"Everything is so close at hand, & being cramped, make one so methodical, that in the end I have been a gainer" -Charles Darwin, letter to his father, 1 March 1832
I suspect, with Darwin's financial heritage, he was not hurting for space. But aboard the Beagle, space was at a premium and forced Darwin to be organized and this he carried into his later days at home as an experimenter.
WEBS went really well yesterday. Fifty girls came by to dissect owl pellets. Skulls were used to identify prey items and I asked them to put the rest of the bones in order and draw them. That part went less well overall although several girls did great. Some teachers were involved others sat and texted or checked sport scores.. or whatever.
Today's a busy day; need to write a lecture for noon, give a guest lecture about coffee and birds, work on a report, and submit a mentoring grant. Yup.
"Whenever I enjoy anything I always either look forward to writing it down either in my log Book (which increases in bulk) or in a letter. -So you must excuse raptures & those raptures badly expressed" -Charles Darwin, letter to his father, 1 March 1832
Many of us that teach ecology or a related course ask our students to keep a field notebook or journal and I think this is a great exercise. It always helps writing to practice writing (why I have this blog) and our memories are always faulty.
Writing reinforces memory and helps us organize thoughts systematically and helps us avoid pareidolia - seeing random patterns as being significant.
As somebody that writes poorly I appreciate Darwin's sentiment here and gives me some solace. Difference being that he was a well published author soon after returning from the Voyage.
Two intro bio labs today and WEBS tonight. We're looking at owl pellets. Should be fun.
"These animals [octopi] also escape detection by a very extraordinary, chameleon-like power of changing their colour" -Charles Darwin,Voyage of the Beagle
Darwin is remarking on the ability of cephalopods to match their backgrounds or to contrast with it. Darwin watched on octopus moving like it was stalking him and it was changing colors as it moved across the tide pool. Question is, does the octopus need to see the back group to match or can the skin see the background. The latter hypothesis may seem absurd but animals, including vertebrates, have molecules in the skin that are related to the photosensitive molecules (rhodopsins) in the eye. The contrasting color was used when the octopus was poked.
Here's a BBC video of an example of adaptive camouflage
A team of researchers from Rutgers (yay!) and Emory University published a paper today in JAMA Neurology showing that folks with Alzheimer Disease (AD) had higher levels of DDE circulating in their blood and risk was also modulated by a genetic component. DDE is one of the products of DDT when it breaks down. In the parlance of environmental chemistry we would just say that DDE is a DDT metabolite. I suspect that the current generation in college has never heard of DDT yet everyone over 45 probably has. This molecule was banned for use in the US in 1972 by the EPA. Yup, we stopped widespread spraying of DDT forty-two years ago. What the hell is it doing in blood at levels that may induce AD? A few points may shed light on this 1. DDT is a persistent organic pesticide that is stored in human body fat - apparently for long periods of time. So those people exposed to DDT in before the ban may still have dangerous levels in their blood 2. DDE is amazingly persistent in soil, such that DDE becomes recirculated in the environment when we dredge (dig in rivers) and through the action of earthworms. Once in the environment, DDE is able to enter food webs and end up in bodies. 3. DDE circulates widely. DDE is stable in water and soil and be transported in the atmosphere. DDE is still showing up in Arctic predators where, to my knowledge, DDT was never used. Birds, particularly fish eating birds, such as pelicans and Bald Eagles, and birds that consume other birds (including those that eat fish), such as Peregrine Falcons still show DDE in eggs and blood. And these birds are not over 40 years old. So there is also the potential that we are still consuming DDE when we eat fish. Is anyone looking for DDE in fish? Not sure. It would be small amounts. But that's the problem with molecules that bioaccumulate, small quantities add up over time. Dilution is not the solution to pollution. Willing or not, we are still consuming many contaminants that accumulate in our bodies including phthalates and flame retardants. The effects? Not sure. But I doubt we can be as indifferent as we were in the past as shown in this video.
Clark, K., et al. (2009). "Organochlorine Pesticides, PCBs, Dioxins, and Metals in Postterm Peregrine Falcon (Falco peregrinus) Eggs from the Mid-Atlantic States, 1993–1999." Archives of Environmental Contamination and Toxicology 57(1): 174-184. Fisk, A. T., et al. (2005). "An assessment of the toxicological significance of anthropogenic contaminants in Canadian arctic wildlife." Science of the Total Environment 351: 57-93. Grier, J. W. (1982). "Ban of DDT and subsequent recovery of Reproduction in bald eagles." Science 218(4578): 1232-1235. Jagannath, A., et al. (2008). "Eggshell pigmentation indicates pesticide contamination." Journal of Applied Ecology 45(1): 133-140.
Nilsen, E., et al. (2014). "Contaminants of legacy and emerging concern in largescale suckers (Catostomus macrocheilus) and the foodweb in the lower Columbia River, Oregon and Washington, USA." Science of the Total Environment(0).
Stemmler, I. and G. Lammel (2009). "Cycling of DDT in the global environment 1950â€“2002: World ocean returns the pollutant." Geophys. Res. Lett. 36.
Plymouth, PA is an old coal mining town that has great potential to be a hip town. When the levee along the Susquehanna River ends is an area called Plymouth Flats. This is a great birding spot with wide open corn fields and brushy edges filled with sparrows. I went out to see one of the zillion snowy owls that have descended upon the East Coast. Didn't turn up any. But I did happen to run into a flock of Tree Sparrows and this very chilly Song Sparrow. I should also note there was a garbage pile burning and some dude and his girlfriend were enjoying the outdoors.
"Another of my occupation was collecting animals of all classes, briefly describing and roughly dissecting many of the marine ones; but from not being able to draw, and from not having sufficient anatomical knowledge, a great pile of MS. which I made during the voyage has proved almost useless" -Charles Darwin, autobiography
"A great pile of MS." - this sentiment I get. I have a number projects that went no where. Some made it submitted manuscripts only to be crushed by reviewers. What I found though, that works, is collaboration with peers. I'm surprised that Darwin did not have a camera lucida with him.
Working on the Biological Conservation special issue. Editing is not, I'm finding, particularly enjoyable though it is interesting. Expecting bitter cold and the birds told us this was coming; flocks of Ring-billed Gulls and two Bald Eagles flew by campus yesterday indicating the freezing over of lakes north of us. May also work on the food web manuscript... speaking of piles of MS.
On a brighter note, ended a section of lectures exactly at the end of class (that never happens), and ecology labs went really well. We used GenBank to download mitochondrial protein sequence data and used this to construct phylogenies. On top of this we're mapping ecological traits or distribution information. It's really nice when labs come together and students don't walk away frustrated or their intelligence insulted - that, I really hate.
"The very first place which I examined, namely St. Jago in the Cape de Verde Islands, showed me clearly the wonderful superiority of Lyell's manner of treating geology" -Charles Darwin, autobiography
Before leaving on the Voyage, Darwin received the first volume of Principles of Geology by Charles Lyell and published by John Murray (who published Origin of Species) in 1830. The other volumes were forthcoming but the first already influenced Darwin. Lyell was a enthusiastic proponent of uniformitarianism - the belief that the laws of nature were constant through time. For geology this meant that processes we observe today (rates of erosion, results of earthquakes, etc) were the same as those working in the past. The uniformitarian view of geology was not widely accepted but was increasing in popularity as the theists, with their laws of nature, were showing scientific success in all areas of science. __________ Two Bald Eagles flew by this morning. I'll take that as a good sign. Teaching phylogentics to ecology course and hopefully showing how some life history traits evolve. Might be interesting.
"I had a net astern the vessel, which caught great numbers of curious animals, & fully occupy my time in my cabin" -Charles Darwin, letter to father, 1 March 1832
An an ornithologist, I appreciate sampling marine environments. To me, it is fishing - just that the organisms are not necessarily fish. I take students to Wallops Island Marine Station for an Ecology field trip (going this year in April) and they love seeing what ends up in the net. These nets typically sample plankton (small organisms that flow with the currents) but also sample nekton (larger organisms that move independently of the current), such as fish and shrimp.
Honey Locust (Gleditsia triacanthos) just off the railroad tracks in Wilkes-Barre. Some of the thorns well exceed 10 cm. Why have such large thorns? I would think it would be some anti-herbivory strategy, its thorny relatives throughout the tropics. But why in North America? Perhaps this warded off the giant ground sloth before their extinction thousands of years ago. Yet the thorns persist. Interesting.
25 Jan 2014: "the misery I endured from sea-sickness is far far beyond what I ever guessed at" -Charles Darwin, letter to his father, 1 March 1832
Darwin is barely out of the English Channel when sea sickness sets upon him after a storm at sea. He is completely miserable and stays in his hammock. The only food he can keep down are raisins his father has sent him. It has only been a few weeks and he founds himself miserable at sea - this is a man who spends another four years and ten months at sea. He notes that he's often to sick to leave his cabin to observe islands they pass. I love being on boats and rough seas don't bother me much. I did however, get sea sick once when I sat on the deck to fix a knot in a fishing reel while in the Florida Keys. I could no longer see the horizon and this did not end well. Enuff said.
24 Jan 2014: "it contains 60 men 5 or 6 officers etc - but is a small vessel.-it will probably be out nearly 3 years" -Charles Darwin, letter to his sister Susan, written 5 September 1831
Conditions were cramped - extremely crampy for a naturalist. But it did force Darwin to organize, label, and take good notes. As for the three year voyage - not so much. Fitzroy extended the trip to five years in order to improve chronological measurements.
Wilkes-Barre is still freezing although we've had far fewer freezing days than the past few decades. Bird-wise there's nothing interesting around but Snowy Owls. There's a distinct absence of winter finches, even our regular American Goldfinches and House Finches are largely absent.
In December 2013, a live Anatolian brown tick (Rhipicephalus bursa) from Macedonia was found on an untanned hide by US Customs and Border Protection agents in Philadelphia. Ticks are vectors of both bacterial and viral pathogens, such as Lyme disease and Rocky Mountain Spotted Fever. This was only the fourth case of this species entering the U.S. Tennessee's state ornithologist Scott Somershoe was catching migrant birds on a coastal island in Georgia and remarked that large numbers of birds were arriving from their wintering grounds in the Caribbean Islands, Central, and South America forests with ticks on them. Given that millions of birds move between continents, I find it surprising that we don't see more cases of ticks establishing themselves in North America. But this amazing migration phenomenon is not new. Birds have been moving between North and South America for millions of years and as far north as Pennsylvania for 20,000 years. One fascinating project would be to pull ticks off birds at places where migrant birds first land or pause (stopover sites) and look at the ectoparasite community and the microbiota they harbor. If ticks and their microbiota differ between sites where the same birds live then why aren't birds homogenizing parasite communities?
23 Jan 2014: "Generally the atmosphere is hazy; and this is caused by the falling of impalpably fine dust" -Charles Darwin, Voyage of the Beagle
Still off the west coast of Africa, Darwin is remarking on the clouds of dust coming from Africa. These clouds are laden with enough dust to bother the eyes and damage equipment. Darwin collected a number of samples and sent them off to be analyzed. The results intrigued Darwin; the dust was primarily composed of the remains of freshwater organisms and plants and to a lesser extent marine organisms.
Darwin's dust samples were taken hundreds of miles away from the African continent. Data suggests that the amount of dust varies by year and decade and can influence climate over the Atlantic (Evan et al. 2011). The amount of dust, in turn, is determined by land use and climate over Africa.
I'm not a trained epidemiologist but I do love reading about diseases. This is an extension of my interest in landscapes and how they affect organisms. I follow the infectious disease literature somewhat and I regularly listen to This Week in Parasitism and This Week in Virology. I also subscribe to Promed Mail - a listerv that sends out infectious disease news. There has been a small outbreak of Chikungunya in the Caribbean Islands that has currently reached 486 known infections. Chikungunya is caused by an arbovirus (short for arthropod borne virus) in the genus Alphavirus. Chikungunya infections are usually not fatal but they can cause long-term joint pain though most infections are cleared in a week. This disease is primarily found in se Asia, central Africa, and some parts of Europe. Why do I think Chukungunya is coming to the US? The virus is carried by mosquitoes are are ubiquitous throughout the Americas. All the virus needs to get a foothold in the US is for an infected individual (say a tourist) to bring the virus back to the Americas while the virus is circulating in their bloodstream. Then an "American" mosquito can bite the infected person, pick up the virus, and the cycle starts anew. Viola! Around 2004, Chikungunya started spreading out from locations around the Indian Ocean and has spreading globally since then with a large bump in 2007 that appears to related to a change in the virus (Staples et al. 2009). References: Staples et al. 2009.http://www.ncbi.nlm.nih.gov/pubmed/19663604
22 Jan 2014: "On the 16th of January 1832 we anchored at Porto Praya, in St. Jago, the chief island of the Cape de Verd archipelago" -Charles Darwin, Voyage of the Beagle
The Beagle is at sea and heading south towards the Canary Islands, where they were scheduled to stop in Teneriffe but were turned away because of the threat of them bringing cholera. The bacterium Vibrium cholerae causes cholera and sufferers essentially shit themselves to death. Mostly due to improved sanitation, cholera has declined in the US thought it is currently an increasing threat to global health (look up cholera in Haiti).
The Beagle comes close enough to the Canary Islands for Darwin to describe them from a distance. Since they were turned away from the Canary Islands, the Beagle makes landing in the Cape Verde Islands, also off the west coast of Africa. Darwin describes the landscape as "utterly sterile" but large numbers of goats (probably over-browsing). The most common bird is the Grey-headed Kingfisher. Despite the name, this species primarily predates lizards and insects.
21 Jan 2014: "The object of the expedition was to complete the survey of Patagonia and Tierra del Fuego ... to survey the shores of Chile and Peru, and of some islands in the Pacific- and to carry a chain of chronometrical measurements round the World" -Charles Darwin, Voyage of the Beagle
The goal wasn't to obliterate creationism and there's no mention of natural history. This was, more or less, a test of new equipment and mapping trip. There was a ship's naturalist and Darwin was on board as Fitzroy's personal naturalist. My guess is that those funding this trip were also interested in new natural products for the Empire.
Took my Ecology class out to our urban park to ID, count, and take dbh of trees. The park was once a zoo and is now a natural area. If you want to see invasive species this is the place. The ground is covered in Japanese knotweed and Japanese hops. However, the overstory is all native trees such as silver maple and black locust. The students were troopers despite the cold. Next week we'll take that data and produce some pretty graphs and see if tree densities differ between the forest edge and interior.
Here's a great video of a camera disguised as a Rockhopper Penguin egg. The egg is removed from the penguin colony by a caracara (think of a hawk that acts like a crow) then is attacked by Turkey Vultures and ten the eggs ends up back in another part of the colony! If anything, this video underscores the fact that egg predation is incredibly common and eggs are highly valued by predators. Link to Youtube video
20 Jan 2014: "The voyage of the Beagle has been the most important event of my life, and has determined my whole career " -Charles Darwin, Voyage of the Beagle
What would be the modern equivalent of Darwin's voyage? Nothing. A recent graduate going around the world, stopping at various ports to collect as much as possible over several years is not something that happens these days. However, I know of several graduate projects that do this piecemeal, such as Auburn's grant to inventory catfish diversity and Utah State's inventory of parasites in se Asia. When we look at the products of these trips, we tend to think publications and new species but we tend to overlook that we also get students that are now highly trained and become highly motivated.
Johns Hopkins researchers show the positive relationship between memory retention and having coffee - and not just increased concentration or attention. Optimal dosage is 200 mg (about one cup). Below this amount there's no measured benefit and above this headaches and nausea (really?). So go get your mug, fill it, and study away.
19 Jan 2014: "Her Majesty's ship Beagle a ten-gun brig, under the command of Captain Fitz Roy, R.N., sailed from Devonport on the 27th of December, 1831" -Charles Darwin, Voyage of the Beagle
Initially Darwin's father didn't want young Darwin to go on this trip but relented at the urging of Darwin's uncle, Josiah Wedgwood. A man he simply describes as being an intelligent and quiet man. Josiah Wedgwood industrialized pottery, became wealthy, and was an ardent abolitionists, which we see in Darwin. Wedgwood china is still popular to this day (it is very nice stuff). Darwin was fresh out of college with a degree in Divinity. Trained in geology, botany, natural history, and skilled at collecting. Bags are stowed, allowances from his father are expected at port. Off they sail...
Blogger James Kennedy has a great blog but has put out a great series of posts on chemophobia, the irrational fear of things we eat with long names. A recent post,which I love, lists the naturally-occurring ingredients of blueberries. To folks that hate anything unnatural the list would be entirely intimidating if presented on their own. Not only are these chemicals natural, many of them are antioxidants, antimicrobials, etc. Ignorance of chemistry and chemophobia is also exploited by the anti-vaccinationists. Their goal is to reduce the immunization rate and leave children more susceptible to preventable diseases.
Sloths are remarkable creatures. Their slow movements seem out of entirely out of place in South and Central American rainforests where fast and efficient predators like jaguars hunt the forest floor and birds of prey hunt from above. While during surveys in a 1-ha forest fragment I happened across a sloth skull.
Here a National Geographic video of a sloth being taken a Harpy Eagle.
I have only seen a single living sloth up close in the wild while it was crossing the road and many more as road kill along the highway that runs north from Manaus. Remarkably, I did see a sloth within the Manaus city limits moving about the Cecropia trees.
A team of researchers published a recent paper in PLOS describing assays of ascomycetes (cup fungi) living on sloth fur and found species that were active against malaria (kills >500,000 people/year), Chagas disease, bacteria, and even cancer cells. They detected 82 operational taxonomic units (essentially species). Sloths are, essentially, their own biome with predators and symbionts, autotrophs and heterotrophs.
Just in case the eagle video gets you down, here's some sloth cuteness
But, whatever you do, don't fall in love in a sloth
18 Jan 2014: "[Fitzroy] defended and praised slavery, which I abominated"Darwin autobiography
Darwin is recounting Fitzroy's personality. A great schism is being formed in European and American societies: those that defend slavery and the abolitionists. Interesting that Darwin gets blamed for so many offenses against humanity yet there's nothing in natural selection, nothing in evolution, and nothing in a materialistic world view that can be used to defend slavery, which is sanctioned in the Bible.
Snowing this morning and very pretty out. Temperatures have been in the 30's yet the increasing day length is inspiring cardinals, song sparrows, and chickadees to sing. Today is laundry-palooza. Catching up on chores.
17 Jan 2014: "I think he was afterwards well satisfied that my nose had spoken falsely"Darwin autobiography
Once Darwin's father finally conceded to the Voyage of the Beagle, Darwin was rushed off to London to meet Captain Fitzroy for a short interview. They got along fabulously but Fitzroy adhered to phrenology principles, which indicated Darwin's laziness.
Submitted a NSF pre-proposal today, lectured on the effect of temperature on organisms, coordinating a submission to the Kaufman foundation. Quite a day.
16 Jan 2014: "Captain Fitz-Roy was willing to give up part of his own cabin to any young man who would volunteer to go with him without pay as naturalist to the Voyage of the Beagle"Darwin autobiography
He was the naturalist, then he wasn't, then he was. I learned that Darwin was the naturalist but only after the official naturalist quit (yup, quit). Now Darwin's account sounds like he was hired as the naturalist from the start. I have heard it suggested that Fitzroy wanted a companion that would complement the ships naturalist; a younger man that was trained as a naturalist.
Working on a National Science Foundation grant to do work on birds in Panama. The deadline is tomorrow and submitting at 10 AM. After that teaching ecology then lunch. Then home for a cigar and a small glass of whiskey. This grant would also transform Women Empowered By Science - increasing enrollment and allowing us to purchase 3D printers so young women can learn the basics of engineers, creating plastic birds that fly. This grant would also train Wilkes students to become physiologists AND conservation biologists.
15 Jan 2014: "science consists in grouping facts to that general laws or conclusions may be drawn from them"Darwin autobiography
In a gravel pit of what probably was glacial till (sediment) a worker claims to have found a tropical shell. Sedgwick dismisses this claim as nonsense because it went against what was known about the origins of the material in the area. The ability to predict observations against a background of derived laws (theories) struck Darwin as being extremely powerful. Such is the nature of science. Though we've replaced "law" with "theory" this is still how we think of science.
Theories are generally accepted explanations. Accepted because they create hypotheses and hypotheses generate predictions and testing predictions is what scientists do. For the rest of Darwin's life, this is how Darwin approached science.
14 Jan 2014: "In my last year at Cambridge, I read with care and profound interest Humbodlt's Personal Narrative [of Travels to the Equinoctial Regions of America]. This work, and Sir J. Hershel's Introduction to the Study of Natural Philosophy, stirred up in me a burning zeal to add even the most humble contribution to the noble structure of Natural Science. "Darwin autobiography
Baron Alexander von Humbolt's Personal Narrative is a description of his travels across northern South America, including the lowlands of Venezuela and the highlands of Andes. He includes natural history, geology, social customs, and reads much like an adventure. I haven't read it myself although I feel like I need to now. It is listed as #1 in the Journal of Natural History Education and Experience's list of 101 natural history books that I should read before I die. Our library has the three volume version and I'll make this my "fun" spring break reading. Humbolt became a world famous traveler and is the namesake of several geological features as well as a penguin (there's a good Welsh word). He inspired Darwin and a number of other natural historians. There's much less information about The Study of Natural Philosophy on the web but Natural Philosophy has deistic origins. When speaking about natural historians of the time, theists viewed God as influencing everyday events, the power of prayer, miracles, etc. This was giving way to the deistic view that God imparted rules onto the natural world and it is the responsibility of the natural philosopher to discover the rules. Pre-Origin of Species this meant that species were perfect and immutable creations. Deistic views were held by many scientists of the time including Darwin, Newton and influenced the American founding fathers (see the Declaration of Independence). I suspect that books on Natural Philosophy were a mix of natural history observations and deistic interpretations. So Darwin is in his last year of college. He's highly motivated to (1) collect organisms, (2) travel, and (3) make contributions to science. He's already an adept collector of insects, birds, bird eggs, plants and marine organisms. He has been trained by Henslow, one of the top botanists of his time. It's time for something. Something big.
13 Jan 2014: "I have not as yet mentioned a circumstance which influenced my whole career more than any other. This was my friendship with Professor Henslow."Darwin autobiography
Darwin was not enjoying his studies. Most of his classes were boring and irrelevant. Then came along Professor Henslow and everything changed. Darwin met John Stevens Henslow Professor in 1828 when Darwin enrolled in his botany course. I mentioned before that Darwin loved Henslow's field trips. It's amazing that field trips and hand-on learning was considered progressive. No wonder Darwin was bored. It's only Jan 13. There will be much more on Henslow. Classes start today and I have Ecology and a very talented bunch of students. I'll have to up my game. In particular, I'd like to learn looping in R code so we can model population changes. Going to be a great semester, we have to coastal field trips scheduled. I'm ready for today's lecture but I need to write up more for the lab. Measuring a bunch of acorns and creating histograms, running simple statistics, and doing some simple statisticals