So polychaetes are funny looking eh?

When I was a lowly museum technician working on the Antarctic invertebrate collections, I remember the funny fat worms with copper-colored bristles. This was my first introduction to polychaetes, aka bristleworms:

Meet Hermadion magalhaensi, an Antarctic representative. I don't know if we are looking at the bottom or top...

Poly + chaetae = many bristles, they always reminded me of those bristly brushes one would use on horses or someone with really fine thick hair. That would be one expensive brush because these critters live mainly in the deep ocean and you would need a lot to make a full brush. Polychaeta is a Class within the larger Phylum Annelida (segmented worms; not to be confused with non-segmented worms, the Nematoda, which include your intestinal parasites!*). Anyways, they are a pretty adaptable group of critters, some live in the uber-hot, chaotic cities of hydrothermal vents, others settle on the cold cold lonely abyssal plains. Some live in self-secreted tubes! Some are free-living! Some are parasitic! You get the picture, very diverse. The ones most people will be familiar with are the christmas tree worms:

"Cuz dey purdy!"

But if you look at one real close up it is a completely different animal:

This one looks like a hungry baby.

This one looks worried. Are those sensors of some sort? The picture is more amusing if I pretend they are eyes. Unfortunately, you don't get much in the way of actual information in this online gallery, still amazing SEM images.

Animal mouths are so weird. The incisor-like teeth and puffy cheeks of the former image actually made me flashback to a critter we had our students learn in Vertebrate Biology lab: pocket gophers!

Family Geoymidae. Look at those claws!

In the Order Rodentia, blah blah blah...burrowing, yup yup....ruining vegetable gardens.....external cheek pouches....Excuse me, what was that last one?? I had to do a double back when I came across this curious aspect of their anatomy. Turns out the 'pocket' in pocket gopher refers to cheek pouches they stuff food in on the outside of their mouths! Being so, they are lined with fur!

Nota bene: see how the lips close behind the front incisors as to not let dirt get into their mouths whilst digging.

I saw an old paper laying out how this might have happened: a particularly deep-dimpled ancestor gopher might have had a nice life because it was able to haul more food. It's babies also had this trait which was carried down through more descendants becoming augmented to the pouches we see today. Evolution leads to some weird forms doesn't it? While grading final exams earlier this month one student had a good zinger that went kind of like this: "Evolution is acting upon all of us, and frankly, I don't think it has any idea what it's doing."
So true :)


* Have you ever looked up how many animal phyla there are? A number like 14 or 20 sounds reasonable right? WRONG! There are currently 35!

Things around me 1

Am home for Winter Break and today I took a long overdue walk in the neighborhood. This isn't an area I grew up in so I had no idea I lived right behind a park! I left my binoculars AND camera in Oregon so all I have is my iPhone...but I am constantly surprised at the crisp images I can take from it. Here are some from my walk:

Who made these tracks?

Of course I ran into some Canada geese and some mallards. Oh the silly squishy sounds of their bills pokin' around the mud.

I was attracted to the shininess of the beetle shell but, alas, it had no head.

These thorny branches grew through this white shelf fungus!

Some kind of little puffball mushroom, there were tons covering this fallen tree. The little holes in their heads means they have released their spores! How cool would it bee to see it like this (!):

This is from Wikipedia

I have no idea what this is. It is kind of hard to look up these tree infections online. The bark itself is not split open, the growth just makes it look like it is. You'd think there would be some "Common tree diseases of Virginia" website...however after much sleuthing I did figure out the following enigma:

So these cork-like growths are quite common for a type of tree called a hackberry. They are pretty common elm-like deciduous trees and apparently grow these when they are young but smooth them out later. I like how the conical ones look like limpets.

Anyways, looking up hackberry was pretty interesting. I had never heard of it before but it is pretty common in northern temperate areas. Super low maintenance in terms of soil type, weather, rainfall, shade, etc. It's got soft bark so its not really used commercially for furniture or building though it is sometimes used for cheap furniture. It is in the elm family (Ulmaceae) and the overall shape/size/leaf is like an elm:

I keep seeing it referred to as a good 'urban tree' though it's features (especially the warty growths!) are not that spectacular. It is a pretty easy-going tree though in terms of living conditions. What a polite, homely tree!

Haiku inspired by National Geographic photos

National Geographic's Photo of the Day: Best of October 2012 (Dragon's Blood Trees, Socotra)

The soft moon rises
The trees stretch, sigh heavenly
Blanketed by light

----------

National Geographic's Photo of the Day: Sep 30, 2012 (Muckross Lake, Ireland)

Thin glassy water

To sink slowly, completely

Cool still - dark silent

*Update Dec 18, 2012 -- "Haiku" is the singular and plural form! I forget who mentioned this to me but the title has thus been changed

The romantic twist of beta sheets

Thomas Cole's Romantic Landscape with Ruined Tower

So I am going further and further into the genomics rabbit hole and I am loving what I am finding! The genetics I remember encountering in undergrad was so dry, so static, so...lacking in dynamism!
How does one compete with the image of an Ecologist, that adventurous, jungle/island/mountain/tundra/desert/reef/volcano/ocean-bound Earth trekker? Any bench-bound Molecular Biologist pipetting fluids from one tube into another tube would seem rather tame, right? I certainly thought so.
But little by little, the more I scratched at the surface the more wonders and curiosities I uncovered. And now, years later (eons it feels like!), I am discovering how completely wrong I was. Somewhere in between learning about the mysterious structure of chromatin and reading about the puzzling habits of enhancers...I think I fell in love.
This world is moodier and more chaotic than a westbound journey 'round Cape Horn!

But I digress. The reason I even thought to post tonight was because I uncovered a delightful bit of protein trivia:
So first off you need to understand that the ability for a protein to function depends on how they fold. There are many different levels of folding which I will not get into too much now, but know that this folding ultimately occurs due to the sequence of amino acids that make up that protein*. As you would imagine, there are tons and tons of proteins that perform diverse activities (some recognizable ones: hemoglobin, insulin, collagen, etc). You would think that there must be a seemingly infinite number of ways to fold a protein in order for it to carry out its specific task - and you are right...but fear not, for there is order in the madness! Those complicated bunches of amino acids can actually be divvied up into many smaller, recognizable structures called structural motifs. Some structural motifs are more common than others and thus can be seen in many different kinds of proteins. One of these is called a Greek key motif:

A snapshot of a segment of amino acids in this protein show us there are 4 connecting beta sheets**. This looping pattern is reminiscent of the common Greek design, the Greek key and is thus aptly named:

Added Oct 12, 2012

This was described and named by Dr. Jane S. Richardson*** who has been a pioneer in the field of protein structure since the 1970s. Lovely, eh? I have to wait til I get on the school network to download the paper but I can't wait to read it! I love finding things like this in science, especially in a field that is not known for quirks. Things like this are just so delightful to find. Obviously this is a reflection on how much I love etymology and taxonomy, there are always so many hidden relationships in words and names. Maybe one day I will discover something and get to name it after some semi-obscure thing students in the future will be compelled to look up and spend over an hour researching!






*So proteins all start of with their DNA sequence which gets transcribed into RNA, spliced [edited] into mRNA, which then feeds into a ribosome that then translates that string of nucleotide bases into a string of amino acids which then scrunch up and twist and fold according to how they came out!

** beta sheets are flat configurations (contrast that to the alpha helix structure)

*** Remember seeing all those 3-D ribbon images of proteins from your textbooks? Well, you can thank Dr. Richardson for those! She created those ribbon diagrams that are now ubiquitous in science textbooks:

Triose phosphate isomerase hand-drawn by Jane Richardson in 1981

Richardson, J. S. 1977. B-sheet topology and the relatedness of proteins. Nature 268: 495-500.

My darling Darlingtonia

For a kid, animals rule. Animals fly, run, hunt, sing, dance, hiss, attack, nap, swim, learn, and even snowboard. Plants are just there for landscape and food*. However, there are certain plants children love because they break the typical mold of what they think a plant should be...

CARNIVOROUS PLANTS!

Ok, maybe not anything like what Rick Moranis encountered on the streets of New York in the 1980s but still, quite striking in their own right:

                   

                     

But let's start at the very beginning, with names. 

King              Philip         Came      Over        From         Geneva    Switzerland. 

Kingdom -> Phylum -> Class -> Order -> Family -> Genus -> species

Carnivorous plants fall into three families: Sarraceniaceae, Nepenthaceae, and Droseraceae

Droseraceae: seen worldwide, these are your venus fly traps (photo: above left)

Nepenthaceae: Old World family (South China, Indonesia, Australia, Philippines, etc), tropical pitcher plants (photo: above right)

and....

Sarraceniaceae: New World family (that's where we are!) with 3 genera; two are in North America and they are roughly split east + west coast. Plants in the Sarracenia genus live on the east coast and has about 8-11 species while Darlingtonia is the west coast representative with just one species...

Do you love my dramatic lighting? It looks as though it might move! Also called the Cobra Lilly for obvious reasons. 

Darlingtonia california, the moody only child of the genus, is a rare find in the field. It was initially stumbled up on by the a certain William Brackenridge, assistant botanist of the U.S. Exploring Expedition on Mount Shasta, California in 1841 (but let's face it, he was pretty much the botanist on the voyage...)! My former supervisor when I was interning for the Wilkes Expedition project told me that his journals revealed he had thought he found a new species of Sarracenia, not realizing he was "collecting the most iconic new species of the U.S.Ex.Ex."

It grows in northern CA and southern OR but the very tip top northernmost reaches of its range can slip past the halfway point up the coast of OR. It was this northernmost population I paid a visit to recently with my botanically inclined friend.

These plants are weird and pretty high maintenance:
- prefer serpentine soils (rich in heavy metals and lacking in nitrogen, phosphorous, potassium)
- needs cool running water (probably from a mountain)
- and likes ample sunshine

You can find them in bogs with the afore mentioned properties. The little population we found did not have that much sunlight (but enough) so their characteristic red color was not present. They still proved beautiful specimens:

This whole thing is actually a modified leaf! What you don't see is the whole plant which consists of many stalks radiating out of the center.

The mustache tips secrete a sugary concoction irresistible to insects! They travel up and into the dome of despair looking for more! Note the 'skylights'...

The 'skylights' are areas of thin plant tissue. A bug might try to leave through these false exits but will eventually tire and fall into the murky depths below... 

The skylights are really nice huh? Love how they attenuate down. 

You can't tell form this picture but the stalks grow in a way so that they don't overlap each other. They twist left or right as they extend upward and lean outward. Some stalks I saw were over a foot tall!

The fun thing about this particular species of pitcher plant is that it does not collect rain water to fill its pitcher. Other pitcher plants you see have an open container while this one takes water from its roots depending on how much dead organic stuff is inside. It also does not have its own digestive enzymes to eat the insects but instead relies on bacteria living in the pitcher to do the job.
So...kind of the opposite of what other pitcher plants do I guess? They just have to be different. Anyways I am discovering there is so much more to these plants but this post is getting a little long in the tooth as it is so I will stop. But if you want more Darlingtonia reading go here and here and here.

Til next time!

* My views on plants have changed since 1993.

Origin of Thoughts!

I took one Philosophy class in undergrad, Knowledge and Reality, and the only thing I really remember is a question our professor asked us on the first day: How do we think?

I still remember, very clearly, the answer was finally shouted out from the back-center row of that amphitheater-style room: in language! Our teacher started off the term by reminding us every thought we ever had, and ever will have, has been constructed and shaped by our language. And isn't that revelatory? That your ideas exist (and exist the way they do) because of language? What about people who speak many languages? My American Sign Language teacher told me the moment you know you have mastered a language is when you begin thinking in it, even sign language. Maybe those lucky folks have very expansive thoughts?
And what if you had no language? What if you were born in the forest Nell-style with sustenance but no society? What would you think? Could it be all instinct and sensation?...

Language is a particularly interesting facet of human history. Apparently, concerning the origin of Indo-European languages* there are two camps:

Camp Steppe - those languages arose from people inhabiting the steppe region north of the Black Sea! They spread out 6000-4000 years ago with their horse-drawn chariots and conquered left and right! Arrr!

(Most people believe this one)








Camp Anatolia - a gentler narrative; these folks are from modern-day Turkey, below the Black Sea. They spread their plowing secrets and language during the agricultural expansion initiated about 9000 years ago.







As summarized in this new NYT article, researchers used some fancy statistical program (this included scoring words known to be heavily used and thus do not change much language-to-language or through time, i.e. "mother") to determine that point to be Anatolia. Score one more for talkative farmers! What is really cool about this project is that they used an approach originally developed to track the origin of viruses!!!! It makes perfect sense right? Viruses evolve and spread all over the globe just like languages. And with each divergence, the new lineage changes a little bit whether it is a nucleotide base pair in a gene or a letter in a word! And so the lineage rolls on and on and becomes ever more removed from its parent over time. It's easy to see how with some savvy statistics you could easily build up a family history of sorts.

Mother was right, everything does back to math. Math can explain the world if you know what to do with the numbers :)

Uzungöl lake near the northern coast of Turkey lining the Black Sea. These researchers do not think the Indo-European origin is from here even though it looks like a lovely place to call home.

* Indo-European languages: English, German, French, Bengali, Russian, Urdu, Hindi, Punjabi, Spanish, ... there are over 400! Somewhere in the 16th century when there was enough travel taking place between the two, people started noticing uncanny similarities between European and Indian languages - thus was born Indo-European linguistics! The elder language from whence all other Indo-European languages come from is called Proto-Indo-European, abbreviated PIE. When I started reading about the topic I kept seeing PIE everywhere and it was initially very confusing.

The Regulars

Because I know you are wondering this fine summer evening, here is a short introduction of some of the regular amphibious inhabitants of Oregon:

One of our outreach animals. I want to do this set over again
and really capture the color and pearly sheen they have about
them. Note the sticky toe pads for climbing!

 Pseudacris regilla (Family Hylidae-tree frogs; Pacific treefrog, Pacific chorus frog): quite numerous, these are the ones you will hear calling persistently and loudly. They are smallish (up to ~ 5 cm says Wikipedia) and are climbers, hence they sticky toe pads. I can tell you they are hard to count and transfer because they are always moving and love to trek to the highest spot. Much like goats.

This is our nice copper-tinted one! If I had a favorite...

They come in simply marvelous hues, the most flashy being a Kermit the Frog green but they can also appear in browns, golds and even, to me at least, a bit copper-ish. (They can also change colors...look that up!) A lot of the ones I have seen in the lab have a cute little Y-shaped mark on the tops of their heads between the eyes. Another feature I like about them is the dark streak that runs through the eye. Sometimes its splotchy and sometimes it is so sharp and smooth it makes me think of Cleopatra's eyeliner!
They are found in largely in the US west of the Rocky Mountains and poking into Mexico and Canada.

Rana cascadae (Family Ranidae; Cascades frog): This is a species I don't have too much familiarity with. They are a ranid species (Rana = Latin for frog) which means they are considered "true frogs," that family has a huge worldwide distribution and they are what we typically think of as frogs -  large sized, strong hind limbs for jumping, and webbed-feet for swimming. Those general characteristics make for a frog that spends much more time in and around the water.

© 1998 Harry Greene from AmphibiaWeb

The Cascades frog does not have as delicate an appearance as the treefrog. Indeed, the first time I handled Cascades frogs I was unimpressed with their bumpier skin, grayish-brown coloring, and haphazard smattering of spots. But, I have grown to admire their spots and hardy nature. Look closely at the photo, the spots are shaped much like the spots of a leopard, no?
Oh, and be careful, they are plucky individuals and quite accomplished escaped artists!
Their range overlaps with P. regilla in the Cascades Mountain range but is much more restricted. Their populations are presently in a decline for a number of usual reasons: habitat loss, non-native predators like some fish, a water mold that attaches to and kills egg masses, etc.

Rana aurora (Family Ranidae; Northern red-legged frog): Another Rana! I liked this frog even before I ever officially met one. That name. What a gloriously seductive name! Aurora, the goddess of the dawn - and here is why:

That strawberry red flush through the legs! I love it! This one might be a young one but there are photos of some with an intense red flush extending all through the legs and up the sides of the stomach creeping on to the backside! So much color!
Like other ranids they are never far from water, smooth skin, strong and long legs for jumping, webbed-feet. Their range includes the western portions of Oregon, Washington, with some populations extending into California and the west coast of Canada.
The Northern red-legged frog is not a species of concern but their close cousin, Rana draytonii, the California red-legged frog is. R. draytonii used to be a subspecies of R. aurora but has now been elevated to a separate full species status.

Wikipedia
See the circle behind its eye? That is called a
tympanum, the ear of the frog.

Lithobates catesbeianus (Family Ranidae; American bullfrog): Ah yes, the uninvited party guest. The philistine who tags along and drinks all the beer, eats all the food and picks fights with everyone! That is the reputation of the bullfrog in amphibian circles.
They occupy a variety of watery environments and can/will eat anything they can stuff into their mouths. In fact, stomach contents have been known to include birds, rodents, and snakes among crazier things! And because they are fairly large (~4-6 in) they not only compete with native frogs for food but will also eat them. 20,000 eggs per egg mass also can't hurt its persistence and spread...
Native to the midwest-to-east coast portion of North America as well as Mexico and Canada, it is now found every where else it seems: Europe, Asia, South American, Hawaii, and is spreading. Notable exceptions are Australia and Africa. They were/are carried outside their native range mainly for food purposes but also in the pet trade and by accident. You wouldn't think it, but a lot more people in the past ate frogs. Back in the late 1800s when the west was filled with hungry gold miners with a penchant for frog legs, someone had the grand idea to ship in tons of bullfrogs from back east to rear in frog farms. Well, you can kind of guess what happens next...


Anaxyrus boreas (Family Bufonidae; Western toad, Boreal toad): Bufo!!! Latin for toad, Bufo are great. After spending so much time looking at ranids and hylids, playing around with toads is a welcomed change. So what is the difference between a frog and a toad? Well, you know a bit about frogs from the species described above, especially the true frogs in the genus Rana. They tend to have:
     - smooth moist skin
     - strong hind limbs for jumping and maybe climbing
     - buggy eyes!
     - lay eggs in large clumps
     - have webbed-feet
     - remain near water

Toads meanwhile in the Bufonidae family, are a bit different for many reasons:

The second goat parallel tonight!

     - drier, thicker, wartier skin
     - stockier shaped body, not tapered at the waist like a    frog
     - short, weak limbs for walking not jumping long distances
     - can be away from water
     - poison glands (!) called parotoid glands
     - lays eggs in strings
     - really cool horizontal pupils...much like...a goat!
 

Anaxyrus boreas are found in the southeastern tip of Alaska, the western half of the US and Canada, and the Baja peninsula. Though they can be found in good numbers around Oregon, overall the species is in decline due to western populations in Colorado, Wyoming, Montana, etc.
As noted above they are quite different in appearance from frogs. I remember after handling and measuring so many ranids for a project when I moved onto A. boreas it was like encountering an alien. Similar body plan...but everything about it was weird: the stocky torso and non-waist, the thin, wiry arms that walked rather than leap, and peering out at me - a tiny, short, rounded face. After working with certain taxa for some time you get habituated to the appearance of it. It is a cool feeling to realize you have memorized its form well enough you can clearly see the morphological departures when comparing it to a similar creature. I remember it happening for all sorts of snails and birds for me in the past :)

A. boreas metamorphs also have what I like to think of as "pants." The skin of their underside changes abruptly from a light speckled color to a darker color right above the waist. Like they are wearing a pair of trousers. I shall snap a picture tomorrow. Until next time!

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: