The ecology of urbanization and things that want to eat you (in the US!)

Here's a science blog about a doctoral student studying puma prey in California. I've been around big cats in the Amazon but that was nothing compared to these cats - jaguars don't eat people (that we know of). 

I really hope they can pull of the wildlife highway tunnel and that starts a movement. 

Winter is coming

Lots of geese in the sky today and freezing rain tonight.

Winter is coming. And working on the "last" game of thrones book as well. My nerd fantasy is to finish this in the snow at the Jacobs property. Thankfully I'm a horribly slow reader. So it might be the end of January when I get there.

The stuff of bird nightmares

Here's a blog post about Eleonora's Falcon (Falco eleonorae) and a unique behavior for a predator. 

The authors of the original paper report that this species caches live, but disabled, prey (small birds) in rocks, purportedly to keep the prey fresh. The falcons disable the prey by removing primaries (outermost 9-10 wing feathers) and retrices (tail feathers) and stashing them in rock crevices. 

I think a commenter in the blog brings up a very good point. Injured prey are very likely to seek out crack and crevices and hide. My students will tell you that if you give a the smallest crack in your hand you'll lose the bird. Like mice, many birds are extremely adept at moving with their feet and I'm skeptical that birds could be held in the manner described.

I suspect that the falcons are exploiting the escape behavior of the birds. Still, and to entirely anthropomorphic, this stuff has got to be terrifying for a small bird.

Goals for winter break

I think having goals is a bad idea. Does anyone ever complete a lists of tasks beyond picking up bread and going to the dentist? So this goes against my better judgement. I have until January 18 to get a bunch of stuff done including 

• Organize the Galapagos trip including a few days in Ecuador
• finalizing logistics
• fundraising 
• Organize the Galapagos course
• what we read and when
• Update Biostatistics notes
• move from OpenOffice to Google Docs
• Update biostatistics lab
• need to spend an afternoon turning verbal hypotheses in equations (this is how I approach statistics when I see a problem for the first time). For example, you might ask "what is the relationship between getting diabetes and the amount of sugar intake and exercise"  ->  p(diabetes) = sugar + exercise 
• Finish the West Georgia manuscript on urbanization and birds
• intro needs work
• results and discussion and graphics (ugh).. why is it that paper is so damn hard to work on? 
• Contact... I totally forgot what I was saying 
• Update the Academic Planning Committee website to include a clickable flowchart 
• Send out the survey of undergraduate programs in ornithology survey to start building up a database of ornithologists at undergraduate institutions  
• Get out to birdwatch four times

Robin singing that strange whistle as a whisper

Mid-December should be the time of the year when most birds are silent but this afternoon there was a robin in the neighbor's yard whisper singing. This is when birds practice their song but at a very low volume. So it was late for behavior. But what was even more interesting was that he was singing/calling this high pitch whistle. 

I had to laugh because I thought it was a nose whistle at first. 

Puppetry and coelacanths

I find these shorts amazing in terms of the artistry and the story. 

http://www.nytimes.com/video/opinion/100000004105667/animated-life-coelacanth.html

Grading palooza begins

Been farting around all day with chores and checking emails. Time to settle down with a cup or two of coffee and get grading. Once done - I'm done. And the writing begins.



(I'm also going to finish the last Game of Thrones book)

Bibliogasm

This morning I was given access to a room on campus with some very special books. Here are some images

Newton's Principia from 1755

Einstein and Infeld's The Evolution of Physics  (signed) 

Darwin's Variation of Animals and Plants

Sitwell's Fine Bird Books 1700-1900

This quetzal page is 4 feet long. 

Darting doves at dusk

My favorite time in the winter is dusk: the way trees are silhouetted and the quietness that comes to the city (even Wilkes-Barre). Last night a flock of snow geese flew overhead - high enough to be out of sight. Moments like this are magical. 

Also, two pairs of mourning doves flew past - not at a normal speed but as if they were being pursued. But no pursuer. I've seen this many times before and always at dusk. Is this part of pair bonding or courtship? Are they trying to escape a predator that was waiting for them to roost at dusk. 

Flame Bowerbird: amazing courtship display

The Flame Bowerbird (Sericulus aureus), a species native to Indonesia, is a member of the the Ptilonorhynchidae - a group of species with very elaborate courtship displays. I have seen this BBC video before and I may have already posted it here. So it goes. I find it remarkable that this behavior and a host of others are coded in this tiny brain.

20,000 views... wut!? wut!?

Hey, I just noticed I went over 20,000 views!

That's awesome! Thanks so much. 

This semester I've been focused on teaching and getting my notes in order online as well as committee tasks. Semester ends in 9 days and I'm ready to head out to the woods and doing some writing. I applied to the study abroad director position and I have an interview with the deans tomorrow. Nervous but I have nothing to lose and I think I have a great vision for the position. 

Reading over my daughter's freshman bio report. Holy cow it's good. 

More later and thanks again peeps. 

For your good behavior.. a pair of Ivory-billed Woodpeckers. 

Kiwis, not the fruit, eat robins eggs, but not those robins.

To a yank like myself, Kiwis are completely mysterious. They're part of a group of birds called ratites, which includes ostriches, emus, and rheas. I tell my classes that Kiwis use their long bills to probe the ground for arthropods. 



Apparently, kiwis have a side to them that was unknown to ornithologists. Apparently, like many many organisms, they enjoy bird eggs. In this case, the New Zealand Robin was the victim. 

Here is a link to the video http://phys.org/news/2015-12-footage-captures-kiwi-robin-revealing.html

What's the most common vertebrate on the planet?

Fish are the most species rich group of vertebrates and there might be over 200,000 species once we're done exploring. But what species is the most abundant. If you look around you it can't be seen. You need to look in the oceans but even a boat won't help. The most abundant vertebrate is a tiny fish deep in the ocean. Here's an excellent story in the NYT about them and deep ocean research. 

Watercolor of Darwin and crew on the Beagle

This is an interesting story in Artlyst.com. There was an artist commissioned on the H.M.S. Beagle that painted a picture of the crew. 

Unfortunately the story doesn't tell us what Darwin is saying. 

A visit to the bird collection at the American Museum of Natural History

Yesterday, I went into NYC to see the collection as the American Museum of Natural History. I didn't go through much of the collection. I decided to sit and work for all but the last 30 minutes of my stay. 

Hard to believe, but despite the view of Central Park and being in the presence of the greatest collection of birds in the world, I reviewed a manuscript that I'm on. What was I thinking????  I've learned that I need to take advantage of those moments when I can concentrate. So it goes. 

Before, I was left to work, one of the bird curators showed my chair, his wife, and the dean's receptionist the type and extinction room. This is the second time I've been around Ivory-billed Woodpeckers and it was just as exciting. Below is a pair of Ivory-bills. The male was from Madison Parish, Louisiana, which is along the Mississippi River near Vicksburg, MS.

The other bird I wanted to see was Topaza pela, the Crimson Topaz, of the Amazon Basin. The males of this species hover over ponds and show off their brilliantly green gorgets and crimson bellies. I saw one of these leks near a pond near a camp called Dimona, north of Manaus. 

After the museum, I met back up with colleagues and visited the 9-11 Memorial. Beautiful but the horror still resonates within my brain. They planted swamp white oaks near the site and we picked up a few. 

Pigeons trained to detect cancer

A paper just came out in PLOS ONE that showed that pigeons can be trained to look at histological slides and diagnose cancerous cells. Amazing stuff. 

The authors, however, make a crucial mistake by saying that they have vision like ours. They don't. Birds' eyes are superior in many ways including spatial resolution, color resolution (they have UV and see more gradations than we do), and a higher flicker rate. 

Knowing this perhaps they could incorporate higher res images that include UV and they could increase single bird efficiency.  Though, even with standard images, a flock of pigeons are 99% accurate! Amazing. 

because I can't resist being a smartass

Some context: 129 people were killed by ISIS in coordinated attacks throughout Paris on November 13, 2015. 

168 people were killed by Tim McVeigh and Terry Nichols - both of Scottish descent - in April 1995. Using Facebook logic we should (1) demand Scots to apologize for their actions and (2) have a moratorium on Scots immigrating to the US.

#keepAmericasafe

Happy Friday the 13th

Last week I was walking down the hallway and saw a bunch of crows flying just next to the building and I went out to investigate and saw this. 

I didn't want the bat to get stepped on or bite a pedestrian so I let it bite a stick and then I lifted it up and off the sidewalk. Of course I picked the stick back up before realizing (like an idiot) that the bat might have rabies and that I might have just exposed myself. 

So I washed my hands and crossed my fingers. One week and feeling (mostly) fine. 

The weevil inside you must die!

So I just learned how to do survivorship analysis. I had no idea how flexible they are. I thought they were just for looking at the effect of some treatment on survivorship rates but they can be applied to such things as time until you have your first child, the effect of being on unemployment on getting a job (here, if you are "killed" you get a job), and anything that is modeled in terms of "time to X".

I was given a data set that was weevils placed in different soils and monitored for 8 weeks - most had died at that time. A previous study showed that weevils survived much better in soil with oak matter so we did another test. Not super happy with it and I'll explain after I impress you.

So weevils do survive much better with soil associated with oaks - and white oaks are not very oaky - in terms of the amount of tannins they produce. In soil from under a black walnut the weevil larvae are whacked. 

Significant results!  Yayyyyyyy.

Hold on a moment. Weevil larvae stay in the soil from October until August so why are all ours dead after 8 weeks?  I'd say the whole experiment is amiss. Unless of course, millions go into the soil and only hundreds emerge. Nobody freaking knows. 

Your halloween treat: acorn weevil larvae!

Students have been cutting up acorn larvae and gathering data for a 20 year data set. These larvae would normally chew their way out of the acorn and go into the soil for a year (or two or three - nobody really knows). We just started looking at soil type to see if that affects survivorship and we're going to start barcoding to see if there are new species out there and to see if there is some sort of specialization out there. 

Home economics: II

One downer about being a graduate student for so long is that you become behind financially - not all of us - but many of us. So, by the time our friends are thinking about a second home or retirement, I'm thinking about living like I have a job. 

The home we live in was flooded in 1972 with Hurricane Agnes and water reached the second floor. We just removed all the paneling and random pieces of wood and were down to the studs. Then the electrician came and the inspector after that. Initially they said two weeks for the whole project but we're in the third week already and we just finished putting up the insulation last night - then immediately went to bed. Who knew insulation became so heavy after three days of installing it. 

The guys are at the house to put up the sheet rock and that is supposed to take three days from start to finish. Exciting just to start the next phase. 

Here's what it looks like with insulation (and you can still see mud on the studs). 

Pin oaks and birds

I remember seeing a bird talk that dissed pin oaks as being a trash species because it was not important to birds. This was in the southeast and pin/willow oaks are super abundant when you don't have fire. So, for some time, I just didn't like them.

But I've made a 180 on pin oaks and I realize they are hugely important to a number of birds in the northeast US (and probably elsewhere pin oak occurs) and probably host a number of invertebrates and other unpopular but crucial species. 

Today I spent an hour on the roof of Cohen and had three species come by. Blue Jays were there grabbing and flying off with several acorns in their crop. The one group of jays was coming from the other side of the Darte Center, which is 500 m away. They're flying over open areas where they could cache. Perplexing!

Crows ignored me and came by and ate a few acorns and took off. A titmouse looked be pounding an acorn to open it - not sure if it was successful. Last year there was a Red-bellied Woodpecker carrying off acorns. So pin oaks are not the fig trees of the tropics (which are known to be eaten by anything that can make up a tree) but they must be crucial to many birds.

Archosaurs class at home

Yesterday [last week.. not sure why this didn't post] we had class at the house and the goal was to get kids to handle wild birds and show them how to get blood, make blood smears, turn blood smears into slides to look for blood parasites and observe different cell types, and get blood in capillary tubes that get centrifuged and we measure hematocrit. 

We ended up catching three house sparrows, a song sparrow, and two white-throated sparrows. Best part of the day was watching the kids I've trained work with the kids in the class. 

DNA barcoding: a road map

I went to a DNA barcoding meeting a few months ago and I've been more inspired to integrate this technique into my own research. I've been working on a food web project but I could also use this to identify parts of birds and the bits in a bird's diet. 

The first application would be to identify the invertebrates we've been catching for our grassland food web project. My idea was that we just needed to get a bit of tissue, amplify the DNA using PCR, send it off, get the sequence, ID the species, and DONE.

If I have gone through with this I could get our critters identified but with lower confidence and the work with be of little use for other researchers. A shame and near waste of work.

At the barcoding meeting, we met up with a Smithsonian scientist, Caroline, that agreed to come up and discuss with us barcoding issues. So, last week, she came up and gave a two day workshop for Ned and I and a number of students. It was incredibly enlightening. We found (many) issues with our protocols and we were pointed to a number of resources to help us with technical issues. More importantly, we were given a work flow that greatly expands on the flow I outlined above. The biggest missing piece is building a library of local organisms that are identified independently of DNA barcodes. These organisms you barcode and then use a reference. This seems a bit circular (and it is) but you can use your reference collection to identify bits of organisms or organisms in other stages, such as larvae and eggs. This sounds simple but it means getting specimens and organizing them. Organizing them. That is completely new to our lab and will be a challenge. But it's a challenge I'm willing to take up. One of the first things to do is to create an outline for the whole project and I'm doing it here. 

So, the workflow is this, get specimens (mostly, go out and collect insects), give them a number, get them identified, pin them in an organized way (presumably by order), bar code a small bit of them, link the barcode to the specimen. Now unknowns can either be ID'ed through the vouchers are barcoded. Everything is organized through BOLD Systems.

It was a hugely useful workshop and Caroline was a blast. She stayed at the Hillard House, which has an awesome breakfast menu. Students enjoyed the workshop as well and I hope they're inspired as well. 

Home economics

We're gutting our downstairs. This means tearing up the carpet, tearing down the panels, the plaster, and the plaster backing. It's mess. 

Our house was flooded in 1972 during Hurricane Agnes and you can still see mud from the flood on the supports. We're going to tweak the electric, insulate, sheet rock, and paint. Looking at a finish date of Thanksgiving. 

Music to write research papers to

I was introduced to the music of Marissa Monte in Brazil in the early 1990's. Great stuff. 

A trip to the American Museum of Natural History: Part 3. Dinosaurs

Last Tuesday I spent the day at the American Museum of Natural History and had my Archosaur students in for some of it. Technically, I think we spent most of our time on the bus and if I'm going to do this again I think I'll take a van. I did this once and, except for the Holland Tunnel, it want very well. This was both expensive and time consuming. Live and learn. 

I posted on the type specimens and other birds and I ran through to get pictures of dinosaurs to integrate into lectures. Never enough time. 

Here are some of the better pictures. If I had a complaint about the museum it would be this - so much glare. So it goes. 

Acanthostega - nice intermediate between fish and amphibians

Allosaurus manuss

Archaeopteryx - close enough to dinosaurs!

Deinonychus manus - note the reduced number of digits and carpels

Deinonychus skull - built for ripping your face off

Diatryma - a bird, taller than me and three times as kick ass

Plateosaurus - an early quasi-bipedal sauropod - note the reduced outer digits

Prestosuchus - early archosaur

Gallimimus - very bird-like dinosaur

Temnospondyl - early amphibian

T. rex!