Friday, February 28, 2014

My Year of Darwin (2/28/2014)

 Charles Darwin

"A person, on first entering a tropical forest, is astonished at the labours of the ants: well-beaten paths branch off in every direction, on which an army of never-failing foragers may be seen, some going forth, an others returning, burdened with pieces of green leaf, often larger than their own bodies." Charles Darwin, Voyage of the Beagle

Darwin is speaking of leaf cutter ants. There were two, at least, species of leaf cutter ants in Manaus. These ants cut leaves into pieces, let them fall, then carry them off to the underground nest. There the leaves are fed to a fungus that uses the sugars in the leaf as a source of energy and the ants eat the fruiting bodies of the ants. Ants create the ideal environmental conditions for the fungus in terms of temperature and humidity and attack competing fungi.  New queens take pieces of the old fungus to start new colonies. 

At camp in Manaus, leaf cutter have raided our food stores and taken off with beans, farinha, and spaghetti!  Their underground liars are immense and the effects of leaf cutters on tropical forests cannot be overstated. Leaf cutters prefer newer growth and will go out into pastures to defoliate young trees thus keeping pastures as pastures and slowing succession. 

Here's a shorter video here:

Here's a longer video here (really cool):

Thursday, February 27, 2014

My Year of Darwin (2/27/2014)

 Charles Darwin

"I was disappointed in the general aspect of the Coleoptera. The number of minute and obscurely coloured beetles is exceedingly great. The cabinets of Europe can, as yet, boast only of the larger species from tropical climates. It is sufficient to disturb the composure of an entomologist's mind, to look forward to the future dimensions of a complete catalogue." Charles Darwin, Voyage of the Beagle

Since Darwin, estimates of beetle diversity are in the millions of species

Wednesday, February 26, 2014

My Year of Darwin (2/26/2014)

 Charles Darwin

"We here see in two distant countries a similar relation between plants and insects of the same families, though the species of both are different. When man is the agent in introducing into a country a new species this relation is often broken ." Charles Darwin, Voyage of the Beagle

This is an incredibly insightful passage on introduced species and why some are so successful. The literature is replete with examples of organisms released by humans into areas where they are non-native and those species become quickly established because they have no predators or pathogens. Likewise, I know of failures of reintroductions because a species important to the target species was missing. The case I'm thinking of is the planting of trees and their subsequent failure because the soil lacked symbiotic fungi that gave the trees water and nutrients. 
A female House Sparrow, native to Europe and now found throughout the world. This one is interesting: note the crossed bill. Why has this species been so successful? 

Tuesday, February 25, 2014

My Year of Darwin (2/25/2014)

 Charles Darwin

"Following a pathway I entered a noble forest, and from a height of five or six hundred feet, once of those splendid views was presented, which are so common on every side of Rio. At this elevation the landscape attains its most brilliant tint; and every form, every shade, so completely surpasses in magnificence all that the European has ever beheld in his own country, that he knows not how to express his feelings." Charles Darwin, Voyage of the Beagle

I need to get to Rio!  

Monday, February 24, 2014

My Year of Darwin (2/24/2014)

 Charles Darwin

"Before seeing them [bread fruit and mango ], I had no idea that any trees could cast so black a shade on the ground." Charles Darwin, Voyage of the Beagle

I have a hard time convincing temperate biologists that the tropical understory is a habitat not seen in temperate forests. Birds of tropical understories experience a dark habitat, year-round, and throughout their entire lives. 

I suspect that the insectivores there have eyes that are adapted to such dark conditions. The adaptations would take the form of gross anatomical (essentially a wider aperture for their eye size) and histological differences (relatively more light sensitive rods). 

Below is an example of Variegated Antpitta. A classic understory bird. Look at that eye!  Look at it!  This species would frustrate me because it would call well before sunrise and I would chase it with my headlamp on and this bird would fly through the dense understory in the dark. How could it do this?

Sunday, February 23, 2014

Lovely day for a run/walk

Participated in the Relay-for-heat organized by the Wilkes University Running Club and in coordination with the Commission on Economic Opportunities. It was a beautiful sunny day in the upper 40's (~10C).  The only problem is that the course was terrible. 

Photo: Relay  4. Heat 2014

I probably did 1 km of running if that. The rest of it was slipping around. Other than a doing something for a good cause, and getting off my butt, the highlights were the birds. They are a House Sparrow (defending a box - seems very early for this), a Dark-eyed Junco, a Black-capped Chickadee grabbing a spruce seed, and a Song Sparrow. 

My Year of Darwin (2/23/2014)

 Charles Darwin

"Nature, in these climes, chooses her vocalists from more humble performers than in Europe. A small frog, of the genus Hyla, sits on a blade of grass about an inch above the surface of the water, and send forth a pleasing chirp; when several are together they sing in harmony on different notes." Charles Darwin, Voyage of the Beagle

Mating frogs at camp 41 of the Biological Dynamics of Forest Fragments Project. Not sure of the species. Several would gather in our PVC drainage pipes and call. No, it wasn't pleasant.


Running in the Relay-4-Heat today. I should say walking though. Out of shape with no training. Bringing the camera and should get some good shots of birds- I hope.

Son's 17th birthday. Miss him terribly. 

Saturday, February 22, 2014

Raising more chicks shortens a bird's life

The Jackdaw is a common and widespread corvid of Europe. In a recent article in Ecology Letters, Jelle Boonekamp and colleagues experimentally showed Jackdaws with enlarged clutches died earlier than those with smaller clutches. 

My Year of Darwin (2/22/2014)

 Charles Darwin

"In England any person fond of natural history enjoys his walks a great advantage, by always having something to attract his attention; but in these fertile climates, teeming with life, the attractions are so numerous, that he scarcely able to walk at all." Charles Darwin, Voyage of the Beagle

Darwin is speaking to his experience in the Brazilian rainforest. Examples that one would use in a introductory biology course to a graduate ecology course are seen at every step. 

Friday, February 21, 2014

My Year of Darwin (2/21/2014)

 Charles Darwin

"It is easy to specify the individual objects of admiration in these grand scenes; but it is not possible to give an adequate idea of the higher feelings of wonder, astonishment, and devotion, which fill and elevate the mind." Charles Darwin, Voyage of the Beagle

Thursday, February 20, 2014

State report done: no effect of natural gas density on avian physiology

When looking across the three years of our study, we have no evidence to say that terrestrial (in this case non-aquatic) birds are exposed to enough contaminants to have glutathione S-transferase, a detoxifying enzyme, increase in their blood. We also didn't find any evidence that barium was making its way into terrestrial food webs. 

The report is in and now to turn it into a paper - hopefully I can get negative results published.  PA DCNR should post the report in a few weeks. Negative results are boring but data is data. 

Now on to a food web paper, a book chapter, and a Amazonian fragmentation paper. 

My Year of Darwin (2/20/2014)

 Charles Darwin

"The woody creepers, themselves covered by other creepers, were of great thickness: of which I measured were two feet in circumference." Charles Darwin, Voyage of the Beagle

Here, Darwin is in a Neotropical forest (tropical forests of South and Central America). Creepers are woody vines (and stalkers on the internet). The largest woody vine on the east coast, US that I have seen was a wild grape and may have been 5-6 cm across. A two foot woody vine is awesome.
Dark understory of an Amazonian forest.

Wednesday, February 19, 2014

My Year of Darwin (2/19/2014)

 Charles Darwin

"I may mention one very trifling anecdote, which at the time struck me more forcibly than any story of cruelty. 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." Charles Darwin - Voyage of the Beagle 

Let us never forget the indignity and injustice of slavery. 

Tuesday, February 18, 2014

Interactive climate map from New Scientist

New Scientist has a great interactive map here. Drag the waypoint to see how temperate has changed since 1880 at a specific location. The map itself is interesting as it shows the change across the globe at once. 

My Year of Darwin (2/18/2014)

 Charles Darwin

"I thought they must belong to an enormous Armadillo, living species of which genus are so abundant here." Charles Darwin - Letter to J.S. Henslow, October 1832

Darwin has explored the Atlantic coast of Brazil and, with great sea-sickness, turned Cape Horn, and is now exploring the west coast of South America. There he finds a huge relative of the modern armadillos. Seeing related but phenotypically different species in the past was key to Darwin's thinking. What forced shaped organisms through time. That was the question. 


Darwin's children and the Origin of Species Manuscript

In the age before laptops, authors would hand write manuscripts on paper (imagine!). Now imagine an interactive father and a houseful of children. 

The result, manuscripts with lots of scribbles and drawings from children. Doubtful Darwin would have been upset. Typesetters are quite able to tell the difference between the author's writing and those of children. 

Blogger Benjamin Breen, writing for The Appendix, has a great essay on the scribbles on drawing found on Darwin's manuscripts. Great stuff. 


Monday, February 17, 2014

My Year of Darwin (2/17/2014)

 Charles Darwin

"Considering the enormous area of Brazil, the proportion of cultivated ground can scarcely be considered as anything compared to that which is left in the state of nature: at some future age, how vast a population it will support." Charles Darwin - Voyage of the Beagle

Indeed, as time has proven, Brazil can have a much larger population. But what a price nature has paid. 

Wilkes is hosting a breakfast for high school students that have high GPAs and SATs. Then we have a poster session. Then I have ecology lab and bio lab and my day ends at 9. That's a nice 13 hour day for me. 

Sunday, February 16, 2014

My Year of Darwin (2/16/2014)

 Charles Darwin

"The Vampire bat is often the cause of much trouble, by biting the horses on their withers." Charles Darwin - Voyage of the Beagle

The horses that Darwin and company would use would often be bitten by vampire bats but they were not observed in the act, which made those in England doubt Darwin's stories. But in Chile, a bat was captured on a horse. The bats were not causing serious problems but would cause local inflammation that would heal in a few days.

Vampire bats feed by licking the site first. Their saliva has an anesthetic so the animal doesn't feel their teeth making a small incision. Their saliva also has an anticoagulant and keeps the blood flowing freely as the bat laps it up with their tongue. 

While sleeping in a apartment on the fourth floor of an apartment complex in Manaus, Brazil, I had a bat running up my leg while I sleeping on the floor. Without looking I though it was just a cockroach and the bat kept returning. I finally flicked on a light and there it was running on the ground. I scooped it on a pillow on flicked it out the window. It was either sick or overfed and it just fell to the ground. I didn't see any cuts on me so I assume it wasn't bit and the bat was just weak. Sorry, I just couldn't make a donation. However, a few weeks later, I was up late reading a paper in a house near the Amazon. Windows were wide open. Just out of "nervous" behavior I started tapping my foot and I noticed that it was in a liquid. So I looked and I was bleeding profusely out of a ~ 1 cm cut on my ankle. The occupants of the house informed me that it was likely a vampire bat. So, I've been bitten by a vampire. I washed it out and nearly 20 years later I feel no effects and I don't like the taste of blood. 

Saturday, February 15, 2014

Reducing the prevalence of Lyme disease: field vaccinations


In the Journal of Infectious Disease, there is an article on the success of a field vaccination program to reduce the prevalence of Borrelia burgdorferi, the cause of Lyme Disease, in ticks. One type of plot (portion of woods) had orally-administered vaccines targeted at White-footed Mice, the primary reservoir, and control plots had mice (as all woods do) that did not receive the vaccines. 

Once the mice are vaccinated, the nymphal ticks carrying Borrelia will not be able to infect the mouse with the bacterium. Transmit, yes - infect, no. Then subsequent ticks feeding on the mouse will not be able to get Borrelia from the mouse - this interrupts the infection-transmission cycle that spills over to humans. For more information on Lyme Disease, visit the CDC page on Lyme Disease

Adult tick. The spike in the front is the hypostome and is the part that is stuck into your body. The barbs keep the tick from being pulled off easily. 

Sorry, can't hear you.. THERE IS A FRUIT FLY LARVA IN MY EAR

This isn't my ear.. but if I ever get a tickly feeling in my ear.. yea, I'm washing it out. 

My Year of Darwin (2/15/2014)

 Charles Darwin

"The trees were very lofty, and remarkable, compared with those of Europe, from the whiteness of their trunks. I see by my notebook, 'wonderful and beautiful flowering parasites,' invariably struck me as the most novel object in these grand scenes." Charles Darwin - Voyage of the Beagle
Midstory in Manaus, Brazil continuous forest site. 

Emergent tree covered in epiphytes at the La Selva Research Station, Costa Rica

State report on natural gas drilling is due Monday, book chapter overdue, exams to be graded, homeworks and labs to be created and past ones graded. Anxiety. Anxiety. Anxiety.

Friday, February 14, 2014

My Year of Darwin (2/14/2014)

 Charles Darwin

"The delight of sitting on a decaying trunk amidst the quiet gloom of the forest is unspeakable & never to be forgotten." July 23,1832, Letter to Henslow


Thursday, February 13, 2014

TMBG - Birdhouse in Your Soul

They Might be Giants: Birdhouse in Your Soul

My Year of Darwin (2/13/2014)

 Charles Darwin

"At this present minute we are at anchor in the mouth of the river: & what a strange scene as it is. - Every thing is in flames, - the sky with lightning, - the water with luminous particles, & even the very masts are pointed with a blue flame." July 23,1832, Letter to Henslow

I have nothing useful to add. This sounds wondrous.

Snow day here and I am thankful for the time to address so many projects. 

Darwin Day Rap

Darwin Day Shenanigans

Yesterday, I had the opportunity to talk about Charles Darwin with Dr. Helen Davis' Victorian Literature class. I'm wearing a Victorian work shirt (stained from washing with a tie-dye) and work pants (too tight!). Here I'm showing an example of pigeons that Darwin described and how quickly pigeon breeders could create a pigeon with desired features.

Before the lecture there was tea and coffee (delicious) as well as cucumber sandwiches, scones (delicious), and cupcakes (delicious). This was in Kirby Hall, which is beautiful (though, I bet, drafty). I think Wilkes U should do a Victorian Week - we have the buildings and the interest and it would be a great way to get the community on campus.

Wednesday, February 12, 2014

Find the Brown Creeper

Lately, there has been a number challenges posted where we are supposed to find a cryptic animal. An orange cat in fall colors, insects that look like flowers, and there's even a game of "find the nightjar". Here's mine. The Brown Creeper (Certhia americana) is one of my favorite birds because they are so, um, not cute but cute and I always thought myself lucky when I came across one. Not only are they cryptic they're also relatively quiet. They creep like woodpeckers with their body vertical and close to the tree trunk. These are not as difficult as the nightjars but one of the more challenging birds to find in Pennsylvania. 

Tuesday, February 11, 2014

My Year of Darwin (2/12/2014)

Happy Darwin Day! 

 Charles Darwin

"If we were lucky, by waiting a couple of hours, we obtained fowls, rice, and farinha." April 9,1832, Voyage of the Beagle

Darwin is describing his terrible experience at an in when we traveled inland from Rio de Janeiro. They keeper told them they could have anything they wanted but were told "No, sir" to every request. The next day they traveled to Campos Novos were they had an excellent meal and were treated graciously.

I could live on chicken, rice and farinha. I know this because I did. I came to enjoy some chicken stew with rice and farinha. 

What is farinha (far een ya)? It's the fibrous starch from mandioc root. There are two (at least) forms of farinha. A fluffier and light farinha that is usually more expensive and a more course yellow form that is much cheaper. Me, I prefer yellow farinha. My favorite meal in Brazil is fish stew PACKED with farinha. I also love bean soup with farinha and there's a brown palm liquid that's excellent with farinha. I love farinha! I miss farinha! I could think of no better way to celebrate Darwin Day than with some farinha sprinkled on something. Maybe next year. 

This photo is yellow farinha taken from

The snow storm cometh... so here's some heat

We're expecting up to a foot of snow on Wednesday night. Just so I might appreciate that. Here's a photo taken from a hillside in Newport Township, PA. Saw a black bear that day early in the morning - too dark for pictures. The temperature went up to 96 F.

Creating terrible and great titles for articles

I don't think problems with titles are as big of an issue for biological sciences as they are social sciences but I found some useful tidbits in this article by Patrick Dunleavy. Although it might be considered poor taste, but I wish that some published examples were given - otherwise we might be arguing a strawman.   

Personally, I like titles that are essentially a statement of the primary result, even if negative results. Vagueness is never a positive attribute in science - unless, of course, results are vague. 

Should scientific results be treated like your naughty bits to be hidden within the results so that only a faithful reader that has stuck with you from your vague abstract to your hypothesis-lacking introduction can finally be enlightened in the final part of your discussion? 


The title should be informative and the results should be up front with accessory information in the end.

"Dynamite causes death in songbirds of northern Wales"
"Periodic outbursts increases parental care in southern chickadees"
"Novel stimuli fails to elicit a response in frozen waterfowl in southern Uganda"