What delicate toes you have!

Updates! It's been quite a while, last term and the first half of the summer was pretty busy. Glad to be free of teaching for the rest of the season!
I am helping carry out two large scale experiments in the lab this summer, a huge collaborative project between us and a companion lab in Pittsburgh (the Relyea group). It's turned out to be a valuable crash course in conducting (and designing) large scale lab experiments! I've done my fair share of lab work in the past but the logistics of running these two projects have been eye opening for me. There are frog shipments every week, multiple species, several treatment combinations, 2x a week feedings, individual housing units to wash and prepare, etc, etc. Our group is a well-oiled machine by now and come each Friday (measurement day for new animals!) everyone knows their posts and duties and can run through hundreds and hundreds of individuals with scarcely a break til noon! It's a mad assembly line but everything runs smoothly and somehow, we all get it done...I remember the first Friday  we started at 8 am and when I finally got home my clock read 8:30 pm!

Anyways, we are deep in summer and though this year will not see me mucking about outside too much, I will nevertheless attempt to fill this space with awesome pictures of frogs among other animals that usually fill up this space.

First off, I staged an impromptu photo shoot with my office pet, Phaeton. He is all grown up as you can see:

No, those vertical lines on the body are NOT ribs, he is well fed thank you very much! They are called costal grooves and they correspond to where the ribs are. They help absorb and transport water to the dorsal (top side) part of the salamander. The  number of groove, from between the front and hind legs, can vary depending on species and are used for identification. 

Did you know amphibians have the largest vertebrate genomes? Humans have over 3 billion base pairs, a mouse ~ 2.7 billion, the bacterium E. coli over 4 million.
But if you think we are impressive take a look at salamanders! Phaeton is a northwestern salamander, Ambystoma gracile, and has over 41 billion base pairs! Even more impressive is the Japanese plant, Paris japonica, with 149 billion base pairs! Yowza! As you may have guessed, having a large genome does not necessarily make one more complex... It does however make for bigger cells. I'll try and remember to discuss this later because it's really a fascinating aspect of amphibian biology I am just starting to learn about myself!

Sometimes you forget

 Sometimes you forget how awesome this planet is. Nothing reminds you of that quicker than a good shot from a helicopter flyby!

Turn up the volume.

*Face Palm*

Left: Ruby-crowned kinglet; right: Hutton's vireo

So everything I've been calling a Hutton's vireo on campus is probably a ruby-crowned kinglet!

I was talking to my Stats professor, who is an avid birder, and he was telling me how nice it is this time of year with all the kinglets hiding out in the patches of rhododendron. And then I said I've been seeing lots of vireos in the rhododendron...And then we did this:
But do they not look very similar?! Arrrrgh! You know this isn't the first time I called a kinglet something else. For some reason my mind never makes that connection. Next time, will note the thinner bill and single wing bar. I also never saw the ruby crest so that would have been an obvious indicator:

Look who's out of the water!

Trapped! In a glass prison!
I was changing his tank yesterday and recreated his beach but this time added a cushy bed of sphagnum moss on top of the pebbles. It holds a lot of moisture and is definitely more comfortable to move around in than the pebbles.

Phaeton completely out of the water now! He lost a lot of weight during the 'Time of Great Change'. I would like to find more varying food sources for him now, though the worms have been great and very nutritious.

Phaeton Update - Hooray for lungs!

One of my favorite pictures of Phaeton. His eyes were so sparkly!

Balancing on his decorative jars.

Learning to breathe!!

I collected this shedding. It was a nice big continuous piece too.

Mar 12 - What welcomed me as I came in this morning! He was trying so hard to get up there! I have to collect some moss and dirt now and fix him up a new tank soon!

"Of the House"

This House Sparrow is a resident of Montmartre! What a life it must lead! The best pastry leftovers to feast on!
My uncle took me here last March (wow a year already!) and these are the most fearless sparrows I have met. I could not have been standing more than 4 ft when I took this shot!

I was originally going to start this piece off by discussing the House Sparrow, Passer domesticus, perhaps the most pedestrian of winged creatures. But I think the bigger story here is how we choose to look at the world and value critters like the "lowly" P. domesticus. So here we go:

I think many of you who know me know that I can easily find most anything interesting and thus worthy of a few minutes of contemplation. But I realize that trait is not present for everyone out there. There have been some posts where I thought readers would lose interest for sure due to the seemingly dull subject matter discussed. You know I can't hold giant birds every week :) So sometimes I do think to myself: "Is anyone going to care about this slug I found on my walk?" or "Will anyone be interested in corn tiling and field drainage?"

Eh. But I start writing anyways because sometimes it's a slow week. And you know what, no matter what it is, there is always a story to be told. Dig deeper and suddenly everything has a fascinating narrative.

There are many people in science who seek out those narratives, who see something overlooked and throw it under a microscope (I can think of a few right now as I type)! Chief among them, in my mind at least, is Rob Dunn of NC State. He is a lover of all creatures, especially ones that are oft under appreciated and/or looked upon scornfully. Thanks to him, Passer domesticus is enjoying a little bit of the lime light this past week due to a great article written by him on Smithsonian.com! It really is awesome so refill your cup, sit back and enjoy :)

He is a proponent of urban ecology which simply seeks to investigate the ecology of urban spaces. Pretty straight forward right? Why hasn't anyone done this before?? Well, what's the first image you have when you think of an ECOLOGIST? Charles Darwin chasing finches on the Galapagos Islands? Jane Goodall hanging with primates? Perhaps Jacques Cousteau descending into the murky depths?

Surely it is not some dude or chick rummaging around the train tracks for bugs! Well, make room at table because there is some new blood up in here! OK, so it's not so new but the field is still very small. The predominate thought, that nature is what happens when people are not around, is simply not true. But as kids (and adults) we grow up on books and media showcasing the lands and organisms of the far-removed African savannah, boreal forests, and colorful reef systems and yet, know extremely little about the very system we are a part of.

I attended an entomology lecture at the Smithsonian Natural History Museum one afternoon long, long ago and though the memory is very blurry, I do recall that a group of scientists did a bug survey in a local marsh-type area near someone's house in Virginia and ended up finding an array of species and abundances they were not expecting. The speaker happily exclaimed that you need not always travel to exotic locales to make fun discoveries. That's not to say everyone should stop doing that research, but just that we ought to take care to not overlook our own backyards, even though the view may not make much of a postcard.

It's obvious that urban systems are their own unique ecosystem. No one planned on building a home for anything else but humans when they made the first cities/settlements. But adapt nature did! There are pigeons, rats, bedbugs, ants, mice, roaches, sparrows and a plenty more! All pests you say? Well, yes - to us. But they are just creatures making the best of it; and how can they resist when we've made it so easy? We give them food, space, shelter and to some, a warm body to snuggle up to at night! Sure, there are things like exterminators and house cats, but somehow I think the bedbug and pigeon populations are managing all right. One interesting note, many of those creatures probably stood out as disease carriers right? It makes sense that many wildlife-to-human diseases are transmitted to us via these hardy critters because those are the guys we live around and thus most commonly come into contact with. *Note to self: discuss this aspect more in detail in a later post.*

Anyways, it is almost midnight now so I leave you with some urban species, mainly of the avian form:

Another Montmartre House sparrow

Paroaria coronata, introduced to Hawaii

Spotted dove, Spilopelia chinensis, introduced all around the Pacific, it is fast replacing native doves in Australia. This one I found on Oahu.
European starling, Sturnus vulgaris. Christ, it's species name is vulgaris! Hahahaha. Ok really, the Latin word vulgaris means 'of the common people' or something to that effect. There are many near my apartment. I actually like the sound these birds make; they are known to be great mimics and are capable of a range of weird quirky noises. They usually have a very mechanical sound which I find infinitely amusing. Is that a machine or bird outside my window??

Evolution...with Crayons!

This video is amazing! I wish I had these animation skills!

This article over at Scientific American explains how it was made.

New Field Guide...for Microbes??

A crazy microbiologist from UC Davis wants to make a field guide for microbes!

Although it probably won't be as popular as the long standing field guides for birds and flowers it will definitely be just as beautiful:

People love knowing the nature around them. You see it in your wild-haired neighbor who plans his trips around bird migrations. OK so not everyone is like this but many are to varying degrees. It feels good to know what lives around you, that's why field guides are so popular. There are whole subcultures of folks who are devoted to a taxa. I remember as a kid my sister and me would check out books about dog, cat and horse breeds from the library and try to learn as many as we could. My brother had his sharks book. And we weren't the only ones, many children are like this! I can distinctly remember a desire to catalog/collect things in my head and put them into some order so I could wrap my mind around it.

When you get older you start doing it with easily 'collectible' things like birds and flowers or shells. There is a satisfying sense of mastery associated with 'collecting.' I often see it in people I meet birding, everyone feeling like like they understand all the ins and outs of their chosen domain. And this is a great thing! (Though it can sometimes come across as conceit). But this is where a lot of natural science people come from!

Ugh, if I had more time we can discuss citizen science and hobbyist vs. professional routes...but alas, such is the fleeting presence of Time in grad school. So this idea of a field guide for microbes is interesting to me. Even as I am getting more and more entrenched in the microbial world I am finding it hard to locate easily digestible pieces written on them. One thing that popular writing in field guides does is make nature more accessible to for everyone. I wonder if it will be hard for people to care though if they don't own a microscope or something to see the critters with but their presence will be appreciated. Most people are aware microbes are everywhere and have a huge impact on our world (even if most don't understand what that impact is).

Anyways before I rush off to my Friday routine here is a quote I'm sure I've posted before from one of my favorite movies, it certainly doesn't wholly apply to everyone but I think the basic sentiment is true:

"There are too may ideas and things and people. Too many directions to go. I was starting to believe the reason it matters to care passionately about something, was that it whittles the world down to a more manageable size." -Adaptation

It's Alive!

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

I found a cool NPR story on a rediscovered stick insect, Dryococelus australis, off the coast of Australia! It was thought to be extinct after a British ship ran aground and the rats onboard made the island their new home and ate all the insects! Some intrepid sleuthing turned up a small population still surviving! Here is the original story:
http://www.npr.org/blogs/krulwich/2012/02/24/147367644/six-legged-giant-finds-secret-hideaway-hides-for-80-years

I love news (and better yet stories!) of rediscovered organisms. It's got a different taste than a story of a newly discovered one, although that is always exciting too. Tales of rediscovery have a a romantic bent to them don't they? The tragic loss of something from this world...stretches of time go by and then one day the local murmurs of the creatures' sighting! A team is hastily put together and sent out! The journey is difficult, expensive, long, tedious, sometimes unfruitful. But sometimes they are not and you have a rediscovered walking stick insect! A rainbow frog back from the dead!

Lots more cool science news. Have not had time to update this blog and there are few field excursions in my life as of late but hang on! Spring and Summer are fast approaching!

Egg collecting

This past Saturday I went with my lab to collect some egg masses. It turned out to be a gorgeous day and the sites were so nice! I could get used to this :)


These are Pseudacris regilla, Pacific Tree frog, eggs. These guys are very common and they have been calling for over a week now. The eggs are smaller than Rana aurora (below) and fresh ones have a pearly yellowish iridescence to them. They remind me of tiger's eye gemstones.
This massive blob belongs to Rana aurora, the Northern Red-legged frog. They quickly became my favorite after I saw some adults for the first time! They were the easiest to see as they are pretty large. Many of the masses had little white dots sprinkled on them like parmesan cheese. That is the evil water mold genus: Saprolegnia. Saprolegnia degrades dead tissue and protein! Ew! People mainly study it as it pertains to fish stock and the aquaculture industry but it can affect amphibians too!
This is a Northwestern salamander, Ambystoma gracile, egg mass. Thus far, the squishy-ness of the red-legged and pacific tree frog masses have not bothered me. They are clear, they look like clear jello/raw egg whites and they certainly feel like that. But these eggs are so weird!!! You see how it has a defined shape in this picture? The other masses are basically a loose blob. But NW salamander eggs are clustered in an oval shaped mass around a rigid reed/stick/stem of some kind. There was one pond that had submerged tree branches and there were TONS of A. gracile masses hanging off those branches.
Here you can see a A. gracile mass out of water. Notice how the shape keeps it forms? When you squeeze one it is very dense and hard. It's soft, squishy and hard at the same time. What?! I know. It's a paradox. OK, not really but still pretty neat!

A quick search revealed the jelly is deposited around the egg in layers and that without it, the egg can't be fertilized...Interesting indeed! The goopy substance is a mix of protein, some things called hexose and hexosamine, and other compounds. I was surprised to see there was not that much stuff out there about the jelly-like substance. I will have to dig around to find out more about it.

In other news, meet my new friend Phaeton:



He is a Northwestern salamander! Yes so he came from one of those dense egg masses! He is two years old (He might be a she, I really have no idea at this point but I'm calling Phaeton a boy). They collected him and his siblings and took them back to the lab where they started eating each other! Typical. So they separated and housed them in plastic cups. They don't do anything with them so me and two other grads students from another amphibian lab took them as office pets. He was the most active of the three constantly swimming up and down in the cup and peering up at me, so I named him after the Greek mythological figure Phaeton. Sharp readers might remember this name from an old blog post about the genus name of the red-tailed tropicbird, Phaeton rubricauda! I thought it was fitting. Although I do not intend to strike him down with a thunderbolt as Zeus did!
In his new tank he has a lot more room to swim; the glass walls let him peer out at his surroundings for the first time! He likes to perch on top of the white tubes sometimes when we have one of our telepathic mind conversations. Right now his home is pretty sparse, just a tank with his 2 white hiding tubes on the bottom, but I am changing his water tomorrow and have brown gravel and a fake plant waiting for him :D