Showing posts from March, 2012

Lighting up life, part 1: Shiny happy organisms

Even those of us from the sad parts of the U.S. where fireflies are not native know what they are. Magical flying insects blink on and off during summer nights, like feral LEDs. They can be caught and put in jars, or rolled up in your katamari to serve as a study lamp. As we get older, our pubescent understanding of their motivation increases: little dudes are blinking for sex, as who would not? Fireflies put on the red light 1 using a chemical called luciferin ("light bearer") and a special enzyme that catalyzes its oxidation, luciferase. Each molecule of luciferin can only be used once -- another word for oxidation is burning. Since it takes energy to produce each luciferin molecule, it's a bit of an expensive way to identify yourself to potential mates, but obviously worthwhile for some. And, of course, many humans find it fascinating and even beautiful: minor molecular subsitutions in the luciferin molecule cause large color changes 2, so a given insect speci…

Weekend links: context and perspective

Spring break special: ammonites

All kids love ammonites! Apparently including tiny, "delicate" Jurassic lobsters (who may or may not have been sexually mature, we can't tell), who liked to hang out inside ammonite shells. The authors deduce based on the lobsters' body positions that they were in there on purpose -- leading to the wonderful, Dogs-in-Elk-evoking subheading "Decapods in cephalopods" -- but they couldn't tell whether the lobsters were eating yummy dead ammonoid or just found an especially classy burrow to hang out in. (Found via Laelaps.) Hermit crabs loved ammonite shells, too. Plenty of other [organism] in [organism] goodness here. Laelaps again: Ammonoid pearls! Sadly there will be no fossilized ammonite-pearl necklaces, since these were the sort of pearl accretions that just result in entombed parasites in the wall of the shell, but that very fact means we can infer coevolution with those parasites over geological time. Lovely. 3D ammonite radula reconstruction

Weekend links: unusual study methods

Playing with Evolution in a Computer

When we think about the process of evolution, we often imagine the slow changing of birds from dinosaurs, or the domestication of crops. Evolution by natural selection is the driving principle behind all of biology, but it can be tricky to wrap your head around. Random mutation, heritability, fitness, environment, populations, allele frequencies and so on are often murky topics especially for the general public. Fortunately not all evolutionary processes require hundreds of years to observe. Microbes (like bacteria and virus) often evolve on the order of years, months, even days. With such fast evolving systems, we can observe evolution in real-time. However what would be really awesome would be to witness evolution take place on the order of seconds or minutes. Short of inventing a time-machine, we have only one system to observe evolution happening on such short time scales, digital systems. Using computational systems, we can look at evolution occurring on populations of digital o…

"Of Flies and Men"


Dammed amphibians

Jared Grummer from the Leaché Lab just submitted a grant for a multi-year project studying amphibian population genetics in the northern Cascades (North Cascades National Park). The proposed study will use high-throughput genomic sequencing technologies to understand what, if any, population-genetic effects have been caused by three dams along the Skagit River. These hydroelectric dams provide the city of Seattle with approximately 25% of our power needs, and have altered the landscape along the river. The study will focus on three amphibian species: coastal tailed frogs (Ascaphus truei), western toads (Anaxyrus boreas), and coastal giant salamanders (Dicamptodon tenebrosus). Jared will find out in late April whether or not this project receives funding; we have our fingers crossed!

Species species of the Week week #1 OR The Whimsey of Nomenclature

Post previously published at Rah Rah Radula. I have been told, and I shall not say by whom, that the scientific name (1) for the green sea urchin is the longest currently assigned. Weighing in at 32 letters, I present: Strongylocentrotus droebachiensis
Ta-da! Oh, to bear the weight of so many syllables! (credit: Now I don't know if this claim is merely intertidal boosterism, but I do know that is a long name and it's not immediately clear how one would know the pronunciation without initiation into a secret society (hint: "STRON-JUH-LO-SEN-TRO-TUS DRO-BAK-EE-EN-SUS"). In addition to being a marine nerd, I'm also a word nerd, and I dig on the etymology of how organisms are named and described by their scientific name, in part because it's both lyrical and logical. Just removed enough from common usage to make you feel like you are gaining insight into the natural world just by knowing the "true" name. Scientists avoid using common name…

Weekend links: graphics and sex

Forensic Strongylocentrotology

One of the S. purpuratus urchins died, and the others ate him, leaving only this skeleton. It smells foul! -Yasmeen