What is a gall, you ask? Good question. A gall is essentially a plant tumor. In many cases (as here) galls are caused by insect parasites. An adult insect lays eggs in the tissue of a plant, and those eggs release hormones that induce the plant to form the gall. Galls can provide food and shelter for their hosts until they are ready to mate and lay new eggs. Galls can be quite complicated structures, the result of parasites evolving very refined control over their hosts over time. As a result, galling insects can frequently be identified by their galls alone. Oak apple galls are caused by a wasp, Andricus quercuscalifornicus, but are exploited by a constellation of at least 20 other arthropods that feed on the galls, A. quercuscalifornicus, and each other.

These aren’t the only galls associated with the Valley Oaks. There are at least two more. One of which is fairly bizarre and the original inspiration for this post: the California Jumping Gall. This gall is also caused by a wasp, Neuroterus saltatorius. In contrast to the oak apple galls, these galls are tiny, only about a millimeter across. What they lack in size, however, they make up for in quantity. These galls form on the undersides of oak leaves by the hundreds of thousands. When they mature, they drop off the leaves, wasp larva still inside. Once on the ground, they start “jumping”. The larvae violently fling themselves around inside the gall, presumably to try to move it into a sheltered spot where they can finish out their life cycle and emerge the following spring to lay new eggs.

The galls are dropping now in my neighborhood, and the result is that sidewalks and gutters under valley oaks appear to be full of jumping grains of sand. It’s a pretty weird sight:

Here’s a link to another video:

ARKive video - California jumping gall wasp - overview

Well, that’s all I’ve got for now. I’ll end on another photo of an amazing Valley Oak.

Quercus lobata VALLEY OAK/ROBLE

Computer Viruses… as art

Computer Virus Catalog, provides us with an illustrated history of the worst computer viruses in history.

It also has an artistic interpretation of each virus, which look really cool! Below are some of my favorites!

HORT---Marburg_905

“Marburg infects .EXE and .SCR files and draws the all too familiar critical error icon everywhere on your screen. The Windows virus spread like crazy in August ’98, when it was included on the master CD of popular MGM/EA game ‘Wargames’”

Lawrence-Slater---Cookie-Monster_905

“Created in the late ’60s, Cookie Monster is the world’s first computer virus. After infection, Cookie Monster freezes all system activity and demands cookies. Don’t sweat it. You simply unlock your computer again by typing the word ‘cookie’_”

Stuxnet

“Stuxnet is a joint effort of the US and Israel, designed to attack Iran’s nuclear facilities. This highly sophisticated Windows worm reportedly destroyed roughly a fifth of Iran’s nuclear centrifuges, by causing them to spin out of control. Mission accomplished_”

Said-Kinos---Ikatako_905

“Ika-Tako (Japanese for squid-octopus) spreads via P2P file sharing network Winny, disguising itself as a music file. When executed, the Windows virus replaces photos, applications and vital system files with images of squids_”

 

Feeling the stress of an academic career? Think happy thoughts!

A recent study published in the journal Stress & Health surveyed the mental health and coping strategies of 200 postdocs at UT Austin and found that individuals who thought positively were better able to cope with the stress of an academic position.

“Thinking positively can do more than bring a transient smile to your face. Postdocs who experience high levels of positive emotions are less likely to suffer from stress-associated anxiety or depression than other postdocs are, according to a recent study of 200 University of Texas (UT), Austin, postdoctoral fellows, 79% of whom work in the sciences. One apparent link between positive thoughts and reduced anxiety and depression is resilience: More positive emotion was correlated with high resilience, which in turn was linked to fewer symptoms of anxiety and depression.”

A happy scientist.

A happy scientist.

Read more about the study here.

SURVEY: How bad was that Science cover and do you care?

The July 11 cover of Sciencegot a lot of press coverage last week. You can read about the variety of responses here, here, here, here or here (to name a few). But if you haven’t heard, Science chose to feature transgender sex workers from Jakarta on the cover of their “Staying a step ahead of HIV/AIDS” special issue, allegedly to highlight this “at risk” group. Unfortunately, the choice felt mostly like objectification and/or exploitation to some because the image was sexual (high heels, short skirts and the women were head/face-less). After a Twitter storm – including some pretty unprofessional responses from a Science editor – Science issued a short apology (cover image can be seen here too).

I’ve been wondering what the masses really think about this.

HERE IS MY 2 QUESTION SURVEY

… for people to please answer as honestly as possible. Basically, how well chosen do you think the cover art was and how much do you care?

Thanks you guys! I’ll post the responses in a week or so. Did I mention please answer? There are even “I don’t know” and “I don’t care”  options, so everyone can participate!

On the scale of Bruce Banner to Incredible Hulk – how angry are you?

PS – All the “Staying a step ahead of HIV/AIDS” articles are open access! Check ‘em out!

Scientists at work among the Joshua trees

When he’s not dismantling racist pseudoscience, Chris Smith studies the evolutionary ecology of species interactions. Willamette University sent along a videographer on Chris’s last field trip to study Joshua trees and the moths that pollinate them in central Nevada, and the result is now posted on Vimeo. It’s mainly geared toward showcasing how Willamette undergraduate students participate in the fieldwork, but I’d say it makes the desert look mighty good, too.

The future of teaching?

Is this cuddly mug the future face of teaching?

I’ve recently become a big fan of IPython Notebook – I use it to keep track of command-line analyses and the thoughts/rationale/questions I have as I’m running them. But Greg Caporaso has another good use – an interactive textbook for teaching bioinformatics. In this blog post, he describes in detail how the textbook came about and how to get a copy for yourself.

Because the IPython Notebooks are interactive, students can (and actually do!) work with the notebooks in class and at home to experiment with the code, which drives active learning of the concepts. For example, one student this semester told us about his experiments with Smith-Waterman gap open penalties of 1000, and about what happens when you make the gap penalties negative (so they effectively become gap rewards; hint: you get a lot of gaps, but if want to see for yourself, install the notebook and try it out).