On deck for the week

For the week of Feb 1, 2016

• I've been putting off letters of recommendation until tomorrow. Need them for pharmacy school (1), student ornithology awards (2), and graduate school (1). 
• Meeting with the provost tomorrow to outline responsibilities for the study abroad directorship. 
• Moving biostatistics lecture material from OpenOffice docs to Google docs (easier to share and collaborate). Ditto for the lab material 
• Need to remember what Ned said to do with the student workers
• Figuring out how I'm getting to Auburn-Montgomery to do their program review
• Work on the math/stats/CS skill document (what we want our bio majors to know when they graduate)
• Need to firm up the Ecuador trip to Wildsumaco research station

Notes on Voyage of the Beagle: Chapter II

Students are supposed to be reading Darwin's Voyage of the Beagle for the class and taking notes. Tonight we're covering Chapter II. We're also supposed to be reading a text on tropical biology but my text hasn't arrived yet. 

To give some perspective on time, they left Devonport on December 27, 1831. Darwin was two months shy of his 22nd birthday and never left England before. 

Chapter II starts April 4, 1832, a year and five months after leaving England. This chapter primarily covers a side trip by Darwin while the ship charts the area around Rio de Janeiro. He meets up with a fellow Englishman and rides off to explore the countryside. 

The first striking passage is about a village of runaway slaves. They were discovered and soldiers dispatched yet "one old woman, who, sooner than again by led into slavery, dashed herself to pieces from the summit of the mountain. In a Roman matron this would have been called the noble love of freedom: in a poor negress it is mere brutal obstinacy."  I know Darwin as a champion of antislavery. Perhaps not yet or maybe he's giving a third-person opinion on the matter. 

Darwin and his party continue to ride along the shore also described here. There is an entertaining exchange when he camps along with way and asks the local property owner if there's anything to eat. The owner responds that he can have anything Darwin desires but he's out of everything that Darwin asks for except for a chicken that they beat to death with a rock. 

Moving on into a coastal forest he sees wonderfully tall forests with parasitic plants, including many orchids, egrets, herons, gastropods, and "ants' nests, which were nearly twelve feet high." These are actually termite mounds and there's an example here. There is a brief mention of vampire bats, which harass horses. 

Coffee is grown in this region and each tree produces about two pounds of coffee beans. And Darwin gives a brief description of mandioc or cassava. All the parts of the plant are eaten save the toxic juice, which much be removed from the root before tapioca and farinha are produced. Apparently slaves work these farms and "I have no doubt the salves pass happy and contented lives."  Oy vey Darwin. 

The next story about slavery was "I was crossing a ferry with a negro, who was uncommonly stupid. In endeavouring to make him understand, I talked loud, and made signs, in doing which I passed my hand near his face. He, I suppose, thought I was in a passion, and was going to strike him; for instantly, with a frightened look and half-shut eyes, he dropped his hands. I shall never forget my feelings of surprise, disgust, and shame, at seeing a great powerful man afraid even to ward off a blow, directed, as he thought, at his face. This man had been trained to a degradation lower than the slavery of the most helpless animal."  Maybe it's sinking in. 

He's then off to Socego, a beach and popular destination. There he encounters an incredible forest, where one man is making a 70' canoe. SEVENTY FEET! The trees are huge and the lianas (woody vines) are also huge being 2' around. 

And this I understand about the rainforest "the attractions are so numerous, the he is scarcely able to walk at all." 

Of all the critters, he focuses on the planarians (flatworms) and fireflies. There's also a paragraphs on the local climate (that's all I'll give it... you can tell meteorology isn't my schtick - unless you're talking very local effects - then I'm very interested). There are so many insects that "It is sufficient to disturb the composure of an entomologist's mind, to look forward to the future dimensions of a complete catalogue." He notes the work of leaf cutter ants and army ants and has a description of a fight between a large wasp (tarantula hunter) and large spider. 

We goes on to describe many spiders and habits, including social spiders. I've encountered these in Manaus. The stuff of nightmares (not really... but if you imagine being tiny and falling into these immense unorganized webs...). 

He commonly messes with invertebrates and cannot just watch. He saves insects from spiders' webs dispatches them so they don't suffer and put them back in the web.

What a curious mind. 

New job!!!! (kinda)

Yesterday I received a phone call from our provost offering the Study Abroad Director position. I accepted. 

Should be a fun challenge learning the ropes and raising money to get students and faculty outside of the U.S. 

Galapagos and tropical ecology course

I'm teaching a 1 + 2 credit sophomore-level course that's part of our "superlab" series inspired by previous HHMI finding. 

We're going to meet once a week and discuss tropical ecology from historical (a chapter in Darwin's Voyage of the Beagle) and current perspectives. 

Here's the website for the course https://sites.google.com/a/wilkes.edu/tropical-ecology/

Too many ecology PhD? From whence?

This is a shot from the hip since I don't have data either way (I need to read this) but I have heard several times that we are producing too many PhDs for the number of potentially new academic positions and many are encouraged to seek employment in other avenues, such as government and consulting.

Since most ecology PhDs are funded through NSF (again, I have no data) or teaching stipends and we reduce the number of PhD students then how are courses covered and will ecology itself suffer if we have fewer folks in the field? In a way this is a selfish thought because I'm thinking of sabbaticals and if we have more funded sabbatical positions then we could help fill the gap by reducing the number of new PhDs. I know I would benefit a great deal from being in a new lab for a semester + summer.  

Just some pre coffee thoughts, sitting in the lounge, waiting for my chair to get in because I left my office keys at home. 

Crow and grackle

This is a picture I thought was a failure and it's been sitting in my Google drive since June. I was trying to get a picture of grackles mobbing a crow. I missed the shot with several grackles nearly on the crow. But I got this and there's something very attractive and a bit spooky about it. I like it. 

Quick note on Endnote

I have 943 references in my > 10,000 reference Endnote library with the keyword fragmentation. I have 400 papers with urbanization as a keyword.

How then, to distill down to the most salient papers?  They actually have a rating system based on stars (1 to 5) and I find this extremely useful. 

The problem (kinda) is that you need to read the paper to figure out how to rate it. Also not available on Endnote Web. Bummer. 

Working on a grant to fund grassland research and I have 218 papers in my collection and it is super inefficient going through each one.  

Ups, downs, and purgatory

2015 was a great year for publications with 6 papers or chapters getting out. 2016 has started out a little bumpier.  A paper on squirrel spatial memory was rejected from Animal Behavior. I did the stats on it... my first mixed model; a repeated measure with a binomial distribution. Journal of Animal Ecology paper on birds and their malarial parasites is in review. 

Just submitted a species richness and urbanization paper to my coauthors to look over. No idea where I'm sending it. 

Question is, what's next?  Dig up the past, do the new? 

The book... the book.  It's calling me.  Neotropical birds: Evolution, Ecology and Conservation. 

South Jersey coastal birding

Got out to Forsythe National Wildlife Refuge today at 730 AM. And a frosty morning it was. Where yesterday at Sandy Hook I overexposed everything, I initially underexposed today. Switched to auto ISO and that helped a ton. 

Did the wildlife drive twice. Was really hoping to pick up a snowy owl but no luck. Also, nobody took over the refuge. 

Gadwall

Hooded Merganser

Hooded Merganser

Pintail

Snow Goose 

American Widgeon

Then I was off to Cape May Audubon/Lighthouse. Super windy and was sand blasted on the ocean side. Still, there's something fun about being the only person around and the wind gusting away. Usually that pays off with a falcon, or gannet, but today is was just sand in the face. 

Gadwall.. damn underexposure

Hooded merganser

Attacking shoveler

Non-attacking shoveler

Tundra Swan

Drive home tonight was really nerve-wracking. Big rigs were throwing that muddy, silty crap on the windows then the wash would freeze so I was driving blind for 3 or so seconds. Horrible.  

North Jersey coastal birding

On a two day trip to my parents' place in Cape May and decided to bird on the way down. Left the house at 6 and finally stepped out of the truck at 10 in Sandy Hook. I haven't been there in twenty years and this trip brought back some nice memories of my fisheries course and Plant Ecology. Very few visitors so that was nice. 

A big part of this trip was figuring my camera. Yea, the one I've had for years. I put everything on manual so I had to pick all the settings except for ISO (because I'm still figuring that one out... in the context of the other settings). 

The first 50 or so pictures were crap - all over exposed.  Clouds came over and the pictures came out better. I'm using a Canon Rebel T1i and I don't think it shows a color histogram but this seems to be the best indicator of overexposure. 

Tomorrow's plan. Forsythe National Wildlife Refuge then Cape May. 

In the meantime, here are today's best pics. 

Surf Scoter

Common Loon - with crab

Dunlin

Young Gannet 

Harlequin Duck

Long-tailed Duck

Purple Sandpiper

Double-crested Cormorant (was hoping for a Great)

Tree Swallow. What. Are. You. Doing?

2016 paper #4 Where the wild meets us

Just finished reading "Bar-Massada, A., V. C. Radeloff and S. I. Stewart, 2014. Biotic and Abiotic Effects of Human Settlement in the wildland-Urban Interface. Bioscience 64, 429-437." 

This paper provides an overview of the changes in ecosystems where wildlands meet or are intermixed with human settlement. It's a bit too brief but provides some great material. It asked some of the same questions I did here about the effects of urbanization but provides more insight. Nothing surprising but nice to see the sources: more generalists, food webs are altered, etc. I take from these papers, however, that food web studies are just getting started. Very cool. Ideas, ideas, ideas.

They also point out that invasive plants radiate out from human settlement and the interaction with habitat modification, primarily edge effects, and how that benefits invasive species. 

We plan on looking at frugivory across the urban gradient this summer. We have an army of "poop traps" ready to be set out.

I'm excited for this summer. Should be interesting! 

2016 paper #3 Climate change and land use

Just gave a very quick read of "Ordonez, A., S. Martinuzzi, V. C. Radeloff and J. W. Williams, 2014. Combined speeds of climate and land-use change of the conterminous US until 2050. Nature Climate Change 4, 811-816."

Ordonez and colleagues present a short article representing lots of work mapping climate change and land use across the US. They examined where climate change and land use change would affect ecosystem most rapidly as independent and combined effects. 

For climate change, the strongest effects will be seen in the Great Plains where there will be no topographic refugia for a warming climate. There will also be high rates of land use change, much of urbanization. So the Plains are screwed. The West appears to have relatively low rates of change for climate and land use. The ne and se US will be mixed.  

Good idea for urban studies (2nd paper of 2016)

Just read a paper from the same group that I did my PhD with. Most of the paper wasn't very relevant to my own work but I did find some inspiration. 

The paper was Styers, D. M., A. H. Chappelka, L. J. Marzen and G. L. Somers, 2010. Scale matters: Indicators of ecological health along the urban-rural interface near Columbus, Georgia. Ecological Indicators 10, 224-233.

They looked at measures of road density and fragmentation along with population measures at different spacial extents. I was disappointed that there was any ecology in this paper. Oh well.

What Styers said that piqued my interest was this "Urbanization effects on natural resources extend well beyond the boundaries of urbanized areas into surrounding wildlland environments (Macie and Hermansen 2002)." This is cool and I haven't thought much about this.  How far do urbanization effects extend beyond what is recognized as being urban? I imagine there are biological and abiotic effects that have the potential to participate in such a phenomenon. How far does the urban heat island radiate across the landscape? Or is it smaller than the urban footprint. I also would think that cats, dogs, and rats have an effect beyond the footprint. 

Then there are questions of ecosystem services/processes. If urban areas have more invasive plants are birds moving them into the larger landscape? Are hummingbirds moving pollen out of urban areas?  Lots of ideas. 

MIddle Creek Wildlife Management Area

Wife and I went to Middle Creek WMA today to do a little birding (and antiquing). MCWMA is just under two hours from Wilkes-Barre - down HWY 81 until Pottsville (home of Yuengling) then country roads for another hour.

Today's goal was to set the camera and manual and see how could do. I would give myself a C-/D. It was cloudy so I turned up the ISO. Most of the photos were overexposed. I used a single point focus and still had issues. So it goes. 

Highlights of the day were a pair of Bald Eagles (wife), Eastern Bluebirds (wife), Shovelers, and Tundra Swans (I'm assuming - they're terribly close to Trumpeters).  And despite acres and acres of fields, there was a noticeable lack of grassland/shrub birds (no Kestrels, Mockingbird, Savannah Sparrows, Horned Larks, etc). 

Ring-necked Duck

Red-tailed Hawk

Northern Shovelers 

Tundra Swans

  

First paper read of 2015: birds and urbanization from 2007

Working on a paper from my work in western Georgia (USA) and catching up on the literature. Been feeling a bit scattered and not sure where my career is going (urbanization?, grasslands?, tropical?, isotopes?, DNA barcoding?, acorns?, blue jays?). 

I could make a career of catching up and I should. I owe it to the people that have invested in me. 

Anyways, just finished Valiela, I. and P. Martinetto, 2007. Changes in Bird Abundance in Eastern North America: Urban Sprawl and Global Footprint? BioScience 57, 360-370. 

I typically read and underline important parts then type in those parts in Endnote. Horribly inefficient. I know some people highlight the pdf. I get it back when I do a search and print out the Endnote hits with annotations. That way I can skim through the annotations and get the gist of the paper that I think is important rather than reading the abstract. 

Here's some of the important findings:

1. Overall, birds are declining in North America but probably not who you expected (long-distance migrants of the forest)

2. Large declines in open habitat birds (their categorization is a little wonky) that are residents or short-distance migrants

3. Wetland birds decline as well

4. Most forest birds, especially residents, are increasing

5. Edge birds (including the Starling?) are not increasing despite what is an increase in the urban-wildland interface 

Rocky Neck State Park, CT

My daughter goes to Connecticut College and I was up last weekend to pick her up and I stopped at Rocky Neck State Park in East Lyme, CT. The day was cold and overcast so not too great for birding. Picked up Horned Larks, Tree Sparrows, Common Loon, and a Surf Scoter. Brant (top) were at a nearby beach and a bunch of Snowy Egrets (bottom) were at the entrance to the park. 

Fourteen years of scholarship

In 2002, I started keeping track of what papers I've been reading by adding the keyword read with the year so if I searched my Endnote files for "read10" I would get all the papers that I read in 2010. Below I graph the number of papers I've read (black) and the the papers I've published (red).

The depressing thing, to me, is the number of years with 0 papers. That would be five out of fourteen years. Hate that. Hard to see in the graph below but I had five papers in 2015. I have at least seven papers I can get out so time to get my ass in gear. 

I had my qualifying exams in 2002 and I read a ton then and that's the giant peak early on. Definitely a decay in the number of papers read but there's no correlation between papers read and my output. I've read more papers in the last two years than what is shown because I've gotten lazy in using my keywords and I've focused on the discussion. 

This frames my goals for the year. Get a few papers out and read more. And teach. And do outreach. And have a life.